source: trunk/src/uvmat.m @ 379

Last change on this file since 379 was 379, checked in by sommeria, 9 years ago

several bugs corrected
set_object.fig rationalized so that read_set_object is replaced by the rgeneral fct read_GUI.

File size: 197.8 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%           .VelType:(char string) type of velocity field selected
45%           .VelType_1:(char string)  REMPLACER LE CELL ACTUEL
46%           .FieldName: (char string) main field selected('image', 'velocity'...)
47%           .FieldName_1:(char string) second field selected('image', 'velocity'...)
48%           .CName: (char string)name of the scalar used for vector colors
49%          .MovieObject: movie object representing an input movie
50%          .MovieObject_1: idem for a second input series (_1)
51%          .filename_1 : last second input file name (to deal with a constant second input without reading again the file)
52%          .VelType_1: last velocity type (VelType, civ2...) for the second input series
53%          .FieldName_1: last field name(velocity, vorticity...) for the second input series
54%          .ZMin, .ZMax: range of the z coordinate
55%..... to complement
56%     - Information on  projection objects
57%           .Object: {[1x1 struct]}
58%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
59%     -Information on the current field (Field{i})
60%            .Txt : text information to display (e.g. error message)
61%            .NbDim: number of dimensions (=0 by default)
62%            .NbCoord: number of vector components
63%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
64%            .dt: time interval for the corresponding image pair
65%            .Mesh: estimated typical distance between vectors
66%            .ZMax:
67%            .ZMin:
68%            .X, .Y, .Z: set of vector coordinates
69%            .U,.V,.W: corresponding set of vector components
70%            .F: corresponding set of warning flags
71%            .FF: corresponding set of false flags, =0 for good vectors
72%            .C: corresponding values of the scalar used for vector color
73%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
74%                     equal to the number of vectors stored in the input open)
75%            .CName: name of the scalar .C
76%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
77%            .A image or scalar
78%            .AX: vector of dimension 2 representing the first and last values
79%              of the X coordinates for the image or scalar known on a regular grid,
80%              or vector of dimension .A for a scaler defined on irregular grid.
81%            .AY: same as .AX along the Y direction
82%            .AName: name of the scalar, ='image' for an image
83
84% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
85%
86% fields are opened and visualised by the sub-function refresh_field.m
87% (called by uvmat_opening, RUN0, runp and runm)
88% The function first reads the name of the input file from the edit boxes  of the GUI
89% A second input file can be introduced for filed comparison
90% It then reads the input file(s) with the appropriate function, read for
91% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf
92% files.
93%               Main input open   second input open(_1)        second image (pair animation)
94%            |                 |                             
95%            |                 |                                               
96%                     Field{1}         Field{2}               
97%                                                                         |
98% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
99%                                                                   Field{i}
100%                                                                    |
101% calc_field.m: calculate scalar or other derived fields (vort, div..).
102%
103% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
104%              Field{i=1->3}.X --> UvData.X                          |
105%                                                                    |
106%                                                                 UvData
107%                                                                    |
108% plot histograms of the whole  field
109% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
110%                                                                    |                                                                          |
111%                                                                ObjectData
112%                                                                    |
113% plot_field.m: plot the projected fields and store them as          |
114% UvData.axes3                                        |
115%                                                                    |
116%                                                                AxeData
117%
118%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
119% scalars are displayed either as an image or countour plot, either as a color of
120% velocity vectors. The scalar values in the first case is represented by
121% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
122% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
123% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
124% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
125% coordinates of the four image corners. The scalar name is represented by
126% the strings .AName and/or .CName.
127% If the scalar exists in an input open (image or scalar stored under its
128% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
129% Else only its name AName is recorded in Field{i}, and its field is then calculated
130%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
131     
132% Properties attached to plotting figures (standard Matlab properties):
133%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
134%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
135%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
136%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
137%    'KeyPressFcn': function called by pressing a key on the key board
138%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
139%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
140
141% Properties attached to plotting axes:
142%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
143%     AxeData:=get(gca,'UserData');
144%     AxeData.Drawing  = create: create a new object
145%                       = deform: modify an existing object by moving its defining create
146%                      = off: no current drawing action
147%                     = translate: translate an existing object
148%                    = calibration: move a calibration point
149%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
150%            .CurrentOrigin: Origin of a curently drawn edit_object
151%            .CurrentLine: currently drawn menuline (A REVOIR)
152%            .CurrentObject: handle of the currently drawn edit_object
153%            .CurrentRectZoom: current rectangle used for CheckZoom
154
155% Properties attached to projection objects (create, menuline, menuplane...):
156%    'Tag'='proj_object': for all projection objects
157%    ObjectData.Type=...: style of projection object:
158%              .ProjMode
159%              .Coord: defines the position of the object
160%              .XMin,YMin....
161%              .XMax,YMax....
