source: trunk/src/uvmat.m @ 444

Last change on this file since 444 was 444, checked in by sommeria, 9 years ago

masks and calibration updated to fit with the new conventions on file organisation.
bug corrected in mouse_up (object creation)
bug corrected in civ in mode TESTciv

File size: 208.0 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
2011if ~isempty(filename)
2012    ObjectName=filename;
2013    FieldName='';%default
2014    VelType='';%default
2015%     FileType=UvData.FileType{1};
2016    switch UvData.FileType{1}
2017        case {'civx','civdata','netcdf'};
2018            list_fields=get(handles.Fields,'String');% list menu fields
2019  %          index_fields=get(handles.Fields,'Value');% selected string index
2020            FieldName= list_fields{get(handles.Fields,'Value')}; % selected field
2021            if ~strcmp(FieldName,'get_field...')
2022                if get(handles.FixVelType,'Value')
2023                    VelTypeList=get(handles.VelType,'String');
2024                    VelType=VelTypeList{get(handles.VelType,'Value')};
2025                end
2026            end
2027            if strcmp(FieldName,'velocity')
2028                list_code=get(handles.ColorCode,'String');% list menu fields
2029                index_code=get(handles.ColorCode,'Value');% selected string index
2030                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2031                    list_code=get(handles.ColorScalar,'String');% list menu fields
2032                    index_code=get(handles.ColorScalar,'Value');% selected string index
2033                    ParamIn.ColorVar= list_code{index_code}; % selected field
2034                end
2035            end
2036        case {'video','mmreader'}
2037            ObjectName=UvData.MovieObject{1};         
2038        case 'vol' %TODO: update
2039            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2040                ParamIn.Npy=UvData.XmlData.Npy;
2041                ParamIn.Npx=UvData.XmlData.Npx;
2042            else           
2043                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2044                return
2045            end
2046    end
2047    ParamIn.FieldName=FieldName;
2048    ParamIn.VelType=VelType;
2049    ParamIn.GUIName='get_field';
2050    [Field{1},ParamOut,errormsg] = read_field(ObjectName,UvData.FileType{1},ParamIn,num_i1);
2051    if ~isempty(errormsg)
2052        errormsg=['error in reading ' filename ': ' errormsg];
2053        return
2054    end 
2055    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2056        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2057        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2058    end
2059    if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2060        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2061    end
2062    if isfield(ParamOut,'TimeValue')
2063        Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2064    end
2065end
2066
2067%% choose and read a second field filename_1 if defined
2068VelType_1=[];%default
2069FieldName_1=[];
2070ParamOut_1=[];
2071if ~isempty(filename_1)
2072    if ~exist(filename_1,'file')
2073        errormsg=['second file ' filename_1 ' does not exist'];
2074        return
2075    end
2076    Name=filename_1;
2077    switch UvData.FileType{2}
2078        case {'civx','civdata','netcdf'};
2079            list_fields=get(handles.Fields_1,'String');% list menu fields
2080            FieldName_1= list_fields{get(handles.Fields_1,'Value')}; % selected field
2081            if ~strcmp(FieldName,'get_field...')
2082                if get(handles.FixVelType,'Value')
2083                    VelTypeList=get(handles.VelType_1,'String');
2084                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2085                end
2086            end
2087            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2088                list_code=get(handles.ColorCode,'String');% list menu fields
2089                index_code=get(handles.ColorCode,'Value');% selected string index
2090                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2091                    list_code=get(handles.ColorScalar,'String');% list menu fields
2092                    index_code=get(handles.ColorScalar,'Value');% selected string index
2093                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2094                end
2095            end
2096        case {'video','mmreader'}
2097            Name=UvData.MovieObject{2};
2098        case 'vol' %TODO: update
2099            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2100                ParamIn_1.Npy=UvData.XmlData.Npy;
2101                ParamIn_1.Npx=UvData.XmlData.Npx;
2102            else
2103                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2104                return
2105            end
2106    end
2107    if isequal(get(handles.NomType_1,'Visible'),'on')
2108    NomType_1=get(handles.NomType_1,'String');
2109    else
2110        NomType_1=get(handles.NomType,'String');
2111    end
2112    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2113    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2114        if isfield(UvData,'filename_1')%&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2115            test_keepdata_1= strcmp(filename_1,UvData.filename_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
2116        end
2117    end
2118    if test_keepdata_1
2119        Field{2}=UvData.Field_1;% keep the stored field
2120        ParamOut_1=UvData.ParamOut_1;
2121    else
2122        ParamIn_1.FieldName=FieldName_1;
2123        ParamIn_1.VelType=VelType_1;
2124        ParamIn_1.GUIName='get_field_1';
2125        [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,num_i1);
2126        if ~isempty(errormsg)
2127            errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
2128            return
2129        end
2130%         UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2131    end
2132end
2133
2134%% update uvmat interface
2135if isfield(ParamOut,'Npx')
2136    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2137    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2138elseif isfield(ParamOut_1,'Npx')
2139    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2140    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2141end
2142
2143%% update the display menu for the first velocity type (first menuline)
2144test_veltype=0;
2145% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2146if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2147    test_veltype=1;
2148    set(handles.VelType,'Visible','on')
2149    set(handles.VelType_1,'Visible','on')
2150    set(handles.FixVelType,'Visible','on')
2151    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2152    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2153    index_val=find(index_menu,1);
2154    if isempty(index_val)
2155        index_val=1;
2156    end
2157    set(handles.VelType,'Value',index_val)
2158    if ~get(handles.SubField,'value')
2159        set(handles.VelType,'String',menu)
2160        set(handles.VelType_1,'Value',1)
2161        set(handles.VelType_1,'String',[{''};menu])
2162    end
2163else
2164    set(handles.VelType,'Visible','off')
2165end
2166% display the Fields menu from the input file and pick the selected one:
2167field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2168set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2169set(handles.Fields,'Value',find(field_index,1))
2170
2171%% update the display menu for the second velocity type (second menuline)
2172test_veltype_1=0;
2173if isempty(filename_1)
2174    set(handles.Fields_1,'Value',1); %update the field menu
2175    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2176elseif ~test_keepdata_1
2177    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2178        set(handles.VelType_1,'Visible','off')
2179    else
2180        test_veltype_1=1;
2181        set(handles.VelType_1,'Visible','on')
2182%         if ~get(handles.FixVelType,'Value')
2183            menu=set_veltype_display(ParamOut_1.CivStage);
2184            index_menu=strcmp(ParamOut_1.VelType,menu);
2185            set(handles.VelType_1,'Value',1+find(index_menu,1))
2186            set(handles.VelType_1,'String',[{''};menu])
2187%         end
2188    end
2189    % update the second field menu: the same quantity
2190    set(handles.Fields_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2191    % display the Fields menu from the input file and pick the selected one:
2192    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2193    set(handles.Fields_1,'Value',find(field_index,1)+1) 
2194%     % synchronise  with the first menu if the first selection is not 'velocity'
2195%     if ~strcmp(ParamOut.FieldName,'velocity')
2196%         field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2197%         set(handles.Fields_1,'Value',field_index); %update the field menu
2198%         ParamOut_1.FieldName=ParamOut.FieldName;
2199%         set(handles.Fields_1,'String',ParamOut_1.FieldList)
2200%     end
2201end
2202if test_veltype||test_veltype_1
2203     set(handles.FixVelType,'Visible','on')
2204else
2205     set(handles.FixVelType,'Visible','off')
2206end
2207
2208% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2209% set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2210% set(handles.Fields,'Value',find(field_index,1))
2211   
2212%% introduce w as background image by default for a new series (only for nbdim=2)
2213if ~isfield(UvData,'NewSeries')
2214    UvData.NewSeries=1;
2215end
2216%put W as background image by default if NbDim=2:
2217if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2218        set(handles.SubField,'Value',1);
2219        set(handles.RootPath_1,'String','"')
2220        set(handles.RootFile_1,'String','"')
2221        set(handles.SubDir_1,'String','"');
2222         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2223        set(handles.FileIndex_1,'String',indices)
2224        set(handles.FileExt_1,'String','"');
2225        set(handles.Fields_1,'Visible','on');
2226        set(handles.Fields_1,'Visible','on');
2227        set(handles.RootPath_1,'Visible','on')
2228        set(handles.RootFile_1,'Visible','on')
2229        set(handles.SubDir_1,'Visible','on');
2230        set(handles.FileIndex_1,'Visible','on');
2231        set(handles.FileExt_1,'Visible','on');
2232        set(handles.Fields_1,'Visible','on');
2233        Field{1}.AName='w';
2234end           
2235
2236%% display time
2237testimedoc=0;
2238TimeUnit='';
2239if isfield(Field{1},'Time')
2240    abstime=Field{1}.Time;%time read from the netcdf input file
2241end
2242if numel(Field)==2 && isfield(Field{2},'Time')
2243    abstime_1=Field{2}.Time;%time read from the netcdf input file
2244end
2245if isfield(Field{1},'Dt')
2246    dt=Field{1}.Dt;%dt read from the netcdf input file
2247    if isfield(Field{1},'TimeUnit')
2248       TimeUnit=Field{1}.TimeUnit;
2249    end
2250elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2251    dt=Field{2}.Dt;%dt read from the netcdf input file
2252    if isfield(Field{2},'TimeUnit')
2253       TimeUnit=Field{2}.TimeUnit;
2254    end
2255end
2256% time from xml file overset previous result
2257if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2258    if isempty(num_i2)||isnan(num_i2)
2259        num_i2=num_i1;
2260    end
2261    if isempty(num_j1)||isnan(num_j1)
2262        num_j1=1;
2263    end
2264    if isempty(num_j2)||isnan(num_j2)
2265        num_j2=num_j1;
2266    end
2267    siz=size(UvData.XmlData{1}.Time);
2268    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2269        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2270        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2271        Field{1}.Dt=dt;
2272        if isfield(UvData.XmlData{1},'TimeUnit')
2273            TimeUnit=UvData.XmlData{1}.TimeUnit;
2274        end
2275    end
2276    if numel(UvData.XmlData)==2
2277        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2278        if isempty(num_i2)
2279            num_i2=num_i1;
2280        end
2281        if isempty(num_j1)
2282            num_j1=1;
2283        end
2284        if isempty(num_j2)
2285            num_j2=num_j1;
2286        end
2287        siz=size(UvData.XmlData{2}.Time);
2288        if ~isempty(num_i1) && siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2289            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
2290            Field{2}.Dt=(UvData.XmlData{2}.Time(num_i2,num_j2)-UvData.XmlData{2}.Time(num_i1,num_j1));
2291        end
2292    end
2293end
2294if ~isequal(numel(abstime),1)
2295    abstime=[];
2296end
2297if ~isequal(numel(abstime_1),1)
2298      abstime_1=[];
2299end 
2300set(handles.abs_time,'String',num2str(abstime,4))
2301set(handles.abs_time_1,'String',num2str(abstime_1,4))
2302% if testimedoc && isfield(UvData,'dt')
2303%     dt=UvData.dt;
2304% end
2305if isempty(dt)||isequal(dt,0)
2306    set(handles.Dt_txt,'String','')
2307else
2308    if  isempty(TimeUnit)
2309        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2310    else
2311        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2312    end
2313end
2314
2315
2316%% store the current open names, fields and vel types in uvmat interface
2317UvData.filename_1=filename_1;
2318
2319%% apply coordinate transform or other user fct
2320XmlData=[];%default
2321XmlData_1=[];%default
2322if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2323    XmlData=UvData.XmlData{1};
2324    if numel(UvData.XmlData)==2
2325        XmlData_1=UvData.XmlData{2};
2326    end
2327end
2328choice_value=get(handles.transform_fct,'Value');
2329transform_list=get(handles.transform_fct,'UserData');
2330transform=transform_list{choice_value};%selected function handles
2331% z index
2332if ~isempty(filename)
2333    Field{1}.ZIndex=z_index;
2334end
2335if ~isempty(transform)
2336    if length(Field)>=2
2337        Field{2}.ZIndex=z_index;
2338        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2339        if isempty(Field{2})
2340            Field(2)=[];
2341        end
2342    else
2343        Field{1}=transform(Field{1},XmlData);
2344    end
2345    %% update tps in phys coordinates if needed
2346    if (strcmp(VelType,'filter1')||strcmp(VelType,'filter2'))&& strcmp(UvData.FileType{1},'civdata')&&isfield(Field{1},'U')&& isfield(Field{1},'V')
2347        Field{1}.X=Field{1}.X(Field{1}.FF==0);
2348        Field{1}.Y=Field{1}.Y(Field{1}.FF==0);
2349        Field{1}.U=Field{1}.U(Field{1}.FF==0);
2350        Field{1}.V=Field{1}.V(Field{1}.FF==0);
2351        [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);
2352    end
2353    if numel(Field)==2 && ~test_keepdata_1 && isequal(UvData.FileType{2}(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2354        %update tps in phys coordinates if needed
2355        if (strcmp(VelType_1,'filter1')||strcmp(VelType_1,'filter2'))&& strcmp(UvData.FileType{2},'civdata')&&isfield(Field{2},'U')&& isfield(Field{2},'V')
2356            Field{2}.X=Field{2}.X(Field{2}.FF==0);
2357            Field{2}.Y=Field{1}.Y(Field{2}.FF==0);
2358            Field{2}.U=Field{1}.U(Field{2}.FF==0);
2359            Field{2}.V=Field{1}.V(Field{2}.FF==0);
2360            [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);
2361        end
2362    end
2363end
2364
2365%% calculate scalar
2366if ~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)%
2367    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2368end
2369if 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...')
