source: trunk/src/uvmat.m @ 483

Last change on this file since 483 was 483, checked in by sommeria, 9 years ago

civ set to accept automatic input in the absence of PARAM.xml. Still problem with run time address
zoom improved to deal with elongated plots
better link between PIV and images in uvmat.

File size: 206.5 KB
Line 
1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%%
8%
9%INPUT:
10% input: input file name (if character chain), or input image matrix to
11% visualize, or Matlab structure representing  netcdf fields (with fields
12% ListVarName....)
13%
14%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15%  Copyright Joel Sommeria,  2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%     This open is part of the toolbox UVMAT.
18%
19%     UVMAT is free software; you can redistribute it and/or modify
20%     it under the terms of the GNU General Public License as published by
21%     the Free Software Foundation; either version 2 of the License, or
22%     (at your option) any later version.
23%
24%     UVMAT is distributed in the hope that it will be useful,
25%     but WITHOUT ANY WARRANTY; without even the implied warranty of
26%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
28%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29%
30% Information stored on the interface:
31%    'Strings' of all edit boxes and menus: get(handles.Tag,'String')
32%    'Values' of all menus and toggle buttons: get(handles.Tag,'Value')
33%     Matlab structure called UvData stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
34%          It contains the following fields:
35%     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn)
36%          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
37%     - Information read in the documentation open of a series (activated by RootPath_Callback) :
38%          .XmlData, with fields:
39%               .Time: matrix of times of the images with index i and j
40%               .GeometryCalib: [1x1 struct]
41%     - Information defined from the interface:
42%           .NewSeries: =1 when the first view of a new field series is displayed, else 0
43%           .FileName:(char string)
44%           .FieldName: (char string) main field selected('image', 'velocity'...)
45%           .CName: (char string)name of the scalar used for vector colors
46%          .MovieObject{1}: movie object representing an input movie
47%          .MovieObject{2}: idem for a second input series (_1)
48%          .FileName_1 : last second input file name (to deal with a constant second input without reading again the file)
49%          .ZMin, .ZMax: range of the z coordinate
50%..... to complement
51%     - Information on  projection objects
52%           .Object: {[1x1 struct]}
53%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
54%     -Information on the current field (Field{i})
55%            .Txt : text information to display (e.g. error message)
56%            .NbDim: number of dimensions (=0 by default)
57%            .NbCoord: number of vector components
58%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
59%            .dt: time interval for the corresponding image pair
60%            .Mesh: estimated typical distance between vectors
61%            .ZMax:
62%            .ZMin:
63%            .X, .Y, .Z: set of vector coordinates
64%            .U,.V,.W: corresponding set of vector components
65%            .F: corresponding set of warning flags
66%            .FF: corresponding set of false flags, =0 for good vectors
67%            .C: corresponding values of the scalar used for vector color
68%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
69%                     equal to the number of vectors stored in the input open)
70%            .CName: name of the scalar .C
71%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
72%            .A image or scalar
73%            .AX: vector of dimension 2 representing the first and last values
74%              of the X coordinates for the image or scalar known on a regular grid,
75%              or vector of dimension .A for a scaler defined on irregular grid.
76%            .AY: same as .AX along the Y direction
77%            .AName: name of the scalar, ='image' for an image
78
79% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
80%
81%
82% 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1
83% (second field), or by the stored file names under  Browse, or as an input of uvmat.
84% 2) These functions call 'display_file_name.m' which detects the file series, and fills the file index boxes
85% 3) Then 'update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file)
86% 4) Then fields are opened and visualised by the main sub-function 'refresh_field.m'
87% The function first reads the name of the input file from the edit boxes  of the GUI
88% A second input file can be introduced for file comparison
89% It then reads the input file(s) with the appropriate function, read for
90% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf
91% files.
92%               Main input open   second input open(_1)        second image (pair animation)
93%            |                 |                             
94%            |                 |                                               
95%                     Field{1}         Field{2}               
96%                                                                         |
97% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
98%                                                                   Field{i}
99%                                                                    |
100% calc_field.m: calculate scalar or other derived fields (vort, div..).
101%
102% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
103%              Field{i=1->3}.X --> UvData.X                          |
104%                                                                    |
105%                                                                 UvData
106%                                                                    |
107% plot histograms of the whole  field
108% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
109%                                                                    |                                                                          |
110%                                                                ObjectData
111%                                                                    |
112% plot_field.m: plot the projected fields and store them as          |
113% UvData.axes3                                        |
114%                                                                    |
115%                                                                AxeData
116%
117%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
118% scalars are displayed either as an image or countour plot, either as a color of
119% velocity vectors. The scalar values in the first case is represented by
120% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
121% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
122% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
123% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
124% coordinates of the four image corners. The scalar name is represented by
125% the strings .AName and/or .CName.
126% If the scalar exists in an input open (image or scalar stored under its
127% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
128% Else only its name AName is recorded in Field{i}, and its field is then calculated
129%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
130     
131% Properties attached to plotting figures (standard Matlab properties):
132%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
133%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
134%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
135%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
136%    'KeyPressFcn': function called by pressing a key on the key board
137%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
138%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
139
140% Properties attached to plotting axes:
141%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
142%     AxeData:=get(gca,'UserData');
143%     AxeData.Drawing  = create: create a new object
144%                       = deform: modify an existing object by moving its defining create
145%                      = off: no current drawing action
146%                     = translate: translate an existing object
147%                    = calibration: move a calibration point
148%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
149%            .CurrentOrigin: Origin of a curently drawn edit_object
150%            .CurrentLine: currently drawn menuline (A REVOIR)
151%            .CurrentObject: handle of the currently drawn edit_object
152%            .CurrentRectZoom: current rectangle used for CheckZoom
153
154% Properties attached to projection objects (create, menuline, menuplane...):
155%    'Tag'='proj_object': for all projection objects
156%    ObjectData.Type=...: style of projection object:
157%              .ProjMode
158%              .Coord: defines the position of the object
159%              .XMin,YMin....
160%              .XMax,YMax....
161%              .DX,DY,DZ
162%              .Phi, .Theta, .Psi : Euler angles
163%              .X,.Y,.U,.V.... : field data projected on the object
164%              .IndexObj: index in the list of UvData.Object
165           %during plotting
166%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
167%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
168% To each projection object #iobj, corresponds an axis
169% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
170% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
171
172%------------------------------------------------------------------------
173%------------------------------------------------------------------------
174%  I - MAIN FUNCTION uvmat
175%------------------------------------------------------------------------
176%------------------------------------------------------------------------
177function varargout = uvmat(varargin)
178
179% Begin initialization code - DO NOT EDIT
180gui_Singleton = 1;
181gui_State = struct('gui_Name',          mfilename, ...
182                   'gui_Singleton',     gui_Singleton, ...
183                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
184                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
185                   'gui_LayoutFcn',     [], ...
186                   'gui_Callback',      []);
187if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
188    gui_State.gui_Callback = str2func(varargin{1});
189end
190
191if nargout
192    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
193else
194    gui_mainfcn(gui_State, varargin{:});
195end
196% End initialization code - DO NOT EDIT
197
198%------------------------------------------------------------------------
199% --- Executes just before the GUI uvmat is made visible.
200function uvmat_OpeningFcn(hObject, eventdata, handles, input )
201%------------------------------------------------------------------------
202
203%% Choose default command menuline output for uvmat (standard GUI)
204handles.output = hObject;
205
206%% Update handles structure (standard GUI)
207guidata(hObject, handles);
208
209%% 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
855nbfield=[];%default
856nbfield_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
862testima=0; %test for image input
863imainfo=[];
864ColorType='falsecolor'; %default
865hhh=[];
866UvData.MovieObject{index}=VideoObject;
867if ~isempty(VideoObject)
868    imainfo=get(VideoObject);
869    testima=1;
870    nbfield_j=1;
871    TimeUnit='s';
872    XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
873    % %         nbfield=imainfo.NumberOfFrames;
874    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
875    ColorType='truecolor';
876elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
877    testima=1;
878    if ~isequal(SubDir,'')
879        RootFile=get(handles.RootFile,'String');
880        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
881    else
882        imainfo=imfinfo([FileBase FileIndices FileExt]);
883    end
884    ColorType=imainfo.ColorType;%='truecolor' for color images
885    if length(imainfo) >1 %case of image with multiple frames
886        nbfield=length(imainfo);
887        nbfield_j=1;
888    end
889end
890if isfield(imainfo,'Width') && isfield(imainfo,'Height')
891    if length(imainfo)>1
892        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
893        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
894    else
895        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
896        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
897    end
898else
899    set(handles.num_Npx,'String','');%fills nbre of pixels x box
900    set(handles.num_Npy,'String','');%fills nbre of pixels x box
901end
902set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
903
904%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
905XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
906[tild,tild,DocExt]=fileparts(XmlFileName);
907warntext='';%default warning message
908NbSlice=1;%default
909set(handles.RootPath,'BackgroundColor',[1 1 1])
910if ~isempty(XmlFileName)
911    set(handles.view_xml,'Visible','on')
912    set(handles.view_xml,'BackgroundColor',[1 1 0])
913    set(handles.view_xml,'String','view .xml')
914    drawnow
915    [XmlDataRead,warntext]=imadoc2struct(XmlFileName);
916    if ~isempty(warntext)
917        msgbox_uvmat('WARNING',warntext)
918    end
919    if isempty(XmlDataRead)
920        set(handles.view_xml,'Visible','off')
921    else
922        set(handles.view_xml,'String',['view ' DocExt])   
923        XmlData=XmlDataRead;
924        if isfield(XmlData,'TimeUnit')
925            if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
926                TimeUnit=XmlData.TimeUnit;
927            end
928        end
929        set(handles.view_xml,'BackgroundColor',[1 1 1])
930        drawnow
931        if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
932            if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
933                set (handles.nb_slice,'String','volume')
934            end
935            hgeometry_calib=findobj('tag','geometry_calib');
936            if ~isempty(hgeometry_calib)
937                GUserData=get(hgeometry_calib,'UserData');
938                if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName))
939                    answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
940                    if strcmp(answer,'Yes')
941                        geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib
942                    end
943                end
944            end
945        end
946    end
947end
948
949%% store last index in handles.lat_i and .last_j
950nbfield=max(max(i2_series));
951if isempty(nbfield)
952    nbfield=max(max(i1_series));
953end
954nbfield_j=max(max(j2_series));
955if isempty(nbfield_j)
956    nbfield_j=max(max(j1_series));
957end
958if ~isempty(XmlData.Time)
959    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
960    if isequal(size(XmlData.Time,1),1)
961        NomType=get(handles.NomType,'String');
962        XmlData.Time=(XmlData.Time)';
963    end
964end
965last_i_cell=get(handles.last_i,'String');
966if isempty(nbfield)
967    last_i_cell{1}='';
968else
969    last_i_cell{1}=num2str(nbfield);
970end
971set(handles.last_i,'String',last_i_cell)
972last_j_cell=get(handles.last_j,'String');
973if isempty(nbfield_j)
974     last_j_cell{1}='';
975else
976     last_j_cell{1}=num2str(nbfield_j);
977end
978set(handles.last_j,'String',last_j_cell);
979
980%% store geometric calibration in UvData
981if isfield(XmlData,'GeometryCalib')
982    GeometryCalib=XmlData.GeometryCalib;
983    if isempty(GeometryCalib)
984        set(handles.pxcm,'String','')
985        set(handles.pycm,'String','')
986        set(handles.transform_fct,'Value',1); %  no transform by default
987    else
988        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
989            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
990            set(handles.pxcm,'String','var')
991            set(handles.pycm,'String','var')
992        elseif isfield(GeometryCalib,'fx_fy')
993            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
994            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
995            set(handles.pxcm,'String',num2str(pixcmx))
996            set(handles.pycm,'String',num2str(pixcmy))
997        end
998        if ~get(handles.CheckFixLimits,'Value')
999            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
1000        end
1001        if isfield(GeometryCalib,'SliceCoord')
1002           
1003           siz=size(GeometryCalib.SliceCoord);
1004           if siz(1)>1
1005               NbSlice=siz(1);
1006               set(handles.slices,'Visible','on')
1007               set(handles.slices,'Value',1)
1008           end
1009           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
1010               set(handles.nb_slice,'String','volume')
1011           else
1012               set(handles.nb_slice,'String',num2str(NbSlice))
1013           end
1014           slices_Callback([],[], handles)
1015        end           
1016    end
1017end
1018
1019%% update the data attached to the uvmat interface
1020if ~isempty(TimeUnit)
1021    set(handles.time_txt,'String',['time (' TimeUnit ')'])
1022end
1023UvData.TimeUnit=TimeUnit;
1024UvData.XmlData{index}=XmlData;
1025UvData.NewSeries=1;
1026% UvData.MovieObject=MovieObject;
1027
1028%display warning message
1029if ~isequal(warntext,'')
1030    msgbox_uvmat('WARNING',warntext);
1031end
1032
1033%% set default options in menu 'Fields'
1034if ~testima
1035    testcivx=0;
1036    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
1037        set(handles_Fields,'Value',1)
1038        set(handles_Fields,'String',{'get_field...'})
1039        UvData=rmfield(UvData,'FieldsString');
1040    else
1041        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
1042        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
1043            FieldList=calc_field;
1044            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
1045            set(handles_Fields,'Value',2) % set menu to 'velocity'
1046            col_vec=FieldList;
1047            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
1048            testcivx=1;
1049        end
1050        if ~testcivx
1051            set(handles_Fields,'Value',1) % set menu to 'get_field...
1052            set(handles_Fields,'String',{'get_field...'})
1053            col_vec={'get_field...'};
1054        end
1055        set(handles.ColorScalar,'String',col_vec)
1056    end
1057end
1058set(handles.uvmat,'UserData',UvData)
1059
1060%% set index navigation options and refresh plots
1061scan_option='i';%default
1062state_j='off'; %default
1063if index==2
1064    if get(handles.scan_j,'Value')
1065        scan_option='j'; %keep the scan option for the second fiel series
1066    end
1067    if strcmp(get(handles.j1,'Visible'),'on')
1068        state_j='on';
1069    end
1070end
1071if ~isempty(j1_series)
1072        state_j='on';
1073        if isequal(nbfield,1) &&index==1
1074            scan_option='j'; %scan j index by default if nbfield=1               
1075        end
1076end
1077if isequal(scan_option,'i')
1078     set(handles.scan_i,'Value',1)
1079     scan_i_Callback([],[], handles);
1080else
1081     set(handles.scan_j,'Value',1)
1082     scan_j_Callback([],[], handles);
1083end
1084set(handles.scan_j,'Visible',state_j)
1085set(handles.j1,'Visible',state_j)
1086set(handles.j2,'Visible',state_j)
1087set(handles.last_j,'Visible',state_j);
1088set(handles.frame_j,'Visible',state_j);
1089set(handles.j_text,'Visible',state_j);
1090if ~isempty(i2_series)||~isempty(j2_series)
1091    set(handles.CheckFixPair,'Visible','on')
1092elseif index==1
1093    set(handles.CheckFixPair,'Visible','off')
1094end
1095
1096%% view the field 
1097run0_Callback([],[], handles); %view field
1098mask_test=get(handles.CheckMask,'value');
1099if mask_test
1100    MaskData=get(handles.CheckMask,'UserData');
1101    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1102          delete(MaskData.maskhandle)    %delete old mask
1103    end
1104    CheckMask_Callback([],[],handles)
1105end
1106
1107%% update list of recent files in the menubar and save it for future opening
1108MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
1109    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
1110str_find=strcmp(FileName,MenuFile);
1111if isempty(find(str_find,1))
1112    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
1113end
1114for ifile=1:min(length(MenuFile),5)
1115    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
1116    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
1117end
1118dir_perso=prefdir;
1119profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1120if exist(profil_perso,'file')
1121    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1122else
1123    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
1124end
1125
1126
1127%------------------------------------------------------------------------
1128% --- switch file index scanning options scan_i and scan_j in an exclusive way
1129function scan_i_Callback(hObject, eventdata, handles)
1130%------------------------------------------------------------------------
1131if get(handles.scan_i,'Value')==1
1132    set(handles.scan_i,'BackgroundColor',[1 1 0])
1133    set(handles.scan_j,'Value',0)
1134else
1135    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1136    set(handles.scan_j,'Value',1)
1137end
1138scan_j_Callback(hObject, eventdata, handles)
1139
1140%------------------------------------------------------------------------
1141% --- switch file index scanning options scan_i and scan_j in an exclusive way
1142function scan_j_Callback(hObject, eventdata, handles)
1143%------------------------------------------------------------------------
1144if get(handles.scan_j,'Value')==1
1145    set(handles.scan_j,'BackgroundColor',[1 1 0])
1146    set(handles.scan_i,'Value',0)
1147    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1148%     NomType=get(handles.NomType,'String');
1149%     switch NomType
1150%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1151%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1152%     otherwise
1153%         set(handles.CheckFixPair,'Visible','off')
1154%     end
1155else
1156    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1157    set(handles.scan_i,'Value',1)
1158    set(handles.scan_i,'BackgroundColor',[1 1 0])
1159    set(handles.CheckFixPair,'Visible','off')
1160end
1161
1162%------------------------------------------------------------------------
1163function i1_Callback(hObject, eventdata, handles)
1164%------------------------------------------------------------------------
1165set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1166NomType=get(handles.NomType,'String');
1167i1=stra2num(get(handles.i1,'String'));
1168i2=stra2num(get(handles.i2,'String'));
1169j1=stra2num(get(handles.j1,'String'));
1170j2=stra2num(get(handles.j2,'String'));
1171indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1172%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1173set(handles.FileIndex,'String',indices)
1174set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1175if get(handles.SubField,'Value')==1
1176    NomType_1=get(handles.NomType_1,'String');
1177    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1178     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1179     set(handles.FileIndex_1,'String',indices)
1180     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1181end
1182
1183%------------------------------------------------------------------------
1184function i2_Callback(hObject, eventdata, handles)
1185%------------------------------------------------------------------------
1186set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1187i1_Callback(hObject, eventdata, handles)
1188
1189%------------------------------------------------------------------------
1190function j1_Callback(hObject, eventdata, handles)
1191%------------------------------------------------------------------------
1192set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1193i1_Callback(hObject, eventdata, handles)
1194
1195%------------------------------------------------------------------------
1196function j2_Callback(hObject, eventdata, handles)
1197%------------------------------------------------------------------------
1198set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1199i1_Callback(hObject, eventdata, handles)
1200
1201%------------------------------------------------------------------------
1202function slices_Callback(hObject, eventdata, handles)
1203%------------------------------------------------------------------------
1204if get(handles.slices,'Value')==1
1205    set(handles.slices,'BackgroundColor',[1 1 0])
1206    set(handles.nb_slice,'Visible','on')
1207    set(handles.z_text,'Visible','on')
1208    set(handles.z_index,'Visible','on')
1209    nb_slice_Callback(hObject, eventdata, handles)
1210else
1211    set(handles.nb_slice,'Visible','off')
1212    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1213    set(handles.z_text,'Visible','off')
1214    set(handles.z_index,'Visible','off')
1215    set(handles.masklevel,'Value',1)
1216    set(handles.masklevel,'String',{'1'})
1217end
1218
1219%------------------------------------------------------------------------
1220function nb_slice_Callback(hObject, eventdata, handles)
1221%------------------------------------------------------------------------
1222nb_slice_str=get(handles.nb_slice,'String');
1223if isequal(nb_slice_str,'volume')
1224    num=stra2num(get(handles.j1,'String'));
1225    last_j=get(handles.last_j,'String');
1226    nbslice=str2double(last_j{1});
1227else
1228    num=str2double(get(handles.i1,'String'));
1229    nbslice=str2double(get(handles.nb_slice,'String'));
1230end
1231z=mod(num-1,nbslice)+1;
1232set(handles.z_index,'String',num2str(z))
1233for ilist=1:nbslice
1234    list_index{ilist,1}=num2str(ilist);
1235end   
1236set(handles.masklevel,'String',list_index)
1237set(handles.masklevel,'Value',z)
1238
1239%------------------------------------------------------------------------
1240% --- Executes on button press in view_xml.