162%              .DX,DY,DZ
163%              .Phi, .Theta, .Psi : Euler angles
164%              .X,.Y,.U,.V.... : field data projected on the object
165%              .IndexObj: index in the list of UvData.Object
166           %during plotting
167%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
168%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
169% To each projection object #iobj, corresponds an axis
170% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
171% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
172
173%------------------------------------------------------------------------
174%------------------------------------------------------------------------
175%  I - MAIN FUNCTION UVMAT (DO NOT MODIFY)
176%------------------------------------------------------------------------
177%------------------------------------------------------------------------
178function varargout = uvmat(varargin)
179
180% Begin initialization code - DO NOT EDIT
181gui_Singleton = 1;
182gui_State = struct('gui_Name',          mfilename, ...
183                   'gui_Singleton',     gui_Singleton, ...
184                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
185                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
186                   'gui_LayoutFcn',     [], ...
187                   'gui_Callback',      []);
188if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
189    gui_State.gui_Callback = str2func(varargin{1});
190end
191
192if nargout
193    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
194else
195    gui_mainfcn(gui_State, varargin{:});
196end
197% End initialization code - DO NOT EDIT
198
199%------------------------------------------------------------------------
200% --- Executes just before the GUI uvmat is made visible.
201function uvmat_OpeningFcn(hObject, eventdata, handles, input )
202%------------------------------------------------------------------------
203
204%% Choose default command menuline output for uvmat (standard GUI)
205handles.output = hObject;
206
207%% Update handles structure (standard GUI)
208guidata(hObject, handles);
209
210%% check the path and date of modification of all functions in uvmat
211path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
212[errormsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m
213date_str=['last modification: ' date_str];
214
215
216%% set the position of colorbar and ancillary GUIs:
217set(hObject,'Units','Normalized')
218movegui(hObject,'center')
219UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
220UvData.OpenParam.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
221UvData.OpenParam.SetObjectSize=[0.3 0.7];
222UvData.OpenParam.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
223UvData.OpenParam.CalSize=[0.28 1];
224UvData.axes3=[];%initiate the record of plotted field
225UvData.axes2=[];
226UvData.axes1=[];
227AxeData.LimEditBox=1; %initialise AxeData
228set(handles.axes3,'UserData',AxeData)
229
230%% set functions for the mouse and keyboard
231set(handles.histo_u,'NextPlot','replacechildren');
232set(handles.histo_v,'NextPlot','replacechildren');
233set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
234set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
235set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
236set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
237set(hObject,'DeleteFcn',{@closefcn})%
238
239%% refresh projection plane
240UvData.Object{1}.ProjMode='projection';%main plotting plane
241set(handles.Fields,'Value',1)
242set(handles.Fields,'string',{''})
243
244%% TRANSFORM menu: builtin fcts
245menu_str={'';'phys';'px';'phys_polar'};
246UvData.OpenParam.NbBuiltin=numel(menu_str); %number of functions
247path_uvmat=fileparts(which('uvmat'));
248addpath (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)
249addpath(fullfile(path_uvmat,'transform_field'))%add the path to transform functions,
250fct_handle{1,1}=[];
251testexist=zeros(size(menu_str'));%default
252testexist(1)=1;
253for ilist=2:length(menu_str)
254    if exist(menu_str{ilist},'file')
255        fct_handle{ilist,1}=str2func(menu_str{ilist});
256        testexist(ilist)=1;
257    else
258        testexist(ilist)=0;
259    end
260end
261rmpath(fullfile(path_uvmat,'transform_field'))
262
263%% load the list of previously browsed files in menus Open and Open_1
264 dir_perso=prefdir; % path to the directory .matlab for personal data
265 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
266 if exist(profil_perso,'file')
267      h=load (profil_perso);
268      if isfield(h,'MenuFile')
269          for ifile=1:min(length(h.MenuFile),5)
270              eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
271               eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
272          end
273      end
274      if isfield(h,'transform_fct') && iscell(h.transform_fct)
275         for ilist=1:length(h.transform_fct);
276             if exist(h.transform_fct{ilist},'file')
277                [path,file]=fileparts(h.transform_fct{ilist});
278                addpath(path)
279                h_func=str2func(file);
280                rmpath(path)
281                testexist=[testexist 1];
282             else
283                file='';
284                h_func=[];
285                testexist=[testexist 0];
286             end
287             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
288             menu_str=[menu_str; {file}];
289         end
290      end
291 end
292menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
293fct_handle=fct_handle(testexist==1);
294menu_str=[menu_str;{'more...'}];
295set(handles.transform_fct,'String',menu_str)
296set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
297
298%% case of an input argument for uvmat
299testinputfield=0;
300inputfile=[];
301Field=[];
302if exist('input','var')
303%     if ~isempty(errormsg)
304%         msgbox_uvmat('WARNING',errormsg)
305%     end
306    if ishandle(handles.UVMAT_title)
307        delete(handles.UVMAT_title)
308    end   
309    if isstruct(input)
310        if isfield(input,'InputFile')
311            inputfile=input.InputFile;
312        end
313        if isfield(input,'TimeIndex')
314            set(handles.i1,num2str(input.TimeIndex))
315        end
316        if isfield(input,'FieldsString')
317%             set(handles.Fields,'Value',1)
318            UvData.FieldsString=input.FieldsString;
319        end
320    elseif ischar(input)% file name introduced as input
321           inputfile=input;
322    elseif isnumeric(input)%simple matrix introduced as input
323        sizinput=size(input);
324        if sizinput(1)<=1 || sizinput(2)<=1
325            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
326            return
327        end
328        UvData.Field.ListVarName={'A','coord_y','coord_x'};
329        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
330        UvData.Field.A=input;
331        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
332        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
333        testinputfield=1;
334    end
335else
336   if ishandle(handles.UVMAT_title)
337       set(handles.UVMAT_title,'String',...