2370     Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2371end
2372
2373%% combine the two input fields (e.g. substract velocity fields)
2374%Field{1}.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}];
2375if numel(Field)==2
2376%    Field{2}.FieldList=[{ParamOut_1.FieldName} {ParamOut_1.ColorVar}];
2377   [UvData.Field,errormsg]=sub_field(Field{1},Field{2}); 
2378   UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2379   UvData.ParamOut_1=ParamOut_1;
2380else
2381   UvData.Field=Field{1};
2382end
2383if ~isempty(errormsg)
2384    errormsg=['error in uvmat/refresh_field/sub_field:' errormsg];
2385    return
2386end
2387%UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation
2388
2389%% analyse input field
2390test_x=0;
2391test_z=0;% test for unstructured z coordinate
2392[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2393if ~isempty(errormsg)
2394    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2395    return
2396end
2397[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);% analyse  the input field structure
2398if ~isempty(errormsg)
2399    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];% display error
2400    return
2401end
2402[NbDim,imax]=max(NbDim);% spatial dimension of the input field
2403if isfield(UvData.Field,'NbDim')
2404    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2405end
2406
2407%% get bounds and mesh (needed for mouse action and to open set_object)
2408if NbDim>1
2409    XName=''; %default
2410    YName='';
2411    %unstructured coordinates
2412    if ~isempty(VarType{imax}.coord_x)&&~isempty(VarType{imax}.coord_y)
2413        XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2414        YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2415        %nbvec=length(UvData.Field.(XName));%nbre of measurement points (e.g. vectors)
2416        test_x=1;%test for unstructured coordinates
2417        if ~isempty(VarType{imax}.coord_z)
2418            ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2419        else
2420            NbDim=2;
2421        end
2422        %structured coordinate
2423    elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0
2424        XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2425        if NbDim> 1 && VarType{imax}.coord(NbDim-1)>0
2426            YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2427        end
2428        % VarIndex=CellVarIndex{imax}; % list of variable indices
2429        DimIndex=VarDimIndex{CellVarIndex{imax}(1)}; %list of dim indices for the variable
2430        nbpoints_x=DimValue(DimIndex(NbDim));
2431        XMax=nbpoints_x;%default
2432        XMin=1;%default
2433    end
2434   
2435    if NbDim==3
2436        if ~test_x
2437            ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2438        end
2439        ZMax=max(UvData.Field.(ZName));
2440        ZMin=min(UvData.Field.(ZName));
2441        UvData.Field.ZMax=ZMax;
2442        UvData.Field.ZMin=ZMin;
2443        test_z=1;
2444        if isequal(ZMin,ZMax)%no z dependency
2445            NbDim=2;
2446            test_z=0;
2447        end
2448    end
2449    if ~isempty (XName)
2450        XMax=max(max(UvData.Field.(XName)));
2451        XMin=min(min(UvData.Field.(XName)));
2452        UvData.Field.NbDim=NbDim;
2453        UvData.Field.XMax=XMax;
2454        UvData.Field.XMin=XMin;
2455        if NbDim >1&& ~isempty(YName)
2456            YMax=max(max(UvData.Field.(YName)));
2457            YMin=min(min(UvData.Field.(YName)));
2458            UvData.Field.YMax=YMax;
2459            UvData.Field.YMin=YMin;
2460        end
2461        nbvec=length(UvData.Field.(XName));
2462        if test_x %unstructured coordinates
2463            if test_z
2464                UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2465                UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2466            else
2467                UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2468            end
2469        end
2470    end
2471    % case of structured coordinates
2472    if ~test_x
2473        DX=(XMax-XMin)/(nbpoints_x-1);
2474        if NbDim >1
2475            nbpoints_y=DimValue(DimIndex(NbDim-1));
2476            if isempty(YName)% if the y coordinate is not expressed, it is taken as the matrix index
2477                DY=1;
2478                UvData.Field.YMax=nbpoints_y;
2479                UvData.Field.YMin=1;
2480            else
2481                DY=(YMax-YMin)/(nbpoints_y-1);
2482            end
2483        end
2484        if NbDim==3
2485            nbpoints_z=DimValue(DimIndex(1));
2486            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2487            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2488            UvData.Field.ZMax=ZMax;
2489            UvData.Field.ZMin=ZMin;
2490        else
2491            UvData.Field.Mesh=DX;%sqrt(DX*DY);
2492        end
2493    end
2494    % adjust the mesh to a value 1, 2 , 5 *10^n
2495    ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude
2496    if UvData.Field.Mesh/ord>=5
2497        UvData.Field.Mesh=5*ord;
2498    elseif UvData.Field.Mesh/ord>=2
2499        UvData.Field.Mesh=2*ord;
2500    else
2501        UvData.Field.Mesh=ord;
2502    end
2503    UvData.Object{1}.Type='plane';%main plotting plane
2504    UvData.Object{1}.ProjMode='projection';%main plotting plane
2505    UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2506    UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2507   
2508    %% 3D case (menuvolume)
2509    if NbDim==3% && UvData.NewSeries
2510        test_set_object=1;
2511        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2512        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2513        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2514        if ~isempty(hset_object) %if set_object is detected
2515            delete(hset_object);% delete the GUI set_object if it does not fit
2516        end
2517        if test_set_object% reinitiate the GUI set_object
2518            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
2519            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2520            UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2521            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2522            UvData.Object{1}.Angle=[0 0 0];
2523            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2524            UvData.Object{1}.Name='1-PLANE';
2525            UvData.Object{1}.enable_plot=1;
2526            set_object(UvData.Object{1},handles,ZBounds);
2527            set(handles.ListObject,'Value',1);
2528            set(handles.ListObject,'String',{'1-PLANE'});
2529            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2530            edit_object_Callback([],[], handles)
2531        end
2532        %multilevel case (single menuplane in a 3D space)
2533    elseif isfield(UvData,'Z')
2534        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2535            XmlData=UvData.XmlData{1};
2536            if isfield(XmlData,'PlanePos')
2537                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2538            end
2539            if isfield(XmlData,'PlaneAngle')
2540                siz=size(XmlData.PlaneAngle);
2541                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2542                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2543            end
2544        elseif isfield(UvData,'ZIndex')
2545            UvData.Object{1}.ZObject=UvData.ZIndex;
2546        end
2547    end
2548end
2549
2550testnewseries=UvData.NewSeries;
2551UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2552set(handles.uvmat,'UserData',UvData)
2553
2554%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2555% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2556%     set(handles.num_MinA,'String','0')
2557%     set(handles.num_MaxA,'String','255')
2558% end
2559
2560%% usual 1D (x,y) plots
2561if NbDim<=1
2562    set(handles.Objects,'Visible','off')
2563    set(handles.ListObject_1_title,'Visible','off')
2564    set(handles.ListObject_1,'Visible','off')
2565    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.axes3,read_GUI(handles.uvmat));
2566    write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2567%     if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2568%         ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2569%     end
2570   
2571%% 2D or 3D fields are generally projected
2572else
2573    set(handles.Objects,'Visible','on')
2574    set(handles.ListObject_1_title,'Visible','on')
2575    set(handles.ListObject_1,'Visible','on')
2576   
2577    %% Plot the projections on the selected  projection objects
2578    % main projection object (uvmat display)
2579    list_object=get(handles.ListObject_1,'String');
2580    if isequal(list_object,{''})%refresh list of objects if the menu is empty
2581        UvData.Object={[]};
2582        set(handles.ListObject_1,'Value',1)
2583    end
2584    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2585    if IndexObj(1)> numel(UvData.Object)
2586        IndexObj(1)=1;%select the first object if the selected one does not exist
2587        set(handles.ListObject_1,'Value',1)
2588    end
2589    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2590    if isequal(IndexObj(2),IndexObj(1))
2591        IndexObj(2)=[];
2592    end
2593    plot_handles{1}=handles;
2594    if isfield(UvData,'plotaxes')%case of movies
2595        haxes(1)=UvData.plotaxes;
2596    else
2597        haxes(1)=handles.axes3;
2598    end
2599    PlotParam{1}=read_GUI(handles.uvmat);
2600    %default settings if vectors not visible
2601    if ~isfield(PlotParam{1},'Vectors')
2602        PlotParam{1}.Vectors.MaxVec=1;
2603        PlotParam{1}.Vectors.MinVec=0;
2604        PlotParam{1}.Vectors.CheckFixVecColor=1;
2605        PlotParam{1}.Vectors.ColCode1=0.33;
2606        PlotParam{1}.Vectors.ColCode2=0.66;
2607        PlotParam{1}.Vectors.ColorScalar={'ima_cor'};
2608        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2609    end
2610    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2611   
2612    %% second projection object (view_field display)
2613    if length( IndexObj)>=2
2614        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2615        if ~isempty(view_field_handle)
2616            plot_handles{2}=guidata(view_field_handle);
2617            haxes(2)=plot_handles{2}.axes3;
2618            PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2619            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2620        end
2621    end
2622   
2623    %% loop on the projection objects: one or two
2624   
2625    for imap=1:numel(IndexObj)
2626        iobj=IndexObj(imap);
2627        %      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)
2628        % %          [ObjectData,errormsg]=calc_field(UvData.Field.FieldList,UvData.Field);
2629        % %      else
2630        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2631        %      end
2632        if ~isempty(errormsg)
2633            return
2634        end
2635        if testnewseries
2636            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2637            if isfield(ObjectData,'CoordUnit')
2638                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2639                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2640            end
2641        end
2642        %use of mask (TODO: check)
2643        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2644            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2645            AX=ObjectData.AX;%x coordiantes for the scalar field
2646            AY=ObjectData.AY;%y coordinates for the scalar field
2647            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2648            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2649            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2650                nxy=size(flag_mask);
2651                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2652                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2653                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2654                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2655                %project on the positions of the scalar
2656                npxy=size(ObjectData.A);
2657                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2658                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2659                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2660                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2661                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2662                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2663            end
2664            AClass=class(ObjectData.A);
2665            ObjectData.A=flag_mask.*double(ObjectData.A);
2666            ObjectData.A=feval(AClass,ObjectData.A);
2667            ind_off=[];
2668            if isfield(ObjectData,'ListVarName')
2669                for ilist=1:length(ObjectData.ListVarName)
2670                    if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2671                        ind_off=[ind_off ilist];
2672                    end
2673                end
2674                ObjectData.ListVarName(ind_off)=[];
2675                VarDimIndex(ind_off)=[];
2676                ind_off=[];
2677                for ilist=1:length(ListDimName)
2678                    if isequal(ListDimName{ilist},'MaskX') || isequal(ListDimName{ilist},'MaskY')
2679                        ind_off=[ind_off ilist];
2680                    end
2681                end
2682                ListDimName(ind_off)=[];
2683                DimValue(ind_off)=[];
2684            end
2685        end
2686        if ~isempty(ObjectData)
2687            PlotType='none'; %default
2688            if imap==2 && isempty(view_field_handle)
2689                view_field(ObjectData)
2690            else
2691                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2692                write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2693                if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2694                    ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2695                end
2696            end
2697            if isequal(PlotType,'none')
2698                hget_field=findobj(allchild(0),'name','get_field');
2699                if isempty(hget_field)
2700                    get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2701                end
2702                errormsg='The field defined by get_field cannot be plotted';
2703                return
2704            end
2705        end
2706    end
2707   
2708    %% update the mask
2709    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2710        update_mask(handles,num_i1,num_i2);
