source: trunk/src/uvmat.m @ 494

Last change on this file since 494 was 494, checked in by sommeria, 9 years ago

various bugs corrected after testing in Windows OS. Introduction
of filter tps

File size: 208.4 KB
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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%% set the position of colorbar and ancillary GUIs:
210set(hObject,'Units','Normalized')
211movegui(hObject,'center')
212UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
213UvData.OpenParam.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
214UvData.OpenParam.SetObjectSize=[0.3 0.7];
215UvData.OpenParam.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
216UvData.OpenParam.CalSize=[0.28 1];
217UvData.axes3=[];%initiate the record of plotted field
218UvData.axes2=[];
219UvData.axes1=[];
220AxeData.LimEditBox=1; %initialise AxeData
221set(handles.axes3,'UserData',AxeData)
222
223%% set functions for the mouse and keyboard
224set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
225set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
226set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
227set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
228set(hObject,'DeleteFcn',{@closefcn})%
229
230%% refresh projection plane
231set(handles.ListObject,'Value',1)% default: empty projection objectproj_field
232set(handles.ListObject,'String',{'plane'})
233set(handles.ListObject_1,'Value',1)% default: empty projection objectproj_field
234set(handles.ListObject_1,'String',{'plane'})
235set(handles.Fields,'Value',1)
236set(handles.Fields,'string',{''})
237
238%% TRANSFORM menu: builtin fcts
239menu_str={'';'phys';'px';'phys_polar'};
240UvData.OpenParam.NbBuiltin=numel(menu_str); %number of functions
241path_uvmat=fileparts(which('uvmat'));
242addpath (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)
243addpath(fullfile(path_uvmat,'transform_field'))%add the path to transform functions,
244fct_handle{1,1}=[];
245testexist=zeros(size(menu_str'));%default
246testexist(1)=1;
247for ilist=2:length(menu_str)
248    if exist(menu_str{ilist},'file')
249        fct_handle{ilist,1}=str2func(menu_str{ilist});
250        testexist(ilist)=1;
251    else
252        testexist(ilist)=0;
253    end
254end
255rmpath(fullfile(path_uvmat,'transform_field'))
256
257%% load the list of previously browsed files in menus Open and Open_1
258 dir_perso=prefdir; % path to the directory .matlab for personal data
259 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
260 if exist(profil_perso,'file')
261      h=load (profil_perso);
262      if isfield(h,'MenuFile')
263          for ifile=1:min(length(h.MenuFile),5)
264              eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
265               eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
266          end
267      end
268      if isfield(h,'transform_fct') && iscell(h.transform_fct)
269         for ilist=1:length(h.transform_fct);
270             if exist(h.transform_fct{ilist},'file')
271                [path,file]=fileparts(h.transform_fct{ilist});
272                addpath(path)
273                h_func=str2func(file);
274                rmpath(path)
275                testexist=[testexist 1];
276             else
277                file='';
278                h_func=[];
279                testexist=[testexist 0];
280             end
281             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
282             menu_str=[menu_str; {file}];
283         end
284      end
285 end
286menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
287fct_handle=fct_handle(testexist==1);
288menu_str=[menu_str;{'more...'}];
289set(handles.transform_fct,'String',menu_str)
290set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
291
292%% case of an input argument for uvmat
293testinputfield=0;
294inputfile=[];
295Field=[];
296if exist('input','var')
297    if ishandle(handles.UVMAT_title)
298        delete(handles.UVMAT_title)
299    end   
300    if isstruct(input)
301        if isfield(input,'InputFile')
302            inputfile=input.InputFile;
303        end
304        if isfield(input,'TimeIndex')
305            set(handles.i1,num2str(input.TimeIndex))
306        end
307        if isfield(input,'FieldsString')
308            UvData.FieldsString=input.FieldsString;
309        end
310    elseif ischar(input)% file name introduced as input
311           inputfile=input;
312    elseif isnumeric(input)%simple matrix introduced as input
313        sizinput=size(input);
314        if sizinput(1)<=1 || sizinput(2)<=1
315            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
316            return
317        end
318        UvData.Field.ListVarName={'A','coord_y','coord_x'};
319        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
320        UvData.Field.A=input;
321        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
322        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
323        testinputfield=1;
324    end
325else
326    %% check the path and date of modification of all functions in uvmat
327    path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
328    [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m   
329    date_str=['last modification: ' date_str];
330    if ishandle(handles.UVMAT_title)
331        set(handles.UVMAT_title,'String',...
332            [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
333            {'GNU General Public License'};...
334            {path_to_uvmat};...
335            {date_str};...
336            infomsg]);
337    end
338end
339set(handles.uvmat,'UserData',UvData)
340if ~isempty(inputfile)
341    %%%%% display the input field %%%%%%%
342    display_file_name(handles,inputfile)
343    %%%%%%%
344    testinputfield=1;
345end
346
347%% plot input field if exists
348if testinputfield
349    %delete drawn objects
350    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
351    for iobj=1:length(hother)
352        delete_object(hother(iobj))
353    end 
354    if isempty(inputfile)
355        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
356        set(handles.MenuTools,'Enable','on')
357        set(handles.OBJECT_txt,'Visible','on')
358        set(handles.edit_object,'Visible','on')
359%         set(handles.ListObject_1,'Visible','on')
360        set(handles.frame_object,'Visible','on')
361        if ~isempty(errormsg)
362            msgbox_uvmat('ERROR',errormsg)
363        end
364    end
365end
366
367set_vec_col_bar(handles) %update the display of color code for vectors
368
369%------------------------------------------------------------------------
370% --- Outputs from this function are returned to the command menuline.
371function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
372varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
373
374%------------------------------------------------------------------------
375% --- executed when closing uvmat: delete or desactivate the associated figures if exist
376function closefcn(gcbo,eventdata)
377%------------------------------------------------------------------------
378hh=findobj(allchild(0),'tag','view_field');
379if ~isempty(hh)
380    delete(hh)
381end
382hh=findobj(allchild(0),'tag','geometry_calib');
383if ~isempty(hh)
384    delete(hh)
385end
386hh=findobj(allchild(0),'tag','set_object');
387if ~isempty(hh)
388    hhh=findobj(hh,'tag','PLOT');
389    set(hhh,'enable','off')
390end
391
392%------------------------------------------------------------------------
393%------------------------------------------------------------------------
394%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
395% automatically sets the global properties when the rootfile name is introduced
396% then activate the view-field action if selected
397% it is activated either by clicking on the RootPath window or by the
398% browser
399%------------------------------------------------------------------------
400%------------------------------------------------------------------------
401% --- Executes on the menu Open/Browse...
402% search the files, recognize their type according to their name and fill the rootfile input windows
403function MenuBrowse_Callback(hObject, eventdata, handles)
404[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
405oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
406if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
407         dir_perso=prefdir;
408         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
409         if exist(profil_perso,'file')
410              h=load (profil_perso);
411             if isfield(h,'MenuFile_1')
412                  oldfile=h.MenuFile_1;
413             end
414         end
415end
416% [FileName, PathName] = uigetfile( ...
417%        {'*.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)';
418%        '*.xml',  '.xml files '; ...
419%         '*.xls',  '.xls files '; ...
420%         '*.civ',  '.civ files '; ...
421%         '*.jpg',' jpeg image files'; ...
422%         '*.png','.png image files'; ...
423%         '*.tif','.tif image files'; ...
424%         '*.avi;*.AVI','.avi movie files'; ...
425%         '*.vol','.volume images (png)'; ...
426%         '*.nc','.netcdf files'; ...
427%         '*.cdf','.netcdf files'; ...
428%         '*.cmx','.cmx text files ';...
429%         '*.fig','.fig files (matlab fig)';...
430%         '*.log','.log text files ';...
431%         '*.dat','.dat text files ';...
432%         '*.bat','.bat system command text files';...
433%         '*.*',  'All Files (*.*)'}, ...
434%         'Pick a file',oldfile);
435
436[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',oldfile);
437fileinput=[PathName FileName];%complete file name
438sizf=size(fileinput);
439if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
440
441% display the selected field and related information
442display_file_name( handles,fileinput)
443
444% -----------------------------------------------------------------------
445% --- Open again the file whose name has been recorded in MenuFile_1
446function MenuFile_1_Callback(hObject, eventdata, handles)
447%------------------------------------------------------------------------
448fileinput=get(handles.MenuFile_1,'Label');
449display_file_name( handles,fileinput)
450
451% -----------------------------------------------------------------------
452% --- Open again the file whose name has been recorded in MenuFile_2
453function MenuFile_2_Callback(hObject, eventdata, handles)
454%------------------------------------------------------------------------
455fileinput=get(handles.MenuFile_2,'Label');
456display_file_name(handles,fileinput)
457
458% -----------------------------------------------------------------------
459% --- Open again the file whose name has been recorded in MenuFile_3
460function MenuFile_3_Callback(hObject, eventdata, handles)
461%------------------------------------------------------------------------
462fileinput=get(handles.MenuFile_3,'Label');
463display_file_name(handles,fileinput)
464
465% -----------------------------------------------------------------------
466% --- Open again the file whose name has been recorded in MenuFile_4
467function MenuFile_4_Callback(hObject, eventdata, handles)
468%------------------------------------------------------------------------
469fileinput=get(handles.MenuFile_4,'Label');
470display_file_name(handles,fileinput)
471
472% -----------------------------------------------------------------------
473% --- Open again the file whose name has been recorded in MenuFile_5
474function MenuFile_5_Callback(hObject, eventdata, handles)
475%------------------------------------------------------------------------
476fileinput=get(handles.MenuFile_5,'Label');
477display_file_name(handles,fileinput)
478
479%------------------------------------------------------------------------
480% --- Executes on the menu Open/Browse_1 for the second input field,
481%     search the files, recognize their type according to their name and fill the rootfile input windows
482function MenuBrowse_1_Callback(hObject, eventdata, handles)
483%------------------------------------------------------------------------
484RootPath=get(handles.RootPath,'String');
485% [FileName, PathName, filterindex] = uigetfile( ...
486%        {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
487%        '*.xml',  '.xml files '; ...
488%         '*.xls',  '.xls files '; ...
489%         '*.civ',  '.civ files '; ...
490%         '*.jpg','.jpg image files'; ...
491%         '*.png','.png image files'; ...
492%         '*.avi;*.AVI','.avi movie files'; ...
493%         '*.nc','.netcdf files'; ...
494%         '*.cdf','.netcdf files'; ...
495%         '*.cmx','.cmx text files';...
496%         '*.cmx2','.cmx2 text files';...
497%         '*.fig','.fig files (matlab fig)';...
498%         '*.log','.log text files ';...
499%         '*.dat','.dat text files ';...
500%         '*.*',  'All Files (*.*)'}, ...
501%         'Pick a second file for comparison',RootPath);
502[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath);
503fileinput_1=[PathName FileName];%complete file name
504sizf=size(fileinput_1);
505if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
506
507% refresh the current displayed field
508set(handles.SubField,'Value',1)
509display_file_name(handles,fileinput_1,2)
510
511%update list of recent files in the menubar
512MenuFile_1=fileinput_1;
513MenuFile_2=get(handles.MenuFile_1,'Label');
514MenuFile_3=get(handles.MenuFile_2,'Label');
515MenuFile_4=get(handles.MenuFile_3,'Label');
516MenuFile_5=get(handles.MenuFile_4,'Label');
517set(handles.MenuFile_1,'Label',MenuFile_1)
518set(handles.MenuFile_2,'Label',MenuFile_2)
519set(handles.MenuFile_3,'Label',MenuFile_3)
520set(handles.MenuFile_4,'Label',MenuFile_4)
521set(handles.MenuFile_5,'Label',MenuFile_5)
522set(handles.MenuFile_1_1,'Label',MenuFile_1)
523set(handles.MenuFile_2_1,'Label',MenuFile_2)
524set(handles.MenuFile_3_1,'Label',MenuFile_3)
525set(handles.MenuFile_4_1,'Label',MenuFile_4)
526set(handles.MenuFile_5_1,'Label',MenuFile_5)
527dir_perso=prefdir;
528profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
529if exist(profil_perso,'file')
530    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
531else
532    txt=ver('MATLAB');
533    Release=txt.Release;
534    relnumb=str2double(Release(3:4));
535    if relnumb >= 14
536        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
537    else
538        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
539    end
540end
541
542% -----------------------------------------------------------------------
543% --- Open again as second field the file whose name has been recorded in MenuFile_1
544function MenuFile_1_1_Callback(hObject, eventdata, handles)
545% -----------------------------------------------------------------------
546fileinput_1=get(handles.MenuFile_1_1,'Label');
547set(handles.SubField,'Value',1)
548display_file_name(handles,fileinput_1,2)
549
550% -----------------------------------------------------------------------
551% --- Open again as second field the file whose name has been recorded in MenuFile_2
552function MenuFile_2_1_Callback(hObject, eventdata, handles)
553% -----------------------------------------------------------------------
554fileinput_1=get(handles.MenuFile_2_1,'Label');
555set(handles.SubField,'Value',1)
556display_file_name(handles,fileinput_1,2)
557
558% -----------------------------------------------------------------------
559% --- Open again as second field the file whose name has been recorded in MenuFile_3
560function MenuFile_3_1_Callback(hObject, eventdata, handles)
561% -----------------------------------------------------------------------
562fileinput_1=get(handles.MenuFile_3_1,'Label');
563set(handles.SubField,'Value',1)
564display_file_name(handles,fileinput_1,2)
565
566% -----------------------------------------------------------------------
567% --- Open again as second field the file whose name has been recorded in MenuFile_4
568function MenuFile_4_1_Callback(hObject, eventdata, handles)
569% -----------------------------------------------------------------------
570fileinput_1=get(handles.MenuFile_4_1,'Label');
571set(handles.SubField,'Value',1)
572display_file_name(handles,fileinput_1,2)
573
574% -----------------------------------------------------------------------
575% --- Open again as second field the file whose name has been recorded in MenuFile_5
576function MenuFile_5_1_Callback(hObject, eventdata, handles)
577% -----------------------------------------------------------------------
578fileinput_1=get(handles.MenuFile_5_1,'Label');
579set(handles.SubField,'Value',1)
580display_file_name(handles,fileinput_1,2)
581
582%------------------------------------------------------------------------
583% --- Called by action in RootPath edit box
584function RootPath_Callback(hObject,eventdata,handles)
585%------------------------------------------------------------------------
586% read the current input file name:
587[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
588if ~exist(fullfile(RootPath,SubDir),'dir')
589    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
590    return
591end
592% detect the file type, get the movie object if relevant, and look for the corresponding file series:
593[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
594% initiate the input file series and refresh the current field view:
595update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);
596
597%-----------------------------------------------------------------------
598% --- Called by action in RootPath_1 edit box
599function RootPath_1_Callback(hObject,eventdata,handles)
600% -----------------------------------------------------------------------
601% update_rootinfo_1(hObject,eventdata,handles)
602[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
603if ~exist(fullfile(RootPath,SubDir),'dir')
604    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
605    return
606end
607% detect the file type, get the movie object if relevant, and look for the corresponding file series:
608[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
609% initiate the input file series and refresh the current field view:
610update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
611
612%------------------------------------------------------------------------
613% --- Called by action in RootFile edit box
614function SubDir_Callback(hObject, eventdata, handles)
615%------------------------------------------------------------------------
616%refresh the menu of input fields
617Fields_Callback(hObject, eventdata, handles);
618% refresh the current field view
619run0_Callback(hObject, eventdata, handles);
620
621%------------------------------------------------------------------------
622% --- Called by action in RootFile edit box
623function RootFile_Callback(hObject, eventdata, handles)
624%------------------------------------------------------------------------
625RootPath_Callback(hObject,eventdata,handles)
626
627%-----------------------------------------------------------------------
628% --- Called by action in RootFile_1 edit box
629function RootFile_1_Callback(hObject, eventdata, handles)
630% -----------------------------------------------------------------------
631RootPath_1_Callback(hObject,eventdata,handles)
632
633%------------------------------------------------------------------------
634% --- Called by action in FileIndex edit box
635function FileIndex_Callback(hObject, eventdata, handles)
636%------------------------------------------------------------------------
637[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
638set(handles.i1,'String',num2str(i1));
639set(handles.i2,'String',num2str(i2));
640set(handles.j1,'String',num2str(j1));
641set(handles.j2,'String',num2str(j2));
642
643% refresh the current field view
644run0_Callback(hObject, eventdata, handles)
645
646%------------------------------------------------------------------------
647% --- Called by action in FileIndex_1 edit box
648function FileIndex_1_Callback(hObject, eventdata, handles)
649%------------------------------------------------------------------------
650run0_Callback(hObject, eventdata, handles)
651
652%------------------------------------------------------------------------
653% --- Called by action in NomType edit box
654function NomType_Callback(hObject, eventdata, handles)
655%------------------------------------------------------------------------
656i1=str2num(get(handles.i1,'String'));
657i2=str2num(get(handles.i2,'String'));
658j1=str2num(get(handles.j1,'String'));
659j2=str2num(get(handles.j2,'String'));
660FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
661set(handles.FileIndex,'String',FileIndex)
662% refresh the current settings and refresh the field view
663RootPath_Callback(hObject,eventdata,handles)
664
665%------------------------------------------------------------------------
666% --- Called by action in NomType edit box
667function NomType_1_Callback(hObject, eventdata, handles)
668%------------------------------------------------------------------------
669i1=str2num(get(handles.i1,'String'));
670i2=str2num(get(handles.i2,'String'));
671j1=str2num(get(handles.j1,'String'));
672j2=str2num(get(handles.j2,'String'));
673FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
674set(handles.FileIndex_1,'String',FileIndex)
675% refresh the current settings and refresh the field view
676RootPath_1_Callback(hObject,eventdata,handles)
677
678%------------------------------------------------------------------------
679% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
680function display_file_name(handles,fileinput,index)
681%------------------------------------------------------------------------
682%% look for the input file existence
683if ~exist(fileinput,'file')
684    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
685    return
686end
687
688%% set the mouse pointer to 'watch'
689set(handles.uvmat,'Pointer','watch')
690set(handles.RootPath,'BackgroundColor',[1 1 0])
691drawnow
692
693%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
694if ~exist('index','var')
695    index=1;
696end
697if index==1
698    handles_RootPath=handles.RootPath;
699    handles_SubDir=handles.SubDir;
700    handles_RootFile=handles.RootFile;
701    handles_FileIndex=handles.FileIndex;
702    handles_NomType=handles.NomType;
703    handles_FileExt=handles.FileExt;
704elseif index==2
705    handles_RootPath=handles.RootPath_1;
706    handles_SubDir=handles.SubDir_1;
707    handles_RootFile=handles.RootFile_1;
708    handles_FileIndex=handles.FileIndex_1;
709    handles_NomType=handles.NomType_1;
710    handles_FileExt=handles.FileExt_1;
711    set(handles.RootPath_1,'Visible','on')
712    set(handles.RootFile_1,'Visible','on')
713    set(handles.SubDir_1,'Visible','on');
714    set(handles.FileIndex_1,'Visible','on');
715    set(handles.FileExt_1,'Visible','on');
716    set(handles.NomType_1,'Visible','on');
717end
718
719%% detect root name, nomenclature and indices in the input file name:
720[FilePath,FileName,FileExt]=fileparts(fileinput);
721% detect the file type, get the movie object if relevant, and look for the corresponding file series:
722% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
723[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
724
725%% open the file or fill the GUI uvmat according to the detected file type
726switch FileType
727    case ''
728        msgbox_uvmat('ERROR','invalid input file type')
729    case 'txt'
730        edit(fileinput)
731    case 'figure'                           %display matlab figure
732        hfig=open(fileinput);
733        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
734        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
735        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
736    case {'xml','xls'}                % edit xml or Excel files
737        editxml(fileinput);
738    otherwise
739        set(handles_RootPath,'String',RootPath);
740        rootname=fullfile(RootPath,SubDir,RootFile);
741        set(handles_SubDir,'String',['/' SubDir]);
742        set(handles_RootFile,'String',['/' RootFile]); %display the separator
743        indices=fileinput(length(rootname)+1:end);
744        indices(end-length(FileExt)+1:end)=[]; %remove extension
745        set(handles_FileIndex,'String',indices);
746        set(handles_NomType,'String',NomType);
747        set(handles_FileExt,'String',FileExt);