338           [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
339           {'GNU General Public License'};...
340           {path_to_uvmat};...
341           {date_str};...
342           {['SVN revision : ' num2str(svn_info.cur_rev)]};...
343           errormsg]);
344   end
345end
346set(handles.uvmat,'UserData',UvData)
347if ~isempty(inputfile)
348    %%%%% display the input field %%%%%%%
349    display_file_name(hObject, eventdata, handles,inputfile)
350    %%%%%%%
351    testinputfield=1;
352end
353
354%% plot input field if exists
355if testinputfield
356    %delete drawn objects
357    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
358    for iobj=1:length(hother)
359        delete_object(hother(iobj))
360    end 
361    if isempty(inputfile)
362        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
363        set(handles.MenuTools,'Enable','on')
364        set(handles.OBJECT_txt,'Visible','on')
365        set(handles.edit_object,'Visible','on')
366        set(handles.ListObject,'Visible','on')
367        set(handles.frame_object,'Visible','on')
368        if ~isempty(errormsg)
369            msgbox_uvmat('ERROR',errormsg)
370        end
371    end
372end
373
374set_vec_col_bar(handles) %update the display of color code for vectors
375
376%------------------------------------------------------------------------
377% --- Outputs from this function are returned to the command menuline.
378function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
379varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
380
381%------------------------------------------------------------------------
382%------------------------------------------------------------------------
383%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
384% automatically sets the global properties when the rootfile name is introduced
385% then activate the view-field action if selected
386% it is activated either by clicking on the RootPath window or by the
387% browser
388%------------------------------------------------------------------------
389%------------------------------------------------------------------------
390% --- Executes on the menu Open/Browse...
391% search the files, recognize their type according to their name and fill the rootfile input windows
392function MenuBrowse_Callback(hObject, eventdata, handles)
393[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
394oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
395% oldfile=read_file_box,es(handles);
396if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
397         dir_perso=prefdir;
398         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
399         if exist(profil_perso,'file')
400              h=load (profil_perso);
401             if isfield(h,'MenuFile_1')
402                  oldfile=h.MenuFile_1;
403             end
404         end
405end
406[FileName, PathName] = uigetfile( ...
407       {'*.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)';
408       '*.xml',  '.xml files '; ...
409        '*.xls',  '.xls files '; ...
410        '*.civ',  '.civ files '; ...
411        '*.jpg',' jpeg image files'; ...
412        '*.png','.png image files'; ...
413        '*.tif','.tif image files'; ...
414        '*.avi;*.AVI','.avi movie files'; ...
415        '*.vol','.volume images (png)'; ...
416        '*.nc','.netcdf files'; ...
417        '*.cdf','.netcdf files'; ...
418        '*.cmx','.cmx text files ';...
419        '*.fig','.fig files (matlab fig)';...
420        '*.log','.log text files ';...
421        '*.dat','.dat text files ';...
422        '*.bat','.bat system command text files';...
423        '*.*',  'All Files (*.*)'}, ...
