source: trunk/src/uvmat.m @ 446

Last change on this file since 446 was 446, checked in by sommeria, 9 years ago

series rationalized. TO BE TESTED.

File size: 208.9 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)
911SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
912filexml=fullfile(RootPath,[SubDirBase '.xml']);% new convention: xml above the image dir
913if ~exist(filexml,'file')
914    filexml=fullfile(RootPath,SubDir,[RootFile '.xml']);%old convention: xml within the image directroy
915end
916warntext='';%default warning message
917NbSlice=1;%default
918set(handles.RootPath,'BackgroundColor',[1 1 1])
919if exist(filexml,'file')
920    set(handles.view_xml,'Visible','on')
921    set(handles.view_xml,'BackgroundColor',[1 1 0])
922    set(handles.view_xml,'String','view .xml')
923    drawnow
924    [XmlData,warntext]=imadoc2struct(filexml);
925    if ~isempty(warntext)
926        msgbox_uvmat('WARNING',warntext)
927    end
928    if isfield(XmlData,'TimeUnit')
929        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
930            TimeUnit=XmlData.TimeUnit;
931        end
932    end
933    set(handles.view_xml,'BackgroundColor',[1 1 1])
934    drawnow
935    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
936        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
937            set (handles.nb_slice,'String','volume')
938        end
939        hgeometry_calib=findobj('tag','geometry_calib');
940        if ~isempty(hgeometry_calib)
941            GUserData=get(hgeometry_calib,'UserData');
942            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
943                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
944                if strcmp(answer,'Yes')
945                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
946                end
947            end
948        end
949    end 
950else
951    fileciv=fullfile(RootPath,SubDir,[RootFile '.civ']);
952    if exist(fileciv,'file')% if .civ file found (very old convention)
953        [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext(fileciv);
954        GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
955        GeometryCalib.Tx=0;
956        GeometryCalib.Ty=0;
957        GeometryCalib.Tz=1;
958        GeometryCalib.dpx=1;
959        GeometryCalib.dpy=1;
960        GeometryCalib.sx=1;
961        GeometryCalib.Cx=0;
962        GeometryCalib.Cy=0;
963        GeometryCalib.f=1;
964        GeometryCalib.kappa1=0;
965        GeometryCalib.CoordUnit='cm';
966        XmlData.GeometryCalib=GeometryCalib;
967        if error==2, warntext=['no file ' fileciv];
968        elseif error==1, warntext='inconsistent number of fields in the .civ file';
969        end
970        set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
971        set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
972        set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
973        set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
974        set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
975        set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
976        set(handles.view_xml,'Visible','on')
977        set(handles.view_xml,'String','view .civ')
978    else
979        set(handles.view_xml,'Visible','off')
980    end
981end
982
983%% store last index in handles.lat_i and .last_j
984nbfield=max(max(i2_series));
985if isempty(nbfield)
986    nbfield=max(max(i1_series));
987end
988nbfield_j=max(max(j2_series));
989if isempty(nbfield_j)
990    nbfield_j=max(max(j1_series));
991end
992if ~isempty(XmlData.Time)
993    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
994    if isequal(size(XmlData.Time,1),1)
995%     if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
996        NomType=get(handles.NomType,'String');
997%         if isempty(nbfield_j)
998%         if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
999            XmlData.Time=(XmlData.Time)';
1000    end
1001end
1002last_i_cell=get(handles.last_i,'String');
1003if isempty(nbfield)
1004    last_i_cell{1}='';
1005else
1006    last_i_cell{1}=num2str(nbfield);
1007end
1008set(handles.last_i,'String',last_i_cell)
1009last_j_cell=get(handles.last_j,'String');
1010if isempty(nbfield_j)
1011     last_j_cell{1}='';
1012else
1013     last_j_cell{1}=num2str(nbfield_j);
1014end
1015set(handles.last_j,'String',last_j_cell);
1016
1017%% store geometric calibration in UvData
1018if isfield(XmlData,'GeometryCalib')
1019    GeometryCalib=XmlData.GeometryCalib;
1020    if isempty(GeometryCalib)
1021        set(handles.pxcm,'String','')
1022        set(handles.pycm,'String','')
1023        set(handles.transform_fct,'Value',1); %  no transform by default
1024    else
1025        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
1026            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
1027            set(handles.pxcm,'String','var')
1028            set(handles.pycm,'String','var')
1029        elseif isfield(GeometryCalib,'fx_fy')
1030            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
1031            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
1032            set(handles.pxcm,'String',num2str(pixcmx))
1033            set(handles.pycm,'String',num2str(pixcmy))
1034        end
1035        if ~get(handles.CheckFixLimits,'Value')
1036            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
1037        end
1038        if isfield(GeometryCalib,'SliceCoord')
1039           
1040           siz=size(GeometryCalib.SliceCoord);
1041           if siz(1)>1
1042               NbSlice=siz(1);
1043               set(handles.slices,'Visible','on')
1044               set(handles.slices,'Value',1)
1045           end
1046           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
1047               set(handles.nb_slice,'String','volume')
1048           else
1049               set(handles.nb_slice,'String',num2str(NbSlice))
1050           end
1051           slices_Callback([],[], handles)
1052        end           
1053    end
1054end
1055
1056%% update the data attached to the uvmat interface
1057if ~isempty(TimeUnit)
1058    set(handles.time_txt,'String',['time (' TimeUnit ')'])
1059end
1060UvData.TimeUnit=TimeUnit;
1061UvData.XmlData{index}=XmlData;
1062UvData.NewSeries=1;
1063% UvData.MovieObject=MovieObject;
1064
1065%display warning message
1066if ~isequal(warntext,'')
1067    msgbox_uvmat('WARNING',warntext);
1068end
1069
1070%% set default options in menu 'Fields'
1071if ~testima
1072    testcivx=0;
1073    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
1074        set(handles_Fields,'Value',1)
1075        set(handles_Fields,'String',{'get_field...'})
1076        UvData=rmfield(UvData,'FieldsString');
1077    else
1078        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
1079        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
1080            FieldList=calc_field;
1081            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
1082            set(handles_Fields,'Value',2) % set menu to 'velocity'
1083            col_vec=FieldList;
1084            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
1085            testcivx=1;
1086        end
1087        if ~testcivx
1088            set(handles_Fields,'Value',1) % set menu to 'get_field...
1089            set(handles_Fields,'String',{'get_field...'})
1090            col_vec={'get_field...'};
1091        end
1092        set(handles.ColorScalar,'String',col_vec)
1093    end
1094end
1095set(handles.uvmat,'UserData',UvData)
1096
1097%% set index navigation options and refresh plots
1098scan_option='i';%default
1099state_j='off'; %default
1100if index==2
1101    if get(handles.scan_j,'Value')
1102        scan_option='j'; %keep the scan option for the second fiel series
1103    end
1104    if strcmp(get(handles.j1,'Visible'),'on')
1105        state_j='on';
1106    end
1107end
1108if ~isempty(j1_series)
1109        state_j='on';
1110        if isequal(nbfield,1) &&index==1
1111            scan_option='j'; %scan j index by default if nbfield=1               
1112        end
1113end
1114if isequal(scan_option,'i')
1115     set(handles.scan_i,'Value',1)
1116     scan_i_Callback([],[], handles);
1117else
1118     set(handles.scan_j,'Value',1)
1119     scan_j_Callback([],[], handles);
1120end
1121set(handles.scan_j,'Visible',state_j)
1122set(handles.j1,'Visible',state_j)
1123set(handles.j2,'Visible',state_j)
1124set(handles.last_j,'Visible',state_j);
1125set(handles.frame_j,'Visible',state_j);
1126set(handles.j_text,'Visible',state_j);
1127if ~isempty(i2_series)||~isempty(j2_series)
1128    set(handles.CheckFixPair,'Visible','on')
1129elseif index==1
1130    set(handles.CheckFixPair,'Visible','off')
1131end
1132
1133%% view the field 
1134run0_Callback([],[], handles); %view field
1135mask_test=get(handles.CheckMask,'value');
1136if mask_test
1137    MaskData=get(handles.CheckMask,'UserData');
1138    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1139          delete(MaskData.maskhandle)    %delete old mask
1140    end
1141    CheckMask_Callback([],[],handles)
1142end
1143
1144%% update list of recent files in the menubar and save it for future opening
1145MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
1146    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
1147str_find=strcmp(FileName,MenuFile);
1148if isempty(find(str_find,1))
1149    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
1150end
1151for ifile=1:min(length(MenuFile),5)
1152    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
1153    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
1154end
1155dir_perso=prefdir;
1156profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1157if exist(profil_perso,'file')
1158    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1159else
1160    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
1161end
1162
1163
1164%------------------------------------------------------------------------
1165% --- switch file index scanning options scan_i and scan_j in an exclusive way
1166function scan_i_Callback(hObject, eventdata, handles)
1167%------------------------------------------------------------------------
1168if get(handles.scan_i,'Value')==1
1169    set(handles.scan_i,'BackgroundColor',[1 1 0])
1170    set(handles.scan_j,'Value',0)
1171else
1172    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1173    set(handles.scan_j,'Value',1)
1174end
1175scan_j_Callback(hObject, eventdata, handles)
1176
1177%------------------------------------------------------------------------
1178% --- switch file index scanning options scan_i and scan_j in an exclusive way
1179function scan_j_Callback(hObject, eventdata, handles)
1180%------------------------------------------------------------------------
1181if get(handles.scan_j,'Value')==1
1182    set(handles.scan_j,'BackgroundColor',[1 1 0])
1183    set(handles.scan_i,'Value',0)
1184    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1185%     NomType=get(handles.NomType,'String');
1186%     switch NomType
1187%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1188%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1189%     otherwise
1190%         set(handles.CheckFixPair,'Visible','off')
1191%     end
1192else
1193    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1194    set(handles.scan_i,'Value',1)
1195    set(handles.scan_i,'BackgroundColor',[1 1 0])
1196    set(handles.CheckFixPair,'Visible','off')
1197end
1198
1199%------------------------------------------------------------------------
1200function i1_Callback(hObject, eventdata, handles)
1201%------------------------------------------------------------------------
1202set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1203NomType=get(handles.NomType,'String');
1204i1=stra2num(get(handles.i1,'String'));
1205i2=stra2num(get(handles.i2,'String'));
1206j1=stra2num(get(handles.j1,'String'));
1207j2=stra2num(get(handles.j2,'String'));
1208indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1209%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1210set(handles.FileIndex,'String',indices)
1211set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1212if get(handles.SubField,'Value')==1
1213    NomType_1=get(handles.NomType_1,'String');
1214    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1215     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1216     set(handles.FileIndex_1,'String',indices)
1217     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1218end
1219
1220%------------------------------------------------------------------------
1221function i2_Callback(hObject, eventdata, handles)
1222%------------------------------------------------------------------------
1223set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1224i1_Callback(hObject, eventdata, handles)
1225
1226%------------------------------------------------------------------------
1227function j1_Callback(hObject, eventdata, handles)
1228%------------------------------------------------------------------------
1229set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1230i1_Callback(hObject, eventdata, handles)
1231
1232%------------------------------------------------------------------------
1233function j2_Callback(hObject, eventdata, handles)
1234%------------------------------------------------------------------------
1235set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1236i1_Callback(hObject, eventdata, handles)
1237
1238%------------------------------------------------------------------------
1239function slices_Callback(hObject, eventdata, handles)
1240%------------------------------------------------------------------------
1241if get(handles.slices,'Value')==1
1242    set(handles.slices,'BackgroundColor',[1 1 0])
1243    set(handles.nb_slice,'Visible','on')
1244    set(handles.z_text,'Visible','on')
1245    set(handles.z_index,'Visible','on')
1246    nb_slice_Callback(hObject, eventdata, handles)
1247else
1248    set(handles.nb_slice,'Visible','off')
1249    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1250    set(handles.z_text,'Visible','off')
1251    set(handles.z_index,'Visible','off')
1252    set(handles.masklevel,'Value',1)
1253    set(handles.masklevel,'String',{'1'})
1254end
1255
1256%------------------------------------------------------------------------
1257function nb_slice_Callback(hObject, eventdata, handles)
1258%------------------------------------------------------------------------
1259nb_slice_str=get(handles.nb_slice,'String');
1260if isequal(nb_slice_str,'volume')
1261    num=stra2num(get(handles.j1,'String'));
1262    last_j=get(handles.last_j,'String');
1263    nbslice=str2double(last_j{1});
1264else
1265    num=str2double(get(handles.i1,'String'));
1266    nbslice=str2double(get(handles.nb_slice,'String'));
1267end
1268z=mod(num-1,nbslice)+1;
1269set(handles.z_index,'String',num2str(z))
1270for ilist=1:nbslice
1271    list_index{ilist,1}=num2str(ilist);
1272end   
1273set(handles.masklevel,'String',list_index)
1274set(handles.masklevel,'Value',z)
1275
1276%------------------------------------------------------------------------
1277% --- Executes on button press in view_xml.
1278function view_xml_Callback(hObject, eventdata, handles)
1279%------------------------------------------------------------------------
1280%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1281 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1282FileBase=fullfile(RootPath,RootFile);
1283option=get(handles.view_xml,'String');
1284if isequal(option,'view .xml')
1285    FileXml=[FileBase '.xml'];
1286    heditxml=editxml(FileXml);
1287end
1288
1289%------------------------------------------------------------------------
1290% --- Executes on button press in CheckMask.
1291function CheckMask_Callback(hObject, eventdata, handles)
1292%------------------------------------------------------------------------
1293%case of view mask selection
1294if isequal(get(handles.CheckMask,'Value'),1)
1295   % [FF,RootPath,FileBase]=read_file_boxes(handles);
1296     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1297     FileBase=fullfile(RootPath,RootFile);
1298    num_i1=stra2num(get(handles.i1,'String'));
1299    num_j1=stra2num(get(handles.j1,'String'));
1300    currentdir=pwd; 
1301    cd(RootPath);
1302    maskfiles=dir('*_*mask_*.png');%look for a mask file
1303    cd(currentdir);%come back to the working directory
1304    mdetect=0;
1305    if ~isempty(maskfiles)
1306        for ilist=1:length(maskfiles)
1307            maskname=maskfiles(ilist).name;% take the first mask file in the list
1308            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1309%             [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1310             [tild,Name]=fileparts(maskname);
1311            Namedouble=double(Name);
1312            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1313            ind_mask=findstr('mask',Name);
1314            i=ind_mask-1;
1315            while val(i)==0 && i>0
1316                i=i-1;
1317            end
1318            nbmask_str=str2num(Name(i+1:ind_mask-1));
1319            if ~isempty(nbmask_str)
1320                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1321            end
1322        end
1323        if isequal(min(nbslice),max(nbslice))
1324            nbslice=nbslice(1);
1325        else
1326            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1327            return
1328        end
1329        if ~isempty(nbslice) && Name(i)=='_'
1330            Mask.Base=[FileBase Name(i:ind_mask+3)];
1331            Mask.NbSlice=nbslice;
1332            num_i1=mod(num_i1-1,nbslice)+1;
1333            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1334            [RootPath,RootFile]=fileparts(Mask.Base);
1335            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1336            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1337            mdetect=exist(maskname,'file');
1338            if mdetect
1339                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1340                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1341                set(handles.CheckMask,'UserData',Mask);
1342                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1343                if nbslice > 1
1344                    set(handles.slices,'value',1)
1345                    slices_Callback(hObject, eventdata, handles)
1346                end
1347            end
1348        end
1349    end
1350    errormsg=[];%default
1351    if mdetect==0
1352        [FileName, PathName, filterindex] = uigetfile( ...
