source: trunk/src/uvmat.m @ 432

Last change on this file since 432 was 432, checked in by sommeria, 9 years ago

system of projection object manipulation with uvmat improved.

File size: 207.7 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 fields (with fields
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:
31%    'Strings' of all edit boxes and menus: get(handles.Tag,'String')
32%    'Values' of all menus and toggle buttons: get(handles.Tag,'Value')
33%     Matlab structure called UvData stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
34%          It contains the following fields:
35%     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn)
36%          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
37%     - Information read in the documentation open of a series (activated by RootPath_Callback) :
38%          .XmlData, with fields:
39%               .Time: matrix of times of the images with index i and j
40%               .GeometryCalib: [1x1 struct]
41%     - Information defined from the interface:
42%           .NewSeries: =1 when the first view of a new field series is displayed, else 0
43%           .filename:(char string)
44%           .FieldName: (char string) main field selected('image', 'velocity'...)
45%           .CName: (char string)name of the scalar used for vector colors
46%          .MovieObject{1}: movie object representing an input movie
47%          .MovieObject{2}: idem for a second input series (_1)
48%          .filename_1 : last second input file name (to deal with a constant second input without reading again the file)
49%          .ZMin, .ZMax: range of the z coordinate
50%..... to complement
51%     - Information on  projection objects
52%           .Object: {[1x1 struct]}
53%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
54%     -Information on the current field (Field{i})
55%            .Txt : text information to display (e.g. error message)
56%            .NbDim: number of dimensions (=0 by default)
57%            .NbCoord: number of vector components
58%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
59%            .dt: time interval for the corresponding image pair
60%            .Mesh: estimated typical distance between vectors
61%            .ZMax:
62%            .ZMin:
63%            .X, .Y, .Z: set of vector coordinates
64%            .U,.V,.W: corresponding set of vector components
65%            .F: corresponding set of warning flags
66%            .FF: corresponding set of false flags, =0 for good vectors
67%            .C: corresponding values of the scalar used for vector color
68%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
69%                     equal to the number of vectors stored in the input open)
70%            .CName: name of the scalar .C
71%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
72%            .A image or scalar
73%            .AX: vector of dimension 2 representing the first and last values
74%              of the X coordinates for the image or scalar known on a regular grid,
75%              or vector of dimension .A for a scaler defined on irregular grid.
76%            .AY: same as .AX along the Y direction
77%            .AName: name of the scalar, ='image' for an image
78
79% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
80%
81%
82% 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1
83% (second field), or by the stored file names under  Browse, or as an input of uvmat.
84% 2) These functions call 'display_file_name.m' which detects the file series, and fills the file index boxes
85% 3) Then 'update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file)
86% 4) Then fields are opened and visualised by the main sub-function 'refresh_field.m'
87% The function first reads the name of the input file from the edit boxes  of the GUI
88% A second input file can be introduced for file comparison
89% It then reads the input file(s) with the appropriate function, read for
90% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf
91% files.
92%               Main input open   second input open(_1)        second image (pair animation)
93%            |                 |                             
94%            |                 |                                               
95%                     Field{1}         Field{2}               
96%                                                                         |
97% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
98%                                                                   Field{i}
99%                                                                    |
100% calc_field.m: calculate scalar or other derived fields (vort, div..).
101%
102% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
103%              Field{i=1->3}.X --> UvData.X                          |
104%                                                                    |
105%                                                                 UvData
106%                                                                    |
107% plot histograms of the whole  field
108% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
109%                                                                    |                                                                          |
110%                                                                ObjectData
111%                                                                    |
112% plot_field.m: plot the projected fields and store them as          |
113% UvData.axes3                                        |
114%                                                                    |
115%                                                                AxeData
116%
117%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
118% scalars are displayed either as an image or countour plot, either as a color of
119% velocity vectors. The scalar values in the first case is represented by
120% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
121% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
122% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
123% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
124% coordinates of the four image corners. The scalar name is represented by
125% the strings .AName and/or .CName.
126% If the scalar exists in an input open (image or scalar stored under its
127% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
128% Else only its name AName is recorded in Field{i}, and its field is then calculated
129%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
130     
131% Properties attached to plotting figures (standard Matlab properties):
132%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
133%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
134%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
135%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
136%    'KeyPressFcn': function called by pressing a key on the key board
137%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
138%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
139
140% Properties attached to plotting axes:
141%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
142%     AxeData:=get(gca,'UserData');
143%     AxeData.Drawing  = create: create a new object
144%                       = deform: modify an existing object by moving its defining create
145%                      = off: no current drawing action
146%                     = translate: translate an existing object
147%                    = calibration: move a calibration point
148%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
149%            .CurrentOrigin: Origin of a curently drawn edit_object
150%            .CurrentLine: currently drawn menuline (A REVOIR)
151%            .CurrentObject: handle of the currently drawn edit_object
152%            .CurrentRectZoom: current rectangle used for CheckZoom
153
154% Properties attached to projection objects (create, menuline, menuplane...):
155%    'Tag'='proj_object': for all projection objects
156%    ObjectData.Type=...: style of projection object:
157%              .ProjMode
158%              .Coord: defines the position of the object
159%              .XMin,YMin....
160%              .XMax,YMax....
161%              .DX,DY,DZ
162%              .Phi, .Theta, .Psi : Euler angles
163%              .X,.Y,.U,.V.... : field data projected on the object
164%              .IndexObj: index in the list of UvData.Object
165           %during plotting
166%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
167%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
168% To each projection object #iobj, corresponds an axis
169% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
170% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
171
172%------------------------------------------------------------------------
173%------------------------------------------------------------------------
174%  I - MAIN FUNCTION uvmat
175%------------------------------------------------------------------------
176%------------------------------------------------------------------------
177function varargout = uvmat(varargin)
178
179% Begin initialization code - DO NOT EDIT
180gui_Singleton = 1;
181gui_State = struct('gui_Name',          mfilename, ...
182                   'gui_Singleton',     gui_Singleton, ...
183                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
184                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
185                   'gui_LayoutFcn',     [], ...
186                   'gui_Callback',      []);
187if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
188    gui_State.gui_Callback = str2func(varargin{1});
189end
190
191if nargout
192    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
193else
194    gui_mainfcn(gui_State, varargin{:});
195end
196% End initialization code - DO NOT EDIT
197
198%------------------------------------------------------------------------
199% --- Executes just before the GUI uvmat is made visible.
200function uvmat_OpeningFcn(hObject, eventdata, handles, input )
201%------------------------------------------------------------------------
202
203%% Choose default command menuline output for uvmat (standard GUI)
204handles.output = hObject;
205
206%% Update handles structure (standard GUI)
207guidata(hObject, handles);
208
209%% check the path and date of modification of all functions in uvmat
210path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
211[errormsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m
212date_str=['last modification: ' date_str];
213
214
215%% set the position of colorbar and ancillary GUIs:
216set(hObject,'Units','Normalized')
217movegui(hObject,'center')
218UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
219UvData.OpenParam.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
220UvData.OpenParam.SetObjectSize=[0.3 0.7];
221UvData.OpenParam.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
222UvData.OpenParam.CalSize=[0.28 1];
223UvData.axes3=[];%initiate the record of plotted field
224UvData.axes2=[];
225UvData.axes1=[];
226AxeData.LimEditBox=1; %initialise AxeData
227set(handles.axes3,'UserData',AxeData)
228
229%% set functions for the mouse and keyboard
230% set(handles.histo_u,'NextPlot','replacechildren');
231% set(handles.histo_v,'NextPlot','replacechildren');
232set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
233set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
234set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
235set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
236set(hObject,'DeleteFcn',{@closefcn})%
237
238%% refresh projection plane
239% UvData.Object{1}.ProjMode='projection';%main plotting plane
240% UvData.Object{1}.DisplayHandle.uvmat=handles.axes3;
241% UvData.Object{1}.DisplayHandle.view_field=[];
242set(handles.ListObject,'Value',1)% default: empty projection objectproj_field
243set(handles.ListObject,'String',{'plane'})
244set(handles.ListObject_1,'Value',1)% default: empty projection objectproj_field
245set(handles.ListObject_1,'String',{'plane'})
246set(handles.Fields,'Value',1)
247set(handles.Fields,'string',{''})
248
249%% TRANSFORM menu: builtin fcts
250menu_str={'';'phys';'px';'phys_polar'};
251UvData.OpenParam.NbBuiltin=numel(menu_str); %number of functions
252path_uvmat=fileparts(which('uvmat'));
253addpath (path_uvmat) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
254addpath(fullfile(path_uvmat,'transform_field'))%add the path to transform functions,
255fct_handle{1,1}=[];
256testexist=zeros(size(menu_str'));%default
257testexist(1)=1;
258for ilist=2:length(menu_str)
259    if exist(menu_str{ilist},'file')
260        fct_handle{ilist,1}=str2func(menu_str{ilist});
261        testexist(ilist)=1;
262    else
263        testexist(ilist)=0;
264    end
265end
266rmpath(fullfile(path_uvmat,'transform_field'))
267
268%% load the list of previously browsed files in menus Open and Open_1
269 dir_perso=prefdir; % path to the directory .matlab for personal data
270 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
271 if exist(profil_perso,'file')
272      h=load (profil_perso);
273      if isfield(h,'MenuFile')
274          for ifile=1:min(length(h.MenuFile),5)
275              eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
276               eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
277          end
278      end
279      if isfield(h,'transform_fct') && iscell(h.transform_fct)
280         for ilist=1:length(h.transform_fct);
281             if exist(h.transform_fct{ilist},'file')
282                [path,file]=fileparts(h.transform_fct{ilist});
283                addpath(path)
284                h_func=str2func(file);
285                rmpath(path)
286                testexist=[testexist 1];
287             else
288                file='';
289                h_func=[];
290                testexist=[testexist 0];
291             end
292             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
293             menu_str=[menu_str; {file}];
294         end
295      end
296 end
297menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
298fct_handle=fct_handle(testexist==1);
299menu_str=[menu_str;{'more...'}];
300set(handles.transform_fct,'String',menu_str)
301set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
302
303%% case of an input argument for uvmat
304testinputfield=0;
305inputfile=[];
306Field=[];
307if exist('input','var')
308%     if ~isempty(errormsg)
309%         msgbox_uvmat('WARNING',errormsg)
310%     end
311    if ishandle(handles.UVMAT_title)
312        delete(handles.UVMAT_title)
313    end   
314    if isstruct(input)
315        if isfield(input,'InputFile')
316            inputfile=input.InputFile;
317        end
318        if isfield(input,'TimeIndex')
319            set(handles.i1,num2str(input.TimeIndex))
320        end
321        if isfield(input,'FieldsString')
322            UvData.FieldsString=input.FieldsString;
323        end
324    elseif ischar(input)% file name introduced as input
325           inputfile=input;
326    elseif isnumeric(input)%simple matrix introduced as input
327        sizinput=size(input);
328        if sizinput(1)<=1 || sizinput(2)<=1
329            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
330            return
331        end
332        UvData.Field.ListVarName={'A','coord_y','coord_x'};
333        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
334        UvData.Field.A=input;
335        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
336        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
337        testinputfield=1;
338    end
339else
340   if ishandle(handles.UVMAT_title)
341       set(handles.UVMAT_title,'String',...
342           [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
343           {'GNU General Public License'};...
344           {path_to_uvmat};...
345           {date_str};...
346           {['SVN revision : ' num2str(svn_info.cur_rev)]};...
347           errormsg]);
348   end
349end
350set(handles.uvmat,'UserData',UvData)
351if ~isempty(inputfile)
352    %%%%% display the input field %%%%%%%
353    display_file_name(handles,inputfile)
354    %%%%%%%
355    testinputfield=1;
356end
357
358%% plot input field if exists
359if testinputfield
360    %delete drawn objects
361    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
362    for iobj=1:length(hother)
363        delete_object(hother(iobj))
364    end 
365    if isempty(inputfile)
366        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
367        set(handles.MenuTools,'Enable','on')
368        set(handles.OBJECT_txt,'Visible','on')
369        set(handles.edit_object,'Visible','on')
370%         set(handles.ListObject_1,'Visible','on')
371        set(handles.frame_object,'Visible','on')
372        if ~isempty(errormsg)
373            msgbox_uvmat('ERROR',errormsg)
374        end
375    end
376end
377
378set_vec_col_bar(handles) %update the display of color code for vectors
379
380%------------------------------------------------------------------------
381% --- Outputs from this function are returned to the command menuline.
382function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
383varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
384
385%------------------------------------------------------------------------
386% --- executed when closing uvmat: delete or desactivate the associated figures if exist
387function closefcn(gcbo,eventdata)
388%------------------------------------------------------------------------
389hh=findobj(allchild(0),'tag','view_field');
390if ~isempty(hh)
391    delete(hh)
392end
393hh=findobj(allchild(0),'tag','geometry_calib');
394if ~isempty(hh)
395    delete(hh)
396end
397hh=findobj(allchild(0),'tag','set_object');
398if ~isempty(hh)
399    hhh=findobj(hh,'tag','PLOT');
400    set(hhh,'enable','off')
401end
402
403%------------------------------------------------------------------------
404%------------------------------------------------------------------------
405%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
406% automatically sets the global properties when the rootfile name is introduced
407% then activate the view-field action if selected
408% it is activated either by clicking on the RootPath window or by the
409% browser
410%------------------------------------------------------------------------
411%------------------------------------------------------------------------
412% --- Executes on the menu Open/Browse...
413% search the files, recognize their type according to their name and fill the rootfile input windows
414function MenuBrowse_Callback(hObject, eventdata, handles)
415[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
416oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
417if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
418         dir_perso=prefdir;
419         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
420         if exist(profil_perso,'file')
421              h=load (profil_perso);
422             if isfield(h,'MenuFile_1')
423                  oldfile=h.MenuFile_1;
424             end
425         end
426end
427% [FileName, PathName] = uigetfile( ...
428%        {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol;*.nc;*.cmx;*.fig;*.log;*.dat;*.bat;', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.vol,*.nc,*.cmx,*.fig,*.log,*.dat,*.bat)';
429%        '*.xml',  '.xml files '; ...
430%         '*.xls',  '.xls files '; ...
431%         '*.civ',  '.civ files '; ...
432%         '*.jpg',' jpeg image files'; ...
433%         '*.png','.png image files'; ...
434%         '*.tif','.tif image files'; ...
435%         '*.avi;*.AVI','.avi movie files'; ...
436%         '*.vol','.volume images (png)'; ...
437%         '*.nc','.netcdf files'; ...
438%         '*.cdf','.netcdf files'; ...
439%         '*.cmx','.cmx text files ';...
440%         '*.fig','.fig files (matlab fig)';...
441%         '*.log','.log text files ';...
442%         '*.dat','.dat text files ';...
443%         '*.bat','.bat system command text files';...
444%         '*.*',  'All Files (*.*)'}, ...
445%         'Pick a file',oldfile);
446
447[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',oldfile);
448fileinput=[PathName FileName];%complete file name
449sizf=size(fileinput);
450if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
451
452% display the selected field and related information
453display_file_name( handles,fileinput)
454
455% -----------------------------------------------------------------------
456% --- Open again the file whose name has been recorded in MenuFile_1
457function MenuFile_1_Callback(hObject, eventdata, handles)
458%------------------------------------------------------------------------
459fileinput=get(handles.MenuFile_1,'Label');
460display_file_name( handles,fileinput)
461
462% -----------------------------------------------------------------------
463% --- Open again the file whose name has been recorded in MenuFile_2
464function MenuFile_2_Callback(hObject, eventdata, handles)
465%------------------------------------------------------------------------
466fileinput=get(handles.MenuFile_2,'Label');
467display_file_name(handles,fileinput)
468
469% -----------------------------------------------------------------------
470% --- Open again the file whose name has been recorded in MenuFile_3
471function MenuFile_3_Callback(hObject, eventdata, handles)
472%------------------------------------------------------------------------
473fileinput=get(handles.MenuFile_3,'Label');
474display_file_name(handles,fileinput)
475
476% -----------------------------------------------------------------------
477% --- Open again the file whose name has been recorded in MenuFile_4
478function MenuFile_4_Callback(hObject, eventdata, handles)
479%------------------------------------------------------------------------
480fileinput=get(handles.MenuFile_4,'Label');
481display_file_name(handles,fileinput)
482
483% -----------------------------------------------------------------------
484% --- Open again the file whose name has been recorded in MenuFile_5
485function MenuFile_5_Callback(hObject, eventdata, handles)
486%------------------------------------------------------------------------
487fileinput=get(handles.MenuFile_5,'Label');
488display_file_name(handles,fileinput)
489
490%------------------------------------------------------------------------
491% --- Executes on the menu Open/Browse_1 for the second input field,
492%     search the files, recognize their type according to their name and fill the rootfile input windows
493function MenuBrowse_1_Callback(hObject, eventdata, handles)
494%------------------------------------------------------------------------
495RootPath=get(handles.RootPath,'String');
496% [FileName, PathName, filterindex] = uigetfile( ...
497%        {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
498%        '*.xml',  '.xml files '; ...
499%         '*.xls',  '.xls files '; ...
500%         '*.civ',  '.civ files '; ...
501%         '*.jpg','.jpg image files'; ...
502%         '*.png','.png image files'; ...
503%         '*.avi;*.AVI','.avi movie files'; ...
504%         '*.nc','.netcdf files'; ...
505%         '*.cdf','.netcdf files'; ...
506%         '*.cmx','.cmx text files';...
507%         '*.cmx2','.cmx2 text files';...
508%         '*.fig','.fig files (matlab fig)';...
509%         '*.log','.log text files ';...
510%         '*.dat','.dat text files ';...
511%         '*.*',  'All Files (*.*)'}, ...