2711    end
2712   
2713    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2714    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2715    ind_skip=[];
2716    % nb_histo=1;
2717    Ustring='';
2718    Vstring='';
2719    % suppress coordinates from the histogram menu
2720    for ivar=1:numel(menu_histo)%l loop on field variables:
2721        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2722            Role=UvData.Field.VarAttribute{ivar}.Role;
2723            switch Role
2724                case {'coord_x','coord_y','coord_z','dimvar'}
2725                    ind_skip=[ind_skip ivar];
2726                case {'vector_x'}
2727                    Ustring=UvData.Field.ListVarName{ivar};
2728                    ind_skip=[ind_skip ivar];
2729                case {'vector_y'}
2730                    Vstring=UvData.Field.ListVarName{ivar};
2731                    ind_skip=[ind_skip ivar];
2732            end
2733        end
2734        DimCell=UvData.Field.VarDimName{ivar};
2735        DimName='';
2736        if ischar(DimCell)
2737            DimName=DimCell;
2738        elseif iscell(DimCell)&& numel(DimCell)==1
2739            DimName=DimCell{1};
2740        end
2741        if strcmp(DimName,menu_histo{ivar})
2742            ind_skip=[ind_skip ivar];
2743        end
2744    end
2745    menu_histo(ind_skip)=[];% remove skipped items
2746    if ~isempty(Ustring)
2747        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2748    end
2749   
2750    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2751    % display menus and plot histograms
2752    test_v=0;
2753    if ~isempty(menu_histo)
2754        set(handles.histo1_menu,'Value',1)
2755        set(handles.histo1_menu,'String',menu_histo)
2756        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2757    end
2758end
2759
2760%------------------------------------------------------------------------
2761function histo1_menu_Callback(hObject, eventdata, handles)
2762%--------------------------------------------
2763%plot first histo
2764%huvmat=get(handles.histo1_menu,'parent');
2765histo_menu=get(handles.histo1_menu,'String');
2766histo_value=get(handles.histo1_menu,'Value');
2767FieldName=histo_menu{histo_value};
2768% update_histo(handles.histo_u,handles.uvmat,FieldName)
2769%
2770% %------------------------------------------------------------------------
2771% function histo2_menu_Callback(hObject, eventdata, handles)
2772% %------------------------------------------------------------------------
2773% %plot second histo
2774% %huvmat=get(handles.histo2_menu,'parent');
2775% histo_menu=get(handles.histo2_menu,'String');
2776% histo_value=get(handles.histo2_menu,'Value');
2777% FieldName=histo_menu{histo_value};
2778% update_histo(handles.histo_v,handles.uvmat,FieldName)
2779%
2780% %------------------------------------------------------------------------
2781% %read the field .Fieldname stored in UvData and plot its histogram
2782% function update_histo(haxes,huvmat,FieldName)
2783%------------------------------------------------------------------------
2784UvData=get(handles.uvmat,'UserData');
2785Field=UvData.Field;
2786r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2787FieldName_2='';
2788if ~isempty(r)
2789    FieldName=r.var1;
2790    FieldName_2=r.var2;
2791end
2792if ~isfield(UvData.Field,FieldName)
2793    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2794    return
2795end
2796FieldHisto=Field.(FieldName);
2797if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2798    indsel=find(Field.FF==0);%find values marked as false
2799    if ~isempty(indsel)
2800        FieldHisto=FieldHisto(indsel);
2801        if ~isempty(FieldName_2)
2802            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2803        end
2804    end
2805end
2806if isempty(Field)
2807    msgbox_uvmat('ERROR',['empty field ' FieldName])
2808else
2809    nxy=size(FieldHisto);
2810    Amin=double(min(min(min(FieldHisto))));%min of field value
2811    Amax=double(max(max(max(FieldHisto))));%max of field value
2812    if isequal(Amin,Amax)
2813        cla(handles.histo_u)
2814    else
2815        Histo.ListVarName={FieldName,'histo'};
2816        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2817            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2818        else
2819            if numel(nxy)==2
2820                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2821            else
2822                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2823            end
2824        end
2825        %unit
2826        units=[]; %default
2827        for ivar=1:numel(Field.ListVarName)
2828            if strcmp(Field.ListVarName{ivar},FieldName)
2829                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2830                    units=Field.VarAttribute{ivar}.units;
2831                    break
2832                end
2833            end
2834        end
2835        if ~isempty(units)
2836            Histo.VarAttribute{1}.units=units;
2837        end
2838        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2839        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2840            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2841            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2842        else
2843            for col=1:size(FieldHisto,3)
2844                B=FieldHisto(:,:,col);
2845                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2846                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2847            end
2848        end
2849        plot_field(Histo,handles.histo_u);
2850        hlegend=legend;
2851        if isempty(FieldName_2)
2852        set(hlegend,'String',FieldName)
2853        else
2854            set(hlegend,'String',{FieldName;FieldName_2})
2855        end
2856%         hh=get(handles.histo_u,'children');
2857%         get(hh(1))
2858%         get(hh(2))
2859    end
2860end
2861
2862%-------------------------------------------------------------------
2863% --- translate coordinate to matrix index
2864%-------------------------------------------------------------------
2865function [indx,indy]=pos2ind(x0,rangx0,nxy)
2866indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2867indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2868
2869
2870%-------------------------------------------------------------------
2871% --- Executes on button press in 'CheckZoom'.
2872%-------------------------------------------------------------------
2873function CheckZoom_Callback(hObject, eventdata, handles)
2874
2875if (get(handles.CheckZoom,'Value') == 1);
2876    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2877    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2878    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2879else
2880    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2881end
2882
2883%-------------------------------------------------------------------
2884% --- Executes on button press in 'CheckFixLimits'.
2885%-------------------------------------------------------------------
2886function CheckFixLimits_Callback(hObject, eventdata, handles)
2887test=get(handles.CheckFixLimits,'Value');
2888if test
2889    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2890else
2891    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2892    update_plot(handles);
2893end
2894
2895%-------------------------------------------------------------------
2896% --- Executes on button press in CheckFixAspectRatio.
2897function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2898%-------------------------------------------------------------------
2899if get(handles.CheckFixAspectRatio,'Value')
2900    set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
2901    update_plot(handles);
2902else
2903    set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
2904    update_plot(handles);
2905end
2906
2907%-------------------------------------------------------------------
2908function num_AspectRatio_Callback(hObject, eventdata, handles)
2909%-------------------------------------------------------------------
2910set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2911set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2912update_plot(handles);
2913%-------------------------------------------------------------------
2914
2915%-------------------------------------------------------------------
2916
2917
2918
2919%-------------------------------------------------------------------
2920%----Executes on button press in 'record': records the current flags of manual correction.
2921%-------------------------------------------------------------------
2922function record_Callback(hObject, eventdata, handles)
2923% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2924[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2925filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2926%filename=read_file_boxes(handles);
2927[erread,message]=fileattrib(filename);
2928if ~isempty(message) && ~isequal(message.UserWrite,1)
2929     msgbox_uvmat('ERROR',['no writting access to ' filename])
2930     return
2931end
2932test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2933test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2934if ~test_civ2 && ~test_civ1
2935    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2936end
2937if test_civ2
2938    nbname='nb_vectors2';
2939   flagname='vec2_FixFlag';
2940   attrname='fix2';
2941end
2942if test_civ1
2943    nbname='nb_vectors';
2944   flagname='vec_FixFlag';
2945   attrname='fix';
2946end
2947%write fix flags in the netcdf file
2948UvData=get(handles.uvmat,'UserData');
2949hhh=which('netcdf.open');% look for built-in matlab netcdf library
2950if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2951    nc=netcdf.open(filename,'NC_WRITE');
2952    netcdf.reDef(nc);
2953    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2954    dimid = netcdf.inqDimID(nc,nbname);
2955    try
2956        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2957    catch
2958        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2959    end
2960    netcdf.endDef(nc);
2961    netcdf.putVar(nc,varid,UvData.axes3.FF);
2962    netcdf.close(nc); 
2963else %old netcdf library
2964    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2965end
2966
2967%-------------------------------------------------------------------
2968%----Correct the netcdf file, using toolbox (old versions of Matlab).
2969%-------------------------------------------------------------------
2970function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2971nc=netcdf(filename,'write'); %open netcdf file
2972result=redef(nc);
2973eval(['nc.' attrname '=1;']);
2974theDim=nc(nbname) ;% get the number of velocity vectors
2975nb_vectors=size(theDim);
2976var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2977var_FixFlag(1:nb_vectors)=AxeData.FF;%
2978fin=close(nc);
2979
2980%-------------------------------------------------------------------
2981% --- Executes on button press in SubField
2982function SubField_Callback(hObject, eventdata, handles)
2983%-------------------------------------------------------------------
2984UvData=get(handles.uvmat,'UserData');
2985if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2986    set(handles.RootPath_1,'String','')
2987    set(handles.RootFile_1,'String','')
2988    set(handles.SubDir_1,'String','');
2989    set(handles.FileIndex_1,'String','');
2990    set(handles.FileExt_1,'String','');
2991    set(handles.RootPath_1,'Visible','off')
2992    set(handles.RootFile_1,'Visible','off')
2993    set(handles.SubDir_1,'Visible','off');
2994    set(handles.NomType_1,'Visible','off');
2995    set(handles.abs_time_1,'Visible','off')
2996    set(handles.FileIndex_1,'Visible','off');
2997    set(handles.FileExt_1,'Visible','off');
2998    set(handles.Fields_1,'Value',1);%set to blank state
2999    set(handles.VelType_1,'Value',1);%set to blank state
3000    set(handles.num_Opacity,'String','')% desactivate opacity setting
3001    if ~strcmp(get(handles.VelType,'Visible'),'on')
3002        set(handles.VelType_1,'Visible','off')
3003    end
3004    if isfield(UvData,'XmlData_1')
3005        UvData=rmfield(UvData,'XmlData_1');
3006    end
3007    set(handles.uvmat,'UserData',UvData);
3008    run0_Callback(hObject, eventdata, handles); %run
3009else
3010    MenuBrowse_1_Callback(hObject, eventdata, handles)
3011end
3012
3013%------------------------------------------------------------------------
3014% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3015
3016function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3017%------------------------------------------------------------------------
3018InputFile=read_GUI(handles.InputFile);
3019RootPath=InputFile.RootPath;
3020SubDir=regexprep(InputFile.SubDir,'/|\','');
3021RootFile=regexprep(InputFile.RootFile,'/|\','');
3022FileIndices=InputFile.FileIndex;
3023FileExt=InputFile.FileExt;
3024
3025
3026%------------------------------------------------------------------------
3027% ---- read the data displayed for the second input rootfile windows
3028function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3029%------------------------------------------------------------------------
3030RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3031if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3032    RootPath_1=get(handles.RootPath,'String');
3033end;
3034SubDir_1=get(handles.SubDir_1,'String');
3035if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3036    SubDir_1=get(handles.SubDir,'String');
3037end
3038SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3039RootFile_1=get(handles.RootFile_1,'String');
3040if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3041    RootFile_1=get(handles.RootFile,'String');
3042end
3043RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3044FileIndex_1=get(handles.FileIndex_1,'String');
3045if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3046    FileIndex_1=get(handles.FileIndex,'String');
3047end
3048FileExt_1=get(handles.FileExt_1,'String');
3049if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3050    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3051end
3052NomType_1=get(handles.NomType_1,'String');
3053if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3054    NomType_1=get(handles.NomType,'String');%read FileExt by default
3055end
3056%------------------------------------------------------------------------
3057% --- Executes on menu selection Fields
3058function Fields_Callback(hObject, eventdata, handles)
3059%------------------------------------------------------------------------
3060list_fields=get(handles.Fields,'String');% list menu fields
3061index_fields=get(handles.Fields,'Value');% selected string index
3062field= list_fields{index_fields(1)}; % selected string
3063if isequal(field,'get_field...')