748        if index==1
749            % fill file index counters if the first file series is opened
750            set(handles.i1,'String',num2str(i1));
751            set(handles.i2,'String',num2str(i2));
752            set(handles.j1,'String',num2stra(j1,NomType));
753            set(handles.j2,'String',num2stra(j2,NomType));
754        else %read the current field index if the second file series is opened
755            i1=str2num(get(handles.i1,'String'));
756            i2=str2num(get(handles.i2,'String'));
757            j1=stra2num(get(handles.j1,'String'));
758            j2=stra2num(get(handles.j2,'String'));
759        end
760       
761        % synchronise indices of the second  input file if it exists
762        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
763            Input=read_GUI(handles.InputFile);
764            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
765                Input.RootPath_1=Input.RootPath;
766            end
767            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
768                Input.SubDir_1=Input.SubDir;
769            end
770            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
771                Input.RootFile_1=Input.RootFile;
772            end
773            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
774                Input.FileExt_1=Input.FileExt;
775            end
776            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
777                Input.NomType_1=Input.NomType;
778            end
779            %updtate the indices of the second field series to correspond to the newly opened one
780            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1,i2,j1,j2);
781            if exist(FileName_1,'file')
782                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
783                set(handles.FileIndex_1,'String',FileIndex_1)
784            else
785                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
786            end
787        end
788       
789        %enable other menus
790        set(handles.MenuOpen_1,'Enable','on')
791        set(handles.MenuFile_1_1,'Enable','on')
792        set(handles.MenuFile_2_1,'Enable','on')
793        set(handles.MenuFile_3_1,'Enable','on')
794        set(handles.MenuFile_4_1,'Enable','on')
795        set(handles.MenuFile_5_1,'Enable','on')
796        set(handles.MenuExport,'Enable','on')
797        set(handles.MenuExportFigure,'Enable','on')
798        set(handles.MenuExportMovie,'Enable','on')
799        set(handles.MenuTools,'Enable','on')
800%         set(handles.OBJECT_txt,'Visible','on')
801%         set(handles.edit_object,'Visible','on')
802%          set(handles.ListObject_1,'Visible','on')
803%          set(handles.ViewObject,'Visible','on')
804%         set(handles.frame_object,'Visible','on')
805       
806        % initiate input file series and refresh the current field view:     
807        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
808
809end
810
811%% set back the mouse pointer to arrow
812set(handles.uvmat,'Pointer','arrow')
813
814
815%------------------------------------------------------------------------
816% --- Update information about a new field series (indices to scan, timing,
817%     calibration from an xml file, then refresh current plots
818function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
819%------------------------------------------------------------------------
820%% define the relevant handles depending on the index (1=first file series, 2= second file series)
821if ~exist('index','var')
822    index=1;
823end
824if index==1
825    handles_RootPath=handles.RootPath;
826    handles_Fields=handles.Fields;
827elseif index==2
828    handles_RootPath=handles.RootPath_1;
829    handles_Fields=handles.Fields_1;
830end
831
832set(handles_RootPath,'BackgroundColor',[1 1 0])
833drawnow
834set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
835UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
836UvData.NewSeries=1; %flag for run0: begin a new series
837UvData.TestInputFile=1;
838UvData.FileType{index}=FileType;
839UvData.i1_series{index}=i1_series;
840UvData.i2_series{index}=i2_series;
841UvData.j1_series{index}=j1_series;
842UvData.j2_series{index}=j2_series;
843set(handles.FixVelType,'Value',0); %desactivate fixed veltype
844if index==1
845    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
846else
847    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
848end
849FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
850FileBase=fullfile(RootPath,RootFile);
851if ~exist(FileName,'file')
852   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
853    return
854end
855% nbfield=[];%default
856% nbfield_j=[];%default
857
858%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
859XmlData.Time=[];%default
860XmlData.GeometryCalib=[];%default
861TimeUnit='';%default
862Time=[];
863testima=0; %test for image input
864imainfo=[];
865ColorType='falsecolor'; %default
866hhh=[];
867UvData.MovieObject{index}=VideoObject;
868if ~isempty(VideoObject)
869    imainfo=get(VideoObject);
870    testima=1;
871%     nbfield_j=1;
872    TimeUnit='s';
873    if isempty(j1_series); %frame index along i
874        Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
875    else
876    Time=ones(size(i1_series,1),1)*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
877    end
878    %nbfield=imainfo.NumberOfFrames;
879    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
880    ColorType='truecolor';
881elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
882    testima=1;
883    if ~isequal(SubDir,'')
884        RootFile=get(handles.RootFile,'String');
885        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
886    else
887        imainfo=imfinfo([FileBase FileIndices FileExt]);
888    end
889    ColorType=imainfo.ColorType;%='truecolor' for color images
890    if length(imainfo) >1 %case of image with multiple frames
891       % nbfield=length(imainfo);
892       % nbfield_j=1;
893    end
894end
895if isfield(imainfo,'Width') && isfield(imainfo,'Height')
896    if length(imainfo)>1
897        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
898        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
899    else
900        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
901        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
902    end
903else
904    set(handles.num_Npx,'String','');%fills nbre of pixels x box
905    set(handles.num_Npy,'String','');%fills nbre of pixels x box
906end
907set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
908
909%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
910XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
911[tild,tild,DocExt]=fileparts(XmlFileName);
912warntext='';%default warning message
913NbSlice=1;%default
914set(handles.RootPath,'BackgroundColor',[1 1 1])
915if ~isempty(XmlFileName)
916    set(handles.view_xml,'Visible','on')
917    set(handles.view_xml,'BackgroundColor',[1 1 0])
918    set(handles.view_xml,'String','view .xml')
919    drawnow
920    [XmlDataRead,warntext]=imadoc2struct(XmlFileName);
921    if ~isempty(warntext)
922        msgbox_uvmat('WARNING',warntext)
923    end
924    if isempty(XmlDataRead)
925        set(handles.view_xml,'Visible','off')
926    else
927        set(handles.view_xml,'String',['view ' DocExt])   
928        XmlData=XmlDataRead;
929        if isfield(XmlData,'TimeUnit')
930            if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
931                TimeUnit=XmlData.TimeUnit;
932            end
933        end
934        set(handles.view_xml,'BackgroundColor',[1 1 1])
935        drawnow
936        if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
937            if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
938                set (handles.nb_slice,'String','volume')
939            end
940            hgeometry_calib=findobj('tag','geometry_calib');
941            if ~isempty(hgeometry_calib)
942                GUserData=get(hgeometry_calib,'UserData');
943                if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName))
944                    answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
945                    if strcmp(answer,'Yes')
946                        geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib
947                    end
948                end
949            end
950        end
951    end
952end
953if ~(isfield(XmlData,'Time')&& ~isempty(XmlData.Time))
954    XmlData.Time=Time; %time set by video
955end
956
957%% store last index in handles.lat_i and .last_j
958nbfield=max(max(i2_series));
959if isempty(nbfield)
960    nbfield=max(max(i1_series));
961end
962nbfield_j=max(max(j2_series));
963if isempty(nbfield_j)
964    nbfield_j=max(max(j1_series));
965end
966if ~isempty(XmlData.Time)
967    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
968    if isequal(size(XmlData.Time,1),1)
969        NomType=get(handles.NomType,'String');
970        XmlData.Time=(XmlData.Time)';
971    end
972end
973last_i_cell=get(handles.last_i,'String');
974if isempty(nbfield)
975    last_i_cell{1}='';
976else
977    last_i_cell{1}=num2str(nbfield);
978end
979set(handles.last_i,'String',last_i_cell)
980last_j_cell=get(handles.last_j,'String');
981if isempty(nbfield_j)
982     last_j_cell{1}='';
983else
984     last_j_cell{1}=num2str(nbfield_j);
985end
986set(handles.last_j,'String',last_j_cell);
987
988%% store geometric calibration in UvData
989if isfield(XmlData,'GeometryCalib')
990    GeometryCalib=XmlData.GeometryCalib;
991    if isempty(GeometryCalib)
992        set(handles.pxcm,'String','')
993        set(handles.pycm,'String','')
994        set(handles.transform_fct,'Value',1); %  no transform by default
995    else
996        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
997            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
998            set(handles.pxcm,'String','var')
999            set(handles.pycm,'String','var')
1000        elseif isfield(GeometryCalib,'fx_fy')
1001            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
1002            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
1003            set(handles.pxcm,'String',num2str(pixcmx))
1004            set(handles.pycm,'String',num2str(pixcmy))
1005        end
1006        if ~get(handles.CheckFixLimits,'Value')
1007            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
1008        end
1009        if isfield(GeometryCalib,'SliceCoord')
1010           
1011           siz=size(GeometryCalib.SliceCoord);
1012           if siz(1)>1
1013               NbSlice=siz(1);
1014               set(handles.slices,'Visible','on')
1015               set(handles.slices,'Value',1)
1016           end
1017           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
1018               set(handles.nb_slice,'String','volume')
1019           else
1020               set(handles.nb_slice,'String',num2str(NbSlice))
1021           end
1022           slices_Callback([],[], handles)
1023        end           
1024    end
1025end
1026
1027%% update the data attached to the uvmat interface
1028if ~isempty(TimeUnit)
1029    set(handles.time_txt,'String',['time (' TimeUnit ')'])
1030end
1031UvData.TimeUnit=TimeUnit;
1032UvData.XmlData{index}=XmlData;
1033UvData.NewSeries=1;
1034% UvData.MovieObject=MovieObject;
1035
1036%display warning message
1037if ~isequal(warntext,'')
1038    msgbox_uvmat('WARNING',warntext);
1039end
1040
1041%% set default options in menu 'Fields'
1042if ~testima
1043    testcivx=0;
1044    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
1045        set(handles_Fields,'Value',1)
1046        set(handles_Fields,'String',{'get_field...'})
1047        UvData=rmfield(UvData,'FieldsString');
1048    else
1049        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
1050        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
1051            FieldList=calc_field;
1052            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
1053            set(handles_Fields,'Value',2) % set menu to 'velocity'
1054            col_vec=FieldList;
1055            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
1056            testcivx=1;
1057        end
1058        if ~testcivx
1059            set(handles_Fields,'Value',1) % set menu to 'get_field...
1060            set(handles_Fields,'String',{'get_field...'})
1061            col_vec={'get_field...'};
1062        end
1063        set(handles.ColorScalar,'String',col_vec)
1064    end
1065end
1066set(handles.uvmat,'UserData',UvData)
1067
1068%% set index navigation options and refresh plots
1069scan_option='i';%default
1070state_j='off'; %default
1071if index==2
1072    if get(handles.scan_j,'Value')
1073        scan_option='j'; %keep the scan option for the second file series
1074    end
1075    if strcmp(get(handles.j1,'Visible'),'on')
1076        state_j='on';
1077    end
1078end
1079[ref_i,ref_j]=find(i1_series);
1080if ~isempty(j1_series)
1081        state_j='on';
1082        if index==1
1083            if isequal(ref_i,ref_i(1)*ones(size(ref_j)))% if ref_i is always equal to its first vzlue
1084                scan_option='j'; %scan j indext               
1085            end
1086        end
1087end
1088if isequal(scan_option,'i')
1089    diff_ref_i=diff(ref_i,1);
1090    if isempty(diff_ref_i)
1091        diff_ref_i=1;
1092    end
1093    if isequal (diff_ref_i,diff_ref_i(1)*ones(size(diff_ref_i)))
1094        set(handles.increment_scan,'String',num2str(diff_ref_i(1)))
1095    end
1096     set(handles.scan_i,'Value',1)
1097     scan_i_Callback([],[], handles);
1098else
1099    diff_ref_j=diff(ref_j);
1100    if isempty(diff_ref_j)
1101        diff_ref_j=1;
1102    end
1103    if isequal (diff_ref_j,diff_ref_j(1)*ones(size(diff_ref_j)))
1104        set(handles.increment_scan,'String',num2str(diff_ref_j(1)))
1105    end
1106     set(handles.scan_j,'Value',1)
1107     scan_j_Callback([],[], handles);
1108end
1109set(handles.scan_j,'Visible',state_j)
1110set(handles.j1,'Visible',state_j)
1111set(handles.j2,'Visible',state_j)
1112set(handles.last_j,'Visible',state_j);
1113set(handles.frame_j,'Visible',state_j);
1114set(handles.j_text,'Visible',state_j);
1115if ~isempty(i2_series)||~isempty(j2_series)
1116    set(handles.CheckFixPair,'Visible','on')
1117elseif index==1
1118    set(handles.CheckFixPair,'Visible','off')
1119end
1120
1121%% view the field 
1122run0_Callback([],[], handles); %view field
1123mask_test=get(handles.CheckMask,'value');
1124if mask_test
1125    MaskData=get(handles.CheckMask,'UserData');
1126    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1127          delete(MaskData.maskhandle)    %delete old mask
1128    end
1129    CheckMask_Callback([],[],handles)
1130end
1131
1132%% update list of recent files in the menubar and save it for future opening
1133MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
1134    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
1135str_find=strcmp(FileName,MenuFile);
1136if isempty(find(str_find,1))
1137    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
1138end
1139for ifile=1:min(length(MenuFile),5)
1140    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
1141    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
1142end
1143dir_perso=prefdir;
1144profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1145if exist(profil_perso,'file')
1146    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1147else
1148    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
1149end
1150
1151
1152%------------------------------------------------------------------------
1153% --- switch file index scanning options scan_i and scan_j in an exclusive way
1154function scan_i_Callback(hObject, eventdata, handles)
1155%------------------------------------------------------------------------
1156if get(handles.scan_i,'Value')==1
1157    set(handles.scan_i,'BackgroundColor',[1 1 0])
1158    set(handles.scan_j,'Value',0)
1159else
1160    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1161    set(handles.scan_j,'Value',1)
1162end
1163scan_j_Callback(hObject, eventdata, handles)
1164
1165%------------------------------------------------------------------------
1166% --- switch file index scanning options scan_i and scan_j in an exclusive way
1167function scan_j_Callback(hObject, eventdata, handles)
1168%------------------------------------------------------------------------
1169if get(handles.scan_j,'Value')==1
1170    set(handles.scan_j,'BackgroundColor',[1 1 0])
1171    set(handles.scan_i,'Value',0)
1172    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1173%     NomType=get(handles.NomType,'String');
1174%     switch NomType
1175%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1176%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1177%     otherwise
1178%         set(handles.CheckFixPair,'Visible','off')
1179%     end
1180else
1181    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1182    set(handles.scan_i,'Value',1)
1183    set(handles.scan_i,'BackgroundColor',[1 1 0])
1184    set(handles.CheckFixPair,'Visible','off')
1185end
1186
1187%------------------------------------------------------------------------
1188function i1_Callback(hObject, eventdata, handles)
1189%------------------------------------------------------------------------
1190set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1191NomType=get(handles.NomType,'String');
1192i1=stra2num(get(handles.i1,'String'));
1193i2=stra2num(get(handles.i2,'String'));
1194j1=stra2num(get(handles.j1,'String'));
1195j2=stra2num(get(handles.j2,'String'));
1196indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1197%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1198set(handles.FileIndex,'String',indices)
1199set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1200if get(handles.SubField,'Value')==1
1201    NomType_1=get(handles.NomType_1,'String');
1202    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1203     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1204     set(handles.FileIndex_1,'String',indices)
1205     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1206end
1207
1208%------------------------------------------------------------------------
1209function i2_Callback(hObject, eventdata, handles)
1210%------------------------------------------------------------------------
1211set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1212i1_Callback(hObject, eventdata, handles)
1213
1214%------------------------------------------------------------------------
1215function j1_Callback(hObject, eventdata, handles)
1216%------------------------------------------------------------------------
1217set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1218i1_Callback(hObject, eventdata, handles)
1219
1220%------------------------------------------------------------------------
1221function j2_Callback(hObject, eventdata, handles)
1222%------------------------------------------------------------------------
1223set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1224i1_Callback(hObject, eventdata, handles)
1225
1226%------------------------------------------------------------------------
1227function slices_Callback(hObject, eventdata, handles)
1228%------------------------------------------------------------------------
1229if get(handles.slices,'Value')==1
1230    set(handles.slices,'BackgroundColor',[1 1 0])
1231    set(handles.nb_slice,'Visible','on')
1232    set(handles.z_text,'Visible','on')
1233    set(handles.z_index,'Visible','on')
1234    nb_slice_Callback(hObject, eventdata, handles)
1235else
1236    set(handles.nb_slice,'Visible','off')
1237    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1238    set(handles.z_text,'Visible','off')
1239    set(handles.z_index,'Visible','off')
1240    set(handles.masklevel,'Value',1)
1241    set(handles.masklevel,'String',{'1'})
1242end
1243
1244%------------------------------------------------------------------------
1245function nb_slice_Callback(hObject, eventdata, handles)
1246%------------------------------------------------------------------------
1247nb_slice_str=get(handles.nb_slice,'String');
1248if isequal(nb_slice_str,'volume')
1249    num=stra2num(get(handles.j1,'String'));
1250    last_j=get(handles.last_j,'String');
1251    nbslice=str2double(last_j{1});
1252else
1253    num=str2double(get(handles.i1,'String'));
1254    nbslice=str2double(get(handles.nb_slice,'String'));
1255end
1256z=mod(num-1,nbslice)+1;
1257set(handles.z_index,'String',num2str(z))
1258for ilist=1:nbslice
1259    list_index{ilist,1}=num2str(ilist);
1260end   
1261set(handles.masklevel,'String',list_index)
1262set(handles.masklevel,'Value',z)
1263
1264%------------------------------------------------------------------------
1265% --- Executes on button press in view_xml.
1266function view_xml_Callback(hObject, eventdata, handles)
1267%------------------------------------------------------------------------
1268%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1269 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1270FileBase=fullfile(RootPath,RootFile);
1271option=get(handles.view_xml,'String');
1272if isequal(option,'view .xml')
1273    FileXml=fullfile(RootPath,[SubDir '.xml']);
1274    if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir
1275        FileXml=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
1276    end
1277    heditxml=editxml(FileXml);
1278end
1279
1280%------------------------------------------------------------------------
1281% --- Executes on button press in CheckMask.
1282function CheckMask_Callback(hObject, eventdata, handles)
1283%------------------------------------------------------------------------
1284%case of view mask selection
1285if isequal(get(handles.CheckMask,'Value'),1)
1286     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1287     FileBase=fullfile(RootPath,RootFile);
1288    num_i1=stra2num(get(handles.i1,'String'));
1289    num_j1=stra2num(get(handles.j1,'String'));
1290    currentdir=pwd; 
1291    cd(RootPath);
1292    maskfiles=dir('*_*mask_*.png');%look for a mask file
1293    cd(currentdir);%come back to the working directory
1294    mdetect=0;
1295    if ~isempty(maskfiles)
1296        for ilist=1:length(maskfiles)
1297            maskname=maskfiles(ilist).name;% take the first mask file in the list
1298            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1299             [tild,Name]=fileparts(maskname);
1300            Namedouble=double(Name);
1301            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1302            ind_mask=findstr('mask',Name);
1303            i=ind_mask-1;
1304            while val(i)==0 && i>0
1305                i=i-1;
1306            end
1307            nbmask_str=str2num(Name(i+1:ind_mask-1));
1308            if ~isempty(nbmask_str)
1309                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1310            end
1311        end
1312        if isequal(min(nbslice),max(nbslice))
1313            nbslice=nbslice(1);
1314        else
1315            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1316            return
1317        end
1318        if ~isempty(nbslice) && Name(i)=='_'
1319            Mask.Base=[FileBase Name(i:ind_mask+3)];
1320            Mask.NbSlice=nbslice;
1321            num_i1=mod(num_i1-1,nbslice)+1;
1322            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1323            [RootPath,RootFile]=fileparts(Mask.Base);
1324            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1325            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1326            mdetect=exist(maskname,'file');
1327            if mdetect
1328                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1329                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1330                set(handles.CheckMask,'UserData',Mask);
1331                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1332                if nbslice > 1
1333                    set(handles.slices,'value',1)
1334                    slices_Callback(hObject, eventdata, handles)
1335                end
1336            end
1337        end
1338    end
1339    errormsg=[];%default
1340    if mdetect==0
1341        [FileName, PathName, filterindex] = uigetfile( ...
1342            {'*.png', ' (*.png)';
1343            '*.png',  '.png files '; ...
1344            '*.*', 'All Files (*.*)'}, ...