512%         'Pick a second file for comparison',RootPath);
513[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath);
514fileinput_1=[PathName FileName];%complete file name
515sizf=size(fileinput_1);
516if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
517
518% refresh the current displayed field
519set(handles.SubField,'Value',1)
520display_file_name(handles,fileinput_1,2)
521
522%update list of recent files in the menubar
523MenuFile_1=fileinput_1;
524MenuFile_2=get(handles.MenuFile_1,'Label');
525MenuFile_3=get(handles.MenuFile_2,'Label');
526MenuFile_4=get(handles.MenuFile_3,'Label');
527MenuFile_5=get(handles.MenuFile_4,'Label');
528set(handles.MenuFile_1,'Label',MenuFile_1)
529set(handles.MenuFile_2,'Label',MenuFile_2)
530set(handles.MenuFile_3,'Label',MenuFile_3)
531set(handles.MenuFile_4,'Label',MenuFile_4)
532set(handles.MenuFile_5,'Label',MenuFile_5)
533set(handles.MenuFile_1_1,'Label',MenuFile_1)
534set(handles.MenuFile_2_1,'Label',MenuFile_2)
535set(handles.MenuFile_3_1,'Label',MenuFile_3)
536set(handles.MenuFile_4_1,'Label',MenuFile_4)
537set(handles.MenuFile_5_1,'Label',MenuFile_5)
538dir_perso=prefdir;
539profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
540if exist(profil_perso,'file')
541    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
542else
543    txt=ver('MATLAB');
544    Release=txt.Release;
545    relnumb=str2double(Release(3:4));
546    if relnumb >= 14
547        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
548    else
549        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
550    end
551end
552
553% -----------------------------------------------------------------------
554% --- Open again as second field the file whose name has been recorded in MenuFile_1
555function MenuFile_1_1_Callback(hObject, eventdata, handles)
556% -----------------------------------------------------------------------
557fileinput_1=get(handles.MenuFile_1_1,'Label');
558set(handles.SubField,'Value',1)
559display_file_name(handles,fileinput_1,2)
560
561% -----------------------------------------------------------------------
562% --- Open again as second field the file whose name has been recorded in MenuFile_2
563function MenuFile_2_1_Callback(hObject, eventdata, handles)
564% -----------------------------------------------------------------------
565fileinput_1=get(handles.MenuFile_2_1,'Label');
566set(handles.SubField,'Value',1)
567display_file_name(handles,fileinput_1,2)
568
569% -----------------------------------------------------------------------
570% --- Open again as second field the file whose name has been recorded in MenuFile_3
571function MenuFile_3_1_Callback(hObject, eventdata, handles)
572% -----------------------------------------------------------------------
573fileinput_1=get(handles.MenuFile_3_1,'Label');
574set(handles.SubField,'Value',1)
575display_file_name(handles,fileinput_1,2)
576
577% -----------------------------------------------------------------------
578% --- Open again as second field the file whose name has been recorded in MenuFile_4
579function MenuFile_4_1_Callback(hObject, eventdata, handles)
580% -----------------------------------------------------------------------
581fileinput_1=get(handles.MenuFile_4_1,'Label');
582set(handles.SubField,'Value',1)
583display_file_name(handles,fileinput_1,2)
584
585% -----------------------------------------------------------------------
586% --- Open again as second field the file whose name has been recorded in MenuFile_5
587function MenuFile_5_1_Callback(hObject, eventdata, handles)
588% -----------------------------------------------------------------------
589fileinput_1=get(handles.MenuFile_5_1,'Label');
590set(handles.SubField,'Value',1)
591display_file_name(handles,fileinput_1,2)
592
593%------------------------------------------------------------------------
594% --- Called by action in RootPath edit box
595function RootPath_Callback(hObject,eventdata,handles)
596%------------------------------------------------------------------------
597% read the current input file name:
598[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
599% detect the file type, get the movie object if relevant, and look for the corresponding file series:
600[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
601% initiate the input file series and refresh the current field view:
602update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);
603
604%-----------------------------------------------------------------------
605% --- Called by action in RootPath_1 edit box
606function RootPath_1_Callback(hObject,eventdata,handles)
607% -----------------------------------------------------------------------
608% update_rootinfo_1(hObject,eventdata,handles)
609[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
610% detect the file type, get the movie object if relevant, and look for the corresponding file series:
611[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
612% initiate the input file series and refresh the current field view:
613update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
614
615%------------------------------------------------------------------------
616% --- Called by action in RootFile edit box
617function SubDir_Callback(hObject, eventdata, handles)
618%------------------------------------------------------------------------
619%refresh the menu of input fields
620Fields_Callback(hObject, eventdata, handles);
621% refresh the current field view
622run0_Callback(hObject, eventdata, handles);
623
624%------------------------------------------------------------------------
625% --- Called by action in RootFile edit box
626function RootFile_Callback(hObject, eventdata, handles)
627%------------------------------------------------------------------------
628RootPath_Callback(hObject,eventdata,handles)
629
630%-----------------------------------------------------------------------
631% --- Called by action in RootFile_1 edit box
632function RootFile_1_Callback(hObject, eventdata, handles)
633% -----------------------------------------------------------------------
634RootPath_1_Callback(hObject,eventdata,handles)
635
636%------------------------------------------------------------------------
637% --- Called by action in FileIndex edit box
638function FileIndex_Callback(hObject, eventdata, handles)
639%------------------------------------------------------------------------
640[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
641set(handles.i1,'String',num2str(i1));
642set(handles.i2,'String',num2str(i2));
643set(handles.j1,'String',num2str(j1));
644set(handles.j2,'String',num2str(j2));
645
646% refresh the current field view
647run0_Callback(hObject, eventdata, handles)
648
649%------------------------------------------------------------------------
650% --- Called by action in FileIndex_1 edit box
651function FileIndex_1_Callback(hObject, eventdata, handles)
652%------------------------------------------------------------------------
653run0_Callback(hObject, eventdata, handles)
654
655%------------------------------------------------------------------------
656% --- Called by action in NomType edit box
657function NomType_Callback(hObject, eventdata, handles)
658%------------------------------------------------------------------------
659i1=str2num(get(handles.i1,'String'));
660i2=str2num(get(handles.i2,'String'));
661j1=str2num(get(handles.j1,'String'));
662j2=str2num(get(handles.j2,'String'));
663FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
664set(handles.FileIndex,'String',FileIndex)
665% refresh the current settings and refresh the field view
666RootPath_Callback(hObject,eventdata,handles)
667
668%------------------------------------------------------------------------
669% --- Called by action in NomType edit box
670function NomType_1_Callback(hObject, eventdata, handles)
671%------------------------------------------------------------------------
672i1=str2num(get(handles.i1,'String'));
673i2=str2num(get(handles.i2,'String'));
674j1=str2num(get(handles.j1,'String'));
675j2=str2num(get(handles.j2,'String'));
676FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
677set(handles.FileIndex_1,'String',FileIndex)
678% refresh the current settings and refresh the field view
679RootPath_1_Callback(hObject,eventdata,handles)
680
681%------------------------------------------------------------------------
682% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
683function display_file_name(handles,fileinput,index)
684%------------------------------------------------------------------------
685%% look for the input file existence
686if ~exist(fileinput,'file')
687    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
688    return
689end
690
691%% set the mouse pointer to 'watch'
692set(handles.uvmat,'Pointer','watch')
693set(handles.RootPath,'BackgroundColor',[1 1 0])
694drawnow
695
696%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
697if ~exist('index','var')
698    index=1;
699end
700if index==1
701    handles_RootPath=handles.RootPath;
702    handles_SubDir=handles.SubDir;
703    handles_RootFile=handles.RootFile;
704    handles_FileIndex=handles.FileIndex;
705    handles_NomType=handles.NomType;
706    handles_FileExt=handles.FileExt;
707elseif index==2
708    handles_RootPath=handles.RootPath_1;
709    handles_SubDir=handles.SubDir_1;
710    handles_RootFile=handles.RootFile_1;
711    handles_FileIndex=handles.FileIndex_1;
712    handles_NomType=handles.NomType_1;
713    handles_FileExt=handles.FileExt_1;
714    set(handles.RootPath_1,'Visible','on')
715    set(handles.RootFile_1,'Visible','on')
716    set(handles.SubDir_1,'Visible','on');
717    set(handles.FileIndex_1,'Visible','on');
718    set(handles.FileExt_1,'Visible','on');
719    set(handles.NomType_1,'Visible','on');
720end
721
722%% detect root name, nomenclature and indices in the input file name:
723[FilePath,FileName,FileExt]=fileparts(fileinput);
724% detect the file type, get the movie object if relevant, and look for the corresponding file series:
725% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
726[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
727
728%% open the file or fill the GUI uvmat according to the detected file type
729switch FileType
730    case ''
731        msgbox_uvmat('ERROR','invalid input file type')
732    case 'txt'
733        edit(fileinput)
734    case 'figure'                           %display matlab figure
735        hfig=open(fileinput);
736        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
737        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
738        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
739    case {'xml','xls'}                % edit xml or Excel files
740        editxml(fileinput);
741    otherwise
742        set(handles_RootPath,'String',RootPath);
743        rootname=fullfile(RootPath,SubDir,RootFile);
744        set(handles_SubDir,'String',['/' SubDir]);
745        set(handles_RootFile,'String',['/' RootFile]); %display the separator
746        indices=fileinput(length(rootname)+1:end);
747        indices(end-length(FileExt)+1:end)=[]; %remove extension
748        set(handles_FileIndex,'String',indices);
749        set(handles_NomType,'String',NomType);
750        set(handles_FileExt,'String',FileExt);
751        if index==1
752            % fill file index counters if the first file series is opened
753            set(handles.i1,'String',num2str(i1));
754            set(handles.i2,'String',num2str(i2));
755            set(handles.j1,'String',num2stra(j1,NomType));
756            set(handles.j2,'String',num2stra(j2,NomType));
757        else %read the current field index if the second file series is opened
758            i1=str2num(get(handles.i1,'String'));
759            i2=str2num(get(handles.i2,'String'));
760            j1=stra2num(get(handles.j1,'String'));
761            j2=stra2num(get(handles.j2,'String'));
762        end
763       
764        % synchronise indices of the second  input file if it exists
765        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
766            Input=read_GUI(handles.InputFile);
767            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
768                Input.RootPath_1=Input.RootPath;
769            end
770            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
771                Input.SubDir_1=Input.SubDir;
772            end
773            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
774                Input.RootFile_1=Input.RootFile;
775            end
776            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
777                Input.FileExt_1=Input.FileExt;
778            end
779            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
780                Input.NomType_1=Input.NomType;
781            end
782            %updtate the indices of the second field series to correspond to the newly opened one
783            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1,i2,j1,j2);
784            if exist(FileName_1,'file')
785                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
786                set(handles.FileIndex_1,'String',FileIndex_1)
787            else
788                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
789%                 set(handles.SubField,'Value',0)
790%                 SubField_Callback([], [], handles)
791            end
792        end
793       
794        %enable other menus
795        set(handles.MenuOpen_1,'Enable','on')
796        set(handles.MenuFile_1_1,'Enable','on')
797        set(handles.MenuFile_2_1,'Enable','on')
798        set(handles.MenuFile_3_1,'Enable','on')
799        set(handles.MenuFile_4_1,'Enable','on')
800        set(handles.MenuFile_5_1,'Enable','on')
801        set(handles.MenuExport,'Enable','on')
802        set(handles.MenuExportFigure,'Enable','on')
803        set(handles.MenuExportMovie,'Enable','on')
804        set(handles.MenuTools,'Enable','on')
805%         set(handles.OBJECT_txt,'Visible','on')
806%         set(handles.edit_object,'Visible','on')
807%          set(handles.ListObject_1,'Visible','on')
808%          set(handles.ViewObject,'Visible','on')
809%         set(handles.frame_object,'Visible','on')
810       
811        % initiate input file series and refresh the current field view:     
812        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
813
814end
815
816%% set back the mouse pointer to arrow
817set(handles.uvmat,'Pointer','arrow')
818
819
820%------------------------------------------------------------------------
821% --- Update information about a new field series (indices to scan, timing,
822%     calibration from an xml file, then refresh current plots
823function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
824%------------------------------------------------------------------------
825%% define the relevant handles depending on the index (1=first file series, 2= second file series)
826if ~exist('index','var')
827    index=1;
828end
829if index==1
830    handles_RootPath=handles.RootPath;
831    handles_Fields=handles.Fields;
832elseif index==2
833    handles_RootPath=handles.RootPath_1;
834    handles_Fields=handles.Fields_1;
835end
836
837set(handles_RootPath,'BackgroundColor',[1 1 0])
838drawnow
839set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
840UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
841UvData.NewSeries=1; %flag for run0: begin a new series
842UvData.TestInputFile=1;
843UvData.FileType{index}=FileType;
844UvData.i1_series{index}=i1_series;
845UvData.i2_series{index}=i2_series;
846UvData.j1_series{index}=j1_series;
847UvData.j2_series{index}=j2_series;
848% set(handles.CheckFixPair,'Value',1) % activate by default the comp_input '-'input window
849set(handles.FixVelType,'Value',0); %desactivate fixed veltype
850if index==1
851    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
852else
853    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
854end
855FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
856FileBase=fullfile(RootPath,RootFile);
857if ~exist(FileName,'file')
858   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
859    return
860end
861nbfield=[];%default
862nbfield_j=[];%default
863
864%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
865XmlData.Time=[];%default
866XmlData.GeometryCalib=[];%default
867TimeUnit=[];%default
868testima=0; %test for image input
869imainfo=[];
870ColorType='falsecolor'; %default
871hhh=[];
872UvData.MovieObject{index}=VideoObject;
873if ~isempty(VideoObject)
874    imainfo=get(VideoObject);
875    testima=1;
876    nbfield_j=1;
877    TimeUnit='s';
878    XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
879    % %         nbfield=imainfo.NumberOfFrames;
880    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
881    ColorType='truecolor';
882elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
883    testima=1;
884    if ~isequal(SubDir,'')
885        RootFile=get(handles.RootFile,'String');
886        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
887    else
888        imainfo=imfinfo([FileBase FileIndices FileExt]);
889    end
890    ColorType=imainfo.ColorType;%='truecolor' for color images
891    if length(imainfo) >1 %case of image with multiple frames
892        nbfield=length(imainfo);
893        nbfield_j=1;
894    end
895end
896if isfield(imainfo,'Width') && isfield(imainfo,'Height')
897    if length(imainfo)>1
898        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
899        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
900    else
901        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
902        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
903    end
904else
905    set(handles.num_Npx,'String','');%fills nbre of pixels x box
906    set(handles.num_Npy,'String','');%fills nbre of pixels x box
907end
908set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
909
910%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
911filexml=[FileBase '.xml'];
912fileciv=[FileBase '.civ'];
913warntext='';%default warning message
914NbSlice=1;%default
915set(handles.RootPath,'BackgroundColor',[1 1 1])
916if exist(filexml,'file')
917    set(handles.view_xml,'Visible','on')
918    set(handles.view_xml,'BackgroundColor',[1 1 0])
919    set(handles.view_xml,'String','view .xml')
920    drawnow
921    [XmlData,warntext]=imadoc2struct(filexml);
922    if ~isempty(warntext)
923        msgbox_uvmat('WARNING',warntext)
924    end
925    if isfield(XmlData,'TimeUnit')
926        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
927            TimeUnit=XmlData.TimeUnit;
928        end
929    end
930    set(handles.view_xml,'BackgroundColor',[1 1 1])
931    drawnow
932    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
933        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
934            set (handles.nb_slice,'String','volume')
935        end
936        hgeometry_calib=findobj('tag','geometry_calib');
937        if ~isempty(hgeometry_calib)
938            GUserData=get(hgeometry_calib,'UserData');
939            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
940                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
941                if strcmp(answer,'Yes')
942                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
943                end
944            end
945        end
946    end 
947elseif exist(fileciv,'file')% if .civ file found
948    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
949    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
950    GeometryCalib.Tx=0;
951    GeometryCalib.Ty=0;
952    GeometryCalib.Tz=1;
953    GeometryCalib.dpx=1;
954    GeometryCalib.dpy=1;
955    GeometryCalib.sx=1;
956    GeometryCalib.Cx=0;
957    GeometryCalib.Cy=0;
958    GeometryCalib.f=1;
959    GeometryCalib.kappa1=0;
960    GeometryCalib.CoordUnit='cm';
961    XmlData.GeometryCalib=GeometryCalib;
962    if error==2, warntext=['no file ' FileBase '.civ'];
963    elseif error==1, warntext='inconsistent number of fields in the .civ file';
964    end 
965    set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
966    set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
967    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
968    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
969    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
970    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
971    set(handles.view_xml,'Visible','on')   
972    set(handles.view_xml,'String','view .civ')
973else
974    set(handles.view_xml,'Visible','off')
975end
976
977%% store last index in handles.lat_i and .last_j
978nbfield=max(max(i2_series));
979if isempty(nbfield)
980    nbfield=max(max(i1_series));
981end
982nbfield_j=max(max(j2_series));
983if isempty(nbfield_j)
984    nbfield_j=max(max(j1_series));
985end
986if ~isempty(XmlData.Time)
987%     nbfield=size(XmlData.Time,1);
988%     nbfield_j=size(XmlData.Time,2);
989    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
990    if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
991        NomType=get(handles.NomType,'String');
992        if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
993            XmlData.Time=(XmlData.Time)';
994%             nbfield=nbfield_j;
995%             nbfield_j=1;
996        end
997    end
998end
999last_i_cell=get(handles.last_i,'String');
1000if isempty(nbfield)
1001    last_i_cell{1}='';
1002else
1003    last_i_cell{1}=num2str(nbfield);
1004end
1005set(handles.last_i,'String',last_i_cell)
1006last_j_cell=get(handles.last_j,'String');
1007if isempty(nbfield_j)
1008     last_j_cell{1}='';
1009else
1010     last_j_cell{1}=num2str(nbfield_j);
1011end
1012set(handles.last_j,'String',last_j_cell);
1013
1014%% store geometric calibration in UvData
1015if isfield(XmlData,'GeometryCalib')
1016    GeometryCalib=XmlData.GeometryCalib;
1017    if isempty(GeometryCalib)
1018        set(handles.pxcm,'String','')
1019        set(handles.pycm,'String','')
1020        set(handles.transform_fct,'Value',1); %  no transform by default
1021    else
1022        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
1023            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
1024            set(handles.pxcm,'String','var')
1025            set(handles.pycm,'String','var')
1026        elseif isfield(GeometryCalib,'fx_fy')
1027            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
1028            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
1029            set(handles.pxcm,'String',num2str(pixcmx))
1030            set(handles.pycm,'String',num2str(pixcmy))
1031        end
1032        if ~get(handles.CheckFixLimits,'Value')
1033            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
1034        end
1035        if isfield(GeometryCalib,'SliceCoord')
1036           
1037           siz=size(GeometryCalib.SliceCoord);
1038           if siz(1)>1
1039               NbSlice=siz(1);
1040               set(handles.slices,'Visible','on')
1041               set(handles.slices,'Value',1)
1042           end
1043           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
1044               set(handles.nb_slice,'String','volume')
1045           else
1046               set(handles.nb_slice,'String',num2str(NbSlice))
1047           end
1048           slices_Callback([],[], handles)
1049        end           
1050    end
1051end
1052
1053%% update the data attached to the uvmat interface
1054if ~isempty(TimeUnit)
1055    set(handles.time_txt,'String',['time (' TimeUnit ')'])
1056end
1057UvData.TimeUnit=TimeUnit;
1058UvData.XmlData{index}=XmlData;
1059UvData.NewSeries=1;
1060% UvData.MovieObject=MovieObject;
1061
1062%display warning message
1063if ~isequal(warntext,'')
1064    msgbox_uvmat('WARNING',warntext);
1065end
1066
1067%% set default options in menu 'Fields'
1068if ~testima
1069    testcivx=0;
1070    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
1071        set(handles_Fields,'Value',1)
1072        set(handles_Fields,'String',{'get_field...'})
1073        UvData=rmfield(UvData,'FieldsString');
1074    else
1075        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
1076        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
1077            FieldList=calc_field;
1078            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
1079            set(handles_Fields,'Value',2) % set menu to 'velocity'
1080            col_vec=FieldList;
1081            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
1082            testcivx=1;
1083        end
1084        if ~testcivx
1085            set(handles_Fields,'Value',1) % set menu to 'get_field...
1086            set(handles_Fields,'String',{'get_field...'})
1087            col_vec={'get_field...'};
1088        end
1089        set(handles.ColorScalar,'String',col_vec)
1090    end
1091end
1092set(handles.uvmat,'UserData',UvData)
1093
1094%% set index navigation options and refresh plots
1095scan_option='i';%default
1096state_j='off'; %default
1097if index==2
1098    if get(handles.scan_j,'Value')
1099        scan_option='j'; %keep the scan option for the second fiel series
1100    end
1101    if strcmp(get(handles.j1,'Visible'),'on')
1102        state_j='on';
1103    end
1104end
1105if ~isempty(j1_series)
1106        state_j='on';
1107        if isequal(nbfield,1) &&index==1
1108            scan_option='j'; %scan j index by default if nbfield=1               
1109        end
1110end
1111if isequal(scan_option,'i')
1112     set(handles.scan_i,'Value',1)
1113     scan_i_Callback([],[], handles);
1114else
1115     set(handles.scan_j,'Value',1)
1116     scan_j_Callback([],[], handles);
1117end
1118set(handles.scan_j,'Visible',state_j)
1119set(handles.j1,'Visible',state_j)
1120set(handles.j2,'Visible',state_j)
1121set(handles.last_j,'Visible',state_j);
1122set(handles.frame_j,'Visible',state_j);
1123set(handles.j_text,'Visible',state_j);
1124if ~isempty(i2_series)||~isempty(j2_series)
1125    set(handles.CheckFixPair,'Visible','on')
1126elseif index==1
1127    set(handles.CheckFixPair,'Visible','off')
1128end
1129
1130%% view the field 
1131run0_Callback([],[], handles); %view field
1132mask_test=get(handles.CheckMask,'value');
1133if mask_test
1134    MaskData=get(handles.CheckMask,'UserData');
1135    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1136          delete(MaskData.maskhandle)    %delete old mask
1137    end
1138    CheckMask_Callback([],[],handles)
1139end
1140
1141%% update list of recent files in the menubar and save it for future opening
1142MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
1143    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
1144str_find=strcmp(FileName,MenuFile);
1145if isempty(find(str_find,1))
1146    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
1147end
1148for ifile=1:min(length(MenuFile),5)
1149    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
1150    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
1151end
1152dir_perso=prefdir;
1153profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1154if exist(profil_perso,'file')
1155    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1156else
1157    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
1158end
1159
1160
1161%------------------------------------------------------------------------
1162% --- switch file index scanning options scan_i and scan_j in an exclusive way
1163function scan_i_Callback(hObject, eventdata, handles)
1164%------------------------------------------------------------------------
1165if get(handles.scan_i,'Value')==1
1166    set(handles.scan_i,'BackgroundColor',[1 1 0])
1167    set(handles.scan_j,'Value',0)
1168else
1169    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1170    set(handles.scan_j,'Value',1)
1171end
1172scan_j_Callback(hObject, eventdata, handles)
1173
1174%------------------------------------------------------------------------
1175% --- switch file index scanning options scan_i and scan_j in an exclusive way
1176function scan_j_Callback(hObject, eventdata, handles)
1177%------------------------------------------------------------------------
1178if get(handles.scan_j,'Value')==1
1179    set(handles.scan_j,'BackgroundColor',[1 1 0])
1180    set(handles.scan_i,'Value',0)
1181    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1182%     NomType=get(handles.NomType,'String');
1183%     switch NomType
1184%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1185%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1186%     otherwise
1187%         set(handles.CheckFixPair,'Visible','off')
1188%     end
1189else
1190    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1191    set(handles.scan_i,'Value',1)
1192    set(handles.scan_i,'BackgroundColor',[1 1 0])
1193    set(handles.CheckFixPair,'Visible','off')
1194end
1195
1196%------------------------------------------------------------------------
1197function i1_Callback(hObject, eventdata, handles)
1198%------------------------------------------------------------------------
1199set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1200NomType=get(handles.NomType,'String');
1201i1=stra2num(get(handles.i1,'String'));
1202i2=stra2num(get(handles.i2,'String'));
1203j1=stra2num(get(handles.j1,'String'));
1204j2=stra2num(get(handles.j2,'String'));
1205indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1206%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1207set(handles.FileIndex,'String',indices)
1208set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1209if get(handles.SubField,'Value')==1
1210    NomType_1=get(handles.NomType_1,'String');
1211    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1212     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1213     set(handles.FileIndex_1,'String',indices)
1214     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1215end
1216
1217%------------------------------------------------------------------------
1218function i2_Callback(hObject, eventdata, handles)
1219%------------------------------------------------------------------------
1220set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1221i1_Callback(hObject, eventdata, handles)
1222
1223%------------------------------------------------------------------------
1224function j1_Callback(hObject, eventdata, handles)
1225%------------------------------------------------------------------------
1226set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1227i1_Callback(hObject, eventdata, handles)
1228
1229%------------------------------------------------------------------------
1230function j2_Callback(hObject, eventdata, handles)
1231%------------------------------------------------------------------------
1232set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1233i1_Callback(hObject, eventdata, handles)
1234
1235%------------------------------------------------------------------------
1236function slices_Callback(hObject, eventdata, handles)
1237%------------------------------------------------------------------------
1238if get(handles.slices,'Value')==1
1239    set(handles.slices,'BackgroundColor',[1 1 0])
1240    set(handles.nb_slice,'Visible','on')
1241    set(handles.z_text,'Visible','on')
1242    set(handles.z_index,'Visible','on')
1243    nb_slice_Callback(hObject, eventdata, handles)
1244else
1245    set(handles.nb_slice,'Visible','off')
1246    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1247    set(handles.z_text,'Visible','off')
1248    set(handles.z_index,'Visible','off')
1249    set(handles.masklevel,'Value',1)
1250    set(handles.masklevel,'String',{'1'})
1251end
1252
1253%------------------------------------------------------------------------
1254function nb_slice_Callback(hObject, eventdata, handles)
1255%------------------------------------------------------------------------
1256nb_slice_str=get(handles.nb_slice,'String');
1257if isequal(nb_slice_str,'volume')
1258    num=stra2num(get(handles.j1,'String'));
1259    last_j=get(handles.last_j,'String');
1260    nbslice=str2double(last_j{1});
1261else
1262    num=str2double(get(handles.i1,'String'));
1263    nbslice=str2double(get(handles.nb_slice,'String'));
1264end
1265z=mod(num-1,nbslice)+1;
1266set(handles.z_index,'String',num2str(z))
1267for ilist=1:nbslice
1268    list_index{ilist,1}=num2str(ilist);
1269end   
1270set(handles.masklevel,'String',list_index)
1271set(handles.masklevel,'Value',z)
1272
1273%------------------------------------------------------------------------
1274% --- Executes on button press in view_xml.