3064    set(handles.FixVelType,'visible','off')
3065    set(handles.VelType,'visible','off')
3066    set(handles.VelType_1,'visible','off')
3067    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3068    filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3069    %filename=read_file_boxes(handles);
3070    hget_field=findobj(allchild(0),'name','get_field');
3071    if ~isempty(hget_field)
3072        delete(hget_field)
3073    end
3074    hget_field=get_field(filename);
3075    set(hget_field,'Name','get_field')
3076    hhget_field=guidata(hget_field);
3077    set(hhget_field.list_fig,'Value',1)
3078    set(hhget_field.list_fig,'String',{'uvmat'})
3079    set(handles.transform_fct,'Value',1)% no transform by default
3080    set(handles.path_transform,'String','')
3081    return %no action
3082end
3083list_fields=get(handles.Fields_1,'String');% list menu fields
3084index_fields=get(handles.Fields_1,'Value');% selected string index
3085field_1= list_fields{index_fields(1)}; % selected string
3086UvData=get(handles.uvmat,'UserData');
3087
3088%read the rootfile input display
3089[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3090FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3091[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3092% NomTypeNew=NomType;%default
3093if isequal(field,'image')
3094%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
3095%         NomTypeNew='_1_1';
3096%     elseif isequal(NomType,'#_ab')
3097%         NomTypeNew='#a';
3098%     elseif isequal(NomType,'_1-2')
3099%         NomTypeNew='_1';
3100%     end
3101    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
3102    if ~exist(imagename,'file')
3103        [FileName,PathName] = uigetfile( ...
3104            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3105            '*.jpg',' jpeg image files'; ...
3106            '*.png','.png image files'; ...
3107            '*.tif','.tif image files'; ...
3108            '*.avi;*.AVI','.avi movie files'; ...
3109            '*.vol','.volume images (png)'; ...
3110            '*.*',  'All Files (*.*)'}, ...
3111            'Pick an image',imagename);   
3112        imagename=[PathName FileName];
3113    end
3114     % display the selected field and related information
3115    display_file_name(handles,imagename)%display the image
3116    return
3117else
3118    ext=get(handles.FileExt,'String');
3119    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3120        [FileName,PathName] = uigetfile( ...
3121            {'*.nc', ' (*.nc)';
3122            '*.nc',' netcdf files'; ...
3123            '*.*',  'All Files (*.*)'}, ...
3124            'Pick a netcdf file',FileBase);
3125        filename=[PathName FileName];
3126        % display the selected field and related information
3127        display_file_name( handles,filename)
3128        return
3129    end
3130end
3131indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3132set(handles.FileIndex,'String',indices)
3133% set(handles.NomType,'String',NomType)
3134
3135%common to Fields_1_Callback
3136if isequal(field,'image')||isequal(field_1,'image')
3137    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3138    set(handles.TitleNpy,'Visible','on')
3139    set(handles.num_Npx,'Visible','on')
3140    set(handles.num_Npy,'Visible','on')
3141else
3142    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3143    set(handles.TitleNpy,'Visible','off')
3144    set(handles.num_Npx,'Visible','off')
3145    set(handles.num_Npy,'Visible','off')
3146end
3147if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3148    run0_Callback(hObject, eventdata, handles)
3149end
3150
3151%---------------------------------------------------
3152% --- Executes on menu selection Fields
3153function Fields_1_Callback(hObject, eventdata, handles)
3154%-------------------------------------------------
3155%% read input data
3156check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3157UvData=get(handles.uvmat,'UserData');
3158if check_new && isfield(UvData,'XmlData')
3159    UvData.XmlData{2}=UvData.XmlData{1};
3160end
3161if isfield(UvData,'Field_1')
3162    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3163end
3164UvData.filename_1='';% desactivate the use of a constant second file
3165list_fields=get(handles.Fields,'String');% list menu fields
3166field= list_fields{get(handles.Fields,'Value')}; % selected string
3167list_fields=get(handles.Fields_1,'String');% list menu fields
3168field_1= list_fields{get(handles.Fields_1,'Value')}; % selected string for the second field
3169if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3170    set(handles.SubField,'Value',0)
3171    SubField_Callback(hObject, eventdata, handles)
3172    return
3173else
3174    set(handles.SubField,'Value',1)%state that a second field is now entered
3175end
3176
3177%% read the rootfile input display
3178[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3179filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3180[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3181% set(handles.FileIndex_1,'Visible','on')
3182% set(handles.FileExt_1,'Visible','on')
3183switch field_1
3184    case 'get_field...'
3185        set_veltype_display(0) % no veltype display
3186        hget_field=findobj(allchild(0),'name','get_field_1');
3187        if ~isempty(hget_field)
3188            delete(hget_field)
3189        end
3190        hget_field=get_field(filename_1);
3191        set(hget_field,'name','get_field_1')
3192        hhget_field=guidata(hget_field);
3193        set(hhget_field.list_fig,'Value',1)
3194        set(hhget_field.list_fig,'String',{'uvmat'})
3195        set(handles.transform_fct,'Value',1)% no transform by default
3196        set(handles.path_transform,'String','')
3197        if check_new
3198            UvData.FileType{2}=UvData.FileType{1};
3199            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3200%             set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3201              set(handles.uvmat,'UserData',UvData)
3202        end
3203    case 'image'
3204        % guess the image name corresponding to the current netcdf name (no unique correspondance)
3205        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3206        if ~exist(imagename,'file') % browse for images if it is not found
3207            [FileName,PathName] = uigetfile( ...
3208                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3209                '*.jpg',' jpeg image files'; ...
3210                '*.png','.png image files'; ...
3211                '*.tif','.tif image files'; ...
3212                '*.avi;*.AVI','.avi movie files'; ...
3213                '*.vol','.volume images (png)'; ...
3214                '*.*',  'All Files (*.*)'}, ...
3215                'Pick an image',imagename);
3216            imagename=[PathName FileName];
3217        end
3218        if ~ischar(imagename)% quit if the browser has  been closed
3219            set(handles.SubField,'Value',0)
3220        else %valid browser input:  display the selected image
3221            set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3222            set(handles.TitleNpy,'Visible','on')
3223            set(handles.num_Npx,'Visible','on')
3224            set(handles.num_Npy,'Visible','on')
3225            display_file_name(handles,imagename,2)%display the imag
3226        end
3227    otherwise
3228        if check_new
3229            UvData.FileType{2}=UvData.FileType{1};
3230            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3231            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3232        end
3233        if ~isequal(field,'image')
3234            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3235            set(handles.TitleNpy,'Visible','off')
3236            set(handles.num_Npx,'Visible','off')
3237            set(handles.num_Npy,'Visible','off')
3238        end
3239        set(handles.uvmat,'UserData',UvData)
3240        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3241            run0_Callback(hObject, eventdata, handles)
3242        end
3243end
3244
3245%------------------------------------------------------------------------
3246% --- set the visibility of relevant velocity type menus:
3247function menu=set_veltype_display(Civ,FileType)
3248%------------------------------------------------------------------------
3249if ~exist('FileType','var')
3250    FileType='civx';
3251end
3252switch FileType
3253    case 'civx'
3254        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3255        if isequal(Civ,0)
3256            imax=0;
3257        elseif isequal(Civ,1) || isequal(Civ,2)
3258            imax=1;
3259        elseif isequal(Civ,3)
3260            imax=3;
3261        elseif isequal(Civ,4) || isequal(Civ,5)
3262            imax=4;
3263        elseif isequal(Civ,6) %patch2
3264            imax=6;
3265        end
3266    case 'civdata'
3267        menu={'civ1';'filter1';'civ2';'filter2'};
3268        if isequal(Civ,0)
3269            imax=0;
3270        elseif isequal(Civ,1) || isequal(Civ,2)
3271            imax=1;
3272        elseif isequal(Civ,3)
3273            imax=2;
3274        elseif isequal(Civ,4) || isequal(Civ,5)
3275            imax=3;
3276        elseif isequal(Civ,6) %patch2
3277            imax=4;
3278        end
3279end
3280menu=menu(1:imax);
3281
3282%------------------------------------------------------------------------
3283% --- Executes on button press in FixVelType.
3284function FixVelType_Callback(hObject, eventdata, handles)
3285%------------------------------------------------------------------------
3286% refresh the current plot if the fixed  veltype is unselected
3287if ~get(handles.FixVelType,'Value')
3288    run0_Callback(hObject, eventdata, handles)
3289end
3290
3291%------------------------------------------------------------------------
3292% --- Executes on button press in VelType.
3293function VelType_Callback(hObject, eventdata, handles)
3294%------------------------------------------------------------------------
3295set(handles.FixVelType,'Value',1)
3296run0_Callback(hObject, eventdata, handles)
3297
3298%------------------------------------------------------------------------
3299% --- Executes on button press in VelType_1.
3300function VelType_1_Callback(hObject, eventdata, handles)
3301%------------------------------------------------------------------------
3302set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3303UvData=get(handles.uvmat,'UserData');
3304%refresh field with a second filename=first file name
3305set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3306drawnow   
3307InputFile=read_GUI(handles.InputFile);
3308[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3309filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3310
3311if isempty(InputFile.VelType_1)
3312        filename_1='';% we plot the current field without the second field
3313        set(handles.SubField,'Value',0)
3314        SubField_Callback(hObject, eventdata, handles)
3315elseif get(handles.SubField,'Value')% if subfield is already 'on'
3316      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3317     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3318else
3319     filename_1=filename;% we compare two fields in the same file by default
3320     UvData.FileType{2}=UvData.FileType{1};
3321     set(handles.SubField,'Value',1)
3322end
3323if isfield(UvData,'Field_1')
3324    UvData=rmfield(UvData,'Field_1');% removes the stored second field if it exists
3325end
3326UvData.filename_1='';% desactivate the use of a constant second file
3327set(handles.uvmat,'UserData',UvData)
3328num_i1=stra2num(get(handles.i1,'String'));
3329num_i2=stra2num(get(handles.i2,'String'));
3330num_j1=stra2num(get(handles.j1,'String'));
3331num_j2=stra2num(get(handles.j2,'String'));
3332
3333errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
3334
3335if ~isempty(errormsg)
3336    msgbox_uvmat('ERROR',errormsg);
3337else
3338    set(handles.i1,'BackgroundColor',[1 1 1])
3339    set(handles.i2,'BackgroundColor',[1 1 1])
3340    set(handles.j1,'BackgroundColor',[1 1 1])
3341    set(handles.j2,'BackgroundColor',[1 1 1])
3342    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3343    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3344end
3345set(handles.run0,'BackgroundColor',[1 0 0])
3346
3347%-----------------------------------------------
3348% --- reset civ buttons
3349function reset_vel_type(handles_civ0,handle1)
3350for ibutton=1:length(handles_civ0)
3351    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3352    set(handles_civ0(ibutton),'Value',0)
3353end
3354if exist('handle1','var')%handles of selected button
3355        set(handle1,'BackgroundColor',[1 1 0]) 
3356end
3357
3358%-------------------------------------------------------
3359% --- Executes on button press in MENUVOLUME.