1345            'Pick a mask file *.png',FileBase);
1346        maskname=fullfile(PathName,FileName);
1347        if ~exist(maskname,'file')
1348            errormsg='no file browsed';
1349        end
1350        [RootDir,SubDir,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1351        Mask.Base=fullfile(RootDir,SubDir,RootFile);
1352        Mask.NbSlice=1;
1353        set(handles.CheckMask,'UserData',Mask);
1354        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1355    end
1356    if isempty(errormsg)
1357        errormsg=update_mask(handles,num_i1,num_j1);
1358    end
1359    if ~isempty(errormsg)
1360            set(handles.CheckMask,'Value',0)
1361            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1362     end
1363else % desactivate mask display
1364    MaskData=get(handles.CheckMask,'UserData');
1365    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1366          delete(MaskData.maskhandle)   
1367    end
1368    set(handles.CheckMask,'UserData',[])   
1369    UvData=get(handles.uvmat,'UserData');
1370    if isfield(UvData,'MaskName')
1371        UvData=rmfield(UvData,'MaskName');
1372        set(handles.uvmat,'UserData',UvData)
1373    end
1374    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1375end
1376
1377%------------------------------------------------------------------------
1378function errormsg=update_mask(handles,num_i1,num_j1)
1379%------------------------------------------------------------------------
1380errormsg=[];%default
1381MaskData=get(handles.CheckMask,'UserData');
1382if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1383    uistack(MaskData.maskhandle,'top');
1384end
1385num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1386[RootPath,RootFile]=fileparts(MaskData.Base);
1387MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1388UvData=get(handles.uvmat,'UserData');
1389%update mask image if the mask is new
1390if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1391    UvData.MaskName=MaskName; %update the recorded name on UvData
1392    set(handles.uvmat,'UserData',UvData);
1393    if ~exist(MaskName,'file')
1394        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1395            delete(MaskData.maskhandle)   
1396        end
1397    else
1398        %read mask image
1399        Mask.AName='image';
1400        Mask.A=imread(MaskName);
1401        npxy=size(Mask.A);
1402        test_error=0;
1403        if length(npxy)>2
1404            errormsg=[MaskName ' is not a grey scale image'];
1405            return
1406        elseif ~isa(Mask.A,'uint8')
1407            errormsg=[MaskName ' is not a 8 bit grey level image'];
1408            return
1409        end
1410        Mask.AX=[0.5 npxy(2)-0.5];
1411        Mask.AY=[npxy(1)-0.5 0.5 ];
1412        Mask.CoordUnit='pixel';
1413        if isequal(get(handles.slices,'Value'),1)
1414           NbSlice=str2num(get(handles.nb_slice,'String'));
1415           num_i1=str2num(get(handles.i1,'String'));
1416           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1417        end
1418        %px to phys or other transform on field
1419         menu_transform=get(handles.transform_fct,'String');
1420        choice_value=get(handles.transform_fct,'Value');
1421        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1422        transform_list=get(handles.transform_fct,'UserData');
1423        transform=transform_list{choice_value};
1424        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1425            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1426                Calib=UvData.XmlData{1}.GeometryCalib;
1427                Mask=transform(Mask,UvData.XmlData{1});
1428            end
1429        end
1430        flagmask=Mask.A < 200;
1431       
1432        %make brown color image
1433        imflag(:,:,1)=0.9*flagmask;
1434        imflag(:,:,2)=0.7*flagmask;
1435        imflag(:,:,3)=zeros(size(flagmask));
1436       
1437        %update mask image
1438        hmask=[]; %default
1439        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1440            hmask=MaskData.maskhandle;
1441        end
1442        if ~isempty(hmask)
1443            set(hmask,'CData',imflag)   
1444            set(hmask,'AlphaData',flagmask*0.6)
1445            set(hmask,'XData',Mask.AX);
1446            set(hmask,'YData',Mask.AY);
1447%             uistack(hmask,'top')
1448        else
1449            axes(handles.axes3)
1450            hold on   
1451            size(flagmask)
1452           % MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1453            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask)));
1454%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1455            set(handles.CheckMask,'UserData',MaskData)
1456        end
1457    end
1458end
1459
1460%------------------------------------------------------------------------
1461%------------------------------------------------------------------------
1462% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1463%------------------------------------------------------------------------
1464
1465%------------------------------------------------------------------------
1466% --- Executes on button press in runplus: make one step forward and call
1467% --- run0. The step forward is along the fields series 1 or 2 depending on
1468% --- the scan_i and scan_j check box (exclusive each other)
1469function runplus_Callback(hObject, eventdata, handles)
1470%------------------------------------------------------------------------
1471set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1472drawnow
1473%TODO: introduce the option: increment ='*' to move to the next available view
1474increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1475% if isnan(increment)
1476%     set(handles.increment_scan,'String','1')%default value
1477%     increment=1;
1478% end
1479errormsg=runpm(hObject,eventdata,handles,increment);
1480if ~isempty(errormsg)
1481    msgbox_uvmat('ERROR',errormsg);
1482end
1483set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1484
1485%------------------------------------------------------------------------
1486% --- Executes on button press in runmin: make one step backward and call
1487% --- run0. The step backward is along the fields series 1 or 2 depending on
1488% --- the scan_i and scan_j check box (exclusive each other)
1489function runmin_Callback(hObject, eventdata, handles)
1490%------------------------------------------------------------------------
1491set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1492drawnow
1493increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1494% if isnan(increment)
1495%     set(handles.increment_scan,'String','1')%default value
1496%     increment=1;
1497% end
1498errormsg=runpm(hObject,eventdata,handles,increment);
1499if ~isempty(errormsg)
1500    msgbox_uvmat('ERROR',errormsg);
1501end
1502set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1503
1504%------------------------------------------------------------------------
1505% -- Executes on button press in Movie: make a series of +> steps
1506function Movie_Callback(hObject, eventdata, handles)
1507%------------------------------------------------------------------------
1508set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1509drawnow
1510increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1511% if isnan(increment)
1512%     set(handles.increment_scan,'String','1')%default value
1513%     increment=1;
1514% end
1515set(handles.STOP,'Visible','on')
1516set(handles.speed,'Visible','on')
1517set(handles.speed_txt,'Visible','on')
1518set(handles.Movie,'BusyAction','queue')
1519UvData=get(handles.uvmat,'UserData');
1520
1521while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1522        errormsg=runpm(hObject,eventdata,handles,increment);
1523        if ~isempty(errormsg)
1524            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1525            return
1526        end
1527        pause(1.02-get(handles.speed,'Value'))% wait for next image
1528end
1529if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1530    UvData.aviobj=close(UvData.aviobj);
1531   set(handles.uvmat,'UserData',UvData);
1532end
1533set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1534
1535%------------------------------------------------------------------------
1536% -- Executes on button press in Movie: make a series of <- steps
1537function MovieBackward_Callback(hObject, eventdata, handles)
1538%------------------------------------------------------------------------
1539set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1540drawnow
1541increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1542set(handles.STOP,'Visible','on')
1543set(handles.speed,'Visible','on')
1544set(handles.speed_txt,'Visible','on')
1545set(handles.MovieBackward,'BusyAction','queue')
1546UvData=get(handles.uvmat,'UserData');
1547
1548while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1549        errormsg=runpm(hObject,eventdata,handles,increment);
1550        if ~isempty(errormsg)
1551            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1552            return
1553        end
1554        pause(1.02-get(handles.speed,'Value'))% wait for next image
1555end
1556if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1557    UvData.aviobj=close(UvData.aviobj);
1558   set(handles.uvmat,'UserData',UvData);
1559end
1560set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1561
1562%------------------------------------------------------------------------
1563function STOP_Callback(hObject, eventdata, handles)
1564%------------------------------------------------------------------------
1565set(handles.movie_pair,'BusyAction','Cancel')
1566set(handles.movie_pair,'value',0)
1567set(handles.Movie,'BusyAction','Cancel')
1568set(handles.MovieBackward,'BusyAction','Cancel')
1569set(handles.MenuExportMovie,'BusyAction','Cancel')
1570set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1571set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1572set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1573
1574%------------------------------------------------------------------------
1575% --- function activated by runplus and run minus
1576function errormsg=runpm(hObject,eventdata,handles,increment)
1577%------------------------------------------------------------------------
1578errormsg='';%default
1579%% check for movie pair status
1580movie_status=get(handles.movie_pair,'Value');
1581if isequal(movie_status,1)
1582    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1583end
1584
1585%% read the current input file name(s) and field indices
1586InputFile=read_GUI(handles.InputFile);
1587InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1588InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1589FileExt=InputFile.FileExt;
1590NomType=get(handles.NomType,'String');
1591i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1592i2=[];%default
1593if strcmp(get(handles.i2,'Visible'),'on')
1594    i2=str2num(get(handles.i2,'String'));
1595end
1596j1=[];
1597if strcmp(get(handles.j1,'Visible'),'on')
1598    j1=stra2num(get(handles.j1,'String'));
1599end
1600j2=j1;
1601if strcmp(get(handles.j2,'Visible'),'on')
1602    j2=stra2num(get(handles.j2,'String'));
1603end
1604sub_value= get(handles.SubField,'Value');
1605if sub_value % a second input file has been entered
1606     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1607    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);
1608%     InputFile.NomType_1=get(handles.NomType_1,'String');
1609else
1610    filename_1=[];
1611end   
1612
1613%% increment (or decrement) the field indices and update the input filename(s)
1614CheckSearch=0;
1615if isempty(increment)
1616    CheckSearch=1;% search for the next available file
1617    set(handles.CheckFixPair,'Value',0)
1618end
1619CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1620
1621% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1622if CheckFixPair
1623    if get(handles.scan_i,'Value')==1% case of scanning along index i
1624        i1=i1+increment;
1625        i2=i2+increment;
1626        if sub_value
1627            i1_1=i1_1+increment;
1628            i2_1=i2_1+increment;
1629        end
1630    else % case of scanning along index j (burst numbers)
1631        j1=j1+increment;
1632        j2=j2+increment;
1633        if sub_value
1634            j1_1=j1_1+increment;
1635            j2_1=j2_1+increment;
1636        end
1637    end
1638   
1639% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected):
1640% the list of existing indices recorded in UvData is used
1641else
1642    UvData=get(handles.uvmat,'UserData');
1643    ref_i=i1;
1644    if ~isempty(i2)
1645        ref_i=floor((i1+i2)/2);% current reference index i
1646    end
1647    ref_j=1;
1648    if ~isempty(j1)
1649        ref_j=j1;
1650        if ~isempty(j2)
1651            ref_j=floor((j1+j2)/2);% current reference index j
1652        end
1653    end
1654    if ~isempty(increment)
1655        if get(handles.scan_i,'Value')==1% case of scanning along index i
1656            ref_i=ref_i+increment;% increment the current reference index i
1657        else % case of scanning along index j (burst numbers)
1658            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1659        end
1660    else % free increment
1661        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
1662            step=1;
1663        else
1664            step=-1;
1665        end
1666        if get(handles.scan_i,'Value')==1% case of scanning along index i
1667            ref_i=ref_i+step;
1668            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
1669                ref_i=ref_i+step;
1670            end
1671        else % case of scanning along index j (burst numbers)
1672            ref_j=ref_j+step;
1673            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
1674                ref_j=ref_j+step;
1675            end
1676        end
1677    end
1678    if ref_i<0
1679        errormsg='minimum i index reached';
1680    elseif ref_j<0
1681        errormsg='minimum j index reached';
1682    elseif ref_i+1>size(UvData.i1_series{1},1)
1683        errormsg='maximum i index reached';
1684    elseif ref_j+1>size(UvData.i1_series{1},2)
1685        errormsg='maximum j index reached';
1686    end
1687    if ~isempty(errormsg)
1688        return
1689    end
1690    i1_subseries=UvData.i1_series{1}(ref_i+1,ref_j+1,:);
1691    i1_subseries=i1_subseries(i1_subseries>0);
1692    if isempty(i1_subseries)
1693        errormsg='no next file';
1694        return
1695    else
1696        i1=i1_subseries(end);
1697    end
1698    if ~isempty(UvData.i2_series{1})
1699        i2_subseries=UvData.i2_series{1}(ref_i+1,ref_j+1,:);
1700        i2_subseries=i2_subseries(i2_subseries>0);
1701        i2=i2_subseries(end);
1702    end
1703    if ~isempty(UvData.j1_series{1})
1704        j1_subseries=UvData.j1_series{1}(ref_i+1,ref_j+1,:);
1705        j1_subseries=j1_subseries(j1_subseries>0);
1706        j1=j1_subseries(end);
1707    end
1708    if ~isempty(UvData.j2_series{1})
1709        j2_subseries=UvData.j2_series{1}(ref_i+1,ref_j+1,:);
1710        j2_subseries=j2_subseries(j2_subseries>0);
1711        j2=j2_subseries(end);
1712    end 
1713    % case of a second file series
1714    if numel(UvData.i1_series)>=2
1715        i1_subseries=UvData.i1_series{2}(ref_i+1,ref_j+1,:);
1716        i1_subseries=i1_subseries(i1_subseries>0);
1717        i1_1=i1_subseries(end);
1718        if ~isempty(UvData.i2_series{2})
1719            i2_subseries=UvData.i2_series{2}(ref_i+1,ref_j+1,:);
1720            i2_subseries=i2_subseries(i2_subseries>0);
1721            i2_1=i2_subseries(end);
1722        end
1723        if ~isempty(UvData.j1_series{2})
1724            j1_subseries=UvData.j1_series{2}(ref_i+1,ref_j+1,:);
1725            j1_subseries=j1_subseries(j1_subseries>0);
1726            j1_1=j1_subseries(end);
1727        end
1728        if ~isempty(UvData.j2_series{2})
1729            j2_subseries=UvData.j2_series{2}(ref_i+1,ref_j+1,:);
1730            j2_subseries=j2_subseries(j2_subseries>0);
1731            j2_1=j2_subseries(end);
1732        end
1733    end
1734end
1735filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1736if sub_value
1737    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);
1738end
1739
1740%% refresh plots
1741errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);
1742
1743%% update the index counters if the index move is successfull
1744if isempty(errormsg)
1745    set(handles.i1,'String',num2stra(i1,NomType,1));
1746    if isequal(i2,i1)
1747        set(handles.i2,'String','');
1748    else
1749        set(handles.i2,'String',num2stra(i2,NomType,1));
1750    end
1751    set(handles.j1,'String',num2stra(j1,NomType,2));
1752    if isequal(j2,j1)
1753        set(handles.j2,'String','');
1754    else
1755        set(handles.j2,'String',num2stra(j2,NomType,2));
1756    end
1757    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1758    set(handles.FileIndex,'String',indices);
1759    if ~isempty(filename_1)
1760        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1761        set(handles.FileIndex_1,'String',indices_1);
1762    end
1763    if isequal(movie_status,1)
1764        set(handles.movie_pair,'Value',1)
1765        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1766    end
1767end
1768
1769%------------------------------------------------------------------------
1770% --- Executes on button press in movie_pair: create an alternating movie with two view
1771function movie_pair_Callback(hObject, eventdata, handles)
1772%------------------------------------------------------------------------
1773%% stop movie action if the movie_pair button is off
1774if ~get(handles.movie_pair,'value')
1775    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1776    set(handles.i2,'String','')
1777    set(handles.j2,'String','')
1778    return
1779else
1780    set(handles.movie_pair,'BusyAction','queue')
1781end
1782
1783%% initialisation
1784set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1785drawnow
1786list_fields=get(handles.Fields,'String');% list menu fields
1787index_fields=get(handles.Fields,'Value');% selected string index
1788FieldName=list_fields{index_fields}; % selected field
1789UvData=get(handles.uvmat,'UserData');
1790if isequal(FieldName,'image')
1791    test_1=0;
1792    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1793    NomType=get(handles.NomType,'String');
1794else
1795    list_fields=get(handles.Fields_1,'String');% list menu fields
1796    index_fields=get(handles.Fields_1,'Value');% selected string index
1797    FieldName=list_fields{index_fields}; % selected field
1798    if isequal(FieldName,'image')
1799        test_1=1;
1800        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1801    else
1802        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1803        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1804        set(handles.movie_pair,'Value',0)
1805        return
1806    end
1807end
1808num_i1=str2num(get(handles.i1,'String'));
1809num_j1=stra2num(get(handles.j1,'String'));
1810num_i2=str2num(get(handles.i2,'String'));
1811num_j2=stra2num(get(handles.j2,'String'));
1812if isempty(num_j2)
1813    if isempty(num_i2)   
1814        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1815        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1816         set(handles.movie_pair,'Value',0)
1817        return
1818    else
1819        num_j2=num_j1;%repeat the index i1 by default
1820    end
1821end
1822if isempty(num_i2)
1823    num_i2=num_i1;%repeat the index i1 by default
1824end
1825% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1826imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
1827if ~exist(imaname_1,'file')
1828      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1829      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1830       set(handles.movie_pair,'Value',0)
1831      return
1832end
1833
1834%% read the second image
1835Field.AName='image';
1836if test_1
1837    Field_a=UvData.Field_1;
1838else
1839    Field_a=UvData.Field;
1840end
1841Field_b.AX=Field_a.AX;
1842Field_b.AY=Field_a.AY;
1843% z index
1844nbslice=str2double(get(handles.nb_slice,'String'));
1845if ~isempty(nbslice)
1846    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1847end
1848Field_b.CoordUnit='pixel';
1849
1850%% determine the input file type
1851if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1852    FileType='movie';
1853elseif isequal(lower(Ext),'.avi')
1854    FileType='avi';
1855elseif isequal(lower(Ext),'.vol')
1856    FileType='vol';
1857else
1858   form=imformats(Ext(2:end));
1859   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1860       if isequal(NomType,'*');
1861           FileType='multimage';
1862       else
1863           FileType='image';
1864       end
1865   end
1866end
1867switch FileType
1868        case 'movie'
1869            if test_1
1870                Field_b.A=read(UvData.MovieObject{2},num_i2);
1871            else
1872                Field_b.A=read(UvData.MovieObject{1},num_i2);
1873            end
1874        case 'avi'
1875            mov=aviread(imaname_1,num_i2);
1876            Field_b.A=frame2im(mov(1));
1877        case 'vol'
1878            Field_b.A=imread(imaname_1);
1879        case 'multimage'
1880            Field_b.A=imread(imaname_1,num_i2);
1881        case 'image'
1882            Field_b.A=imread(imaname_1);
1883end
1884if get(handles.slices,'Value')
1885    Field.ZIndex=str2double(get(handles.z_index,'String'));
1886end
1887
1888%px to phys or other transform on field
1889menu_transform=get(handles.transform_fct,'String');
1890choice_value=get(handles.transform_fct,'Value');
1891transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1892transform_list=get(handles.transform_fct,'UserData');
1893transform=transform_list{choice_value};
1894if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1895    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
1896        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
1897        Field_b=transform(Field_b,UvData.XmlData{2});
1898    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
1899        Field_b=transform(Field_b,UvData.XmlData{1});
1900    end
1901end
1902
1903 % make movie until movie speed is set to 0 or STOP is activated
1904hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1905set(handles.STOP,'Visible','on')
1906set(handles.speed,'Visible','on')
1907set(handles.speed_txt,'Visible','on')
1908while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1909    % read and plot the series of images in non erase mode
1910    set(hima,'CData',Field_b.A);
1911    pause(1.02-get(handles.speed,'Value'));% wait for next image
1912    set(hima,'CData',Field_a.A);
1913    pause(1.02-get(handles.speed,'Value'));% wait for next image
1914end
1915set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1916 set(handles.movie_pair,'Value',0)
1917
1918%------------------------------------------------------------------------
1919% --- Executes on button press in run0.
1920function run0_Callback(hObject, eventdata, handles)
1921%------------------------------------------------------------------------
1922set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1923drawnow
1924[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1925filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1926filename_1=[];%default
1927if get(handles.SubField,'Value')
1928    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
1929    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
1930end
1931num_i1=stra2num(get(handles.i1,'String'));
1932num_i2=stra2num(get(handles.i2,'String'));
1933num_j1=stra2num(get(handles.j1,'String'));
1934num_j2=stra2num(get(handles.j2,'String'));
1935
1936errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
1937
1938if ~isempty(errormsg)
1939      msgbox_uvmat('ERROR',errormsg);
1940else
1941    set(handles.i1,'BackgroundColor',[1 1 1])
1942    set(handles.i2,'BackgroundColor',[1 1 1])
1943    set(handles.j1,'BackgroundColor',[1 1 1])
1944    set(handles.j2,'BackgroundColor',[1 1 1])
1945    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1946    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1947end   
1948set(handles.run0,'BackgroundColor',[1 0 0])
1949
1950
1951%------------------------------------------------------------------------
1952% --- read the input files and refresh all the plots, including projection.