1275function view_xml_Callback(hObject, eventdata, handles)
1276%------------------------------------------------------------------------
1277%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1278 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1279FileBase=fullfile(RootPath,RootFile);
1280option=get(handles.view_xml,'String');
1281if isequal(option,'view .xml')
1282    FileXml=[FileBase '.xml'];
1283    heditxml=editxml(FileXml);
1284end
1285
1286%------------------------------------------------------------------------
1287% --- Executes on button press in CheckMask.
1288function CheckMask_Callback(hObject, eventdata, handles)
1289%------------------------------------------------------------------------
1290%case of view mask selection
1291if isequal(get(handles.CheckMask,'Value'),1)
1292   % [FF,RootPath,FileBase]=read_file_boxes(handles);
1293     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1294     FileBase=fullfile(RootPath,RootFile);
1295    num_i1=stra2num(get(handles.i1,'String'));
1296    num_j1=stra2num(get(handles.j1,'String'));
1297    currentdir=pwd; 
1298    cd(RootPath);
1299    maskfiles=dir('*_*mask_*.png');%look for a mask file
1300    cd(currentdir);%come back to the working directory
1301    mdetect=0;
1302    if ~isempty(maskfiles)
1303        for ilist=1:length(maskfiles)
1304            maskname=maskfiles(ilist).name;% take the first mask file in the list
1305            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1306%             [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1307             [tild,Name]=fileparts(maskname);
1308            Namedouble=double(Name);
1309            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1310            ind_mask=findstr('mask',Name);
1311            i=ind_mask-1;
1312            while val(i)==0 && i>0
1313                i=i-1;
1314            end
1315            nbmask_str=str2num(Name(i+1:ind_mask-1));
1316            if ~isempty(nbmask_str)
1317                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1318            end
1319        end
1320        if isequal(min(nbslice),max(nbslice))
1321            nbslice=nbslice(1);
1322        else
1323            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1324            return
1325        end
1326        if ~isempty(nbslice) && Name(i)=='_'
1327            Mask.Base=[FileBase Name(i:ind_mask+3)];
1328            Mask.NbSlice=nbslice;
1329            num_i1=mod(num_i1-1,nbslice)+1;
1330            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1331            [RootPath,RootFile]=fileparts(Mask.Base);
1332            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1333            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1334            mdetect=exist(maskname,'file');
1335            if mdetect
1336                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1337                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1338                set(handles.CheckMask,'UserData',Mask);
1339                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1340                if nbslice > 1
1341                    set(handles.slices,'value',1)
1342                    slices_Callback(hObject, eventdata, handles)
1343                end
1344            end
1345        end
1346    end
1347    errormsg=[];%default
1348    if mdetect==0
1349        [FileName, PathName, filterindex] = uigetfile( ...
1350            {'*.png', ' (*.png)';
1351            '*.png',  '.png files '; ...
1352            '*.*', 'All Files (*.*)'}, ...
1353            'Pick a mask file *.png',FileBase);
1354        maskname=fullfile(PathName,FileName);
1355        if ~exist(maskname,'file')
1356            errormsg='no file browsed';
1357        end
1358        [RootDir,tild,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1359%         [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1360        Mask.Base=fullfile(RootDir,RootFile);
1361        Mask.NbSlice=1;
1362        set(handles.CheckMask,'UserData',Mask);
1363        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1364    end
1365    if isempty(errormsg)
1366        errormsg=update_mask(handles,num_i1,num_j1);
1367    end
1368    if ~isempty(errormsg)
1369            set(handles.CheckMask,'Value',0)
1370            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1371     end
1372else % desactivate mask display
1373    MaskData=get(handles.CheckMask,'UserData');
1374    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1375          delete(MaskData.maskhandle)   
1376    end
1377    set(handles.CheckMask,'UserData',[])   
1378    UvData=get(handles.uvmat,'UserData');
1379    if isfield(UvData,'MaskName')
1380        UvData=rmfield(UvData,'MaskName');
1381        set(handles.uvmat,'UserData',UvData)
1382    end
1383    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1384end
1385
1386%------------------------------------------------------------------------
1387function errormsg=update_mask(handles,num_i1,num_j1)
1388%------------------------------------------------------------------------
1389errormsg=[];%default
1390MaskData=get(handles.CheckMask,'UserData');
1391if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1392    uistack(MaskData.maskhandle,'top');
1393end
1394num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1395[RootPath,RootFile]=fileparts(MaskData.Base);
1396MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1397%MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1398% huvmat=get(handles.CheckMask,'parent');
1399UvData=get(handles.uvmat,'UserData');
1400%update mask image if the mask is new
1401if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1402    UvData.MaskName=MaskName; %update the recorded name on UvData
1403    set(handles.uvmat,'UserData',UvData);
1404    if ~exist(MaskName,'file')
1405        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1406            delete(MaskData.maskhandle)   
1407        end
1408    else
1409        %read mask image
1410        Mask.AName='image';
1411        Mask.A=imread(MaskName);
1412        npxy=size(Mask.A);
1413        test_error=0;
1414        if length(npxy)>2
1415            errormsg=[MaskName ' is not a grey scale image'];
1416            return
1417        elseif ~isa(Mask.A,'uint8')
1418            errormsg=[MaskName ' is not a 8 bit grey level image'];
1419            return
1420        end
1421        Mask.AX=[0.5 npxy(2)-0.5];
1422        Mask.AY=[npxy(1)-0.5 0.5 ];
1423        Mask.CoordUnit='pixel';
1424        if isequal(get(handles.slices,'Value'),1)
1425           NbSlice=str2num(get(handles.nb_slice,'String'));
1426           num_i1=str2num(get(handles.i1,'String'));
1427           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1428        end
1429        %px to phys or other transform on field
1430         menu_transform=get(handles.transform_fct,'String');
1431        choice_value=get(handles.transform_fct,'Value');
1432        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1433        transform_list=get(handles.transform_fct,'UserData');
1434        transform=transform_list{choice_value};
1435        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1436            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1437                Calib=UvData.XmlData{1}.GeometryCalib;
1438                Mask=transform(Mask,UvData.XmlData{1});
1439            end
1440        end
1441        flagmask=Mask.A < 200;
1442       
1443        %make brown color image
1444        imflag(:,:,1)=0.9*flagmask;
1445        imflag(:,:,2)=0.7*flagmask;
1446        imflag(:,:,3)=zeros(size(flagmask));
1447       
1448        %update mask image
1449        hmask=[]; %default
1450        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1451            hmask=MaskData.maskhandle;
1452        end
1453        if ~isempty(hmask)
1454            set(hmask,'CData',imflag)   
1455            set(hmask,'AlphaData',flagmask*0.6)
1456            set(hmask,'XData',Mask.AX);
1457            set(hmask,'YData',Mask.AY);
1458%             uistack(hmask,'top')
1459        else
1460            axes(handles.axes3)
1461            hold on   
1462            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1463%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1464            set(handles.CheckMask,'UserData',MaskData)
1465        end
1466    end
1467end
1468
1469%------------------------------------------------------------------------
1470%------------------------------------------------------------------------
1471% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1472%------------------------------------------------------------------------
1473
1474%------------------------------------------------------------------------
1475% --- Executes on button press in runplus: make one step forward and call
1476% --- run0. The step forward is along the fields series 1 or 2 depending on
1477% --- the scan_i and scan_j check box (exclusive each other)
1478function runplus_Callback(hObject, eventdata, handles)
1479%------------------------------------------------------------------------
1480set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1481drawnow
1482%TODO: introduce the option: increment ='*' to move to the next available view
1483increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1484% if isnan(increment)
1485%     set(handles.increment_scan,'String','1')%default value
1486%     increment=1;
1487% end
1488errormsg=runpm(hObject,eventdata,handles,increment);
1489if ~isempty(errormsg)
1490    msgbox_uvmat('ERROR',errormsg);
1491end
1492set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1493
1494%------------------------------------------------------------------------
1495% --- Executes on button press in runmin: make one step backward and call
1496% --- run0. The step backward is along the fields series 1 or 2 depending on
1497% --- the scan_i and scan_j check box (exclusive each other)
1498function runmin_Callback(hObject, eventdata, handles)
1499%------------------------------------------------------------------------
1500set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1501drawnow
1502increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1503% if isnan(increment)
1504%     set(handles.increment_scan,'String','1')%default value
1505%     increment=1;
1506% end
1507errormsg=runpm(hObject,eventdata,handles,increment);
1508if ~isempty(errormsg)
1509    msgbox_uvmat('ERROR',errormsg);
1510end
1511set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1512
1513%------------------------------------------------------------------------
1514% -- Executes on button press in Movie: make a series of +> steps
1515function Movie_Callback(hObject, eventdata, handles)
1516%------------------------------------------------------------------------
1517set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1518drawnow
1519increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1520% if isnan(increment)
1521%     set(handles.increment_scan,'String','1')%default value
1522%     increment=1;
1523% end
1524set(handles.STOP,'Visible','on')
1525set(handles.speed,'Visible','on')
1526set(handles.speed_txt,'Visible','on')
1527set(handles.Movie,'BusyAction','queue')
1528UvData=get(handles.uvmat,'UserData');
1529
1530while get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1531        errormsg=runpm(hObject,eventdata,handles,increment);
1532        if ~isempty(errormsg)
1533            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1534            return
1535        end
1536        pause(1.02-get(handles.speed,'Value'))% wait for next image
1537end
1538if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1539    UvData.aviobj=close(UvData.aviobj);
1540   set(handles.uvmat,'UserData',UvData);
1541end
1542set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1543
1544%------------------------------------------------------------------------
1545% -- Executes on button press in Movie: make a series of <- steps
1546function MovieBackward_Callback(hObject, eventdata, handles)
1547%------------------------------------------------------------------------
1548set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1549drawnow
1550increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1551set(handles.STOP,'Visible','on')
1552set(handles.speed,'Visible','on')
1553set(handles.speed_txt,'Visible','on')
1554set(handles.MovieBackward,'BusyAction','queue')
1555UvData=get(handles.uvmat,'UserData');
1556
1557while get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1558        errormsg=runpm(hObject,eventdata,handles,increment);
1559        if ~isempty(errormsg)
1560            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1561            return
1562        end
1563        pause(1.02-get(handles.speed,'Value'))% wait for next image
1564end
1565if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1566    UvData.aviobj=close(UvData.aviobj);
1567   set(handles.uvmat,'UserData',UvData);
1568end
1569set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1570
1571%------------------------------------------------------------------------
1572function STOP_Callback(hObject, eventdata, handles)
1573%------------------------------------------------------------------------
1574set(handles.movie_pair,'BusyAction','Cancel')
1575set(handles.movie_pair,'value',0)
1576set(handles.Movie,'BusyAction','Cancel')
1577set(handles.MovieBackward,'BusyAction','Cancel')
1578set(handles.MenuExportMovie,'BusyAction','Cancel')
1579set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1580set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1581set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1582
1583%------------------------------------------------------------------------
1584% --- function activated by runplus and run minus
1585function errormsg=runpm(hObject,eventdata,handles,increment)
1586%------------------------------------------------------------------------
1587errormsg='';%default
1588%% check for movie pair status
1589movie_status=get(handles.movie_pair,'Value');
1590if isequal(movie_status,1)
1591    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1592end
1593
1594%% read the current input file name(s) and field indices
1595InputFile=read_GUI(handles.InputFile);
1596InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1597InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1598FileExt=InputFile.FileExt;
1599NomType=get(handles.NomType,'String');
1600i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1601i2=[];%default
1602if strcmp(get(handles.i2,'Visible'),'on')
1603    i2=str2num(get(handles.i2,'String'));
1604end
1605j1=[];
1606if strcmp(get(handles.j1,'Visible'),'on')
1607    j1=stra2num(get(handles.j1,'String'));
1608end
1609j2=j1;
1610if strcmp(get(handles.j2,'Visible'),'on')
1611    j2=stra2num(get(handles.j2,'String'));
1612end
1613sub_value= get(handles.SubField,'Value');
1614if sub_value % a second input file has been entered
1615     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1616    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);
1617%     InputFile.NomType_1=get(handles.NomType_1,'String');
1618else
1619    filename_1=[];
1620end   
1621
1622%% increment (or decrement) the field indices and update the input filename(s)
1623CheckSearch=0;
1624if isempty(increment)
1625    CheckSearch=1;% search for the next available file
1626    set(handles.CheckFixPair,'Value',0)
1627end
1628CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1629
1630% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1631if CheckFixPair
1632    if get(handles.scan_i,'Value')==1% case of scanning along index i
1633        i1=i1+increment;
1634        i2=i2+increment;
1635        if sub_value
1636            i1_1=i1_1+increment;
1637            i2_1=i2_1+increment;
1638        end
1639    else % case of scanning along index j (burst numbers)
1640        j1=j1+increment;
1641        j2=j2+increment;
1642        if sub_value
1643            j1_1=j1_1+increment;
1644            j2_1=j2_1+increment;
1645        end
1646    end
1647   
1648% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected):
1649% the list of existing indices recorded in UvData is used
1650else
1651    UvData=get(handles.uvmat,'UserData');
1652    ref_i=i1;
1653    if ~isempty(i2)
1654        ref_i=floor((i1+i2)/2);% current reference index i
1655    end
1656    ref_j=1;
1657    if ~isempty(j1)
1658        ref_j=j1;
1659        if ~isempty(j2)
1660            ref_j=floor((j1+j2)/2);% current reference index j
1661        end
1662    end
1663    if ~isempty(increment)
1664        if get(handles.scan_i,'Value')==1% case of scanning along index i
1665            ref_i=ref_i+increment;% increment the current reference index i
1666        else % case of scanning along index j (burst numbers)
1667            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1668        end
1669    else % free increment
1670        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
1671            step=1;
1672        else
1673            step=-1;
1674        end
1675        if get(handles.scan_i,'Value')==1% case of scanning along index i
1676            ref_i=ref_i+step;
1677            while ref_i>=0  && size(UvData.i1_series{1},1)>=ref_i+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
1678                ref_i=ref_i+step;
1679            end
1680        else % case of scanning along index j (burst numbers)
1681            ref_j=ref_j+step;
1682            while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
1683                ref_j=ref_j+step;
1684            end
1685        end
1686    end
1687    if ref_i<0
1688        errormsg='minimum i index reached';
1689    elseif ref_j<0
1690        errormsg='minimum j index reached';
1691    elseif ref_i+1>size(UvData.i1_series{1},1)
1692        errormsg='maximum i index reached';
1693    elseif ref_j+1>size(UvData.i1_series{1},2)
1694        errormsg='maximum j index reached';
1695    end
1696    if ~isempty(errormsg)
1697        return
1698    end
1699    i1_subseries=UvData.i1_series{1}(ref_i+1,ref_j+1,:);
1700    i1_subseries=i1_subseries(i1_subseries>0);
1701    if isempty(i1_subseries)
1702        errormsg='no next file';
1703        return
1704    else
1705        i1=i1_subseries(end);
1706    end
1707    if ~isempty(UvData.i2_series{1})
1708        i2_subseries=UvData.i2_series{1}(ref_i+1,ref_j+1,:);
1709        i2_subseries=i2_subseries(i2_subseries>0);
1710        i2=i2_subseries(end);
1711    end
1712    if ~isempty(UvData.j1_series{1})
1713        j1_subseries=UvData.j1_series{1}(ref_i+1,ref_j+1,:);
1714        j1_subseries=j1_subseries(j1_subseries>0);
1715        j1=j1_subseries(end);
1716    end
1717    if ~isempty(UvData.j2_series{1})
1718        j2_subseries=UvData.j2_series{1}(ref_i+1,ref_j+1,:);
1719        j2_subseries=j2_subseries(j2_subseries>0);
1720        j2=j2_subseries(end);
1721    end 
1722    % case of a second file series
1723    if numel(UvData.i1_series)>=2
1724        i1_subseries=UvData.i1_series{2}(ref_i+1,ref_j+1,:);
1725        i1_subseries=i1_subseries(i1_subseries>0);
1726        i1_1=i1_subseries(end);
1727        if ~isempty(UvData.i2_series{2})
1728            i2_subseries=UvData.i2_series{2}(ref_i+1,ref_j+1,:);
1729            i2_subseries=i2_subseries(i2_subseries>0);
1730            i2_1=i2_subseries(end);
1731        end
1732        if ~isempty(UvData.j1_series{2})
1733            j1_subseries=UvData.j1_series{2}(ref_i+1,ref_j+1,:);
1734            j1_subseries=j1_subseries(j1_subseries>0);
1735            j1_1=j1_subseries(end);
1736        end
1737        if ~isempty(UvData.j2_series{2})
1738            j2_subseries=UvData.j2_series{2}(ref_i+1,ref_j+1,:);
1739            j2_subseries=j2_subseries(j2_subseries>0);
1740            j2_1=j2_subseries(end);
1741        end
1742    end
1743end
1744filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1745if sub_value
1746    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);
1747end
1748
1749%% refresh plots
1750errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);
1751
1752%% update the index counters if the index move is successfull
1753if isempty(errormsg)
1754    set(handles.i1,'String',num2stra(i1,NomType,1));
1755    if isequal(i2,i1)
1756        set(handles.i2,'String','');
1757    else
1758        set(handles.i2,'String',num2stra(i2,NomType,1));
1759    end
1760    set(handles.j1,'String',num2stra(j1,NomType,2));
1761    if isequal(j2,j1)
1762        set(handles.j2,'String','');
1763    else
1764        set(handles.j2,'String',num2stra(j2,NomType,2));
1765    end
1766    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1767    set(handles.FileIndex,'String',indices);
1768    if ~isempty(filename_1)
1769        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1770        set(handles.FileIndex_1,'String',indices_1);
1771    end
1772    if isequal(movie_status,1)
1773        set(handles.movie_pair,'Value',1)
1774        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1775    end
1776end
1777
1778%------------------------------------------------------------------------
1779% --- Executes on button press in movie_pair: create an alternating movie with two view
1780function movie_pair_Callback(hObject, eventdata, handles)
1781%------------------------------------------------------------------------
1782%% stop movie action if the movie_pair button is off
1783if ~get(handles.movie_pair,'value')
1784    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1785    set(handles.i2,'String','')
1786    set(handles.j2,'String','')
1787    return
1788else
1789    set(handles.movie_pair,'BusyAction','queue')
1790end
1791
1792%% initialisation
1793set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1794drawnow
1795list_fields=get(handles.Fields,'String');% list menu fields
1796index_fields=get(handles.Fields,'Value');% selected string index
1797FieldName=list_fields{index_fields}; % selected field
1798UvData=get(handles.uvmat,'UserData');
1799if isequal(FieldName,'image')
1800    test_1=0;
1801    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1802    NomType=get(handles.NomType,'String');
1803else
1804    list_fields=get(handles.Fields_1,'String');% list menu fields
1805    index_fields=get(handles.Fields_1,'Value');% selected string index
1806    FieldName=list_fields{index_fields}; % selected field
1807    if isequal(FieldName,'image')
1808        test_1=1;
1809        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1810    else
1811        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1812        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1813        set(handles.movie_pair,'Value',0)
1814        return
1815    end
1816end
1817num_i1=str2num(get(handles.i1,'String'));
1818num_j1=stra2num(get(handles.j1,'String'));
1819num_i2=str2num(get(handles.i2,'String'));
1820num_j2=stra2num(get(handles.j2,'String'));
1821if isempty(num_j2)
1822    if isempty(num_i2)   
1823        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1824        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1825         set(handles.movie_pair,'Value',0)
1826        return
1827    else
1828        num_j2=num_j1;%repeat the index i1 by default
1829    end
1830end
1831if isempty(num_i2)
1832    num_i2=num_i1;%repeat the index i1 by default
1833end
1834% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1835imaname_1=fullfile_uvmat(RootPath,'',RootFile,Ext,NomType,num_i2,[],num_j2);
1836if ~exist(imaname_1,'file')
1837      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1838      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1839       set(handles.movie_pair,'Value',0)
1840      return
1841end
1842
1843%% read the second image
1844Field.AName='image';
1845if test_1
1846    Field_a=UvData.Field_1;
1847else
1848    Field_a=UvData.Field;
1849end
1850Field_b.AX=Field_a.AX;
1851Field_b.AY=Field_a.AY;
1852% z index
1853nbslice=str2double(get(handles.nb_slice,'String'));
1854if ~isempty(nbslice)
1855    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1856end
1857Field_b.CoordUnit='pixel';
1858
1859%% determine the input file type
1860if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1861    FileType='movie';
1862elseif isequal(lower(Ext),'.avi')
1863    FileType='avi';
1864elseif isequal(lower(Ext),'.vol')
1865    FileType='vol';
1866else
1867   form=imformats(Ext(2:end));
1868   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1869       if isequal(NomType,'*');
1870           FileType='multimage';
1871       else
1872           FileType='image';
1873       end
1874   end
1875end
1876switch FileType
1877        case 'movie'
1878            if test_1
1879                Field_b.A=read(UvData.MovieObject{2},num_i2);
1880            else
1881                Field_b.A=read(UvData.MovieObject{1},num_i2);
1882            end
1883        case 'avi'
1884            mov=aviread(imaname_1,num_i2);
1885            Field_b.A=frame2im(mov(1));
1886        case 'vol'
1887            Field_b.A=imread(imaname_1);
1888        case 'multimage'
1889            Field_b.A=imread(imaname_1,num_i2);
1890        case 'image'
1891            Field_b.A=imread(imaname_1);
1892end
1893if get(handles.slices,'Value')
1894    Field.ZIndex=str2double(get(handles.z_index,'String'));
1895end
1896
1897%px to phys or other transform on field
1898menu_transform=get(handles.transform_fct,'String');
1899choice_value=get(handles.transform_fct,'Value');
1900transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1901transform_list=get(handles.transform_fct,'UserData');
1902transform=transform_list{choice_value};
1903if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1904    if test_1 && isfield(UvData,'XmlData') && numel(UvData.XmlData)==2 && isfield(UvData.XmlData{2},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1905        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
1906        Field_b=transform(Field_b,UvData.XmlData{2});
1907    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
1908        Field_b=transform(Field_b,UvData.XmlData{1});
1909    end
1910end
1911
1912 % make movie until movie speed is set to 0 or STOP is activated
1913hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1914set(handles.STOP,'Visible','on')
1915set(handles.speed,'Visible','on')
1916set(handles.speed_txt,'Visible','on')
1917while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1918    % read and plot the series of images in non erase mode
1919    set(hima,'CData',Field_b.A);
1920    pause(1.02-get(handles.speed,'Value'));% wait for next image
1921    set(hima,'CData',Field_a.A);
1922    pause(1.02-get(handles.speed,'Value'));% wait for next image
1923end
1924set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1925 set(handles.movie_pair,'Value',0)
1926
1927%------------------------------------------------------------------------
1928% --- Executes on button press in run0.