424        'Pick a file',oldfile);
425fileinput=[PathName FileName];%complete file name
426sizf=size(fileinput);
427if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
428
429% display the selected field and related information
430display_file_name(hObject, eventdata, handles,fileinput)
431
432% -----------------------------------------------------------------------
433% --- Open again the file whose name has been recorded in MenuFile_1
434function MenuFile_1_Callback(hObject, eventdata, handles)
435%------------------------------------------------------------------------
436fileinput=get(handles.MenuFile_1,'Label');
437display_file_name(hObject, eventdata, handles,fileinput)
438
439% -----------------------------------------------------------------------
440% --- Open again the file whose name has been recorded in MenuFile_2
441function MenuFile_2_Callback(hObject, eventdata, handles)
442%------------------------------------------------------------------------
443fileinput=get(handles.MenuFile_2,'Label');
444display_file_name(hObject, eventdata, handles,fileinput)
445
446% -----------------------------------------------------------------------
447% --- Open again the file whose name has been recorded in MenuFile_3
448function MenuFile_3_Callback(hObject, eventdata, handles)
449%------------------------------------------------------------------------
450fileinput=get(handles.MenuFile_3,'Label');
451display_file_name(hObject, eventdata, handles,fileinput)
452
453% -----------------------------------------------------------------------
454% --- Open again the file whose name has been recorded in MenuFile_4
455function MenuFile_4_Callback(hObject, eventdata, handles)
456%------------------------------------------------------------------------
457fileinput=get(handles.MenuFile_4,'Label');
458display_file_name(hObject, eventdata, handles,fileinput)
459
460% -----------------------------------------------------------------------
461% --- Open again the file whose name has been recorded in MenuFile_5
462function MenuFile_5_Callback(hObject, eventdata, handles)
463%------------------------------------------------------------------------
464fileinput=get(handles.MenuFile_5,'Label');
465display_file_name(hObject, eventdata, handles,fileinput)
466
467%------------------------------------------------------------------------
468% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
469function display_file_name(hObject, eventdata, handles,fileinput,index)
470%------------------------------------------------------------------------
471%% look for the input file existence
472if ~exist(fileinput,'file')
473    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
474    return
475end
476
477%% set the mouse pointer to 'watch'
478set(handles.uvmat,'Pointer','watch')
479set(handles.RootPath,'BackgroundColor',[1 1 0])
480drawnow
481
482%% define the relevant handles for the first fiel series (index=1) or the second file series (index=2)
483if ~exist('index','var')
484    index=1;
485end
486if index==1
487    handles_RootPath=handles.RootPath;
488    handles_SubDir=handles.SubDir;
489    handles_RootFile=handles.RootFile;
490    handles_FileIndex=handles.FileIndex;
491    handles_NomType=handles.NomType;
492    handles_FileExt=handles.FileExt;
493    handles_Fields=handles.Fields;
494elseif index==2
495    handles_RootPath=handles.RootPath_1;
496    handles_SubDir=handles.SubDir_1;
497    handles_RootFile=handles.RootFile_1;
498    handles_FileIndex=handles.FileIndex_1;
499    handles_NomType=handles.NomType_1;
500    handles_FileExt=handles.FileExt_1;
501    handles_Fields=handles.Fields_1;
502    set(handles.RootPath_1,'Visible','on')
503    set(handles.RootFile_1,'Visible','on')
504    set(handles.SubDir_1,'Visible','on');
505    set(handles.FileIndex_1,'Visible','on');
506    set(handles.FileExt_1,'Visible','on');
507    set(handles.NomType_1,'Visible','on');
508end
509
510%% detect root name, nomenclature and indices in the input file name:
511[RootPath,SubDir,tild,i1,i2,j1,j2]=fileparts_uvmat(fileinput);
512[tild,FileName,FileExt]=fileparts(fileinput);
513% detect the file type, get the movie object if relevant, and look for the corresponding file series:
514[RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[FileName FileExt]);
515if strcmp(NomType,'*')% movies will be opened at the first frame
516    i1=1;
517    i2=[];
518    j1=[];
519    j2=[];
520end 
521
522%% open the file or fill the GUI uvmat according to the detected file type
523switch FileType
524    case ''
525        msgbox_uvmat('ERROR','invalid input file type')
526    case 'txt'
527        edit(fileinput)
528    case 'figure'                           %display matlab figure
529        hfig=open(fileinput);
530        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
531        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
532        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
533    case {'xml','xls'}                % edit xml or Excel files
534        editxml(fileinput);
535    otherwise
536        set(handles_RootPath,'String',RootPath);
537        rootname=fullfile(RootPath,SubDir,RootFile);
538        set(handles_SubDir,'String',['/' SubDir]);
539        set(handles_RootFile,'String',['/' RootFile]); %display the separator
540        indices=fileinput(length(rootname)+1:end);
541        indices(end-length(FileExt)+1:end)=[]; %remove extension
542        set(handles_FileIndex,'String',indices);
543        set(handles_NomType,'String',NomType);
544        set(handles_FileExt,'String',FileExt);
545        if index==1
546            % fill file index counters if the first file series is opened
547            set(handles.i1,'String',num2str(i1));
548            set(handles.i2,'String',num2str(i2));
549            set(handles.j1,'String',num2stra(j1,NomType));
550            set(handles.j2,'String',num2stra(j2,NomType));
551        else %read the current field index if the second file series is opened