1353            {'*.png', ' (*.png)';
1354            '*.png',  '.png files '; ...
1355            '*.*', 'All Files (*.*)'}, ...
1356            'Pick a mask file *.png',FileBase);
1357        maskname=fullfile(PathName,FileName);
1358        if ~exist(maskname,'file')
1359            errormsg='no file browsed';
1360        end
1361        [RootDir,SubDir,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1362        Mask.Base=fullfile(RootDir,SubDir,RootFile);
1363        Mask.NbSlice=1;
1364        set(handles.CheckMask,'UserData',Mask);
1365        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1366    end
1367    if isempty(errormsg)
1368        errormsg=update_mask(handles,num_i1,num_j1);
1369    end
1370    if ~isempty(errormsg)
1371            set(handles.CheckMask,'Value',0)
1372            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1373     end
1374else % desactivate mask display
1375    MaskData=get(handles.CheckMask,'UserData');
1376    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1377          delete(MaskData.maskhandle)   
1378    end
1379    set(handles.CheckMask,'UserData',[])   
1380    UvData=get(handles.uvmat,'UserData');
1381    if isfield(UvData,'MaskName')
1382        UvData=rmfield(UvData,'MaskName');
1383        set(handles.uvmat,'UserData',UvData)
1384    end
1385    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1386end
1387
1388%------------------------------------------------------------------------
1389function errormsg=update_mask(handles,num_i1,num_j1)
1390%------------------------------------------------------------------------
1391errormsg=[];%default
1392MaskData=get(handles.CheckMask,'UserData');
1393if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1394    uistack(MaskData.maskhandle,'top');
1395end
1396num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1397[RootPath,RootFile]=fileparts(MaskData.Base);
1398MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
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.Movie,'Value')==1 && 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.MovieBackward,'Value')==1 && 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,SubDir,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
2011frame_index=1;%default
2012if ~isempty(filename)
2013    ObjectName=filename;
2014    FieldName='';%default
2015    VelType='';%default
2016%     FileType=UvData.FileType{1};
2017    switch UvData.FileType{1}
2018        case {'civx','civdata','netcdf'};
2019            list_fields=get(handles.Fields,'String');% list menu fields
2020  %          index_fields=get(handles.Fields,'Value');% selected string index
2021            FieldName= list_fields{get(handles.Fields,'Value')}; % selected field
2022            if ~strcmp(FieldName,'get_field...')
2023                if get(handles.FixVelType,'Value')
2024                    VelTypeList=get(handles.VelType,'String');
2025                    VelType=VelTypeList{get(handles.VelType,'Value')};
2026                end
2027            end
2028            if strcmp(FieldName,'velocity')
2029                list_code=get(handles.ColorCode,'String');% list menu fields
2030                index_code=get(handles.ColorCode,'Value');% selected string index
2031                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2032                    list_code=get(handles.ColorScalar,'String');% list menu fields
2033                    index_code=get(handles.ColorScalar,'Value');% selected string index
2034                    ParamIn.ColorVar= list_code{index_code}; % selected field
2035                end
2036            end
2037        case {'video','mmreader'}
2038            ObjectName=UvData.MovieObject{1};     
2039            if ~strcmp(NomType,'*')
2040                frame_index=num_j1;%frame index for movies or multimage
2041            else
2042                frame_index=num_i1;
2043            end
2044        case 'multimage'
2045            if ~strcmp(NomType,'*')
2046                frame_index=num_j1;%frame index for movies or multimage
2047            else
2048                frame_index=num_i1;
2049            end
2050        case 'vol' %TODO: update
2051            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2052                ParamIn.Npy=UvData.XmlData.Npy;
2053                ParamIn.Npx=UvData.XmlData.Npx;
2054            else           
2055                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2056                return
2057            end
2058    end
2059    ParamIn.FieldName=FieldName;
2060    ParamIn.VelType=VelType;
2061    ParamIn.GUIName='get_field';
2062    [Field{1},ParamOut,errormsg] = read_field(ObjectName,UvData.FileType{1},ParamIn,frame_index);
2063    if ~isempty(errormsg)
2064        errormsg=['error in reading ' filename ': ' errormsg];
2065        return
2066    end 
2067    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2068        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2069        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2070    end
2071    if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2072        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2073    end
2074    if isfield(ParamOut,'TimeValue')
2075        Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2076    end
2077end
2078
2079%% choose and read a second field filename_1 if defined
2080VelType_1=[];%default
2081FieldName_1=[];
2082ParamOut_1=[];
2083frame_index_1=1;
2084if ~isempty(filename_1)
2085    if ~exist(filename_1,'file')
2086        errormsg=['second file ' filename_1 ' does not exist'];
2087        return
2088    end
2089    Name=filename_1;
2090    switch UvData.FileType{2}
2091        case {'civx','civdata','netcdf'};
2092            list_fields=get(handles.Fields_1,'String');% list menu fields
2093            FieldName_1= list_fields{get(handles.Fields_1,'Value')}; % selected field
2094            if ~strcmp(FieldName,'get_field...')
2095                if get(handles.FixVelType,'Value')
2096                    VelTypeList=get(handles.VelType_1,'String');
2097                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2098                end
2099            end
2100            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2101                list_code=get(handles.ColorCode,'String');% list menu fields
2102                index_code=get(handles.ColorCode,'Value');% selected string index
2103                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2104                    list_code=get(handles.ColorScalar,'String');% list menu fields
2105                    index_code=get(handles.ColorScalar,'Value');% selected string index
2106                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2107                end
2108            end
2109        case {'video','mmreader'}
2110            Name=UvData.MovieObject{2};
2111                        if ~strcmp(NomType_1,'*')
2112                frame_index_1=num_j1;%frame index for movies or multimage
2113            else
2114                frame_index_1=num_i1;
2115            end 
2116         case 'multimage'
2117            if ~strcmp(NomType_1,'*')
2118                frame_index_1=num_j1;%frame index for movies or multimage
2119            else
2120                frame_index_1=num_i1;
2121            end   
2122        case 'vol' %TODO: update
2123            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2124                ParamIn_1.Npy=UvData.XmlData.Npy;
2125                ParamIn_1.Npx=UvData.XmlData.Npx;
2126            else
2127                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2128                return
2129            end
2130    end
2131    if isequal(get(handles.NomType_1,'Visible'),'on')
2132    NomType_1=get(handles.NomType_1,'String');
2133    else
2134        NomType_1=get(handles.NomType,'String');
2135    end
2136    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2137    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2138        if isfield(UvData,'filename_1')%&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2139            test_keepdata_1= strcmp(filename_1,UvData.filename_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
2140        end
2141    end
2142    if test_keepdata_1
2143        Field{2}=UvData.Field_1;% keep the stored field
2144        ParamOut_1=UvData.ParamOut_1;
2145    else
2146        ParamIn_1.FieldName=FieldName_1;
2147        ParamIn_1.VelType=VelType_1;
2148        ParamIn_1.GUIName='get_field_1';
2149        [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,frame_index_1);
2150        if ~isempty(errormsg)
2151            errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
2152            return
2153        end
2154%         UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2155    end
2156end
2157
2158%% update uvmat interface
2159if isfield(ParamOut,'Npx')
2160    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2161    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2162elseif isfield(ParamOut_1,'Npx')
2163    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2164    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2165end
2166
2167%% update the display menu for the first velocity type (first menuline)
2168test_veltype=0;
2169% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2170if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2171    test_veltype=1;
2172    set(handles.VelType,'Visible','on')
2173    set(handles.VelType_1,'Visible','on')
2174    set(handles.FixVelType,'Visible','on')
2175    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2176    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2177    index_val=find(index_menu,1);
2178    if isempty(index_val)
2179        index_val=1;
2180    end
2181    set(handles.VelType,'Value',index_val)
2182    if ~get(handles.SubField,'value')
2183        set(handles.VelType,'String',menu)
2184        set(handles.VelType_1,'Value',1)
2185        set(handles.VelType_1,'String',[{''};menu])
2186    end
2187else
2188    set(handles.VelType,'Visible','off')
2189end
2190% display the Fields menu from the input file and pick the selected one:
2191field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2192set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2193set(handles.Fields,'Value',find(field_index,1))
2194
2195%% update the display menu for the second velocity type (second menuline)
2196test_veltype_1=0;
2197if isempty(filename_1)
2198    set(handles.Fields_1,'Value',1); %update the field menu
2199    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2200elseif ~test_keepdata_1
2201    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2202        set(handles.VelType_1,'Visible','off')
2203    else
2204        test_veltype_1=1;
2205        set(handles.VelType_1,'Visible','on')
2206%         if ~get(handles.FixVelType,'Value')
2207            menu=set_veltype_display(ParamOut_1.CivStage);
2208            index_menu=strcmp(ParamOut_1.VelType,menu);
2209            set(handles.VelType_1,'Value',1+find(index_menu,1))
2210            set(handles.VelType_1,'String',[{''};menu])
2211%         end
2212    end
2213    % update the second field menu: the same quantity
2214    set(handles.Fields_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2215    % display the Fields menu from the input file and pick the selected one:
2216    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2217    set(handles.Fields_1,'Value',find(field_index,1)+1) 
2218%     % synchronise  with the first menu if the first selection is not 'velocity'
2219%     if ~strcmp(ParamOut.FieldName,'velocity')
2220%         field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2221%         set(handles.Fields_1,'Value',field_index); %update the field menu
2222%         ParamOut_1.FieldName=ParamOut.FieldName;
2223%         set(handles.Fields_1,'String',ParamOut_1.FieldList)
2224%     end
2225end
2226if test_veltype||test_veltype_1
2227     set(handles.FixVelType,'Visible','on')
2228else
2229     set(handles.FixVelType,'Visible','off')
2230end
2231
2232% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2233% set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2234% set(handles.Fields,'Value',find(field_index,1))
2235   
2236%% introduce w as background image by default for a new series (only for nbdim=2)
2237if ~isfield(UvData,'NewSeries')
2238    UvData.NewSeries=1;
2239end
2240%put W as background image by default if NbDim=2:
2241if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2242        set(handles.SubField,'Value',1);
2243        set(handles.RootPath_1,'String','"')
2244        set(handles.RootFile_1,'String','"')
2245        set(handles.SubDir_1,'String','"');
2246         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2247        set(handles.FileIndex_1,'String',indices)
2248        set(handles.FileExt_1,'String','"');
2249        set(handles.Fields_1,'Visible','on');
2250        set(handles.Fields_1,'Visible','on');
2251        set(handles.RootPath_1,'Visible','on')
2252        set(handles.RootFile_1,'Visible','on')
2253        set(handles.SubDir_1,'Visible','on');
2254        set(handles.FileIndex_1,'Visible','on');
2255        set(handles.FileExt_1,'Visible','on');
2256        set(handles.Fields_1,'Visible','on');
2257        Field{1}.AName='w';
2258end           
2259
2260%% display time
2261testimedoc=0;
2262TimeUnit='';
2263if isfield(Field{1},'Time')
2264    abstime=Field{1}.Time;%time read from the netcdf input file
2265end
2266if numel(Field)==2 && isfield(Field{2},'Time')
2267    abstime_1=Field{2}.Time;%time read from the netcdf input file
2268end
2269if isfield(Field{1},'Dt')
2270    dt=Field{1}.Dt;%dt read from the netcdf input file
2271    if isfield(Field{1},'TimeUnit')
2272       TimeUnit=Field{1}.TimeUnit;
2273    end
2274elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2275    dt=Field{2}.Dt;%dt read from the netcdf input file
2276    if isfield(Field{2},'TimeUnit')
2277       TimeUnit=Field{2}.TimeUnit;
2278    end
2279end
2280% time from xml file overset previous result
2281if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2282    if isempty(num_i2)||isnan(num_i2)
2283        num_i2=num_i1;
2284    end
2285    if isempty(num_j1)||isnan(num_j1)
2286        num_j1=1;
2287    end
2288    if isempty(num_j2)||isnan(num_j2)
2289        num_j2=num_j1;
2290    end
2291    siz=size(UvData.XmlData{1}.Time);
2292    if ~isempty(num_i1)&& ~isempty(num_i2)&&siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2293        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2294        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2295        Field{1}.Dt=dt;
2296        if isfield(UvData.XmlData{1},'TimeUnit')
2297            TimeUnit=UvData.XmlData{1}.TimeUnit;
2298        end
2299    end
2300    if numel(UvData.XmlData)==2
2301        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2302        if isempty(num_i2)
2303            num_i2=num_i1;
2304        end
2305        if isempty(num_j1)
2306            num_j1=1;
2307        end
2308        if isempty(num_j2)
2309            num_j2=num_j1;
2310        end
2311        siz=size(UvData.XmlData{2}.Time);
2312        if ~isempty(num_i1) && siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2313            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
2314            Field{2}.Dt=(UvData.XmlData{2}.Time(num_i2,num_j2)-UvData.XmlData{2}.Time(num_i1,num_j1));
2315        end
2316    end
2317end
2318if ~isequal(numel(abstime),1)
2319    abstime=[];
2320end
2321if ~isequal(numel(abstime_1),1)
2322      abstime_1=[];
2323end 
2324set(handles.abs_time,'String',num2str(abstime,4))
2325set(handles.abs_time_1,'String',num2str(abstime_1,4))
2326% if testimedoc && isfield(UvData,'dt')
2327%     dt=UvData.dt;
2328% end
2329if isempty(dt)||isequal(dt,0)
2330    set(handles.Dt_txt,'String','')
2331else
2332    if  isempty(TimeUnit)
2333        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2334    else
2335        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2336    end
2337end
2338
2339
2340%% store the current open names, fields and vel types in uvmat interface
2341UvData.filename_1=filename_1;
2342
2343%% apply coordinate transform or other user fct
2344XmlData=[];%default
2345XmlData_1=[];%default
2346if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2347    XmlData=UvData.XmlData{1};
2348    if numel(UvData.XmlData)==2
2349        XmlData_1=UvData.XmlData{2};
2350    end
2351end
2352choice_value=get(handles.transform_fct,'Value');
2353transform_list=get(handles.transform_fct,'UserData');
2354transform=transform_list{choice_value};%selected function handles
2355% z index
2356if ~isempty(filename)
2357    Field{1}.ZIndex=z_index;
2358end
2359if ~isempty(transform)
2360    if length(Field)>=2
2361        Field{2}.ZIndex=z_index;
2362        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2363        if isempty(Field{2})
2364            Field(2)=[];
2365        end
2366    else
2367        Field{1}=transform(Field{1},XmlData);
2368    end
2369    %% update tps in phys coordinates if needed
2370    if (strcmp(VelType,'filter1')||strcmp(VelType,'filter2'))&& strcmp(UvData.FileType{1},'civdata')&&isfield(Field{1},'U')&& isfield(Field{1},'V')
2371        Field{1}.X=Field{1}.X(Field{1}.FF==0);
2372        Field{1}.Y=Field{1}.Y(Field{1}.FF==0);
2373        Field{1}.U=Field{1}.U(Field{1}.FF==0);
2374        Field{1}.V=Field{1}.V(Field{1}.FF==0);
2375        [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);
2376    end
2377    if numel(Field)==2 && ~test_keepdata_1 && isequal(UvData.FileType{2}(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2378        %update tps in phys coordinates if needed
2379        if (strcmp(VelType_1,'filter1')||strcmp(VelType_1,'filter2'))&& strcmp(UvData.FileType{2},'civdata')&&isfield(Field{2},'U')&& isfield(Field{2},'V')
2380            Field{2}.X=Field{2}.X(Field{2}.FF==0);
2381            Field{2}.Y=Field{1}.Y(Field{2}.FF==0);
2382            Field{2}.U=Field{1}.U(Field{2}.FF==0);
2383            Field{2}.V=Field{1}.V(Field{2}.FF==0);
2384            [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);
2385        end
2386    end
2387end
2388
2389%% calculate scalar
2390if ~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)%
2391    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2392end
2393if 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...')