1929function run0_Callback(hObject, eventdata, handles)
1930%------------------------------------------------------------------------
1931set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1932drawnow
1933[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1934filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1935filename_1=[];%default
1936if get(handles.SubField,'Value')
1937    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
1938    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
1939end
1940num_i1=stra2num(get(handles.i1,'String'));
1941num_i2=stra2num(get(handles.i2,'String'));
1942num_j1=stra2num(get(handles.j1,'String'));
1943num_j2=stra2num(get(handles.j2,'String'));
1944
1945errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
1946
1947if ~isempty(errormsg)
1948      msgbox_uvmat('ERROR',errormsg);
1949else
1950    set(handles.i1,'BackgroundColor',[1 1 1])
1951    set(handles.i2,'BackgroundColor',[1 1 1])
1952    set(handles.j1,'BackgroundColor',[1 1 1])
1953    set(handles.j2,'BackgroundColor',[1 1 1])
1954    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1955    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1956end   
1957set(handles.run0,'BackgroundColor',[1 0 0])
1958
1959
1960%------------------------------------------------------------------------
1961% --- read the input files and refresh all the plots, including projection.
1962% OUTPUT:
1963%  errormsg: error message char string  =[] by default
1964% INPUT:
1965% filename: first input file (=[] in the absence of input file)
1966% filename_1: second input file (=[] in the asbsenc of secodn input file)
1967% num_i1,num_i2,num_j1,num_j2; frame indices
1968% Field: structure describing an optional input field (then replace the input file)
1969
1970function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
1971%------------------------------------------------------------------------
1972
1973%% initialisation
1974abstime=[];
1975abstime_1=[];
1976dt=[];
1977if ~exist('Field','var')
1978    Field={};
1979end
1980UvData=get(handles.uvmat,'UserData');
1981if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1982    delete(handles.UVMAT_title)
1983end
1984
1985%% determine the main input file information for action
1986FileType=[];%default
1987if ~exist(filename,'file')
1988    errormsg=['input file ' filename ' does not exist'];
1989    return
1990end
1991NomType=get(handles.NomType,'String');
1992% NomType=get(handles.FileIndex,'UserData');
1993%update the z position index
1994nbslice_str=get(handles.nb_slice,'String');
1995if isequal(nbslice_str,'volume')%NOT USED
1996    z_index=num_j1;
1997    set(handles.z_index,'String',num2str(z_index))
1998else
1999    nbslice=str2num(nbslice_str);
2000    z_index=mod(num_i1-1,nbslice)+1;
2001    set(handles.z_index,'String',num2str(z_index))
2002end
2003% refresh menu for save_mask if relevant
2004masknumber=get(handles.masklevel,'String');
2005if length(masknumber)>=z_index
2006    set(handles.masklevel,'Value',z_index)
2007end
2008
2009%% read the first input field if a filename has been introduced
2010ParamIn.ColorVar='';%default variable name for vector color
2011if ~isempty(filename)
2012    ObjectName=filename;
2013    FieldName='';%default
2014    VelType='';%default
2015%     FileType=UvData.FileType{1};
2016    switch UvData.FileType{1}
2017        case {'civx','civdata','netcdf'};
2018            list_fields=get(handles.Fields,'String');% list menu fields
2019  %          index_fields=get(handles.Fields,'Value');% selected string index
2020            FieldName= list_fields{get(handles.Fields,'Value')}; % selected field
2021            if ~strcmp(FieldName,'get_field...')
2022                if get(handles.FixVelType,'Value')
2023                    VelTypeList=get(handles.VelType,'String');
2024                    VelType=VelTypeList{get(handles.VelType,'Value')};
2025                end
2026            end
2027            if strcmp(FieldName,'velocity')
2028                list_code=get(handles.ColorCode,'String');% list menu fields
2029                index_code=get(handles.ColorCode,'Value');% selected string index
2030                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2031                    list_code=get(handles.ColorScalar,'String');% list menu fields
2032                    index_code=get(handles.ColorScalar,'Value');% selected string index
2033                    ParamIn.ColorVar= list_code{index_code}; % selected field
2034                end
2035            end
2036        case 'video'
2037            ObjectName=UvData.MovieObject{1};         
2038        case 'vol' %TODO: update
2039            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2040                ParamIn.Npy=UvData.XmlData.Npy;
2041                ParamIn.Npx=UvData.XmlData.Npx;
2042            else           
2043                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2044                return
2045            end
2046    end
2047    ParamIn.FieldName=FieldName;
2048    ParamIn.VelType=VelType;
2049    ParamIn.GUIName='get_field';
2050    [Field{1},ParamOut,errormsg] = read_field(ObjectName,UvData.FileType{1},ParamIn,num_i1);
2051    if ~isempty(errormsg)
2052        errormsg=['error in reading ' filename ': ' errormsg];
2053        return
2054    end 
2055    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2056        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2057        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2058    end
2059    if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2060        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2061    end
2062    if isfield(ParamOut,'TimeValue')
2063        Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2064    end
2065end
2066
2067%% choose and read a second field filename_1 if defined
2068VelType_1=[];%default
2069FieldName_1=[];
2070ParamOut_1=[];
2071if ~isempty(filename_1)
2072    if ~exist(filename_1,'file')
2073        errormsg=['second file ' filename_1 ' does not exist'];
2074        return
2075    end
2076    Name=filename_1;
2077    switch UvData.FileType{2}
2078        case {'civx','civdata','netcdf'};
2079            list_fields=get(handles.Fields_1,'String');% list menu fields
2080            FieldName_1= list_fields{get(handles.Fields_1,'Value')}; % selected field
2081            if ~strcmp(FieldName,'get_field...')
2082                if get(handles.FixVelType,'Value')
2083                    VelTypeList=get(handles.VelType_1,'String');
2084                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2085                end
2086            end
2087            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2088                list_code=get(handles.ColorCode,'String');% list menu fields
2089                index_code=get(handles.ColorCode,'Value');% selected string index
2090                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2091                    list_code=get(handles.ColorScalar,'String');% list menu fields
2092                    index_code=get(handles.ColorScalar,'Value');% selected string index
2093                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2094                end
2095            end
2096        case 'video'
2097            Name=UvData.MovieObject{2};
2098        case 'vol' %TODO: update
2099            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2100                ParamIn_1.Npy=UvData.XmlData.Npy;
2101                ParamIn_1.Npx=UvData.XmlData.Npx;
2102            else
2103                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2104                return
2105            end
2106    end
2107    if isequal(get(handles.NomType_1,'Visible'),'on')
2108    NomType_1=get(handles.NomType_1,'String');
2109    else
2110        NomType_1=get(handles.NomType,'String');
2111    end
2112    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2113    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2114        if isfield(UvData,'filename_1')%&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2115            test_keepdata_1= strcmp(filename_1,UvData.filename_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
2116        end
2117    end
2118    if test_keepdata_1
2119        Field{2}=UvData.Field_1;% keep the stored field
2120        ParamOut_1=UvData.ParamOut_1;
2121    else
2122        ParamIn_1.FieldName=FieldName_1;
2123        ParamIn_1.VelType=VelType_1;
2124        ParamIn_1.GUIName='get_field_1';
2125        [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,num_i1);
2126        if ~isempty(errormsg)
2127            errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
2128            return
2129        end
2130%         UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2131    end
2132end
2133
2134%% update uvmat interface
2135if isfield(ParamOut,'Npx')
2136    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2137    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2138elseif isfield(ParamOut_1,'Npx')
2139    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2140    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2141end
2142
2143%% update the display menu for the first velocity type (first menuline)
2144test_veltype=0;
2145% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2146if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2147    test_veltype=1;
2148    set(handles.VelType,'Visible','on')
2149    set(handles.VelType_1,'Visible','on')
2150    set(handles.FixVelType,'Visible','on')
2151    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2152    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2153    index_val=find(index_menu,1);
2154    if isempty(index_val)
2155        index_val=1;
2156    end
2157    set(handles.VelType,'Value',index_val)
2158    if ~get(handles.SubField,'value')
2159        set(handles.VelType,'String',menu)
2160        set(handles.VelType_1,'Value',1)
2161        set(handles.VelType_1,'String',[{''};menu])
2162    end
2163else
2164    set(handles.VelType,'Visible','off')
2165end
2166% display the Fields menu from the input file and pick the selected one:
2167field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2168set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2169set(handles.Fields,'Value',find(field_index,1))
2170
2171%% update the display menu for the second velocity type (second menuline)
2172
2173test_veltype_1=0;
2174if isempty(filename_1)
2175    set(handles.Fields_1,'Value',1); %update the field menu
2176    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2177elseif ~test_keepdata_1
2178    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2179        set(handles.VelType_1,'Visible','off')
2180    else
2181        test_veltype_1=1;
2182        set(handles.VelType_1,'Visible','on')
2183%         if ~get(handles.FixVelType,'Value')
2184            menu=set_veltype_display(ParamOut_1.CivStage);
2185            index_menu=strcmp(ParamOut_1.VelType,menu);
2186            set(handles.VelType_1,'Value',1+find(index_menu,1))
2187            set(handles.VelType_1,'String',[{''};menu])
2188%         end
2189    end
2190    % update the second field menu: the same quantity
2191    set(handles.Fields_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2192    % display the Fields menu from the input file and pick the selected one:
2193    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2194    set(handles.Fields_1,'Value',find(field_index,1)+1) 
2195%     % synchronise  with the first menu if the first selection is not 'velocity'
2196%     if ~strcmp(ParamOut.FieldName,'velocity')
2197%         field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2198%         set(handles.Fields_1,'Value',field_index); %update the field menu
2199%         ParamOut_1.FieldName=ParamOut.FieldName;
2200%         set(handles.Fields_1,'String',ParamOut_1.FieldList)
2201%     end
2202end
2203if test_veltype||test_veltype_1
2204     set(handles.FixVelType,'Visible','on')
2205else
2206     set(handles.FixVelType,'Visible','off')
2207end
2208
2209% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2210% set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2211% set(handles.Fields,'Value',find(field_index,1))
2212   
2213%% introduce w as background image by default for a new series (only for nbdim=2)
2214if ~isfield(UvData,'NewSeries')
2215    UvData.NewSeries=1;
2216end
2217%put W as background image by default if NbDim=2:
2218if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2219        set(handles.SubField,'Value',1);
2220        set(handles.RootPath_1,'String','"')
2221        set(handles.RootFile_1,'String','"')
2222        set(handles.SubDir_1,'String','"');
2223         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2224        set(handles.FileIndex_1,'String',indices)
2225        set(handles.FileExt_1,'String','"');
2226        set(handles.Fields_1,'Visible','on');
2227        set(handles.Fields_1,'Visible','on');
2228        set(handles.RootPath_1,'Visible','on')
2229        set(handles.RootFile_1,'Visible','on')
2230        set(handles.SubDir_1,'Visible','on');
2231        set(handles.FileIndex_1,'Visible','on');
2232        set(handles.FileExt_1,'Visible','on');
2233        set(handles.Fields_1,'Visible','on');
2234        Field{1}.AName='w';
2235end           
2236
2237
2238
2239%% display time
2240testimedoc=0;
2241TimeUnit='';
2242if isfield(Field{1},'Time')
2243    abstime=Field{1}.Time;%time read from the netcdf input file
2244end
2245if numel(Field)==2 && isfield(Field{2},'Time')
2246    abstime_1=Field{2}.Time;%time read from the netcdf input file
2247end
2248if isfield(Field{1},'Dt')
2249    dt=Field{1}.Dt;%dt read from the netcdf input file
2250    if isfield(Field{1},'TimeUnit')
2251       TimeUnit=Field{1}.TimeUnit;
2252    end
2253elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2254    dt=Field{2}.Dt;%dt read from the netcdf input file
2255    if isfield(Field{2},'TimeUnit')
2256       TimeUnit=Field{2}.TimeUnit;
2257    end
2258end
2259% time from xml file overset previous result
2260if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2261    if isempty(num_i2)||isnan(num_i2)
2262        num_i2=num_i1;
2263    end
2264    if isempty(num_j1)||isnan(num_j1)
2265        num_j1=1;
2266    end
2267    if isempty(num_j2)||isnan(num_j2)
2268        num_j2=num_j1;
2269    end
2270    siz=size(UvData.XmlData{1}.Time);
2271    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2272        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2273        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2274        Field{1}.Dt=dt;
2275        if isfield(UvData.XmlData{1},'TimeUnit')
2276            TimeUnit=UvData.XmlData{1}.TimeUnit;
2277        end
2278    end
2279    if numel(UvData.XmlData)==2
2280        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2281        if isempty(num_i2)
2282            num_i2=num_i1;
2283        end
2284        if isempty(num_j1)
2285            num_j1=1;
2286        end
2287        if isempty(num_j2)
2288            num_j2=num_j1;
2289        end
2290        siz=size(UvData.XmlData{2}.Time);
2291        if ~isempty(num_i1) && siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2292            abstime_1=(UvData.XmlData{2}.Time(num_i1,num_j1)+UvData.XmlData{2}.Time(num_i2,num_j2))/2;%overset the time read from files
2293            Field{2}.Dt=(UvData.XmlData{2}.Time(num_i2,num_j2)-UvData.XmlData{2}.Time(num_i1,num_j1));
2294        end
2295    end
2296end
2297if ~isequal(numel(abstime),1)
2298    abstime=[];
2299end
2300if ~isequal(numel(abstime_1),1)
2301      abstime_1=[];
2302end 
2303set(handles.abs_time,'String',num2str(abstime,4))
2304set(handles.abs_time_1,'String',num2str(abstime_1,4))
2305% if testimedoc && isfield(UvData,'dt')
2306%     dt=UvData.dt;
2307% end
2308if isempty(dt)||isequal(dt,0)
2309    set(handles.Dt_txt,'String','')
2310else
2311    if  isempty(TimeUnit)
2312        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2313    else
2314        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2315    end
2316end
2317
2318
2319%% store the current open names, fields and vel types in uvmat interface
2320UvData.filename_1=filename_1;
2321
2322%% apply coordinate transform or other user fct
2323XmlData=[];%default
2324XmlData_1=[];%default
2325if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2326    XmlData=UvData.XmlData{1};
2327    if numel(UvData.XmlData)==2
2328        XmlData_1=UvData.XmlData{2};
2329    end
2330end
2331choice_value=get(handles.transform_fct,'Value');
2332transform_list=get(handles.transform_fct,'UserData');
2333transform=transform_list{choice_value};%selected function handles
2334% z index
2335if ~isempty(filename)
2336    Field{1}.ZIndex=z_index;
2337end
2338if ~isempty(transform)
2339    if length(Field)>=2
2340        Field{2}.ZIndex=z_index;
2341        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2342        if isempty(Field{2})
2343            Field(2)=[];
2344        end
2345    else
2346        Field{1}=transform(Field{1},XmlData);
2347    end
2348    %% update tps in phys coordinates if needed
2349    if (strcmp(VelType,'filter1')||strcmp(VelType,'filter2'))&& strcmp(UvData.FileType{1},'civdata')&&isfield(Field{1},'U')&& isfield(Field{1},'V')
2350        Field{1}.X=Field{1}.X(Field{1}.FF==0);
2351        Field{1}.Y=Field{1}.Y(Field{1}.FF==0);
2352        Field{1}.U=Field{1}.U(Field{1}.FF==0);
2353        Field{1}.V=Field{1}.V(Field{1}.FF==0);
2354        [Field{1}.SubRange,Field{1}.NbSites,Field{1}.Coord_tps,Field{1}.U_tps,Field{1}.V_tps]=filter_tps([Field{1}.X Field{1}.Y],Field{1}.U,Field{1}.V,[],Field{1}.Patch1_SubDomain,0);
2355    end
2356    if numel(Field)==2 && ~test_keepdata_1 && isequal(UvData.FileType{2}(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2357        %update tps in phys coordinates if needed
2358        if (strcmp(VelType_1,'filter1')||strcmp(VelType_1,'filter2'))&& strcmp(UvData.FileType{2},'civdata')&&isfield(Field{2},'U')&& isfield(Field{2},'V')
2359            Field{2}.X=Field{2}.X(Field{2}.FF==0);
2360            Field{2}.Y=Field{1}.Y(Field{2}.FF==0);
2361            Field{2}.U=Field{1}.U(Field{2}.FF==0);
2362            Field{2}.V=Field{1}.V(Field{2}.FF==0);
2363            [Field{2}.SubRange,Field{2}.NbSites,Field{2}.Coord_tps,Field{2}.U_tps,Field{2}.V_tps]=filter_tps([Field{2}.X Field{2}.Y],Field{2}.U,Field{2}.V,[],1500,0);
2364        end
2365    end
2366end
2367
2368%% calculate scalar
2369if ~strcmp(ParamOut.FieldName,'get_field...')&& (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))%&&~strcmp(ParamOut.FieldName,'velocity')&& ~strcmp(ParamOut.FieldName,'get_field...');% ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
2370    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2371end
2372if numel(Field)==2 && ~strcmp(ParamOut_1.FieldName,'get_field...')&& ~test_keepdata_1 && (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))  &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2373     Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2374end
2375
2376%% combine the two input fields (e.g. substract velocity fields)
2377%Field{1}.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}];
2378if numel(Field)==2
2379%    Field{2}.FieldList=[{ParamOut_1.FieldName} {ParamOut_1.ColorVar}];
2380   [UvData.Field,errormsg]=sub_field(Field{1},Field{2}); 
2381   UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2382   UvData.ParamOut_1=ParamOut_1;
2383else
2384   UvData.Field=Field{1};
2385end
2386if ~isempty(errormsg)
2387    errormsg=['error in uvmat/refresh_field/sub_field:' errormsg];
2388    return
2389end
2390%UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation
2391
2392
2393%% get bounds and mesh (needed for mouse action and to open set_object)
2394test_x=0;
2395test_z=0;% test for unstructured z coordinate
2396[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);
2397if ~isempty(errormsg)
2398    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];
2399    return
2400end
2401[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);
2402if ~isempty(errormsg)
2403    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];
2404    return
2405end
2406[NbDim,imax]=max(NbDim);% spatial dimension of the input field
2407if isfield(UvData.Field,'NbDim')
2408    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2409end
2410XName=''; %default
2411YName='';
2412if ~isempty(VarType{imax}.coord_x)  && ~isempty(VarType{imax}.coord_y)    %unstructured coordinates
2413    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2414    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2415    nbvec=length(UvData.Field.(XName));%nbre of measurement points (e.g. vectors)
2416    test_x=1;%test for unstructured coordinates
2417    if ~isempty(VarType{imax}.coord_z)
2418        ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2419    else
2420        NbDim=2;
2421    end
2422elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0 %structured coordinate
2423    XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2424    if NbDim> 1 && VarType{imax}.coord(NbDim-1)>0
2425        YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2426    end
2427    VarIndex=CellVarIndex{imax}; % list of variable indices
2428    DimIndex=VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2429    nbpoints_x=DimValue(DimIndex(NbDim));
2430    XMax=nbpoints_x;%default
2431    XMin=1;%default
2432end
2433%% object visibility
2434if NbDim>=2
2435    set(handles.Objects,'Visible','on')
2436    set(handles.ListObject_1_title,'Visible','on')
2437    set(handles.ListObject_1,'Visible','on')
2438else% usual (x,y) plots: no projection object
2439    set(handles.Objects,'Visible','off')
2440    set(handles.ListObject_title,'Visible','off')
2441    set(handles.ListObject_1,'Visible','off')
2442end
2443if NbDim==3
2444    if ~test_x
2445        ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2446    end
2447    eval(['ZMax=max(UvData.Field.' ZName ');'])
2448    eval(['ZMin=min(UvData.Field.' ZName ');'])
2449    UvData.Field.ZMax=ZMax;
2450    UvData.Field.ZMin=ZMin;
2451    test_z=1;
2452    if isequal(ZMin,ZMax)%no z dependency
2453        NbDim=2;
2454        test_z=0;
2455    end
2456end
2457
2458if ~isempty (XName)
2459    XMax=max(max(UvData.Field.(XName)));
2460    XMin=min(min(UvData.Field.(XName)));