552            i1=str2num(get(handles.i1,'String'));
553            i2=str2num(get(handles.i2,'String'));
554            j1=stra2num(get(handles.j1,'String'));
555            j2=stra2num(get(handles.j2,'String'));
556        end
557       
558        % synchronise indices of the second  input file if it exists
559        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
560            Input=read_GUI(handles.InputFile);
561            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
562                Input.RootPath_1=Input.RootPath;
563            end
564            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
565                Input.SubDir_1=Input.SubDir;
566            end
567            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
568                Input.RootFile_1=Input.RootFile;
569            end
570            %updtate the indices of the second field series to correspond to the newly opened one
571            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1,i2,j1,j2);
572            if exist(FileName_1,'file')
573                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
574                set(handles.FileIndex_1,'String',FileIndex_1)
575            else
576                set(handles.SubField,'Value',0)
577                SubField_Callback(hObject, eventdata, handles)
578            end
579        end
580       
581        %enable other menus
582        set(handles.MenuOpen_1,'Enable','on')
583        set(handles.MenuFile_1_1,'Enable','on')
584        set(handles.MenuFile_2_1,'Enable','on')
585        set(handles.MenuFile_3_1,'Enable','on')
586        set(handles.MenuFile_4_1,'Enable','on')
587        set(handles.MenuFile_5_1,'Enable','on')
588        set(handles.MenuExport,'Enable','on')
589        set(handles.MenuExportFigure,'Enable','on')
590        set(handles.MenuExportMovie,'Enable','on')
591        set(handles.MenuTools,'Enable','on')
592        set(handles.OBJECT_txt,'Visible','on')
593        set(handles.edit_object,'Visible','on')
594        set(handles.ListObject,'Visible','on')
595        set(handles.frame_object,'Visible','on')
596       
597        % initiate input file series and refresh the current field view:     
598        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
599
600end
601
602%% set back the mouse pointer to arrow
603set(handles.uvmat,'Pointer','arrow')
604
605%------------------------------------------------------------------------
606% --- Called by action in RootPath edit box
607function RootPath_Callback(hObject,eventdata,handles)
608%------------------------------------------------------------------------
609% read the current input file name:
610[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
611%fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
612% detect the file type, get the movie object if relevant, and look for the corresponding file series:
613[tild,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
614% initiate the input file series and refresh the current field view:
615update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject);
616
617%------------------------------------------------------------------------
618% --- Called by action in RootFile edit box
619function SubDir_Callback(hObject, eventdata, handles)
620%------------------------------------------------------------------------
621%refresh the menu of input fields
622Fields_Callback(hObject, eventdata, handles);
623% refresh the current field view
624run0_Callback(hObject, eventdata, handles);
625
626%------------------------------------------------------------------------
627% --- Called by action in RootFile edit box
628function RootFile_Callback(hObject, eventdata, handles)
629%------------------------------------------------------------------------
630RootPath_Callback(hObject,eventdata,handles)
631
632%------------------------------------------------------------------------
633% --- Called by action in FileIndex edit box
634function FileIndex_Callback(hObject, eventdata, handles)
635%------------------------------------------------------------------------
636[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
637set(handles.i1,'String',num2str(i1));
638set(handles.i2,'String',num2str(i2));
639set(handles.j1,'String',num2str(j1));
640set(handles.j2,'String',num2str(j2));
641
642% refresh the current field view
643run0_Callback(hObject, eventdata, handles)
644
645%------------------------------------------------------------------------
646% --- Update information about a new field series (indices to scan, timing,
647%     calibration from an xml file, then refresh current plots
648function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index)
649%------------------------------------------------------------------------
650%% define the relevant handles depending on the index (1=first file series, 2= second file series)
651if ~exist('index','var')
652    index=1;
653end
654if index==1
655    handles_RootPath=handles.RootPath;
656    handles_Fields=handles.Fields;
657elseif index==2
658    handles_RootPath=handles.RootPath_1;
659    handles_Fields=handles.Fields_1;
660end
661
662set(handles_RootPath,'BackgroundColor',[1 1 0])
663drawnow
664set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
665UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
666UvData.NewSeries=1; %flag for run0: begin a new series
667UvData.TestInputFile=1;
668UvData.FileType{index}=FileType;
669UvData.i1_series{index}=i1_series;
670UvData.i2_series{index}=i2_series;
671UvData.j1_series{index}=j1_series;
672UvData.j2_series{index}=j2_series;
673% set(handles.CheckFixPair,'Value',1) % activate by default the comp_input '-'input window
674set(handles.FixVelType,'Value',0); %desactivate fixed veltype
675if index==1
676    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
677else
678    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
679end
680FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