1241function view_xml_Callback(hObject, eventdata, handles)
1242%------------------------------------------------------------------------
1243%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1244 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1245FileBase=fullfile(RootPath,RootFile);
1246option=get(handles.view_xml,'String');
1247if isequal(option,'view .xml')
1248    FileXml=[FileBase '.xml'];
1249    heditxml=editxml(FileXml);
1250end
1251
1252%------------------------------------------------------------------------
1253% --- Executes on button press in CheckMask.
1254function CheckMask_Callback(hObject, eventdata, handles)
1255%------------------------------------------------------------------------
1256%case of view mask selection
1257if isequal(get(handles.CheckMask,'Value'),1)
1258   % [FF,RootPath,FileBase]=read_file_boxes(handles);
1259     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1260     FileBase=fullfile(RootPath,RootFile);
1261    num_i1=stra2num(get(handles.i1,'String'));
1262    num_j1=stra2num(get(handles.j1,'String'));
1263    currentdir=pwd; 
1264    cd(RootPath);
1265    maskfiles=dir('*_*mask_*.png');%look for a mask file
1266    cd(currentdir);%come back to the working directory
1267    mdetect=0;
1268    if ~isempty(maskfiles)
1269        for ilist=1:length(maskfiles)
1270            maskname=maskfiles(ilist).name;% take the first mask file in the list
1271            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1272%             [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1273             [tild,Name]=fileparts(maskname);
1274            Namedouble=double(Name);
1275            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1276            ind_mask=findstr('mask',Name);
1277            i=ind_mask-1;
1278            while val(i)==0 && i>0
1279                i=i-1;
1280            end
1281            nbmask_str=str2num(Name(i+1:ind_mask-1));
1282            if ~isempty(nbmask_str)
1283                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1284            end
1285        end
1286        if isequal(min(nbslice),max(nbslice))
1287            nbslice=nbslice(1);
1288        else
1289            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1290            return
1291        end
1292        if ~isempty(nbslice) && Name(i)=='_'
1293            Mask.Base=[FileBase Name(i:ind_mask+3)];
1294            Mask.NbSlice=nbslice;
1295            num_i1=mod(num_i1-1,nbslice)+1;
1296            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1297            [RootPath,RootFile]=fileparts(Mask.Base);
1298            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1299            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1300            mdetect=exist(maskname,'file');
1301            if mdetect
1302                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1303                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1304                set(handles.CheckMask,'UserData',Mask);
1305                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1306                if nbslice > 1
1307                    set(handles.slices,'value',1)
1308                    slices_Callback(hObject, eventdata, handles)
1309                end
1310            end
1311        end
1312    end
1313    errormsg=[];%default
1314    if mdetect==0
1315        [FileName, PathName, filterindex] = uigetfile( ...
1316            {'*.png', ' (*.png)';
1317            '*.png',  '.png files '; ...
1318            '*.*', 'All Files (*.*)'}, ...
1319            'Pick a mask file *.png',FileBase);
1320        maskname=fullfile(PathName,FileName);
1321        if ~exist(maskname,'file')
1322            errormsg='no file browsed';
1323        end
1324        [RootDir,SubDir,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1325        Mask.Base=fullfile(RootDir,SubDir,RootFile);
1326        Mask.NbSlice=1;
1327        set(handles.CheckMask,'UserData',Mask);
1328        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1329    end
1330    if isempty(errormsg)
1331        errormsg=update_mask(handles,num_i1,num_j1);
1332    end
1333    if ~isempty(errormsg)
1334            set(handles.CheckMask,'Value',0)
1335            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1336     end
1337else % desactivate mask display
1338    MaskData=get(handles.CheckMask,'UserData');
1339    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1340          delete(MaskData.maskhandle)   
1341    end
1342    set(handles.CheckMask,'UserData',[])   
1343    UvData=get(handles.uvmat,'UserData');
1344    if isfield(UvData,'MaskName')
1345        UvData=rmfield(UvData,'MaskName');
1346        set(handles.uvmat,'UserData',UvData)
1347    end
1348    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1349end
1350
1351%------------------------------------------------------------------------
1352function errormsg=update_mask(handles,num_i1,num_j1)
1353%------------------------------------------------------------------------
1354errormsg=[];%default
1355MaskData=get(handles.CheckMask,'UserData');
1356if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1357    uistack(MaskData.maskhandle,'top');
1358end
1359num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1360[RootPath,RootFile]=fileparts(MaskData.Base);
1361MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1362UvData=get(handles.uvmat,'UserData');
1363%update mask image if the mask is new
1364if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1365    UvData.MaskName=MaskName; %update the recorded name on UvData
1366    set(handles.uvmat,'UserData',UvData);
1367    if ~exist(MaskName,'file')
1368        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1369            delete(MaskData.maskhandle)   
1370        end
1371    else
1372        %read mask image
1373        Mask.AName='image';
1374        Mask.A=imread(MaskName);
1375        npxy=size(Mask.A);
1376        test_error=0;
1377        if length(npxy)>2
1378            errormsg=[MaskName ' is not a grey scale image'];
1379            return
1380        elseif ~isa(Mask.A,'uint8')
1381            errormsg=[MaskName ' is not a 8 bit grey level image'];
1382            return
1383        end
1384        Mask.AX=[0.5 npxy(2)-0.5];
1385        Mask.AY=[npxy(1)-0.5 0.5 ];
1386        Mask.CoordUnit='pixel';
1387        if isequal(get(handles.slices,'Value'),1)
1388           NbSlice=str2num(get(handles.nb_slice,'String'));
1389           num_i1=str2num(get(handles.i1,'String'));
1390           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1391        end
1392        %px to phys or other transform on field
1393         menu_transform=get(handles.transform_fct,'String');
1394        choice_value=get(handles.transform_fct,'Value');
1395        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1396        transform_list=get(handles.transform_fct,'UserData');
1397        transform=transform_list{choice_value};
1398        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1399            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1400                Calib=UvData.XmlData{1}.GeometryCalib;
1401                Mask=transform(Mask,UvData.XmlData{1});
1402            end
1403        end
1404        flagmask=Mask.A < 200;
1405       
1406        %make brown color image
1407        imflag(:,:,1)=0.9*flagmask;
1408        imflag(:,:,2)=0.7*flagmask;
1409        imflag(:,:,3)=zeros(size(flagmask));
1410       
1411        %update mask image
1412        hmask=[]; %default
1413        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1414            hmask=MaskData.maskhandle;
1415        end
1416        if ~isempty(hmask)
1417            set(hmask,'CData',imflag)   
1418            set(hmask,'AlphaData',flagmask*0.6)
1419            set(hmask,'XData',Mask.AX);
1420            set(hmask,'YData',Mask.AY);
1421%             uistack(hmask,'top')
1422        else
1423            axes(handles.axes3)
1424            hold on   
1425            size(flagmask)
1426           % MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1427            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask)));
1428%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1429            set(handles.CheckMask,'UserData',MaskData)
1430        end
1431    end
1432end
1433
1434%------------------------------------------------------------------------
1435%------------------------------------------------------------------------
1436% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1437%------------------------------------------------------------------------
1438
1439%------------------------------------------------------------------------
1440% --- Executes on button press in runplus: make one step forward and call
1441% --- run0. The step forward is along the fields series 1 or 2 depending on
1442% --- the scan_i and scan_j check box (exclusive each other)
1443function runplus_Callback(hObject, eventdata, handles)
1444%------------------------------------------------------------------------
1445set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1446drawnow
1447%TODO: introduce the option: increment ='*' to move to the next available view
1448increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1449% if isnan(increment)
1450%     set(handles.increment_scan,'String','1')%default value
1451%     increment=1;
1452% end
1453errormsg=runpm(hObject,eventdata,handles,increment);
1454if ~isempty(errormsg)
1455    msgbox_uvmat('ERROR',errormsg);
1456end
1457set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1458
1459%------------------------------------------------------------------------
1460% --- Executes on button press in runmin: make one step backward and call
1461% --- run0. The step backward is along the fields series 1 or 2 depending on
1462% --- the scan_i and scan_j check box (exclusive each other)
1463function runmin_Callback(hObject, eventdata, handles)
1464%------------------------------------------------------------------------
1465set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1466drawnow
1467increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1468% if isnan(increment)
1469%     set(handles.increment_scan,'String','1')%default value
1470%     increment=1;
1471% end
1472errormsg=runpm(hObject,eventdata,handles,increment);
1473if ~isempty(errormsg)
1474    msgbox_uvmat('ERROR',errormsg);
1475end
1476set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1477
1478%------------------------------------------------------------------------
1479% -- Executes on button press in Movie: make a series of +> steps
1480function Movie_Callback(hObject, eventdata, handles)
1481%------------------------------------------------------------------------
1482set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1483drawnow
1484increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1485% if isnan(increment)
1486%     set(handles.increment_scan,'String','1')%default value
1487%     increment=1;
1488% end
1489set(handles.STOP,'Visible','on')
1490set(handles.speed,'Visible','on')
1491set(handles.speed_txt,'Visible','on')
1492set(handles.Movie,'BusyAction','queue')
1493UvData=get(handles.uvmat,'UserData');
1494
1495while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1496        errormsg=runpm(hObject,eventdata,handles,increment);
1497        if ~isempty(errormsg)
1498            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1499            return
1500        end
1501        pause(1.02-get(handles.speed,'Value'))% wait for next image
1502end
1503if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1504    UvData.aviobj=close(UvData.aviobj);
1505   set(handles.uvmat,'UserData',UvData);
1506end
1507set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1508
1509%------------------------------------------------------------------------
1510% -- Executes on button press in Movie: make a series of <- steps
1511function MovieBackward_Callback(hObject, eventdata, handles)
1512%------------------------------------------------------------------------
1513set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1514drawnow
1515increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1516set(handles.STOP,'Visible','on')
1517set(handles.speed,'Visible','on')
1518set(handles.speed_txt,'Visible','on')
1519set(handles.MovieBackward,'BusyAction','queue')
1520UvData=get(handles.uvmat,'UserData');
1521
1522while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1523        errormsg=runpm(hObject,eventdata,handles,increment);
1524        if ~isempty(errormsg)
1525            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1526            return
1527        end
1528        pause(1.02-get(handles.speed,'Value'))% wait for next image
1529end
1530if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1531    UvData.aviobj=close(UvData.aviobj);
1532   set(handles.uvmat,'UserData',UvData);
1533end
1534set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1535
1536%------------------------------------------------------------------------
1537function STOP_Callback(hObject, eventdata, handles)
1538%------------------------------------------------------------------------
1539set(handles.movie_pair,'BusyAction','Cancel')
1540set(handles.movie_pair,'value',0)
1541set(handles.Movie,'BusyAction','Cancel')
1542set(handles.MovieBackward,'BusyAction','Cancel')
1543set(handles.MenuExportMovie,'BusyAction','Cancel')
1544set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1545set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1546set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1547
1548%------------------------------------------------------------------------
1549% --- function activated by runplus and run minus
1550function errormsg=runpm(hObject,eventdata,handles,increment)
1551%------------------------------------------------------------------------
1552errormsg='';%default
1553%% check for movie pair status
1554movie_status=get(handles.movie_pair,'Value');
1555if isequal(movie_status,1)
1556    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1557end
1558
1559%% read the current input file name(s) and field indices
1560InputFile=read_GUI(handles.InputFile);
1561InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1562InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1563FileExt=InputFile.FileExt;
1564NomType=get(handles.NomType,'String');
1565i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1566i2=[];%default
1567if strcmp(get(handles.i2,'Visible'),'on')
1568    i2=str2num(get(handles.i2,'String'));
1569end
1570j1=[];
1571if strcmp(get(handles.j1,'Visible'),'on')
1572    j1=stra2num(get(handles.j1,'String'));
1573end
1574j2=j1;
1575if strcmp(get(handles.j2,'Visible'),'on')
1576    j2=stra2num(get(handles.j2,'String'));
1577end
1578sub_value= get(handles.SubField,'Value');
1579if sub_value % a second input file has been entered
1580     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1581    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);
1582%     InputFile.NomType_1=get(handles.NomType_1,'String');
1583else
1584    filename_1=[];
1585end   
1586
1587%% increment (or decrement) the field indices and update the input filename(s)
1588CheckSearch=0;
1589if isempty(increment)
1590    CheckSearch=1;% search for the next available file
1591    set(handles.CheckFixPair,'Value',0)
1592end
1593CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1594
1595% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1596if CheckFixPair
1597    if get(handles.scan_i,'Value')==1% case of scanning along index i
1598        i1=i1+increment;
1599        i2=i2+increment;
1600        if sub_value
1601            i1_1=i1_1+increment;
1602            i2_1=i2_1+increment;
1603        end
1604    else % case of scanning along index j (burst numbers)
1605        j1=j1+increment;
1606        j2=j2+increment;
1607        if sub_value
1608            j1_1=j1_1+increment;
1609            j2_1=j2_1+increment;
1610        end
1611    end
1612   
1613% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected):
1614% the list of existing indices recorded in UvData is used
1615else
1616    UvData=get(handles.uvmat,'UserData');
1617    ref_i=i1;
1618    if ~isempty(i2)
1619        ref_i=floor((i1+i2)/2);% current reference index i
1620    end
1621    ref_j=1;
1622    if ~isempty(j1)
1623        ref_j=j1;
1624        if ~isempty(j2)
1625            ref_j=floor((j1+j2)/2);% current reference index j
1626        end
1627    end
1628    if ~isempty(increment)
1629        if get(handles.scan_i,'Value')==1% case of scanning along index i
1630            ref_i=ref_i+increment;% increment the current reference index i
1631        else % case of scanning along index j (burst numbers)
1632            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1633        end
1634    else % free increment
1635        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
1636            step=1;
1637        else
1638            step=-1;
1639        end
1640        if get(handles.scan_i,'Value')==1% case of scanning along index i
1641            ref_i=ref_i+step;
1642            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
1643                ref_i=ref_i+step;
1644            end
1645        else % case of scanning along index j (burst numbers)
1646            ref_j=ref_j+step;
1647            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
1648                ref_j=ref_j+step;
1649            end
1650        end
1651    end
1652    if ref_i<0
1653        errormsg='minimum i index reached';
1654    elseif ref_j<0
1655        errormsg='minimum j index reached';
1656    elseif ref_i+1>size(UvData.i1_series{1},1)
1657        errormsg='maximum i index reached';
1658    elseif ref_j+1>size(UvData.i1_series{1},2)
1659        errormsg='maximum j index reached';
1660    end
1661    if ~isempty(errormsg)
1662        return
1663    end
1664    i1_subseries=UvData.i1_series{1}(ref_i+1,ref_j+1,:);
1665    i1_subseries=i1_subseries(i1_subseries>0);
1666    if isempty(i1_subseries)
1667        errormsg='no next file';
1668        return
1669    else
1670        i1=i1_subseries(end);
1671    end
1672    if ~isempty(UvData.i2_series{1})
1673        i2_subseries=UvData.i2_series{1}(ref_i+1,ref_j+1,:);
1674        i2_subseries=i2_subseries(i2_subseries>0);
1675        i2=i2_subseries(end);
1676    end
1677    if ~isempty(UvData.j1_series{1})
1678        j1_subseries=UvData.j1_series{1}(ref_i+1,ref_j+1,:);
1679        j1_subseries=j1_subseries(j1_subseries>0);
1680        j1=j1_subseries(end);
1681    end
1682    if ~isempty(UvData.j2_series{1})
1683        j2_subseries=UvData.j2_series{1}(ref_i+1,ref_j+1,:);
1684        j2_subseries=j2_subseries(j2_subseries>0);
1685        j2=j2_subseries(end);
1686    end 
1687    % case of a second file series
1688    if numel(UvData.i1_series)>=2
1689        i1_subseries=UvData.i1_series{2}(ref_i+1,ref_j+1,:);
1690        i1_subseries=i1_subseries(i1_subseries>0);
1691        i1_1=i1_subseries(end);
1692        if ~isempty(UvData.i2_series{2})
1693            i2_subseries=UvData.i2_series{2}(ref_i+1,ref_j+1,:);
1694            i2_subseries=i2_subseries(i2_subseries>0);
1695            i2_1=i2_subseries(end);
1696        end
1697        if ~isempty(UvData.j1_series{2})
1698            j1_subseries=UvData.j1_series{2}(ref_i+1,ref_j+1,:);
1699            j1_subseries=j1_subseries(j1_subseries>0);
1700            j1_1=j1_subseries(end);
1701        end
1702        if ~isempty(UvData.j2_series{2})
1703            j2_subseries=UvData.j2_series{2}(ref_i+1,ref_j+1,:);
1704            j2_subseries=j2_subseries(j2_subseries>0);
1705            j2_1=j2_subseries(end);
1706        end
1707    end
1708end
1709filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1710if sub_value
1711    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);
1712end
1713
1714%% refresh plots
1715errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);
1716
1717%% update the index counters if the index move is successfull
1718if isempty(errormsg)
1719    set(handles.i1,'String',num2stra(i1,NomType,1));
1720    if isequal(i2,i1)
1721        set(handles.i2,'String','');
1722    else
1723        set(handles.i2,'String',num2stra(i2,NomType,1));
1724    end
1725    set(handles.j1,'String',num2stra(j1,NomType,2));
1726    if isequal(j2,j1)
1727        set(handles.j2,'String','');
1728    else
1729        set(handles.j2,'String',num2stra(j2,NomType,2));
1730    end
1731    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1732    set(handles.FileIndex,'String',indices);
1733    if ~isempty(filename_1)
1734        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1735        set(handles.FileIndex_1,'String',indices_1);
1736    end
1737    if isequal(movie_status,1)
1738        set(handles.movie_pair,'Value',1)
1739        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1740    end
1741end
1742
1743%------------------------------------------------------------------------
1744% --- Executes on button press in movie_pair: create an alternating movie with two view
1745function movie_pair_Callback(hObject, eventdata, handles)
1746%------------------------------------------------------------------------
1747%% stop movie action if the movie_pair button is off
1748if ~get(handles.movie_pair,'value')
1749    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1750    set(handles.i2,'String','')
1751    set(handles.j2,'String','')
1752    return
1753else
1754    set(handles.movie_pair,'BusyAction','queue')
1755end
1756
1757%% initialisation
1758set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1759drawnow
1760list_fields=get(handles.Fields,'String');% list menu fields
1761index_fields=get(handles.Fields,'Value');% selected string index
1762FieldName=list_fields{index_fields}; % selected field
1763UvData=get(handles.uvmat,'UserData');
1764if isequal(FieldName,'image')
1765    test_1=0;
1766    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1767    NomType=get(handles.NomType,'String');
1768else
1769    list_fields=get(handles.Fields_1,'String');% list menu fields
1770    index_fields=get(handles.Fields_1,'Value');% selected string index
1771    FieldName=list_fields{index_fields}; % selected field
1772    if isequal(FieldName,'image')
1773        test_1=1;
1774        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1775    else
1776        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1777        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1778        set(handles.movie_pair,'Value',0)
1779        return
1780    end
1781end