2461    UvData.Field.NbDim=NbDim;
2462    UvData.Field.XMax=XMax;
2463    UvData.Field.XMin=XMin;
2464    if NbDim >1&& ~isempty(YName)
2465        YMax=max(max(UvData.Field.(YName)));
2466        YMin=min(min(UvData.Field.(YName)));
2467        UvData.Field.YMax=YMax;
2468        UvData.Field.YMin=YMin;
2469    end
2470    nbvec=length(UvData.Field.(XName));
2471    if test_x %unstructured coordinates
2472        if test_z
2473            UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2474            UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2475        else
2476            UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2477        end
2478    end
2479end
2480if ~test_x
2481    %         VarIndex=CellVarIndex{imax}; % list of variable indices
2482    %         DimIndex=VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2483    %         nbpoints_x=DimValue(DimIndex(NbDim));
2484    DX=(XMax-XMin)/(nbpoints_x-1);
2485    if NbDim >1
2486        nbpoints_y=DimValue(DimIndex(NbDim-1));
2487        if isempty(YName)% if the y coordinate is not expressed, it is taken as the matrix index
2488            DY=1;
2489            UvData.Field.YMax=nbpoints_y;
2490            UvData.Field.YMin=1;
2491        else
2492            DY=(YMax-YMin)/(nbpoints_y-1);
2493        end
2494    end
2495    if NbDim==3
2496        nbpoints_z=DimValue(DimIndex(1));
2497        DZ=(ZMax-ZMin)/(nbpoints_z-1);
2498        UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2499        UvData.Field.ZMax=ZMax;
2500        UvData.Field.ZMin=ZMin;
2501    else
2502        UvData.Field.Mesh=DX;%sqrt(DX*DY);
2503    end
2504end
2505% adjust the mesh to a value 1, 2 , 5 *10^n
2506ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude
2507if UvData.Field.Mesh/ord>=5
2508    UvData.Field.Mesh=5*ord;
2509elseif UvData.Field.Mesh/ord>=2
2510    UvData.Field.Mesh=2*ord;
2511else
2512    UvData.Field.Mesh=ord;
2513end
2514        UvData.Object{1}.Type='plane';%main plotting plane
2515        UvData.Object{1}.ProjMode='projection';%main plotting plane
2516        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2517        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2518
2519%% 3D case (menuvolume)
2520if NbDim==3% && UvData.NewSeries
2521    test_set_object=1;
2522    hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2523    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2524    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2525    if ~isempty(hset_object) %if set_object is detected
2526          delete(hset_object);% delete the GUI set_object if it does not fit
2527    end
2528    if test_set_object% reinitiate the GUI set_object
2529        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
2530%         UvData.Object{1}.Type='plane';%main plotting plane
2531%         UvData.Object{1}.ProjMode='projection';%main plotting plane
2532%         UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2533%         UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2534        UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2535        UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2536        UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2537        UvData.Object{1}.Angle=[0 0 0];
2538        UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2539        UvData.Object{1}.Name='1-PLANE';
2540        UvData.Object{1}.enable_plot=1;
2541        set_object(UvData.Object{1},handles,ZBounds);
2542        set(handles.ListObject,'Value',1);
2543        set(handles.ListObject,'String',{'1-PLANE'});
2544        set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2545        edit_object_Callback([],[], handles)
2546    end
2547    %multilevel case (single menuplane in a 3D space)
2548elseif isfield(UvData,'Z')
2549    if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2550        XmlData=UvData.XmlData{1};
2551        if isfield(XmlData,'PlanePos')
2552            UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2553        end
2554        if isfield(XmlData,'PlaneAngle')
2555            siz=size(XmlData.PlaneAngle);
2556            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2557            UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2558        end
2559    elseif isfield(UvData,'ZIndex')
2560        UvData.Object{1}.ZObject=UvData.ZIndex;
2561    end
2562else
2563%     % create a default projection
2564%     UvData.Object{1}.ProjMode='projection';%main plotting plane
2565%     UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2566%     set(handles.ListObject,'Value',1);
2567%     list_object=get(handles.ListObject,'String');
2568%     if isempty(list_object)
2569%         list_object={''};
2570%     elseif ~isempty(list_object{1})
2571%         list_object=[{''};list_object];
2572%     end
2573%     set(handles.ListObject,'String',list_object);
2574% %     set(handles.list_object_2,'String',list_object);
2575end
2576testnewseries=UvData.NewSeries;
2577UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2578set(handles.uvmat,'UserData',UvData)
2579
2580%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2581% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2582%     set(handles.num_MinA,'String','0')
2583%     set(handles.num_MaxA,'String','255')
2584% end
2585
2586%% Plot the projections on the selected  projection objects
2587% main projection object (uvmat display)
2588list_object=get(handles.ListObject_1,'String');
2589if isequal(list_object,{''})%refresh list of objects if the menu is empty
2590    UvData.Object={[]};
2591    set(handles.ListObject_1,'Value',1)
2592end
2593IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2594if IndexObj(1)> numel(UvData.Object)
2595    IndexObj(1)=1;%select the first object if the selected one does not exist
2596    set(handles.ListObject_1,'Value',1)
2597end
2598IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2599if isequal(IndexObj(2),IndexObj(1))
2600    IndexObj(2)=[];
2601end
2602plot_handles{1}=handles;
2603if isfield(UvData,'plotaxes')%case of movies
2604    haxes(1)=UvData.plotaxes;
2605else
2606    haxes(1)=handles.axes3;
2607end
2608%PlotParam{1}=read_plot_param(handles);%read plotting parameters on the uvmat interfac
2609PlotParam{1}=read_GUI(handles.uvmat);
2610%default settings if vectors not visible
2611if ~isfield(PlotParam{1},'Vectors')
2612    PlotParam{1}.Vectors.MaxVec=1;
2613    PlotParam{1}.Vectors.MinVec=0;
2614    PlotParam{1}.Vectors.CheckFixVecColor=1;
2615    PlotParam{1}.Vectors.ColCode1=0.33;
2616    PlotParam{1}.Vectors.ColCode2=0.66;
2617    PlotParam{1}.Vectors.ColorScalar={'ima_cor'};
2618    PlotParam{1}.Vectors.ColorCode= {'rgb'};
2619end
2620%keeplim(1)=get(handles.CheckFixLimits,'Value');% test for fixed graph limits
2621PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2622
2623% second projection object (view_field display)
2624if length( IndexObj)>=2
2625    view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2626    if ~isempty(view_field_handle)
2627        plot_handles{2}=guidata(view_field_handle);
2628        haxes(2)=plot_handles{2}.axes3;
2629        PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2630        PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2631    end
2632end
2633
2634%% loop on the projection objects: one or two
2635for imap=1:numel(IndexObj)
2636    iobj=IndexObj(imap);
2637%      if imap==2 || check_proj==0  % field not yet projected) && ~isfield(UvData.Object{iobj},'Type')% case with no projection (only for the first empty object)
2638% %          [ObjectData,errormsg]=calc_field(UvData.Field.FieldList,UvData.Field);
2639% %      else
2640        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2641%      end
2642    if ~isempty(errormsg)
2643        return
2644    end
2645    if testnewseries
2646        PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2647        if isfield(ObjectData,'CoordUnit')
2648        PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2649        PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2650        end
2651    end
2652    %use of mask (TODO: check)
2653    if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2654        flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2655        AX=ObjectData.AX;%x coordiantes for the scalar field
2656        AY=ObjectData.AY;%y coordinates for the scalar field
2657        MaskX=ObjectData.MaskX;%x coordiantes for the mask
2658        MaskY=ObjectData.MaskY;%y coordiantes for the mask
2659        if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2660            nxy=size(flag_mask);
2661            sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2662            sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2663            x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2664            y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2665            %project on the positions of the scalar
2666            npxy=size(ObjectData.A);
2667            dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2668            dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2669            xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2670            yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2671            [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2672            flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2673        end
2674        AClass=class(ObjectData.A);
2675        ObjectData.A=flag_mask.*double(ObjectData.A);
2676        ObjectData.A=feval(AClass,ObjectData.A);
2677        ind_off=[];
2678        if isfield(ObjectData,'ListVarName')
2679            for ilist=1:length(ObjectData.ListVarName)
2680                if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2681                    ind_off=[ind_off ilist];
2682                end
2683            end
2684            ObjectData.ListVarName(ind_off)=[];
2685            VarDimIndex(ind_off)=[];
2686            ind_off=[];
2687            for ilist=1:length(ListDimName)
2688                if isequal(ListDimName{ilist},'MaskX') || isequal(ListDimName{ilist},'MaskY')
2689                    ind_off=[ind_off ilist];
2690                end
2691            end
2692            ListDimName(ind_off)=[];
2693            DimValue(ind_off)=[];
2694        end
2695    end
2696    if ~isempty(ObjectData)
2697       
2698        PlotType='none'; %default
2699        if imap==2 && isempty(view_field_handle)
2700            view_field(ObjectData)
2701        else
2702            [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2703            write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2704            if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2705                ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2706            end
2707        end
2708        if isequal(PlotType,'none')
2709            hget_field=findobj(allchild(0),'name','get_field');
2710            if isempty(hget_field)
2711                get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2712            end
2713            errormsg='The field defined by get_field cannot be plotted';
2714            return
2715        end
2716    end
2717end
2718
2719%% update the mask
2720if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2721   update_mask(handles,num_i1,num_i2);
2722end
2723
2724%% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2725menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2726ind_skip=[];
2727% nb_histo=1;
2728Ustring='';
2729Vstring='';
2730% suppress coordinates from the histogram menu
2731for ivar=1:numel(menu_histo)%l loop on field variables:
2732    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2733        Role=UvData.Field.VarAttribute{ivar}.Role;
2734        switch Role
2735            case {'coord_x','coord_y','coord_z','dimvar'}
2736                ind_skip=[ind_skip ivar];
2737            case {'vector_x'}
2738                Ustring=UvData.Field.ListVarName{ivar};
2739                ind_skip=[ind_skip ivar];
2740            case {'vector_y'}
2741                Vstring=UvData.Field.ListVarName{ivar};
2742                ind_skip=[ind_skip ivar];
2743        end
2744    end
2745    DimCell=UvData.Field.VarDimName{ivar};
2746    DimName='';
2747    if ischar(DimCell)
2748        DimName=DimCell;
2749    elseif iscell(DimCell)&& numel(DimCell)==1
2750        DimName=DimCell{1};
2751    end
2752    if strcmp(DimName,menu_histo{ivar})
2753        ind_skip=[ind_skip ivar];
2754    end
2755end
2756menu_histo(ind_skip)=[];% remove skipped items
2757if ~isempty(Ustring)
2758    menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2759end
2760
2761%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2762% display menus and plot histograms
2763test_v=0;
2764if ~isempty(menu_histo)
2765    set(handles.histo1_menu,'Value',1)
2766    set(handles.histo1_menu,'String',menu_histo)
2767    histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2768    % case of more than one variables (eg vector components)
2769%     if nb_histo > 1
2770%         test_v=1;
2771%         set(handles.histo2_menu,'Visible','on')
2772%         set(handles.histo_v,'Visible','on')
2773%         set(handles.histo2_menu,'String',menu_histo)
2774%         set(handles.histo2_menu,'Value',2)
2775%         histo2_menu_Callback(handles.histo2_menu,[], handles)% plot second histogram
2776%     end
2777end
2778% if ~test_v
2779%     set(handles.histo2_menu,'Visible','off')
2780%     set(handles.histo_v,'Visible','off')
2781%     cla(handles.histo_v)
2782%     set(handles.histo2_menu,'Value',1)
2783% end
2784%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2785%------------------------------------------------------------------------
2786function histo1_menu_Callback(hObject, eventdata, handles)
2787%--------------------------------------------
2788%plot first histo
2789%huvmat=get(handles.histo1_menu,'parent');
2790histo_menu=get(handles.histo1_menu,'String');
2791histo_value=get(handles.histo1_menu,'Value');
2792FieldName=histo_menu{histo_value};
2793% update_histo(handles.histo_u,handles.uvmat,FieldName)
2794%
2795% %------------------------------------------------------------------------
2796% function histo2_menu_Callback(hObject, eventdata, handles)
2797% %------------------------------------------------------------------------
2798% %plot second histo
2799% %huvmat=get(handles.histo2_menu,'parent');
2800% histo_menu=get(handles.histo2_menu,'String');
2801% histo_value=get(handles.histo2_menu,'Value');
2802% FieldName=histo_menu{histo_value};
2803% update_histo(handles.histo_v,handles.uvmat,FieldName)
2804%
2805% %------------------------------------------------------------------------
2806% %read the field .Fieldname stored in UvData and plot its histogram
2807% function update_histo(haxes,huvmat,FieldName)
2808%------------------------------------------------------------------------
2809UvData=get(handles.uvmat,'UserData');
2810Field=UvData.Field;
2811r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2812FieldName_2='';
2813if ~isempty(r)
2814    FieldName=r.var1;
2815    FieldName_2=r.var2;
2816end
2817if ~isfield(UvData.Field,FieldName)
2818    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2819    return
2820end
2821FieldHisto=Field.(FieldName);
2822if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2823    indsel=find(Field.FF==0);%find values marked as false
2824    if ~isempty(indsel)
2825        FieldHisto=FieldHisto(indsel);
2826        if ~isempty(FieldName_2)
2827            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2828        end
2829    end
2830end
2831if isempty(Field)
2832    msgbox_uvmat('ERROR',['empty field ' FieldName])
2833else
2834    nxy=size(FieldHisto);
2835    Amin=double(min(min(min(FieldHisto))));%min of field value
2836    Amax=double(max(max(max(FieldHisto))));%max of field value
2837    if isequal(Amin,Amax)
2838        cla(handles.histo_u)
2839    else
2840        Histo.ListVarName={FieldName,'histo'};
2841        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2842            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2843        else
2844            if numel(nxy)==2
2845                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2846            else
2847                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2848            end
2849        end
2850        %unit
2851        units=[]; %default
2852        for ivar=1:numel(Field.ListVarName)
2853            if strcmp(Field.ListVarName{ivar},FieldName)
2854                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2855                    units=Field.VarAttribute{ivar}.units;
2856                    break
2857                end
2858            end
2859        end
2860        if ~isempty(units)
2861            Histo.VarAttribute{1}.units=units;
2862        end
2863        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2864        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2865            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2866            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2867        else
2868            for col=1:size(FieldHisto,3)
2869                B=FieldHisto(:,:,col);
2870                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2871                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2872            end
2873        end
2874        plot_field(Histo,handles.histo_u);
2875        hlegend=legend;
2876        if isempty(FieldName_2)
2877        set(hlegend,'String',FieldName)
2878        else
2879            set(hlegend,'String',{FieldName;FieldName_2})
2880        end
2881%         hh=get(handles.histo_u,'children');
2882%         get(hh(1))
2883%         get(hh(2))
2884    end
2885end
2886
2887%-------------------------------------------------------------------
2888% --- translate coordinate to matrix index
2889%-------------------------------------------------------------------
2890function [indx,indy]=pos2ind(x0,rangx0,nxy)
2891indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2892indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2893
2894
2895%-------------------------------------------------------------------
2896% --- Executes on button press in 'CheckZoom'.
2897%-------------------------------------------------------------------
2898function CheckZoom_Callback(hObject, eventdata, handles)
2899
2900if (get(handles.CheckZoom,'Value') == 1);
2901    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2902    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2903    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2904else
2905    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2906end
2907
2908%-------------------------------------------------------------------
2909% --- Executes on button press in 'CheckFixLimits'.
2910%-------------------------------------------------------------------
2911function CheckFixLimits_Callback(hObject, eventdata, handles)
2912test=get(handles.CheckFixLimits,'Value');
2913if test
2914    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2915else
2916    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2917    update_plot(handles);
2918end
2919
2920%-------------------------------------------------------------------
2921% --- Executes on button press in CheckFixAspectRatio.
2922function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2923%-------------------------------------------------------------------
2924if get(handles.CheckFixAspectRatio,'Value')
2925    set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
2926    update_plot(handles);
2927else
2928    set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
2929    update_plot(handles);
2930end
2931
2932%-------------------------------------------------------------------
2933function num_AspectRatio_Callback(hObject, eventdata, handles)
2934%-------------------------------------------------------------------
2935set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2936set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2937update_plot(handles);
2938%-------------------------------------------------------------------
2939
2940%-------------------------------------------------------------------
2941
2942
2943
2944%-------------------------------------------------------------------
2945%----Executes on button press in 'record': records the current flags of manual correction.
2946%-------------------------------------------------------------------
2947function record_Callback(hObject, eventdata, handles)
2948% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2949[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2950filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2951%filename=read_file_boxes(handles);
2952[erread,message]=fileattrib(filename);
2953if ~isempty(message) && ~isequal(message.UserWrite,1)
2954     msgbox_uvmat('ERROR',['no writting access to ' filename])
2955     return
2956end
2957test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2958test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2959if ~test_civ2 && ~test_civ1
2960    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2961end
2962if test_civ2
2963    nbname='nb_vectors2';
2964   flagname='vec2_FixFlag';
2965   attrname='fix2';
2966end
2967if test_civ1
2968    nbname='nb_vectors';
2969   flagname='vec_FixFlag';
2970   attrname='fix';
2971end
2972%write fix flags in the netcdf file
2973UvData=get(handles.uvmat,'UserData');
2974hhh=which('netcdf.open');% look for built-in matlab netcdf library
2975if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2976    nc=netcdf.open(filename,'NC_WRITE');
2977    netcdf.reDef(nc);
2978    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2979    dimid = netcdf.inqDimID(nc,nbname);
2980    try
2981        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2982    catch
2983        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2984    end
2985    netcdf.endDef(nc);
2986    netcdf.putVar(nc,varid,UvData.axes3.FF);
2987    netcdf.close(nc); 
2988else %old netcdf library
2989    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2990end
2991
2992%-------------------------------------------------------------------
2993%----Correct the netcdf file, using toolbox (old versions of Matlab).