1953% OUTPUT:
1954%  errormsg: error message char string  =[] by default
1955% INPUT:
1956% filename: first input file (=[] in the absence of input file)
1957% filename_1: second input file (=[] in the asbsenc of secodn input file)
1958% num_i1,num_i2,num_j1,num_j2; frame indices
1959% Field: structure describing an optional input field (then replace the input file)
1960
1961function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,Field)
1962%------------------------------------------------------------------------
1963
1964%% initialisation
1965abstime=[];
1966abstime_1=[];
1967dt=[];
1968if ~exist('Field','var')
1969    Field={};
1970end
1971UvData=get(handles.uvmat,'UserData');
1972if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1973    delete(handles.UVMAT_title)
1974end
1975
1976%% determine the main input file information for action
1977FileType=[];%default
1978if ~exist(FileName,'file')
1979    errormsg=['input file ' FileName ' does not exist'];
1980    return
1981end
1982NomType=get(handles.NomType,'String');
1983NomType_1='';
1984if strcmp(get(handles.NomType_1,'Visible'),'on')
1985    NomType_1=get(handles.NomType_1,'String');
1986end
1987% NomType=get(handles.FileIndex,'UserData');
1988%update the z position index
1989nbslice_str=get(handles.nb_slice,'String');
1990if isequal(nbslice_str,'volume')%NOT USED
1991    z_index=num_j1;
1992    set(handles.z_index,'String',num2str(z_index))
1993else
1994    nbslice=str2num(nbslice_str);
1995    z_index=mod(num_i1-1,nbslice)+1;
1996    set(handles.z_index,'String',num2str(z_index))
1997end
1998% refresh menu for save_mask if relevant
1999masknumber=get(handles.masklevel,'String');
2000if length(masknumber)>=z_index
2001    set(handles.masklevel,'Value',z_index)
2002end
2003
2004%% read the first input field if a filename has been introduced
2005ParamIn.ColorVar='';%default variable name for vector color
2006frame_index=1;%default
2007if ~isempty(FileName)
2008    FieldName='';%default
2009    VelType='';%default
2010%     FileType=UvData.FileType{1};
2011    switch UvData.FileType{1}
2012        case {'civx','civdata','netcdf'};
2013            list_fields=get(handles.Fields,'String');% list menu fields
2014  %          index_fields=get(handles.Fields,'Value');% selected string index
2015            FieldName= list_fields{get(handles.Fields,'Value')}; % selected field
2016            if ~strcmp(FieldName,'get_field...')
2017                if get(handles.FixVelType,'Value')
2018                    VelTypeList=get(handles.VelType,'String');
2019                    VelType=VelTypeList{get(handles.VelType,'Value')};
2020                end
2021            end
2022            if strcmp(FieldName,'velocity')
2023                list_code=get(handles.ColorCode,'String');% list menu fields
2024                index_code=get(handles.ColorCode,'Value');% selected string index
2025                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2026                    list_code=get(handles.ColorScalar,'String');% list menu fields
2027                    index_code=get(handles.ColorScalar,'Value');% selected string index
2028                    ParamIn.ColorVar= list_code{index_code}; % selected field
2029                end
2030            end
2031        case {'video','mmreader'}
2032            ParamIn=UvData.MovieObject{1};     
2033            if ~strcmp(NomType,'*')
2034                frame_index=num_j1;%frame index for movies or multimage
2035            else
2036                frame_index=num_i1;
2037            end
2038        case 'multimage'
2039            if ~strcmp(NomType,'*')
2040                frame_index=num_j1;%frame index for movies or multimage
2041            else
2042                frame_index=num_i1;
2043            end
2044        case 'vol' %TODO: update
2045            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2046                ParamIn.Npy=UvData.XmlData.Npy;
2047                ParamIn.Npx=UvData.XmlData.Npx;
2048            else           
2049                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2050                return
2051            end
2052    end
2053    if isstruct (ParamIn)
2054    ParamIn.FieldName=FieldName;
2055    ParamIn.VelType=VelType;
2056    ParamIn.GUIName='get_field';
2057    end
2058    [Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index);
2059    if ~isempty(errormsg)
2060        errormsg=['error in reading ' FileName ': ' errormsg];
2061        return
2062    end 
2063    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2064        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2065        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2066    end
2067    if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2068        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2069    end
2070    if isfield(ParamOut,'TimeValue')
2071        Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2072    end
2073end
2074
2075%% choose and read a second field FileName_1 if defined
2076VelType_1=[];%default
2077FieldName_1=[];
2078ParamOut_1=[];
2079frame_index_1=1;
2080if ~isempty(FileName_1)
2081    if ~exist(FileName_1,'file')
2082        errormsg=['second file ' FileName_1 ' does not exist'];
2083        return
2084    end
2085    Name=FileName_1;
2086    switch UvData.FileType{2}
2087        case {'civx','civdata','netcdf'};
2088            list_fields=get(handles.Fields_1,'String');% list menu fields
2089            FieldName_1= list_fields{get(handles.Fields_1,'Value')}; % selected field
2090            if ~strcmp(FieldName,'get_field...')
2091                if get(handles.FixVelType,'Value')
2092                    VelTypeList=get(handles.VelType_1,'String');
2093                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2094                end
2095            end
2096            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2097                list_code=get(handles.ColorCode,'String');% list menu fields
2098                index_code=get(handles.ColorCode,'Value');% selected string index
2099                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2100                    list_code=get(handles.ColorScalar,'String');% list menu fields
2101                    index_code=get(handles.ColorScalar,'Value');% selected string index
2102                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2103                end
2104            end
2105        case {'video','mmreader'}
2106            ParamIn_1=UvData.MovieObject{2};
2107                        if ~strcmp(NomType_1,'*')
2108                frame_index_1=num_j1;%frame index for movies or multimage
2109            else
2110                frame_index_1=num_i1;
2111            end 
2112         case 'multimage'
2113            if ~strcmp(NomType_1,'*')
2114                frame_index_1=num_j1;%frame index for movies or multimage
2115            else
2116                frame_index_1=num_i1;
2117            end   
2118        case 'vol' %TODO: update
2119            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2120                ParamIn_1.Npy=UvData.XmlData.Npy;
2121                ParamIn_1.Npx=UvData.XmlData.Npx;
2122            else
2123                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2124                return
2125            end
2126    end
2127    if isequal(get(handles.NomType_1,'Visible'),'on')
2128    NomType_1=get(handles.NomType_1,'String');
2129    else
2130        NomType_1=get(handles.NomType,'String');
2131    end
2132    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2133    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2134        if isfield(UvData,'FileName_1')%&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2135            test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
2136        end
2137    end
2138    if test_keepdata_1
2139        Field{2}=UvData.Field_1;% keep the stored field
2140        ParamOut_1=UvData.ParamOut_1;
2141    else
2142        if isstruct(ParamIn_1)
2143        ParamIn_1.FieldName=FieldName_1;
2144        ParamIn_1.VelType=VelType_1;
2145        ParamIn_1.GUIName='get_field_1';
2146        end
2147        [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,frame_index_1);
2148        if ~isempty(errormsg)
2149            errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg];
2150            return
2151        end
2152%         UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2153    end
2154end
2155
2156%% update uvmat interface
2157if isfield(ParamOut,'Npx')
2158    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2159    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2160elseif isfield(ParamOut_1,'Npx')
2161    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2162    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2163end
2164
2165%% update the display menu for the first velocity type (first menuline)
2166test_veltype=0;
2167% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2168if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2169    test_veltype=1;
2170    set(handles.VelType,'Visible','on')
2171    set(handles.VelType_1,'Visible','on')
2172    set(handles.FixVelType,'Visible','on')
2173    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2174    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2175    index_val=find(index_menu,1);
2176    if isempty(index_val)
2177        index_val=1;
2178    end
2179    set(handles.VelType,'Value',index_val)
2180    if ~get(handles.SubField,'value')
2181        set(handles.VelType,'String',menu)
2182        set(handles.VelType_1,'Value',1)
2183        set(handles.VelType_1,'String',[{''};menu])
2184    end
2185else
2186    set(handles.VelType,'Visible','off')
2187end
2188% display the Fields menu from the input file and pick the selected one:
2189if isstruct(ParamOut)
2190field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2191set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2192set(handles.Fields,'Value',find(field_index,1))
2193end
2194
2195%% update the display menu for the second velocity type (second menuline)
2196test_veltype_1=0;
2197if isempty(FileName_1)
2198    set(handles.Fields_1,'Value',1); %update the field menu
2199    if isstruct(ParamOut)
2200    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2201    end
2202elseif ~test_keepdata_1
2203    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2204        set(handles.VelType_1,'Visible','off')
2205    else
2206        test_veltype_1=1;
2207        set(handles.VelType_1,'Visible','on')
2208        menu=set_veltype_display(ParamOut_1.CivStage);
2209        index_menu=strcmp(ParamOut_1.VelType,menu);
2210        set(handles.VelType_1,'Value',1+find(index_menu,1))
2211        set(handles.VelType_1,'String',[{''};menu])
2212    end
2213    % update the second field menu: the same quantity
2214    if isstruct(ParamOut_1)
2215    set(handles.Fields_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2216    % display the Fields menu from the input file and pick the selected one:
2217    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2218    set(handles.Fields_1,'Value',find(field_index,1)+1) 
2219    end
2220   
2221end
2222if test_veltype||test_veltype_1
2223     set(handles.FixVelType,'Visible','on')
2224else
2225     set(handles.FixVelType,'Visible','off')
2226end
2227
2228% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2229% set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2230% set(handles.Fields,'Value',find(field_index,1))
2231   
2232%% introduce w as background image by default for a new series (only for nbdim=2)
2233if ~isfield(UvData,'NewSeries')
2234    UvData.NewSeries=1;
2235end
2236%put W as background image by default if NbDim=2:
2237if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2238        set(handles.SubField,'Value',1);
2239        set(handles.RootPath_1,'String','"')
2240        set(handles.RootFile_1,'String','"')
2241        set(handles.SubDir_1,'String','"');
2242         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2243        set(handles.FileIndex_1,'String',indices)
2244        set(handles.FileExt_1,'String','"');
2245        set(handles.Fields_1,'Visible','on');
2246        set(handles.Fields_1,'Visible','on');
2247        set(handles.RootPath_1,'Visible','on')
2248        set(handles.RootFile_1,'Visible','on')
2249        set(handles.SubDir_1,'Visible','on');
2250        set(handles.FileIndex_1,'Visible','on');
2251        set(handles.FileExt_1,'Visible','on');
2252        set(handles.Fields_1,'Visible','on');
2253        Field{1}.AName='w';
2254end           
2255
2256%% display time
2257testimedoc=0;
2258TimeUnit='';
2259if isfield(Field{1},'Time')
2260    abstime=Field{1}.Time;%time read from the netcdf input file
2261end
2262if numel(Field)==2 && isfield(Field{2},'Time')
2263    abstime_1=Field{2}.Time;%time read from the netcdf input file
2264end
2265if isfield(Field{1},'Dt')
2266    dt=Field{1}.Dt;%dt read from the netcdf input file
2267    if isfield(Field{1},'TimeUnit')
2268       TimeUnit=Field{1}.TimeUnit;
2269    end
2270elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2271    dt=Field{2}.Dt;%dt read from the netcdf input file
2272    if isfield(Field{2},'TimeUnit')
2273       TimeUnit=Field{2}.TimeUnit;
2274    end
2275end
2276% time from xml file overset previous result
2277if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2278    if isempty(num_i2)||isnan(num_i2)
2279        num_i2=num_i1;
2280    end
2281    if isempty(num_j1)||isnan(num_j1)
2282        num_j1=1;
2283    end
2284    if isempty(num_j2)||isnan(num_j2)
2285        num_j2=num_j1;
2286    end
2287    siz=size(UvData.XmlData{1}.Time);
2288    if ~isempty(num_i1)&& ~isempty(num_i2)&&siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2289        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2290        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2291        Field{1}.Dt=dt;
2292        if isfield(UvData.XmlData{1},'TimeUnit')
2293            TimeUnit=UvData.XmlData{1}.TimeUnit;
2294        end
2295    end
2296    if numel(UvData.XmlData)==2
2297        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2298        if isempty(num_i2)
2299            num_i2=num_i1;
2300        end
2301        if isempty(num_j1)
2302            num_j1=1;
2303        end
2304        if isempty(num_j2)
2305            num_j2=num_j1;
2306        end
2307        siz=size(UvData.XmlData{2}.Time);
2308        if ~isempty(num_i1) && siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2309            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
2310            Field{2}.Dt=(UvData.XmlData{2}.Time(num_i2,num_j2)-UvData.XmlData{2}.Time(num_i1,num_j1));
2311        end
2312    end
2313end
2314if ~isequal(numel(abstime),1)
2315    abstime=[];
2316end
2317if ~isequal(numel(abstime_1),1)
2318      abstime_1=[];
2319end 
2320set(handles.abs_time,'String',num2str(abstime,5))
2321set(handles.abs_time_1,'String',num2str(abstime_1,5))
2322% if testimedoc && isfield(UvData,'dt')
2323%     dt=UvData.dt;
2324% end
2325if isempty(dt)||isequal(dt,0)
2326    set(handles.Dt_txt,'String','')
2327else
2328    if  isempty(TimeUnit)
2329        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2330    else
2331        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2332    end
2333end
2334
2335
2336%% store the current open names, fields and vel types in uvmat interface
2337UvData.FileName_1=FileName_1;
2338
2339%% apply coordinate transform or other user fct
2340XmlData=[];%default
2341XmlData_1=[];%default
2342if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2343    XmlData=UvData.XmlData{1};
2344    if numel(UvData.XmlData)==2
2345        XmlData_1=UvData.XmlData{2};
2346    end
2347end
2348choice_value=get(handles.transform_fct,'Value');
2349transform_list=get(handles.transform_fct,'UserData');
2350transform=transform_list{choice_value};%selected function handles
2351% z index
2352if ~isempty(FileName)
2353    Field{1}.ZIndex=z_index;
2354end
2355if ~isempty(transform)
2356    if length(Field)>=2
2357        Field{2}.ZIndex=z_index;
2358        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2359        if isempty(Field{2})
2360            Field(2)=[];
2361        end
2362    else
2363        Field{1}=transform(Field{1},XmlData);
2364    end
2365   
2366    %% check whether tps is needed, then calculate tps coefficients if needed
2367    check_tps=0;
2368    if strcmp(UvData.FileType{1},'civdata')|| strcmp(UvData.FileType{1},'civx')
2369        switch ParamOut.FieldName
2370            case {'vort','div','strain'}
2371                check_tps=1;
2372            otherwise
2373                check_tps=0;
2374                if isfield(UvData,'Object')
2375                for iobj=1:numel(UvData.Object)
2376                    UvData.Object{iobj}
2377                    if isfield(UvData.Object{iobj},'ProjMode')&& strcmp(UvData.Object{iobj}.ProjMode,'filter')
2378                        check_tps=1;
2379                        break
2380                    end
2381                end
2382                end
2383        end
2384    end
2385    if check_tps
2386        SubDomain=1500; %default, estimated nbre of vectors in a subdomain used for tps
2387        if isfield(Field{1},'SubDomain')
2388            SubDomain=Field{1}.SubDomain;%
2389        end
2390        [Field{1}.SubRange,Field{1}.NbSites,Field{1}.Coord_tps,Field{1}.U_tps,Field{1}.V_tps,tild,U_smooth,V_smooth,W_smooth,FF] =...
2391           filter_tps([Field{1}.X(Field{1}.FF==0) Field{1}.Y(Field{1}.FF==0)],Field{1}.U(Field{1}.FF==0),Field{1}.V(Field{1}.FF==0),[],SubDomain,0);
2392        nbvar=numel(Field{1}.ListVarName);
2393        Field{1}.ListVarName=[Field{1}.ListVarName {'SubRange','NbSites','Coord_tps','U_tps','V_tps'}];
2394        Field{1}.VarDimName=[Field{1}.VarDimName {{'nb_coord','nb_bounds','nb_subdomain'},{'nb_subdomain'},...
2395            {'nb_tps','nb_coord','nb_subdomain'},{'nb_tps','nb_subdomain'},{'nb_tps','nb_subdomain'}}];
2396        Field{1}.VarAttribute{nbvar+3}.Role='coord_tps';
2397        Field{1}.VarAttribute{nbvar+4}.Role='vector_x';
2398        Field{1}.VarAttribute{nbvar+5}.Role='vector_y';
2399        if isfield(Field{1},'ListDimName')%cleaning
2400            Field{1}=rmfield(Field{1},'ListDimName');
2401        end
2402        if isfield(Field{1},'DimValue')%cleaning
2403            Field{1}=rmfield(Field{1},'DimValue');
2404        end
2405    end
2406end
2407
2408%% calculate scalar
2409if isstruct(ParamOut)&&~strcmp(ParamOut.FieldName,'get_field...')&& (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))
2410    if isfield(Field{1},'Coord_tps')
2411        Field{1}.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}];
2412    else
2413    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2414    end
2415end
2416if isstruct(ParamOut_1)&& numel(Field)==2 && ~strcmp(ParamOut_1.FieldName,'get_field...')&& ~test_keepdata_1 && (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))...