681FileBase=fullfile(RootPath,RootFile);
682if ~exist(FileName,'file')
683   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
684    return
685end
686nbfield=[];%default
687nbfield_j=[];%default
688
689%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
690XmlData.Time=[];%default
691XmlData.GeometryCalib=[];%default
692TimeUnit=[];%default
693testima=0; %test for image input
694imainfo=[];
695ColorType='falsecolor'; %default
696hhh='';
697if isequal(lower(FileExt),'.avi') %.avi file
698    testima=1;
699    imainfo=aviinfo([FileName]);
700    nbfield=imainfo.NumFrames;
701    nbfield_j=1;
702    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
703    XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
704    TimeUnit='s';
705    hhh=which('mmreader');
706    ColorType=imainfo.ImageType;%='truecolor' for color images
707elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
708    testima=1;
709    if ~isequal(SubDir,'')
710       RootFile=get(handles.RootFile,'String');
711        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
712    else
713        imainfo=imfinfo([FileBase FileIndices FileExt]);
714    end
715    ColorType=imainfo.ColorType;%='truecolor' for color images
716    if length(imainfo) >1 %case of image with multiple frames
717        nbfield=length(imainfo);
718        nbfield_j=1;
719    end
720end
721if ~strcmp(hhh,'')% if the function mmreader is found (recent version of matlab)
722    UvData.MovieObject{index}=mmreader([FileBase FileIndices FileExt]);
723else
724    UvData.MovieObject{index}=[];
725end
726if isfield(imainfo,'Width') && isfield(imainfo,'Height')
727    if length(imainfo)>1
728        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
729        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
730    else
731        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
732        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
733    end
734else
735    set(handles.num_Npx,'String','');%fills nbre of pixels x box
736    set(handles.num_Npy,'String','');%fills nbre of pixels x box
737end
738set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
739
740%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
741filexml=[FileBase '.xml'];
742fileciv=[FileBase '.civ'];
743warntext='';%default warning message
744NbSlice=1;%default
745set(handles.RootPath,'BackgroundColor',[1 1 1])
746if exist(filexml,'file')
747    set(handles.view_xml,'Visible','on')
748    set(handles.view_xml,'BackgroundColor',[1 1 0])
749    set(handles.view_xml,'String','view .xml')
750    drawnow
751    [XmlData,warntext]=imadoc2struct(filexml);
752    if ~isempty(warntext)
753        msgbox_uvmat('WARNING',warntext)
754    end
755    if isfield(XmlData,'TimeUnit')
756        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
757            TimeUnit=XmlData.TimeUnit;
758        end
759    end
760    set(handles.view_xml,'BackgroundColor',[1 1 1])
761    drawnow
762    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
763        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
764            set (handles.nb_slice,'String','volume')
765        end
766        hgeometry_calib=findobj('tag','geometry_calib');
767        if ~isempty(hgeometry_calib)
768            GUserData=get(hgeometry_calib,'UserData');
769            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
770                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
771                if strcmp(answer,'Yes')
772                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
773                end
774            end
775        end
776    end 
777elseif exist(fileciv,'file')% if .civ file found
778    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
779    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
780    GeometryCalib.Tx=0;
781    GeometryCalib.Ty=0;
782    GeometryCalib.Tz=1;
783    GeometryCalib.dpx=1;
784    GeometryCalib.dpy=1;
785    GeometryCalib.sx=1;
786    GeometryCalib.Cx=0;
787    GeometryCalib.Cy=0;
788    GeometryCalib.f=1;
789    GeometryCalib.kappa1=0;
790    GeometryCalib.CoordUnit='cm';
791    XmlData.GeometryCalib=GeometryCalib;
792    if error==2, warntext=['no file ' FileBase '.civ'];
793    elseif error==1, warntext='inconsistent number of fields in the .civ file';
794    end 
795    set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
796    set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
797    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
798    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
799    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
800    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
801    set(handles.view_xml,'Visible','on')   
802    set(handles.view_xml,'String','view .civ')
803else
804    set(handles.view_xml,'Visible','off')
805end
806
807%% store last index in handles.lat_i and .last_j
808nbfield=max(max(i2_series));
809if isempty(nbfield)
810    nbfield=max(max(i1_series));
811end
812nbfield_j=max(max(j2_series));
813if isempty(nbfield_j)
814    nbfield_j=max(max(j1_series));
815end
816if ~isempty(XmlData.Time)
817%     nbfield=size(XmlData.Time,1);
818%     nbfield_j=size(XmlData.Time,2);
819    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
820    if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
821        NomType=get(handles.NomType,'String');
822        if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
823            XmlData.Time=(XmlData.Time)';
824%             nbfield=nbfield_j;
825%             nbfield_j=1;
826        end
827    end
828end
829last_i_cell=get(handles.last_i,'String');
830if isempty(nbfield)
831    last_i_cell{1}='';
832else
833    last_i_cell{1}=num2str(nbfield);
834end
835set(handles.last_i,'String',last_i_cell)
836last_j_cell=get(handles.last_j,'String');
837if isempty(nbfield_j)
838     last_j_cell{1}='';
839else
840     last_j_cell{1}=num2str(nbfield_j);
841end