2994%-------------------------------------------------------------------
2995function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2996nc=netcdf(filename,'write'); %open netcdf file
2997result=redef(nc);
2998eval(['nc.' attrname '=1;']);
2999theDim=nc(nbname) ;% get the number of velocity vectors
3000nb_vectors=size(theDim);
3001var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
3002var_FixFlag(1:nb_vectors)=AxeData.FF;%
3003fin=close(nc);
3004
3005%-------------------------------------------------------------------
3006% --- Executes on button press in SubField
3007function SubField_Callback(hObject, eventdata, handles)
3008%-------------------------------------------------------------------
3009UvData=get(handles.uvmat,'UserData');
3010if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
3011    set(handles.RootPath_1,'String','')
3012    set(handles.RootFile_1,'String','')
3013    set(handles.SubDir_1,'String','');
3014    set(handles.FileIndex_1,'String','');
3015    set(handles.FileExt_1,'String','');
3016    set(handles.RootPath_1,'Visible','off')
3017    set(handles.RootFile_1,'Visible','off')
3018    set(handles.SubDir_1,'Visible','off');
3019    set(handles.NomType_1,'Visible','off');
3020    set(handles.abs_time_1,'Visible','off')
3021    set(handles.FileIndex_1,'Visible','off');
3022    set(handles.FileExt_1,'Visible','off');
3023    set(handles.Fields_1,'Value',1);%set to blank state
3024    set(handles.VelType_1,'Value',1);%set to blank state
3025    set(handles.num_Opacity,'String','')% desactivate opacity setting
3026    if ~strcmp(get(handles.VelType,'Visible'),'on')
3027        set(handles.VelType_1,'Visible','off')
3028    end
3029    if isfield(UvData,'XmlData_1')
3030        UvData=rmfield(UvData,'XmlData_1');
3031    end
3032    set(handles.uvmat,'UserData',UvData);
3033    run0_Callback(hObject, eventdata, handles); %run
3034else
3035    MenuBrowse_1_Callback(hObject, eventdata, handles)
3036end
3037
3038%------------------------------------------------------------------------
3039% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3040
3041function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3042%------------------------------------------------------------------------
3043InputFile=read_GUI(handles.InputFile);
3044RootPath=InputFile.RootPath;
3045SubDir=regexprep(InputFile.SubDir,'/|\','');
3046RootFile=regexprep(InputFile.RootFile,'/|\','');
3047FileIndices=InputFile.FileIndex;
3048FileExt=InputFile.FileExt;
3049
3050
3051%------------------------------------------------------------------------
3052% ---- read the data displayed for the second input rootfile windows
3053function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3054%------------------------------------------------------------------------
3055RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3056if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3057    RootPath_1=get(handles.RootPath,'String');
3058end;
3059SubDir_1=get(handles.SubDir_1,'String');
3060if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3061    SubDir_1=get(handles.SubDir,'String');
3062end
3063SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3064RootFile_1=get(handles.RootFile_1,'String');
3065if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3066    RootFile_1=get(handles.RootFile,'String');
3067end
3068RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3069FileIndex_1=get(handles.FileIndex_1,'String');
3070if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3071    FileIndex_1=get(handles.FileIndex,'String');
3072end
3073FileExt_1=get(handles.FileExt_1,'String');
3074if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3075    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3076end
3077NomType_1=get(handles.NomType_1,'String');
3078if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3079    NomType_1=get(handles.NomType,'String');%read FileExt by default
3080end
3081%------------------------------------------------------------------------
3082% --- Executes on menu selection Fields
3083function Fields_Callback(hObject, eventdata, handles)
3084%------------------------------------------------------------------------
3085list_fields=get(handles.Fields,'String');% list menu fields
3086index_fields=get(handles.Fields,'Value');% selected string index
3087field= list_fields{index_fields(1)}; % selected string
3088if isequal(field,'get_field...')
3089    set(handles.FixVelType,'visible','off')
3090    set(handles.VelType,'visible','off')
3091    set(handles.VelType_1,'visible','off')
3092    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3093    filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3094    %filename=read_file_boxes(handles);
3095    hget_field=findobj(allchild(0),'name','get_field');
3096    if ~isempty(hget_field)
3097        delete(hget_field)
3098    end
3099    hget_field=get_field(filename);
3100    set(hget_field,'Name','get_field')
3101    hhget_field=guidata(hget_field);
3102    set(hhget_field.list_fig,'Value',1)
3103    set(hhget_field.list_fig,'String',{'uvmat'})
3104    set(handles.transform_fct,'Value',1)% no transform by default
3105    set(handles.path_transform,'String','')
3106    return %no action
3107end
3108list_fields=get(handles.Fields_1,'String');% list menu fields
3109index_fields=get(handles.Fields_1,'Value');% selected string index
3110field_1= list_fields{index_fields(1)}; % selected string
3111UvData=get(handles.uvmat,'UserData');
3112
3113%read the rootfile input display
3114[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3115FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3116[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3117% NomTypeNew=NomType;%default
3118if isequal(field,'image')
3119%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
3120%         NomTypeNew='_1_1';
3121%     elseif isequal(NomType,'#_ab')
3122%         NomTypeNew='#a';
3123%     elseif isequal(NomType,'_1-2')
3124%         NomTypeNew='_1';
3125%     end
3126    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
3127    if ~exist(imagename,'file')
3128        [FileName,PathName] = uigetfile( ...
3129            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3130            '*.jpg',' jpeg image files'; ...
3131            '*.png','.png image files'; ...
3132            '*.tif','.tif image files'; ...
3133            '*.avi;*.AVI','.avi movie files'; ...
3134            '*.vol','.volume images (png)'; ...
3135            '*.*',  'All Files (*.*)'}, ...
3136            'Pick an image',imagename);   
3137        imagename=[PathName FileName];
3138    end
3139     % display the selected field and related information
3140    display_file_name(handles,imagename)%display the image
3141    return
3142else
3143    ext=get(handles.FileExt,'String');
3144    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3145        [FileName,PathName] = uigetfile( ...
3146            {'*.nc', ' (*.nc)';
3147            '*.nc',' netcdf files'; ...
3148            '*.*',  'All Files (*.*)'}, ...
3149            'Pick a netcdf file',FileBase);
3150        filename=[PathName FileName];
3151        % display the selected field and related information
3152        display_file_name( handles,filename)
3153        return
3154    end
3155end
3156indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3157set(handles.FileIndex,'String',indices)
3158% set(handles.NomType,'String',NomType)
3159
3160%common to Fields_1_Callback
3161if isequal(field,'image')||isequal(field_1,'image')
3162    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3163    set(handles.TitleNpy,'Visible','on')
3164    set(handles.num_Npx,'Visible','on')
3165    set(handles.num_Npy,'Visible','on')
3166else
3167    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3168    set(handles.TitleNpy,'Visible','off')
3169    set(handles.num_Npx,'Visible','off')
3170    set(handles.num_Npy,'Visible','off')
3171end
3172if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3173    run0_Callback(hObject, eventdata, handles)
3174end
3175
3176%---------------------------------------------------
3177% --- Executes on menu selection Fields
3178function Fields_1_Callback(hObject, eventdata, handles)
3179%-------------------------------------------------
3180%% read input data
3181check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3182UvData=get(handles.uvmat,'UserData');
3183if check_new && isfield(UvData,'XmlData')
3184    UvData.XmlData{2}=UvData.XmlData{1};
3185end
3186if isfield(UvData,'Field_1')
3187    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3188end
3189UvData.filename_1='';% desactivate the use of a constant second file
3190list_fields=get(handles.Fields,'String');% list menu fields
3191field= list_fields{get(handles.Fields,'Value')}; % selected string
3192list_fields=get(handles.Fields_1,'String');% list menu fields
3193field_1= list_fields{get(handles.Fields_1,'Value')}; % selected string for the second field
3194if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3195    set(handles.SubField,'Value',0)
3196    SubField_Callback(hObject, eventdata, handles)
3197    return
3198else
3199    set(handles.SubField,'Value',1)%state that a second field is now entered
3200end
3201
3202%% read the rootfile input display
3203[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3204filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3205[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3206% set(handles.FileIndex_1,'Visible','on')
3207% set(handles.FileExt_1,'Visible','on')
3208switch field_1
3209    case 'get_field...'
3210        set_veltype_display(0) % no veltype display
3211        hget_field=findobj(allchild(0),'name','get_field_1');
3212        if ~isempty(hget_field)
3213            delete(hget_field)
3214        end
3215        hget_field=get_field(filename_1);
3216        set(hget_field,'name','get_field_1')
3217        hhget_field=guidata(hget_field);
3218        set(hhget_field.list_fig,'Value',1)
3219        set(hhget_field.list_fig,'String',{'uvmat'})
3220        set(handles.transform_fct,'Value',1)% no transform by default
3221        set(handles.path_transform,'String','')
3222        if check_new
3223            UvData.FileType{2}=UvData.FileType{1};
3224            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3225%             set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3226              set(handles.uvmat,'UserData',UvData)
3227        end
3228    case 'image'
3229        % guess the image name corresponding to the current netcdf name (no unique correspondance)
3230        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3231        if ~exist(imagename,'file') % browse for images if it is not found
3232            [FileName,PathName] = uigetfile( ...
3233                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3234                '*.jpg',' jpeg image files'; ...
3235                '*.png','.png image files'; ...
3236                '*.tif','.tif image files'; ...
3237                '*.avi;*.AVI','.avi movie files'; ...
3238                '*.vol','.volume images (png)'; ...
3239                '*.*',  'All Files (*.*)'}, ...
3240                'Pick an image',imagename);
3241            imagename=[PathName FileName];
3242        end
3243        if ~ischar(imagename)% quit if the browser has  been closed
3244            set(handles.SubField,'Value',0)
3245        else %valid browser input:  display the selected image
3246            set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3247            set(handles.TitleNpy,'Visible','on')
3248            set(handles.num_Npx,'Visible','on')
3249            set(handles.num_Npy,'Visible','on')
3250            display_file_name(handles,imagename,2)%display the imag
3251        end
3252    otherwise
3253        if check_new
3254            UvData.FileType{2}=UvData.FileType{1};
3255            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3256            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3257        end
3258        if ~isequal(field,'image')
3259            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3260            set(handles.TitleNpy,'Visible','off')
3261            set(handles.num_Npx,'Visible','off')
3262            set(handles.num_Npy,'Visible','off')
3263        end
3264        set(handles.uvmat,'UserData',UvData)
3265        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3266            run0_Callback(hObject, eventdata, handles)
3267        end
3268end
3269
3270%------------------------------------------------------------------------
3271% --- set the visibility of relevant velocity type menus:
3272function menu=set_veltype_display(Civ,FileType)
3273%------------------------------------------------------------------------
3274if ~exist('FileType','var')
3275    FileType='civx';
3276end
3277switch FileType
3278    case 'civx'
3279        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3280        if isequal(Civ,0)
3281            imax=0;
3282        elseif isequal(Civ,1) || isequal(Civ,2)
3283            imax=1;
3284        elseif isequal(Civ,3)
3285            imax=3;
3286        elseif isequal(Civ,4) || isequal(Civ,5)
3287            imax=4;
3288        elseif isequal(Civ,6) %patch2
3289            imax=6;
3290        end
3291    case 'civdata'
3292        menu={'civ1';'filter1';'civ2';'filter2'};
3293        if isequal(Civ,0)
3294            imax=0;
3295        elseif isequal(Civ,1) || isequal(Civ,2)
3296            imax=1;
3297        elseif isequal(Civ,3)
3298            imax=2;
3299        elseif isequal(Civ,4) || isequal(Civ,5)
3300            imax=3;
3301        elseif isequal(Civ,6) %patch2
3302            imax=4;
3303        end
3304end
3305menu=menu(1:imax);
3306
3307%------------------------------------------------------------------------
3308% --- Executes on button press in FixVelType.
3309function FixVelType_Callback(hObject, eventdata, handles)
3310%------------------------------------------------------------------------
3311% refresh the current plot if the fixed  veltype is unselected
3312if ~get(handles.FixVelType,'Value')
3313    run0_Callback(hObject, eventdata, handles)
3314end
3315
3316%------------------------------------------------------------------------
3317% --- Executes on button press in VelType.
3318function VelType_Callback(hObject, eventdata, handles)
3319%------------------------------------------------------------------------
3320set(handles.FixVelType,'Value',1)
3321run0_Callback(hObject, eventdata, handles)
3322
3323%------------------------------------------------------------------------
3324% --- Executes on button press in VelType_1.
3325function VelType_1_Callback(hObject, eventdata, handles)
3326%------------------------------------------------------------------------
3327set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3328UvData=get(handles.uvmat,'UserData');
3329%refresh field with a second filename=first file name
3330set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3331drawnow   
3332InputFile=read_GUI(handles.InputFile);
3333[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3334filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3335
3336if isempty(InputFile.VelType_1)
3337        filename_1='';% we plot the current field without the second field
3338        set(handles.SubField,'Value',0)
3339        SubField_Callback(hObject, eventdata, handles)
3340elseif get(handles.SubField,'Value')% if subfield is already 'on'
3341      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3342     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3343else
3344     filename_1=filename;% we compare two fields in the same file by default
3345     UvData.FileType{2}=UvData.FileType{1};
3346     set(handles.SubField,'Value',1)
3347end
3348if isfield(UvData,'Field_1')
3349    UvData=rmfield(UvData,'Field_1');% removes the stored second field if it exists
3350end
3351UvData.filename_1='';% desactivate the use of a constant second file
3352set(handles.uvmat,'UserData',UvData)
3353num_i1=stra2num(get(handles.i1,'String'));
3354num_i2=stra2num(get(handles.i2,'String'));
3355num_j1=stra2num(get(handles.j1,'String'));
3356num_j2=stra2num(get(handles.j2,'String'));
3357
3358errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
3359
3360if ~isempty(errormsg)
3361    msgbox_uvmat('ERROR',errormsg);
3362else
3363    set(handles.i1,'BackgroundColor',[1 1 1])
3364    set(handles.i2,'BackgroundColor',[1 1 1])
3365    set(handles.j1,'BackgroundColor',[1 1 1])
3366    set(handles.j2,'BackgroundColor',[1 1 1])
3367    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3368    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3369end
3370set(handles.run0,'BackgroundColor',[1 0 0])
3371
3372%-----------------------------------------------
3373% --- reset civ buttons
3374function reset_vel_type(handles_civ0,handle1)
3375for ibutton=1:length(handles_civ0)
3376    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3377    set(handles_civ0(ibutton),'Value',0)
3378end
3379if exist('handle1','var')%handles of selected button
3380        set(handle1,'BackgroundColor',[1 1 0]) 
3381end
3382
3383%-------------------------------------------------------
3384% --- Executes on button press in MENUVOLUME.
3385%-------------------------------------------------------
3386function VOLUME_Callback(hObject, eventdata, handles)
3387%errordlg('command VOL not implemented yet')
3388if ishandle(handles.UVMAT_title)
3389    delete(handles.UVMAT_title)
3390end
3391UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3392if isequal(get(handles.VOLUME,'Value'),1)
3393    set(handles.CheckZoom,'Value',0)
3394    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3395    set(handles.edit_vect,'Value',0)
3396    edit_vect_Callback(hObject, eventdata, handles)
3397    set(handles.edit_object,'Value',0)
3398    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3399%     set(handles.cal,'Value',0)
3400%     set(handles.cal,'BackgroundColor',[0 1 0])
3401    set(handles.edit_vect,'Value',0)
3402    edit_vect_Callback(hObject, eventdata, handles)
3403    %initiate set_object GUI
3404    data.Name='VOLUME';
3405    if isfield(UvData,'CoordType')
3406        data.CoordType=UvData.CoordType;
3407    end
3408    if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh)
3409        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3410        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3411        data.DX=UvData.Field.Mesh;
3412        data.DY=UvData.Field.Mesh;
3413    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3414        np=size(UvData.Field.A);
3415        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3416        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3417        data.RangeY=max(meshx,meshy);
3418        data.RangeX=max(meshx,meshy);
3419        data.DX=max(meshx,meshy);
3420    end
3421    data.ParentButton=handles.VOLUME;
3422    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3423    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3424                                                      % associate the set_object interface handle to the plotting axes
3425    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3426    pos_uvmat=get(handles.uvmat,'Position');
3427    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3428    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3429    set(hset_object,'Position',pos_set_object)
3430    end
3431    UvData.MouseAction='create_object';
3432else
3433    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3434    UvData.MouseAction='none';
3435end
3436set(handles.uvmat,'UserData',UvData)
3437
3438%-------------------------------------------------------
3439function edit_vect_Callback(hObject, eventdata, handles)
3440%-------------------------------------------------------
3441%
3442% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3443if isequal(get(handles.edit_vect,'Value'),1)
3444    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3445    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3446    if ~test_civ2 && ~test_civ1
3447        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3448    end
3449    set(handles.record,'Visible','on')
3450    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3451    set(handles.edit_object,'Value',0)
3452    set(handles.CheckZoom,'Value',0)
3453    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3454%     set(handles.create,'Value',0)
3455%     set(handles.create,'BackgroundColor',[0 1 0])
3456    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3457    set(gcf,'Pointer','arrow')
3458%     UvData.MouseAction='edit_vect';
3459else
3460    set(handles.record,'Visible','off')
3461    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3462%     UvData.MouseAction='none';
3463end
3464% set(handles.uvmat,'UserData',UvData)
3465
3466%----------------------------------------------
3467function save_mask_Callback(hObject, eventdata, handles)
3468%-----------------------------------------------------------------------
3469UvData=get(handles.uvmat,'UserData');
3470
3471flag=1;
3472npx=size(UvData.Field.A,2);
3473npy=size(UvData.Field.A,1);
3474xi=0.5:npx-0.5;
3475yi=0.5:npy-0.5;
3476[Xi,Yi]=meshgrid(xi,yi);
3477if isfield(UvData,'Object')
3478    for iobj=1:length(UvData.Object)
3479        ObjectData=UvData.Object{iobj};
3480        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3481            flagobj=1;
3482            testphys=0; %coordinates in pixels by default
3483            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3484                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3485                    Calib=UvData.XmlData{1}.GeometryCalib;
3486                    testphys=1;
3487                end
3488            end
3489            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3490                if isequal(ObjectData.Type,'polygon')
3491                    X=ObjectData.Coord(:,1);
3492                    Y=ObjectData.Coord(:,2);
3493                    if testphys
3494                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3495                    end
3496                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3497                elseif isequal(ObjectData.Type,'ellipse')
3498                    if testphys
3499                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3500                    end
3501                    RangeX=max(ObjectData.RangeX);
3502                    RangeY=max(ObjectData.RangeY);
3503                    X2Max=RangeX*RangeX;
3504                    Y2Max=RangeY*RangeY;
3505                    distX=(Xi-ObjectData.Coord(1,1));
3506                    distY=(Yi-ObjectData.Coord(1,2));
3507                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3508                elseif isequal(ObjectData.Type,'rectangle')
3509                    if testphys
3510                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3511                    end
3512                    distX=abs(Xi-ObjectData.Coord(1,1));
3513                    distY=abs(Yi-ObjectData.Coord(1,2));
3514                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3515                end
3516                if isequal(ObjectData.ProjMode,'mask_outside')
3517                    flagobj=~flagobj;
3518                end
3519                flag=flag & flagobj;
3520            end
3521        end
3522    end
3523end
3524% flag=~flag;
3525%mask name
3526RootPath=get(handles.RootPath,'String');
3527RootFile=get(handles.RootFile,'String');
3528RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3529filebase=fullfile(RootPath,RootFile);
3530list=get(handles.masklevel,'String');
3531masknumber=num2str(length(list));
3532maskindex=get(handles.masklevel,'Value');
3533mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3534%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3535imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3536imflag=flipdim(imflag,1);
3537% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3538msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3539imwrite(imflag,mask_name,'BitDepth',8);
3540
3541%display the mask
3542figure;
3543vec=linspace(0,1,256);%define a linear greyscale colormap
3544map=[vec' vec' vec'];
3545colormap(map)
3546
3547image(imflag);
3548
3549%-------------------------------------------------------------------
3550%-------------------------------------------------------------------
3551%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3552
3553%------------------------------------------------------------------
3554%-------------------------------------------------------------
3555% --- Executes on selection change in transform_fct.
3556function transform_fct_Callback(hObject, eventdata, handles)
3557%-------------------------------------------------------------
3558UvData=get(handles.uvmat,'UserData');
3559menu=get(handles.transform_fct,'String');
3560ind_coord=get(handles.transform_fct,'Value');
3561coord_option=menu{ind_coord};
3562list_transform=get(handles.transform_fct,'UserData');
3563ff=functions(list_transform{end}); 
3564if isequal(coord_option,'more...');
3565    coord_fct='';
3566    prompt = {'Enter the name of the transform function'};
3567    dlg_title = 'user defined transform';
3568    num_lines= 1;
3569    [FileName, PathName] = uigetfile( ...
3570       {'*.m', ' (*.m)';
3571        '*.m',  '.m files '; ...
3572        '*.*', 'All Files (*.*)'}, ...