2417        &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2418    if isfield(Field{2},'Coord_tps')
2419        Field{2}.FieldList=[{ParamOut_1.FieldName} {ParamOut_1.ColorVar}];
2420    else
2421     Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2422    end
2423end
2424
2425%% combine the two input fields (e.g. substract velocity fields)
2426%Field{1}.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}];
2427if numel(Field)==2
2428   [UvData.Field,errormsg]=sub_field(Field{1},Field{2}); 
2429   UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2430   UvData.ParamOut_1=ParamOut_1;
2431else
2432   UvData.Field=Field{1};
2433end
2434if ~isempty(errormsg)
2435    errormsg=['error in uvmat/refresh_field/sub_field:' errormsg];
2436    return
2437end
2438%UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation
2439
2440%% analyse input field
2441test_x=0;
2442test_z=0;% test for unstructured z coordinate
2443[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2444if ~isempty(errormsg)
2445    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2446    return
2447end
2448[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);% analyse  the input field structure
2449if ~isempty(errormsg)
2450    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];% display error
2451    return
2452end
2453[NbDim,imax]=max(NbDim);% spatial dimension of the input field
2454if isfield(UvData.Field,'NbDim')
2455    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2456end
2457
2458%% get bounds and mesh (needed for mouse action and to open set_object)
2459if NbDim>1
2460    XName=''; %default
2461    YName='';
2462    %unstructured coordinates
2463    if ~isempty(VarType{imax}.coord_x)&&~isempty(VarType{imax}.coord_y)
2464        XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2465        YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2466        %nbvec=length(UvData.Field.(XName));%nbre of measurement points (e.g. vectors)
2467        test_x=1;%test for unstructured coordinates
2468        if ~isempty(VarType{imax}.coord_z)
2469            ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2470        else
2471            NbDim=2;
2472        end
2473        %structured coordinate
2474    elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0
2475        XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2476        if NbDim> 1 && VarType{imax}.coord(NbDim-1)>0
2477            YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2478        end
2479        % VarIndex=CellVarIndex{imax}; % list of variable indices
2480        DimIndex=VarDimIndex{CellVarIndex{imax}(1)}; %list of dim indices for the variable
2481        nbpoints_x=DimValue(DimIndex(NbDim));
2482        XMax=nbpoints_x;%default
2483        XMin=1;%default
2484    end
2485   
2486    if NbDim==3
2487        if ~test_x
2488            ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2489        end
2490        ZMax=max(UvData.Field.(ZName));
2491        ZMin=min(UvData.Field.(ZName));
2492        UvData.Field.ZMax=ZMax;
2493        UvData.Field.ZMin=ZMin;
2494        test_z=1;
2495        if isequal(ZMin,ZMax)%no z dependency
2496            NbDim=2;
2497            test_z=0;
2498        end
2499    end
2500    if ~isempty (XName)
2501        XMax=max(max(UvData.Field.(XName)));
2502        XMin=min(min(UvData.Field.(XName)));
2503        UvData.Field.NbDim=NbDim;
2504        UvData.Field.XMax=XMax;
2505        UvData.Field.XMin=XMin;
2506        if NbDim >1&& ~isempty(YName)
2507            YMax=max(max(UvData.Field.(YName)));
2508            YMin=min(min(UvData.Field.(YName)));
2509            UvData.Field.YMax=YMax;
2510            UvData.Field.YMin=YMin;
2511        end
2512        nbvec=length(UvData.Field.(XName));
2513        if test_x %unstructured coordinates
2514            if test_z
2515                UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2516                UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2517            else
2518                UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2519            end
2520        end
2521    end
2522    % case of structured coordinates
2523    if ~test_x
2524        DX=(XMax-XMin)/(nbpoints_x-1);
2525        if NbDim >1
2526            nbpoints_y=DimValue(DimIndex(NbDim-1));
2527            if isempty(YName)% if the y coordinate is not expressed, it is taken as the matrix index
2528                DY=1;
2529                UvData.Field.YMax=nbpoints_y;
2530                UvData.Field.YMin=1;
2531            else
2532                DY=(YMax-YMin)/(nbpoints_y-1);
2533            end
2534        end
2535        if NbDim==3
2536            nbpoints_z=DimValue(DimIndex(1));
2537            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2538            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2539            UvData.Field.ZMax=ZMax;
2540            UvData.Field.ZMin=ZMin;
2541        else
2542            UvData.Field.Mesh=DX;%sqrt(DX*DY);
2543        end
2544    end
2545    % adjust the mesh to a value 1, 2 , 5 *10^n
2546    ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude
2547    if UvData.Field.Mesh/ord>=5
2548        UvData.Field.Mesh=5*ord;
2549    elseif UvData.Field.Mesh/ord>=2
2550        UvData.Field.Mesh=2*ord;
2551    else
2552        UvData.Field.Mesh=ord;
2553    end
2554    % default projection plane
2555    if ~isfield(UvData,'Object')
2556        UvData.Object{1}.Type='plane';%main plotting plane
2557        UvData.Object{1}.ProjMode='projection';%main plotting plane
2558        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2559        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2560    end
2561    %% 3D case (menuvolume)
2562    if NbDim==3% && UvData.NewSeries
2563        test_set_object=1;
2564        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2565        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2566        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2567        if ~isempty(hset_object) %if set_object is detected
2568            delete(hset_object);% delete the GUI set_object if it does not fit
2569        end
2570        if test_set_object% reinitiate the GUI set_object
2571            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
2572            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2573            UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2574            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2575            UvData.Object{1}.Angle=[0 0 0];
2576            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2577            UvData.Object{1}.Name='1-PLANE';
2578            UvData.Object{1}.enable_plot=1;
2579            set_object(UvData.Object{1},handles,ZBounds);
2580            set(handles.ListObject,'Value',1);
2581            set(handles.ListObject,'String',{'1-PLANE'});
2582            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2583            edit_object_Callback([],[], handles)
2584        end
2585        %multilevel case (single menuplane in a 3D space)
2586    elseif isfield(UvData,'Z')
2587        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2588            XmlData=UvData.XmlData{1};
2589            if isfield(XmlData,'PlanePos')
2590                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2591            end
2592            if isfield(XmlData,'PlaneAngle')
2593                siz=size(XmlData.PlaneAngle);
2594                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2595                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2596            end
2597        elseif isfield(UvData,'ZIndex')
2598            UvData.Object{1}.ZObject=UvData.ZIndex;
2599        end
2600    end
2601end
2602
2603testnewseries=UvData.NewSeries;
2604UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2605set(handles.uvmat,'UserData',UvData)
2606
2607%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2608% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2609%     set(handles.num_MinA,'String','0')
2610%     set(handles.num_MaxA,'String','255')
2611% end
2612
2613%% usual 1D (x,y) plots
2614if NbDim<=1
2615    set(handles.Objects,'Visible','off')
2616    set(handles.ListObject_1_title,'Visible','off')
2617    set(handles.ListObject_1,'Visible','off')
2618    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.axes3,read_GUI(handles.uvmat));
2619    write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2620%     if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2621%         ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2622%     end
2623   
2624%% 2D or 3D fields are generally projected
2625else
2626    set(handles.Objects,'Visible','on')
2627    set(handles.ListObject_1_title,'Visible','on')
2628    set(handles.ListObject_1,'Visible','on')
2629   
2630    %% Plot the projections on the selected  projection objects
2631    % main projection object (uvmat display)
2632    list_object=get(handles.ListObject_1,'String');
2633    if isequal(list_object,{''})%refresh list of objects if the menu is empty
2634        UvData.Object={[]};
2635        set(handles.ListObject_1,'Value',1)
2636    end
2637    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2638    if IndexObj(1)> numel(UvData.Object)
2639        IndexObj(1)=1;%select the first object if the selected one does not exist
2640        set(handles.ListObject_1,'Value',1)
2641    end
2642    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2643    if isequal(IndexObj(2),IndexObj(1))
2644        IndexObj(2)=[];
2645    end
2646    plot_handles{1}=handles;
2647    if isfield(UvData,'plotaxes')%case of movies
2648        haxes(1)=UvData.plotaxes;
2649    else
2650        haxes(1)=handles.axes3;
2651    end
2652    PlotParam{1}=read_GUI(handles.uvmat);
2653    %default settings if vectors not visible
2654    if ~isfield(PlotParam{1},'Vectors')
2655        PlotParam{1}.Vectors.MaxVec=1;
2656        PlotParam{1}.Vectors.MinVec=0;
2657        PlotParam{1}.Vectors.CheckFixVecColor=1;
2658        PlotParam{1}.Vectors.ColCode1=0.33;
2659        PlotParam{1}.Vectors.ColCode2=0.66;
2660        PlotParam{1}.Vectors.ColorScalar={'ima_cor'};
2661        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2662    end
2663    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2664   
2665    %% second projection object (view_field display)
2666    if length( IndexObj)>=2
2667        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2668        if ~isempty(view_field_handle)
2669            plot_handles{2}=guidata(view_field_handle);
2670            haxes(2)=plot_handles{2}.axes3;
2671            PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2672            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2673        end
2674    end
2675   
2676    %% loop on the projection objects: one or two
2677   
2678    for imap=1:numel(IndexObj)
2679        iobj=IndexObj(imap);
2680        %      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)
2681        % %          [ObjectData,errormsg]=calc_field(UvData.Field.FieldList,UvData.Field);
2682        % %      else
2683        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2684        %      end
2685        if ~isempty(errormsg)
2686            return
2687        end
2688        if testnewseries
2689            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2690            if isfield(ObjectData,'CoordUnit')
2691                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2692                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2693            end
2694        end
2695        %use of mask (TODO: check)
2696        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2697            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2698            AX=ObjectData.AX;%x coordiantes for the scalar field
2699            AY=ObjectData.AY;%y coordinates for the scalar field
2700            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2701            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2702            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2703                nxy=size(flag_mask);
2704                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2705                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2706                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2707                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2708                %project on the positions of the scalar
2709                npxy=size(ObjectData.A);
2710                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2711                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2712                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2713                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2714                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2715                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2716            end
2717            AClass=class(ObjectData.A);
2718            ObjectData.A=flag_mask.*double(ObjectData.A);
2719            ObjectData.A=feval(AClass,ObjectData.A);
2720            ind_off=[];
2721            if isfield(ObjectData,'ListVarName')
2722                for ilist=1:length(ObjectData.ListVarName)
2723                    if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2724                        ind_off=[ind_off ilist];
2725                    end
2726                end
2727                ObjectData.ListVarName(ind_off)=[];
2728                VarDimIndex(ind_off)=[];
2729                ind_off=[];
2730                for ilist=1:length(ListDimName)
2731                    if isequal(ListDimName{ilist},'MaskX') || isequal(ListDimName{ilist},'MaskY')
2732                        ind_off=[ind_off ilist];
2733                    end
2734                end
2735                ListDimName(ind_off)=[];
2736                DimValue(ind_off)=[];
2737            end
2738        end
2739        if ~isempty(ObjectData)
2740            PlotType='none'; %default
2741            if imap==2 && isempty(view_field_handle)
2742                view_field(ObjectData)
2743            else
2744                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2745                write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2746                if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2747                    ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2748                end
2749            end
2750            if isequal(PlotType,'none')
2751                hget_field=findobj(allchild(0),'name','get_field');
2752                if isempty(hget_field)
2753                    get_field(FileName)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2754                end
2755                errormsg='The field defined by get_field cannot be plotted';
2756                return
2757            end
2758        end
2759    end
2760   
2761    %% update the mask
2762    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2763        update_mask(handles,num_i1,num_i2);
2764    end
2765   
2766    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2767    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2768    ind_skip=[];
2769    % nb_histo=1;
2770    Ustring='';
2771    Vstring='';
2772    % suppress coordinates from the histogram menu
2773    for ivar=1:numel(menu_histo)%l loop on field variables:
2774        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2775            Role=UvData.Field.VarAttribute{ivar}.Role;
2776            switch Role
2777                case {'coord_x','coord_y','coord_z','dimvar'}
2778                    ind_skip=[ind_skip ivar];
2779                case {'vector_x'}
2780                    Ustring=UvData.Field.ListVarName{ivar};
2781                    ind_skip=[ind_skip ivar];
2782                case {'vector_y'}
2783                    Vstring=UvData.Field.ListVarName{ivar};
2784                    ind_skip=[ind_skip ivar];
2785            end
2786        end
2787        DimCell=UvData.Field.VarDimName{ivar};
2788        DimName='';
2789        if ischar(DimCell)
2790            DimName=DimCell;
2791        elseif iscell(DimCell)&& numel(DimCell)==1
2792            DimName=DimCell{1};
2793        end
2794        if strcmp(DimName,menu_histo{ivar})
2795            ind_skip=[ind_skip ivar];
2796        end
2797    end
2798    menu_histo(ind_skip)=[];% remove skipped items
2799    if ~isempty(Ustring)
2800        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2801    end
2802   
2803    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2804    % display menus and plot histograms
2805    test_v=0;
2806    if ~isempty(menu_histo)
2807        set(handles.histo1_menu,'Value',1)
2808        set(handles.histo1_menu,'String',menu_histo)
2809        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2810    end
2811end
2812
2813%------------------------------------------------------------------------
2814function histo1_menu_Callback(hObject, eventdata, handles)
2815%--------------------------------------------
2816%plot first histo
2817%huvmat=get(handles.histo1_menu,'parent');
2818histo_menu=get(handles.histo1_menu,'String');
2819histo_value=get(handles.histo1_menu,'Value');
2820FieldName=histo_menu{histo_value};
2821% update_histo(handles.histo_u,handles.uvmat,FieldName)
2822%
2823% %------------------------------------------------------------------------
2824% function histo2_menu_Callback(hObject, eventdata, handles)
2825% %------------------------------------------------------------------------
2826% %plot second histo
2827% %huvmat=get(handles.histo2_menu,'parent');
2828% histo_menu=get(handles.histo2_menu,'String');
2829% histo_value=get(handles.histo2_menu,'Value');
2830% FieldName=histo_menu{histo_value};
2831% update_histo(handles.histo_v,handles.uvmat,FieldName)
2832%
2833% %------------------------------------------------------------------------
2834% %read the field .Fieldname stored in UvData and plot its histogram
2835% function update_histo(haxes,huvmat,FieldName)
2836%------------------------------------------------------------------------
2837UvData=get(handles.uvmat,'UserData');
2838Field=UvData.Field;
2839r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2840FieldName_2='';
2841if ~isempty(r)
2842    FieldName=r.var1;
2843    FieldName_2=r.var2;
2844end
2845if ~isfield(UvData.Field,FieldName)
2846    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2847    return
2848end
2849FieldHisto=Field.(FieldName);
2850if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2851    indsel=find(Field.FF==0);%find values marked as false
2852    if ~isempty(indsel)
2853        FieldHisto=FieldHisto(indsel);
2854        if ~isempty(FieldName_2)
2855            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2856        end
2857    end
2858end
2859if isempty(Field)
2860    msgbox_uvmat('ERROR',['empty field ' FieldName])
2861else
2862    nxy=size(FieldHisto);
2863    Amin=double(min(min(min(FieldHisto))));%min of field value
2864    Amax=double(max(max(max(FieldHisto))));%max of field value
2865    if isequal(Amin,Amax)
2866        cla(handles.histo_u)
2867    else
2868        Histo.ListVarName={FieldName,'histo'};
2869        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2870            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2871        else
2872            if numel(nxy)==2
2873                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2874            else
2875                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2876            end
2877        end
2878        %unit
2879        units=[]; %default
2880        for ivar=1:numel(Field.ListVarName)
2881            if strcmp(Field.ListVarName{ivar},FieldName)
2882                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2883                    units=Field.VarAttribute{ivar}.units;
2884                    break
2885                end
2886            end
2887        end
2888        if ~isempty(units)
2889            Histo.VarAttribute{1}.units=units;
2890        end
2891        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2892        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2893            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2894            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2895        else
2896            for col=1:size(FieldHisto,3)
2897                B=FieldHisto(:,:,col);
2898                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2899                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2900            end
2901        end
2902        plot_field(Histo,handles.histo_u);
2903        hlegend=legend;
2904        if isempty(FieldName_2)
2905        set(hlegend,'String',FieldName)
2906        else
2907            set(hlegend,'String',{FieldName;FieldName_2})
2908        end
2909%         hh=get(handles.histo_u,'children');
2910%         get(hh(1))
2911%         get(hh(2))
2912    end
2913end
2914
2915%-------------------------------------------------------------------
2916% --- translate coordinate to matrix index
2917%-------------------------------------------------------------------
2918function [indx,indy]=pos2ind(x0,rangx0,nxy)
2919indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2920indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2921
2922
2923%-------------------------------------------------------------------
2924% --- Executes on button press in 'CheckZoom'.
2925%-------------------------------------------------------------------
2926function CheckZoom_Callback(hObject, eventdata, handles)
2927
2928if (get(handles.CheckZoom,'Value') == 1);
2929    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2930    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2931    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2932else
2933    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2934end
2935
2936%-------------------------------------------------------------------
2937% --- Executes on button press in 'CheckFixLimits'.
2938%-------------------------------------------------------------------
2939function CheckFixLimits_Callback(hObject, eventdata, handles)
2940test=get(handles.CheckFixLimits,'Value');
2941if test
2942    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2943else
2944    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2945    update_plot(handles);
2946end
2947
2948%-------------------------------------------------------------------
2949% --- Executes on button press in CheckFixAspectRatio.
2950function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2951%-------------------------------------------------------------------
2952if get(handles.CheckFixAspectRatio,'Value')
2953    set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
2954    update_plot(handles);
2955else
2956    set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
2957    update_plot(handles);
2958end
2959
2960%-------------------------------------------------------------------
2961function num_AspectRatio_Callback(hObject, eventdata, handles)
2962%-------------------------------------------------------------------
2963set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2964set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2965update_plot(handles);
2966%-------------------------------------------------------------------
2967
2968%-------------------------------------------------------------------
2969
2970
2971
2972%-------------------------------------------------------------------
2973%----Executes on button press in 'record': records the current flags of manual correction.
2974%-------------------------------------------------------------------
2975function record_Callback(hObject, eventdata, handles)
2976% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2977[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2978FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2979%FileName=read_file_boxes(handles);
2980[erread,message]=fileattrib(FileName);
2981if ~isempty(message) && ~isequal(message.UserWrite,1)
2982     msgbox_uvmat('ERROR',['no writting access to ' FileName])
2983     return
2984end
2985test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2986test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2987if ~test_civ2 && ~test_civ1
2988    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2989end
2990if test_civ2
2991    nbname='nb_vectors2';
2992   flagname='vec2_FixFlag';
2993   attrname='fix2';
2994end
2995if test_civ1
2996    nbname='nb_vectors';
2997   flagname='vec_FixFlag';
2998   attrname='fix';
2999end
3000%write fix flags in the netcdf file
3001UvData=get(handles.uvmat,'UserData');
3002hhh=which('netcdf.open');% look for built-in matlab netcdf library
3003if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
3004    nc=netcdf.open(FileName,'NC_WRITE');
3005    netcdf.reDef(nc);
3006    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
3007    dimid = netcdf.inqDimID(nc,nbname);
3008    try
3009        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
3010    catch
3011        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
3012    end
3013    netcdf.endDef(nc);
3014    netcdf.putVar(nc,varid,UvData.axes3.FF);
3015    netcdf.close(nc); 
3016else %old netcdf library
3017    netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
3018end
3019
3020%-------------------------------------------------------------------
3021%----Correct the netcdf file, using toolbox (old versions of Matlab).
3022%-------------------------------------------------------------------
3023function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
3024nc=netcdf(FileName,'write'); %open netcdf file
3025result=redef(nc);
3026eval(['nc.' attrname '=1;']);
3027theDim=nc(nbname) ;% get the number of velocity vectors
3028nb_vectors=size(theDim);
3029var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
3030var_FixFlag(1:nb_vectors)=AxeData.FF;%
3031fin=close(nc);
3032
3033%-------------------------------------------------------------------
3034% --- Executes on button press in SubField
3035function SubField_Callback(hObject, eventdata, handles)
3036%-------------------------------------------------------------------
3037UvData=get(handles.uvmat,'UserData');
3038if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
3039    set(handles.RootPath_1,'String','')
3040    set(handles.RootFile_1,'String','')
3041    set(handles.SubDir_1,'String','');
3042    set(handles.FileIndex_1,'String','');
3043    set(handles.FileExt_1,'String','');
3044    set(handles.RootPath_1,'Visible','off')
3045    set(handles.RootFile_1,'Visible','off')
3046    set(handles.SubDir_1,'Visible','off');
3047    set(handles.NomType_1,'Visible','off');
3048    set(handles.abs_time_1,'Visible','off')
3049    set(handles.FileIndex_1,'Visible','off');
3050    set(handles.FileExt_1,'Visible','off');
3051    set(handles.Fields_1,'Value',1);%set to blank state
3052    set(handles.VelType_1,'Value',1);%set to blank state
3053    set(handles.num_Opacity,'String','')% desactivate opacity setting
3054    if ~strcmp(get(handles.VelType,'Visible'),'on')
3055        set(handles.VelType_1,'Visible','off')
3056    end
3057    if isfield(UvData,'XmlData_1')
3058        UvData=rmfield(UvData,'XmlData_1');
3059    end
3060    set(handles.uvmat,'UserData',UvData);
3061    run0_Callback(hObject, eventdata, handles); %run
3062else
3063    MenuBrowse_1_Callback(hObject, eventdata, handles)
3064end
3065
3066%------------------------------------------------------------------------
3067% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3068
3069function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3070%------------------------------------------------------------------------
3071InputFile=read_GUI(handles.InputFile);
3072RootPath=InputFile.RootPath;
3073SubDir=regexprep(InputFile.SubDir,'/|\','');
3074RootFile=regexprep(InputFile.RootFile,'/|\','');
3075FileIndices=InputFile.FileIndex;
3076FileExt=InputFile.FileExt;
3077
3078
3079%------------------------------------------------------------------------
3080% ---- read the data displayed for the second input rootfile windows
3081function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3082%------------------------------------------------------------------------
3083RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3084if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3085    RootPath_1=get(handles.RootPath,'String');
3086end;
3087SubDir_1=get(handles.SubDir_1,'String');
3088if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3089    SubDir_1=get(handles.SubDir,'String');
3090end
3091SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3092RootFile_1=get(handles.RootFile_1,'String');
3093if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3094    RootFile_1=get(handles.RootFile,'String');
3095end
3096RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3097FileIndex_1=get(handles.FileIndex_1,'String');
3098if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3099    FileIndex_1=get(handles.FileIndex,'String');
3100end
3101FileExt_1=get(handles.FileExt_1,'String');
3102if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3103    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3104end
3105NomType_1=get(handles.NomType_1,'String');
3106if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3107    NomType_1=get(handles.NomType,'String');%read FileExt by default
3108end
3109%------------------------------------------------------------------------
3110% --- Executes on menu selection Fields
3111function Fields_Callback(hObject, eventdata, handles)
3112%------------------------------------------------------------------------
3113list_fields=get(handles.Fields,'String');% list menu fields
3114index_fields=get(handles.Fields,'Value');% selected string index
3115field= list_fields{index_fields(1)}; % selected string
3116if isequal(field,'get_field...')