3360%-------------------------------------------------------
3361function VOLUME_Callback(hObject, eventdata, handles)
3362%errordlg('command VOL not implemented yet')
3363if ishandle(handles.UVMAT_title)
3364    delete(handles.UVMAT_title)
3365end
3366UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3367if isequal(get(handles.VOLUME,'Value'),1)
3368    set(handles.CheckZoom,'Value',0)
3369    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3370    set(handles.edit_vect,'Value',0)
3371    edit_vect_Callback(hObject, eventdata, handles)
3372    set(handles.edit_object,'Value',0)
3373    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3374%     set(handles.cal,'Value',0)
3375%     set(handles.cal,'BackgroundColor',[0 1 0])
3376    set(handles.edit_vect,'Value',0)
3377    edit_vect_Callback(hObject, eventdata, handles)
3378    %initiate set_object GUI
3379    data.Name='VOLUME';
3380    if isfield(UvData,'CoordType')
3381        data.CoordType=UvData.CoordType;
3382    end
3383    if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh)
3384        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3385        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3386        data.DX=UvData.Field.Mesh;
3387        data.DY=UvData.Field.Mesh;
3388    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3389        np=size(UvData.Field.A);
3390        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3391        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3392        data.RangeY=max(meshx,meshy);
3393        data.RangeX=max(meshx,meshy);
3394        data.DX=max(meshx,meshy);
3395    end
3396    data.ParentButton=handles.VOLUME;
3397    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3398    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3399                                                      % associate the set_object interface handle to the plotting axes
3400    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3401    pos_uvmat=get(handles.uvmat,'Position');
3402    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3403    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3404    set(hset_object,'Position',pos_set_object)
3405    end
3406    UvData.MouseAction='create_object';
3407else
3408    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3409    UvData.MouseAction='none';
3410end
3411set(handles.uvmat,'UserData',UvData)
3412
3413%-------------------------------------------------------
3414function edit_vect_Callback(hObject, eventdata, handles)
3415%-------------------------------------------------------
3416%
3417% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3418if isequal(get(handles.edit_vect,'Value'),1)
3419    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3420    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3421    if ~test_civ2 && ~test_civ1
3422        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3423    end
3424    set(handles.record,'Visible','on')
3425    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3426    set(handles.edit_object,'Value',0)
3427    set(handles.CheckZoom,'Value',0)
3428    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3429%     set(handles.create,'Value',0)
3430%     set(handles.create,'BackgroundColor',[0 1 0])
3431    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3432    set(gcf,'Pointer','arrow')
3433%     UvData.MouseAction='edit_vect';
3434else
3435    set(handles.record,'Visible','off')
3436    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3437%     UvData.MouseAction='none';
3438end
3439% set(handles.uvmat,'UserData',UvData)
3440
3441%----------------------------------------------
3442function save_mask_Callback(hObject, eventdata, handles)
3443%-----------------------------------------------------------------------
3444UvData=get(handles.uvmat,'UserData');
3445
3446flag=1;
3447npx=size(UvData.Field.A,2);
3448npy=size(UvData.Field.A,1);
3449xi=0.5:npx-0.5;
3450yi=0.5:npy-0.5;
3451[Xi,Yi]=meshgrid(xi,yi);
3452if isfield(UvData,'Object')
3453    for iobj=1:length(UvData.Object)
3454        ObjectData=UvData.Object{iobj};
3455        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3456            flagobj=1;
3457            testphys=0; %coordinates in pixels by default
3458            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3459                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3460                    Calib=UvData.XmlData{1}.GeometryCalib;
3461                    testphys=1;
3462                end
3463            end
3464            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3465                if isequal(ObjectData.Type,'polygon')
3466                    X=ObjectData.Coord(:,1);
3467                    Y=ObjectData.Coord(:,2);
3468                    if testphys
3469                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3470                    end
3471                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3472                elseif isequal(ObjectData.Type,'ellipse')
3473                    if testphys
3474                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3475                    end
3476                    RangeX=max(ObjectData.RangeX);
3477                    RangeY=max(ObjectData.RangeY);
3478                    X2Max=RangeX*RangeX;
3479                    Y2Max=RangeY*RangeY;
3480                    distX=(Xi-ObjectData.Coord(1,1));
3481                    distY=(Yi-ObjectData.Coord(1,2));
3482                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3483                elseif isequal(ObjectData.Type,'rectangle')
3484                    if testphys
3485                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3486                    end
3487                    distX=abs(Xi-ObjectData.Coord(1,1));
3488                    distY=abs(Yi-ObjectData.Coord(1,2));
3489                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3490                end
3491                if isequal(ObjectData.ProjMode,'mask_outside')
3492                    flagobj=~flagobj;
3493                end
3494                flag=flag & flagobj;
3495            end
3496        end
3497    end
3498end
3499% flag=~flag;
3500%mask name
3501RootPath=get(handles.RootPath,'String');
3502RootFile=get(handles.RootFile,'String');
3503RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3504filebase=fullfile(RootPath,RootFile);
3505list=get(handles.masklevel,'String');
3506masknumber=num2str(length(list));
3507maskindex=get(handles.masklevel,'Value');
3508mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3509%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3510imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3511imflag=flipdim(imflag,1);
3512% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3513msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3514imwrite(imflag,mask_name,'BitDepth',8);
3515
3516%display the mask
3517figure;
3518vec=linspace(0,1,256);%define a linear greyscale colormap
3519map=[vec' vec' vec'];
3520colormap(map)
3521
3522image(imflag);
3523
3524%-------------------------------------------------------------------
3525%-------------------------------------------------------------------
3526%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3527
3528%------------------------------------------------------------------
3529%-------------------------------------------------------------
3530% --- Executes on selection change in transform_fct.
3531function transform_fct_Callback(hObject, eventdata, handles)
3532%-------------------------------------------------------------
3533UvData=get(handles.uvmat,'UserData');
3534menu=get(handles.transform_fct,'String');
3535ind_coord=get(handles.transform_fct,'Value');
3536coord_option=menu{ind_coord};
3537list_transform=get(handles.transform_fct,'UserData');
3538ff=functions(list_transform{end}); 
3539if isequal(coord_option,'more...');
3540    coord_fct='';
3541    prompt = {'Enter the name of the transform function'};
3542    dlg_title = 'user defined transform';
3543    num_lines= 1;
3544    [FileName, PathName] = uigetfile( ...
3545       {'*.m', ' (*.m)';
3546        '*.m',  '.m files '; ...
3547        '*.*', 'All Files (*.*)'}, ...
3548        'Pick a file', ff.file);
3549    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3550        PathName(end)=[];
3551    end
3552    transform_selected =fullfile(PathName,FileName);
3553    if ~exist(transform_selected,'file')
3554           return
3555    end
3556   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3557   if ~isequal(ext_fct,'.m')
3558        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3559        return
3560   end
3561   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3562   ind_coord=get(handles.transform_fct,'Value');
3563   addpath(PathName)
3564   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3565   set(handles.transform_fct,'UserData',list_transform)
3566   rmpath(PathName)
3567   % save the new menu in the personal file 'uvmat_perso.mat'
3568   dir_perso=prefdir;%personal Matalb directory
3569   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3570   if exist(profil_perso,'file')
3571       nb_builtin=UvData.OpenParam.NbBuiltin;
3572       for ilist=nb_builtin+1:numel(list_transform)
3573           ff=functions(list_transform{ilist});
3574           transform_fct{ilist-nb_builtin}=ff.file;
3575       end
3576        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3577   end   
3578end
3579
3580%% check the current path to the selected function
3581if isa(list_transform{ind_coord},'function_handle')
3582    func=functions(list_transform{ind_coord});
3583    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3584else
3585    set(handles.path_transform,'String','')
3586end
3587
3588set(handles.CheckFixLimits,'Value',0)
3589set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3590
3591%% delete drawn objects
3592hother=findobj('Tag','proj_object');%find all the proj objects
3593for iobj=1:length(hother)
3594    delete_object(hother(iobj))
3595end
3596hother=findobj('Tag','DeformPoint');%find all the proj objects
3597for iobj=1:length(hother)
3598    delete_object(hother(iobj))
3599end
3600hh=findobj('Tag','calib_points');
3601if ~isempty(hh)
3602    delete(hh)
3603end
3604hhh=findobj('Tag','calib_marker');
3605if ~isempty(hhh)
3606    delete(hhh)
3607end
3608if isfield(UvData,'Object')
3609     UvData.Object=UvData.Object(1);
3610end
3611set(handles.ListObject,'Value',1)
3612set(handles.ListObject,'String',{'plane'})
3613set(handles.ListObject_1,'Value',1)
3614set(handles.ListObject_1,'String',{'plane'})
3615
3616%delete mask if it is displayed
3617% if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3618%    UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3619% end
3620set(handles.uvmat,'UserData',UvData)
3621run0_Callback(hObject, eventdata, handles)
3622
3623
3624
3625%------------------------------------------------
3626%CALLBACKS FOR PLOTTING PARAMETERS
3627%-------------------------------------------------
3628%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3629% Plot coordinates
3630%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3631%------------------------------------------------------------------------
3632function num_MinX_Callback(hObject, eventdata, handles)
3633%------------------------------------------------------------------------
3634set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3635set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3636update_plot(handles);
3637
3638%------------------------------------------------------------------------
3639function num_MaxX_Callback(hObject, eventdata, handles)
3640%------------------------------------------------------------------------
3641set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3642set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3643update_plot(handles);
3644
3645%------------------------------------------------------------------------
3646function num_MinY_Callback(hObject, eventdata, handles)
3647%------------------------------------------
3648set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3649set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3650update_plot(handles);
3651
3652%------------------------------------------------------------------------
3653function num_MaxY_Callback(hObject, eventdata, handles)
3654%------------------------------------------------------------------------
3655set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3656set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3657update_plot(handles);
3658
3659%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3660% Scalar or image representation
3661%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3662%------------------------------------------------------------------------
3663function num_MinA_Callback(hObject, eventdata, handles)
3664%------------------------------------------
3665set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3666set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3667MinA=str2double(get(handles.num_MinA,'String'));
3668MaxA=str2double(get(handles.num_MaxA,'String'));
3669if MinA>MaxA% switch minA and maxA in case of error
3670    MinA_old=MinA;
3671    MinA=MaxA;
3672    MaxA=MinA_old;
3673    set(handles.num_MinA,'String',num2str(MinA,5));
3674    set(handles.num_MaxA,'String',num2str(MaxA,5));
3675end
3676update_plot(handles);
3677
3678%------------------------------------------------------------------------
3679function num_MaxA_Callback(hObject, eventdata, handles)
3680%------------------------------------------------------------------------
3681set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3682set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3683MinA=str2double(get(handles.num_MinA,'String'));
3684MaxA=str2double(get(handles.num_MaxA,'String'));
3685if MinA>MaxA% switch minA and maxA in case of error
3686        MinA_old=MinA;
3687    MinA=MaxA;
3688    MaxA=MinA_old;
3689    set(handles.num_MinA,'String',num2str(MinA,5));
3690    set(handles.num_MaxA,'String',num2str(MaxA,5));
3691end
3692update_plot(handles);
3693
3694%------------------------------------------------------------------------
3695function CheckFixScalar_Callback(hObject, eventdata, handles)
3696%------------------------------------------------------------------------
3697test=get(handles.CheckFixScalar,'Value');
3698if test
3699    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3700else
3701    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3702    update_plot(handles);
3703end
3704
3705%-------------------------------------------------------------------
3706function CheckBW_Callback(hObject, eventdata, handles)
3707%-------------------------------------------------------------------
3708update_plot(handles);
3709
3710%-------------------------------------------------------------------
3711function num_Opacity_Callback(hObject, eventdata, handles)
3712update_plot(handles);
3713%-------------------------------------------------------------------
3714
3715%-------------------------------------------------------------------
3716function ListContour_Callback(hObject, eventdata, handles)
3717%-------------------------------------------------------------------
3718val=get(handles.ListContour,'Value');
3719if val==2
3720    set(handles.interval_txt,'Visible','on')
3721    set(handles.num_IncrA,'Visible','on')
3722else
3723    set(handles.interval_txt,'Visible','off')
3724    set(handles.num_IncrA,'Visible','off')
3725end
3726update_plot(handles);
3727
3728%-------------------------------------------------------------------
3729function num_IncrA_Callback(hObject, eventdata, handles)
3730%-------------------------------------------------------------------
3731update_plot(handles);
3732
3733
3734%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3735% Vector representation
3736%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3737%-------------------------------------------------------------------
3738function CheckHideWarning_Callback(hObject, eventdata, handles)
3739%-------------------------------------------------------------------
3740update_plot(handles);
3741
3742%-------------------------------------------------------------------
3743function CheckHideFalse_Callback(hObject, eventdata, handles)
3744%-------------------------------------------------------------------
3745update_plot(handles);
3746
3747%-------------------------------------------------------------------
3748function num_VecScale_Callback(hObject, eventdata, handles)
3749%-------------------------------------------------------------------
3750set(handles.CheckFixVectors,'Value',1);
3751set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3752update_plot(handles);
3753
3754%-------------------------------------------------------------------
3755function CheckFixVectors_Callback(hObject, eventdata, handles)
3756%-------------------------------------------------------------------
3757test=get(handles.CheckFixVectors,'Value');
3758if test
3759    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3760else
3761    update_plot(handles);
3762    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3763    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3764end
3765
3766%------------------------------------------------------------------------
3767% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3768function CheckDecimate4_Callback(hObject, eventdata, handles)
3769%------------------------------------------------------------------------
3770update_plot(handles);
3771
3772%------------------------------------------------------------------------
3773% --- Executes on selection change in ColorCode menu
3774function ColorCode_Callback(hObject, eventdata, handles)
3775%------------------------------------------------------------------------
3776% edit the choice for color code
3777update_color_code_boxes(handles);
3778update_plot(handles);
3779
3780%------------------------------------------------------------------------
3781function update_color_code_boxes(handles)
3782%------------------------------------------------------------------------
3783list_code=get(handles.ColorCode,'String');% list menu fields
3784colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3785enable_slider='off';%default
3786enable_bounds='off';%default
3787enable_scalar='off';%default
3788switch colcode
3789    case {'rgb','bgr'}
3790        enable_slider='on';
3791        enable_bounds='on';
3792        enable_scalar='on';
3793    case '64 colors'
3794        enable_bounds='on';
3795        enable_scalar='on';
3796end
3797set(handles.Slider1,'Visible',enable_slider)
3798set(handles.Slider2,'Visible', enable_slider)
3799set(handles.num_ColCode1,'Visible',enable_slider)
3800set(handles.num_ColCode2,'Visible',enable_slider)
3801set(handles.TitleColCode1,'Visible',enable_slider)
3802set(handles.TitleColCode2,'Visible',enable_slider)
3803set(handles.CheckFixVecColor,'Visible',enable_bounds)
3804set(handles.num_MinVec,'Visible',enable_bounds)
3805set(handles.num_MaxVec,'Visible',enable_bounds)
3806set(handles.ColorScalar,'Visible',enable_scalar)
3807set_vec_col_bar(handles)
3808
3809%------------------------------------------------------------------
3810% --- Executes on selection change in ColorScalar: choice of the color code.