2394     Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2395end
2396
2397%% combine the two input fields (e.g. substract velocity fields)
2398%Field{1}.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}];
2399if numel(Field)==2
2400%    Field{2}.FieldList=[{ParamOut_1.FieldName} {ParamOut_1.ColorVar}];
2401   [UvData.Field,errormsg]=sub_field(Field{1},Field{2}); 
2402   UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2403   UvData.ParamOut_1=ParamOut_1;
2404else
2405   UvData.Field=Field{1};
2406end
2407if ~isempty(errormsg)
2408    errormsg=['error in uvmat/refresh_field/sub_field:' errormsg];
2409    return
2410end
2411%UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation
2412
2413%% analyse input field
2414test_x=0;
2415test_z=0;% test for unstructured z coordinate
2416[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2417if ~isempty(errormsg)
2418    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2419    return
2420end
2421[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);% analyse  the input field structure
2422if ~isempty(errormsg)
2423    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];% display error
2424    return
2425end
2426[NbDim,imax]=max(NbDim);% spatial dimension of the input field
2427if isfield(UvData.Field,'NbDim')
2428    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2429end
2430
2431%% get bounds and mesh (needed for mouse action and to open set_object)
2432if NbDim>1
2433    XName=''; %default
2434    YName='';
2435    %unstructured coordinates
2436    if ~isempty(VarType{imax}.coord_x)&&~isempty(VarType{imax}.coord_y)
2437        XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2438        YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2439        %nbvec=length(UvData.Field.(XName));%nbre of measurement points (e.g. vectors)
2440        test_x=1;%test for unstructured coordinates
2441        if ~isempty(VarType{imax}.coord_z)
2442            ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2443        else
2444            NbDim=2;
2445        end
2446        %structured coordinate
2447    elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0
2448        XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2449        if NbDim> 1 && VarType{imax}.coord(NbDim-1)>0
2450            YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2451        end
2452        % VarIndex=CellVarIndex{imax}; % list of variable indices
2453        DimIndex=VarDimIndex{CellVarIndex{imax}(1)}; %list of dim indices for the variable
2454        nbpoints_x=DimValue(DimIndex(NbDim));
2455        XMax=nbpoints_x;%default
2456        XMin=1;%default
2457    end
2458   
2459    if NbDim==3
2460        if ~test_x
2461            ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2462        end
2463        ZMax=max(UvData.Field.(ZName));
2464        ZMin=min(UvData.Field.(ZName));
2465        UvData.Field.ZMax=ZMax;
2466        UvData.Field.ZMin=ZMin;
2467        test_z=1;
2468        if isequal(ZMin,ZMax)%no z dependency
2469            NbDim=2;
2470            test_z=0;
2471        end
2472    end
2473    if ~isempty (XName)
2474        XMax=max(max(UvData.Field.(XName)));
2475        XMin=min(min(UvData.Field.(XName)));
2476        UvData.Field.NbDim=NbDim;
2477        UvData.Field.XMax=XMax;
2478        UvData.Field.XMin=XMin;
2479        if NbDim >1&& ~isempty(YName)
2480            YMax=max(max(UvData.Field.(YName)));
2481            YMin=min(min(UvData.Field.(YName)));
2482            UvData.Field.YMax=YMax;
2483            UvData.Field.YMin=YMin;
2484        end
2485        nbvec=length(UvData.Field.(XName));
2486        if test_x %unstructured coordinates
2487            if test_z
2488                UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2489                UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2490            else
2491                UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2492            end
2493        end
2494    end
2495    % case of structured coordinates
2496    if ~test_x
2497        DX=(XMax-XMin)/(nbpoints_x-1);
2498        if NbDim >1
2499            nbpoints_y=DimValue(DimIndex(NbDim-1));
2500            if isempty(YName)% if the y coordinate is not expressed, it is taken as the matrix index
2501                DY=1;
2502                UvData.Field.YMax=nbpoints_y;
2503                UvData.Field.YMin=1;
2504            else
2505                DY=(YMax-YMin)/(nbpoints_y-1);
2506            end
2507        end
2508        if NbDim==3
2509            nbpoints_z=DimValue(DimIndex(1));
2510            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2511            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2512            UvData.Field.ZMax=ZMax;
2513            UvData.Field.ZMin=ZMin;
2514        else
2515            UvData.Field.Mesh=DX;%sqrt(DX*DY);
2516        end
2517    end
2518    % adjust the mesh to a value 1, 2 , 5 *10^n
2519    ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude
2520    if UvData.Field.Mesh/ord>=5
2521        UvData.Field.Mesh=5*ord;
2522    elseif UvData.Field.Mesh/ord>=2
2523        UvData.Field.Mesh=2*ord;
2524    else
2525        UvData.Field.Mesh=ord;
2526    end
2527    UvData.Object{1}.Type='plane';%main plotting plane
2528    UvData.Object{1}.ProjMode='projection';%main plotting plane
2529    UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2530    UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2531   
2532    %% 3D case (menuvolume)
2533    if NbDim==3% && UvData.NewSeries
2534        test_set_object=1;
2535        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2536        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2537        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2538        if ~isempty(hset_object) %if set_object is detected
2539            delete(hset_object);% delete the GUI set_object if it does not fit
2540        end
2541        if test_set_object% reinitiate the GUI set_object
2542            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
2543            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2544            UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2545            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2546            UvData.Object{1}.Angle=[0 0 0];
2547            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2548            UvData.Object{1}.Name='1-PLANE';
2549            UvData.Object{1}.enable_plot=1;
2550            set_object(UvData.Object{1},handles,ZBounds);
2551            set(handles.ListObject,'Value',1);
2552            set(handles.ListObject,'String',{'1-PLANE'});
2553            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2554            edit_object_Callback([],[], handles)
2555        end
2556        %multilevel case (single menuplane in a 3D space)
2557    elseif isfield(UvData,'Z')
2558        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2559            XmlData=UvData.XmlData{1};
2560            if isfield(XmlData,'PlanePos')
2561                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2562            end
2563            if isfield(XmlData,'PlaneAngle')
2564                siz=size(XmlData.PlaneAngle);
2565                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2566                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2567            end
2568        elseif isfield(UvData,'ZIndex')
2569            UvData.Object{1}.ZObject=UvData.ZIndex;
2570        end
2571    end
2572end
2573
2574testnewseries=UvData.NewSeries;
2575UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2576set(handles.uvmat,'UserData',UvData)
2577
2578%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2579% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2580%     set(handles.num_MinA,'String','0')
2581%     set(handles.num_MaxA,'String','255')
2582% end
2583
2584%% usual 1D (x,y) plots
2585if NbDim<=1
2586    set(handles.Objects,'Visible','off')
2587    set(handles.ListObject_1_title,'Visible','off')
2588    set(handles.ListObject_1,'Visible','off')
2589    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.axes3,read_GUI(handles.uvmat));
2590    write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2591%     if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2592%         ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2593%     end
2594   
2595%% 2D or 3D fields are generally projected
2596else
2597    set(handles.Objects,'Visible','on')
2598    set(handles.ListObject_1_title,'Visible','on')
2599    set(handles.ListObject_1,'Visible','on')
2600   
2601    %% Plot the projections on the selected  projection objects
2602    % main projection object (uvmat display)
2603    list_object=get(handles.ListObject_1,'String');
2604    if isequal(list_object,{''})%refresh list of objects if the menu is empty
2605        UvData.Object={[]};
2606        set(handles.ListObject_1,'Value',1)
2607    end
2608    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2609    if IndexObj(1)> numel(UvData.Object)
2610        IndexObj(1)=1;%select the first object if the selected one does not exist
2611        set(handles.ListObject_1,'Value',1)
2612    end
2613    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2614    if isequal(IndexObj(2),IndexObj(1))
2615        IndexObj(2)=[];
2616    end
2617    plot_handles{1}=handles;
2618    if isfield(UvData,'plotaxes')%case of movies
2619        haxes(1)=UvData.plotaxes;
2620    else
2621        haxes(1)=handles.axes3;
2622    end
2623    PlotParam{1}=read_GUI(handles.uvmat);
2624    %default settings if vectors not visible
2625    if ~isfield(PlotParam{1},'Vectors')
2626        PlotParam{1}.Vectors.MaxVec=1;
2627        PlotParam{1}.Vectors.MinVec=0;
2628        PlotParam{1}.Vectors.CheckFixVecColor=1;
2629        PlotParam{1}.Vectors.ColCode1=0.33;
2630        PlotParam{1}.Vectors.ColCode2=0.66;
2631        PlotParam{1}.Vectors.ColorScalar={'ima_cor'};
2632        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2633    end
2634    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2635   
2636    %% second projection object (view_field display)
2637    if length( IndexObj)>=2
2638        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2639        if ~isempty(view_field_handle)
2640            plot_handles{2}=guidata(view_field_handle);
2641            haxes(2)=plot_handles{2}.axes3;
2642            PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2643            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2644        end
2645    end
2646   
2647    %% loop on the projection objects: one or two
2648   
2649    for imap=1:numel(IndexObj)
2650        iobj=IndexObj(imap);
2651        %      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)
2652        % %          [ObjectData,errormsg]=calc_field(UvData.Field.FieldList,UvData.Field);
2653        % %      else
2654        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2655        %      end
2656        if ~isempty(errormsg)
2657            return
2658        end
2659        if testnewseries
2660            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2661            if isfield(ObjectData,'CoordUnit')
2662                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2663                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2664            end
2665        end
2666        %use of mask (TODO: check)
2667        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2668            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2669            AX=ObjectData.AX;%x coordiantes for the scalar field
2670            AY=ObjectData.AY;%y coordinates for the scalar field
2671            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2672            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2673            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2674                nxy=size(flag_mask);
2675                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2676                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2677                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2678                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2679                %project on the positions of the scalar
2680                npxy=size(ObjectData.A);
2681                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2682                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2683                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2684                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2685                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2686                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2687            end
2688            AClass=class(ObjectData.A);
2689            ObjectData.A=flag_mask.*double(ObjectData.A);
2690            ObjectData.A=feval(AClass,ObjectData.A);
2691            ind_off=[];
2692            if isfield(ObjectData,'ListVarName')
2693                for ilist=1:length(ObjectData.ListVarName)
2694                    if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2695                        ind_off=[ind_off ilist];
2696                    end
2697                end
2698                ObjectData.ListVarName(ind_off)=[];
2699                VarDimIndex(ind_off)=[];
2700                ind_off=[];
2701                for ilist=1:length(ListDimName)
2702                    if isequal(ListDimName{ilist},'MaskX') || isequal(ListDimName{ilist},'MaskY')
2703                        ind_off=[ind_off ilist];
2704                    end
2705                end
2706                ListDimName(ind_off)=[];
2707                DimValue(ind_off)=[];
2708            end
2709        end
2710        if ~isempty(ObjectData)
2711            PlotType='none'; %default
2712            if imap==2 && isempty(view_field_handle)
2713                view_field(ObjectData)
2714            else
2715                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2716                write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2717                if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2718                    ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2719                end
2720            end
2721            if isequal(PlotType,'none')
2722                hget_field=findobj(allchild(0),'name','get_field');
2723                if isempty(hget_field)
2724                    get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2725                end
2726                errormsg='The field defined by get_field cannot be plotted';
2727                return
2728            end
2729        end
2730    end
2731   
2732    %% update the mask
2733    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2734        update_mask(handles,num_i1,num_i2);
2735    end
2736   
2737    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2738    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2739    ind_skip=[];
2740    % nb_histo=1;
2741    Ustring='';
2742    Vstring='';
2743    % suppress coordinates from the histogram menu
2744    for ivar=1:numel(menu_histo)%l loop on field variables:
2745        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2746            Role=UvData.Field.VarAttribute{ivar}.Role;
2747            switch Role
2748                case {'coord_x','coord_y','coord_z','dimvar'}
2749                    ind_skip=[ind_skip ivar];
2750                case {'vector_x'}
2751                    Ustring=UvData.Field.ListVarName{ivar};
2752                    ind_skip=[ind_skip ivar];
2753                case {'vector_y'}
2754                    Vstring=UvData.Field.ListVarName{ivar};
2755                    ind_skip=[ind_skip ivar];
2756            end
2757        end
2758        DimCell=UvData.Field.VarDimName{ivar};
2759        DimName='';
2760        if ischar(DimCell)
2761            DimName=DimCell;
2762        elseif iscell(DimCell)&& numel(DimCell)==1
2763            DimName=DimCell{1};
2764        end
2765        if strcmp(DimName,menu_histo{ivar})
2766            ind_skip=[ind_skip ivar];
2767        end
2768    end
2769    menu_histo(ind_skip)=[];% remove skipped items
2770    if ~isempty(Ustring)
2771        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2772    end
2773   
2774    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2775    % display menus and plot histograms
2776    test_v=0;
2777    if ~isempty(menu_histo)
2778        set(handles.histo1_menu,'Value',1)
2779        set(handles.histo1_menu,'String',menu_histo)
2780        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2781    end
2782end
2783
2784%------------------------------------------------------------------------
2785function histo1_menu_Callback(hObject, eventdata, handles)
2786%--------------------------------------------
2787%plot first histo
2788%huvmat=get(handles.histo1_menu,'parent');
2789histo_menu=get(handles.histo1_menu,'String');
2790histo_value=get(handles.histo1_menu,'Value');
2791FieldName=histo_menu{histo_value};
2792% update_histo(handles.histo_u,handles.uvmat,FieldName)
2793%
2794% %------------------------------------------------------------------------
2795% function histo2_menu_Callback(hObject, eventdata, handles)
2796% %------------------------------------------------------------------------
2797% %plot second histo
2798% %huvmat=get(handles.histo2_menu,'parent');
2799% histo_menu=get(handles.histo2_menu,'String');
2800% histo_value=get(handles.histo2_menu,'Value');
2801% FieldName=histo_menu{histo_value};
2802% update_histo(handles.histo_v,handles.uvmat,FieldName)
2803%
2804% %------------------------------------------------------------------------
2805% %read the field .Fieldname stored in UvData and plot its histogram
2806% function update_histo(haxes,huvmat,FieldName)
2807%------------------------------------------------------------------------
2808UvData=get(handles.uvmat,'UserData');
2809Field=UvData.Field;
2810r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2811FieldName_2='';
2812if ~isempty(r)
2813    FieldName=r.var1;
2814    FieldName_2=r.var2;
2815end
2816if ~isfield(UvData.Field,FieldName)
2817    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2818    return
2819end
2820FieldHisto=Field.(FieldName);
2821if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2822    indsel=find(Field.FF==0);%find values marked as false
2823    if ~isempty(indsel)
2824        FieldHisto=FieldHisto(indsel);
2825        if ~isempty(FieldName_2)
2826            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2827        end
2828    end
2829end
2830if isempty(Field)
2831    msgbox_uvmat('ERROR',['empty field ' FieldName])
2832else
2833    nxy=size(FieldHisto);
2834    Amin=double(min(min(min(FieldHisto))));%min of field value
2835    Amax=double(max(max(max(FieldHisto))));%max of field value
2836    if isequal(Amin,Amax)
2837        cla(handles.histo_u)
2838    else
2839        Histo.ListVarName={FieldName,'histo'};
2840        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2841            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2842        else
2843            if numel(nxy)==2
2844                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2845            else
2846                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2847            end
2848        end
2849        %unit
2850        units=[]; %default
2851        for ivar=1:numel(Field.ListVarName)
2852            if strcmp(Field.ListVarName{ivar},FieldName)
2853                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2854                    units=Field.VarAttribute{ivar}.units;
2855                    break
2856                end
2857            end
2858        end
2859        if ~isempty(units)
2860            Histo.VarAttribute{1}.units=units;
2861        end
2862        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2863        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2864            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2865            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2866        else
2867            for col=1:size(FieldHisto,3)
2868                B=FieldHisto(:,:,col);
2869                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2870                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2871            end
2872        end
2873        plot_field(Histo,handles.histo_u);
2874        hlegend=legend;
2875        if isempty(FieldName_2)
2876        set(hlegend,'String',FieldName)
2877        else
2878            set(hlegend,'String',{FieldName;FieldName_2})
2879        end
2880%         hh=get(handles.histo_u,'children');
2881%         get(hh(1))
2882%         get(hh(2))
2883    end
2884end
2885
2886%-------------------------------------------------------------------
2887% --- translate coordinate to matrix index
2888%-------------------------------------------------------------------
2889function [indx,indy]=pos2ind(x0,rangx0,nxy)
2890indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2891indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2892
2893
2894%-------------------------------------------------------------------
2895% --- Executes on button press in 'CheckZoom'.