1782num_i1=str2num(get(handles.i1,'String'));
1783num_j1=stra2num(get(handles.j1,'String'));
1784num_i2=str2num(get(handles.i2,'String'));
1785num_j2=stra2num(get(handles.j2,'String'));
1786if isempty(num_j2)
1787    if isempty(num_i2)   
1788        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1789        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1790         set(handles.movie_pair,'Value',0)
1791        return
1792    else
1793        num_j2=num_j1;%repeat the index i1 by default
1794    end
1795end
1796if isempty(num_i2)
1797    num_i2=num_i1;%repeat the index i1 by default
1798end
1799% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1800imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
1801if ~exist(imaname_1,'file')
1802      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1803      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1804       set(handles.movie_pair,'Value',0)
1805      return
1806end
1807
1808%% read the second image
1809Field.AName='image';
1810if test_1
1811    Field_a=UvData.Field_1;
1812else
1813    Field_a=UvData.Field;
1814end
1815Field_b.AX=Field_a.AX;
1816Field_b.AY=Field_a.AY;
1817% z index
1818nbslice=str2double(get(handles.nb_slice,'String'));
1819if ~isempty(nbslice)
1820    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1821end
1822Field_b.CoordUnit='pixel';
1823
1824%% determine the input file type
1825if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1826    FileType='movie';
1827elseif isequal(lower(Ext),'.avi')
1828    FileType='avi';
1829elseif isequal(lower(Ext),'.vol')
1830    FileType='vol';
1831else
1832   form=imformats(Ext(2:end));
1833   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1834       if isequal(NomType,'*');
1835           FileType='multimage';
1836       else
1837           FileType='image';
1838       end
1839   end
1840end
1841switch FileType
1842        case 'movie'
1843            if test_1
1844                Field_b.A=read(UvData.MovieObject{2},num_i2);
1845            else
1846                Field_b.A=read(UvData.MovieObject{1},num_i2);
1847            end
1848        case 'avi'
1849            mov=aviread(imaname_1,num_i2);
1850            Field_b.A=frame2im(mov(1));
1851        case 'vol'
1852            Field_b.A=imread(imaname_1);
1853        case 'multimage'
1854            Field_b.A=imread(imaname_1,num_i2);
1855        case 'image'
1856            Field_b.A=imread(imaname_1);
1857end
1858if get(handles.slices,'Value')
1859    Field.ZIndex=str2double(get(handles.z_index,'String'));
1860end
1861
1862%px to phys or other transform on field
1863menu_transform=get(handles.transform_fct,'String');
1864choice_value=get(handles.transform_fct,'Value');
1865transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1866transform_list=get(handles.transform_fct,'UserData');
1867transform=transform_list{choice_value};
1868if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1869    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
1870        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
1871        Field_b=transform(Field_b,UvData.XmlData{2});
1872    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
1873        Field_b=transform(Field_b,UvData.XmlData{1});
1874    end
1875end
1876
1877 % make movie until movie speed is set to 0 or STOP is activated
1878hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1879set(handles.STOP,'Visible','on')
1880set(handles.speed,'Visible','on')
1881set(handles.speed_txt,'Visible','on')
1882while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1883    % read and plot the series of images in non erase mode
1884    set(hima,'CData',Field_b.A);
1885    pause(1.02-get(handles.speed,'Value'));% wait for next image
1886    set(hima,'CData',Field_a.A);
1887    pause(1.02-get(handles.speed,'Value'));% wait for next image
1888end
1889set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1890 set(handles.movie_pair,'Value',0)
1891
1892%------------------------------------------------------------------------
1893% --- Executes on button press in run0.
1894function run0_Callback(hObject, eventdata, handles)
1895%------------------------------------------------------------------------
1896set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1897drawnow
1898[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1899filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1900filename_1=[];%default
1901if get(handles.SubField,'Value')
1902    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
1903    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
1904end
1905num_i1=stra2num(get(handles.i1,'String'));
1906num_i2=stra2num(get(handles.i2,'String'));
1907num_j1=stra2num(get(handles.j1,'String'));
1908num_j2=stra2num(get(handles.j2,'String'));
1909
1910errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
1911
1912if ~isempty(errormsg)
1913      msgbox_uvmat('ERROR',errormsg);
1914else
1915    set(handles.i1,'BackgroundColor',[1 1 1])
1916    set(handles.i2,'BackgroundColor',[1 1 1])
1917    set(handles.j1,'BackgroundColor',[1 1 1])
1918    set(handles.j2,'BackgroundColor',[1 1 1])
1919    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1920    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1921end   
1922set(handles.run0,'BackgroundColor',[1 0 0])
1923
1924
1925%------------------------------------------------------------------------
1926% --- read the input files and refresh all the plots, including projection.
1927% OUTPUT:
1928%  errormsg: error message char string  =[] by default
1929% INPUT:
1930% filename: first input file (=[] in the absence of input file)
1931% filename_1: second input file (=[] in the asbsenc of secodn input file)
1932% num_i1,num_i2,num_j1,num_j2; frame indices
1933% Field: structure describing an optional input field (then replace the input file)
1934
1935function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,Field)
1936%------------------------------------------------------------------------
1937
1938%% initialisation
1939abstime=[];
1940abstime_1=[];
1941dt=[];
1942if ~exist('Field','var')
1943    Field={};
1944end
1945UvData=get(handles.uvmat,'UserData');
1946if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1947    delete(handles.UVMAT_title)
1948end
1949
1950%% determine the main input file information for action
1951FileType=[];%default
1952if ~exist(FileName,'file')
1953    errormsg=['input file ' FileName ' does not exist'];
1954    return
1955end
1956NomType=get(handles.NomType,'String');
1957% NomType=get(handles.FileIndex,'UserData');
1958%update the z position index
1959nbslice_str=get(handles.nb_slice,'String');
1960if isequal(nbslice_str,'volume')%NOT USED
1961    z_index=num_j1;
1962    set(handles.z_index,'String',num2str(z_index))
1963else
1964    nbslice=str2num(nbslice_str);
1965    z_index=mod(num_i1-1,nbslice)+1;
1966    set(handles.z_index,'String',num2str(z_index))
1967end
1968% refresh menu for save_mask if relevant
1969masknumber=get(handles.masklevel,'String');
1970if length(masknumber)>=z_index
1971    set(handles.masklevel,'Value',z_index)
1972end
1973
1974%% read the first input field if a filename has been introduced
1975ParamIn.ColorVar='';%default variable name for vector color
1976frame_index=1;%default
1977if ~isempty(FileName)
1978    FieldName='';%default
1979    VelType='';%default
1980%     FileType=UvData.FileType{1};
1981    switch UvData.FileType{1}
1982        case {'civx','civdata','netcdf'};
1983            list_fields=get(handles.Fields,'String');% list menu fields
1984  %          index_fields=get(handles.Fields,'Value');% selected string index
1985            FieldName= list_fields{get(handles.Fields,'Value')}; % selected field
1986            if ~strcmp(FieldName,'get_field...')
1987                if get(handles.FixVelType,'Value')
1988                    VelTypeList=get(handles.VelType,'String');
1989                    VelType=VelTypeList{get(handles.VelType,'Value')};
1990                end
1991            end
1992            if strcmp(FieldName,'velocity')
1993                list_code=get(handles.ColorCode,'String');% list menu fields
1994                index_code=get(handles.ColorCode,'Value');% selected string index
1995                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
1996                    list_code=get(handles.ColorScalar,'String');% list menu fields
1997                    index_code=get(handles.ColorScalar,'Value');% selected string index
1998                    ParamIn.ColorVar= list_code{index_code}; % selected field
1999                end
2000            end
2001        case {'video','mmreader'}
2002            ParamIn=UvData.MovieObject{1};     
2003            if ~strcmp(NomType,'*')
2004                frame_index=num_j1;%frame index for movies or multimage
2005            else
2006                frame_index=num_i1;
2007            end
2008        case 'multimage'
2009            if ~strcmp(NomType,'*')
2010                frame_index=num_j1;%frame index for movies or multimage
2011            else
2012                frame_index=num_i1;
2013            end
2014        case 'vol' %TODO: update
2015            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2016                ParamIn.Npy=UvData.XmlData.Npy;
2017                ParamIn.Npx=UvData.XmlData.Npx;
2018            else           
2019                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2020                return
2021            end
2022    end
2023    if isstruct (ParamIn)
2024    ParamIn.FieldName=FieldName;
2025    ParamIn.VelType=VelType;
2026    ParamIn.GUIName='get_field';
2027    end
2028    [Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index);
2029    if ~isempty(errormsg)
2030        errormsg=['error in reading ' FileName ': ' errormsg];
2031        return
2032    end 
2033    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2034        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2035        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2036    end
2037    if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2038        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2039    end
2040    if isfield(ParamOut,'TimeValue')
2041        Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2042    end
2043end
2044
2045%% choose and read a second field FileName_1 if defined
2046VelType_1=[];%default
2047FieldName_1=[];
2048ParamOut_1=[];
2049frame_index_1=1;
2050if ~isempty(FileName_1)
2051    if ~exist(FileName_1,'file')
2052        errormsg=['second file ' FileName_1 ' does not exist'];
2053        return
2054    end
2055    Name=FileName_1;
2056    switch UvData.FileType{2}
2057        case {'civx','civdata','netcdf'};
2058            list_fields=get(handles.Fields_1,'String');% list menu fields
2059            FieldName_1= list_fields{get(handles.Fields_1,'Value')}; % selected field
2060            if ~strcmp(FieldName,'get_field...')
2061                if get(handles.FixVelType,'Value')
2062                    VelTypeList=get(handles.VelType_1,'String');
2063                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2064                end
2065            end
2066            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2067                list_code=get(handles.ColorCode,'String');% list menu fields
2068                index_code=get(handles.ColorCode,'Value');% selected string index
2069                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2070                    list_code=get(handles.ColorScalar,'String');% list menu fields
2071                    index_code=get(handles.ColorScalar,'Value');% selected string index
2072                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2073                end
2074            end
2075        case {'video','mmreader'}
2076            ParamIn_1=UvData.MovieObject{2};
2077                        if ~strcmp(NomType_1,'*')
2078                frame_index_1=num_j1;%frame index for movies or multimage
2079            else
2080                frame_index_1=num_i1;
2081            end 
2082         case 'multimage'
2083            if ~strcmp(NomType_1,'*')
2084                frame_index_1=num_j1;%frame index for movies or multimage
2085            else
2086                frame_index_1=num_i1;
2087            end   
2088        case 'vol' %TODO: update
2089            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2090                ParamIn_1.Npy=UvData.XmlData.Npy;
2091                ParamIn_1.Npx=UvData.XmlData.Npx;
2092            else
2093                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2094                return
2095            end
2096    end
2097    if isequal(get(handles.NomType_1,'Visible'),'on')
2098    NomType_1=get(handles.NomType_1,'String');
2099    else
2100        NomType_1=get(handles.NomType,'String');
2101    end
2102    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2103    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2104        if isfield(UvData,'FileName_1')%&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2105            test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
2106        end
2107    end
2108    if test_keepdata_1
2109        Field{2}=UvData.Field_1;% keep the stored field
2110        ParamOut_1=UvData.ParamOut_1;
2111    else
2112        ParamIn_1.FieldName=FieldName_1;
2113        ParamIn_1.VelType=VelType_1;
2114        ParamIn_1.GUIName='get_field_1';
2115        [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,frame_index_1);
2116        if ~isempty(errormsg)
2117            errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg];
2118            return
2119        end
2120%         UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2121    end
2122end
2123
2124%% update uvmat interface
2125if isfield(ParamOut,'Npx')
2126    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2127    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2128elseif isfield(ParamOut_1,'Npx')
2129    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2130    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2131end
2132
2133%% update the display menu for the first velocity type (first menuline)
2134test_veltype=0;
2135% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2136if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2137    test_veltype=1;
2138    set(handles.VelType,'Visible','on')
2139    set(handles.VelType_1,'Visible','on')
2140    set(handles.FixVelType,'Visible','on')
2141    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2142    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2143    index_val=find(index_menu,1);
2144    if isempty(index_val)
2145        index_val=1;
2146    end
2147    set(handles.VelType,'Value',index_val)
2148    if ~get(handles.SubField,'value')
2149        set(handles.VelType,'String',menu)
2150        set(handles.VelType_1,'Value',1)
2151        set(handles.VelType_1,'String',[{''};menu])
2152    end
2153else
2154    set(handles.VelType,'Visible','off')
2155end
2156% display the Fields menu from the input file and pick the selected one:
2157if isstruct(ParamOut)
2158field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2159set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2160set(handles.Fields,'Value',find(field_index,1))
2161end
2162
2163%% update the display menu for the second velocity type (second menuline)
2164test_veltype_1=0;
2165if isempty(FileName_1)
2166    set(handles.Fields_1,'Value',1); %update the field menu
2167    if isstruct(ParamOut)
2168    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2169    end
2170elseif ~test_keepdata_1
2171    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2172        set(handles.VelType_1,'Visible','off')
2173    else
2174        test_veltype_1=1;
2175        set(handles.VelType_1,'Visible','on')
2176%         if ~get(handles.FixVelType,'Value')
2177            menu=set_veltype_display(ParamOut_1.CivStage);
2178            index_menu=strcmp(ParamOut_1.VelType,menu);
2179            set(handles.VelType_1,'Value',1+find(index_menu,1))
2180            set(handles.VelType_1,'String',[{''};menu])
2181%         end
2182    end
2183    % update the second field menu: the same quantity
2184    set(handles.Fields_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2185    % display the Fields menu from the input file and pick the selected one:
2186    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2187    set(handles.Fields_1,'Value',find(field_index,1)+1) 
2188%     % synchronise  with the first menu if the first selection is not 'velocity'
2189%     if ~strcmp(ParamOut.FieldName,'velocity')
2190%         field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2191%         set(handles.Fields_1,'Value',field_index); %update the field menu
2192%         ParamOut_1.FieldName=ParamOut.FieldName;
2193%         set(handles.Fields_1,'String',ParamOut_1.FieldList)
2194%     end
2195end
2196if test_veltype||test_veltype_1
2197     set(handles.FixVelType,'Visible','on')
2198else
2199     set(handles.FixVelType,'Visible','off')
2200end
2201
2202% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2203% set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2204% set(handles.Fields,'Value',find(field_index,1))
2205   
2206%% introduce w as background image by default for a new series (only for nbdim=2)
2207if ~isfield(UvData,'NewSeries')
2208    UvData.NewSeries=1;
2209end
2210%put W as background image by default if NbDim=2:
2211if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2212        set(handles.SubField,'Value',1);
2213        set(handles.RootPath_1,'String','"')
2214        set(handles.RootFile_1,'String','"')
2215        set(handles.SubDir_1,'String','"');
2216         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2217        set(handles.FileIndex_1,'String',indices)
2218        set(handles.FileExt_1,'String','"');
2219        set(handles.Fields_1,'Visible','on');
2220        set(handles.Fields_1,'Visible','on');
2221        set(handles.RootPath_1,'Visible','on')
2222        set(handles.RootFile_1,'Visible','on')
2223        set(handles.SubDir_1,'Visible','on');
2224        set(handles.FileIndex_1,'Visible','on');
2225        set(handles.FileExt_1,'Visible','on');
2226        set(handles.Fields_1,'Visible','on');
2227        Field{1}.AName='w';
2228end           
2229
2230%% display time
2231testimedoc=0;
2232TimeUnit='';
2233if isfield(Field{1},'Time')
2234    abstime=Field{1}.Time;%time read from the netcdf input file
2235end
2236if numel(Field)==2 && isfield(Field{2},'Time')
2237    abstime_1=Field{2}.Time;%time read from the netcdf input file
2238end
2239if isfield(Field{1},'Dt')
2240    dt=Field{1}.Dt;%dt read from the netcdf input file
2241    if isfield(Field{1},'TimeUnit')
2242       TimeUnit=Field{1}.TimeUnit;
2243    end
2244elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2245    dt=Field{2}.Dt;%dt read from the netcdf input file
2246    if isfield(Field{2},'TimeUnit')
2247       TimeUnit=Field{2}.TimeUnit;
2248    end
2249end
2250% time from xml file overset previous result
2251if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2252    if isempty(num_i2)||isnan(num_i2)
2253        num_i2=num_i1;
2254    end
2255    if isempty(num_j1)||isnan(num_j1)
2256        num_j1=1;
2257    end
2258    if isempty(num_j2)||isnan(num_j2)
2259        num_j2=num_j1;
2260    end
2261    siz=size(UvData.XmlData{1}.Time);
2262    if ~isempty(num_i1)&& ~isempty(num_i2)&&siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2263        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2264        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2265        Field{1}.Dt=dt;
2266        if isfield(UvData.XmlData{1},'TimeUnit')
2267            TimeUnit=UvData.XmlData{1}.TimeUnit;
2268        end
2269    end
2270    if numel(UvData.XmlData)==2
2271        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2272        if isempty(num_i2)
2273            num_i2=num_i1;
2274        end
2275        if isempty(num_j1)
2276            num_j1=1;
2277        end
2278        if isempty(num_j2)
2279            num_j2=num_j1;
2280        end
2281        siz=size(UvData.XmlData{2}.Time);
2282        if ~isempty(num_i1) && siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2283            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
2284            Field{2}.Dt=(UvData.XmlData{2}.Time(num_i2,num_j2)-UvData.XmlData{2}.Time(num_i1,num_j1));
2285        end
2286    end
2287end
2288if ~isequal(numel(abstime),1)
2289    abstime=[];
2290end
2291if ~isequal(numel(abstime_1),1)
2292      abstime_1=[];
2293end 
2294set(handles.abs_time,'String',num2str(abstime,5))
2295set(handles.abs_time_1,'String',num2str(abstime_1,5))
2296% if testimedoc && isfield(UvData,'dt')
2297%     dt=UvData.dt;
2298% end
2299if isempty(dt)||isequal(dt,0)
2300    set(handles.Dt_txt,'String','')
2301else
2302    if  isempty(TimeUnit)
2303        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2304    else
2305        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2306    end
2307end
2308
2309
2310%% store the current open names, fields and vel types in uvmat interface
2311UvData.FileName_1=FileName_1;
2312
2313%% apply coordinate transform or other user fct
2314XmlData=[];%default
2315XmlData_1=[];%default
2316if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2317    XmlData=UvData.XmlData{1};
2318    if numel(UvData.XmlData)==2
2319        XmlData_1=UvData.XmlData{2};
2320    end
2321end
2322choice_value=get(handles.transform_fct,'Value');
2323transform_list=get(handles.transform_fct,'UserData');
2324transform=transform_list{choice_value};%selected function handles
2325% z index
2326if ~isempty(FileName)
2327    Field{1}.ZIndex=z_index;
2328end
2329if ~isempty(transform)
2330    if length(Field)>=2
2331        Field{2}.ZIndex=z_index;
2332        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2333        if isempty(Field{2})
2334            Field(2)=[];
2335        end
2336    else
2337        Field{1}=transform(Field{1},XmlData);
2338    end
2339    %% update tps in phys coordinates if needed
2340    if (strcmp(VelType,'filter1')||strcmp(VelType,'filter2'))&& strcmp(UvData.FileType{1},'civdata')&&isfield(Field{1},'U')&& isfield(Field{1},'V')
2341        Field{1}.X=Field{1}.X(Field{1}.FF==0);
2342        Field{1}.Y=Field{1}.Y(Field{1}.FF==0);
2343        Field{1}.U=Field{1}.U(Field{1}.FF==0);
2344        Field{1}.V=Field{1}.V(Field{1}.FF==0);
2345        [Field{1}.SubRange,Field{1}.NbSites,Field{1}.Coord_tps,Field{1}.U_tps,Field{1}.V_tps]=filter_tps([Field{1}.X Field{1}.Y],Field{1}.U,Field{1}.V,[],Field{1}.Patch1_SubDomain,0);