3117    set(handles.FixVelType,'visible','off')
3118    set(handles.VelType,'visible','off')
3119    set(handles.VelType_1,'visible','off')
3120    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3121    FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3122    %FileName=read_file_boxes(handles);
3123    hget_field=findobj(allchild(0),'name','get_field');
3124    if ~isempty(hget_field)
3125        delete(hget_field)
3126    end
3127    hget_field=get_field(FileName);
3128    set(hget_field,'Name','get_field')
3129    hhget_field=guidata(hget_field);
3130    set(hhget_field.list_fig,'Value',1)
3131    set(hhget_field.list_fig,'String',{'uvmat'})
3132    set(handles.transform_fct,'Value',1)% no transform by default
3133    set(handles.path_transform,'String','')
3134    return %no action
3135end
3136list_fields=get(handles.Fields_1,'String');% list menu fields
3137index_fields=get(handles.Fields_1,'Value');% selected string index
3138field_1= list_fields{index_fields(1)}; % selected string
3139UvData=get(handles.uvmat,'UserData');
3140
3141%read the rootfile input display
3142[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3143FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3144[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3145if isequal(field,'image')
3146    if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3147        imagename=UvData.Field.Civ2_ImageA;
3148    elseif isfield(UvData.Field,'Civ1_ImageA')%
3149        imagename=UvData.Field.Civ1_ImageA;
3150    else
3151        SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3152        imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3153    end
3154    if ~exist(imagename,'file')
3155        [FileName,PathName] = uigetfile( ...
3156            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3157            '*.jpg',' jpeg image files'; ...
3158            '*.png','.png image files'; ...
3159            '*.tif','.tif image files'; ...
3160            '*.avi;*.AVI','.avi movie files'; ...
3161            '*.vol','.volume images (png)'; ...
3162            '*.*',  'All Files (*.*)'}, ...
3163            'Pick an image',imagename);   
3164        imagename=[PathName FileName];
3165    end
3166     % display the selected field and related information
3167    display_file_name(handles,imagename)%display the image
3168    return
3169else
3170    ext=get(handles.FileExt,'String');
3171    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3172        [FileName,PathName] = uigetfile( ...
3173            {'*.nc', ' (*.nc)';
3174            '*.nc',' netcdf files'; ...
3175            '*.*',  'All Files (*.*)'}, ...
3176            'Pick a netcdf file',FileBase);
3177        FullFileName=[PathName FileName];
3178        % display the selected field and related information
3179        display_file_name( handles,FullFileName)
3180        return
3181    end
3182end
3183indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3184set(handles.FileIndex,'String',indices)
3185% set(handles.NomType,'String',NomType)
3186
3187%common to Fields_1_Callback
3188if isequal(field,'image')||isequal(field_1,'image')
3189    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3190    set(handles.TitleNpy,'Visible','on')
3191    set(handles.num_Npx,'Visible','on')
3192    set(handles.num_Npy,'Visible','on')
3193else
3194    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3195    set(handles.TitleNpy,'Visible','off')
3196    set(handles.num_Npx,'Visible','off')
3197    set(handles.num_Npy,'Visible','off')
3198end
3199if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3200    run0_Callback(hObject, eventdata, handles)
3201end
3202
3203%---------------------------------------------------
3204% --- Executes on menu selection Fields
3205function Fields_1_Callback(hObject, eventdata, handles)
3206%-------------------------------------------------
3207%% read input data
3208check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3209UvData=get(handles.uvmat,'UserData');
3210if check_new && isfield(UvData,'XmlData')
3211    UvData.XmlData{2}=UvData.XmlData{1};
3212end
3213if isfield(UvData,'Field_1')
3214    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3215end
3216UvData.FileName_1='';% desactivate the use of a constant second file
3217list_fields=get(handles.Fields,'String');% list menu fields
3218field= list_fields{get(handles.Fields,'Value')}; % selected string
3219list_fields=get(handles.Fields_1,'String');% list menu fields
3220field_1= list_fields{get(handles.Fields_1,'Value')}; % selected string for the second field
3221if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3222    set(handles.SubField,'Value',0)
3223    SubField_Callback(hObject, eventdata, handles)
3224    return
3225else
3226    set(handles.SubField,'Value',1)%state that a second field is now entered
3227end
3228
3229%% read the rootfile input display
3230[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3231FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3232[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3233% set(handles.FileIndex_1,'Visible','on')
3234% set(handles.FileExt_1,'Visible','on')
3235switch field_1
3236    case 'get_field...'
3237        set_veltype_display(0) % no veltype display
3238        hget_field=findobj(allchild(0),'name','get_field_1');
3239        if ~isempty(hget_field)
3240            delete(hget_field)
3241        end
3242        hget_field=get_field(FileName_1);
3243        set(hget_field,'name','get_field_1')
3244        hhget_field=guidata(hget_field);
3245        set(hhget_field.list_fig,'Value',1)
3246        set(hhget_field.list_fig,'String',{'uvmat'})
3247        set(handles.transform_fct,'Value',1)% no transform by default
3248        set(handles.path_transform,'String','')
3249        if check_new
3250            UvData.FileType{2}=UvData.FileType{1};
3251            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3252%             set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3253              set(handles.uvmat,'UserData',UvData)
3254        end
3255    case 'image'
3256        % get the image name corresponding to the current netcdf name (no unique correspondance)
3257        if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3258            imagename=UvData.Field.Civ2_ImageA;
3259        elseif isfield(UvData.Field,'Civ1_ImageA')%
3260            imagename=UvData.Field.Civ1_ImageA;
3261        else
3262            SubDirBase=regexprep(SubDir_1,'\..*','');%take the root part of SubDir, before the first dot '.'
3263            imagename=fullfile_uvmat(RootPath_1,SubDirBase,RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3264        end
3265        if ~exist(imagename,'file') % browse for images if it is not found
3266            [FileName,PathName] = uigetfile( ...
3267                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3268                '*.jpg',' jpeg image files'; ...
3269                '*.png','.png image files'; ...
3270                '*.tif','.tif image files'; ...
3271                '*.avi;*.AVI','.avi movie files'; ...
3272                '*.vol','.volume images (png)'; ...
3273                '*.*',  'All Files (*.*)'}, ...
3274                'Pick an image',imagename);
3275            imagename=[PathName FileName];
3276        end
3277        if ~ischar(imagename)% quit if the browser has  been closed
3278            set(handles.SubField,'Value',0)
3279        else %valid browser input:  display the selected image
3280            set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3281            set(handles.TitleNpy,'Visible','on')
3282            set(handles.num_Npx,'Visible','on')
3283            set(handles.num_Npy,'Visible','on')
3284            display_file_name(handles,imagename,2)%display the imag
3285        end
3286    otherwise
3287        if check_new
3288            UvData.FileType{2}=UvData.FileType{1};
3289            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3290            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3291        end
3292        if ~isequal(field,'image')
3293            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3294            set(handles.TitleNpy,'Visible','off')
3295            set(handles.num_Npx,'Visible','off')
3296            set(handles.num_Npy,'Visible','off')
3297        end
3298        set(handles.uvmat,'UserData',UvData)
3299        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3300            run0_Callback(hObject, eventdata, handles)
3301        end
3302end
3303
3304%------------------------------------------------------------------------
3305% --- set the visibility of relevant velocity type menus:
3306function menu=set_veltype_display(Civ,FileType)
3307%------------------------------------------------------------------------
3308if ~exist('FileType','var')
3309    FileType='civx';
3310end
3311switch FileType
3312    case 'civx'
3313        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3314        if isequal(Civ,0)
3315            imax=0;
3316        elseif isequal(Civ,1) || isequal(Civ,2)
3317            imax=1;
3318        elseif isequal(Civ,3)
3319            imax=3;
3320        elseif isequal(Civ,4) || isequal(Civ,5)
3321            imax=4;
3322        elseif isequal(Civ,6) %patch2
3323            imax=6;
3324        end
3325    case 'civdata'
3326        menu={'civ1';'filter1';'civ2';'filter2'};
3327        if isequal(Civ,0)
3328            imax=0;
3329        elseif isequal(Civ,1) || isequal(Civ,2)
3330            imax=1;
3331        elseif isequal(Civ,3)
3332            imax=2;
3333        elseif isequal(Civ,4) || isequal(Civ,5)
3334            imax=3;
3335        elseif isequal(Civ,6) %patch2
3336            imax=4;
3337        end
3338end
3339menu=menu(1:imax);
3340
3341%------------------------------------------------------------------------
3342% --- Executes on button press in FixVelType.
3343function FixVelType_Callback(hObject, eventdata, handles)
3344%------------------------------------------------------------------------
3345% refresh the current plot if the fixed  veltype is unselected
3346if ~get(handles.FixVelType,'Value')
3347    run0_Callback(hObject, eventdata, handles)
3348end
3349
3350%------------------------------------------------------------------------
3351% --- Executes on button press in VelType.
3352function VelType_Callback(hObject, eventdata, handles)
3353%------------------------------------------------------------------------
3354set(handles.FixVelType,'Value',1)
3355run0_Callback(hObject, eventdata, handles)
3356
3357%------------------------------------------------------------------------
3358% --- Executes on button press in VelType_1.
3359function VelType_1_Callback(hObject, eventdata, handles)
3360%------------------------------------------------------------------------
3361set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3362UvData=get(handles.uvmat,'UserData');
3363%refresh field with a second FileName=first file name
3364set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3365drawnow   
3366InputFile=read_GUI(handles.InputFile);
3367[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3368FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3369
3370if isempty(InputFile.VelType_1)
3371        FileName_1='';% we plot the current field without the second field
3372        set(handles.SubField,'Value',0)
3373        SubField_Callback(hObject, eventdata, handles)
3374elseif get(handles.SubField,'Value')% if subfield is already 'on'
3375      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3376     FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3377else
3378     FileName_1=FileName;% we compare two fields in the same file by default
3379     UvData.FileType{2}=UvData.FileType{1};
3380     set(handles.SubField,'Value',1)
3381end
3382if isfield(UvData,'Field_1')
3383    UvData=rmfield(UvData,'Field_1');% removes the stored second field if it exists
3384end
3385UvData.FileName_1='';% desactivate the use of a constant second file
3386set(handles.uvmat,'UserData',UvData)
3387num_i1=stra2num(get(handles.i1,'String'));
3388num_i2=stra2num(get(handles.i2,'String'));
3389num_j1=stra2num(get(handles.j1,'String'));
3390num_j2=stra2num(get(handles.j2,'String'));
3391
3392errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2);
3393
3394if ~isempty(errormsg)
3395    msgbox_uvmat('ERROR',errormsg);
3396else
3397    set(handles.i1,'BackgroundColor',[1 1 1])
3398    set(handles.i2,'BackgroundColor',[1 1 1])
3399    set(handles.j1,'BackgroundColor',[1 1 1])
3400    set(handles.j2,'BackgroundColor',[1 1 1])
3401    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3402    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3403end
3404set(handles.run0,'BackgroundColor',[1 0 0])
3405
3406%-----------------------------------------------
3407% --- reset civ buttons
3408function reset_vel_type(handles_civ0,handle1)
3409for ibutton=1:length(handles_civ0)
3410    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3411    set(handles_civ0(ibutton),'Value',0)
3412end
3413if exist('handle1','var')%handles of selected button
3414        set(handle1,'BackgroundColor',[1 1 0]) 
3415end
3416
3417%-------------------------------------------------------
3418% --- Executes on button press in MENUVOLUME.
3419%-------------------------------------------------------
3420function VOLUME_Callback(hObject, eventdata, handles)
3421%errordlg('command VOL not implemented yet')
3422if ishandle(handles.UVMAT_title)
3423    delete(handles.UVMAT_title)
3424end
3425UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3426if isequal(get(handles.VOLUME,'Value'),1)
3427    set(handles.CheckZoom,'Value',0)
3428    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3429    set(handles.edit_vect,'Value',0)
3430    edit_vect_Callback(hObject, eventdata, handles)
3431    set(handles.edit_object,'Value',0)
3432    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3433%     set(handles.cal,'Value',0)
3434%     set(handles.cal,'BackgroundColor',[0 1 0])
3435    set(handles.edit_vect,'Value',0)
3436    edit_vect_Callback(hObject, eventdata, handles)
3437    %initiate set_object GUI
3438    data.Name='VOLUME';
3439    if isfield(UvData,'CoordType')
3440        data.CoordType=UvData.CoordType;
3441    end
3442    if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh)
3443        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3444        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3445        data.DX=UvData.Field.Mesh;
3446        data.DY=UvData.Field.Mesh;
3447    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3448        np=size(UvData.Field.A);
3449        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3450        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3451        data.RangeY=max(meshx,meshy);
3452        data.RangeX=max(meshx,meshy);
3453        data.DX=max(meshx,meshy);
3454    end
3455    data.ParentButton=handles.VOLUME;
3456    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3457    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3458                                                      % associate the set_object interface handle to the plotting axes
3459    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3460    pos_uvmat=get(handles.uvmat,'Position');
3461    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3462    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3463    set(hset_object,'Position',pos_set_object)
3464    end
3465    UvData.MouseAction='create_object';
3466else
3467    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3468    UvData.MouseAction='none';
3469end
3470set(handles.uvmat,'UserData',UvData)
3471
3472%-------------------------------------------------------
3473function edit_vect_Callback(hObject, eventdata, handles)
3474%-------------------------------------------------------
3475%
3476% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3477if isequal(get(handles.edit_vect,'Value'),1)
3478    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3479    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3480    if ~test_civ2 && ~test_civ1
3481        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3482    end
3483    set(handles.record,'Visible','on')
3484    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3485    set(handles.edit_object,'Value',0)
3486    set(handles.CheckZoom,'Value',0)
3487    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3488%     set(handles.create,'Value',0)
3489%     set(handles.create,'BackgroundColor',[0 1 0])
3490    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3491    set(gcf,'Pointer','arrow')
3492%     UvData.MouseAction='edit_vect';
3493else
3494    set(handles.record,'Visible','off')
3495    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3496%     UvData.MouseAction='none';
3497end
3498% set(handles.uvmat,'UserData',UvData)
3499
3500%----------------------------------------------
3501function save_mask_Callback(hObject, eventdata, handles)
3502%-----------------------------------------------------------------------
3503UvData=get(handles.uvmat,'UserData');
3504
3505flag=1;
3506npx=size(UvData.Field.A,2);
3507npy=size(UvData.Field.A,1);
3508xi=0.5:npx-0.5;
3509yi=0.5:npy-0.5;
3510[Xi,Yi]=meshgrid(xi,yi);
3511if isfield(UvData,'Object')
3512    for iobj=1:length(UvData.Object)
3513        ObjectData=UvData.Object{iobj};
3514        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3515            flagobj=1;
3516            testphys=0; %coordinates in pixels by default
3517            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3518                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3519                    Calib=UvData.XmlData{1}.GeometryCalib;
3520                    testphys=1;
3521                end
3522            end
3523            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3524                if isequal(ObjectData.Type,'polygon')
3525                    X=ObjectData.Coord(:,1);
3526                    Y=ObjectData.Coord(:,2);
3527                    if testphys
3528                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3529                    end
3530                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3531                elseif isequal(ObjectData.Type,'ellipse')
3532                    if testphys
3533                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3534                    end
3535                    RangeX=max(ObjectData.RangeX);
3536                    RangeY=max(ObjectData.RangeY);
3537                    X2Max=RangeX*RangeX;
3538                    Y2Max=RangeY*RangeY;
3539                    distX=(Xi-ObjectData.Coord(1,1));
3540                    distY=(Yi-ObjectData.Coord(1,2));
3541                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3542                elseif isequal(ObjectData.Type,'rectangle')
3543                    if testphys
3544                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3545                    end
3546                    distX=abs(Xi-ObjectData.Coord(1,1));
3547                    distY=abs(Yi-ObjectData.Coord(1,2));
3548                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3549                end
3550                if isequal(ObjectData.ProjMode,'mask_outside')
3551                    flagobj=~flagobj;
3552                end
3553                flag=flag & flagobj;
3554            end
3555        end
3556    end
3557end
3558% flag=~flag;
3559%mask name
3560RootPath=get(handles.RootPath,'String');
3561RootFile=get(handles.RootFile,'String');
3562RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3563filebase=fullfile(RootPath,RootFile);
3564list=get(handles.masklevel,'String');
3565masknumber=num2str(length(list));
3566maskindex=get(handles.masklevel,'Value');
3567mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3568%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3569imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3570imflag=flipdim(imflag,1);
3571% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3572msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3573imwrite(imflag,mask_name,'BitDepth',8);
3574
3575%display the mask
3576figure;
3577vec=linspace(0,1,256);%define a linear greyscale colormap
3578map=[vec' vec' vec'];
3579colormap(map)
3580
3581image(imflag);
3582
3583%-------------------------------------------------------------------
3584%-------------------------------------------------------------------
3585%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3586
3587%------------------------------------------------------------------
3588%-------------------------------------------------------------
3589% --- Executes on selection change in transform_fct.
3590function transform_fct_Callback(hObject, eventdata, handles)
3591%-------------------------------------------------------------
3592UvData=get(handles.uvmat,'UserData');
3593menu=get(handles.transform_fct,'String');
3594ind_coord=get(handles.transform_fct,'Value');
3595coord_option=menu{ind_coord};
3596list_transform=get(handles.transform_fct,'UserData');
3597ff=functions(list_transform{end}); 
3598if isequal(coord_option,'more...');
3599    coord_fct='';
3600    prompt = {'Enter the name of the transform function'};
3601    dlg_title = 'user defined transform';
3602    num_lines= 1;
3603    [FileName, PathName] = uigetfile( ...
3604       {'*.m', ' (*.m)';
3605        '*.m',  '.m files '; ...
3606        '*.*', 'All Files (*.*)'}, ...