2896%-------------------------------------------------------------------
2897function CheckZoom_Callback(hObject, eventdata, handles)
2898
2899if (get(handles.CheckZoom,'Value') == 1);
2900    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2901    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2902    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2903else
2904    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2905end
2906
2907%-------------------------------------------------------------------
2908% --- Executes on button press in 'CheckFixLimits'.
2909%-------------------------------------------------------------------
2910function CheckFixLimits_Callback(hObject, eventdata, handles)
2911test=get(handles.CheckFixLimits,'Value');
2912if test
2913    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2914else
2915    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2916    update_plot(handles);
2917end
2918
2919%-------------------------------------------------------------------
2920% --- Executes on button press in CheckFixAspectRatio.
2921function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2922%-------------------------------------------------------------------
2923if get(handles.CheckFixAspectRatio,'Value')
2924    set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
2925    update_plot(handles);
2926else
2927    set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
2928    update_plot(handles);
2929end
2930
2931%-------------------------------------------------------------------
2932function num_AspectRatio_Callback(hObject, eventdata, handles)
2933%-------------------------------------------------------------------
2934set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2935set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2936update_plot(handles);
2937%-------------------------------------------------------------------
2938
2939%-------------------------------------------------------------------
2940
2941
2942
2943%-------------------------------------------------------------------
2944%----Executes on button press in 'record': records the current flags of manual correction.
2945%-------------------------------------------------------------------
2946function record_Callback(hObject, eventdata, handles)
2947% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2948[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2949filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2950%filename=read_file_boxes(handles);
2951[erread,message]=fileattrib(filename);
2952if ~isempty(message) && ~isequal(message.UserWrite,1)
2953     msgbox_uvmat('ERROR',['no writting access to ' filename])
2954     return
2955end
2956test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2957test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2958if ~test_civ2 && ~test_civ1
2959    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2960end
2961if test_civ2
2962    nbname='nb_vectors2';
2963   flagname='vec2_FixFlag';
2964   attrname='fix2';
2965end
2966if test_civ1
2967    nbname='nb_vectors';
2968   flagname='vec_FixFlag';
2969   attrname='fix';
2970end
2971%write fix flags in the netcdf file
2972UvData=get(handles.uvmat,'UserData');
2973hhh=which('netcdf.open');% look for built-in matlab netcdf library
2974if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2975    nc=netcdf.open(filename,'NC_WRITE');
2976    netcdf.reDef(nc);
2977    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2978    dimid = netcdf.inqDimID(nc,nbname);
2979    try
2980        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2981    catch
2982        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2983    end
2984    netcdf.endDef(nc);
2985    netcdf.putVar(nc,varid,UvData.axes3.FF);
2986    netcdf.close(nc); 
2987else %old netcdf library
2988    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2989end
2990
2991%-------------------------------------------------------------------
2992%----Correct the netcdf file, using toolbox (old versions of Matlab).
2993%-------------------------------------------------------------------
2994function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2995nc=netcdf(filename,'write'); %open netcdf file
2996result=redef(nc);
2997eval(['nc.' attrname '=1;']);
2998theDim=nc(nbname) ;% get the number of velocity vectors
2999nb_vectors=size(theDim);
3000var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
3001var_FixFlag(1:nb_vectors)=AxeData.FF;%
3002fin=close(nc);
3003
3004%-------------------------------------------------------------------
3005% --- Executes on button press in SubField
3006function SubField_Callback(hObject, eventdata, handles)
3007%-------------------------------------------------------------------
3008UvData=get(handles.uvmat,'UserData');
3009if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
3010    set(handles.RootPath_1,'String','')
3011    set(handles.RootFile_1,'String','')
3012    set(handles.SubDir_1,'String','');
3013    set(handles.FileIndex_1,'String','');
3014    set(handles.FileExt_1,'String','');
3015    set(handles.RootPath_1,'Visible','off')
3016    set(handles.RootFile_1,'Visible','off')
3017    set(handles.SubDir_1,'Visible','off');
3018    set(handles.NomType_1,'Visible','off');
3019    set(handles.abs_time_1,'Visible','off')
3020    set(handles.FileIndex_1,'Visible','off');
3021    set(handles.FileExt_1,'Visible','off');
3022    set(handles.Fields_1,'Value',1);%set to blank state
3023    set(handles.VelType_1,'Value',1);%set to blank state
3024    set(handles.num_Opacity,'String','')% desactivate opacity setting
3025    if ~strcmp(get(handles.VelType,'Visible'),'on')
3026        set(handles.VelType_1,'Visible','off')
3027    end
3028    if isfield(UvData,'XmlData_1')
3029        UvData=rmfield(UvData,'XmlData_1');
3030    end
3031    set(handles.uvmat,'UserData',UvData);
3032    run0_Callback(hObject, eventdata, handles); %run
3033else
3034    MenuBrowse_1_Callback(hObject, eventdata, handles)
3035end
3036
3037%------------------------------------------------------------------------
3038% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3039
3040function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3041%------------------------------------------------------------------------
3042InputFile=read_GUI(handles.InputFile);
3043RootPath=InputFile.RootPath;
3044SubDir=regexprep(InputFile.SubDir,'/|\','');
3045RootFile=regexprep(InputFile.RootFile,'/|\','');
3046FileIndices=InputFile.FileIndex;
3047FileExt=InputFile.FileExt;
3048
3049
3050%------------------------------------------------------------------------
3051% ---- read the data displayed for the second input rootfile windows
3052function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3053%------------------------------------------------------------------------
3054RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3055if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3056    RootPath_1=get(handles.RootPath,'String');
3057end;
3058SubDir_1=get(handles.SubDir_1,'String');
3059if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3060    SubDir_1=get(handles.SubDir,'String');
3061end
3062SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3063RootFile_1=get(handles.RootFile_1,'String');
3064if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3065    RootFile_1=get(handles.RootFile,'String');
3066end
3067RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3068FileIndex_1=get(handles.FileIndex_1,'String');
3069if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3070    FileIndex_1=get(handles.FileIndex,'String');
3071end
3072FileExt_1=get(handles.FileExt_1,'String');
3073if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3074    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3075end
3076NomType_1=get(handles.NomType_1,'String');
3077if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3078    NomType_1=get(handles.NomType,'String');%read FileExt by default
3079end
3080%------------------------------------------------------------------------
3081% --- Executes on menu selection Fields
3082function Fields_Callback(hObject, eventdata, handles)
3083%------------------------------------------------------------------------
3084list_fields=get(handles.Fields,'String');% list menu fields
3085index_fields=get(handles.Fields,'Value');% selected string index
3086field= list_fields{index_fields(1)}; % selected string
3087if isequal(field,'get_field...')
3088    set(handles.FixVelType,'visible','off')
3089    set(handles.VelType,'visible','off')
3090    set(handles.VelType_1,'visible','off')
3091    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3092    filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3093    %filename=read_file_boxes(handles);
3094    hget_field=findobj(allchild(0),'name','get_field');
3095    if ~isempty(hget_field)
3096        delete(hget_field)
3097    end
3098    hget_field=get_field(filename);
3099    set(hget_field,'Name','get_field')
3100    hhget_field=guidata(hget_field);
3101    set(hhget_field.list_fig,'Value',1)
3102    set(hhget_field.list_fig,'String',{'uvmat'})
3103    set(handles.transform_fct,'Value',1)% no transform by default
3104    set(handles.path_transform,'String','')
3105    return %no action
3106end
3107list_fields=get(handles.Fields_1,'String');% list menu fields
3108index_fields=get(handles.Fields_1,'Value');% selected string index
3109field_1= list_fields{index_fields(1)}; % selected string
3110UvData=get(handles.uvmat,'UserData');
3111
3112%read the rootfile input display
3113[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3114FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3115[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3116% NomTypeNew=NomType;%default
3117if isequal(field,'image')
3118%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
3119%         NomTypeNew='_1_1';
3120%     elseif isequal(NomType,'#_ab')
3121%         NomTypeNew='#a';
3122%     elseif isequal(NomType,'_1-2')
3123%         NomTypeNew='_1';
3124%     end
3125    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
3126    if ~exist(imagename,'file')
3127        [FileName,PathName] = uigetfile( ...
3128            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3129            '*.jpg',' jpeg image files'; ...
3130            '*.png','.png image files'; ...
3131            '*.tif','.tif image files'; ...
3132            '*.avi;*.AVI','.avi movie files'; ...
3133            '*.vol','.volume images (png)'; ...
3134            '*.*',  'All Files (*.*)'}, ...
3135            'Pick an image',imagename);   
3136        imagename=[PathName FileName];
3137    end
3138     % display the selected field and related information
3139    display_file_name(handles,imagename)%display the image
3140    return
3141else
3142    ext=get(handles.FileExt,'String');
3143    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3144        [FileName,PathName] = uigetfile( ...
3145            {'*.nc', ' (*.nc)';
3146            '*.nc',' netcdf files'; ...
3147            '*.*',  'All Files (*.*)'}, ...
3148            'Pick a netcdf file',FileBase);
3149        filename=[PathName FileName];
3150        % display the selected field and related information
3151        display_file_name( handles,filename)
3152        return
3153    end
3154end
3155indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3156set(handles.FileIndex,'String',indices)
3157% set(handles.NomType,'String',NomType)
3158
3159%common to Fields_1_Callback
3160if isequal(field,'image')||isequal(field_1,'image')
3161    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3162    set(handles.TitleNpy,'Visible','on')
3163    set(handles.num_Npx,'Visible','on')
3164    set(handles.num_Npy,'Visible','on')
3165else
3166    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3167    set(handles.TitleNpy,'Visible','off')
3168    set(handles.num_Npx,'Visible','off')
3169    set(handles.num_Npy,'Visible','off')
3170end
3171if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3172    run0_Callback(hObject, eventdata, handles)
3173end
3174
3175%---------------------------------------------------
3176% --- Executes on menu selection Fields
3177function Fields_1_Callback(hObject, eventdata, handles)
3178%-------------------------------------------------
3179%% read input data
3180check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3181UvData=get(handles.uvmat,'UserData');
3182if check_new && isfield(UvData,'XmlData')
3183    UvData.XmlData{2}=UvData.XmlData{1};
3184end
3185if isfield(UvData,'Field_1')
3186    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3187end
3188UvData.filename_1='';% desactivate the use of a constant second file
3189list_fields=get(handles.Fields,'String');% list menu fields
3190field= list_fields{get(handles.Fields,'Value')}; % selected string
3191list_fields=get(handles.Fields_1,'String');% list menu fields
3192field_1= list_fields{get(handles.Fields_1,'Value')}; % selected string for the second field
3193if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3194    set(handles.SubField,'Value',0)
3195    SubField_Callback(hObject, eventdata, handles)
3196    return
3197else
3198    set(handles.SubField,'Value',1)%state that a second field is now entered
3199end
3200
3201%% read the rootfile input display
3202[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3203filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3204[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3205% set(handles.FileIndex_1,'Visible','on')
3206% set(handles.FileExt_1,'Visible','on')
3207switch field_1
3208    case 'get_field...'