2346    end
2347    if numel(Field)==2 && ~test_keepdata_1 && isequal(UvData.FileType{2}(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2348        %update tps in phys coordinates if needed
2349        if (strcmp(VelType_1,'filter1')||strcmp(VelType_1,'filter2'))&& strcmp(UvData.FileType{2},'civdata')&&isfield(Field{2},'U')&& isfield(Field{2},'V')
2350            Field{2}.X=Field{2}.X(Field{2}.FF==0);
2351            Field{2}.Y=Field{1}.Y(Field{2}.FF==0);
2352            Field{2}.U=Field{1}.U(Field{2}.FF==0);
2353            Field{2}.V=Field{1}.V(Field{2}.FF==0);
2354            [Field{2}.SubRange,Field{2}.NbSites,Field{2}.Coord_tps,Field{2}.U_tps,Field{2}.V_tps]=filter_tps([Field{2}.X Field{2}.Y],Field{2}.U,Field{2}.V,[],1500,0);
2355        end
2356    end
2357end
2358
2359%% calculate scalar
2360if isstruct(ParamOut)&&~strcmp(ParamOut.FieldName,'get_field...')&& (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))%&&~strcmp(ParamOut.FieldName,'velocity')&& ~strcmp(ParamOut.FieldName,'get_field...');% ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
2361    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2362end
2363if 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'))  &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2364     Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2365end
2366
2367%% combine the two input fields (e.g. substract velocity fields)
2368%Field{1}.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}];
2369if numel(Field)==2
2370%    Field{2}.FieldList=[{ParamOut_1.FieldName} {ParamOut_1.ColorVar}];
2371   [UvData.Field,errormsg]=sub_field(Field{1},Field{2}); 
2372   UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2373   UvData.ParamOut_1=ParamOut_1;
2374else
2375   UvData.Field=Field{1};
2376end
2377if ~isempty(errormsg)
2378    errormsg=['error in uvmat/refresh_field/sub_field:' errormsg];
2379    return
2380end
2381%UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation
2382
2383%% analyse input field
2384test_x=0;
2385test_z=0;% test for unstructured z coordinate
2386[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2387if ~isempty(errormsg)
2388    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2389    return
2390end
2391[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);% analyse  the input field structure
2392if ~isempty(errormsg)
2393    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];% display error
2394    return
2395end
2396[NbDim,imax]=max(NbDim);% spatial dimension of the input field
2397if isfield(UvData.Field,'NbDim')
2398    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2399end
2400
2401%% get bounds and mesh (needed for mouse action and to open set_object)
2402if NbDim>1
2403    XName=''; %default
2404    YName='';
2405    %unstructured coordinates
2406    if ~isempty(VarType{imax}.coord_x)&&~isempty(VarType{imax}.coord_y)
2407        XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2408        YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2409        %nbvec=length(UvData.Field.(XName));%nbre of measurement points (e.g. vectors)
2410        test_x=1;%test for unstructured coordinates
2411        if ~isempty(VarType{imax}.coord_z)
2412            ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2413        else
2414            NbDim=2;
2415        end
2416        %structured coordinate
2417    elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0
2418        XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2419        if NbDim> 1 && VarType{imax}.coord(NbDim-1)>0
2420            YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2421        end
2422        % VarIndex=CellVarIndex{imax}; % list of variable indices
2423        DimIndex=VarDimIndex{CellVarIndex{imax}(1)}; %list of dim indices for the variable
2424        nbpoints_x=DimValue(DimIndex(NbDim));
2425        XMax=nbpoints_x;%default
2426        XMin=1;%default
2427    end
2428   
2429    if NbDim==3
2430        if ~test_x
2431            ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2432        end
2433        ZMax=max(UvData.Field.(ZName));
2434        ZMin=min(UvData.Field.(ZName));
2435        UvData.Field.ZMax=ZMax;
2436        UvData.Field.ZMin=ZMin;
2437        test_z=1;
2438        if isequal(ZMin,ZMax)%no z dependency
2439            NbDim=2;
2440            test_z=0;
2441        end
2442    end
2443    if ~isempty (XName)
2444        XMax=max(max(UvData.Field.(XName)));
2445        XMin=min(min(UvData.Field.(XName)));
2446        UvData.Field.NbDim=NbDim;
2447        UvData.Field.XMax=XMax;
2448        UvData.Field.XMin=XMin;
2449        if NbDim >1&& ~isempty(YName)
2450            YMax=max(max(UvData.Field.(YName)));
2451            YMin=min(min(UvData.Field.(YName)));
2452            UvData.Field.YMax=YMax;
2453            UvData.Field.YMin=YMin;
2454        end
2455        nbvec=length(UvData.Field.(XName));
2456        if test_x %unstructured coordinates
2457            if test_z
2458                UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2459                UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2460            else
2461                UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2462            end
2463        end
2464    end
2465    % case of structured coordinates
2466    if ~test_x
2467        DX=(XMax-XMin)/(nbpoints_x-1);
2468        if NbDim >1
2469            nbpoints_y=DimValue(DimIndex(NbDim-1));
2470            if isempty(YName)% if the y coordinate is not expressed, it is taken as the matrix index
2471                DY=1;
2472                UvData.Field.YMax=nbpoints_y;
2473                UvData.Field.YMin=1;
2474            else
2475                DY=(YMax-YMin)/(nbpoints_y-1);
2476            end
2477        end
2478        if NbDim==3
2479            nbpoints_z=DimValue(DimIndex(1));
2480            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2481            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2482            UvData.Field.ZMax=ZMax;
2483            UvData.Field.ZMin=ZMin;
2484        else
2485            UvData.Field.Mesh=DX;%sqrt(DX*DY);
2486        end
2487    end
2488    % adjust the mesh to a value 1, 2 , 5 *10^n
2489    ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude
2490    if UvData.Field.Mesh/ord>=5
2491        UvData.Field.Mesh=5*ord;
2492    elseif UvData.Field.Mesh/ord>=2
2493        UvData.Field.Mesh=2*ord;
2494    else
2495        UvData.Field.Mesh=ord;
2496    end
2497    UvData.Object{1}.Type='plane';%main plotting plane
2498    UvData.Object{1}.ProjMode='projection';%main plotting plane
2499    UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2500    UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2501   
2502    %% 3D case (menuvolume)
2503    if NbDim==3% && UvData.NewSeries
2504        test_set_object=1;
2505        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2506        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2507        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2508        if ~isempty(hset_object) %if set_object is detected
2509            delete(hset_object);% delete the GUI set_object if it does not fit
2510        end
2511        if test_set_object% reinitiate the GUI set_object
2512            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
2513            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2514            UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2515            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2516            UvData.Object{1}.Angle=[0 0 0];
2517            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2518            UvData.Object{1}.Name='1-PLANE';
2519            UvData.Object{1}.enable_plot=1;
2520            set_object(UvData.Object{1},handles,ZBounds);
2521            set(handles.ListObject,'Value',1);
2522            set(handles.ListObject,'String',{'1-PLANE'});
2523            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2524            edit_object_Callback([],[], handles)
2525        end
2526        %multilevel case (single menuplane in a 3D space)
2527    elseif isfield(UvData,'Z')
2528        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2529            XmlData=UvData.XmlData{1};
2530            if isfield(XmlData,'PlanePos')
2531                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2532            end
2533            if isfield(XmlData,'PlaneAngle')
2534                siz=size(XmlData.PlaneAngle);
2535                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2536                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2537            end
2538        elseif isfield(UvData,'ZIndex')
2539            UvData.Object{1}.ZObject=UvData.ZIndex;
2540        end
2541    end
2542end
2543
2544testnewseries=UvData.NewSeries;
2545UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2546set(handles.uvmat,'UserData',UvData)
2547
2548%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2549% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2550%     set(handles.num_MinA,'String','0')
2551%     set(handles.num_MaxA,'String','255')
2552% end
2553
2554%% usual 1D (x,y) plots
2555if NbDim<=1
2556    set(handles.Objects,'Visible','off')
2557    set(handles.ListObject_1_title,'Visible','off')
2558    set(handles.ListObject_1,'Visible','off')
2559    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.axes3,read_GUI(handles.uvmat));
2560    write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2561%     if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2562%         ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2563%     end
2564   
2565%% 2D or 3D fields are generally projected
2566else
2567    set(handles.Objects,'Visible','on')
2568    set(handles.ListObject_1_title,'Visible','on')
2569    set(handles.ListObject_1,'Visible','on')
2570   
2571    %% Plot the projections on the selected  projection objects
2572    % main projection object (uvmat display)
2573    list_object=get(handles.ListObject_1,'String');
2574    if isequal(list_object,{''})%refresh list of objects if the menu is empty
2575        UvData.Object={[]};
2576        set(handles.ListObject_1,'Value',1)
2577    end
2578    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2579    if IndexObj(1)> numel(UvData.Object)
2580        IndexObj(1)=1;%select the first object if the selected one does not exist
2581        set(handles.ListObject_1,'Value',1)
2582    end
2583    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2584    if isequal(IndexObj(2),IndexObj(1))
2585        IndexObj(2)=[];
2586    end
2587    plot_handles{1}=handles;
2588    if isfield(UvData,'plotaxes')%case of movies
2589        haxes(1)=UvData.plotaxes;
2590    else
2591        haxes(1)=handles.axes3;
2592    end
2593    PlotParam{1}=read_GUI(handles.uvmat);
2594    %default settings if vectors not visible
2595    if ~isfield(PlotParam{1},'Vectors')
2596        PlotParam{1}.Vectors.MaxVec=1;
2597        PlotParam{1}.Vectors.MinVec=0;
2598        PlotParam{1}.Vectors.CheckFixVecColor=1;
2599        PlotParam{1}.Vectors.ColCode1=0.33;
2600        PlotParam{1}.Vectors.ColCode2=0.66;
2601        PlotParam{1}.Vectors.ColorScalar={'ima_cor'};
2602        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2603    end
2604    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2605   
2606    %% second projection object (view_field display)
2607    if length( IndexObj)>=2
2608        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2609        if ~isempty(view_field_handle)
2610            plot_handles{2}=guidata(view_field_handle);
2611            haxes(2)=plot_handles{2}.axes3;
2612            PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2613            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2614        end
2615    end
2616   
2617    %% loop on the projection objects: one or two
2618   
2619    for imap=1:numel(IndexObj)
2620        iobj=IndexObj(imap);
2621        %      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)
2622        % %          [ObjectData,errormsg]=calc_field(UvData.Field.FieldList,UvData.Field);
2623        % %      else
2624        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2625        %      end
2626        if ~isempty(errormsg)
2627            return
2628        end
2629        if testnewseries
2630            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2631            if isfield(ObjectData,'CoordUnit')
2632                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2633                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2634            end
2635        end
2636        %use of mask (TODO: check)
2637        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2638            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2639            AX=ObjectData.AX;%x coordiantes for the scalar field
2640            AY=ObjectData.AY;%y coordinates for the scalar field
2641            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2642            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2643            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2644                nxy=size(flag_mask);
2645                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2646                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2647                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2648                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2649                %project on the positions of the scalar
2650                npxy=size(ObjectData.A);
2651                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2652                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2653                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2654                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2655                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2656                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2657            end
2658            AClass=class(ObjectData.A);
2659            ObjectData.A=flag_mask.*double(ObjectData.A);
2660            ObjectData.A=feval(AClass,ObjectData.A);
2661            ind_off=[];
2662            if isfield(ObjectData,'ListVarName')
2663                for ilist=1:length(ObjectData.ListVarName)
2664                    if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2665                        ind_off=[ind_off ilist];
2666                    end
2667                end
2668                ObjectData.ListVarName(ind_off)=[];
2669                VarDimIndex(ind_off)=[];
2670                ind_off=[];
2671                for ilist=1:length(ListDimName)
2672                    if isequal(ListDimName{ilist},'MaskX') || isequal(ListDimName{ilist},'MaskY')
2673                        ind_off=[ind_off ilist];
2674                    end
2675                end
2676                ListDimName(ind_off)=[];
2677                DimValue(ind_off)=[];
2678            end
2679        end
2680        if ~isempty(ObjectData)
2681            PlotType='none'; %default
2682            if imap==2 && isempty(view_field_handle)
2683                view_field(ObjectData)
2684            else
2685                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2686                write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2687                if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2688                    ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2689                end
2690            end
2691            if isequal(PlotType,'none')
2692                hget_field=findobj(allchild(0),'name','get_field');
2693                if isempty(hget_field)
2694                    get_field(FileName)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2695                end
2696                errormsg='The field defined by get_field cannot be plotted';
2697                return
2698            end
2699        end
2700    end
2701   
2702    %% update the mask
2703    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2704        update_mask(handles,num_i1,num_i2);
2705    end
2706   
2707    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2708    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2709    ind_skip=[];
2710    % nb_histo=1;
2711    Ustring='';
2712    Vstring='';
2713    % suppress coordinates from the histogram menu
2714    for ivar=1:numel(menu_histo)%l loop on field variables:
2715        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2716            Role=UvData.Field.VarAttribute{ivar}.Role;
2717            switch Role
2718                case {'coord_x','coord_y','coord_z','dimvar'}
2719                    ind_skip=[ind_skip ivar];
2720                case {'vector_x'}
2721                    Ustring=UvData.Field.ListVarName{ivar};
2722                    ind_skip=[ind_skip ivar];
2723                case {'vector_y'}
2724                    Vstring=UvData.Field.ListVarName{ivar};
2725                    ind_skip=[ind_skip ivar];
2726            end
2727        end
2728        DimCell=UvData.Field.VarDimName{ivar};
2729        DimName='';
2730        if ischar(DimCell)
2731            DimName=DimCell;
2732        elseif iscell(DimCell)&& numel(DimCell)==1
2733            DimName=DimCell{1};
2734        end
2735        if strcmp(DimName,menu_histo{ivar})
2736            ind_skip=[ind_skip ivar];
2737        end
2738    end
2739    menu_histo(ind_skip)=[];% remove skipped items
2740    if ~isempty(Ustring)
2741        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2742    end
2743   
2744    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2745    % display menus and plot histograms
2746    test_v=0;
2747    if ~isempty(menu_histo)
2748        set(handles.histo1_menu,'Value',1)
2749        set(handles.histo1_menu,'String',menu_histo)
2750        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2751    end
2752end
2753
2754%------------------------------------------------------------------------
2755function histo1_menu_Callback(hObject, eventdata, handles)
2756%--------------------------------------------
2757%plot first histo
2758%huvmat=get(handles.histo1_menu,'parent');
2759histo_menu=get(handles.histo1_menu,'String');
2760histo_value=get(handles.histo1_menu,'Value');
2761FieldName=histo_menu{histo_value};
2762% update_histo(handles.histo_u,handles.uvmat,FieldName)
2763%
2764% %------------------------------------------------------------------------
2765% function histo2_menu_Callback(hObject, eventdata, handles)
2766% %------------------------------------------------------------------------
2767% %plot second histo
2768% %huvmat=get(handles.histo2_menu,'parent');
2769% histo_menu=get(handles.histo2_menu,'String');
2770% histo_value=get(handles.histo2_menu,'Value');
2771% FieldName=histo_menu{histo_value};
2772% update_histo(handles.histo_v,handles.uvmat,FieldName)
2773%
2774% %------------------------------------------------------------------------
2775% %read the field .Fieldname stored in UvData and plot its histogram
2776% function update_histo(haxes,huvmat,FieldName)
2777%------------------------------------------------------------------------
2778UvData=get(handles.uvmat,'UserData');
2779Field=UvData.Field;
2780r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2781FieldName_2='';
2782if ~isempty(r)
2783    FieldName=r.var1;
2784    FieldName_2=r.var2;
2785end
2786if ~isfield(UvData.Field,FieldName)
2787    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2788    return
2789end
2790FieldHisto=Field.(FieldName);
2791if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2792    indsel=find(Field.FF==0);%find values marked as false
2793    if ~isempty(indsel)
2794        FieldHisto=FieldHisto(indsel);
2795        if ~isempty(FieldName_2)
2796            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2797        end
2798    end
2799end
2800if isempty(Field)
2801    msgbox_uvmat('ERROR',['empty field ' FieldName])
2802else
2803    nxy=size(FieldHisto);
2804    Amin=double(min(min(min(FieldHisto))));%min of field value
2805    Amax=double(max(max(max(FieldHisto))));%max of field value
2806    if isequal(Amin,Amax)
2807        cla(handles.histo_u)
2808    else
2809        Histo.ListVarName={FieldName,'histo'};
2810        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2811            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2812        else
2813            if numel(nxy)==2
2814                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2815            else
2816                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2817            end
2818        end
2819        %unit
2820        units=[]; %default
2821        for ivar=1:numel(Field.ListVarName)
2822            if strcmp(Field.ListVarName{ivar},FieldName)
2823                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2824                    units=Field.VarAttribute{ivar}.units;
2825                    break
2826                end
2827            end
2828        end
2829        if ~isempty(units)
2830            Histo.VarAttribute{1}.units=units;
2831        end
2832        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2833        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2834            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2835            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2836        else
2837            for col=1:size(FieldHisto,3)
2838                B=FieldHisto(:,:,col);
2839                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2840                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2841            end
2842        end
2843        plot_field(Histo,handles.histo_u);
2844        hlegend=legend;
2845        if isempty(FieldName_2)
2846        set(hlegend,'String',FieldName)
2847        else
2848            set(hlegend,'String',{FieldName;FieldName_2})
2849        end
2850%         hh=get(handles.histo_u,'children');
2851%         get(hh(1))
2852%         get(hh(2))
2853    end
2854end
2855
2856%-------------------------------------------------------------------
2857% --- translate coordinate to matrix index
2858%-------------------------------------------------------------------
2859function [indx,indy]=pos2ind(x0,rangx0,nxy)
2860indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2861indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2862
2863
2864%-------------------------------------------------------------------
2865% --- Executes on button press in 'CheckZoom'.