3607        'Pick a file', ff.file);
3608    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3609        PathName(end)=[];
3610    end
3611    transform_selected =fullfile(PathName,FileName);
3612    if ~exist(transform_selected,'file')
3613           return
3614    end
3615   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3616   if ~isequal(ext_fct,'.m')
3617        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3618        return
3619   end
3620   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3621   ind_coord=get(handles.transform_fct,'Value');
3622   addpath(PathName)
3623   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3624   set(handles.transform_fct,'UserData',list_transform)
3625   rmpath(PathName)
3626   % save the new menu in the personal file 'uvmat_perso.mat'
3627   dir_perso=prefdir;%personal Matalb directory
3628   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3629   if exist(profil_perso,'file')
3630       nb_builtin=UvData.OpenParam.NbBuiltin;
3631       for ilist=nb_builtin+1:numel(list_transform)
3632           ff=functions(list_transform{ilist});
3633           transform_fct{ilist-nb_builtin}=ff.file;
3634       end
3635        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3636   end   
3637end
3638
3639%% check the current path to the selected function
3640if isa(list_transform{ind_coord},'function_handle')
3641    func=functions(list_transform{ind_coord});
3642    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3643else
3644    set(handles.path_transform,'String','')
3645end
3646
3647set(handles.CheckFixLimits,'Value',0)
3648set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3649
3650%% delete drawn objects
3651hother=findobj('Tag','proj_object');%find all the proj objects
3652for iobj=1:length(hother)
3653    delete_object(hother(iobj))
3654end
3655hother=findobj('Tag','DeformPoint');%find all the proj objects
3656for iobj=1:length(hother)
3657    delete_object(hother(iobj))
3658end
3659hh=findobj('Tag','calib_points');
3660if ~isempty(hh)
3661    delete(hh)
3662end
3663hhh=findobj('Tag','calib_marker');
3664if ~isempty(hhh)
3665    delete(hhh)
3666end
3667if isfield(UvData,'Object')
3668     UvData.Object=UvData.Object(1);
3669end
3670set(handles.ListObject,'Value',1)
3671set(handles.ListObject,'String',{'plane'})
3672set(handles.ListObject_1,'Value',1)
3673set(handles.ListObject_1,'String',{'plane'})
3674
3675%delete mask if it is displayed
3676% if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3677%    UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3678% end
3679set(handles.uvmat,'UserData',UvData)
3680run0_Callback(hObject, eventdata, handles)
3681
3682
3683
3684%------------------------------------------------
3685%CALLBACKS FOR PLOTTING PARAMETERS
3686%-------------------------------------------------
3687%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3688% Plot coordinates
3689%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3690%------------------------------------------------------------------------
3691function num_MinX_Callback(hObject, eventdata, handles)
3692%------------------------------------------------------------------------
3693set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3694set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3695update_plot(handles);
3696
3697%------------------------------------------------------------------------
3698function num_MaxX_Callback(hObject, eventdata, handles)
3699%------------------------------------------------------------------------
3700set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3701set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3702update_plot(handles);
3703
3704%------------------------------------------------------------------------
3705function num_MinY_Callback(hObject, eventdata, handles)
3706%------------------------------------------
3707set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3708set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3709update_plot(handles);
3710
3711%------------------------------------------------------------------------
3712function num_MaxY_Callback(hObject, eventdata, handles)
3713%------------------------------------------------------------------------
3714set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3715set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3716update_plot(handles);
3717
3718%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3719% Scalar or image representation
3720%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3721%------------------------------------------------------------------------
3722function num_MinA_Callback(hObject, eventdata, handles)
3723%------------------------------------------
3724set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3725set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3726MinA=str2double(get(handles.num_MinA,'String'));
3727MaxA=str2double(get(handles.num_MaxA,'String'));
3728if MinA>MaxA% switch minA and maxA in case of error
3729    MinA_old=MinA;
3730    MinA=MaxA;
3731    MaxA=MinA_old;
3732    set(handles.num_MinA,'String',num2str(MinA,5));
3733    set(handles.num_MaxA,'String',num2str(MaxA,5));
3734end
3735update_plot(handles);
3736
3737%------------------------------------------------------------------------
3738function num_MaxA_Callback(hObject, eventdata, handles)
3739%------------------------------------------------------------------------
3740set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3741set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3742MinA=str2double(get(handles.num_MinA,'String'));
3743MaxA=str2double(get(handles.num_MaxA,'String'));
3744if MinA>MaxA% switch minA and maxA in case of error
3745        MinA_old=MinA;
3746    MinA=MaxA;
3747    MaxA=MinA_old;
3748    set(handles.num_MinA,'String',num2str(MinA,5));
3749    set(handles.num_MaxA,'String',num2str(MaxA,5));
3750end
3751update_plot(handles);
3752
3753%------------------------------------------------------------------------
3754function CheckFixScalar_Callback(hObject, eventdata, handles)
3755%------------------------------------------------------------------------
3756test=get(handles.CheckFixScalar,'Value');
3757if test
3758    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3759else
3760    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3761    update_plot(handles);
3762end
3763
3764%-------------------------------------------------------------------
3765function CheckBW_Callback(hObject, eventdata, handles)
3766%-------------------------------------------------------------------
3767update_plot(handles);
3768
3769%-------------------------------------------------------------------
3770function num_Opacity_Callback(hObject, eventdata, handles)
3771update_plot(handles);
3772%-------------------------------------------------------------------
3773
3774%-------------------------------------------------------------------
3775function ListContour_Callback(hObject, eventdata, handles)
3776%-------------------------------------------------------------------
3777val=get(handles.ListContour,'Value');
3778if val==2
3779    set(handles.interval_txt,'Visible','on')
3780    set(handles.num_IncrA,'Visible','on')
3781else
3782    set(handles.interval_txt,'Visible','off')
3783    set(handles.num_IncrA,'Visible','off')
3784end
3785update_plot(handles);
3786
3787%-------------------------------------------------------------------
3788function num_IncrA_Callback(hObject, eventdata, handles)
3789%-------------------------------------------------------------------
3790update_plot(handles);
3791
3792
3793%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3794% Vector representation
3795%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3796%-------------------------------------------------------------------
3797function CheckHideWarning_Callback(hObject, eventdata, handles)
3798%-------------------------------------------------------------------
3799update_plot(handles);
3800
3801%-------------------------------------------------------------------
3802function CheckHideFalse_Callback(hObject, eventdata, handles)
3803%-------------------------------------------------------------------
3804update_plot(handles);
3805
3806%-------------------------------------------------------------------
3807function num_VecScale_Callback(hObject, eventdata, handles)
3808%-------------------------------------------------------------------
3809set(handles.CheckFixVectors,'Value',1);
3810set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3811update_plot(handles);
3812
3813%-------------------------------------------------------------------
3814function CheckFixVectors_Callback(hObject, eventdata, handles)
3815%-------------------------------------------------------------------
3816test=get(handles.CheckFixVectors,'Value');
3817if test
3818    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3819else
3820    update_plot(handles);
3821    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3822    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3823end
3824
3825%------------------------------------------------------------------------
3826% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3827function CheckDecimate4_Callback(hObject, eventdata, handles)
3828%------------------------------------------------------------------------
3829update_plot(handles);
3830
3831%------------------------------------------------------------------------
3832% --- Executes on selection change in ColorCode menu
3833function ColorCode_Callback(hObject, eventdata, handles)
3834%------------------------------------------------------------------------
3835% edit the choice for color code
3836update_color_code_boxes(handles);
3837update_plot(handles);
3838
3839%------------------------------------------------------------------------
3840function update_color_code_boxes(handles)
3841%------------------------------------------------------------------------
3842list_code=get(handles.ColorCode,'String');% list menu fields
3843colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3844enable_slider='off';%default
3845enable_bounds='off';%default
3846enable_scalar='off';%default
3847switch colcode
3848    case {'rgb','bgr'}
3849        enable_slider='on';
3850        enable_bounds='on';
3851        enable_scalar='on';
3852    case '64 colors'
3853        enable_bounds='on';
3854        enable_scalar='on';
3855end
3856set(handles.Slider1,'Visible',enable_slider)
3857set(handles.Slider2,'Visible', enable_slider)
3858set(handles.num_ColCode1,'Visible',enable_slider)
3859set(handles.num_ColCode2,'Visible',enable_slider)
3860set(handles.TitleColCode1,'Visible',enable_slider)
3861set(handles.TitleColCode2,'Visible',enable_slider)
3862set(handles.CheckFixVecColor,'Visible',enable_bounds)
3863set(handles.num_MinVec,'Visible',enable_bounds)
3864set(handles.num_MaxVec,'Visible',enable_bounds)
3865set(handles.ColorScalar,'Visible',enable_scalar)
3866set_vec_col_bar(handles)
3867
3868%------------------------------------------------------------------
3869% --- Executes on selection change in ColorScalar: choice of the color code.
3870function ColorScalar_Callback(hObject, eventdata, handles)
3871%------------------------------------------------------------------
3872% edit the choice for color code
3873list_scalar=get(handles.ColorScalar,'String');% list menu fields
3874col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3875if isequal(col_scalar,'ima_cor')
3876    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3877    ColorCode='rgb';
3878    set(handles.num_MinVec,'String','0')
3879    set(handles.num_MaxVec,'String','1')
3880    set(handles.num_ColCode1,'String','0.333')
3881    set(handles.num_ColCode2,'String','0.666')
3882else
3883    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3884    ColorCode='64 colors';
3885end
3886ColorCodeList=get(handles.ColorCode,'String');
3887ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3888set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3889
3890update_color_code_boxes(handles);
3891%replot the current graph
3892run0_Callback(hObject, eventdata, handles)
3893
3894%----------------------------------------------------------------
3895% -- Executes on slider movement to set the color code
3896%
3897function Slider1_Callback(hObject, eventdata, handles)
3898%------------------------------------------------------------------
3899slider1=get(handles.Slider1,'Value');
3900min_val=str2num(get(handles.num_MinVec,'String'));
3901max_val=str2num(get(handles.num_MaxVec,'String'));
3902col=min_val+(max_val-min_val)*slider1;
3903set(handles.num_ColCode1,'String',num2str(col))
3904if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3905    set(handles.Slider2,'Value',col)
3906    set(handles.num_ColCode2,'String',num2str(col))
3907end
3908set_vec_col_bar(handles)
3909update_plot(handles);
3910
3911%----------------------------------------------------------------
3912% Executes on slider movement to set the color code
3913%----------------------------------------------------------------
3914function Slider2_Callback(hObject, eventdata, handles)
3915slider2=get(handles.Slider2,'Value');
3916min_val=str2num(get(handles.num_MinVec,'String'));
3917max_val=str2num(get(handles.num_MaxVec,'String'));
3918col=min_val+(max_val-min_val)*slider2;
3919set(handles.num_ColCode2,'String',num2str(col))
3920if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3921    set(handles.Slider1,'Value',col)
3922    set(handles.num_ColCode1,'String',num2str(col))
3923end
3924set_vec_col_bar(handles)
3925update_plot(handles);
3926
3927%----------------------------------------------------------------
3928% --- Execute on return carriage on the edit box corresponding to slider 1
3929%----------------------------------------------------------------
3930function num_ColCode1_Callback(hObject, eventdata, handles)
3931set_vec_col_bar(handles)
3932update_plot(handles);
3933
3934%----------------------------------------------------------------
3935% --- Execute on return carriage on the edit box corresponding to slider 2
3936%----------------------------------------------------------------
3937function num_ColCode2_Callback(hObject, eventdata, handles)
3938set_vec_col_bar(handles)
3939update_plot(handles);
3940%------------------------------------------------------------------------
3941%-------------------------------------------------------
3942% --- Executes on button press in CheckFixVecColor.
3943%-------------------------------------------------------
3944function VecColBar_Callback(hObject, eventdata, handles)
3945set_vec_col_bar(handles)
3946
3947%------------------------------------------------------------------------
3948% --- Executes on button press in CheckFixVecColor.
3949function CheckFixVecColor_Callback(hObject, eventdata, handles)
3950%------------------------------------------------------------------------
3951if ~get(handles.CheckFixVecColor,'Value')
3952    update_plot(handles);
3953end
3954
3955%------------------------------------------------------------------------
3956% --- Executes on selection change in num_MaxVec.
3957function num_MinVec_Callback(hObject, eventdata, handles)
3958%------------------------------------------------------------------------
3959max_vec_Callback(hObject, eventdata, handles)
3960
3961%------------------------------------------------------------------------
3962% --- Executes on selection change in num_MaxVec.
3963function num_MaxVec_Callback(hObject, eventdata, handles)
3964%------------------------------------------------------------------------
3965set(handles.CheckFixVecColor,'Value',1)
3966CheckFixVecColor_Callback(hObject, eventdata, handles)
3967min_val=str2num(get(handles.num_MinVec,'String'));
3968max_val=str2num(get(handles.num_MaxVec,'String'));
3969slider1=get(handles.Slider1,'Value');
3970slider2=get(handles.Slider2,'Value');
3971colcode1=min_val+(max_val-min_val)*slider1;
3972colcode2=min_val+(max_val-min_val)*slider2;
3973set(handles.num_ColCode1,'String',num2str(colcode1))
3974set(handles.num_ColCode2,'String',num2str(colcode2))
3975update_plot(handles);
3976
3977%------------------------------------------------------------------------
3978% --- update the display of color code for vectors (on vecColBar)
3979function set_vec_col_bar(handles)
3980%------------------------------------------------------------------------
3981%get the image of the color display button 'VecColBar' in pixels
3982set(handles.VecColBar,'Unit','pixel');
3983pos_vert=get(handles.VecColBar,'Position');
3984set(handles.VecColBar,'Unit','Normalized');
3985width=ceil(pos_vert(3));
3986height=ceil(pos_vert(4));
3987
3988%get slider indications
3989list=get(handles.ColorCode,'String');
3990ichoice=get(handles.ColorCode,'Value');
3991colcode.ColorCode=list{ichoice};
3992colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3993colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3994test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
3995if test3color
3996    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3997    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3998end
3999vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
4000[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4001oneheight=ones(1,height);
4002A1=colorlist(col_vec,1)*oneheight;
4003A2=colorlist(col_vec,2)*oneheight;
4004A3=colorlist(col_vec,3)*oneheight;
4005A(:,:,1)=A1';
4006A(:,:,2)=A2';
4007A(:,:,3)=A3';
4008set(handles.VecColBar,'Cdata',A)
4009
4010%-------------------------------------------------------------------
4011function update_plot(handles)
4012%-------------------------------------------------------------------
4013UvData=get(handles.uvmat,'UserData');
4014AxeData=UvData.axes3;% retrieve the current plotted data
4015PlotParam=read_GUI(handles.uvmat);
4016[tild,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
4017write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4018
4019%------------------------------------------------------------------------
4020%------------------------------------------------------------------------
4021%   SELECTION AND EDITION OF PROJECTION OBJECTS
4022%------------------------------------------------------------------------
4023%------------------------------------------------------------------------
4024
4025% --- Executes on selection change in ListObject_1.
4026function ListObject_1_Callback(hObject, eventdata, handles)
4027list_str=get(handles.ListObject,'String');
4028UvData=get(handles.uvmat,'UserData');
4029ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
4030
4031%% update the projection plot on uvmat
4032ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
4033plot_field(ProjData,handles.axes3,read_GUI(handles.uvmat));% plot the projected field;
4034%replot all the objects within the new projected field
4035for IndexObj=1:numel(list_str)
4036    IndexObj
4037        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat
4038        if isempty(hobject) || ~ishandle(hobject)
4039            hobject=handles.axes3
4040        end
4041        if isequal(IndexObj,get(handles.ListObject,'Value'))
4042            objectcolor='m'; %paint in magenta the currently selected object in ListObject
4043        else
4044            objectcolor='b';
4045        end
4046        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
4047end
4048set(handles.uvmat,'UserData',UvData)
4049
4050%% display the object parameters if the GUI set_object is already opened
4051if ~get(handles.ViewObject,'Value')
4052    ZBounds=0; % default
4053    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4054        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4055        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4056    end
4057    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
4058    set_object(ObjectData,[],ZBounds);
4059    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
4060end
4061
4062%  desactivate the edit object mode
4063set(handles.edit_object,'Value',0)
4064set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4065
4066%------------------------------------------------------------------------
4067% --- Executes on selection change in ListObject.
4068function ListObject_Callback(hObject, eventdata, handles)
4069%------------------------------------------------------------------------
4070list_str=get(handles.ListObject,'String');
4071IndexObj=get(handles.ListObject,'Value');%present object selection
4072
4073%% The object  is displayed in set_object if this GUI is already opened
4074UvData=get(handles.uvmat,'UserData');
4075ObjectData=UvData.Object{IndexObj};
4076hset_object=findobj(allchild(0),'tag','set_object');
4077if ~isempty(hset_object)
4078    ZBounds=0; % default
4079    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4080        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4081        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4082    end
4083    ObjectData.Name=list_str{IndexObj};
4084    set_object(ObjectData,[],ZBounds);
4085    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4086end
4087
4088%%  desactivate the edit object mode
4089set(handles.edit_object,'Value',0)
4090set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4091
4092%% update the  plot on view_field if view_field is already openened
4093hview_field=findobj(allchild(0),'tag','view_field');
4094if isempty(hview_field)
4095    hhview_field.axes3=[];
4096else
4097    Data=get(hview_field,'UserData');
4098    hhview_field=guidata(hview_field);
4099    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4100    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
4101    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4102    haxes=findobj(hview_field,'tag','axes3');
4103    pos=get(hview_field,'Position'); 
4104    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4105        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4106        pos_table=get(h_TableDisplay,'Position');
4107        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4108        drawnow% needed to change position before the next command
4109        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4110    else
4111        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4112    end
4113end
4114
4115%% update the color of the graphic object representation: the selected object in magenta, others in blue
4116update_object_color(handles.axes3,hhview_field.axes3,UvData.Object{IndexObj}.DisplayHandle.uvmat)
4117
4118%------------------------------------------------------------------------
4119%--- update the color representation of objects (indicating the selected ones)
4120function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4121%------------------------------------------------------------------------
4122if isempty(axes_view_field)% case with no view_field plot
4123hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4124else
4125hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4126findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4127end
4128for iobj=1:length(hother)
4129    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4130        set(hother(iobj),'EdgeColor','b')
4131        if isequal(get(hother(iobj),'FaceColor'),'m')
4132            set(hother(iobj),'FaceColor','b')
4133        end
4134    elseif isequal(get(hother(iobj),'Type'),'image')
4135        Acolor=get(hother(iobj),'CData');
4136        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4137        set(hother(iobj),'CData',Acolor);
4138    else
4139        set(hother(iobj),'Color','b')
4140    end
4141    set(hother(iobj),'Selected','off')
4142end
4143if ishandle(DisplayHandle)
4144    linetype=get(DisplayHandle,'Type');
4145    if isequal(linetype,'line')
4146        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4147    elseif isequal(linetype,'rectangle')
4148        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4149    elseif isequal(linetype,'patch')
4150        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4151    end
4152    SubObjectData=get(DisplayHandle,'UserData');
4153    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4154        for iobj=1:length(SubObjectData.SubObject)
4155            hsub=SubObjectData.SubObject(iobj);
4156            if isequal(get(hsub,'Type'),'rectangle')
4157                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4158            elseif isequal(get(hsub,'Type'),'image')
4159                Acolor=get(hsub,'CData');
4160                Acolor(:,:,1)=Acolor(:,:,3);
4161                set(hsub,'CData',Acolor);
4162            else
4163                set(hsub,'Color','m')
4164            end
4165        end
4166    end
4167    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4168        set(SubObjectData.DeformPoint,'Color','m')
4169    end
4170end
4171
4172%-------------------------------------------------------------------
4173% --- Executes on selection change in edit_object.
4174function edit_object_Callback(hObject, eventdata, handles)
4175%-------------------------------------------------------------------
4176UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4177hset_object=findobj(allchild(0),'Tag','set_object');
4178if get(handles.edit_object,'Value')
4179    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4180    %suppress the other options
4181    set(handles.CheckZoom,'Value',0)
4182    CheckZoom_Callback(hObject, eventdata, handles)
4183    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4184    if ishandle(hgeometry_calib)
4185        hhgeometry_calib=guidata(hgeometry_calib);
4186        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4187        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4188    end
4189    set(handles.ViewObject,'value',1)
4190    ViewObject_Callback(hObject, eventdata, handles)
4191else % desctivate object edit mode
4192    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4193    if ~isempty(hset_object)% open the
4194        hhset_object=guidata(hset_object);
4195        set(hhset_object.PLOT,'enable','off');
4196        set(get(hset_object,'children'),'enable','inactive')
4197    end
4198end
4199
4200
4201%------------------------------------------------------------------------
4202% --- Executes on button press in ViewObject.
4203function ViewObject_Callback(hObject, eventdata, handles)
4204%------------------------------------------------------------------------
4205check_view=get(handles.ViewObject,'Value');
4206
4207if check_view %activate set_object   
4208    IndexObj=get(handles.ListObject,'Value');
4209    list_object=get(handles.ListObject,'String');
4210    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4211    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4212    if numel(UvData.Object)<IndexObj;% error in UvData
4213        msgbox_uvmat('ERROR','invalid object list')
4214        return
4215    end
4216    ZBounds=0; % default
4217    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4218        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4219        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4220    end
4221%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4222    data=UvData.Object{IndexObj};
4223    if ~isfield(data,'Type')% default plane
4224        data.Type='plane';
4225    end
4226    if isfield(UvData,'Field')
4227        Field=UvData.Field;
4228        if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4229            data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4230            if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4231                data.RangeY=UvData.Field.Mesh;
4232            else
4233                data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4234            end
4235            data.DX=UvData.Field.Mesh;
4236            data.DY=UvData.Field.Mesh;
4237        end
4238        if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4239            data.Coord=[0 0 0]; %default
4240        end
4241        if isfield(Field,'CoordUnit')
4242            data.CoordUnit=Field.CoordUnit;
4243        end
4244    end
4245    hset_object=set_object(data,[],ZBounds);
4246    hhset_object=guidata(hset_object);
4247    if get(handles.edit_object,'Value')% edit mode
4248        set(hhset_object.PLOT,'Enable','on')
4249        set(get(hset_object,'children'),'enable','on')
4250    else
4251        set(hhset_object.PLOT,'Enable','off')
4252        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4253        set(hhset_object.SAVE,'Enable','on')
4254    end
4255else
4256    hset_object=findobj(allchild(0),'tag','set_object');
4257    if ~isempty(hset_object)
4258        delete(hset_object)% delete existing version of set_object
4259    end
4260end
4261 
4262
4263%------------------------------------------------------------------------
4264% --- Executes on button press in ViewField.
4265function ViewField_Callback(hObject, eventdata, handles)
4266%------------------------------------------------------------------------
4267check_view=get(handles.ViewField,'Value');
4268
4269if check_view
4270    IndexObj=get(handles.ListObject,'Value');
4271    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4272    if numel(UvData.Object)<IndexObj(end);% error in UvData
4273        msgbox_uvmat('ERROR','invalid object list')
4274        return
4275    end
4276    ZBounds=0; % default
4277    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4278        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4279        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4280    end
4281    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4282    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4283        UvData.Object{IndexObj(1)}.Type='plane';
4284    end
4285    list_object=get(handles.ListObject,'String');
4286    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4287   
4288    %% show the projection of the selected object on view_field
4289    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
4290    hview_field=findobj(allchild(0),'tag','view_field');
4291    if isempty(hview_field)
4292        hview_field=view_field;
4293    end
4294    hhview_field=guidata(hview_field);
4295    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4296    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4297    haxes=findobj(hview_field,'tag','axes3');
4298    pos=get(hview_field,'Position');
4299    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4300        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4301        pos_table=get(h_TableDisplay,'Position');
4302        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4303    else
4304        Data=get(hview_field,'UserData');
4305        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4306    end
4307else
4308    hview_field=findobj(allchild(0),'tag','view_field');
4309    if ~isempty(hview_field)
4310        delete(hview_field)% delete existing version of set_object
4311    end
4312end
4313
4314
4315%------------------------------------------------------------------------
4316% --- Executes on button press in delete_object.