3209        set_veltype_display(0) % no veltype display
3210        hget_field=findobj(allchild(0),'name','get_field_1');
3211        if ~isempty(hget_field)
3212            delete(hget_field)
3213        end
3214        hget_field=get_field(filename_1);
3215        set(hget_field,'name','get_field_1')
3216        hhget_field=guidata(hget_field);
3217        set(hhget_field.list_fig,'Value',1)
3218        set(hhget_field.list_fig,'String',{'uvmat'})
3219        set(handles.transform_fct,'Value',1)% no transform by default
3220        set(handles.path_transform,'String','')
3221        if check_new
3222            UvData.FileType{2}=UvData.FileType{1};
3223            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3224%             set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3225              set(handles.uvmat,'UserData',UvData)
3226        end
3227    case 'image'
3228        % guess the image name corresponding to the current netcdf name (no unique correspondance)
3229        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3230        if ~exist(imagename,'file') % browse for images if it is not found
3231            [FileName,PathName] = uigetfile( ...
3232                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3233                '*.jpg',' jpeg image files'; ...
3234                '*.png','.png image files'; ...
3235                '*.tif','.tif image files'; ...
3236                '*.avi;*.AVI','.avi movie files'; ...
3237                '*.vol','.volume images (png)'; ...
3238                '*.*',  'All Files (*.*)'}, ...
3239                'Pick an image',imagename);
3240            imagename=[PathName FileName];
3241        end
3242        if ~ischar(imagename)% quit if the browser has  been closed
3243            set(handles.SubField,'Value',0)
3244        else %valid browser input:  display the selected image
3245            set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3246            set(handles.TitleNpy,'Visible','on')
3247            set(handles.num_Npx,'Visible','on')
3248            set(handles.num_Npy,'Visible','on')
3249            display_file_name(handles,imagename,2)%display the imag
3250        end
3251    otherwise
3252        if check_new
3253            UvData.FileType{2}=UvData.FileType{1};
3254            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3255            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3256        end
3257        if ~isequal(field,'image')
3258            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3259            set(handles.TitleNpy,'Visible','off')
3260            set(handles.num_Npx,'Visible','off')
3261            set(handles.num_Npy,'Visible','off')
3262        end
3263        set(handles.uvmat,'UserData',UvData)
3264        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3265            run0_Callback(hObject, eventdata, handles)
3266        end
3267end
3268
3269%------------------------------------------------------------------------
3270% --- set the visibility of relevant velocity type menus:
3271function menu=set_veltype_display(Civ,FileType)
3272%------------------------------------------------------------------------
3273if ~exist('FileType','var')
3274    FileType='civx';
3275end
3276switch FileType
3277    case 'civx'
3278        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3279        if isequal(Civ,0)
3280            imax=0;
3281        elseif isequal(Civ,1) || isequal(Civ,2)
3282            imax=1;
3283        elseif isequal(Civ,3)
3284            imax=3;
3285        elseif isequal(Civ,4) || isequal(Civ,5)
3286            imax=4;
3287        elseif isequal(Civ,6) %patch2
3288            imax=6;
3289        end
3290    case 'civdata'
3291        menu={'civ1';'filter1';'civ2';'filter2'};
3292        if isequal(Civ,0)
3293            imax=0;
3294        elseif isequal(Civ,1) || isequal(Civ,2)
3295            imax=1;
3296        elseif isequal(Civ,3)
3297            imax=2;
3298        elseif isequal(Civ,4) || isequal(Civ,5)
3299            imax=3;
3300        elseif isequal(Civ,6) %patch2
3301            imax=4;
3302        end
3303end
3304menu=menu(1:imax);
3305
3306%------------------------------------------------------------------------
3307% --- Executes on button press in FixVelType.
3308function FixVelType_Callback(hObject, eventdata, handles)
3309%------------------------------------------------------------------------
3310% refresh the current plot if the fixed  veltype is unselected
3311if ~get(handles.FixVelType,'Value')
3312    run0_Callback(hObject, eventdata, handles)
3313end
3314
3315%------------------------------------------------------------------------
3316% --- Executes on button press in VelType.
3317function VelType_Callback(hObject, eventdata, handles)
3318%------------------------------------------------------------------------
3319set(handles.FixVelType,'Value',1)
3320run0_Callback(hObject, eventdata, handles)
3321
3322%------------------------------------------------------------------------
3323% --- Executes on button press in VelType_1.
3324function VelType_1_Callback(hObject, eventdata, handles)
3325%------------------------------------------------------------------------
3326set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3327UvData=get(handles.uvmat,'UserData');
3328%refresh field with a second filename=first file name
3329set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3330drawnow   
3331InputFile=read_GUI(handles.InputFile);
3332[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3333filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3334
3335if isempty(InputFile.VelType_1)
3336        filename_1='';% we plot the current field without the second field
3337        set(handles.SubField,'Value',0)
3338        SubField_Callback(hObject, eventdata, handles)
3339elseif get(handles.SubField,'Value')% if subfield is already 'on'
3340      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3341     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3342else
3343     filename_1=filename;% we compare two fields in the same file by default
3344     UvData.FileType{2}=UvData.FileType{1};
3345     set(handles.SubField,'Value',1)
3346end
3347if isfield(UvData,'Field_1')
3348    UvData=rmfield(UvData,'Field_1');% removes the stored second field if it exists
3349end
3350UvData.filename_1='';% desactivate the use of a constant second file
3351set(handles.uvmat,'UserData',UvData)
3352num_i1=stra2num(get(handles.i1,'String'));
3353num_i2=stra2num(get(handles.i2,'String'));
3354num_j1=stra2num(get(handles.j1,'String'));
3355num_j2=stra2num(get(handles.j2,'String'));
3356
3357errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
3358
3359if ~isempty(errormsg)
3360    msgbox_uvmat('ERROR',errormsg);
3361else
3362    set(handles.i1,'BackgroundColor',[1 1 1])
3363    set(handles.i2,'BackgroundColor',[1 1 1])
3364    set(handles.j1,'BackgroundColor',[1 1 1])
3365    set(handles.j2,'BackgroundColor',[1 1 1])
3366    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3367    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3368end
3369set(handles.run0,'BackgroundColor',[1 0 0])
3370
3371%-----------------------------------------------
3372% --- reset civ buttons
3373function reset_vel_type(handles_civ0,handle1)
3374for ibutton=1:length(handles_civ0)
3375    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3376    set(handles_civ0(ibutton),'Value',0)
3377end
3378if exist('handle1','var')%handles of selected button
3379        set(handle1,'BackgroundColor',[1 1 0]) 
3380end
3381
3382%-------------------------------------------------------
3383% --- Executes on button press in MENUVOLUME.
3384%-------------------------------------------------------
3385function VOLUME_Callback(hObject, eventdata, handles)
3386%errordlg('command VOL not implemented yet')
3387if ishandle(handles.UVMAT_title)
3388    delete(handles.UVMAT_title)
3389end
3390UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3391if isequal(get(handles.VOLUME,'Value'),1)
3392    set(handles.CheckZoom,'Value',0)
3393    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3394    set(handles.edit_vect,'Value',0)
3395    edit_vect_Callback(hObject, eventdata, handles)
3396    set(handles.edit_object,'Value',0)
3397    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3398%     set(handles.cal,'Value',0)
3399%     set(handles.cal,'BackgroundColor',[0 1 0])
3400    set(handles.edit_vect,'Value',0)
3401    edit_vect_Callback(hObject, eventdata, handles)
3402    %initiate set_object GUI
3403    data.Name='VOLUME';
3404    if isfield(UvData,'CoordType')
3405        data.CoordType=UvData.CoordType;
3406    end
3407    if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh)
3408        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3409        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3410        data.DX=UvData.Field.Mesh;
3411        data.DY=UvData.Field.Mesh;
3412    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3413        np=size(UvData.Field.A);
3414        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3415        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3416        data.RangeY=max(meshx,meshy);
3417        data.RangeX=max(meshx,meshy);
3418        data.DX=max(meshx,meshy);
3419    end
3420    data.ParentButton=handles.VOLUME;
3421    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3422    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3423                                                      % associate the set_object interface handle to the plotting axes
3424    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3425    pos_uvmat=get(handles.uvmat,'Position');
3426    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3427    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3428    set(hset_object,'Position',pos_set_object)
3429    end
3430    UvData.MouseAction='create_object';
3431else
3432    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3433    UvData.MouseAction='none';
3434end
3435set(handles.uvmat,'UserData',UvData)
3436
3437%-------------------------------------------------------
3438function edit_vect_Callback(hObject, eventdata, handles)
3439%-------------------------------------------------------
3440%
3441% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3442if isequal(get(handles.edit_vect,'Value'),1)
3443    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3444    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3445    if ~test_civ2 && ~test_civ1
3446        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3447    end
3448    set(handles.record,'Visible','on')
3449    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3450    set(handles.edit_object,'Value',0)
3451    set(handles.CheckZoom,'Value',0)
3452    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3453%     set(handles.create,'Value',0)
3454%     set(handles.create,'BackgroundColor',[0 1 0])
3455    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3456    set(gcf,'Pointer','arrow')
3457%     UvData.MouseAction='edit_vect';
3458else
3459    set(handles.record,'Visible','off')
3460    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3461%     UvData.MouseAction='none';
3462end
3463% set(handles.uvmat,'UserData',UvData)
3464
3465%----------------------------------------------
3466function save_mask_Callback(hObject, eventdata, handles)
3467%-----------------------------------------------------------------------
3468UvData=get(handles.uvmat,'UserData');
3469
3470flag=1;
3471npx=size(UvData.Field.A,2);
3472npy=size(UvData.Field.A,1);
3473xi=0.5:npx-0.5;
3474yi=0.5:npy-0.5;
3475[Xi,Yi]=meshgrid(xi,yi);
3476if isfield(UvData,'Object')
3477    for iobj=1:length(UvData.Object)
3478        ObjectData=UvData.Object{iobj};
3479        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3480            flagobj=1;
3481            testphys=0; %coordinates in pixels by default
3482            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3483                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3484                    Calib=UvData.XmlData{1}.GeometryCalib;
3485                    testphys=1;
3486                end
3487            end
3488            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3489                if isequal(ObjectData.Type,'polygon')
3490                    X=ObjectData.Coord(:,1);
3491                    Y=ObjectData.Coord(:,2);
3492                    if testphys
3493                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3494                    end
3495                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3496                elseif isequal(ObjectData.Type,'ellipse')
3497                    if testphys
3498                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3499                    end
3500                    RangeX=max(ObjectData.RangeX);
3501                    RangeY=max(ObjectData.RangeY);
3502                    X2Max=RangeX*RangeX;
3503                    Y2Max=RangeY*RangeY;
3504                    distX=(Xi-ObjectData.Coord(1,1));
3505                    distY=(Yi-ObjectData.Coord(1,2));
3506                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3507                elseif isequal(ObjectData.Type,'rectangle')
3508                    if testphys
3509                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3510                    end
3511                    distX=abs(Xi-ObjectData.Coord(1,1));
3512                    distY=abs(Yi-ObjectData.Coord(1,2));
3513                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3514                end
3515                if isequal(ObjectData.ProjMode,'mask_outside')
3516                    flagobj=~flagobj;
3517                end
3518                flag=flag & flagobj;
3519            end
3520        end
3521    end
3522end
3523% flag=~flag;
3524%mask name
3525RootPath=get(handles.RootPath,'String');
3526RootFile=get(handles.RootFile,'String');
3527RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3528filebase=fullfile(RootPath,RootFile);
3529list=get(handles.masklevel,'String');
3530masknumber=num2str(length(list));
3531maskindex=get(handles.masklevel,'Value');
3532mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3533%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3534imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3535imflag=flipdim(imflag,1);
3536% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3537msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3538imwrite(imflag,mask_name,'BitDepth',8);
3539
3540%display the mask
3541figure;
3542vec=linspace(0,1,256);%define a linear greyscale colormap
3543map=[vec' vec' vec'];
3544colormap(map)
3545
3546image(imflag);
3547
3548%-------------------------------------------------------------------
3549%-------------------------------------------------------------------
3550%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3551
3552%------------------------------------------------------------------
3553%-------------------------------------------------------------
3554% --- Executes on selection change in transform_fct.
3555function transform_fct_Callback(hObject, eventdata, handles)
3556%-------------------------------------------------------------
3557UvData=get(handles.uvmat,'UserData');
3558menu=get(handles.transform_fct,'String');
3559ind_coord=get(handles.transform_fct,'Value');
3560coord_option=menu{ind_coord};
3561list_transform=get(handles.transform_fct,'UserData');
3562ff=functions(list_transform{end}); 
3563if isequal(coord_option,'more...');
3564    coord_fct='';
3565    prompt = {'Enter the name of the transform function'};
3566    dlg_title = 'user defined transform';
3567    num_lines= 1;
3568    [FileName, PathName] = uigetfile( ...
3569       {'*.m', ' (*.m)';
3570        '*.m',  '.m files '; ...
3571        '*.*', 'All Files (*.*)'}, ...