2866%-------------------------------------------------------------------
2867function CheckZoom_Callback(hObject, eventdata, handles)
2868
2869if (get(handles.CheckZoom,'Value') == 1);
2870    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2871    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2872    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2873else
2874    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2875end
2876
2877%-------------------------------------------------------------------
2878% --- Executes on button press in 'CheckFixLimits'.
2879%-------------------------------------------------------------------
2880function CheckFixLimits_Callback(hObject, eventdata, handles)
2881test=get(handles.CheckFixLimits,'Value');
2882if test
2883    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2884else
2885    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2886    update_plot(handles);
2887end
2888
2889%-------------------------------------------------------------------
2890% --- Executes on button press in CheckFixAspectRatio.
2891function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2892%-------------------------------------------------------------------
2893if get(handles.CheckFixAspectRatio,'Value')
2894    set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
2895    update_plot(handles);
2896else
2897    set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
2898    update_plot(handles);
2899end
2900
2901%-------------------------------------------------------------------
2902function num_AspectRatio_Callback(hObject, eventdata, handles)
2903%-------------------------------------------------------------------
2904set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2905set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2906update_plot(handles);
2907%-------------------------------------------------------------------
2908
2909%-------------------------------------------------------------------
2910
2911
2912
2913%-------------------------------------------------------------------
2914%----Executes on button press in 'record': records the current flags of manual correction.
2915%-------------------------------------------------------------------
2916function record_Callback(hObject, eventdata, handles)
2917% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2918[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2919FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2920%FileName=read_file_boxes(handles);
2921[erread,message]=fileattrib(FileName);
2922if ~isempty(message) && ~isequal(message.UserWrite,1)
2923     msgbox_uvmat('ERROR',['no writting access to ' FileName])
2924     return
2925end
2926test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2927test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2928if ~test_civ2 && ~test_civ1
2929    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2930end
2931if test_civ2
2932    nbname='nb_vectors2';
2933   flagname='vec2_FixFlag';
2934   attrname='fix2';
2935end
2936if test_civ1
2937    nbname='nb_vectors';
2938   flagname='vec_FixFlag';
2939   attrname='fix';
2940end
2941%write fix flags in the netcdf file
2942UvData=get(handles.uvmat,'UserData');
2943hhh=which('netcdf.open');% look for built-in matlab netcdf library
2944if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2945    nc=netcdf.open(FileName,'NC_WRITE');
2946    netcdf.reDef(nc);
2947    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2948    dimid = netcdf.inqDimID(nc,nbname);
2949    try
2950        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2951    catch
2952        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2953    end
2954    netcdf.endDef(nc);
2955    netcdf.putVar(nc,varid,UvData.axes3.FF);
2956    netcdf.close(nc); 
2957else %old netcdf library
2958    netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2959end
2960
2961%-------------------------------------------------------------------
2962%----Correct the netcdf file, using toolbox (old versions of Matlab).
2963%-------------------------------------------------------------------
2964function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2965nc=netcdf(FileName,'write'); %open netcdf file
2966result=redef(nc);
2967eval(['nc.' attrname '=1;']);
2968theDim=nc(nbname) ;% get the number of velocity vectors
2969nb_vectors=size(theDim);
2970var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2971var_FixFlag(1:nb_vectors)=AxeData.FF;%
2972fin=close(nc);
2973
2974%-------------------------------------------------------------------
2975% --- Executes on button press in SubField
2976function SubField_Callback(hObject, eventdata, handles)
2977%-------------------------------------------------------------------
2978UvData=get(handles.uvmat,'UserData');
2979if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2980    set(handles.RootPath_1,'String','')
2981    set(handles.RootFile_1,'String','')
2982    set(handles.SubDir_1,'String','');
2983    set(handles.FileIndex_1,'String','');
2984    set(handles.FileExt_1,'String','');
2985    set(handles.RootPath_1,'Visible','off')
2986    set(handles.RootFile_1,'Visible','off')
2987    set(handles.SubDir_1,'Visible','off');
2988    set(handles.NomType_1,'Visible','off');
2989    set(handles.abs_time_1,'Visible','off')
2990    set(handles.FileIndex_1,'Visible','off');
2991    set(handles.FileExt_1,'Visible','off');
2992    set(handles.Fields_1,'Value',1);%set to blank state
2993    set(handles.VelType_1,'Value',1);%set to blank state
2994    set(handles.num_Opacity,'String','')% desactivate opacity setting
2995    if ~strcmp(get(handles.VelType,'Visible'),'on')
2996        set(handles.VelType_1,'Visible','off')
2997    end
2998    if isfield(UvData,'XmlData_1')
2999        UvData=rmfield(UvData,'XmlData_1');
3000    end
3001    set(handles.uvmat,'UserData',UvData);
3002    run0_Callback(hObject, eventdata, handles); %run
3003else
3004    MenuBrowse_1_Callback(hObject, eventdata, handles)
3005end
3006
3007%------------------------------------------------------------------------
3008% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3009
3010function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3011%------------------------------------------------------------------------
3012InputFile=read_GUI(handles.InputFile);
3013RootPath=InputFile.RootPath;
3014SubDir=regexprep(InputFile.SubDir,'/|\','');
3015RootFile=regexprep(InputFile.RootFile,'/|\','');
3016FileIndices=InputFile.FileIndex;
3017FileExt=InputFile.FileExt;
3018
3019
3020%------------------------------------------------------------------------
3021% ---- read the data displayed for the second input rootfile windows
3022function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3023%------------------------------------------------------------------------
3024RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3025if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3026    RootPath_1=get(handles.RootPath,'String');
3027end;
3028SubDir_1=get(handles.SubDir_1,'String');
3029if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3030    SubDir_1=get(handles.SubDir,'String');
3031end
3032SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3033RootFile_1=get(handles.RootFile_1,'String');
3034if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3035    RootFile_1=get(handles.RootFile,'String');
3036end
3037RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3038FileIndex_1=get(handles.FileIndex_1,'String');
3039if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3040    FileIndex_1=get(handles.FileIndex,'String');
3041end
3042FileExt_1=get(handles.FileExt_1,'String');
3043if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3044    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3045end
3046NomType_1=get(handles.NomType_1,'String');
3047if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3048    NomType_1=get(handles.NomType,'String');%read FileExt by default
3049end
3050%------------------------------------------------------------------------
3051% --- Executes on menu selection Fields
3052function Fields_Callback(hObject, eventdata, handles)
3053%------------------------------------------------------------------------
3054list_fields=get(handles.Fields,'String');% list menu fields
3055index_fields=get(handles.Fields,'Value');% selected string index
3056field= list_fields{index_fields(1)}; % selected string
3057if isequal(field,'get_field...')
3058    set(handles.FixVelType,'visible','off')
3059    set(handles.VelType,'visible','off')
3060    set(handles.VelType_1,'visible','off')
3061    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3062    FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3063    %FileName=read_file_boxes(handles);
3064    hget_field=findobj(allchild(0),'name','get_field');
3065    if ~isempty(hget_field)
3066        delete(hget_field)
3067    end
3068    hget_field=get_field(FileName);
3069    set(hget_field,'Name','get_field')
3070    hhget_field=guidata(hget_field);
3071    set(hhget_field.list_fig,'Value',1)
3072    set(hhget_field.list_fig,'String',{'uvmat'})
3073    set(handles.transform_fct,'Value',1)% no transform by default
3074    set(handles.path_transform,'String','')
3075    return %no action
3076end
3077list_fields=get(handles.Fields_1,'String');% list menu fields
3078index_fields=get(handles.Fields_1,'Value');% selected string index
3079field_1= list_fields{index_fields(1)}; % selected string
3080UvData=get(handles.uvmat,'UserData');
3081
3082%read the rootfile input display
3083[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3084FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3085[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3086if isequal(field,'image')
3087    SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3088    imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3089    if ~exist(imagename,'file')
3090        [FileName,PathName] = uigetfile( ...
3091            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3092            '*.jpg',' jpeg image files'; ...
3093            '*.png','.png image files'; ...
3094            '*.tif','.tif image files'; ...
3095            '*.avi;*.AVI','.avi movie files'; ...
3096            '*.vol','.volume images (png)'; ...
3097            '*.*',  'All Files (*.*)'}, ...
3098            'Pick an image',imagename);   
3099        imagename=[PathName FileName];
3100    end
3101     % display the selected field and related information
3102    display_file_name(handles,imagename)%display the image
3103    return
3104else
3105    ext=get(handles.FileExt,'String');
3106    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3107        [FileName,PathName] = uigetfile( ...
3108            {'*.nc', ' (*.nc)';
3109            '*.nc',' netcdf files'; ...
3110            '*.*',  'All Files (*.*)'}, ...
3111            'Pick a netcdf file',FileBase);
3112        FullFileName=[PathName FileName];
3113        % display the selected field and related information
3114        display_file_name( handles,FullFileName)
3115        return
3116    end
3117end
3118indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3119set(handles.FileIndex,'String',indices)
3120% set(handles.NomType,'String',NomType)
3121
3122%common to Fields_1_Callback
3123if isequal(field,'image')||isequal(field_1,'image')
3124    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3125    set(handles.TitleNpy,'Visible','on')
3126    set(handles.num_Npx,'Visible','on')
3127    set(handles.num_Npy,'Visible','on')
3128else
3129    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3130    set(handles.TitleNpy,'Visible','off')
3131    set(handles.num_Npx,'Visible','off')
3132    set(handles.num_Npy,'Visible','off')
3133end
3134if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3135    run0_Callback(hObject, eventdata, handles)
3136end
3137
3138%---------------------------------------------------
3139% --- Executes on menu selection Fields
3140function Fields_1_Callback(hObject, eventdata, handles)
3141%-------------------------------------------------
3142%% read input data
3143check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3144UvData=get(handles.uvmat,'UserData');
3145if check_new && isfield(UvData,'XmlData')
3146    UvData.XmlData{2}=UvData.XmlData{1};
3147end
3148if isfield(UvData,'Field_1')
3149    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3150end
3151UvData.FileName_1='';% desactivate the use of a constant second file
3152list_fields=get(handles.Fields,'String');% list menu fields
3153field= list_fields{get(handles.Fields,'Value')}; % selected string
3154list_fields=get(handles.Fields_1,'String');% list menu fields
3155field_1= list_fields{get(handles.Fields_1,'Value')}; % selected string for the second field
3156if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3157    set(handles.SubField,'Value',0)
3158    SubField_Callback(hObject, eventdata, handles)
3159    return
3160else
3161    set(handles.SubField,'Value',1)%state that a second field is now entered
3162end
3163
3164%% read the rootfile input display
3165[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3166FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3167[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3168% set(handles.FileIndex_1,'Visible','on')
3169% set(handles.FileExt_1,'Visible','on')
3170switch field_1
3171    case 'get_field...'
3172        set_veltype_display(0) % no veltype display
3173        hget_field=findobj(allchild(0),'name','get_field_1');
3174        if ~isempty(hget_field)
3175            delete(hget_field)
3176        end
3177        hget_field=get_field(FileName_1);
3178        set(hget_field,'name','get_field_1')
3179        hhget_field=guidata(hget_field);
3180        set(hhget_field.list_fig,'Value',1)
3181        set(hhget_field.list_fig,'String',{'uvmat'})
3182        set(handles.transform_fct,'Value',1)% no transform by default
3183        set(handles.path_transform,'String','')
3184        if check_new
3185            UvData.FileType{2}=UvData.FileType{1};
3186            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3187%             set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3188              set(handles.uvmat,'UserData',UvData)
3189        end
3190    case 'image'
3191        % guess the image name corresponding to the current netcdf name (no unique correspondance)
3192        SubDirBase=regexprep(SubDir_1,'\..*','');%take the root part of SubDir, before the first dot '.'
3193        imagename=fullfile_uvmat(RootPath_1,SubDirBase,RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3194        if ~exist(imagename,'file') % browse for images if it is not found
3195            [FileName,PathName] = uigetfile( ...
3196                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3197                '*.jpg',' jpeg image files'; ...
3198                '*.png','.png image files'; ...
3199                '*.tif','.tif image files'; ...
3200                '*.avi;*.AVI','.avi movie files'; ...
3201                '*.vol','.volume images (png)'; ...
3202                '*.*',  'All Files (*.*)'}, ...
3203                'Pick an image',imagename);
3204            imagename=[PathName FileName];
3205        end
3206        if ~ischar(imagename)% quit if the browser has  been closed
3207            set(handles.SubField,'Value',0)
3208        else %valid browser input:  display the selected image
3209            set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3210            set(handles.TitleNpy,'Visible','on')
3211            set(handles.num_Npx,'Visible','on')
3212            set(handles.num_Npy,'Visible','on')
3213            display_file_name(handles,imagename,2)%display the imag
3214        end
3215    otherwise
3216        if check_new
3217            UvData.FileType{2}=UvData.FileType{1};
3218            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3219            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3220        end
3221        if ~isequal(field,'image')
3222            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3223            set(handles.TitleNpy,'Visible','off')
3224            set(handles.num_Npx,'Visible','off')
3225            set(handles.num_Npy,'Visible','off')
3226        end
3227        set(handles.uvmat,'UserData',UvData)
3228        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3229            run0_Callback(hObject, eventdata, handles)
3230        end
3231end
3232
3233%------------------------------------------------------------------------
3234% --- set the visibility of relevant velocity type menus:
3235function menu=set_veltype_display(Civ,FileType)
3236%------------------------------------------------------------------------
3237if ~exist('FileType','var')
3238    FileType='civx';
3239end
3240switch FileType
3241    case 'civx'
3242        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3243        if isequal(Civ,0)
3244            imax=0;
3245        elseif isequal(Civ,1) || isequal(Civ,2)
3246            imax=1;
3247        elseif isequal(Civ,3)
3248            imax=3;
3249        elseif isequal(Civ,4) || isequal(Civ,5)
3250            imax=4;
3251        elseif isequal(Civ,6) %patch2
3252            imax=6;
3253        end
3254    case 'civdata'
3255        menu={'civ1';'filter1';'civ2';'filter2'};
3256        if isequal(Civ,0)
3257            imax=0;
3258        elseif isequal(Civ,1) || isequal(Civ,2)
3259            imax=1;
3260        elseif isequal(Civ,3)
3261            imax=2;
3262        elseif isequal(Civ,4) || isequal(Civ,5)
3263            imax=3;
3264        elseif isequal(Civ,6) %patch2
3265            imax=4;
3266        end
3267end
3268menu=menu(1:imax);
3269
3270%------------------------------------------------------------------------
3271% --- Executes on button press in FixVelType.