4317function delete_object_Callback(hObject, eventdata, handles)
4318%------------------------------------------------------------------------
4319IndexObj=get(handles.ListObject,'Value');
4320IndexObj_1=get(handles.ListObject_1,'Value');
4321if IndexObj>1 && ~isequal(IndexObj,IndexObj_1)
4322    delete_object(IndexObj)
4323end
4324
4325%------------------------------------------------------------------------
4326%------------------------------------------------------------------------
4327%  II - TOOLS FROM THE UPPER MENU BAR
4328%------------------------------------------------------------------------
4329%------------------------------------------------------------------------
4330
4331%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4332% Export  Menu Callbacks
4333%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4334%------------------------------------------------------------------------
4335% --- Executes on button press in Menu/Export/field in workspace.
4336function MenuExportField_Callback(hObject, eventdata, handles)
4337%------------------------------------------------------------------------
4338global Data_uvmat
4339Data_uvmat=get(handles.uvmat,'UserData');
4340evalin('base','global Data_uvmat')%make CurData global in the workspace
4341display('current field :')
4342evalin('base','Data_uvmat') %display CurData in the workspace
4343commandwindow; %brings the Matlab command window to the front
4344
4345%------------------------------------------------------------------------
4346% --- Executes on button press in Menu/Export/extract figure.
4347function MenuExportFigure_Callback(hObject, eventdata, handles)
4348%------------------------------------------------------------------------
4349% huvmat=get(handles.MenuExport,'parent');
4350hfig=figure;
4351copyobj(handles.axes3,hfig);
4352map=colormap(handles.axes3);
4353colormap(map);%transmit the current colormap to the zoom fig
4354colorbar
4355
4356% %------------------------------------------------------
4357% % --- Executes on button press in Menu/Export/extract figure.
4358% %------------------------------------------------------
4359% function MenuExport_plot_Callback(hObject, eventdata, handles)
4360% huvmat=get(handles.MenuExport_plot,'parent');
4361% UvData=get(huvmat,'UserData');
4362% hfig=figure;
4363% newaxes=copyobj(handles.axes3,hfig);
4364% map=colormap(handles.axes3);
4365% colormap(map);%transmit the current colormap to the zoom fig
4366% colorbar
4367
4368%
4369% % --------------------------------------------------------------------
4370% function Insert_Callback(hObject, eventdata, handles)
4371%
4372
4373%------------------------------------------------------------------------
4374% --------------------------------------------------------------------
4375function MenuExportMovie_Callback(hObject, eventdata, handles)
4376% --------------------------------------------------------------------
4377set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4378huvmat=get(handles.run0,'parent');
4379UvData=get(huvmat,'UserData');
4380%[xx,xx,FileBase]=read_file_boxes(handles);
4381[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4382FileBase=fullfile(RootPath,RootFile);
4383 %read the current input file name
4384prompt = {'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)'};
4385dlg_title = 'select properties of the output avi movie';
4386num_lines= 1;
4387% nbfield_cell=get(handles.last_i,'String');
4388def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4389answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4390aviname=answer{1};
4391fps=str2double(answer{2});
4392% check for existing file with output name aviname
4393if exist(aviname,'file')
4394    backup=aviname;
4395    testexist=2;
4396    while testexist==2
4397        backup=[backup '~'];
4398        testexist=exist(backup,'file');     
4399    end
4400    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4401    if isequal(success,1)
4402        delete(aviname)%delete existing file
4403    else
4404        msgbox_uvmat('ERROR',message)
4405        return
4406    end
4407end
4408%create avi open
4409aviobj=avifile(aviname,'Compression','None','fps',fps);
4410
4411%display first view for tests
4412newfig=figure;
4413newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4414set(newaxes,'Tag','movieaxes')
4415nbpix=[512 384]*str2double(answer{3});
4416set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4417set(newaxes,'Position',eval(answer{4}));
4418map=colormap(handles.axes3);
4419colormap(map);%transmit the current colormap to the zoom fig
4420msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4421        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4422UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4423set(huvmat,'UserData',UvData);
4424increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4425set(handles.STOP,'Visible','on')
4426set(handles.speed,'Visible','on')
4427set(handles.speed_txt,'Visible','on')
4428set(handles.Movie,'BusyAction','queue')
4429
4430%imin=str2double(get(handles.i1,'String'));
4431imax=str2double(answer{5});
4432% if isfield(UvData,'Time')
4433htitle=get(newaxes,'Title');
4434xlim=get(newaxes,'XLim');
4435ylim=get(newaxes,'YLim');
4436set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4437time_str=get(handles.abs_time,'String');
4438set(htitle,'String',['t=' time_str])
4439set(handles.speed,'Value',1)
4440for i=1:imax
4441    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4442            runpm(hObject,eventdata,handles,increment)% run plus
4443            drawnow
4444            time_str=get(handles.abs_time,'String');
4445            if ishandle(htitle)
4446             set(htitle,'String',['t=' time_str])
4447            end
4448            mov=getframe(newfig);
4449            aviobj=addframe(aviobj,mov);
4450    end
4451end
4452aviobj=close(aviobj);
4453UvData=rmfield(UvData,'plotaxes');
4454%UvData.Object{1}.plotaxes=handles.axes3;
4455set(huvmat,'UserData',UvData);
4456msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4457
4458
4459%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4460% Projection Objects Menu Callbacks
4461%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4462
4463% -----------------------------------------------------------------------
4464function Menupoints_Callback(hObject, eventdata, handles)
4465%------------------------------------------------------------------------
4466data.Type='points';
4467data.ProjMode='projection';%default
4468data.ProjModeMenu={};% do not restrict ProjMode menus
4469create_object(data,handles)
4470
4471% -----------------------------------------------------------------------
4472function Menuline_Callback(hObject, eventdata, handles)
4473%------------------------------------------------------------------------
4474data.Type='line';
4475data.ProjMode='projection';%default
4476data.ProjModeMenu={};% do not restrict ProjMode menus
4477create_object(data,handles)
4478
4479%------------------------------------------------------------------------
4480function Menupolyline_Callback(hObject, eventdata, handles)
4481%------------------------------------------------------------------------
4482data.Type='polyline';
4483data.ProjMode='projection';%default
4484data.ProjModeMenu={};% do not restrict ProjMode menus
4485create_object(data,handles)
4486
4487%------------------------------------------------------------------------
4488function Menupolygon_Callback(hObject, eventdata, handles)
4489%------------------------------------------------------------------------
4490data.Type='polygon';
4491data.ProjMode='inside';%default
4492data.ProjModeMenu={};% do not restrict ProjMode menus
4493create_object(data,handles)
4494
4495%------------------------------------------------------------------------
4496function Menurectangle_Callback(hObject, eventdata, handles)
4497%------------------------------------------------------------------------
4498data.Type='rectangle';
4499data.ProjMode='inside';%default
4500data.ProjModeMenu={};% do not restrict ProjMode menus
4501create_object(data,handles)
4502
4503%------------------------------------------------------------------------
4504function Menuellipse_Callback(hObject, eventdata, handles)
4505%------------------------------------------------------------------------
4506data.Type='ellipse';
4507data.ProjMode='inside';%default
4508data.ProjModeMenu={};% do not restrict ProjMode menus
4509create_object(data,handles)
4510
4511%------------------------------------------------------------------------
4512function MenuMaskObject_Callback(hObject, eventdata, handles)
4513%------------------------------------------------------------------------
4514data.Type='polygon';
4515data.TypeMenu={'polygon'};
4516data.ProjMode='mask_inside';%default
4517data.ProjModeMenu={'mask_inside';'mask_outside'};
4518create_object(data,handles)
4519
4520%------------------------------------------------------------------------
4521function Menuplane_Callback(hObject, eventdata, handles)
4522%------------------------------------------------------------------------
4523data.Type='plane';
4524data.ProjMode='projection';%default
4525data.ProjModeMenu={};% do not restrict ProjMode menus
4526create_object(data,handles)
4527
4528%------------------------------------------------------------------------
4529function Menuvolume_Callback(hObject, eventdata, handles)
4530%------------------------------------------------------------------------
4531data.Type='volume';
4532data.ProjMode='interp';%default
4533data.ProjModeMenu={};
4534% set(handles.create,'Visible','on')
4535% set(handles.create,'Value',1)
4536% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4537create_object(data,handles)
4538
4539%------------------------------------------------------------------------
4540% --- generic function used for the creation of a projection object
4541function create_object(data,handles)
4542%------------------------------------------------------------------------
4543% desactivate geometric calibration if opened
4544hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4545if ishandle(hgeometry_calib)
4546    hhgeometry_calib=guidata(hgeometry_calib);
4547    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4548    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4549end
4550set(handles.edit_object,'Value',0); %suppress the object edit mode
4551set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4552ListObject=get(handles.ListObject,'String');
4553if ~strcmp(ListObject{end},'')
4554    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4555    set(handles.ListObject,'String',ListObject)
4556end
4557IndexObj=length(ListObject);
4558set(handles.ListObject,'Value',IndexObj)
4559UvData=get(handles.uvmat,'UserData');
4560UvData.Object{IndexObj}=[]; %create a new empty object
4561UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.axes3; % axes for plot_object
4562UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4563data.Name=data.Type;% default name=type
4564data.Coord=[0 0]; %default
4565if isfield(UvData,'Field')
4566    Field=UvData.Field;
4567    if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4568        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4569        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4570            data.RangeY=UvData.Field.Mesh;
4571        else
4572            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4573        end
4574        data.DX=UvData.Field.Mesh;
4575        data.DY=UvData.Field.Mesh;
4576    end
4577    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4578         data.Coord=[0 0 0]; %default
4579    end
4580    if isfield(Field,'CoordUnit')
4581        data.CoordUnit=Field.CoordUnit;
4582    end
4583end
4584if ishandle(handles.UVMAT_title)
4585    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4586end
4587hset_object=set_object(data,handles);% call the set_object interface
4588hhset_object=guidata(hset_object);
4589hchild=get(hset_object,'children');
4590set(hchild,'enable','on')
4591set(handles.uvmat,'UserData',UvData)
4592set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
4593CheckZoom_Callback(handles.uvmat, [], handles)
4594set(handles.delete_object,'Visible','on')
4595
4596%------------------------------------------------------------------------
4597function MenuBrowseObject_Callback(hObject, eventdata, handles)
4598%------------------------------------------------------------------------
4599%get the object file
4600[FileName, PathName, filterindex] = uigetfile( ...
4601       {'*.xml;*.mat', ' (*.xml,*.mat)';
4602       '*.xml',  '.xml files '; ...
4603        '*.mat',  '.mat matlab files '}, ...
4604        'Pick an xml Object file',get(handles.RootPath,'String'));
4605fileinput=[PathName FileName];%complete file name
4606sizf=size(fileinput);
4607if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4608
4609%read the file
4610[data,heading]=xml2struct(fileinput);
4611if ~strcmp(heading,'ProjObject')
4612    msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects')
4613end
4614[tild,data.Name]=fileparts(FileName);% object name set as file name
4615ListObject=get(handles.ListObject,'String');
4616if ~strcmp(ListObject{end},'')
4617    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4618    set(handles.ListObject,'String',ListObject)
4619end
4620IndexObj=length(ListObject);
4621
4622UvData=get(handles.uvmat,'UserData');
4623UvData.Object{IndexObj}=[]; %create a new empty object
4624UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4625UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4626set(handles.uvmat,'UserData',UvData)
4627set(handles.ListObject,'Value',IndexObj)
4628hset_object=set_object(data);% call the set_object interface
4629set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4630set(handles.edit_object,'Value',0); %suppress the object edit mode
4631set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4632set(handles.delete_object,'Visible','on')
4633
4634
4635%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4636% MenuEdit Callbacks
4637%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4638%------------------------------------------------------------------------
4639function MenuEditObject_Callback(hObject, eventdata, handles)
4640%------------------------------------------------------------------------
4641set(handles.edit_object,'Value',1)
4642edit_Callback(hObject, eventdata, handles)
4643
4644%------------------------------------------------------------------------
4645function MenuEditVectors_Callback(hObject, eventdata, handles)
4646%------------------------------------------------------------------------
4647set(handles.edit_vect,'Visible','on')
4648set(handles.edit_vect,'Value',1)
4649edit_vect_Callback(hObject, eventdata, handles)
4650
4651%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4652% MenuTools Callbacks
4653%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4654%------------------------------------------------------------------------
4655function MenuCalib_Callback(hObject, eventdata, handles)
4656%------------------------------------------------------------------------
4657
4658UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4659
4660%suppress competing options
4661set(handles.CheckZoom,'Value',0)
4662set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4663set(handles.ListObject,'Value',1)     
4664% initiate display of GUI geometry_calib
4665data=[]; %default
4666if isfield(UvData,'CoordType')
4667    data.CoordType=UvData.CoordType;
4668end
4669pos=get(handles.uvmat,'Position');
4670pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4671pos(2)=pos(2)-0.02;
4672[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4673FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4674set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4675if isfield(UvData.OpenParam,'CalOrigin')
4676    pos_uvmat=get(handles.uvmat,'Position');
4677    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4678    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4679    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4680end
4681geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4682set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4683set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4684
4685%------------------------------------------------------------------------
4686function MenuMask_Callback(hObject, eventdata, handles)
4687%------------------------------------------------------------------------
4688UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4689ListObj=UvData.Object;
4690select=zeros(1,numel(ListObj));
4691for iobj=1:numel(ListObj);
4692    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4693        select(iobj)=1;
4694    end
4695end
4696val=find(select);
4697if isempty(val)
4698    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4699    return
4700else
4701%     set(handles.ListObject,'Max',2);%allow multiple selection
4702    set(handles.ListObject,'Value',val);
4703    flag=1;
4704    npx=size(UvData.Field.A,2);
4705    npy=size(UvData.Field.A,1);
4706    xi=0.5:npx-0.5;
4707    yi=0.5:npy-0.5;
4708    [Xi,Yi]=meshgrid(xi,yi);
4709    if isfield(UvData,'Object')
4710        for iobj=1:length(UvData.Object)
4711            ObjectData=UvData.Object{iobj};
4712            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4713                flagobj=1;
4714                testphys=0; %coordinates in pixels by default
4715                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4716                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4717                        Calib=UvData.XmlData{1}.GeometryCalib;
4718                        testphys=1;
4719                    end
4720                end
4721                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4722                    if isequal(ObjectData.Type,'polygon')
4723                        X=ObjectData.Coord(:,1);
4724                        Y=ObjectData.Coord(:,2);
4725                        if testphys
4726                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4727                        end
4728                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4729                    elseif isequal(ObjectData.Type,'ellipse')
4730                        if testphys
4731                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4732                        end
4733                        RangeX=max(ObjectData.RangeX);
4734                        RangeY=max(ObjectData.RangeY);
4735                        X2Max=RangeX*RangeX;
4736                        Y2Max=RangeY*RangeY;
4737                        distX=(Xi-ObjectData.Coord(1,1));
4738                        distY=(Yi-ObjectData.Coord(1,2));
4739                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4740                    elseif isequal(ObjectData.Type,'rectangle')
4741                        if testphys
4742                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4743                        end
4744                        distX=abs(Xi-ObjectData.Coord(1,1));
4745                        distY=abs(Yi-ObjectData.Coord(1,2));
4746                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4747                    end
4748                    if isequal(ObjectData.ProjMode,'mask_outside')
4749                        flagobj=~flagobj;
4750                    end
4751                    flag=flag & flagobj;
4752                end
4753            end
4754        end
4755    end
4756    %mask name
4757    RootPath=get(handles.RootPath,'String');
4758    SubDir=get(handles.SubDir,'String');
4759    RootFile=get(handles.RootFile,'String');
4760    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4761        RootFile(1)=[];
4762    end
4763   % filebase=fullfile(RootPath,RootFile);
4764    list=get(handles.masklevel,'String');
4765    masknumber=num2str(length(list));
4766    maskindex=get(handles.masklevel,'Value');
4767   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4768    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
4769    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4770    imflag=flipdim(imflag,1);
4771
4772    %display the mask
4773    hfigmask=figure;
4774    set(hfigmask,'Name','mask image')
4775    vec=linspace(0,1,256);%define a linear greyscale colormap
4776    map=[vec' vec' vec'];
4777    colormap(map)
4778    image(imflag);
4779    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4780    if ~strcmp(answer,'Cancel')
4781        mask_dir=fileparts(answer);
4782        if ~exist(mask_dir,'dir')
4783            [xx,msg1]=mkdir(mask_dir);
4784            if ~strcmp(msg1,'')
4785                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
4786                return
4787            end
4788        end
4789        imwrite(imflag,answer,'BitDepth',8);
4790    end
4791    set(handles.ListObject,'Value',1)
4792end
4793
4794%------------------------------------------------------------------------
4795%-- open the GUI set_grid.fig to create grid
4796function MenuGrid_Callback(hObject, eventdata, handles)
4797%------------------------------------------------------------------------
4798%suppress the other options if grid is chosen
4799set(handles.edit_vect,'Value',0)
4800edit_vect_Callback(hObject, eventdata, handles)
4801set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4802set(handles.ListObject,'Value',1)     
4803
4804%prepare display of the set_grid GUI
4805[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4806FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4807CoordList=get(handles.transform_fct,'String');
4808val=get(handles.transform_fct,'Value');
4809set_grid(FileName,CoordList{val});% call the set_object interface
4810
4811
4812%------------------------------------------------------------------------
4813function MenuRuler_Callback(hObject, eventdata, handles)
4814%------------------------------------------------------------------------
4815set(handles.CheckZoom,'Value',0)
4816CheckZoom_Callback(handles.uvmat, [], handles)
4817set(handles.MenuRuler,'checked','on')
4818UvData=get(handles.uvmat,'UserData');
4819UvData.MouseAction='ruler';
4820set(handles.uvmat,'UserData',UvData);
4821
4822%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4823% MenuRun Callbacks
4824%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4825
4826%------------------------------------------------------------------------
4827% open the GUI 'series'
4828function MenuSeries_Callback(hObject, eventdata, handles)
4829%------------------------------------------------------------------------
4830series; %first display of the GUI to fill waiting time
4831[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4832param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4833if isequal(get(handles.SubField,'Value'),1)
4834    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
4835    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
4836    if ~isequal(FileName_1,param.FileName)
4837        param.FileName_1=FileName_1;
4838    end
4839end
4840param.NomType=get(handles.NomType,'String');
4841param.NomType_1=get(handles.NomType_1,'String');
4842param.CheckFixPair=get(handles.CheckFixPair,'Value');
4843huvmat=get(handles.MenuSeries,'parent');
4844UvData=get(huvmat,'UserData');
4845if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4846    param.Time=UvData.XmlData{1}.Time;
4847end
4848if isequal(get(handles.scan_i,'Value'),1)
4849    param.incr_i=str2num(get(handles.increment_scan,'String'));
4850elseif isequal(get(handles.scan_j,'Value'),1)
4851    param.incr_j=str2num(get(handles.increment_scan,'String'));
4852end
4853param.list_fields=get(handles.Fields,'String');% list menu fields
4854param.list_fields(1)=[]; %suppress  'image' option
4855param.index_fields=get(handles.Fields,'Value');% selected string index
4856if param.index_fields>1
4857    param.index_fields=param.index_fields-1;
4858end
4859param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4860param.list_fields_1(1)=[]; %suppress  'image' option
4861param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4862if param.index_fields_1>1
4863    param.index_fields_1=param.index_fields_1-1;
4864end
4865param.menu_coord_str=get(handles.transform_fct,'String');
4866param.menu_coord_val=get(handles.transform_fct,'Value');
4867series(param); %run the series interface
4868
4869%------------------------------------------------------------------------
4870% -- open the GUI civ.fig for PIV
4871function MenuPIV_Callback(hObject, eventdata, handles)
4872%------------------------------------------------------------------------
4873 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4874 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4875civ(FileName);% interface de civ(not in the uvmat file)
4876
4877% --------------------------------------------------------------------
4878function MenuHelp_Callback(hObject, eventdata, handles)
4879% --------------------------------------------------------------------
4880path_to_uvmat=which ('uvmat');% check the path of uvmat
4881pathelp=fileparts(path_to_uvmat);
4882helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4883if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4884else
4885    addpath (fullfile(pathelp,'uvmat_doc'))
4886    web(helpfile);
4887end
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