3572        'Pick a file', ff.file);
3573    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3574        PathName(end)=[];
3575    end
3576    transform_selected =fullfile(PathName,FileName);
3577    if ~exist(transform_selected,'file')
3578           return
3579    end
3580   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3581   if ~isequal(ext_fct,'.m')
3582        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3583        return
3584   end
3585   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3586   ind_coord=get(handles.transform_fct,'Value');
3587   addpath(PathName)
3588   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3589   set(handles.transform_fct,'UserData',list_transform)
3590   rmpath(PathName)
3591   % save the new menu in the personal file 'uvmat_perso.mat'
3592   dir_perso=prefdir;%personal Matalb directory
3593   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3594   if exist(profil_perso,'file')
3595       nb_builtin=UvData.OpenParam.NbBuiltin;
3596       for ilist=nb_builtin+1:numel(list_transform)
3597           ff=functions(list_transform{ilist});
3598           transform_fct{ilist-nb_builtin}=ff.file;
3599       end
3600        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3601   end   
3602end
3603
3604%% check the current path to the selected function
3605if isa(list_transform{ind_coord},'function_handle')
3606    func=functions(list_transform{ind_coord});
3607    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3608else
3609    set(handles.path_transform,'String','')
3610end
3611
3612set(handles.CheckFixLimits,'Value',0)
3613set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3614
3615%% delete drawn objects
3616hother=findobj('Tag','proj_object');%find all the proj objects
3617for iobj=1:length(hother)
3618    delete_object(hother(iobj))
3619end
3620hother=findobj('Tag','DeformPoint');%find all the proj objects
3621for iobj=1:length(hother)
3622    delete_object(hother(iobj))
3623end
3624hh=findobj('Tag','calib_points');
3625if ~isempty(hh)
3626    delete(hh)
3627end
3628hhh=findobj('Tag','calib_marker');
3629if ~isempty(hhh)
3630    delete(hhh)
3631end
3632if isfield(UvData,'Object')
3633     UvData.Object=UvData.Object(1);
3634end
3635set(handles.ListObject,'Value',1)
3636set(handles.ListObject,'String',{'plane'})
3637set(handles.ListObject_1,'Value',1)
3638set(handles.ListObject_1,'String',{'plane'})
3639
3640%delete mask if it is displayed
3641% if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3642%    UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3643% end
3644set(handles.uvmat,'UserData',UvData)
3645run0_Callback(hObject, eventdata, handles)
3646
3647
3648
3649%------------------------------------------------
3650%CALLBACKS FOR PLOTTING PARAMETERS
3651%-------------------------------------------------
3652%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3653% Plot coordinates
3654%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3655%------------------------------------------------------------------------
3656function num_MinX_Callback(hObject, eventdata, handles)
3657%------------------------------------------------------------------------
3658set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3659set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3660update_plot(handles);
3661
3662%------------------------------------------------------------------------
3663function num_MaxX_Callback(hObject, eventdata, handles)
3664%------------------------------------------------------------------------
3665set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3666set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3667update_plot(handles);
3668
3669%------------------------------------------------------------------------
3670function num_MinY_Callback(hObject, eventdata, handles)
3671%------------------------------------------
3672set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3673set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3674update_plot(handles);
3675
3676%------------------------------------------------------------------------
3677function num_MaxY_Callback(hObject, eventdata, handles)
3678%------------------------------------------------------------------------
3679set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3680set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3681update_plot(handles);
3682
3683%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3684% Scalar or image representation
3685%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3686%------------------------------------------------------------------------
3687function num_MinA_Callback(hObject, eventdata, handles)
3688%------------------------------------------
3689set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3690set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3691MinA=str2double(get(handles.num_MinA,'String'));
3692MaxA=str2double(get(handles.num_MaxA,'String'));
3693if MinA>MaxA% switch minA and maxA in case of error
3694    MinA_old=MinA;
3695    MinA=MaxA;
3696    MaxA=MinA_old;
3697    set(handles.num_MinA,'String',num2str(MinA,5));
3698    set(handles.num_MaxA,'String',num2str(MaxA,5));
3699end
3700update_plot(handles);
3701
3702%------------------------------------------------------------------------
3703function num_MaxA_Callback(hObject, eventdata, handles)
3704%------------------------------------------------------------------------
3705set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3706set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3707MinA=str2double(get(handles.num_MinA,'String'));
3708MaxA=str2double(get(handles.num_MaxA,'String'));
3709if MinA>MaxA% switch minA and maxA in case of error
3710        MinA_old=MinA;
3711    MinA=MaxA;
3712    MaxA=MinA_old;
3713    set(handles.num_MinA,'String',num2str(MinA,5));
3714    set(handles.num_MaxA,'String',num2str(MaxA,5));
3715end
3716update_plot(handles);
3717
3718%------------------------------------------------------------------------
3719function CheckFixScalar_Callback(hObject, eventdata, handles)
3720%------------------------------------------------------------------------
3721test=get(handles.CheckFixScalar,'Value');
3722if test
3723    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3724else
3725    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3726    update_plot(handles);
3727end
3728
3729%-------------------------------------------------------------------
3730function CheckBW_Callback(hObject, eventdata, handles)
3731%-------------------------------------------------------------------
3732update_plot(handles);
3733
3734%-------------------------------------------------------------------
3735function num_Opacity_Callback(hObject, eventdata, handles)
3736update_plot(handles);
3737%-------------------------------------------------------------------
3738
3739%-------------------------------------------------------------------
3740function ListContour_Callback(hObject, eventdata, handles)
3741%-------------------------------------------------------------------
3742val=get(handles.ListContour,'Value');
3743if val==2
3744    set(handles.interval_txt,'Visible','on')
3745    set(handles.num_IncrA,'Visible','on')
3746else
3747    set(handles.interval_txt,'Visible','off')
3748    set(handles.num_IncrA,'Visible','off')
3749end
3750update_plot(handles);
3751
3752%-------------------------------------------------------------------
3753function num_IncrA_Callback(hObject, eventdata, handles)
3754%-------------------------------------------------------------------
3755update_plot(handles);
3756
3757
3758%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3759% Vector representation
3760%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3761%-------------------------------------------------------------------
3762function CheckHideWarning_Callback(hObject, eventdata, handles)
3763%-------------------------------------------------------------------
3764update_plot(handles);
3765
3766%-------------------------------------------------------------------
3767function CheckHideFalse_Callback(hObject, eventdata, handles)
3768%-------------------------------------------------------------------
3769update_plot(handles);
3770
3771%-------------------------------------------------------------------
3772function num_VecScale_Callback(hObject, eventdata, handles)
3773%-------------------------------------------------------------------
3774set(handles.CheckFixVectors,'Value',1);
3775set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3776update_plot(handles);
3777
3778%-------------------------------------------------------------------
3779function CheckFixVectors_Callback(hObject, eventdata, handles)
3780%-------------------------------------------------------------------
3781test=get(handles.CheckFixVectors,'Value');
3782if test
3783    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3784else
3785    update_plot(handles);
3786    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3787    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3788end
3789
3790%------------------------------------------------------------------------
3791% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3792function CheckDecimate4_Callback(hObject, eventdata, handles)
3793%------------------------------------------------------------------------
3794update_plot(handles);
3795
3796%------------------------------------------------------------------------
3797% --- Executes on selection change in ColorCode menu
3798function ColorCode_Callback(hObject, eventdata, handles)
3799%------------------------------------------------------------------------
3800% edit the choice for color code
3801update_color_code_boxes(handles);
3802update_plot(handles);
3803
3804%------------------------------------------------------------------------
3805function update_color_code_boxes(handles)
3806%------------------------------------------------------------------------
3807list_code=get(handles.ColorCode,'String');% list menu fields
3808colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3809enable_slider='off';%default
3810enable_bounds='off';%default
3811enable_scalar='off';%default
3812switch colcode
3813    case {'rgb','bgr'}
3814        enable_slider='on';
3815        enable_bounds='on';
3816        enable_scalar='on';
3817    case '64 colors'
3818        enable_bounds='on';
3819        enable_scalar='on';
3820end
3821set(handles.Slider1,'Visible',enable_slider)
3822set(handles.Slider2,'Visible', enable_slider)
3823set(handles.num_ColCode1,'Visible',enable_slider)
3824set(handles.num_ColCode2,'Visible',enable_slider)
3825set(handles.TitleColCode1,'Visible',enable_slider)
3826set(handles.TitleColCode2,'Visible',enable_slider)
3827set(handles.CheckFixVecColor,'Visible',enable_bounds)
3828set(handles.num_MinVec,'Visible',enable_bounds)
3829set(handles.num_MaxVec,'Visible',enable_bounds)
3830set(handles.ColorScalar,'Visible',enable_scalar)
3831set_vec_col_bar(handles)
3832
3833%------------------------------------------------------------------
3834% --- Executes on selection change in ColorScalar: choice of the color code.
3835function ColorScalar_Callback(hObject, eventdata, handles)
3836%------------------------------------------------------------------
3837% edit the choice for color code
3838list_scalar=get(handles.ColorScalar,'String');% list menu fields
3839col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3840if isequal(col_scalar,'ima_cor')
3841    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3842    ColorCode='rgb';
3843    set(handles.num_MinVec,'String','0')
3844    set(handles.num_MaxVec,'String','1')
3845    set(handles.num_ColCode1,'String','0.333')
3846    set(handles.num_ColCode2,'String','0.666')
3847else
3848    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3849    ColorCode='64 colors';
3850end
3851ColorCodeList=get(handles.ColorCode,'String');
3852ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3853set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3854
3855update_color_code_boxes(handles);
3856%replot the current graph
3857run0_Callback(hObject, eventdata, handles)
3858
3859%----------------------------------------------------------------
3860% -- Executes on slider movement to set the color code
3861%
3862function Slider1_Callback(hObject, eventdata, handles)
3863%------------------------------------------------------------------
3864slider1=get(handles.Slider1,'Value');
3865min_val=str2num(get(handles.num_MinVec,'String'));
3866max_val=str2num(get(handles.num_MaxVec,'String'));
3867col=min_val+(max_val-min_val)*slider1;
3868set(handles.num_ColCode1,'String',num2str(col))
3869if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3870    set(handles.Slider2,'Value',col)
3871    set(handles.num_ColCode2,'String',num2str(col))
3872end
3873set_vec_col_bar(handles)
3874update_plot(handles);
3875
3876%----------------------------------------------------------------
3877% Executes on slider movement to set the color code
3878%----------------------------------------------------------------
3879function Slider2_Callback(hObject, eventdata, handles)
3880slider2=get(handles.Slider2,'Value');
3881min_val=str2num(get(handles.num_MinVec,'String'));
3882max_val=str2num(get(handles.num_MaxVec,'String'));
3883col=min_val+(max_val-min_val)*slider2;
3884set(handles.num_ColCode2,'String',num2str(col))
3885if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3886    set(handles.Slider1,'Value',col)
3887    set(handles.num_ColCode1,'String',num2str(col))
3888end
3889set_vec_col_bar(handles)
3890update_plot(handles);
3891
3892%----------------------------------------------------------------
3893% --- Execute on return carriage on the edit box corresponding to slider 1
3894%----------------------------------------------------------------
3895function num_ColCode1_Callback(hObject, eventdata, handles)
3896set_vec_col_bar(handles)
3897update_plot(handles);
3898
3899%----------------------------------------------------------------
3900% --- Execute on return carriage on the edit box corresponding to slider 2
3901%----------------------------------------------------------------
3902function num_ColCode2_Callback(hObject, eventdata, handles)
3903set_vec_col_bar(handles)
3904update_plot(handles);
3905%------------------------------------------------------------------------
3906%-------------------------------------------------------
3907% --- Executes on button press in CheckFixVecColor.
3908%-------------------------------------------------------
3909function VecColBar_Callback(hObject, eventdata, handles)
3910set_vec_col_bar(handles)
3911
3912%------------------------------------------------------------------------
3913% --- Executes on button press in CheckFixVecColor.
3914function CheckFixVecColor_Callback(hObject, eventdata, handles)
3915%------------------------------------------------------------------------
3916if ~get(handles.CheckFixVecColor,'Value')
3917    update_plot(handles);
3918end
3919
3920%------------------------------------------------------------------------
3921% --- Executes on selection change in num_MaxVec.
3922function num_MinVec_Callback(hObject, eventdata, handles)
3923%------------------------------------------------------------------------
3924max_vec_Callback(hObject, eventdata, handles)
3925
3926%------------------------------------------------------------------------
3927% --- Executes on selection change in num_MaxVec.
3928function num_MaxVec_Callback(hObject, eventdata, handles)
3929%------------------------------------------------------------------------
3930set(handles.CheckFixVecColor,'Value',1)
3931CheckFixVecColor_Callback(hObject, eventdata, handles)
3932min_val=str2num(get(handles.num_MinVec,'String'));
3933max_val=str2num(get(handles.num_MaxVec,'String'));
3934slider1=get(handles.Slider1,'Value');
3935slider2=get(handles.Slider2,'Value');
3936colcode1=min_val+(max_val-min_val)*slider1;
3937colcode2=min_val+(max_val-min_val)*slider2;
3938set(handles.num_ColCode1,'String',num2str(colcode1))
3939set(handles.num_ColCode2,'String',num2str(colcode2))
3940update_plot(handles);
3941
3942%------------------------------------------------------------------------
3943% --- update the display of color code for vectors (on vecColBar)
3944function set_vec_col_bar(handles)
3945%------------------------------------------------------------------------
3946%get the image of the color display button 'VecColBar' in pixels
3947set(handles.VecColBar,'Unit','pixel');
3948pos_vert=get(handles.VecColBar,'Position');
3949set(handles.VecColBar,'Unit','Normalized');
3950width=ceil(pos_vert(3));
3951height=ceil(pos_vert(4));
3952
3953%get slider indications
3954list=get(handles.ColorCode,'String');
3955ichoice=get(handles.ColorCode,'Value');
3956colcode.ColorCode=list{ichoice};
3957colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3958colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3959test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
3960if test3color
3961    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3962    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3963end
3964vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3965[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3966oneheight=ones(1,height);
3967A1=colorlist(col_vec,1)*oneheight;
3968A2=colorlist(col_vec,2)*oneheight;
3969A3=colorlist(col_vec,3)*oneheight;
3970A(:,:,1)=A1';
3971A(:,:,2)=A2';
3972A(:,:,3)=A3';
3973set(handles.VecColBar,'Cdata',A)
3974
3975%-------------------------------------------------------------------
3976function update_plot(handles)
3977%-------------------------------------------------------------------
3978UvData=get(handles.uvmat,'UserData');
3979AxeData=UvData.axes3;% retrieve the current plotted data
3980PlotParam=read_GUI(handles.uvmat);
3981[tild,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
3982write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3983
3984%------------------------------------------------------------------------
3985%------------------------------------------------------------------------
3986%   SELECTION AND EDITION OF PROJECTION OBJECTS
3987%------------------------------------------------------------------------
3988%------------------------------------------------------------------------
3989
3990% --- Executes on selection change in ListObject_1.
3991function ListObject_1_Callback(hObject, eventdata, handles)
3992list_str=get(handles.ListObject,'String');
3993UvData=get(handles.uvmat,'UserData');
3994ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
3995
3996%% update the projection plot on uvmat
3997ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
3998plot_field(ProjData,handles.axes3,read_GUI(handles.uvmat));% plot the projected field;
3999%replot all the objects within the new projected field
4000for IndexObj=1:numel(list_str)
4001    IndexObj
4002        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat
4003        if isempty(hobject) || ~ishandle(hobject)
4004            hobject=handles.axes3
4005        end
4006        if isequal(IndexObj,get(handles.ListObject,'Value'))
4007            objectcolor='m'; %paint in magenta the currently selected object in ListObject
4008        else
4009            objectcolor='b';
4010        end
4011        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
4012end
4013set(handles.uvmat,'UserData',UvData)
4014
4015%% display the object parameters if the GUI set_object is already opened
4016if ~get(handles.ViewObject,'Value')
4017    ZBounds=0; % default
4018    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4019        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4020        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4021    end
4022    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
4023    set_object(ObjectData,[],ZBounds);
4024    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
4025end
4026
4027%  desactivate the edit object mode
4028set(handles.edit_object,'Value',0)
4029set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4030
4031%------------------------------------------------------------------------
4032% --- Executes on selection change in ListObject.