3811function ColorScalar_Callback(hObject, eventdata, handles)
3812%------------------------------------------------------------------
3813% edit the choice for color code
3814list_scalar=get(handles.ColorScalar,'String');% list menu fields
3815col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3816if isequal(col_scalar,'ima_cor')
3817    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3818    ColorCode='rgb';
3819    set(handles.num_MinVec,'String','0')
3820    set(handles.num_MaxVec,'String','1')
3821    set(handles.num_ColCode1,'String','0.333')
3822    set(handles.num_ColCode2,'String','0.666')
3823else
3824    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3825    ColorCode='64 colors';
3826end
3827ColorCodeList=get(handles.ColorCode,'String');
3828ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3829set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3830
3831update_color_code_boxes(handles);
3832%replot the current graph
3833run0_Callback(hObject, eventdata, handles)
3834
3835%----------------------------------------------------------------
3836% -- Executes on slider movement to set the color code
3837%
3838function Slider1_Callback(hObject, eventdata, handles)
3839%------------------------------------------------------------------
3840slider1=get(handles.Slider1,'Value');
3841min_val=str2num(get(handles.num_MinVec,'String'));
3842max_val=str2num(get(handles.num_MaxVec,'String'));
3843col=min_val+(max_val-min_val)*slider1;
3844set(handles.num_ColCode1,'String',num2str(col))
3845if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3846    set(handles.Slider2,'Value',col)
3847    set(handles.num_ColCode2,'String',num2str(col))
3848end
3849set_vec_col_bar(handles)
3850update_plot(handles);
3851
3852%----------------------------------------------------------------
3853% Executes on slider movement to set the color code
3854%----------------------------------------------------------------
3855function Slider2_Callback(hObject, eventdata, handles)
3856slider2=get(handles.Slider2,'Value');
3857min_val=str2num(get(handles.num_MinVec,'String'));
3858max_val=str2num(get(handles.num_MaxVec,'String'));
3859col=min_val+(max_val-min_val)*slider2;
3860set(handles.num_ColCode2,'String',num2str(col))
3861if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3862    set(handles.Slider1,'Value',col)
3863    set(handles.num_ColCode1,'String',num2str(col))
3864end
3865set_vec_col_bar(handles)
3866update_plot(handles);
3867
3868%----------------------------------------------------------------
3869% --- Execute on return carriage on the edit box corresponding to slider 1
3870%----------------------------------------------------------------
3871function num_ColCode1_Callback(hObject, eventdata, handles)
3872set_vec_col_bar(handles)
3873update_plot(handles);
3874
3875%----------------------------------------------------------------
3876% --- Execute on return carriage on the edit box corresponding to slider 2
3877%----------------------------------------------------------------
3878function num_ColCode2_Callback(hObject, eventdata, handles)
3879set_vec_col_bar(handles)
3880update_plot(handles);
3881%------------------------------------------------------------------------
3882%-------------------------------------------------------
3883% --- Executes on button press in CheckFixVecColor.
3884%-------------------------------------------------------
3885function VecColBar_Callback(hObject, eventdata, handles)
3886set_vec_col_bar(handles)
3887
3888%------------------------------------------------------------------------
3889% --- Executes on button press in CheckFixVecColor.
3890function CheckFixVecColor_Callback(hObject, eventdata, handles)
3891%------------------------------------------------------------------------
3892if ~get(handles.CheckFixVecColor,'Value')
3893    update_plot(handles);
3894end
3895
3896%------------------------------------------------------------------------
3897% --- Executes on selection change in num_MaxVec.
3898function num_MinVec_Callback(hObject, eventdata, handles)
3899%------------------------------------------------------------------------
3900max_vec_Callback(hObject, eventdata, handles)
3901
3902%------------------------------------------------------------------------
3903% --- Executes on selection change in num_MaxVec.
3904function num_MaxVec_Callback(hObject, eventdata, handles)
3905%------------------------------------------------------------------------
3906set(handles.CheckFixVecColor,'Value',1)
3907CheckFixVecColor_Callback(hObject, eventdata, handles)
3908min_val=str2num(get(handles.num_MinVec,'String'));
3909max_val=str2num(get(handles.num_MaxVec,'String'));
3910slider1=get(handles.Slider1,'Value');
3911slider2=get(handles.Slider2,'Value');
3912colcode1=min_val+(max_val-min_val)*slider1;
3913colcode2=min_val+(max_val-min_val)*slider2;
3914set(handles.num_ColCode1,'String',num2str(colcode1))
3915set(handles.num_ColCode2,'String',num2str(colcode2))
3916update_plot(handles);
3917
3918%------------------------------------------------------------------------
3919% --- update the display of color code for vectors (on vecColBar)
3920function set_vec_col_bar(handles)
3921%------------------------------------------------------------------------
3922%get the image of the color display button 'VecColBar' in pixels
3923set(handles.VecColBar,'Unit','pixel');
3924pos_vert=get(handles.VecColBar,'Position');
3925set(handles.VecColBar,'Unit','Normalized');
3926width=ceil(pos_vert(3));
3927height=ceil(pos_vert(4));
3928
3929%get slider indications
3930list=get(handles.ColorCode,'String');
3931ichoice=get(handles.ColorCode,'Value');
3932colcode.ColorCode=list{ichoice};
3933colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3934colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3935test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
3936if test3color
3937    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3938    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3939end
3940vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3941[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3942oneheight=ones(1,height);
3943A1=colorlist(col_vec,1)*oneheight;
3944A2=colorlist(col_vec,2)*oneheight;
3945A3=colorlist(col_vec,3)*oneheight;
3946A(:,:,1)=A1';
3947A(:,:,2)=A2';
3948A(:,:,3)=A3';
3949set(handles.VecColBar,'Cdata',A)
3950
3951%-------------------------------------------------------------------
3952function update_plot(handles)
3953%-------------------------------------------------------------------
3954UvData=get(handles.uvmat,'UserData');
3955AxeData=UvData.axes3;% retrieve the current plotted data
3956PlotParam=read_GUI(handles.uvmat);
3957[tild,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
3958write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3959
3960%------------------------------------------------------------------------
3961%------------------------------------------------------------------------
3962%   SELECTION AND EDITION OF PROJECTION OBJECTS
3963%------------------------------------------------------------------------
3964%------------------------------------------------------------------------
3965
3966% --- Executes on selection change in ListObject_1.
3967function ListObject_1_Callback(hObject, eventdata, handles)
3968list_str=get(handles.ListObject,'String');
3969UvData=get(handles.uvmat,'UserData');
3970ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
3971
3972%% update the projection plot on uvmat
3973ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
3974plot_field(ProjData,handles.axes3,read_GUI(handles.uvmat));% plot the projected field;
3975%replot all the objects within the new projected field
3976for IndexObj=1:numel(list_str)
3977    IndexObj
3978        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat
3979        if isempty(hobject) || ~ishandle(hobject)
3980            hobject=handles.axes3
3981        end
3982        if isequal(IndexObj,get(handles.ListObject,'Value'))
3983            objectcolor='m'; %paint in magenta the currently selected object in ListObject
3984        else
3985            objectcolor='b';
3986        end
3987        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
3988end
3989set(handles.uvmat,'UserData',UvData)
3990
3991%% display the object parameters if the GUI set_object is already opened
3992if ~get(handles.ViewObject,'Value')
3993    ZBounds=0; % default
3994    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3995        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3996        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3997    end
3998    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
3999    set_object(ObjectData,[],ZBounds);
4000    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
4001end
4002
4003%  desactivate the edit object mode
4004set(handles.edit_object,'Value',0)
4005set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4006
4007%------------------------------------------------------------------------
4008% --- Executes on selection change in ListObject.
4009function ListObject_Callback(hObject, eventdata, handles)
4010%------------------------------------------------------------------------
4011list_str=get(handles.ListObject,'String');
4012IndexObj=get(handles.ListObject,'Value');%present object selection
4013
4014%% The object  is displayed in set_object if this GUI is already opened
4015UvData=get(handles.uvmat,'UserData');
4016ObjectData=UvData.Object{IndexObj};
4017hset_object=findobj(allchild(0),'tag','set_object');
4018if ~isempty(hset_object)
4019    ZBounds=0; % default
4020    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4021        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4022        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4023    end
4024    ObjectData.Name=list_str{IndexObj};
4025    set_object(ObjectData,[],ZBounds);
4026    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4027end
4028
4029%%  desactivate the edit object mode
4030set(handles.edit_object,'Value',0)
4031set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4032
4033%% update the  plot on view_field if view_field is already openened
4034hview_field=findobj(allchild(0),'tag','view_field');
4035if isempty(hview_field)
4036    hhview_field.axes3=[];
4037else
4038    Data=get(hview_field,'UserData');
4039    hhview_field=guidata(hview_field);
4040    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4041    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
4042    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4043    haxes=findobj(hview_field,'tag','axes3');
4044    pos=get(hview_field,'Position'); 
4045    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4046        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4047        pos_table=get(h_TableDisplay,'Position');
4048        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4049        drawnow% needed to change position before the next command
4050        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4051    else
4052        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4053    end
4054end
4055
4056%% update the color of the graphic object representation: the selected object in magenta, others in blue
4057update_object_color(handles.axes3,hhview_field.axes3,UvData.Object{IndexObj}.DisplayHandle.uvmat)
4058
4059%------------------------------------------------------------------------
4060%--- update the color representation of objects (indicating the selected ones)
4061function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4062%------------------------------------------------------------------------
4063if isempty(axes_view_field)% case with no view_field plot
4064hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4065else
4066hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4067findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4068end
4069for iobj=1:length(hother)
4070    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4071        set(hother(iobj),'EdgeColor','b')
4072        if isequal(get(hother(iobj),'FaceColor'),'m')
4073            set(hother(iobj),'FaceColor','b')
4074        end
4075    elseif isequal(get(hother(iobj),'Type'),'image')
4076        Acolor=get(hother(iobj),'CData');
4077        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4078        set(hother(iobj),'CData',Acolor);
4079    else
4080        set(hother(iobj),'Color','b')
4081    end
4082    set(hother(iobj),'Selected','off')
4083end
4084if ishandle(DisplayHandle)
4085    linetype=get(DisplayHandle,'Type');
4086    if isequal(linetype,'line')
4087        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4088    elseif isequal(linetype,'rectangle')
4089        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4090    elseif isequal(linetype,'patch')
4091        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4092    end
4093    SubObjectData=get(DisplayHandle,'UserData');
4094    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4095        for iobj=1:length(SubObjectData.SubObject)
4096            hsub=SubObjectData.SubObject(iobj);
4097            if isequal(get(hsub,'Type'),'rectangle')
4098                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4099            elseif isequal(get(hsub,'Type'),'image')
4100                Acolor=get(hsub,'CData');
4101                Acolor(:,:,1)=Acolor(:,:,3);
4102                set(hsub,'CData',Acolor);
4103            else
4104                set(hsub,'Color','m')
4105            end
4106        end
4107    end
4108    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4109        set(SubObjectData.DeformPoint,'Color','m')
4110    end
4111end
4112
4113%-------------------------------------------------------------------
4114% --- Executes on selection change in edit_object.
4115function edit_object_Callback(hObject, eventdata, handles)
4116%-------------------------------------------------------------------
4117UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4118hset_object=findobj(allchild(0),'Tag','set_object');
4119if get(handles.edit_object,'Value')
4120    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4121    %suppress the other options
4122    set(handles.CheckZoom,'Value',0)
4123    CheckZoom_Callback(hObject, eventdata, handles)
4124    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4125    if ishandle(hgeometry_calib)
4126        hhgeometry_calib=guidata(hgeometry_calib);
4127        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4128        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4129    end
4130    set(handles.ViewObject,'value',1)
4131    ViewObject_Callback(hObject, eventdata, handles)
4132%     if isempty(hset_object)% open the GUI set_object with data of the currently selected object
4133%         ViewObject_Callback(hObject, eventdata, handles)
4134%         %         hset_object=findobj(allchild(0),'Tag','set_object');
4135%     else
4136%         hhset_object=guidata(hset_object);
4137%         set(hhset_object.PLOT,'enable','on');
4138%         set(get(hset_object,'children'),'enable','on')
4139%     end
4140else % desctivate object edit mode
4141    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4142    if ~isempty(hset_object)% open the
4143        hhset_object=guidata(hset_object);
4144        set(hhset_object.PLOT,'enable','off');
4145        set(get(hset_object,'children'),'enable','inactive')
4146    end
4147end
4148
4149
4150%------------------------------------------------------------------------
4151% --- Executes on button press in ViewObject.