842set(handles.last_j,'String',last_j_cell);
843
844%% store geometric calibration in UvData
845if isfield(XmlData,'GeometryCalib')
846    GeometryCalib=XmlData.GeometryCalib;
847    if isempty(GeometryCalib)
848        set(handles.pxcm,'String','')
849        set(handles.pycm,'String','')
850        set(handles.transform_fct,'Value',1); %  no transform by default
851    else
852        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
853            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
854            set(handles.pxcm,'String','var')
855            set(handles.pycm,'String','var')
856        elseif isfield(GeometryCalib,'fx_fy')
857            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
858            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
859            set(handles.pxcm,'String',num2str(pixcmx))
860            set(handles.pycm,'String',num2str(pixcmy))
861        end
862        if ~get(handles.CheckFixLimits,'Value')
863            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
864        end
865        if isfield(GeometryCalib,'SliceCoord')
866           
867           siz=size(GeometryCalib.SliceCoord);
868           if siz(1)>1
869               NbSlice=siz(1);
870               set(handles.slices,'Visible','on')
871               set(handles.slices,'Value',1)
872           end
873           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
874               set(handles.nb_slice,'String','volume')
875           else
876               set(handles.nb_slice,'String',num2str(NbSlice))
877           end
878           slices_Callback([],[], handles)
879        end           
880    end
881end
882
883%% update the data attached to the uvmat interface
884if ~isempty(TimeUnit)
885    set(handles.time_txt,'String',['time (' TimeUnit ')'])
886end
887UvData.TimeUnit=TimeUnit;
888UvData.XmlData{index}=XmlData;
889UvData.NewSeries=1;
890% UvData.MovieObject=MovieObject;
891
892%display warning message
893if ~isequal(warntext,'')
894    msgbox_uvmat('WARNING',warntext);
895end
896
897%% set default options in menu 'Fields'
898if ~testima
899    testcivx=0;
900    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
901        set(handles_Fields,'Value',1)
902        set(handles_Fields,'String',{'get_field...'})
903        UvData=rmfield(UvData,'FieldsString');
904    else
905        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
906        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
907            FieldList=calc_field;
908            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
909            set(handles_Fields,'Value',2) % set menu to 'velocity'
910            col_vec=FieldList;
911            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
912            testcivx=1;
913        end
914        if ~testcivx
915            set(handles_Fields,'Value',1) % set menu to 'get_field...
916            set(handles_Fields,'String',{'get_field...'})
917            col_vec={'get_field...'};
918        end
919        set(handles.ListColorScalar,'String',col_vec)
920    end
921end
922set(handles.uvmat,'UserData',UvData)
923
924%% set index navigation options and refresh plots
925scan_option='i';%default
926state_j='off'; %default
927if index==2
928    if get(handles.scan_j,'Value')
929        scan_option='j'; %keep the scan option for the second fiel series
930    end
931    if strcmp(get(handles.j1,'Visible'),'on')
932        state_j='on';
933    end
934end
935if ~isempty(j1_series)
936        state_j='on';
937        if isequal(nbfield,1) &&index==1
938            scan_option='j'; %scan j index by default if nbfield=1               
939        end
940end
941if isequal(scan_option,'i')
942     set(handles.scan_i,'Value',1)
943     scan_i_Callback([],[], handles);
944else
945     set(handles.scan_j,'Value',1)
946     scan_j_Callback([],[], handles);
947end
948set(handles.scan_j,'Visible',state_j)
949set(handles.j1,'Visible',state_j)
950set(handles.j2,'Visible',state_j)
951set(handles.last_j,'Visible',state_j);
952set(handles.frame_j,'Visible',state_j);
953set(handles.j_text,'Visible',state_j);
954if ~isempty(i2_series)||~isempty(j2_series)
955    set(handles.CheckFixPair,'Visible','on')
956elseif index==1
957    set(handles.CheckFixPair,'Visible','off')
958end
959
960%% view the field 
961run0_Callback([],[], handles); %view field
962mask_test=get(handles.CheckMask,'value');
963if mask_test
964    MaskData=get(handles.CheckMask,'UserData');
965    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
966          delete(MaskData.maskhandle)    %delete old mask
967    end
968    CheckMask_Callback([],[],handles)
969end
970
971%% update list of recent files in the menubar
972MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
973    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
974str_find=strcmp(FileName,MenuFile);
975if isempty(find(str_find,1))
976    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
977end
978for ifile=1:min(length(MenuFile),5)
979    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
980    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
981end
982dir_perso=prefdir;
983profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
984if exist(profil_perso,'file')
985    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
986else
987    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
988end
989
990
991%------------------------------------------------------------------------
992% --- Executes on the menu Open/Browse_1 for the second input field,
993%     search the files, recognize their type according to their name and fill the rootfile input windows
994function MenuBrowse_1_Callback(hObject, eventdata, handles)
995%------------------------------------------------------------------------
996% huvmat=get(handles.run0,'parent');
997UvData=get(handles.uvmat,'UserData');
998
999RootPath=get(handles.RootPath,'String');
1000[FileName, PathName, filterindex] = uigetfile( ...