4033function ListObject_Callback(hObject, eventdata, handles)
4034%------------------------------------------------------------------------
4035list_str=get(handles.ListObject,'String');
4036IndexObj=get(handles.ListObject,'Value');%present object selection
4037
4038%% The object  is displayed in set_object if this GUI is already opened
4039UvData=get(handles.uvmat,'UserData');
4040ObjectData=UvData.Object{IndexObj};
4041hset_object=findobj(allchild(0),'tag','set_object');
4042if ~isempty(hset_object)
4043    ZBounds=0; % default
4044    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4045        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4046        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4047    end
4048    ObjectData.Name=list_str{IndexObj};
4049    set_object(ObjectData,[],ZBounds);
4050    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4051end
4052
4053%%  desactivate the edit object mode
4054set(handles.edit_object,'Value',0)
4055set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4056
4057%% update the  plot on view_field if view_field is already openened
4058hview_field=findobj(allchild(0),'tag','view_field');
4059if isempty(hview_field)
4060    hhview_field.axes3=[];
4061else
4062    Data=get(hview_field,'UserData');
4063    hhview_field=guidata(hview_field);
4064    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4065    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
4066    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4067    haxes=findobj(hview_field,'tag','axes3');
4068    pos=get(hview_field,'Position'); 
4069    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4070        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4071        pos_table=get(h_TableDisplay,'Position');
4072        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4073        drawnow% needed to change position before the next command
4074        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4075    else
4076        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4077    end
4078end
4079
4080%% update the color of the graphic object representation: the selected object in magenta, others in blue
4081update_object_color(handles.axes3,hhview_field.axes3,UvData.Object{IndexObj}.DisplayHandle.uvmat)
4082
4083%------------------------------------------------------------------------
4084%--- update the color representation of objects (indicating the selected ones)
4085function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4086%------------------------------------------------------------------------
4087if isempty(axes_view_field)% case with no view_field plot
4088hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4089else
4090hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4091findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4092end
4093for iobj=1:length(hother)
4094    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4095        set(hother(iobj),'EdgeColor','b')
4096        if isequal(get(hother(iobj),'FaceColor'),'m')
4097            set(hother(iobj),'FaceColor','b')
4098        end
4099    elseif isequal(get(hother(iobj),'Type'),'image')
4100        Acolor=get(hother(iobj),'CData');
4101        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4102        set(hother(iobj),'CData',Acolor);
4103    else
4104        set(hother(iobj),'Color','b')
4105    end
4106    set(hother(iobj),'Selected','off')
4107end
4108if ishandle(DisplayHandle)
4109    linetype=get(DisplayHandle,'Type');
4110    if isequal(linetype,'line')
4111        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4112    elseif isequal(linetype,'rectangle')
4113        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4114    elseif isequal(linetype,'patch')
4115        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4116    end
4117    SubObjectData=get(DisplayHandle,'UserData');
4118    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4119        for iobj=1:length(SubObjectData.SubObject)
4120            hsub=SubObjectData.SubObject(iobj);
4121            if isequal(get(hsub,'Type'),'rectangle')
4122                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4123            elseif isequal(get(hsub,'Type'),'image')
4124                Acolor=get(hsub,'CData');
4125                Acolor(:,:,1)=Acolor(:,:,3);
4126                set(hsub,'CData',Acolor);
4127            else
4128                set(hsub,'Color','m')
4129            end
4130        end
4131    end
4132    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4133        set(SubObjectData.DeformPoint,'Color','m')
4134    end
4135end
4136
4137%-------------------------------------------------------------------
4138% --- Executes on selection change in edit_object.
4139function edit_object_Callback(hObject, eventdata, handles)
4140%-------------------------------------------------------------------
4141UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4142hset_object=findobj(allchild(0),'Tag','set_object');
4143if get(handles.edit_object,'Value')
4144    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4145    %suppress the other options
4146    set(handles.CheckZoom,'Value',0)
4147    CheckZoom_Callback(hObject, eventdata, handles)
4148    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4149    if ishandle(hgeometry_calib)
4150        hhgeometry_calib=guidata(hgeometry_calib);
4151        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4152        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4153    end
4154    set(handles.ViewObject,'value',1)
4155    ViewObject_Callback(hObject, eventdata, handles)
4156%     if isempty(hset_object)% open the GUI set_object with data of the currently selected object
4157%         ViewObject_Callback(hObject, eventdata, handles)
4158%         %         hset_object=findobj(allchild(0),'Tag','set_object');
4159%     else
4160%         hhset_object=guidata(hset_object);
4161%         set(hhset_object.PLOT,'enable','on');
4162%         set(get(hset_object,'children'),'enable','on')
4163%     end
4164else % desctivate object edit mode
4165    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4166    if ~isempty(hset_object)% open the
4167        hhset_object=guidata(hset_object);
4168        set(hhset_object.PLOT,'enable','off');
4169        set(get(hset_object,'children'),'enable','inactive')
4170    end
4171end
4172
4173
4174%------------------------------------------------------------------------
4175% --- Executes on button press in ViewObject.
4176function ViewObject_Callback(hObject, eventdata, handles)
4177%------------------------------------------------------------------------
4178check_view=get(handles.ViewObject,'Value');
4179
4180if check_view %activate set_object   
4181    IndexObj=get(handles.ListObject,'Value');
4182    list_object=get(handles.ListObject,'String');
4183    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4184    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4185    if numel(UvData.Object)<IndexObj;% error in UvData
4186        msgbox_uvmat('ERROR','invalid object list')
4187        return
4188    end
4189    ZBounds=0; % default
4190    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4191        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4192        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4193    end
4194%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4195    data=UvData.Object{IndexObj};
4196    if ~isfield(data,'Type')% default plane
4197        data.Type='plane';
4198    end
4199    if isfield(UvData,'Field')
4200        Field=UvData.Field;
4201        if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4202            data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4203            if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4204                data.RangeY=UvData.Field.Mesh;
4205            else
4206                data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4207            end
4208            data.DX=UvData.Field.Mesh;
4209            data.DY=UvData.Field.Mesh;
4210        end
4211        if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4212            data.Coord=[0 0 0]; %default
4213        end
4214        if isfield(Field,'CoordUnit')
4215            data.CoordUnit=Field.CoordUnit;
4216        end
4217    end
4218    hset_object=set_object(data,[],ZBounds);
4219    hhset_object=guidata(hset_object);
4220    if get(handles.edit_object,'Value')% edit mode
4221        set(hhset_object.PLOT,'Enable','on')
4222        set(get(hset_object,'children'),'enable','on')
4223    else
4224        set(hhset_object.PLOT,'Enable','off')
4225        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4226        set(hhset_object.SAVE,'Enable','on')
4227    end
4228else
4229    hset_object=findobj(allchild(0),'tag','set_object');
4230    if ~isempty(hset_object)
4231        delete(hset_object)% delete existing version of set_object
4232    end
4233end
4234 
4235
4236%------------------------------------------------------------------------
4237% --- Executes on button press in ViewField.
4238function ViewField_Callback(hObject, eventdata, handles)
4239%------------------------------------------------------------------------
4240check_view=get(handles.ViewField,'Value');
4241
4242if check_view
4243    IndexObj=get(handles.ListObject,'Value');
4244    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4245    if numel(UvData.Object)<IndexObj(end);% error in UvData
4246        msgbox_uvmat('ERROR','invalid object list')
4247        return
4248    end
4249    ZBounds=0; % default
4250    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4251        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4252        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4253    end
4254    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4255    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4256        UvData.Object{IndexObj(1)}.Type='plane';
4257    end
4258    list_object=get(handles.ListObject,'String');
4259    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4260   
4261    %% show the projection of the selected object on view_field
4262    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
4263    hview_field=findobj(allchild(0),'tag','view_field');
4264    if isempty(hview_field)
4265        hview_field=view_field;
4266    end
4267    hhview_field=guidata(hview_field);
4268    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4269    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4270    haxes=findobj(hview_field,'tag','axes3');
4271    pos=get(hview_field,'Position');
4272    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4273        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4274        pos_table=get(h_TableDisplay,'Position');
4275        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4276    else
4277        Data=get(hview_field,'UserData');
4278        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4279    end
4280else
4281    hview_field=findobj(allchild(0),'tag','view_field');
4282    if ~isempty(hview_field)
4283        delete(hview_field)% delete existing version of set_object
4284    end
4285end
4286
4287
4288%------------------------------------------------------------------------
4289% --- Executes on button press in delete_object.
4290function delete_object_Callback(hObject, eventdata, handles)
4291%------------------------------------------------------------------------
4292IndexObj=get(handles.ListObject,'Value');
4293IndexObj_1=get(handles.ListObject_1,'Value');
4294if IndexObj>1 && ~isequal(IndexObj,IndexObj_1)
4295    delete_object(IndexObj)
4296end
4297
4298%------------------------------------------------------------------------
4299%------------------------------------------------------------------------
4300%  II - TOOLS FROM THE UPPER MENU BAR
4301%------------------------------------------------------------------------
4302%------------------------------------------------------------------------
4303
4304%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4305% Export  Menu Callbacks
4306%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4307%------------------------------------------------------------------------
4308% --- Executes on button press in Menu/Export/field in workspace.
4309function MenuExportField_Callback(hObject, eventdata, handles)
4310%------------------------------------------------------------------------
4311global Data_uvmat
4312Data_uvmat=get(handles.uvmat,'UserData');
4313evalin('base','global Data_uvmat')%make CurData global in the workspace
4314display('current field :')
4315evalin('base','Data_uvmat') %display CurData in the workspace
4316commandwindow; %brings the Matlab command window to the front
4317
4318%------------------------------------------------------------------------
4319% --- Executes on button press in Menu/Export/extract figure.
4320function MenuExportFigure_Callback(hObject, eventdata, handles)
4321%------------------------------------------------------------------------
4322% huvmat=get(handles.MenuExport,'parent');
4323hfig=figure;
4324copyobj(handles.axes3,hfig);
4325map=colormap(handles.axes3);
4326colormap(map);%transmit the current colormap to the zoom fig
4327colorbar
4328
4329% %------------------------------------------------------
4330% % --- Executes on button press in Menu/Export/extract figure.
4331% %------------------------------------------------------
4332% function MenuExport_plot_Callback(hObject, eventdata, handles)
4333% huvmat=get(handles.MenuExport_plot,'parent');
4334% UvData=get(huvmat,'UserData');
4335% hfig=figure;
4336% newaxes=copyobj(handles.axes3,hfig);
4337% map=colormap(handles.axes3);
4338% colormap(map);%transmit the current colormap to the zoom fig
4339% colorbar
4340
4341%
4342% % --------------------------------------------------------------------
4343% function Insert_Callback(hObject, eventdata, handles)
4344%
4345
4346%------------------------------------------------------------------------
4347% --------------------------------------------------------------------
4348function MenuExportMovie_Callback(hObject, eventdata, handles)
4349% --------------------------------------------------------------------
4350set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4351huvmat=get(handles.run0,'parent');
4352UvData=get(huvmat,'UserData');
4353%[xx,xx,FileBase]=read_file_boxes(handles);
4354[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4355FileBase=fullfile(RootPath,RootFile);
4356 %read the current input file name
4357prompt = {'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)'};
4358dlg_title = 'select properties of the output avi movie';
4359num_lines= 1;
4360% nbfield_cell=get(handles.last_i,'String');
4361def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4362answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4363aviname=answer{1};
4364fps=str2double(answer{2});
4365% check for existing file with output name aviname
4366if exist(aviname,'file')
4367    backup=aviname;
4368    testexist=2;
4369    while testexist==2
4370        backup=[backup '~'];
4371        testexist=exist(backup,'file');     
4372    end
4373    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4374    if isequal(success,1)
4375        delete(aviname)%delete existing file
4376    else
4377        msgbox_uvmat('ERROR',message)
4378        return
4379    end
4380end
4381%create avi open
4382aviobj=avifile(aviname,'Compression','None','fps',fps);
4383
4384%display first view for tests
4385newfig=figure;
4386newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4387set(newaxes,'Tag','movieaxes')
4388nbpix=[512 384]*str2double(answer{3});
4389set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4390set(newaxes,'Position',eval(answer{4}));
4391map=colormap(handles.axes3);
4392colormap(map);%transmit the current colormap to the zoom fig
4393msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4394        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4395UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4396set(huvmat,'UserData',UvData);
4397increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4398set(handles.STOP,'Visible','on')
4399set(handles.speed,'Visible','on')
4400set(handles.speed_txt,'Visible','on')
4401set(handles.Movie,'BusyAction','queue')
4402
4403%imin=str2double(get(handles.i1,'String'));
4404imax=str2double(answer{5});
4405% if isfield(UvData,'Time')
4406htitle=get(newaxes,'Title');
4407xlim=get(newaxes,'XLim');
4408ylim=get(newaxes,'YLim');
4409set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4410time_str=get(handles.abs_time,'String');
4411set(htitle,'String',['t=' time_str])
4412set(handles.speed,'Value',1)
4413for i=1:imax
4414    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4415            runpm(hObject,eventdata,handles,increment)% run plus
4416            drawnow
4417            time_str=get(handles.abs_time,'String');
4418            if ishandle(htitle)
4419             set(htitle,'String',['t=' time_str])
4420            end
4421            mov=getframe(newfig);
4422            aviobj=addframe(aviobj,mov);
4423    end
4424end
4425aviobj=close(aviobj);
4426UvData=rmfield(UvData,'plotaxes');
4427%UvData.Object{1}.plotaxes=handles.axes3;
4428set(huvmat,'UserData',UvData);
4429msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4430
4431
4432%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4433% Projection Objects Menu Callbacks
4434%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4435
4436% -----------------------------------------------------------------------
4437function Menupoints_Callback(hObject, eventdata, handles)
4438%------------------------------------------------------------------------
4439data.Type='points';
4440data.ProjMode='projection';%default
4441data.ProjModeMenu={};% do not restrict ProjMode menus
4442create_object(data,handles)
4443
4444% -----------------------------------------------------------------------
4445function Menuline_Callback(hObject, eventdata, handles)
4446%------------------------------------------------------------------------
4447data.Type='line';
4448data.ProjMode='projection';%default
4449data.ProjModeMenu={};% do not restrict ProjMode menus
4450create_object(data,handles)
4451
4452%------------------------------------------------------------------------
4453function Menupolyline_Callback(hObject, eventdata, handles)
4454%------------------------------------------------------------------------
4455data.Type='polyline';
4456data.ProjMode='projection';%default
4457data.ProjModeMenu={};% do not restrict ProjMode menus
4458create_object(data,handles)
4459
4460%------------------------------------------------------------------------
4461function Menupolygon_Callback(hObject, eventdata, handles)
4462%------------------------------------------------------------------------
4463data.Type='polygon';
4464data.ProjMode='inside';%default
4465data.ProjModeMenu={};% do not restrict ProjMode menus
4466create_object(data,handles)
4467
4468%------------------------------------------------------------------------
4469function Menurectangle_Callback(hObject, eventdata, handles)
4470%------------------------------------------------------------------------
4471data.Type='rectangle';
4472data.ProjMode='inside';%default
4473data.ProjModeMenu={};% do not restrict ProjMode menus
4474create_object(data,handles)
4475
4476%------------------------------------------------------------------------
4477function Menuellipse_Callback(hObject, eventdata, handles)
4478%------------------------------------------------------------------------
4479data.Type='ellipse';
4480data.ProjMode='inside';%default
4481data.ProjModeMenu={};% do not restrict ProjMode menus
4482create_object(data,handles)
4483
4484%------------------------------------------------------------------------
4485function MenuMaskObject_Callback(hObject, eventdata, handles)
4486%------------------------------------------------------------------------
4487data.Type='polygon';
4488data.TypeMenu={'polygon'};
4489data.ProjMode='mask_inside';%default
4490data.ProjModeMenu={'mask_inside';'mask_outside'};
4491create_object(data,handles)
4492
4493%------------------------------------------------------------------------
4494function Menuplane_Callback(hObject, eventdata, handles)
4495%------------------------------------------------------------------------
4496data.Type='plane';
4497data.ProjMode='projection';%default
4498data.ProjModeMenu={};% do not restrict ProjMode menus
4499create_object(data,handles)
4500
4501%------------------------------------------------------------------------
4502function Menuvolume_Callback(hObject, eventdata, handles)
4503%------------------------------------------------------------------------
4504data.Type='volume';
4505data.ProjMode='interp';%default
4506data.ProjModeMenu={};
4507% set(handles.create,'Visible','on')
4508% set(handles.create,'Value',1)
4509% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4510create_object(data,handles)
4511
4512%------------------------------------------------------------------------
4513% --- generic function used for the creation of a projection object
4514function create_object(data,handles)
4515%------------------------------------------------------------------------
4516% desactivate geometric calibration if opened
4517hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4518if ishandle(hgeometry_calib)
4519    hhgeometry_calib=guidata(hgeometry_calib);
4520    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4521    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4522end
4523set(handles.edit_object,'Value',0); %suppress the object edit mode
4524set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4525ListObject=get(handles.ListObject,'String');
4526if ~strcmp(ListObject{end},'')
4527    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4528    set(handles.ListObject,'String',ListObject)
4529end
4530IndexObj=length(ListObject);
4531set(handles.ListObject,'Value',IndexObj)
4532UvData=get(handles.uvmat,'UserData');
4533UvData.Object{IndexObj}=[]; %create a new empty object
4534UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.axes3; % axes for plot_object
4535UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4536data.Name=data.Type;% default name=type
4537data.Coord=[0 0]; %default
4538if isfield(UvData,'Field')
4539    Field=UvData.Field;
4540    if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4541        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4542        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4543            data.RangeY=UvData.Field.Mesh;
4544        else
4545            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4546        end
4547        data.DX=UvData.Field.Mesh;
4548        data.DY=UvData.Field.Mesh;
4549    end
4550    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4551         data.Coord=[0 0 0]; %default
4552    end
4553    if isfield(Field,'CoordUnit')
4554        data.CoordUnit=Field.CoordUnit;
4555    end
4556end
4557if ishandle(handles.UVMAT_title)
4558    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4559end
4560hset_object=set_object(data,handles);% call the set_object interface
4561hhset_object=guidata(hset_object);
4562hchild=get(hset_object,'children');
4563set(hchild,'enable','on')
4564set(handles.uvmat,'UserData',UvData)
4565set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
4566CheckZoom_Callback(handles.uvmat, [], handles)
4567set(handles.delete_object,'Visible','on')
4568
4569%------------------------------------------------------------------------
4570function MenuBrowseObject_Callback(hObject, eventdata, handles)
4571%------------------------------------------------------------------------
4572%get the object file
4573[FileName, PathName, filterindex] = uigetfile( ...