4152function ViewObject_Callback(hObject, eventdata, handles)
4153%------------------------------------------------------------------------
4154check_view=get(handles.ViewObject,'Value');
4155
4156if check_view %activate set_object   
4157    IndexObj=get(handles.ListObject,'Value');
4158    list_object=get(handles.ListObject,'String');
4159    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4160    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4161    if numel(UvData.Object)<IndexObj;% error in UvData
4162        msgbox_uvmat('ERROR','invalid object list')
4163        return
4164    end
4165    ZBounds=0; % default
4166    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4167        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4168        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4169    end
4170%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4171    data=UvData.Object{IndexObj};
4172    if ~isfield(data,'Type')% default plane
4173        data.Type='plane';
4174    end
4175    if isfield(UvData,'Field')
4176        Field=UvData.Field;
4177        if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4178            data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4179            if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4180                data.RangeY=UvData.Field.Mesh;
4181            else
4182                data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4183            end
4184            data.DX=UvData.Field.Mesh;
4185            data.DY=UvData.Field.Mesh;
4186        end
4187        if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4188            data.Coord=[0 0 0]; %default
4189        end
4190        if isfield(Field,'CoordUnit')
4191            data.CoordUnit=Field.CoordUnit;
4192        end
4193    end
4194    hset_object=set_object(data,[],ZBounds);
4195    hhset_object=guidata(hset_object);
4196    if get(handles.edit_object,'Value')% edit mode
4197        set(hhset_object.PLOT,'Enable','on')
4198        set(get(hset_object,'children'),'enable','on')
4199    else
4200        set(hhset_object.PLOT,'Enable','off')
4201        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4202        set(hhset_object.SAVE,'Enable','on')
4203    end
4204else
4205    hset_object=findobj(allchild(0),'tag','set_object');
4206    if ~isempty(hset_object)
4207        delete(hset_object)% delete existing version of set_object
4208    end
4209end
4210 
4211
4212%------------------------------------------------------------------------
4213% --- Executes on button press in ViewField.
4214function ViewField_Callback(hObject, eventdata, handles)
4215%------------------------------------------------------------------------
4216check_view=get(handles.ViewField,'Value');
4217
4218if check_view
4219    IndexObj=get(handles.ListObject,'Value');
4220    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4221    if numel(UvData.Object)<IndexObj(end);% error in UvData
4222        msgbox_uvmat('ERROR','invalid object list')
4223        return
4224    end
4225    ZBounds=0; % default
4226    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4227        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4228        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4229    end
4230    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4231    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4232        UvData.Object{IndexObj(1)}.Type='plane';
4233    end
4234    list_object=get(handles.ListObject,'String');
4235    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4236   
4237    %% show the projection of the selected object on view_field
4238    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
4239    hview_field=findobj(allchild(0),'tag','view_field');
4240    if isempty(hview_field)
4241        hview_field=view_field;
4242    end
4243    hhview_field=guidata(hview_field);
4244    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4245    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4246    haxes=findobj(hview_field,'tag','axes3');
4247    pos=get(hview_field,'Position');
4248    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4249        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4250        pos_table=get(h_TableDisplay,'Position');
4251        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4252    else
4253        Data=get(hview_field,'UserData');
4254        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4255    end
4256else
4257    hview_field=findobj(allchild(0),'tag','view_field');
4258    if ~isempty(hview_field)
4259        delete(hview_field)% delete existing version of set_object
4260    end
4261end
4262
4263
4264%------------------------------------------------------------------------
4265% --- Executes on button press in delete_object.
4266function delete_object_Callback(hObject, eventdata, handles)
4267%------------------------------------------------------------------------
4268IndexObj=get(handles.ListObject,'Value');
4269IndexObj_1=get(handles.ListObject_1,'Value');
4270if IndexObj>1 && ~isequal(IndexObj,IndexObj_1)
4271    delete_object(IndexObj)
4272end
4273
4274%------------------------------------------------------------------------
4275%------------------------------------------------------------------------
4276%  II - TOOLS FROM THE UPPER MENU BAR
4277%------------------------------------------------------------------------
4278%------------------------------------------------------------------------
4279
4280%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4281% Export  Menu Callbacks
4282%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4283%------------------------------------------------------------------------
4284% --- Executes on button press in Menu/Export/field in workspace.
4285function MenuExportField_Callback(hObject, eventdata, handles)
4286%------------------------------------------------------------------------
4287global Data_uvmat
4288Data_uvmat=get(handles.uvmat,'UserData');
4289evalin('base','global Data_uvmat')%make CurData global in the workspace
4290display('current field :')
4291evalin('base','Data_uvmat') %display CurData in the workspace
4292commandwindow; %brings the Matlab command window to the front
4293
4294%------------------------------------------------------------------------
4295% --- Executes on button press in Menu/Export/extract figure.
4296function MenuExportFigure_Callback(hObject, eventdata, handles)
4297%------------------------------------------------------------------------
4298% huvmat=get(handles.MenuExport,'parent');
4299hfig=figure;
4300copyobj(handles.axes3,hfig);
4301map=colormap(handles.axes3);
4302colormap(map);%transmit the current colormap to the zoom fig
4303colorbar
4304
4305% %------------------------------------------------------
4306% % --- Executes on button press in Menu/Export/extract figure.
4307% %------------------------------------------------------
4308% function MenuExport_plot_Callback(hObject, eventdata, handles)
4309% huvmat=get(handles.MenuExport_plot,'parent');
4310% UvData=get(huvmat,'UserData');
4311% hfig=figure;
4312% newaxes=copyobj(handles.axes3,hfig);
4313% map=colormap(handles.axes3);
4314% colormap(map);%transmit the current colormap to the zoom fig
4315% colorbar
4316
4317%
4318% % --------------------------------------------------------------------
4319% function Insert_Callback(hObject, eventdata, handles)
4320%
4321
4322%------------------------------------------------------------------------
4323% --------------------------------------------------------------------
4324function MenuExportMovie_Callback(hObject, eventdata, handles)
4325% --------------------------------------------------------------------
4326set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4327huvmat=get(handles.run0,'parent');
4328UvData=get(huvmat,'UserData');
4329%[xx,xx,FileBase]=read_file_boxes(handles);
4330[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4331FileBase=fullfile(RootPath,RootFile);
4332 %read the current input file name
4333prompt = {'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)'};
4334dlg_title = 'select properties of the output avi movie';
4335num_lines= 1;
4336% nbfield_cell=get(handles.last_i,'String');
4337def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4338answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4339aviname=answer{1};
4340fps=str2double(answer{2});
4341% check for existing file with output name aviname
4342if exist(aviname,'file')
4343    backup=aviname;
4344    testexist=2;
4345    while testexist==2
4346        backup=[backup '~'];
4347        testexist=exist(backup,'file');     
4348    end
4349    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4350    if isequal(success,1)
4351        delete(aviname)%delete existing file
4352    else
4353        msgbox_uvmat('ERROR',message)
4354        return
4355    end
4356end
4357%create avi open
4358aviobj=avifile(aviname,'Compression','None','fps',fps);
4359
4360%display first view for tests
4361newfig=figure;
4362newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4363set(newaxes,'Tag','movieaxes')
4364nbpix=[512 384]*str2double(answer{3});
4365set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4366set(newaxes,'Position',eval(answer{4}));
4367map=colormap(handles.axes3);
4368colormap(map);%transmit the current colormap to the zoom fig
4369msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4370        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4371UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4372set(huvmat,'UserData',UvData);
4373increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4374set(handles.STOP,'Visible','on')
4375set(handles.speed,'Visible','on')
4376set(handles.speed_txt,'Visible','on')
4377set(handles.Movie,'BusyAction','queue')
4378
4379%imin=str2double(get(handles.i1,'String'));
4380imax=str2double(answer{5});
4381% if isfield(UvData,'Time')
4382htitle=get(newaxes,'Title');
4383xlim=get(newaxes,'XLim');
4384ylim=get(newaxes,'YLim');
4385set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4386time_str=get(handles.abs_time,'String');
4387set(htitle,'String',['t=' time_str])
4388set(handles.speed,'Value',1)
4389for i=1:imax
4390    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4391            runpm(hObject,eventdata,handles,increment)% run plus
4392            drawnow
4393            time_str=get(handles.abs_time,'String');
4394            if ishandle(htitle)
4395             set(htitle,'String',['t=' time_str])
4396            end
4397            mov=getframe(newfig);
4398            aviobj=addframe(aviobj,mov);
4399    end
4400end
4401aviobj=close(aviobj);
4402UvData=rmfield(UvData,'plotaxes');
4403%UvData.Object{1}.plotaxes=handles.axes3;
4404set(huvmat,'UserData',UvData);
4405msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4406
4407
4408%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4409% Projection Objects Menu Callbacks
4410%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4411
4412% -----------------------------------------------------------------------
4413function Menupoints_Callback(hObject, eventdata, handles)
4414%------------------------------------------------------------------------
4415data.Type='points';
4416data.ProjMode='projection';%default
4417data.ProjModeMenu={};% do not restrict ProjMode menus
4418create_object(data,handles)
4419
4420% -----------------------------------------------------------------------
4421function Menuline_Callback(hObject, eventdata, handles)
4422%------------------------------------------------------------------------
4423data.Type='line';
4424data.ProjMode='projection';%default
4425data.ProjModeMenu={};% do not restrict ProjMode menus
4426create_object(data,handles)
4427
4428%------------------------------------------------------------------------
4429function Menupolyline_Callback(hObject, eventdata, handles)
4430%------------------------------------------------------------------------
4431data.Type='polyline';
4432data.ProjMode='projection';%default
4433data.ProjModeMenu={};% do not restrict ProjMode menus
4434create_object(data,handles)
4435
4436%------------------------------------------------------------------------
4437function Menupolygon_Callback(hObject, eventdata, handles)
4438%------------------------------------------------------------------------
4439data.Type='polygon';
4440data.ProjMode='inside';%default
4441data.ProjModeMenu={};% do not restrict ProjMode menus
4442create_object(data,handles)
4443
4444%------------------------------------------------------------------------
4445function Menurectangle_Callback(hObject, eventdata, handles)
4446%------------------------------------------------------------------------
4447data.Type='rectangle';
4448data.ProjMode='inside';%default
4449data.ProjModeMenu={};% do not restrict ProjMode menus
4450create_object(data,handles)
4451
4452%------------------------------------------------------------------------
4453function Menuellipse_Callback(hObject, eventdata, handles)
4454%------------------------------------------------------------------------
4455data.Type='ellipse';
4456data.ProjMode='inside';%default
4457data.ProjModeMenu={};% do not restrict ProjMode menus
4458create_object(data,handles)
4459
4460%------------------------------------------------------------------------
4461function MenuMaskObject_Callback(hObject, eventdata, handles)
4462%------------------------------------------------------------------------
4463data.Type='polygon';
4464data.TypeMenu={'polygon'};
4465data.ProjMode='mask_inside';%default
4466data.ProjModeMenu={'mask_inside';'mask_outside'};
4467create_object(data,handles)
4468
4469%------------------------------------------------------------------------
4470function Menuplane_Callback(hObject, eventdata, handles)
4471%------------------------------------------------------------------------
4472data.Type='plane';
4473data.ProjMode='projection';%default
4474data.ProjModeMenu={};% do not restrict ProjMode menus
4475create_object(data,handles)
4476
4477%------------------------------------------------------------------------
4478function Menuvolume_Callback(hObject, eventdata, handles)
4479%------------------------------------------------------------------------
4480data.Type='volume';
4481data.ProjMode='interp';%default
4482data.ProjModeMenu={};
4483% set(handles.create,'Visible','on')
4484% set(handles.create,'Value',1)
4485% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4486create_object(data,handles)
4487
4488%------------------------------------------------------------------------
4489% --- generic function used for the creation of a projection object
4490function create_object(data,handles)
4491%------------------------------------------------------------------------
4492% desactivate geometric calibration if opened
4493hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4494if ishandle(hgeometry_calib)
4495    hhgeometry_calib=guidata(hgeometry_calib);
4496    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4497    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4498end
4499set(handles.edit_object,'Value',0); %suppress the object edit mode
4500set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4501ListObject=get(handles.ListObject,'String');
4502if ~strcmp(ListObject{end},'')
4503    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4504    set(handles.ListObject,'String',ListObject)
4505end
4506IndexObj=length(ListObject);
4507set(handles.ListObject,'Value',IndexObj)
4508UvData=get(handles.uvmat,'UserData');
4509UvData.Object{IndexObj}=[]; %create a new empty object
4510UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.axes3; % axes for plot_object
4511UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4512data.Name=data.Type;% default name=type
4513data.Coord=[0 0]; %default
4514if isfield(UvData,'Field')
4515    Field=UvData.Field;
4516    if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4517        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4518        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4519            data.RangeY=UvData.Field.Mesh;
4520        else
4521            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4522        end
4523        data.DX=UvData.Field.Mesh;
4524        data.DY=UvData.Field.Mesh;
4525    end
4526    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4527         data.Coord=[0 0 0]; %default
4528    end
4529    if isfield(Field,'CoordUnit')
4530        data.CoordUnit=Field.CoordUnit;
4531    end
4532end
4533if ishandle(handles.UVMAT_title)
4534    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4535end
4536hset_object=set_object(data,handles);% call the set_object interface
4537hhset_object=guidata(hset_object);
4538hchild=get(hset_object,'children');
4539set(hchild,'enable','on')
4540set(handles.uvmat,'UserData',UvData)
4541set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
4542CheckZoom_Callback(handles.uvmat, [], handles)
4543set(handles.delete_object,'Visible','on')
4544
4545%------------------------------------------------------------------------
4546function MenuBrowseObject_Callback(hObject, eventdata, handles)
4547%------------------------------------------------------------------------
4548%get the object file
4549[FileName, PathName, filterindex] = uigetfile( ...