3272function FixVelType_Callback(hObject, eventdata, handles)
3273%------------------------------------------------------------------------
3274% refresh the current plot if the fixed  veltype is unselected
3275if ~get(handles.FixVelType,'Value')
3276    run0_Callback(hObject, eventdata, handles)
3277end
3278
3279%------------------------------------------------------------------------
3280% --- Executes on button press in VelType.
3281function VelType_Callback(hObject, eventdata, handles)
3282%------------------------------------------------------------------------
3283set(handles.FixVelType,'Value',1)
3284run0_Callback(hObject, eventdata, handles)
3285
3286%------------------------------------------------------------------------
3287% --- Executes on button press in VelType_1.
3288function VelType_1_Callback(hObject, eventdata, handles)
3289%------------------------------------------------------------------------
3290set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3291UvData=get(handles.uvmat,'UserData');
3292%refresh field with a second FileName=first file name
3293set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3294drawnow   
3295InputFile=read_GUI(handles.InputFile);
3296[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3297FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3298
3299if isempty(InputFile.VelType_1)
3300        FileName_1='';% we plot the current field without the second field
3301        set(handles.SubField,'Value',0)
3302        SubField_Callback(hObject, eventdata, handles)
3303elseif get(handles.SubField,'Value')% if subfield is already 'on'
3304      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3305     FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3306else
3307     FileName_1=FileName;% we compare two fields in the same file by default
3308     UvData.FileType{2}=UvData.FileType{1};
3309     set(handles.SubField,'Value',1)
3310end
3311if isfield(UvData,'Field_1')
3312    UvData=rmfield(UvData,'Field_1');% removes the stored second field if it exists
3313end
3314UvData.FileName_1='';% desactivate the use of a constant second file
3315set(handles.uvmat,'UserData',UvData)
3316num_i1=stra2num(get(handles.i1,'String'));
3317num_i2=stra2num(get(handles.i2,'String'));
3318num_j1=stra2num(get(handles.j1,'String'));
3319num_j2=stra2num(get(handles.j2,'String'));
3320
3321errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2);
3322
3323if ~isempty(errormsg)
3324    msgbox_uvmat('ERROR',errormsg);
3325else
3326    set(handles.i1,'BackgroundColor',[1 1 1])
3327    set(handles.i2,'BackgroundColor',[1 1 1])
3328    set(handles.j1,'BackgroundColor',[1 1 1])
3329    set(handles.j2,'BackgroundColor',[1 1 1])
3330    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3331    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3332end
3333set(handles.run0,'BackgroundColor',[1 0 0])
3334
3335%-----------------------------------------------
3336% --- reset civ buttons
3337function reset_vel_type(handles_civ0,handle1)
3338for ibutton=1:length(handles_civ0)
3339    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3340    set(handles_civ0(ibutton),'Value',0)
3341end
3342if exist('handle1','var')%handles of selected button
3343        set(handle1,'BackgroundColor',[1 1 0]) 
3344end
3345
3346%-------------------------------------------------------
3347% --- Executes on button press in MENUVOLUME.
3348%-------------------------------------------------------
3349function VOLUME_Callback(hObject, eventdata, handles)
3350%errordlg('command VOL not implemented yet')
3351if ishandle(handles.UVMAT_title)
3352    delete(handles.UVMAT_title)
3353end
3354UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3355if isequal(get(handles.VOLUME,'Value'),1)
3356    set(handles.CheckZoom,'Value',0)
3357    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3358    set(handles.edit_vect,'Value',0)
3359    edit_vect_Callback(hObject, eventdata, handles)
3360    set(handles.edit_object,'Value',0)
3361    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3362%     set(handles.cal,'Value',0)
3363%     set(handles.cal,'BackgroundColor',[0 1 0])
3364    set(handles.edit_vect,'Value',0)
3365    edit_vect_Callback(hObject, eventdata, handles)
3366    %initiate set_object GUI
3367    data.Name='VOLUME';
3368    if isfield(UvData,'CoordType')
3369        data.CoordType=UvData.CoordType;
3370    end
3371    if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh)
3372        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3373        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3374        data.DX=UvData.Field.Mesh;
3375        data.DY=UvData.Field.Mesh;
3376    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3377        np=size(UvData.Field.A);
3378        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3379        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3380        data.RangeY=max(meshx,meshy);
3381        data.RangeX=max(meshx,meshy);
3382        data.DX=max(meshx,meshy);
3383    end
3384    data.ParentButton=handles.VOLUME;
3385    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3386    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3387                                                      % associate the set_object interface handle to the plotting axes
3388    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3389    pos_uvmat=get(handles.uvmat,'Position');
3390    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3391    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3392    set(hset_object,'Position',pos_set_object)
3393    end
3394    UvData.MouseAction='create_object';
3395else
3396    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3397    UvData.MouseAction='none';
3398end
3399set(handles.uvmat,'UserData',UvData)
3400
3401%-------------------------------------------------------
3402function edit_vect_Callback(hObject, eventdata, handles)
3403%-------------------------------------------------------
3404%
3405% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3406if isequal(get(handles.edit_vect,'Value'),1)
3407    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3408    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3409    if ~test_civ2 && ~test_civ1
3410        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3411    end
3412    set(handles.record,'Visible','on')
3413    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3414    set(handles.edit_object,'Value',0)
3415    set(handles.CheckZoom,'Value',0)
3416    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3417%     set(handles.create,'Value',0)
3418%     set(handles.create,'BackgroundColor',[0 1 0])
3419    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3420    set(gcf,'Pointer','arrow')
3421%     UvData.MouseAction='edit_vect';
3422else
3423    set(handles.record,'Visible','off')
3424    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3425%     UvData.MouseAction='none';
3426end
3427% set(handles.uvmat,'UserData',UvData)
3428
3429%----------------------------------------------
3430function save_mask_Callback(hObject, eventdata, handles)
3431%-----------------------------------------------------------------------
3432UvData=get(handles.uvmat,'UserData');
3433
3434flag=1;
3435npx=size(UvData.Field.A,2);
3436npy=size(UvData.Field.A,1);
3437xi=0.5:npx-0.5;
3438yi=0.5:npy-0.5;
3439[Xi,Yi]=meshgrid(xi,yi);
3440if isfield(UvData,'Object')
3441    for iobj=1:length(UvData.Object)
3442        ObjectData=UvData.Object{iobj};
3443        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3444            flagobj=1;
3445            testphys=0; %coordinates in pixels by default
3446            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3447                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3448                    Calib=UvData.XmlData{1}.GeometryCalib;
3449                    testphys=1;
3450                end
3451            end
3452            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3453                if isequal(ObjectData.Type,'polygon')
3454                    X=ObjectData.Coord(:,1);
3455                    Y=ObjectData.Coord(:,2);
3456                    if testphys
3457                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3458                    end
3459                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3460                elseif isequal(ObjectData.Type,'ellipse')
3461                    if testphys
3462                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3463                    end
3464                    RangeX=max(ObjectData.RangeX);
3465                    RangeY=max(ObjectData.RangeY);
3466                    X2Max=RangeX*RangeX;
3467                    Y2Max=RangeY*RangeY;
3468                    distX=(Xi-ObjectData.Coord(1,1));
3469                    distY=(Yi-ObjectData.Coord(1,2));
3470                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3471                elseif isequal(ObjectData.Type,'rectangle')
3472                    if testphys
3473                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3474                    end
3475                    distX=abs(Xi-ObjectData.Coord(1,1));
3476                    distY=abs(Yi-ObjectData.Coord(1,2));
3477                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3478                end
3479                if isequal(ObjectData.ProjMode,'mask_outside')
3480                    flagobj=~flagobj;
3481                end
3482                flag=flag & flagobj;
3483            end
3484        end
3485    end
3486end
3487% flag=~flag;
3488%mask name
3489RootPath=get(handles.RootPath,'String');
3490RootFile=get(handles.RootFile,'String');
3491RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3492filebase=fullfile(RootPath,RootFile);
3493list=get(handles.masklevel,'String');
3494masknumber=num2str(length(list));
3495maskindex=get(handles.masklevel,'Value');
3496mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3497%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3498imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3499imflag=flipdim(imflag,1);
3500% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3501msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3502imwrite(imflag,mask_name,'BitDepth',8);
3503
3504%display the mask
3505figure;
3506vec=linspace(0,1,256);%define a linear greyscale colormap
3507map=[vec' vec' vec'];
3508colormap(map)
3509
3510image(imflag);
3511
3512%-------------------------------------------------------------------
3513%-------------------------------------------------------------------
3514%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3515
3516%------------------------------------------------------------------
3517%-------------------------------------------------------------
3518% --- Executes on selection change in transform_fct.
3519function transform_fct_Callback(hObject, eventdata, handles)
3520%-------------------------------------------------------------
3521UvData=get(handles.uvmat,'UserData');
3522menu=get(handles.transform_fct,'String');
3523ind_coord=get(handles.transform_fct,'Value');
3524coord_option=menu{ind_coord};
3525list_transform=get(handles.transform_fct,'UserData');
3526ff=functions(list_transform{end}); 
3527if isequal(coord_option,'more...');
3528    coord_fct='';
3529    prompt = {'Enter the name of the transform function'};
3530    dlg_title = 'user defined transform';
3531    num_lines= 1;
3532    [FileName, PathName] = uigetfile( ...
3533       {'*.m', ' (*.m)';
3534        '*.m',  '.m files '; ...
3535        '*.*', 'All Files (*.*)'}, ...
3536        'Pick a file', ff.file);
3537    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3538        PathName(end)=[];
3539    end
3540    transform_selected =fullfile(PathName,FileName);
3541    if ~exist(transform_selected,'file')
3542           return
3543    end
3544   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3545   if ~isequal(ext_fct,'.m')
3546        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3547        return
3548   end
3549   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3550   ind_coord=get(handles.transform_fct,'Value');
3551   addpath(PathName)
3552   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3553   set(handles.transform_fct,'UserData',list_transform)
3554   rmpath(PathName)
3555   % save the new menu in the personal file 'uvmat_perso.mat'
3556   dir_perso=prefdir;%personal Matalb directory
3557   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3558   if exist(profil_perso,'file')
3559       nb_builtin=UvData.OpenParam.NbBuiltin;
3560       for ilist=nb_builtin+1:numel(list_transform)
3561           ff=functions(list_transform{ilist});
3562           transform_fct{ilist-nb_builtin}=ff.file;
3563       end
3564        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3565   end   
3566end
3567
3568%% check the current path to the selected function
3569if isa(list_transform{ind_coord},'function_handle')
3570    func=functions(list_transform{ind_coord});
3571    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3572else
3573    set(handles.path_transform,'String','')
3574end
3575
3576set(handles.CheckFixLimits,'Value',0)
3577set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3578
3579%% delete drawn objects
3580hother=findobj('Tag','proj_object');%find all the proj objects
3581for iobj=1:length(hother)
3582    delete_object(hother(iobj))
3583end
3584hother=findobj('Tag','DeformPoint');%find all the proj objects
3585for iobj=1:length(hother)
3586    delete_object(hother(iobj))
3587end
3588hh=findobj('Tag','calib_points');
3589if ~isempty(hh)
3590    delete(hh)
3591end
3592hhh=findobj('Tag','calib_marker');
3593if ~isempty(hhh)
3594    delete(hhh)
3595end
3596if isfield(UvData,'Object')
3597     UvData.Object=UvData.Object(1);
3598end
3599set(handles.ListObject,'Value',1)
3600set(handles.ListObject,'String',{'plane'})
3601set(handles.ListObject_1,'Value',1)
3602set(handles.ListObject_1,'String',{'plane'})
3603
3604%delete mask if it is displayed
3605% if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3606%    UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3607% end
3608set(handles.uvmat,'UserData',UvData)
3609run0_Callback(hObject, eventdata, handles)
3610
3611
3612
3613%------------------------------------------------
3614%CALLBACKS FOR PLOTTING PARAMETERS
3615%-------------------------------------------------
3616%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3617% Plot coordinates
3618%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3619%------------------------------------------------------------------------
3620function num_MinX_Callback(hObject, eventdata, handles)
3621%------------------------------------------------------------------------
3622set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3623set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3624update_plot(handles);
3625
3626%------------------------------------------------------------------------
3627function num_MaxX_Callback(hObject, eventdata, handles)
3628%------------------------------------------------------------------------
3629set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3630set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3631update_plot(handles);
3632
3633%------------------------------------------------------------------------
3634function num_MinY_Callback(hObject, eventdata, handles)
3635%------------------------------------------
3636set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3637set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3638update_plot(handles);
3639
3640%------------------------------------------------------------------------
3641function num_MaxY_Callback(hObject, eventdata, handles)
3642%------------------------------------------------------------------------
3643set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3644set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3645update_plot(handles);
3646
3647%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3648% Scalar or image representation
3649%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3650%------------------------------------------------------------------------
3651function num_MinA_Callback(hObject, eventdata, handles)
3652%------------------------------------------
3653set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3654set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3655MinA=str2double(get(handles.num_MinA,'String'));
3656MaxA=str2double(get(handles.num_MaxA,'String'));
3657if MinA>MaxA% switch minA and maxA in case of error
3658    MinA_old=MinA;
3659    MinA=MaxA;
3660    MaxA=MinA_old;
3661    set(handles.num_MinA,'String',num2str(MinA,5));
3662    set(handles.num_MaxA,'String',num2str(MaxA,5));
3663end
3664update_plot(handles);
3665
3666%------------------------------------------------------------------------
3667function num_MaxA_Callback(hObject, eventdata, handles)
3668%------------------------------------------------------------------------
3669set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3670set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3671MinA=str2double(get(handles.num_MinA,'String'));
3672MaxA=str2double(get(handles.num_MaxA,'String'));
3673if MinA>MaxA% switch minA and maxA in case of error
3674        MinA_old=MinA;
3675    MinA=MaxA;
3676    MaxA=MinA_old;
3677    set(handles.num_MinA,'String',num2str(MinA,5));
3678    set(handles.num_MaxA,'String',num2str(MaxA,5));
3679end
3680update_plot(handles);
3681
3682%------------------------------------------------------------------------
3683function CheckFixScalar_Callback(hObject, eventdata, handles)
3684%------------------------------------------------------------------------
3685test=get(handles.CheckFixScalar,'Value');
3686if test
3687    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3688else
3689    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3690    update_plot(handles);
3691end
3692
3693%-------------------------------------------------------------------
3694function CheckBW_Callback(hObject, eventdata, handles)
3695%-------------------------------------------------------------------
3696update_plot(handles);
3697
3698%-------------------------------------------------------------------
3699function num_Opacity_Callback(hObject, eventdata, handles)
3700update_plot(handles);
3701%-------------------------------------------------------------------
3702
3703%-------------------------------------------------------------------
3704function ListContour_Callback(hObject, eventdata, handles)
3705%-------------------------------------------------------------------
3706val=get(handles.ListContour,'Value');
3707if val==2
3708    set(handles.interval_txt,'Visible','on')
3709    set(handles.num_IncrA,'Visible','on')
3710else
3711    set(handles.interval_txt,'Visible','off')
3712    set(handles.num_IncrA,'Visible','off')
3713end
3714update_plot(handles);
3715
3716%-------------------------------------------------------------------
3717function num_IncrA_Callback(hObject, eventdata, handles)
3718%-------------------------------------------------------------------
3719update_plot(handles);
3720
3721
3722%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3723% Vector representation
3724%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3725%-------------------------------------------------------------------
3726function CheckHideWarning_Callback(hObject, eventdata, handles)
3727%-------------------------------------------------------------------
3728update_plot(handles);
3729
3730%-------------------------------------------------------------------
3731function CheckHideFalse_Callback(hObject, eventdata, handles)
3732%-------------------------------------------------------------------
3733update_plot(handles);
3734
3735%-------------------------------------------------------------------
3736function num_VecScale_Callback(hObject, eventdata, handles)
3737%-------------------------------------------------------------------
3738set(handles.CheckFixVectors,'Value',1);
3739set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3740update_plot(handles);
3741
3742%-------------------------------------------------------------------
3743function CheckFixVectors_Callback(hObject, eventdata, handles)
3744%-------------------------------------------------------------------
3745test=get(handles.CheckFixVectors,'Value');
3746if test
3747    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3748else
3749    update_plot(handles);
3750    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3751    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3752end
3753
3754%------------------------------------------------------------------------
3755% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3756function CheckDecimate4_Callback(hObject, eventdata, handles)
3757%------------------------------------------------------------------------
3758update_plot(handles);
3759
3760%------------------------------------------------------------------------
3761% --- Executes on selection change in ColorCode menu
3762function ColorCode_Callback(hObject, eventdata, handles)
3763%------------------------------------------------------------------------
3764% edit the choice for color code
3765update_color_code_boxes(handles);
3766update_plot(handles);
3767
3768%------------------------------------------------------------------------
3769function update_color_code_boxes(handles)
3770%------------------------------------------------------------------------
3771list_code=get(handles.ColorCode,'String');% list menu fields
3772colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3773enable_slider='off';%default
3774enable_bounds='off';%default
3775enable_scalar='off';%default
3776switch colcode
3777    case {'rgb','bgr'}
3778        enable_slider='on';
3779        enable_bounds='on';
3780        enable_scalar='on';
3781    case '64 colors'
3782        enable_bounds='on';
3783        enable_scalar='on';
3784end
3785set(handles.Slider1,'Visible',enable_slider)
3786set(handles.Slider2,'Visible', enable_slider)
3787set(handles.num_ColCode1,'Visible',enable_slider)
3788set(handles.num_ColCode2,'Visible',enable_slider)
3789set(handles.TitleColCode1,'Visible',enable_slider)
3790set(handles.TitleColCode2,'Visible',enable_slider)
3791set(handles.CheckFixVecColor,'Visible',enable_bounds)
3792set(handles.num_MinVec,'Visible',enable_bounds)
3793set(handles.num_MaxVec,'Visible',enable_bounds)
3794set(handles.ColorScalar,'Visible',enable_scalar)
3795set_vec_col_bar(handles)
3796
3797%------------------------------------------------------------------
3798% --- Executes on selection change in ColorScalar: choice of the color code.