3573        'Pick a file', ff.file);
3574    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3575        PathName(end)=[];
3576    end
3577    transform_selected =fullfile(PathName,FileName);
3578    if ~exist(transform_selected,'file')
3579           return
3580    end
3581   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3582   if ~isequal(ext_fct,'.m')
3583        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3584        return
3585   end
3586   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3587   ind_coord=get(handles.transform_fct,'Value');
3588   addpath(PathName)
3589   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3590   set(handles.transform_fct,'UserData',list_transform)
3591   rmpath(PathName)
3592   % save the new menu in the personal file 'uvmat_perso.mat'
3593   dir_perso=prefdir;%personal Matalb directory
3594   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3595   if exist(profil_perso,'file')
3596       nb_builtin=UvData.OpenParam.NbBuiltin;
3597       for ilist=nb_builtin+1:numel(list_transform)
3598           ff=functions(list_transform{ilist});
3599           transform_fct{ilist-nb_builtin}=ff.file;
3600       end
3601        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3602   end   
3603end
3604
3605%% check the current path to the selected function
3606if isa(list_transform{ind_coord},'function_handle')
3607    func=functions(list_transform{ind_coord});
3608    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3609else
3610    set(handles.path_transform,'String','')
3611end
3612
3613set(handles.CheckFixLimits,'Value',0)
3614set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3615
3616%% delete drawn objects
3617hother=findobj('Tag','proj_object');%find all the proj objects
3618for iobj=1:length(hother)
3619    delete_object(hother(iobj))
3620end
3621hother=findobj('Tag','DeformPoint');%find all the proj objects
3622for iobj=1:length(hother)
3623    delete_object(hother(iobj))
3624end
3625hh=findobj('Tag','calib_points');
3626if ~isempty(hh)
3627    delete(hh)
3628end
3629hhh=findobj('Tag','calib_marker');
3630if ~isempty(hhh)
3631    delete(hhh)
3632end
3633if isfield(UvData,'Object')
3634     UvData.Object=UvData.Object(1);
3635end
3636set(handles.ListObject,'Value',1)
3637set(handles.ListObject,'String',{'plane'})
3638set(handles.ListObject_1,'Value',1)
3639set(handles.ListObject_1,'String',{'plane'})
3640
3641%delete mask if it is displayed
3642% if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3643%    UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3644% end
3645set(handles.uvmat,'UserData',UvData)
3646run0_Callback(hObject, eventdata, handles)
3647
3648
3649
3650%------------------------------------------------
3651%CALLBACKS FOR PLOTTING PARAMETERS
3652%-------------------------------------------------
3653%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3654% Plot coordinates
3655%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3656%------------------------------------------------------------------------
3657function num_MinX_Callback(hObject, eventdata, handles)
3658%------------------------------------------------------------------------
3659set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3660set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3661update_plot(handles);
3662
3663%------------------------------------------------------------------------
3664function num_MaxX_Callback(hObject, eventdata, handles)
3665%------------------------------------------------------------------------
3666set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3667set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3668update_plot(handles);
3669
3670%------------------------------------------------------------------------
3671function num_MinY_Callback(hObject, eventdata, handles)
3672%------------------------------------------
3673set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3674set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3675update_plot(handles);
3676
3677%------------------------------------------------------------------------
3678function num_MaxY_Callback(hObject, eventdata, handles)
3679%------------------------------------------------------------------------
3680set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3681set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3682update_plot(handles);
3683
3684%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3685% Scalar or image representation
3686%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3687%------------------------------------------------------------------------
3688function num_MinA_Callback(hObject, eventdata, handles)
3689%------------------------------------------
3690set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3691set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3692MinA=str2double(get(handles.num_MinA,'String'));
3693MaxA=str2double(get(handles.num_MaxA,'String'));
3694if MinA>MaxA% switch minA and maxA in case of error
3695    MinA_old=MinA;
3696    MinA=MaxA;
3697    MaxA=MinA_old;
3698    set(handles.num_MinA,'String',num2str(MinA,5));
3699    set(handles.num_MaxA,'String',num2str(MaxA,5));
3700end
3701update_plot(handles);
3702
3703%------------------------------------------------------------------------
3704function num_MaxA_Callback(hObject, eventdata, handles)
3705%------------------------------------------------------------------------
3706set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3707set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3708MinA=str2double(get(handles.num_MinA,'String'));
3709MaxA=str2double(get(handles.num_MaxA,'String'));
3710if MinA>MaxA% switch minA and maxA in case of error
3711        MinA_old=MinA;
3712    MinA=MaxA;
3713    MaxA=MinA_old;
3714    set(handles.num_MinA,'String',num2str(MinA,5));
3715    set(handles.num_MaxA,'String',num2str(MaxA,5));
3716end
3717update_plot(handles);
3718
3719%------------------------------------------------------------------------
3720function CheckFixScalar_Callback(hObject, eventdata, handles)
3721%------------------------------------------------------------------------
3722test=get(handles.CheckFixScalar,'Value');
3723if test
3724    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3725else
3726    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3727    update_plot(handles);
3728end
3729
3730%-------------------------------------------------------------------
3731function CheckBW_Callback(hObject, eventdata, handles)
3732%-------------------------------------------------------------------
3733update_plot(handles);
3734
3735%-------------------------------------------------------------------
3736function num_Opacity_Callback(hObject, eventdata, handles)
3737update_plot(handles);
3738%-------------------------------------------------------------------
3739
3740%-------------------------------------------------------------------
3741function ListContour_Callback(hObject, eventdata, handles)
3742%-------------------------------------------------------------------
3743val=get(handles.ListContour,'Value');
3744if val==2
3745    set(handles.interval_txt,'Visible','on')
3746    set(handles.num_IncrA,'Visible','on')
3747else
3748    set(handles.interval_txt,'Visible','off')
3749    set(handles.num_IncrA,'Visible','off')
3750end
3751update_plot(handles);
3752
3753%-------------------------------------------------------------------
3754function num_IncrA_Callback(hObject, eventdata, handles)
3755%-------------------------------------------------------------------
3756update_plot(handles);
3757
3758
3759%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3760% Vector representation
3761%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3762%-------------------------------------------------------------------
3763function CheckHideWarning_Callback(hObject, eventdata, handles)
3764%-------------------------------------------------------------------
3765update_plot(handles);
3766
3767%-------------------------------------------------------------------
3768function CheckHideFalse_Callback(hObject, eventdata, handles)
3769%-------------------------------------------------------------------
3770update_plot(handles);
3771
3772%-------------------------------------------------------------------
3773function num_VecScale_Callback(hObject, eventdata, handles)
3774%-------------------------------------------------------------------
3775set(handles.CheckFixVectors,'Value',1);
3776set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3777update_plot(handles);
3778
3779%-------------------------------------------------------------------
3780function CheckFixVectors_Callback(hObject, eventdata, handles)
3781%-------------------------------------------------------------------
3782test=get(handles.CheckFixVectors,'Value');
3783if test
3784    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3785else
3786    update_plot(handles);
3787    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3788    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3789end
3790
3791%------------------------------------------------------------------------
3792% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3793function CheckDecimate4_Callback(hObject, eventdata, handles)
3794%------------------------------------------------------------------------
3795update_plot(handles);
3796
3797%------------------------------------------------------------------------
3798% --- Executes on selection change in ColorCode menu
3799function ColorCode_Callback(hObject, eventdata, handles)
3800%------------------------------------------------------------------------
3801% edit the choice for color code
3802update_color_code_boxes(handles);
3803update_plot(handles);
3804
3805%------------------------------------------------------------------------
3806function update_color_code_boxes(handles)
3807%------------------------------------------------------------------------
3808list_code=get(handles.ColorCode,'String');% list menu fields
3809colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3810enable_slider='off';%default
3811enable_bounds='off';%default
3812enable_scalar='off';%default
3813switch colcode
3814    case {'rgb','bgr'}
3815        enable_slider='on';
3816        enable_bounds='on';
3817        enable_scalar='on';
3818    case '64 colors'
3819        enable_bounds='on';
3820        enable_scalar='on';
3821end
3822set(handles.Slider1,'Visible',enable_slider)
3823set(handles.Slider2,'Visible', enable_slider)
3824set(handles.num_ColCode1,'Visible',enable_slider)
3825set(handles.num_ColCode2,'Visible',enable_slider)
3826set(handles.TitleColCode1,'Visible',enable_slider)
3827set(handles.TitleColCode2,'Visible',enable_slider)
3828set(handles.CheckFixVecColor,'Visible',enable_bounds)
3829set(handles.num_MinVec,'Visible',enable_bounds)
3830set(handles.num_MaxVec,'Visible',enable_bounds)
3831set(handles.ColorScalar,'Visible',enable_scalar)
3832set_vec_col_bar(handles)
3833
3834%------------------------------------------------------------------
3835% --- Executes on selection change in ColorScalar: choice of the color code.
3836function ColorScalar_Callback(hObject, eventdata, handles)
3837%------------------------------------------------------------------
3838% edit the choice for color code
3839list_scalar=get(handles.ColorScalar,'String');% list menu fields
3840col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3841if isequal(col_scalar,'ima_cor')
3842    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3843    ColorCode='rgb';
3844    set(handles.num_MinVec,'String','0')
3845    set(handles.num_MaxVec,'String','1')
3846    set(handles.num_ColCode1,'String','0.333')
3847    set(handles.num_ColCode2,'String','0.666')
3848else
3849    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3850    ColorCode='64 colors';
3851end
3852ColorCodeList=get(handles.ColorCode,'String');
3853ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3854set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3855
3856update_color_code_boxes(handles);
3857%replot the current graph
3858run0_Callback(hObject, eventdata, handles)
3859
3860%----------------------------------------------------------------
3861% -- Executes on slider movement to set the color code
3862%
3863function Slider1_Callback(hObject, eventdata, handles)
3864%------------------------------------------------------------------
3865slider1=get(handles.Slider1,'Value');
3866min_val=str2num(get(handles.num_MinVec,'String'));
3867max_val=str2num(get(handles.num_MaxVec,'String'));
3868col=min_val+(max_val-min_val)*slider1;
3869set(handles.num_ColCode1,'String',num2str(col))
3870if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3871    set(handles.Slider2,'Value',col)
3872    set(handles.num_ColCode2,'String',num2str(col))
3873end
3874set_vec_col_bar(handles)
3875update_plot(handles);
3876
3877%----------------------------------------------------------------
3878% Executes on slider movement to set the color code
3879%----------------------------------------------------------------
3880function Slider2_Callback(hObject, eventdata, handles)
3881slider2=get(handles.Slider2,'Value');
3882min_val=str2num(get(handles.num_MinVec,'String'));
3883max_val=str2num(get(handles.num_MaxVec,'String'));
3884col=min_val+(max_val-min_val)*slider2;
3885set(handles.num_ColCode2,'String',num2str(col))
3886if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3887    set(handles.Slider1,'Value',col)
3888    set(handles.num_ColCode1,'String',num2str(col))
3889end
3890set_vec_col_bar(handles)
3891update_plot(handles);
3892
3893%----------------------------------------------------------------
3894% --- Execute on return carriage on the edit box corresponding to slider 1
3895%----------------------------------------------------------------
3896function num_ColCode1_Callback(hObject, eventdata, handles)
3897set_vec_col_bar(handles)
3898update_plot(handles);
3899
3900%----------------------------------------------------------------
3901% --- Execute on return carriage on the edit box corresponding to slider 2
3902%----------------------------------------------------------------
3903function num_ColCode2_Callback(hObject, eventdata, handles)
3904set_vec_col_bar(handles)
3905update_plot(handles);
3906%------------------------------------------------------------------------
3907%-------------------------------------------------------
3908% --- Executes on button press in CheckFixVecColor.
3909%-------------------------------------------------------
3910function VecColBar_Callback(hObject, eventdata, handles)
3911set_vec_col_bar(handles)
3912
3913%------------------------------------------------------------------------
3914% --- Executes on button press in CheckFixVecColor.
3915function CheckFixVecColor_Callback(hObject, eventdata, handles)
3916%------------------------------------------------------------------------
3917if ~get(handles.CheckFixVecColor,'Value')
3918    update_plot(handles);
3919end
3920
3921%------------------------------------------------------------------------
3922% --- Executes on selection change in num_MaxVec.
3923function num_MinVec_Callback(hObject, eventdata, handles)
3924%------------------------------------------------------------------------
3925max_vec_Callback(hObject, eventdata, handles)
3926
3927%------------------------------------------------------------------------
3928% --- Executes on selection change in num_MaxVec.
3929function num_MaxVec_Callback(hObject, eventdata, handles)
3930%------------------------------------------------------------------------
3931set(handles.CheckFixVecColor,'Value',1)
3932CheckFixVecColor_Callback(hObject, eventdata, handles)
3933min_val=str2num(get(handles.num_MinVec,'String'));
3934max_val=str2num(get(handles.num_MaxVec,'String'));
3935slider1=get(handles.Slider1,'Value');
3936slider2=get(handles.Slider2,'Value');
3937colcode1=min_val+(max_val-min_val)*slider1;
3938colcode2=min_val+(max_val-min_val)*slider2;
3939set(handles.num_ColCode1,'String',num2str(colcode1))
3940set(handles.num_ColCode2,'String',num2str(colcode2))
3941update_plot(handles);
3942
3943%------------------------------------------------------------------------
3944% --- update the display of color code for vectors (on vecColBar)
3945function set_vec_col_bar(handles)
3946%------------------------------------------------------------------------
3947%get the image of the color display button 'VecColBar' in pixels
3948set(handles.VecColBar,'Unit','pixel');
3949pos_vert=get(handles.VecColBar,'Position');
3950set(handles.VecColBar,'Unit','Normalized');
3951width=ceil(pos_vert(3));
3952height=ceil(pos_vert(4));
3953
3954%get slider indications
3955list=get(handles.ColorCode,'String');
3956ichoice=get(handles.ColorCode,'Value');
3957colcode.ColorCode=list{ichoice};
3958colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3959colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3960test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
3961if test3color
3962    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3963    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3964end
3965vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3966[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3967oneheight=ones(1,height);
3968A1=colorlist(col_vec,1)*oneheight;
3969A2=colorlist(col_vec,2)*oneheight;
3970A3=colorlist(col_vec,3)*oneheight;
3971A(:,:,1)=A1';
3972A(:,:,2)=A2';
3973A(:,:,3)=A3';
3974set(handles.VecColBar,'Cdata',A)
3975
3976%-------------------------------------------------------------------
3977function update_plot(handles)
3978%-------------------------------------------------------------------
3979UvData=get(handles.uvmat,'UserData');
3980AxeData=UvData.axes3;% retrieve the current plotted data
3981PlotParam=read_GUI(handles.uvmat);
3982[tild,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
3983write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3984
3985%------------------------------------------------------------------------
3986%------------------------------------------------------------------------
3987%   SELECTION AND EDITION OF PROJECTION OBJECTS
3988%------------------------------------------------------------------------
3989%------------------------------------------------------------------------
3990
3991% --- Executes on selection change in ListObject_1.
3992function ListObject_1_Callback(hObject, eventdata, handles)
3993list_str=get(handles.ListObject,'String');
3994UvData=get(handles.uvmat,'UserData');
3995ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
3996
3997%% update the projection plot on uvmat
3998ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
3999plot_field(ProjData,handles.axes3,read_GUI(handles.uvmat));% plot the projected field;
4000%replot all the objects within the new projected field
4001for IndexObj=1:numel(list_str)
4002    IndexObj
4003        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat
4004        if isempty(hobject) || ~ishandle(hobject)
4005            hobject=handles.axes3
4006        end
4007        if isequal(IndexObj,get(handles.ListObject,'Value'))
4008            objectcolor='m'; %paint in magenta the currently selected object in ListObject
4009        else
4010            objectcolor='b';
4011        end
4012        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
4013end
4014set(handles.uvmat,'UserData',UvData)
4015
4016%% display the object parameters if the GUI set_object is already opened
4017if ~get(handles.ViewObject,'Value')
4018    ZBounds=0; % default
4019    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4020        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4021        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4022    end
4023    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
4024    set_object(ObjectData,[],ZBounds);
4025    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
4026end
4027
4028%  desactivate the edit object mode
4029set(handles.edit_object,'Value',0)
4030set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4031
4032%------------------------------------------------------------------------
4033% --- Executes on selection change in ListObject.
4034function ListObject_Callback(hObject, eventdata, handles)
4035%------------------------------------------------------------------------
4036list_str=get(handles.ListObject,'String');
4037IndexObj=get(handles.ListObject,'Value');%present object selection
4038
4039%% The object  is displayed in set_object if this GUI is already opened
4040UvData=get(handles.uvmat,'UserData');
4041ObjectData=UvData.Object{IndexObj};
4042hset_object=findobj(allchild(0),'tag','set_object');
4043if ~isempty(hset_object)
4044    ZBounds=0; % default
4045    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4046        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4047        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4048    end
4049    ObjectData.Name=list_str{IndexObj};
4050    set_object(ObjectData,[],ZBounds);
4051    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4052end
4053
4054%%  desactivate the edit object mode
4055set(handles.edit_object,'Value',0)
4056set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4057
4058%% update the  plot on view_field if view_field is already openened
4059hview_field=findobj(allchild(0),'tag','view_field');
4060if isempty(hview_field)
4061    hhview_field.axes3=[];
4062else
4063    Data=get(hview_field,'UserData');
4064    hhview_field=guidata(hview_field);
4065    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4066    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
4067    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4068    haxes=findobj(hview_field,'tag','axes3');
4069    pos=get(hview_field,'Position'); 
4070    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4071        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4072        pos_table=get(h_TableDisplay,'Position');
4073        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4074        drawnow% needed to change position before the next command
4075        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4076    else
4077        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4078    end
4079end
4080
4081%% update the color of the graphic object representation: the selected object in magenta, others in blue
4082update_object_color(handles.axes3,hhview_field.axes3,UvData.Object{IndexObj}.DisplayHandle.uvmat)
4083
4084%------------------------------------------------------------------------
4085%--- update the color representation of objects (indicating the selected ones)
4086function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4087%------------------------------------------------------------------------
4088if isempty(axes_view_field)% case with no view_field plot
4089hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4090else
4091hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4092findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4093end
4094for iobj=1:length(hother)
4095    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4096        set(hother(iobj),'EdgeColor','b')
4097        if isequal(get(hother(iobj),'FaceColor'),'m')
4098            set(hother(iobj),'FaceColor','b')
4099        end
4100    elseif isequal(get(hother(iobj),'Type'),'image')
4101        Acolor=get(hother(iobj),'CData');
4102        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4103        set(hother(iobj),'CData',Acolor);
4104    else
4105        set(hother(iobj),'Color','b')
4106    end
4107    set(hother(iobj),'Selected','off')
4108end
4109if ishandle(DisplayHandle)
4110    linetype=get(DisplayHandle,'Type');
4111    if isequal(linetype,'line')
4112        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4113    elseif isequal(linetype,'rectangle')
4114        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4115    elseif isequal(linetype,'patch')
4116        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4117    end
4118    SubObjectData=get(DisplayHandle,'UserData');
4119    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4120        for iobj=1:length(SubObjectData.SubObject)
4121            hsub=SubObjectData.SubObject(iobj);
4122            if isequal(get(hsub,'Type'),'rectangle')
4123                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4124            elseif isequal(get(hsub,'Type'),'image')
4125                Acolor=get(hsub,'CData');
4126                Acolor(:,:,1)=Acolor(:,:,3);
4127                set(hsub,'CData',Acolor);
4128            else
4129                set(hsub,'Color','m')
4130            end
4131        end
4132    end
4133    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4134        set(SubObjectData.DeformPoint,'Color','m')
4135    end
4136end
4137
4138%-------------------------------------------------------------------
4139% --- Executes on selection change in edit_object.
4140function edit_object_Callback(hObject, eventdata, handles)
4141%-------------------------------------------------------------------
4142UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4143hset_object=findobj(allchild(0),'Tag','set_object');
4144if get(handles.edit_object,'Value')
4145    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4146    %suppress the other options
4147    set(handles.CheckZoom,'Value',0)
4148    CheckZoom_Callback(hObject, eventdata, handles)
4149    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4150    if ishandle(hgeometry_calib)
4151        hhgeometry_calib=guidata(hgeometry_calib);
4152        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4153        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4154    end
4155    set(handles.ViewObject,'value',1)
4156    ViewObject_Callback(hObject, eventdata, handles)
4157%     if isempty(hset_object)% open the GUI set_object with data of the currently selected object
4158%         ViewObject_Callback(hObject, eventdata, handles)
4159%         %         hset_object=findobj(allchild(0),'Tag','set_object');
4160%     else
4161%         hhset_object=guidata(hset_object);
4162%         set(hhset_object.PLOT,'enable','on');
4163%         set(get(hset_object,'children'),'enable','on')
4164%     end
4165else % desctivate object edit mode
4166    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4167    if ~isempty(hset_object)% open the
4168        hhset_object=guidata(hset_object);
4169        set(hhset_object.PLOT,'enable','off');
4170        set(get(hset_object,'children'),'enable','inactive')
4171    end
4172end
4173
4174
4175%------------------------------------------------------------------------
4176% --- Executes on button press in ViewObject.
4177function ViewObject_Callback(hObject, eventdata, handles)
4178%------------------------------------------------------------------------
4179check_view=get(handles.ViewObject,'Value');
4180
4181if check_view %activate set_object   
4182    IndexObj=get(handles.ListObject,'Value');
4183    list_object=get(handles.ListObject,'String');
4184    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4185    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4186    if numel(UvData.Object)<IndexObj;% error in UvData
4187        msgbox_uvmat('ERROR','invalid object list')
4188        return
4189    end
4190    ZBounds=0; % default
4191    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4192        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4193        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4194    end
4195%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4196    data=UvData.Object{IndexObj};
4197    if ~isfield(data,'Type')% default plane
4198        data.Type='plane';
4199    end
4200    if isfield(UvData,'Field')
4201        Field=UvData.Field;
4202        if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4203            data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4204            if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4205                data.RangeY=UvData.Field.Mesh;
4206            else
4207                data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4208            end
4209            data.DX=UvData.Field.Mesh;
4210            data.DY=UvData.Field.Mesh;
4211        end
4212        if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4213            data.Coord=[0 0 0]; %default
4214        end
4215        if isfield(Field,'CoordUnit')
4216            data.CoordUnit=Field.CoordUnit;
4217        end
4218    end
4219    hset_object=set_object(data,[],ZBounds);
4220    hhset_object=guidata(hset_object);
4221    if get(handles.edit_object,'Value')% edit mode
4222        set(hhset_object.PLOT,'Enable','on')
4223        set(get(hset_object,'children'),'enable','on')
4224    else
4225        set(hhset_object.PLOT,'Enable','off')
4226        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4227        set(hhset_object.SAVE,'Enable','on')
4228    end
4229else
4230    hset_object=findobj(allchild(0),'tag','set_object');
4231    if ~isempty(hset_object)
4232        delete(hset_object)% delete existing version of set_object
4233    end
4234end
4235 
4236
4237%------------------------------------------------------------------------
4238% --- Executes on button press in ViewField.