4574       {'*.xml;*.mat', ' (*.xml,*.mat)';
4575       '*.xml',  '.xml files '; ...
4576        '*.mat',  '.mat matlab files '}, ...
4577        'Pick an xml Object file',get(handles.RootPath,'String'));
4578fileinput=[PathName FileName];%complete file name
4579sizf=size(fileinput);
4580if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4581
4582%read the file
4583data=xml2struct(fileinput);
4584
4585[tild,data.Name]=fileparts(FileName);% object name set as file name
4586ListObject=get(handles.ListObject,'String');
4587if ~strcmp(ListObject{end},'')
4588    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4589    set(handles.ListObject,'String',ListObject)
4590end
4591
4592IndexObj=length(ListObject);
4593
4594UvData=get(handles.uvmat,'UserData');
4595UvData.Object{IndexObj}=[]; %create a new empty object
4596UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4597UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4598set(handles.uvmat,'UserData',UvData)
4599set(handles.ListObject,'Value',IndexObj)
4600hset_object=set_object(data);% call the set_object interface
4601set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4602set(handles.edit_object,'Value',0); %suppress the object edit mode
4603set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4604set(handles.delete_object,'Visible','on')
4605
4606
4607%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4608% MenuEdit Callbacks
4609%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4610%------------------------------------------------------------------------
4611function MenuEditObject_Callback(hObject, eventdata, handles)
4612%------------------------------------------------------------------------
4613set(handles.edit_object,'Value',1)
4614edit_Callback(hObject, eventdata, handles)
4615
4616% %------------------------------------------------------------------------
4617% function enable_transform(handles,state)
4618% %------------------------------------------------------------------------
4619% set(handles.transform_fct,'Visible',state)
4620% set(handles.TRANSFORM_txt,'Visible',state)   
4621% set(handles.transform_fct,'Visible',state) 
4622% set(handles.path_transform,'Visible',state)
4623% set(handles.pxcmx_txt,'Visible',state)
4624% set(handles.pxcmy_txt,'Visible',state)
4625% set(handles.pxcm,'Visible',state)
4626% set(handles.pycm,'Visible',state)
4627
4628%------------------------------------------------------------------------
4629function MenuEditVectors_Callback(hObject, eventdata, handles)
4630%------------------------------------------------------------------------
4631set(handles.edit_vect,'Visible','on')
4632set(handles.edit_vect,'Value',1)
4633edit_vect_Callback(hObject, eventdata, handles)
4634
4635%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4636% MenuTools Callbacks
4637%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4638%------------------------------------------------------------------------
4639function MenuCalib_Callback(hObject, eventdata, handles)
4640%------------------------------------------------------------------------
4641
4642UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4643
4644%suppress competing options
4645set(handles.CheckZoom,'Value',0)
4646set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4647set(handles.ListObject,'Value',1)     
4648% initiate display of GUI geometry_calib
4649data=[]; %default
4650if isfield(UvData,'CoordType')
4651    data.CoordType=UvData.CoordType;
4652end
4653pos=get(handles.uvmat,'Position');
4654pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4655pos(2)=pos(2)-0.02;
4656[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4657FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4658set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4659if isfield(UvData.OpenParam,'CalOrigin')
4660    pos_uvmat=get(handles.uvmat,'Position');
4661    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4662    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4663    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4664end
4665geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4666set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4667set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4668
4669%------------------------------------------------------------------------
4670function MenuMask_Callback(hObject, eventdata, handles)
4671%------------------------------------------------------------------------
4672UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4673ListObj=UvData.Object;
4674select=zeros(1,numel(ListObj));
4675for iobj=1:numel(ListObj);
4676    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4677        select(iobj)=1;
4678    end
4679end
4680val=find(select);
4681if isempty(val)
4682    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4683    return
4684else
4685%     set(handles.ListObject,'Max',2);%allow multiple selection
4686    set(handles.ListObject,'Value',val);
4687    flag=1;
4688    npx=size(UvData.Field.A,2);
4689    npy=size(UvData.Field.A,1);
4690    xi=0.5:npx-0.5;
4691    yi=0.5:npy-0.5;
4692    [Xi,Yi]=meshgrid(xi,yi);
4693    if isfield(UvData,'Object')
4694        for iobj=1:length(UvData.Object)
4695            ObjectData=UvData.Object{iobj};
4696            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4697                flagobj=1;
4698                testphys=0; %coordinates in pixels by default
4699                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4700                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4701                        Calib=UvData.XmlData{1}.GeometryCalib;
4702                        testphys=1;
4703                    end
4704                end
4705                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4706                    if isequal(ObjectData.Type,'polygon')
4707                        X=ObjectData.Coord(:,1);
4708                        Y=ObjectData.Coord(:,2);
4709                        if testphys
4710                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4711                        end
4712                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4713                    elseif isequal(ObjectData.Type,'ellipse')
4714                        if testphys
4715                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4716                        end
4717                        RangeX=max(ObjectData.RangeX);
4718                        RangeY=max(ObjectData.RangeY);
4719                        X2Max=RangeX*RangeX;
4720                        Y2Max=RangeY*RangeY;
4721                        distX=(Xi-ObjectData.Coord(1,1));
4722                        distY=(Yi-ObjectData.Coord(1,2));
4723                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4724                    elseif isequal(ObjectData.Type,'rectangle')
4725                        if testphys
4726                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4727                        end
4728                        distX=abs(Xi-ObjectData.Coord(1,1));
4729                        distY=abs(Yi-ObjectData.Coord(1,2));
4730                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4731                    end
4732                    if isequal(ObjectData.ProjMode,'mask_outside')
4733                        flagobj=~flagobj;
4734                    end
4735                    flag=flag & flagobj;
4736                end
4737            end
4738        end
4739    end
4740    %mask name
4741    RootPath=get(handles.RootPath,'String');
4742    SubDir=get(handles.SubDir,'String');
4743    RootFile=get(handles.RootFile,'String');
4744    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4745        RootFile(1)=[];
4746    end
4747   % filebase=fullfile(RootPath,RootFile);
4748    list=get(handles.masklevel,'String');
4749    masknumber=num2str(length(list));
4750    maskindex=get(handles.masklevel,'Value');
4751   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4752    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
4753    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4754    imflag=flipdim(imflag,1);
4755
4756    %display the mask
4757    hfigmask=figure;
4758    set(hfigmask,'Name','mask image')
4759    vec=linspace(0,1,256);%define a linear greyscale colormap
4760    map=[vec' vec' vec'];
4761    colormap(map)
4762    image(imflag);
4763    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4764    if ~strcmp(answer,'Cancel')
4765        mask_dir=fileparts(answer);
4766        if ~exist(mask_dir,'dir')
4767            [xx,msg1]=mkdir(mask_dir);
4768            if ~strcmp(msg1,'')
4769                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
4770                return
4771            end
4772        end
4773        imwrite(imflag,answer,'BitDepth',8);
4774    end
4775    set(handles.ListObject,'Value',1)
4776end
4777
4778%------------------------------------------------------------------------
4779%-- open the GUI set_grid.fig to create grid
4780function MenuGrid_Callback(hObject, eventdata, handles)
4781%------------------------------------------------------------------------
4782%suppress the other options if grid is chosen
4783set(handles.edit_vect,'Value',0)
4784edit_vect_Callback(hObject, eventdata, handles)
4785set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4786set(handles.ListObject,'Value',1)     
4787
4788%prepare display of the set_grid GUI
4789[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4790FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4791CoordList=get(handles.transform_fct,'String');
4792val=get(handles.transform_fct,'Value');
4793set_grid(FileName,CoordList{val});% call the set_object interface
4794
4795
4796%------------------------------------------------------------------------
4797function MenuRuler_Callback(hObject, eventdata, handles)
4798%------------------------------------------------------------------------
4799set(handles.CheckZoom,'Value',0)
4800CheckZoom_Callback(handles.uvmat, [], handles)
4801set(handles.MenuRuler,'checked','on')
4802UvData=get(handles.uvmat,'UserData');
4803UvData.MouseAction='ruler';
4804set(handles.uvmat,'UserData',UvData);
4805
4806%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4807% MenuRun Callbacks
4808%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4809
4810%------------------------------------------------------------------------
4811% open the GUI 'series'
4812function MenuSeries_Callback(hObject, eventdata, handles)
4813%------------------------------------------------------------------------
4814series; %first display of the GUI to fill waiting time
4815[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4816param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4817if isequal(get(handles.SubField,'Value'),1)
4818    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
4819    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
4820    if ~isequal(FileName_1,param.FileName)
4821        param.FileName_1=FileName_1;
4822    end
4823end
4824param.NomType=get(handles.NomType,'String');
4825param.NomType_1=get(handles.NomType_1,'String');
4826param.CheckFixPair=get(handles.CheckFixPair,'Value');
4827huvmat=get(handles.MenuSeries,'parent');
4828UvData=get(huvmat,'UserData');
4829if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4830    param.Time=UvData.XmlData{1}.Time;
4831end
4832if isequal(get(handles.scan_i,'Value'),1)
4833    param.incr_i=str2num(get(handles.increment_scan,'String'));
4834elseif isequal(get(handles.scan_j,'Value'),1)
4835    param.incr_j=str2num(get(handles.increment_scan,'String'));
4836end
4837param.list_fields=get(handles.Fields,'String');% list menu fields
4838param.list_fields(1)=[]; %suppress  'image' option
4839param.index_fields=get(handles.Fields,'Value');% selected string index
4840if param.index_fields>1
4841    param.index_fields=param.index_fields-1;
4842end
4843param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4844param.list_fields_1(1)=[]; %suppress  'image' option
4845param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4846if param.index_fields_1>1
4847    param.index_fields_1=param.index_fields_1-1;
4848end
4849param.menu_coord_str=get(handles.transform_fct,'String');
4850param.menu_coord_val=get(handles.transform_fct,'Value');
4851series(param); %run the series interface
4852
4853%------------------------------------------------------------------------
4854% -- open the GUI civ.fig for PIV
4855function MenuPIV_Callback(hObject, eventdata, handles)
4856%------------------------------------------------------------------------
4857 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4858 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4859civ(FileName);% interface de civ(not in the uvmat file)
4860
4861% --------------------------------------------------------------------
4862function MenuHelp_Callback(hObject, eventdata, handles)
4863% --------------------------------------------------------------------
4864path_to_uvmat=which ('uvmat');% check the path of uvmat
4865pathelp=fileparts(path_to_uvmat);
4866helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4867if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4868else
4869    addpath (fullfile(pathelp,'uvmat_doc'))
4870    web(helpfile);
4871end
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