3799function ColorScalar_Callback(hObject, eventdata, handles)
3800%------------------------------------------------------------------
3801% edit the choice for color code
3802list_scalar=get(handles.ColorScalar,'String');% list menu fields
3803col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3804if isequal(col_scalar,'ima_cor')
3805    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3806    ColorCode='rgb';
3807    set(handles.num_MinVec,'String','0')
3808    set(handles.num_MaxVec,'String','1')
3809    set(handles.num_ColCode1,'String','0.333')
3810    set(handles.num_ColCode2,'String','0.666')
3811else
3812    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3813    ColorCode='64 colors';
3814end
3815ColorCodeList=get(handles.ColorCode,'String');
3816ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3817set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3818
3819update_color_code_boxes(handles);
3820%replot the current graph
3821run0_Callback(hObject, eventdata, handles)
3822
3823%----------------------------------------------------------------
3824% -- Executes on slider movement to set the color code
3825%
3826function Slider1_Callback(hObject, eventdata, handles)
3827%------------------------------------------------------------------
3828slider1=get(handles.Slider1,'Value');
3829min_val=str2num(get(handles.num_MinVec,'String'));
3830max_val=str2num(get(handles.num_MaxVec,'String'));
3831col=min_val+(max_val-min_val)*slider1;
3832set(handles.num_ColCode1,'String',num2str(col))
3833if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3834    set(handles.Slider2,'Value',col)
3835    set(handles.num_ColCode2,'String',num2str(col))
3836end
3837set_vec_col_bar(handles)
3838update_plot(handles);
3839
3840%----------------------------------------------------------------
3841% Executes on slider movement to set the color code
3842%----------------------------------------------------------------
3843function Slider2_Callback(hObject, eventdata, handles)
3844slider2=get(handles.Slider2,'Value');
3845min_val=str2num(get(handles.num_MinVec,'String'));
3846max_val=str2num(get(handles.num_MaxVec,'String'));
3847col=min_val+(max_val-min_val)*slider2;
3848set(handles.num_ColCode2,'String',num2str(col))
3849if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3850    set(handles.Slider1,'Value',col)
3851    set(handles.num_ColCode1,'String',num2str(col))
3852end
3853set_vec_col_bar(handles)
3854update_plot(handles);
3855
3856%----------------------------------------------------------------
3857% --- Execute on return carriage on the edit box corresponding to slider 1
3858%----------------------------------------------------------------
3859function num_ColCode1_Callback(hObject, eventdata, handles)
3860set_vec_col_bar(handles)
3861update_plot(handles);
3862
3863%----------------------------------------------------------------
3864% --- Execute on return carriage on the edit box corresponding to slider 2
3865%----------------------------------------------------------------
3866function num_ColCode2_Callback(hObject, eventdata, handles)
3867set_vec_col_bar(handles)
3868update_plot(handles);
3869%------------------------------------------------------------------------
3870%-------------------------------------------------------
3871% --- Executes on button press in CheckFixVecColor.
3872%-------------------------------------------------------
3873function VecColBar_Callback(hObject, eventdata, handles)
3874set_vec_col_bar(handles)
3875
3876%------------------------------------------------------------------------
3877% --- Executes on button press in CheckFixVecColor.
3878function CheckFixVecColor_Callback(hObject, eventdata, handles)
3879%------------------------------------------------------------------------
3880if ~get(handles.CheckFixVecColor,'Value')
3881    update_plot(handles);
3882end
3883
3884%------------------------------------------------------------------------
3885% --- Executes on selection change in num_MaxVec.
3886function num_MinVec_Callback(hObject, eventdata, handles)
3887%------------------------------------------------------------------------
3888max_vec_Callback(hObject, eventdata, handles)
3889
3890%------------------------------------------------------------------------
3891% --- Executes on selection change in num_MaxVec.
3892function num_MaxVec_Callback(hObject, eventdata, handles)
3893%------------------------------------------------------------------------
3894set(handles.CheckFixVecColor,'Value',1)
3895CheckFixVecColor_Callback(hObject, eventdata, handles)
3896min_val=str2num(get(handles.num_MinVec,'String'));
3897max_val=str2num(get(handles.num_MaxVec,'String'));
3898slider1=get(handles.Slider1,'Value');
3899slider2=get(handles.Slider2,'Value');
3900colcode1=min_val+(max_val-min_val)*slider1;
3901colcode2=min_val+(max_val-min_val)*slider2;
3902set(handles.num_ColCode1,'String',num2str(colcode1))
3903set(handles.num_ColCode2,'String',num2str(colcode2))
3904update_plot(handles);
3905
3906%------------------------------------------------------------------------
3907% --- update the display of color code for vectors (on vecColBar)
3908function set_vec_col_bar(handles)
3909%------------------------------------------------------------------------
3910%get the image of the color display button 'VecColBar' in pixels
3911set(handles.VecColBar,'Unit','pixel');
3912pos_vert=get(handles.VecColBar,'Position');
3913set(handles.VecColBar,'Unit','Normalized');
3914width=ceil(pos_vert(3));
3915height=ceil(pos_vert(4));
3916
3917%get slider indications
3918list=get(handles.ColorCode,'String');
3919ichoice=get(handles.ColorCode,'Value');
3920colcode.ColorCode=list{ichoice};
3921colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3922colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3923test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
3924if test3color
3925    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3926    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3927end
3928vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3929[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3930oneheight=ones(1,height);
3931A1=colorlist(col_vec,1)*oneheight;
3932A2=colorlist(col_vec,2)*oneheight;
3933A3=colorlist(col_vec,3)*oneheight;
3934A(:,:,1)=A1';
3935A(:,:,2)=A2';
3936A(:,:,3)=A3';
3937set(handles.VecColBar,'Cdata',A)
3938
3939%-------------------------------------------------------------------
3940function update_plot(handles)
3941%-------------------------------------------------------------------
3942UvData=get(handles.uvmat,'UserData');
3943AxeData=UvData.axes3;% retrieve the current plotted data
3944PlotParam=read_GUI(handles.uvmat);
3945[tild,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
3946write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3947
3948%------------------------------------------------------------------------
3949%------------------------------------------------------------------------
3950%   SELECTION AND EDITION OF PROJECTION OBJECTS
3951%------------------------------------------------------------------------
3952%------------------------------------------------------------------------
3953
3954% --- Executes on selection change in ListObject_1.
3955function ListObject_1_Callback(hObject, eventdata, handles)
3956list_str=get(handles.ListObject,'String');
3957UvData=get(handles.uvmat,'UserData');
3958ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
3959
3960%% update the projection plot on uvmat
3961ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
3962plot_field(ProjData,handles.axes3,read_GUI(handles.uvmat));% plot the projected field;
3963%replot all the objects within the new projected field
3964for IndexObj=1:numel(list_str)
3965    IndexObj
3966        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat
3967        if isempty(hobject) || ~ishandle(hobject)
3968            hobject=handles.axes3
3969        end
3970        if isequal(IndexObj,get(handles.ListObject,'Value'))
3971            objectcolor='m'; %paint in magenta the currently selected object in ListObject
3972        else
3973            objectcolor='b';
3974        end
3975        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
3976end
3977set(handles.uvmat,'UserData',UvData)
3978
3979%% display the object parameters if the GUI set_object is already opened
3980if ~get(handles.ViewObject,'Value')
3981    ZBounds=0; % default
3982    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3983        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3984        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3985    end
3986    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
3987    set_object(ObjectData,[],ZBounds);
3988    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
3989end
3990
3991%  desactivate the edit object mode
3992set(handles.edit_object,'Value',0)
3993set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
3994
3995%------------------------------------------------------------------------
3996% --- Executes on selection change in ListObject.
3997function ListObject_Callback(hObject, eventdata, handles)
3998%------------------------------------------------------------------------
3999list_str=get(handles.ListObject,'String');
4000IndexObj=get(handles.ListObject,'Value');%present object selection
4001
4002%% The object  is displayed in set_object if this GUI is already opened
4003UvData=get(handles.uvmat,'UserData');
4004ObjectData=UvData.Object{IndexObj};
4005hset_object=findobj(allchild(0),'tag','set_object');
4006if ~isempty(hset_object)
4007    ZBounds=0; % default
4008    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4009        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4010        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4011    end
4012    ObjectData.Name=list_str{IndexObj};
4013    set_object(ObjectData,[],ZBounds);
4014    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4015end
4016
4017%%  desactivate the edit object mode
4018set(handles.edit_object,'Value',0)
4019set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4020
4021%% update the  plot on view_field if view_field is already openened
4022hview_field=findobj(allchild(0),'tag','view_field');
4023if isempty(hview_field)
4024    hhview_field.axes3=[];
4025else
4026    Data=get(hview_field,'UserData');
4027    hhview_field=guidata(hview_field);
4028    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4029    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
4030    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4031    haxes=findobj(hview_field,'tag','axes3');
4032    pos=get(hview_field,'Position'); 
4033    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4034        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4035        pos_table=get(h_TableDisplay,'Position');
4036        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4037        drawnow% needed to change position before the next command
4038        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4039    else
4040        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4041    end
4042end
4043
4044%% update the color of the graphic object representation: the selected object in magenta, others in blue
4045update_object_color(handles.axes3,hhview_field.axes3,UvData.Object{IndexObj}.DisplayHandle.uvmat)
4046
4047%------------------------------------------------------------------------
4048%--- update the color representation of objects (indicating the selected ones)
4049function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4050%------------------------------------------------------------------------
4051if isempty(axes_view_field)% case with no view_field plot
4052hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4053else
4054hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4055findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4056end
4057for iobj=1:length(hother)
4058    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4059        set(hother(iobj),'EdgeColor','b')
4060        if isequal(get(hother(iobj),'FaceColor'),'m')
4061            set(hother(iobj),'FaceColor','b')
4062        end
4063    elseif isequal(get(hother(iobj),'Type'),'image')
4064        Acolor=get(hother(iobj),'CData');
4065        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4066        set(hother(iobj),'CData',Acolor);
4067    else
4068        set(hother(iobj),'Color','b')
4069    end
4070    set(hother(iobj),'Selected','off')
4071end
4072if ishandle(DisplayHandle)
4073    linetype=get(DisplayHandle,'Type');
4074    if isequal(linetype,'line')
4075        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4076    elseif isequal(linetype,'rectangle')
4077        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4078    elseif isequal(linetype,'patch')
4079        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4080    end
4081    SubObjectData=get(DisplayHandle,'UserData');
4082    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4083        for iobj=1:length(SubObjectData.SubObject)
4084            hsub=SubObjectData.SubObject(iobj);
4085            if isequal(get(hsub,'Type'),'rectangle')
4086                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4087            elseif isequal(get(hsub,'Type'),'image')
4088                Acolor=get(hsub,'CData');
4089                Acolor(:,:,1)=Acolor(:,:,3);
4090                set(hsub,'CData',Acolor);
4091            else
4092                set(hsub,'Color','m')
4093            end
4094        end
4095    end
4096    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4097        set(SubObjectData.DeformPoint,'Color','m')
4098    end
4099end
4100
4101%-------------------------------------------------------------------
4102% --- Executes on selection change in edit_object.
4103function edit_object_Callback(hObject, eventdata, handles)
4104%-------------------------------------------------------------------
4105UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4106hset_object=findobj(allchild(0),'Tag','set_object');
4107if get(handles.edit_object,'Value')
4108    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4109    %suppress the other options
4110    set(handles.CheckZoom,'Value',0)
4111    CheckZoom_Callback(hObject, eventdata, handles)
4112    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4113    if ishandle(hgeometry_calib)
4114        hhgeometry_calib=guidata(hgeometry_calib);
4115        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4116        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4117    end
4118    set(handles.ViewObject,'value',1)
4119    ViewObject_Callback(hObject, eventdata, handles)
4120else % desctivate object edit mode
4121    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4122    if ~isempty(hset_object)% open the
4123        hhset_object=guidata(hset_object);
4124        set(hhset_object.PLOT,'enable','off');
4125        set(get(hset_object,'children'),'enable','inactive')
4126    end
4127end
4128
4129
4130%------------------------------------------------------------------------
4131% --- Executes on button press in ViewObject.
4132function ViewObject_Callback(hObject, eventdata, handles)
4133%------------------------------------------------------------------------
4134check_view=get(handles.ViewObject,'Value');
4135
4136if check_view %activate set_object   
4137    IndexObj=get(handles.ListObject,'Value');
4138    list_object=get(handles.ListObject,'String');
4139    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4140    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4141    if numel(UvData.Object)<IndexObj;% error in UvData
4142        msgbox_uvmat('ERROR','invalid object list')
4143        return
4144    end
4145    ZBounds=0; % default
4146    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4147        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4148        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4149    end
4150%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4151    data=UvData.Object{IndexObj};
4152    if ~isfield(data,'Type')% default plane
4153        data.Type='plane';
4154    end
4155    if isfield(UvData,'Field')
4156        Field=UvData.Field;
4157        if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4158            data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4159            if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4160                data.RangeY=UvData.Field.Mesh;
4161            else
4162                data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4163            end
4164            data.DX=UvData.Field.Mesh;
4165            data.DY=UvData.Field.Mesh;
4166        end
4167        if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4168            data.Coord=[0 0 0]; %default
4169        end
4170        if isfield(Field,'CoordUnit')
4171            data.CoordUnit=Field.CoordUnit;
4172        end
4173    end
4174    hset_object=set_object(data,[],ZBounds);
4175    hhset_object=guidata(hset_object);
4176    if get(handles.edit_object,'Value')% edit mode
4177        set(hhset_object.PLOT,'Enable','on')
4178        set(get(hset_object,'children'),'enable','on')
4179    else
4180        set(hhset_object.PLOT,'Enable','off')
4181        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4182        set(hhset_object.SAVE,'Enable','on')
4183    end
4184else
4185    hset_object=findobj(allchild(0),'tag','set_object');
4186    if ~isempty(hset_object)
4187        delete(hset_object)% delete existing version of set_object
4188    end
4189end
4190 
4191
4192%------------------------------------------------------------------------
4193% --- Executes on button press in ViewField.
4194function ViewField_Callback(hObject, eventdata, handles)
4195%------------------------------------------------------------------------
4196check_view=get(handles.ViewField,'Value');
4197
4198if check_view
4199    IndexObj=get(handles.ListObject,'Value');
4200    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4201    if numel(UvData.Object)<IndexObj(end);% error in UvData
4202        msgbox_uvmat('ERROR','invalid object list')
4203        return
4204    end
4205    ZBounds=0; % default
4206    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4207        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4208        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4209    end
4210    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4211    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4212        UvData.Object{IndexObj(1)}.Type='plane';
4213    end
4214    list_object=get(handles.ListObject,'String');
4215    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4216   
4217    %% show the projection of the selected object on view_field
4218    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
4219    hview_field=findobj(allchild(0),'tag','view_field');
4220    if isempty(hview_field)
4221        hview_field=view_field;
4222    end
4223    hhview_field=guidata(hview_field);
4224    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4225    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4226    haxes=findobj(hview_field,'tag','axes3');
4227    pos=get(hview_field,'Position');
4228    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4229        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4230        pos_table=get(h_TableDisplay,'Position');
4231        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4232    else
4233        Data=get(hview_field,'UserData');
4234        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4235    end
4236else
4237    hview_field=findobj(allchild(0),'tag','view_field');
4238    if ~isempty(hview_field)
4239        delete(hview_field)% delete existing version of set_object
4240    end
4241end
4242
4243
4244%------------------------------------------------------------------------
4245% --- Executes on button press in delete_object.
4246function delete_object_Callback(hObject, eventdata, handles)
4247%------------------------------------------------------------------------
4248IndexObj=get(handles.ListObject,'Value');
4249IndexObj_1=get(handles.ListObject_1,'Value');
4250if IndexObj>1 && ~isequal(IndexObj,IndexObj_1)
4251    delete_object(IndexObj)
4252end
4253
4254%------------------------------------------------------------------------
4255%------------------------------------------------------------------------
4256%  II - TOOLS FROM THE UPPER MENU BAR
4257%------------------------------------------------------------------------
4258%------------------------------------------------------------------------
4259
4260%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4261% Export  Menu Callbacks
4262%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4263%------------------------------------------------------------------------
4264% --- Executes on button press in Menu/Export/field in workspace.
4265function MenuExportField_Callback(hObject, eventdata, handles)
4266%------------------------------------------------------------------------
4267global Data_uvmat
4268Data_uvmat=get(handles.uvmat,'UserData');
4269evalin('base','global Data_uvmat')%make CurData global in the workspace
4270display('current field :')
4271evalin('base','Data_uvmat') %display CurData in the workspace
4272commandwindow; %brings the Matlab command window to the front
4273
4274%------------------------------------------------------------------------
4275% --- Executes on button press in Menu/Export/extract figure.
4276function MenuExportFigure_Callback(hObject, eventdata, handles)
4277%------------------------------------------------------------------------
4278% huvmat=get(handles.MenuExport,'parent');
4279hfig=figure;
4280copyobj(handles.axes3,hfig);
4281map=colormap(handles.axes3);
4282colormap(map);%transmit the current colormap to the zoom fig
4283colorbar
4284
4285% %------------------------------------------------------
4286% % --- Executes on button press in Menu/Export/extract figure.