4239function ViewField_Callback(hObject, eventdata, handles)
4240%------------------------------------------------------------------------
4241check_view=get(handles.ViewField,'Value');
4242
4243if check_view
4244    IndexObj=get(handles.ListObject,'Value');
4245    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4246    if numel(UvData.Object)<IndexObj(end);% error in UvData
4247        msgbox_uvmat('ERROR','invalid object list')
4248        return
4249    end
4250    ZBounds=0; % default
4251    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4252        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4253        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4254    end
4255    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4256    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4257        UvData.Object{IndexObj(1)}.Type='plane';
4258    end
4259    list_object=get(handles.ListObject,'String');
4260    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4261   
4262    %% show the projection of the selected object on view_field
4263    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
4264    hview_field=findobj(allchild(0),'tag','view_field');
4265    if isempty(hview_field)
4266        hview_field=view_field;
4267    end
4268    hhview_field=guidata(hview_field);
4269    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4270    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4271    haxes=findobj(hview_field,'tag','axes3');
4272    pos=get(hview_field,'Position');
4273    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4274        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4275        pos_table=get(h_TableDisplay,'Position');
4276        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4277    else
4278        Data=get(hview_field,'UserData');
4279        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4280    end
4281else
4282    hview_field=findobj(allchild(0),'tag','view_field');
4283    if ~isempty(hview_field)
4284        delete(hview_field)% delete existing version of set_object
4285    end
4286end
4287
4288
4289%------------------------------------------------------------------------
4290% --- Executes on button press in delete_object.
4291function delete_object_Callback(hObject, eventdata, handles)
4292%------------------------------------------------------------------------
4293IndexObj=get(handles.ListObject,'Value');
4294IndexObj_1=get(handles.ListObject_1,'Value');
4295if IndexObj>1 && ~isequal(IndexObj,IndexObj_1)
4296    delete_object(IndexObj)
4297end
4298
4299%------------------------------------------------------------------------
4300%------------------------------------------------------------------------
4301%  II - TOOLS FROM THE UPPER MENU BAR
4302%------------------------------------------------------------------------
4303%------------------------------------------------------------------------
4304
4305%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4306% Export  Menu Callbacks
4307%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4308%------------------------------------------------------------------------
4309% --- Executes on button press in Menu/Export/field in workspace.
4310function MenuExportField_Callback(hObject, eventdata, handles)
4311%------------------------------------------------------------------------
4312global Data_uvmat
4313Data_uvmat=get(handles.uvmat,'UserData');
4314evalin('base','global Data_uvmat')%make CurData global in the workspace
4315display('current field :')
4316evalin('base','Data_uvmat') %display CurData in the workspace
4317commandwindow; %brings the Matlab command window to the front
4318
4319%------------------------------------------------------------------------
4320% --- Executes on button press in Menu/Export/extract figure.
4321function MenuExportFigure_Callback(hObject, eventdata, handles)
4322%------------------------------------------------------------------------
4323% huvmat=get(handles.MenuExport,'parent');
4324hfig=figure;
4325copyobj(handles.axes3,hfig);
4326map=colormap(handles.axes3);
4327colormap(map);%transmit the current colormap to the zoom fig
4328colorbar
4329
4330% %------------------------------------------------------
4331% % --- Executes on button press in Menu/Export/extract figure.
4332% %------------------------------------------------------
4333% function MenuExport_plot_Callback(hObject, eventdata, handles)
4334% huvmat=get(handles.MenuExport_plot,'parent');
4335% UvData=get(huvmat,'UserData');
4336% hfig=figure;
4337% newaxes=copyobj(handles.axes3,hfig);
4338% map=colormap(handles.axes3);
4339% colormap(map);%transmit the current colormap to the zoom fig
4340% colorbar
4341
4342%
4343% % --------------------------------------------------------------------
4344% function Insert_Callback(hObject, eventdata, handles)
4345%
4346
4347%------------------------------------------------------------------------
4348% --------------------------------------------------------------------
4349function MenuExportMovie_Callback(hObject, eventdata, handles)
4350% --------------------------------------------------------------------
4351set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4352huvmat=get(handles.run0,'parent');
4353UvData=get(huvmat,'UserData');
4354%[xx,xx,FileBase]=read_file_boxes(handles);
4355[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4356FileBase=fullfile(RootPath,RootFile);
4357 %read the current input file name
4358prompt = {'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)'};
4359dlg_title = 'select properties of the output avi movie';
4360num_lines= 1;
4361% nbfield_cell=get(handles.last_i,'String');
4362def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4363answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4364aviname=answer{1};
4365fps=str2double(answer{2});
4366% check for existing file with output name aviname
4367if exist(aviname,'file')
4368    backup=aviname;
4369    testexist=2;
4370    while testexist==2
4371        backup=[backup '~'];
4372        testexist=exist(backup,'file');     
4373    end
4374    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4375    if isequal(success,1)
4376        delete(aviname)%delete existing file
4377    else
4378        msgbox_uvmat('ERROR',message)
4379        return
4380    end
4381end
4382%create avi open
4383aviobj=avifile(aviname,'Compression','None','fps',fps);
4384
4385%display first view for tests
4386newfig=figure;
4387newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4388set(newaxes,'Tag','movieaxes')
4389nbpix=[512 384]*str2double(answer{3});
4390set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4391set(newaxes,'Position',eval(answer{4}));
4392map=colormap(handles.axes3);
4393colormap(map);%transmit the current colormap to the zoom fig
4394msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4395        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4396UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4397set(huvmat,'UserData',UvData);
4398increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4399set(handles.STOP,'Visible','on')
4400set(handles.speed,'Visible','on')
4401set(handles.speed_txt,'Visible','on')
4402set(handles.Movie,'BusyAction','queue')
4403
4404%imin=str2double(get(handles.i1,'String'));
4405imax=str2double(answer{5});
4406% if isfield(UvData,'Time')
4407htitle=get(newaxes,'Title');
4408xlim=get(newaxes,'XLim');
4409ylim=get(newaxes,'YLim');
4410set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4411time_str=get(handles.abs_time,'String');
4412set(htitle,'String',['t=' time_str])
4413set(handles.speed,'Value',1)
4414for i=1:imax
4415    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4416            runpm(hObject,eventdata,handles,increment)% run plus
4417            drawnow
4418            time_str=get(handles.abs_time,'String');
4419            if ishandle(htitle)
4420             set(htitle,'String',['t=' time_str])
4421            end
4422            mov=getframe(newfig);
4423            aviobj=addframe(aviobj,mov);
4424    end
4425end
4426aviobj=close(aviobj);
4427UvData=rmfield(UvData,'plotaxes');
4428%UvData.Object{1}.plotaxes=handles.axes3;
4429set(huvmat,'UserData',UvData);
4430msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4431
4432
4433%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4434% Projection Objects Menu Callbacks
4435%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4436
4437% -----------------------------------------------------------------------
4438function Menupoints_Callback(hObject, eventdata, handles)
4439%------------------------------------------------------------------------
4440data.Type='points';
4441data.ProjMode='projection';%default
4442data.ProjModeMenu={};% do not restrict ProjMode menus
4443create_object(data,handles)
4444
4445% -----------------------------------------------------------------------
4446function Menuline_Callback(hObject, eventdata, handles)
4447%------------------------------------------------------------------------
4448data.Type='line';
4449data.ProjMode='projection';%default
4450data.ProjModeMenu={};% do not restrict ProjMode menus
4451create_object(data,handles)
4452
4453%------------------------------------------------------------------------
4454function Menupolyline_Callback(hObject, eventdata, handles)
4455%------------------------------------------------------------------------
4456data.Type='polyline';
4457data.ProjMode='projection';%default
4458data.ProjModeMenu={};% do not restrict ProjMode menus
4459create_object(data,handles)
4460
4461%------------------------------------------------------------------------
4462function Menupolygon_Callback(hObject, eventdata, handles)
4463%------------------------------------------------------------------------
4464data.Type='polygon';
4465data.ProjMode='inside';%default
4466data.ProjModeMenu={};% do not restrict ProjMode menus
4467create_object(data,handles)
4468
4469%------------------------------------------------------------------------
4470function Menurectangle_Callback(hObject, eventdata, handles)
4471%------------------------------------------------------------------------
4472data.Type='rectangle';
4473data.ProjMode='inside';%default
4474data.ProjModeMenu={};% do not restrict ProjMode menus
4475create_object(data,handles)
4476
4477%------------------------------------------------------------------------
4478function Menuellipse_Callback(hObject, eventdata, handles)
4479%------------------------------------------------------------------------
4480data.Type='ellipse';
4481data.ProjMode='inside';%default
4482data.ProjModeMenu={};% do not restrict ProjMode menus
4483create_object(data,handles)
4484
4485%------------------------------------------------------------------------
4486function MenuMaskObject_Callback(hObject, eventdata, handles)
4487%------------------------------------------------------------------------
4488data.Type='polygon';
4489data.TypeMenu={'polygon'};
4490data.ProjMode='mask_inside';%default
4491data.ProjModeMenu={'mask_inside';'mask_outside'};
4492create_object(data,handles)
4493
4494%------------------------------------------------------------------------
4495function Menuplane_Callback(hObject, eventdata, handles)
4496%------------------------------------------------------------------------
4497data.Type='plane';
4498data.ProjMode='projection';%default
4499data.ProjModeMenu={};% do not restrict ProjMode menus
4500create_object(data,handles)
4501
4502%------------------------------------------------------------------------
4503function Menuvolume_Callback(hObject, eventdata, handles)
4504%------------------------------------------------------------------------
4505data.Type='volume';
4506data.ProjMode='interp';%default
4507data.ProjModeMenu={};
4508% set(handles.create,'Visible','on')
4509% set(handles.create,'Value',1)
4510% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4511create_object(data,handles)
4512
4513%------------------------------------------------------------------------
4514% --- generic function used for the creation of a projection object
4515function create_object(data,handles)
4516%------------------------------------------------------------------------
4517% desactivate geometric calibration if opened
4518hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4519if ishandle(hgeometry_calib)
4520    hhgeometry_calib=guidata(hgeometry_calib);
4521    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4522    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4523end
4524set(handles.edit_object,'Value',0); %suppress the object edit mode
4525set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4526ListObject=get(handles.ListObject,'String');
4527if ~strcmp(ListObject{end},'')
4528    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4529    set(handles.ListObject,'String',ListObject)
4530end
4531IndexObj=length(ListObject);
4532set(handles.ListObject,'Value',IndexObj)
4533UvData=get(handles.uvmat,'UserData');
4534UvData.Object{IndexObj}=[]; %create a new empty object
4535UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.axes3; % axes for plot_object
4536UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4537data.Name=data.Type;% default name=type
4538data.Coord=[0 0]; %default
4539if isfield(UvData,'Field')
4540    Field=UvData.Field;
4541    if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4542        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4543        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4544            data.RangeY=UvData.Field.Mesh;
4545        else
4546            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4547        end
4548        data.DX=UvData.Field.Mesh;
4549        data.DY=UvData.Field.Mesh;
4550    end
4551    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4552         data.Coord=[0 0 0]; %default
4553    end
4554    if isfield(Field,'CoordUnit')
4555        data.CoordUnit=Field.CoordUnit;
4556    end
4557end
4558if ishandle(handles.UVMAT_title)
4559    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4560end
4561hset_object=set_object(data,handles);% call the set_object interface
4562hhset_object=guidata(hset_object);
4563hchild=get(hset_object,'children');
4564set(hchild,'enable','on')
4565set(handles.uvmat,'UserData',UvData)
4566set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
4567CheckZoom_Callback(handles.uvmat, [], handles)
4568set(handles.delete_object,'Visible','on')
4569
4570%------------------------------------------------------------------------
4571function MenuBrowseObject_Callback(hObject, eventdata, handles)
4572%------------------------------------------------------------------------
4573%get the object file
4574[FileName, PathName, filterindex] = uigetfile( ...
4575       {'*.xml;*.mat', ' (*.xml,*.mat)';
4576       '*.xml',  '.xml files '; ...
4577        '*.mat',  '.mat matlab files '}, ...
4578        'Pick an xml Object file',get(handles.RootPath,'String'));
4579fileinput=[PathName FileName];%complete file name
4580sizf=size(fileinput);
4581if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4582
4583%read the file
4584data=xml2struct(fileinput);
4585
4586[tild,data.Name]=fileparts(FileName);% object name set as file name
4587ListObject=get(handles.ListObject,'String');
4588if ~strcmp(ListObject{end},'')
4589    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4590    set(handles.ListObject,'String',ListObject)
4591end
4592UvData=get(handles.uvmat,'UserData');
4593UvData.Object{IndexObj}=[]; %create a new empty object
4594UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4595UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4596set(handles.uvmat,'UserData',UvData)
4597set(handles.ListObject,'Value',length(ListObject))
4598hset_object=set_object(data);% call the set_object interface
4599set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4600set(handles.edit_object,'Value',0); %suppress the object edit mode
4601set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4602set(handles.delete_object,'Visible','on')
4603
4604
4605%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4606% MenuEdit Callbacks
4607%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4608%------------------------------------------------------------------------
4609function MenuEditObject_Callback(hObject, eventdata, handles)
4610%------------------------------------------------------------------------
4611set(handles.edit_object,'Value',1)
4612edit_Callback(hObject, eventdata, handles)
4613
4614% %------------------------------------------------------------------------
4615% function enable_transform(handles,state)
4616% %------------------------------------------------------------------------
4617% set(handles.transform_fct,'Visible',state)
4618% set(handles.TRANSFORM_txt,'Visible',state)   
4619% set(handles.transform_fct,'Visible',state) 
4620% set(handles.path_transform,'Visible',state)
4621% set(handles.pxcmx_txt,'Visible',state)
4622% set(handles.pxcmy_txt,'Visible',state)
4623% set(handles.pxcm,'Visible',state)
4624% set(handles.pycm,'Visible',state)
4625
4626%------------------------------------------------------------------------
4627function MenuEditVectors_Callback(hObject, eventdata, handles)
4628%------------------------------------------------------------------------
4629set(handles.edit_vect,'Visible','on')
4630set(handles.edit_vect,'Value',1)
4631edit_vect_Callback(hObject, eventdata, handles)
4632
4633%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4634% MenuTools Callbacks
4635%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4636%------------------------------------------------------------------------
4637function MenuCalib_Callback(hObject, eventdata, handles)
4638%------------------------------------------------------------------------
4639
4640UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4641
4642%suppress competing options
4643set(handles.CheckZoom,'Value',0)
4644set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4645set(handles.ListObject,'Value',1)     
4646% initiate display of GUI geometry_calib
4647data=[]; %default
4648if isfield(UvData,'CoordType')
4649    data.CoordType=UvData.CoordType;
4650end
4651pos=get(handles.uvmat,'Position');
4652pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4653pos(2)=pos(2)-0.02;
4654[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4655FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4656set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4657if isfield(UvData.OpenParam,'CalOrigin')
4658    pos_uvmat=get(handles.uvmat,'Position');
4659    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4660    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4661    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4662end
4663geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4664set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4665set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4666
4667%------------------------------------------------------------------------
4668function MenuMask_Callback(hObject, eventdata, handles)
4669%------------------------------------------------------------------------
4670UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4671ListObj=UvData.Object;
4672select=zeros(1,numel(ListObj));
4673for iobj=1:numel(ListObj);
4674    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4675        select(iobj)=1;
4676    end
4677end
4678val=find(select);
4679if isempty(val)
4680    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4681    return
4682else
4683%     set(handles.ListObject,'Max',2);%allow multiple selection
4684    set(handles.ListObject,'Value',val);
4685    flag=1;
4686    npx=size(UvData.Field.A,2);
4687    npy=size(UvData.Field.A,1);
4688    xi=0.5:npx-0.5;
4689    yi=0.5:npy-0.5;
4690    [Xi,Yi]=meshgrid(xi,yi);
4691    if isfield(UvData,'Object')
4692        for iobj=1:length(UvData.Object)
4693            ObjectData=UvData.Object{iobj};
4694            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4695                flagobj=1;
4696                testphys=0; %coordinates in pixels by default
4697                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4698                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4699                        Calib=UvData.XmlData{1}.GeometryCalib;
4700                        testphys=1;
4701                    end
4702                end
4703                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4704                    if isequal(ObjectData.Type,'polygon')
4705                        X=ObjectData.Coord(:,1);
4706                        Y=ObjectData.Coord(:,2);
4707                        if testphys
4708                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4709                        end
4710                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4711                    elseif isequal(ObjectData.Type,'ellipse')
4712                        if testphys
4713                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4714                        end
4715                        RangeX=max(ObjectData.RangeX);
4716                        RangeY=max(ObjectData.RangeY);
4717                        X2Max=RangeX*RangeX;
4718                        Y2Max=RangeY*RangeY;
4719                        distX=(Xi-ObjectData.Coord(1,1));
4720                        distY=(Yi-ObjectData.Coord(1,2));
4721                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4722                    elseif isequal(ObjectData.Type,'rectangle')
4723                        if testphys
4724                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4725                        end
4726                        distX=abs(Xi-ObjectData.Coord(1,1));
4727                        distY=abs(Yi-ObjectData.Coord(1,2));
4728                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4729                    end
4730                    if isequal(ObjectData.ProjMode,'mask_outside')
4731                        flagobj=~flagobj;
4732                    end
4733                    flag=flag & flagobj;
4734                end
4735            end
4736        end
4737    end
4738    %mask name
4739    RootPath=get(handles.RootPath,'String');
4740    RootFile=get(handles.RootFile,'String');
4741    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4742        RootFile(1)=[];
4743    end
4744    filebase=fullfile(RootPath,RootFile);
4745    list=get(handles.masklevel,'String');
4746    masknumber=num2str(length(list));
4747    maskindex=get(handles.masklevel,'Value');
4748    mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4749    %mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4750    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4751    imflag=flipdim(imflag,1);
4752
4753    %display the mask
4754    hfigmask=figure;
4755    set(hfigmask,'Name','mask image')
4756    vec=linspace(0,1,256);%define a linear greyscale colormap
4757    map=[vec' vec' vec'];
4758    colormap(map)
4759    image(imflag);
4760    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4761    if ~strcmp(answer,'Cancel')
4762        mask_dir=fileparts(answer);
4763        if ~exist(mask_dir,'dir')
4764            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4765            return
4766        end
4767        imwrite(imflag,answer,'BitDepth',8);
4768    end
4769    set(handles.ListObject,'Value',1)
4770%     set(handles.ListObject,'Max',1)
4771end
4772
4773%------------------------------------------------------------------------
4774%-- open the GUI set_grid.fig to create grid
4775function MenuGrid_Callback(hObject, eventdata, handles)
4776%------------------------------------------------------------------------
4777%suppress the other options if grid is chosen
4778set(handles.edit_vect,'Value',0)
4779edit_vect_Callback(hObject, eventdata, handles)
4780set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4781set(handles.ListObject,'Value',1)     
4782
4783%prepare display of the set_grid GUI
4784[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4785FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4786CoordList=get(handles.transform_fct,'String');
4787val=get(handles.transform_fct,'Value');
4788set_grid(FileName,CoordList{val});% call the set_object interface
4789
4790
4791%------------------------------------------------------------------------
4792function MenuRuler_Callback(hObject, eventdata, handles)
4793%------------------------------------------------------------------------
4794set(handles.CheckZoom,'Value',0)
4795CheckZoom_Callback(handles.uvmat, [], handles)
4796set(handles.MenuRuler,'checked','on')
4797UvData=get(handles.uvmat,'UserData');
4798UvData.MouseAction='ruler';
4799set(handles.uvmat,'UserData',UvData);
4800
4801%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4802% MenuRun Callbacks
4803%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4804
4805%------------------------------------------------------------------------
4806% open the GUI 'series'
4807function MenuSeries_Callback(hObject, eventdata, handles)
4808%------------------------------------------------------------------------
4809series; %first display of the GUI to fill waiting time
4810[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4811param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4812if isequal(get(handles.SubField,'Value'),1)
4813    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
4814    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
4815    if ~isequal(FileName_1,param.FileName)
4816        param.FileName_1=FileName_1;
4817    end
4818end
4819param.NomType=get(handles.NomType,'String');
4820param.NomType_1=get(handles.NomType_1,'String');
4821param.CheckFixPair=get(handles.CheckFixPair,'Value');
4822huvmat=get(handles.MenuSeries,'parent');
4823UvData=get(huvmat,'UserData');
4824if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4825    param.Time=UvData.XmlData{1}.Time;
4826end
4827if isequal(get(handles.scan_i,'Value'),1)
4828    param.incr_i=str2num(get(handles.increment_scan,'String'));
4829elseif isequal(get(handles.scan_j,'Value'),1)
4830    param.incr_j=str2num(get(handles.increment_scan,'String'));
4831end
4832param.list_fields=get(handles.Fields,'String');% list menu fields
4833param.list_fields(1)=[]; %suppress  'image' option
4834param.index_fields=get(handles.Fields,'Value');% selected string index
4835if param.index_fields>1
4836    param.index_fields=param.index_fields-1;
4837end
4838param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4839param.list_fields_1(1)=[]; %suppress  'image' option
4840param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4841if param.index_fields_1>1
4842    param.index_fields_1=param.index_fields_1-1;
4843end
4844param.menu_coord_str=get(handles.transform_fct,'String');
4845param.menu_coord_val=get(handles.transform_fct,'Value');
4846series(param); %run the series interface
4847
4848%------------------------------------------------------------------------
4849% -- open the GUI civ.fig for PIV
4850function MenuPIV_Callback(hObject, eventdata, handles)
4851%------------------------------------------------------------------------
4852 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4853 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4854civ(FileName);% interface de civ(not in the uvmat file)
4855
4856% --------------------------------------------------------------------
4857function MenuHelp_Callback(hObject, eventdata, handles)
4858% --------------------------------------------------------------------
4859path_to_uvmat=which ('uvmat');% check the path of uvmat
4860pathelp=fileparts(path_to_uvmat);
4861helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4862if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4863else
4864    addpath (fullfile(pathelp,'uvmat_doc'))
4865    web(helpfile);
4866end
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