4550       {'*.xml;*.mat', ' (*.xml,*.mat)';
4551       '*.xml',  '.xml files '; ...
4552        '*.mat',  '.mat matlab files '}, ...
4553        'Pick an xml Object file',get(handles.RootPath,'String'));
4554fileinput=[PathName FileName];%complete file name
4555sizf=size(fileinput);
4556if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4557
4558%read the file
4559data=xml2struct(fileinput);
4560
4561[tild,data.Name]=fileparts(FileName);% object name set as file name
4562ListObject=get(handles.ListObject,'String');
4563if ~strcmp(ListObject{end},'')
4564    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4565    set(handles.ListObject,'String',ListObject)
4566end
4567UvData=get(handles.uvmat,'UserData');
4568UvData.Object{IndexObj}=[]; %create a new empty object
4569UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4570UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4571set(handles.uvmat,'UserData',UvData)
4572set(handles.ListObject,'Value',length(ListObject))
4573hset_object=set_object(data);% call the set_object interface
4574set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4575set(handles.edit_object,'Value',0); %suppress the object edit mode
4576set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4577set(handles.delete_object,'Visible','on')
4578
4579
4580%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4581% MenuEdit Callbacks
4582%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4583%------------------------------------------------------------------------
4584function MenuEditObject_Callback(hObject, eventdata, handles)
4585%------------------------------------------------------------------------
4586set(handles.edit_object,'Value',1)
4587edit_Callback(hObject, eventdata, handles)
4588
4589% %------------------------------------------------------------------------
4590% function enable_transform(handles,state)
4591% %------------------------------------------------------------------------
4592% set(handles.transform_fct,'Visible',state)
4593% set(handles.TRANSFORM_txt,'Visible',state)   
4594% set(handles.transform_fct,'Visible',state) 
4595% set(handles.path_transform,'Visible',state)
4596% set(handles.pxcmx_txt,'Visible',state)
4597% set(handles.pxcmy_txt,'Visible',state)
4598% set(handles.pxcm,'Visible',state)
4599% set(handles.pycm,'Visible',state)
4600
4601%------------------------------------------------------------------------
4602function MenuEditVectors_Callback(hObject, eventdata, handles)
4603%------------------------------------------------------------------------
4604set(handles.edit_vect,'Visible','on')
4605set(handles.edit_vect,'Value',1)
4606edit_vect_Callback(hObject, eventdata, handles)
4607
4608%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4609% MenuTools Callbacks
4610%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4611%------------------------------------------------------------------------
4612function MenuCalib_Callback(hObject, eventdata, handles)
4613%------------------------------------------------------------------------
4614
4615UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4616
4617%suppress competing options
4618set(handles.CheckZoom,'Value',0)
4619set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4620set(handles.ListObject,'Value',1)     
4621% initiate display of GUI geometry_calib
4622data=[]; %default
4623if isfield(UvData,'CoordType')
4624    data.CoordType=UvData.CoordType;
4625end
4626pos=get(handles.uvmat,'Position');
4627pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4628pos(2)=pos(2)-0.02;
4629[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4630FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4631set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4632if isfield(UvData.OpenParam,'CalOrigin')
4633    pos_uvmat=get(handles.uvmat,'Position');
4634    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4635    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4636    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4637end
4638geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4639set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4640set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4641
4642%------------------------------------------------------------------------
4643function MenuMask_Callback(hObject, eventdata, handles)
4644%------------------------------------------------------------------------
4645UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4646ListObj=UvData.Object;
4647select=zeros(1,numel(ListObj));
4648for iobj=1:numel(ListObj);
4649    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4650        select(iobj)=1;
4651    end
4652end
4653val=find(select);
4654if isempty(val)
4655    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4656    return
4657else
4658%     set(handles.ListObject,'Max',2);%allow multiple selection
4659    set(handles.ListObject,'Value',val);
4660    flag=1;
4661    npx=size(UvData.Field.A,2);
4662    npy=size(UvData.Field.A,1);
4663    xi=0.5:npx-0.5;
4664    yi=0.5:npy-0.5;
4665    [Xi,Yi]=meshgrid(xi,yi);
4666    if isfield(UvData,'Object')
4667        for iobj=1:length(UvData.Object)
4668            ObjectData=UvData.Object{iobj};
4669            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4670                flagobj=1;
4671                testphys=0; %coordinates in pixels by default
4672                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4673                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4674                        Calib=UvData.XmlData{1}.GeometryCalib;
4675                        testphys=1;
4676                    end
4677                end
4678                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4679                    if isequal(ObjectData.Type,'polygon')
4680                        X=ObjectData.Coord(:,1);
4681                        Y=ObjectData.Coord(:,2);
4682                        if testphys
4683                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4684                        end
4685                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4686                    elseif isequal(ObjectData.Type,'ellipse')
4687                        if testphys
4688                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4689                        end
4690                        RangeX=max(ObjectData.RangeX);
4691                        RangeY=max(ObjectData.RangeY);
4692                        X2Max=RangeX*RangeX;
4693                        Y2Max=RangeY*RangeY;
4694                        distX=(Xi-ObjectData.Coord(1,1));
4695                        distY=(Yi-ObjectData.Coord(1,2));
4696                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4697                    elseif isequal(ObjectData.Type,'rectangle')
4698                        if testphys
4699                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4700                        end
4701                        distX=abs(Xi-ObjectData.Coord(1,1));
4702                        distY=abs(Yi-ObjectData.Coord(1,2));
4703                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4704                    end
4705                    if isequal(ObjectData.ProjMode,'mask_outside')
4706                        flagobj=~flagobj;
4707                    end
4708                    flag=flag & flagobj;
4709                end
4710            end
4711        end
4712    end
4713    %mask name
4714    RootPath=get(handles.RootPath,'String');
4715    SubDir=get(handles.SubDir,'String');
4716    RootFile=get(handles.RootFile,'String');
4717    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4718        RootFile(1)=[];
4719    end
4720   % filebase=fullfile(RootPath,RootFile);
4721    list=get(handles.masklevel,'String');
4722    masknumber=num2str(length(list));
4723    maskindex=get(handles.masklevel,'Value');
4724   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4725    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
4726    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4727    imflag=flipdim(imflag,1);
4728
4729    %display the mask
4730    hfigmask=figure;
4731    set(hfigmask,'Name','mask image')
4732    vec=linspace(0,1,256);%define a linear greyscale colormap
4733    map=[vec' vec' vec'];
4734    colormap(map)
4735    image(imflag);
4736    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4737    if ~strcmp(answer,'Cancel')
4738        mask_dir=fileparts(answer);
4739        if ~exist(mask_dir,'dir')
4740            [xx,msg1]=mkdir(mask_dir);
4741            if ~strcmp(msg1,'')
4742                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
4743                return
4744            end
4745        end
4746        imwrite(imflag,answer,'BitDepth',8);
4747    end
4748    set(handles.ListObject,'Value',1)
4749end
4750
4751%------------------------------------------------------------------------
4752%-- open the GUI set_grid.fig to create grid
4753function MenuGrid_Callback(hObject, eventdata, handles)
4754%------------------------------------------------------------------------
4755%suppress the other options if grid is chosen
4756set(handles.edit_vect,'Value',0)
4757edit_vect_Callback(hObject, eventdata, handles)
4758set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4759set(handles.ListObject,'Value',1)     
4760
4761%prepare display of the set_grid GUI
4762[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4763FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4764CoordList=get(handles.transform_fct,'String');
4765val=get(handles.transform_fct,'Value');
4766set_grid(FileName,CoordList{val});% call the set_object interface
4767
4768
4769%------------------------------------------------------------------------
4770function MenuRuler_Callback(hObject, eventdata, handles)
4771%------------------------------------------------------------------------
4772set(handles.CheckZoom,'Value',0)
4773CheckZoom_Callback(handles.uvmat, [], handles)
4774set(handles.MenuRuler,'checked','on')
4775UvData=get(handles.uvmat,'UserData');
4776UvData.MouseAction='ruler';
4777set(handles.uvmat,'UserData',UvData);
4778
4779%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4780% MenuRun Callbacks
4781%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4782
4783%------------------------------------------------------------------------
4784% open the GUI 'series'
4785function MenuSeries_Callback(hObject, eventdata, handles)
4786%------------------------------------------------------------------------
4787series; %first display of the GUI to fill waiting time
4788[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4789param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4790if isequal(get(handles.SubField,'Value'),1)
4791    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
4792    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
4793    if ~isequal(FileName_1,param.FileName)
4794        param.FileName_1=FileName_1;
4795    end
4796end
4797param.NomType=get(handles.NomType,'String');
4798param.NomType_1=get(handles.NomType_1,'String');
4799param.CheckFixPair=get(handles.CheckFixPair,'Value');
4800huvmat=get(handles.MenuSeries,'parent');
4801UvData=get(huvmat,'UserData');
4802if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4803    param.Time=UvData.XmlData{1}.Time;
4804end
4805if isequal(get(handles.scan_i,'Value'),1)
4806    param.incr_i=str2num(get(handles.increment_scan,'String'));
4807elseif isequal(get(handles.scan_j,'Value'),1)
4808    param.incr_j=str2num(get(handles.increment_scan,'String'));
4809end
4810param.list_fields=get(handles.Fields,'String');% list menu fields
4811param.list_fields(1)=[]; %suppress  'image' option
4812param.index_fields=get(handles.Fields,'Value');% selected string index
4813if param.index_fields>1
4814    param.index_fields=param.index_fields-1;
4815end
4816param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4817param.list_fields_1(1)=[]; %suppress  'image' option
4818param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4819if param.index_fields_1>1
4820    param.index_fields_1=param.index_fields_1-1;
4821end
4822param.menu_coord_str=get(handles.transform_fct,'String');
4823param.menu_coord_val=get(handles.transform_fct,'Value');
4824series(param); %run the series interface
4825
4826%------------------------------------------------------------------------
4827% -- open the GUI civ.fig for PIV
4828function MenuPIV_Callback(hObject, eventdata, handles)
4829%------------------------------------------------------------------------
4830 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4831 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4832civ(FileName);% interface de civ(not in the uvmat file)
4833
4834% --------------------------------------------------------------------
4835function MenuHelp_Callback(hObject, eventdata, handles)
4836% --------------------------------------------------------------------
4837path_to_uvmat=which ('uvmat');% check the path of uvmat
4838pathelp=fileparts(path_to_uvmat);
4839helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4840if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4841else
4842    addpath (fullfile(pathelp,'uvmat_doc'))
4843    web(helpfile);
4844end
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