4287% %------------------------------------------------------
4288% function MenuExport_plot_Callback(hObject, eventdata, handles)
4289% huvmat=get(handles.MenuExport_plot,'parent');
4290% UvData=get(huvmat,'UserData');
4291% hfig=figure;
4292% newaxes=copyobj(handles.axes3,hfig);
4293% map=colormap(handles.axes3);
4294% colormap(map);%transmit the current colormap to the zoom fig
4295% colorbar
4296
4297%
4298% % --------------------------------------------------------------------
4299% function Insert_Callback(hObject, eventdata, handles)
4300%
4301
4302%------------------------------------------------------------------------
4303% --------------------------------------------------------------------
4304function MenuExportMovie_Callback(hObject, eventdata, handles)
4305% --------------------------------------------------------------------
4306set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4307huvmat=get(handles.run0,'parent');
4308UvData=get(huvmat,'UserData');
4309%[xx,xx,FileBase]=read_file_boxes(handles);
4310[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4311FileBase=fullfile(RootPath,RootFile);
4312 %read the current input file name
4313prompt = {'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)'};
4314dlg_title = 'select properties of the output avi movie';
4315num_lines= 1;
4316% nbfield_cell=get(handles.last_i,'String');
4317def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4318answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4319aviname=answer{1};
4320fps=str2double(answer{2});
4321% check for existing file with output name aviname
4322if exist(aviname,'file')
4323    backup=aviname;
4324    testexist=2;
4325    while testexist==2
4326        backup=[backup '~'];
4327        testexist=exist(backup,'file');     
4328    end
4329    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4330    if isequal(success,1)
4331        delete(aviname)%delete existing file
4332    else
4333        msgbox_uvmat('ERROR',message)
4334        return
4335    end
4336end
4337%create avi open
4338aviobj=avifile(aviname,'Compression','None','fps',fps);
4339
4340%display first view for tests
4341newfig=figure;
4342newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4343set(newaxes,'Tag','movieaxes')
4344nbpix=[512 384]*str2double(answer{3});
4345set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4346set(newaxes,'Position',eval(answer{4}));
4347map=colormap(handles.axes3);
4348colormap(map);%transmit the current colormap to the zoom fig
4349msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4350        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4351UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4352set(huvmat,'UserData',UvData);
4353increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4354set(handles.STOP,'Visible','on')
4355set(handles.speed,'Visible','on')
4356set(handles.speed_txt,'Visible','on')
4357set(handles.Movie,'BusyAction','queue')
4358
4359%imin=str2double(get(handles.i1,'String'));
4360imax=str2double(answer{5});
4361% if isfield(UvData,'Time')
4362htitle=get(newaxes,'Title');
4363xlim=get(newaxes,'XLim');
4364ylim=get(newaxes,'YLim');
4365set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4366time_str=get(handles.abs_time,'String');
4367set(htitle,'String',['t=' time_str])
4368set(handles.speed,'Value',1)
4369for i=1:imax
4370    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4371            runpm(hObject,eventdata,handles,increment)% run plus
4372            drawnow
4373            time_str=get(handles.abs_time,'String');
4374            if ishandle(htitle)
4375             set(htitle,'String',['t=' time_str])
4376            end
4377            mov=getframe(newfig);
4378            aviobj=addframe(aviobj,mov);
4379    end
4380end
4381aviobj=close(aviobj);
4382UvData=rmfield(UvData,'plotaxes');
4383%UvData.Object{1}.plotaxes=handles.axes3;
4384set(huvmat,'UserData',UvData);
4385msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4386
4387
4388%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4389% Projection Objects Menu Callbacks
4390%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4391
4392% -----------------------------------------------------------------------
4393function Menupoints_Callback(hObject, eventdata, handles)
4394%------------------------------------------------------------------------
4395data.Type='points';
4396data.ProjMode='projection';%default
4397data.ProjModeMenu={};% do not restrict ProjMode menus
4398create_object(data,handles)
4399
4400% -----------------------------------------------------------------------
4401function Menuline_Callback(hObject, eventdata, handles)
4402%------------------------------------------------------------------------
4403data.Type='line';
4404data.ProjMode='projection';%default
4405data.ProjModeMenu={};% do not restrict ProjMode menus
4406create_object(data,handles)
4407
4408%------------------------------------------------------------------------
4409function Menupolyline_Callback(hObject, eventdata, handles)
4410%------------------------------------------------------------------------
4411data.Type='polyline';
4412data.ProjMode='projection';%default
4413data.ProjModeMenu={};% do not restrict ProjMode menus
4414create_object(data,handles)
4415
4416%------------------------------------------------------------------------
4417function Menupolygon_Callback(hObject, eventdata, handles)
4418%------------------------------------------------------------------------
4419data.Type='polygon';
4420data.ProjMode='inside';%default
4421data.ProjModeMenu={};% do not restrict ProjMode menus
4422create_object(data,handles)
4423
4424%------------------------------------------------------------------------
4425function Menurectangle_Callback(hObject, eventdata, handles)
4426%------------------------------------------------------------------------
4427data.Type='rectangle';
4428data.ProjMode='inside';%default
4429data.ProjModeMenu={};% do not restrict ProjMode menus
4430create_object(data,handles)
4431
4432%------------------------------------------------------------------------
4433function Menuellipse_Callback(hObject, eventdata, handles)
4434%------------------------------------------------------------------------
4435data.Type='ellipse';
4436data.ProjMode='inside';%default
4437data.ProjModeMenu={};% do not restrict ProjMode menus
4438create_object(data,handles)
4439
4440%------------------------------------------------------------------------
4441function MenuMaskObject_Callback(hObject, eventdata, handles)
4442%------------------------------------------------------------------------
4443data.Type='polygon';
4444data.TypeMenu={'polygon'};
4445data.ProjMode='mask_inside';%default
4446data.ProjModeMenu={'mask_inside';'mask_outside'};
4447create_object(data,handles)
4448
4449%------------------------------------------------------------------------
4450function Menuplane_Callback(hObject, eventdata, handles)
4451%------------------------------------------------------------------------
4452data.Type='plane';
4453data.ProjMode='projection';%default
4454data.ProjModeMenu={};% do not restrict ProjMode menus
4455create_object(data,handles)
4456
4457%------------------------------------------------------------------------
4458function Menuvolume_Callback(hObject, eventdata, handles)
4459%------------------------------------------------------------------------
4460data.Type='volume';
4461data.ProjMode='interp';%default
4462data.ProjModeMenu={};
4463% set(handles.create,'Visible','on')
4464% set(handles.create,'Value',1)
4465% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4466create_object(data,handles)
4467
4468%------------------------------------------------------------------------
4469% --- generic function used for the creation of a projection object
4470function create_object(data,handles)
4471%------------------------------------------------------------------------
4472% desactivate geometric calibration if opened
4473hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4474if ishandle(hgeometry_calib)
4475    hhgeometry_calib=guidata(hgeometry_calib);
4476    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4477    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4478end
4479set(handles.edit_object,'Value',0); %suppress the object edit mode
4480set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4481ListObject=get(handles.ListObject,'String');
4482if ~strcmp(ListObject{end},'')
4483    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4484    set(handles.ListObject,'String',ListObject)
4485end
4486IndexObj=length(ListObject);
4487set(handles.ListObject,'Value',IndexObj)
4488UvData=get(handles.uvmat,'UserData');
4489UvData.Object{IndexObj}=[]; %create a new empty object
4490UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.axes3; % axes for plot_object
4491UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4492data.Name=data.Type;% default name=type
4493data.Coord=[0 0]; %default
4494if isfield(UvData,'Field')
4495    Field=UvData.Field;
4496    if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4497        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4498        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4499            data.RangeY=UvData.Field.Mesh;
4500        else
4501            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4502        end
4503        data.DX=UvData.Field.Mesh;
4504        data.DY=UvData.Field.Mesh;
4505    end
4506    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4507         data.Coord=[0 0 0]; %default
4508    end
4509    if isfield(Field,'CoordUnit')
4510        data.CoordUnit=Field.CoordUnit;
4511    end
4512end
4513if ishandle(handles.UVMAT_title)
4514    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4515end
4516hset_object=set_object(data,handles);% call the set_object interface
4517hhset_object=guidata(hset_object);
4518hchild=get(hset_object,'children');
4519set(hchild,'enable','on')
4520set(handles.uvmat,'UserData',UvData)
4521set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
4522CheckZoom_Callback(handles.uvmat, [], handles)
4523set(handles.delete_object,'Visible','on')
4524
4525%------------------------------------------------------------------------
4526function MenuBrowseObject_Callback(hObject, eventdata, handles)
4527%------------------------------------------------------------------------
4528%get the object file
4529[FileName, PathName, filterindex] = uigetfile( ...
4530       {'*.xml;*.mat', ' (*.xml,*.mat)';
4531       '*.xml',  '.xml files '; ...
4532        '*.mat',  '.mat matlab files '}, ...
4533        'Pick an xml Object file',get(handles.RootPath,'String'));
4534fileinput=[PathName FileName];%complete file name
4535sizf=size(fileinput);
4536if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4537
4538%read the file
4539[data,heading]=xml2struct(fileinput);
4540if ~strcmp(heading,'ProjObject')
4541    msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects')
4542end
4543[tild,data.Name]=fileparts(FileName);% object name set as file name
4544ListObject=get(handles.ListObject,'String');
4545if ~strcmp(ListObject{end},'')
4546    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4547    set(handles.ListObject,'String',ListObject)
4548end
4549IndexObj=length(ListObject);
4550
4551UvData=get(handles.uvmat,'UserData');
4552UvData.Object{IndexObj}=[]; %create a new empty object
4553UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4554UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4555set(handles.uvmat,'UserData',UvData)
4556set(handles.ListObject,'Value',IndexObj)
4557hset_object=set_object(data);% call the set_object interface
4558set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4559set(handles.edit_object,'Value',0); %suppress the object edit mode
4560set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4561set(handles.delete_object,'Visible','on')
4562
4563
4564%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4565% MenuEdit Callbacks
4566%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4567%------------------------------------------------------------------------
4568function MenuEditObject_Callback(hObject, eventdata, handles)
4569%------------------------------------------------------------------------
4570set(handles.edit_object,'Value',1)
4571edit_Callback(hObject, eventdata, handles)
4572
4573%------------------------------------------------------------------------
4574function MenuEditVectors_Callback(hObject, eventdata, handles)
4575%------------------------------------------------------------------------
4576set(handles.edit_vect,'Visible','on')
4577set(handles.edit_vect,'Value',1)
4578edit_vect_Callback(hObject, eventdata, handles)
4579
4580%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4581% MenuTools Callbacks
4582%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4583%------------------------------------------------------------------------
4584function MenuCalib_Callback(hObject, eventdata, handles)
4585%------------------------------------------------------------------------
4586
4587UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4588
4589%suppress competing options
4590set(handles.CheckZoom,'Value',0)
4591set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4592set(handles.ListObject,'Value',1)     
4593% initiate display of GUI geometry_calib
4594data=[]; %default
4595if isfield(UvData,'CoordType')
4596    data.CoordType=UvData.CoordType;
4597end
4598pos=get(handles.uvmat,'Position');
4599pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4600pos(2)=pos(2)-0.02;
4601[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4602FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4603set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4604if isfield(UvData.OpenParam,'CalOrigin')
4605    pos_uvmat=get(handles.uvmat,'Position');
4606    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4607    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4608    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4609end
4610geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4611set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4612set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4613
4614%------------------------------------------------------------------------
4615function MenuMask_Callback(hObject, eventdata, handles)
4616%------------------------------------------------------------------------
4617UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4618ListObj=UvData.Object;
4619select=zeros(1,numel(ListObj));
4620for iobj=1:numel(ListObj);
4621    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4622        select(iobj)=1;
4623    end
4624end
4625val=find(select);
4626if isempty(val)
4627    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4628    return
4629else
4630%     set(handles.ListObject,'Max',2);%allow multiple selection
4631    set(handles.ListObject,'Value',val);
4632    flag=1;
4633    npx=size(UvData.Field.A,2);
4634    npy=size(UvData.Field.A,1);
4635    xi=0.5:npx-0.5;
4636    yi=0.5:npy-0.5;
4637    [Xi,Yi]=meshgrid(xi,yi);
4638    if isfield(UvData,'Object')
4639        for iobj=1:length(UvData.Object)
4640            ObjectData=UvData.Object{iobj};
4641            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4642                flagobj=1;
4643                testphys=0; %coordinates in pixels by default
4644                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4645                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4646                        Calib=UvData.XmlData{1}.GeometryCalib;
4647                        testphys=1;
4648                    end
4649                end
4650                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4651                    if isequal(ObjectData.Type,'polygon')
4652                        X=ObjectData.Coord(:,1);
4653                        Y=ObjectData.Coord(:,2);
4654                        if testphys
4655                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4656                        end
4657                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4658                    elseif isequal(ObjectData.Type,'ellipse')
4659                        if testphys
4660                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4661                        end
4662                        RangeX=max(ObjectData.RangeX);
4663                        RangeY=max(ObjectData.RangeY);
4664                        X2Max=RangeX*RangeX;
4665                        Y2Max=RangeY*RangeY;
4666                        distX=(Xi-ObjectData.Coord(1,1));
4667                        distY=(Yi-ObjectData.Coord(1,2));
4668                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4669                    elseif isequal(ObjectData.Type,'rectangle')
4670                        if testphys
4671                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4672                        end
4673                        distX=abs(Xi-ObjectData.Coord(1,1));
4674                        distY=abs(Yi-ObjectData.Coord(1,2));
4675                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4676                    end
4677                    if isequal(ObjectData.ProjMode,'mask_outside')
4678                        flagobj=~flagobj;
4679                    end
4680                    flag=flag & flagobj;
4681                end
4682            end
4683        end
4684    end
4685    %mask name
4686    RootPath=get(handles.RootPath,'String');
4687    SubDir=get(handles.SubDir,'String');
4688    RootFile=get(handles.RootFile,'String');
4689    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4690        RootFile(1)=[];
4691    end
4692   % filebase=fullfile(RootPath,RootFile);
4693    list=get(handles.masklevel,'String');
4694    masknumber=num2str(length(list));
4695    maskindex=get(handles.masklevel,'Value');
4696   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4697    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
4698    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4699    imflag=flipdim(imflag,1);
4700
4701    %display the mask
4702    hfigmask=figure;
4703    set(hfigmask,'Name','mask image')
4704    vec=linspace(0,1,256);%define a linear greyscale colormap
4705    map=[vec' vec' vec'];
4706    colormap(map)
4707    image(imflag);
4708    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4709    if ~strcmp(answer,'Cancel')
4710        mask_dir=fileparts(answer);
4711        if ~exist(mask_dir,'dir')
4712            [xx,msg1]=mkdir(mask_dir);
4713            if ~strcmp(msg1,'')
4714                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
4715                return
4716            end
4717        end
4718        imwrite(imflag,answer,'BitDepth',8);
4719    end
4720    set(handles.ListObject,'Value',1)
4721end
4722
4723%------------------------------------------------------------------------
4724%-- open the GUI set_grid.fig to create grid
4725function MenuGrid_Callback(hObject, eventdata, handles)
4726%------------------------------------------------------------------------
4727%suppress the other options if grid is chosen
4728set(handles.edit_vect,'Value',0)
4729edit_vect_Callback(hObject, eventdata, handles)
4730set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4731set(handles.ListObject,'Value',1)     
4732
4733%prepare display of the set_grid GUI
4734[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4735FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4736CoordList=get(handles.transform_fct,'String');
4737val=get(handles.transform_fct,'Value');
4738set_grid(FileName,CoordList{val});% call the set_object interface
4739
4740
4741%------------------------------------------------------------------------
4742function MenuRuler_Callback(hObject, eventdata, handles)
4743%------------------------------------------------------------------------
4744set(handles.CheckZoom,'Value',0)
4745CheckZoom_Callback(handles.uvmat, [], handles)
4746set(handles.MenuRuler,'checked','on')
4747UvData=get(handles.uvmat,'UserData');
4748UvData.MouseAction='ruler';
4749set(handles.uvmat,'UserData',UvData);
4750
4751%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4752% MenuRun Callbacks
4753%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4754
4755%------------------------------------------------------------------------
4756% open the GUI 'series'
4757function MenuSeries_Callback(hObject, eventdata, handles)
4758%------------------------------------------------------------------------
4759series; %first display of the GUI to fill waiting time
4760[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4761param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4762if isequal(get(handles.SubField,'Value'),1)
4763    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
4764    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
4765    if ~isequal(FileName_1,param.FileName)
4766        param.FileName_1=FileName_1;
4767    end
4768end
4769param.NomType=get(handles.NomType,'String');
4770param.NomType_1=get(handles.NomType_1,'String');
4771param.CheckFixPair=get(handles.CheckFixPair,'Value');
4772huvmat=get(handles.MenuSeries,'parent');
4773UvData=get(huvmat,'UserData');
4774if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4775    param.Time=UvData.XmlData{1}.Time;
4776end
4777if isequal(get(handles.scan_i,'Value'),1)
4778    param.incr_i=str2num(get(handles.increment_scan,'String'));
4779elseif isequal(get(handles.scan_j,'Value'),1)
4780    param.incr_j=str2num(get(handles.increment_scan,'String'));
4781end
4782param.list_fields=get(handles.Fields,'String');% list menu fields
4783param.list_fields(1)=[]; %suppress  'image' option
4784param.index_fields=get(handles.Fields,'Value');% selected string index
4785if param.index_fields>1
4786    param.index_fields=param.index_fields-1;
4787end
4788param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4789param.list_fields_1(1)=[]; %suppress  'image' option
4790param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4791if param.index_fields_1>1
4792    param.index_fields_1=param.index_fields_1-1;
4793end
4794param.menu_coord_str=get(handles.transform_fct,'String');
4795param.menu_coord_val=get(handles.transform_fct,'Value');
4796series(param); %run the series interface
4797
4798%------------------------------------------------------------------------
4799% -- open the GUI civ.fig for PIV
4800function MenuPIV_Callback(hObject, eventdata, handles)
4801%------------------------------------------------------------------------
4802 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4803 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4804civ(FileName);% interface de civ(not in the uvmat file)
4805
4806% --------------------------------------------------------------------
4807function MenuHelp_Callback(hObject, eventdata, handles)
4808% --------------------------------------------------------------------
4809path_to_uvmat=which ('uvmat');% check the path of uvmat
4810pathelp=fileparts(path_to_uvmat);
4811helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4812if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4813else
4814    addpath (fullfile(pathelp,'uvmat_doc'))
4815    web(helpfile);
4816end
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