1001       {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
1002       '*.xml',  '.xml files '; ...
1003        '*.xls',  '.xls files '; ...
1004        '*.civ',  '.civ files '; ...
1005        '*.jpg','.jpg image files'; ...
1006        '*.png','.png image files'; ...
1007        '*.avi;*.AVI','.avi movie files'; ...
1008        '*.nc','.netcdf files'; ...
1009        '*.cdf','.netcdf files'; ...
1010        '*.cmx','.cmx text files';...
1011        '*.cmx2','.cmx2 text files';...
1012        '*.fig','.fig files (matlab fig)';...
1013        '*.log','.log text files ';...
1014        '*.dat','.dat text files ';...
1015        '*.*',  'All Files (*.*)'}, ...
1016        'Pick a second file for comparison',RootPath);
1017fileinput_1=[PathName FileName];%complete file name
1018sizf=size(fileinput_1);
1019if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
1020
1021% refresh the current displayed field
1022set(handles.SubField,'Value',1)
1023display_file_name(hObject,eventdata,handles,fileinput_1,2)
1024
1025%update list of recent files in the menubar
1026MenuFile_1=fileinput_1;
1027MenuFile_2=get(handles.MenuFile_1,'Label');
1028MenuFile_3=get(handles.MenuFile_2,'Label');
1029MenuFile_4=get(handles.MenuFile_3,'Label');
1030MenuFile_5=get(handles.MenuFile_4,'Label');
1031set(handles.MenuFile_1,'Label',MenuFile_1)
1032set(handles.MenuFile_2,'Label',MenuFile_2)
1033set(handles.MenuFile_3,'Label',MenuFile_3)
1034set(handles.MenuFile_4,'Label',MenuFile_4)
1035set(handles.MenuFile_5,'Label',MenuFile_5)
1036set(handles.MenuFile_1_1,'Label',MenuFile_1)
1037set(handles.MenuFile_2_1,'Label',MenuFile_2)
1038set(handles.MenuFile_3_1,'Label',MenuFile_3)
1039set(handles.MenuFile_4_1,'Label',MenuFile_4)
1040set(handles.MenuFile_5_1,'Label',MenuFile_5)
1041dir_perso=prefdir;
1042profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1043if exist(profil_perso,'file')
1044    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
1045else
1046    txt=ver('MATLAB');
1047    Release=txt.Release;
1048    relnumb=str2double(Release(3:4));
1049    if relnumb >= 14
1050        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
1051    else
1052        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
1053    end
1054end
1055
1056% -----------------------------------------------------------------------
1057% --- Open again as second field the file whose name has been recorded in MenuFile_1
1058function MenuFile_1_1_Callback(hObject, eventdata, handles)
1059% -----------------------------------------------------------------------
1060fileinput_1=get(handles.MenuFile_1_1,'Label');
1061set(handles.SubField,'Value',1)
1062display_file_name(hObject,eventdata,handles,fileinput_1,2)
1063
1064% -----------------------------------------------------------------------
1065% --- Open again as second field the file whose name has been recorded in MenuFile_2
1066function MenuFile_2_1_Callback(hObject, eventdata, handles)
1067% -----------------------------------------------------------------------
1068fileinput_1=get(handles.MenuFile_2_1,'Label');
1069set(handles.SubField,'Value',1)
1070display_file_name(hObject,eventdata,handles,fileinput_1,2)
1071
1072% -----------------------------------------------------------------------
1073% --- Open again as second field the file whose name has been recorded in MenuFile_3
1074function MenuFile_3_1_Callback(hObject, eventdata, handles)
1075% -----------------------------------------------------------------------
1076fileinput_1=get(handles.MenuFile_3_1,'Label');
1077set(handles.SubField,'Value',1)
1078display_file_name(hObject,eventdata,handles,fileinput_1,2)
1079
1080% -----------------------------------------------------------------------
1081% --- Open again as second field the file whose name has been recorded in MenuFile_4
1082function MenuFile_4_1_Callback(hObject, eventdata, handles)
1083% -----------------------------------------------------------------------
1084fileinput_1=get(handles.MenuFile_4_1,'Label');
1085set(handles.SubField,'Value',1)
1086display_file_name(hObject,eventdata,handles,fileinput_1,2)
1087
1088% -----------------------------------------------------------------------
1089% --- Open again as second field the file whose name has been recorded in MenuFile_5
1090function MenuFile_5_1_Callback(hObject, eventdata, handles)
1091% -----------------------------------------------------------------------
1092fileinput_1=get(handles.MenuFile_5_1,'Label');
1093set(handles.SubField,'Value',1)
1094display_file_name(hObject,eventdata,handles,fileinput_1,2)
1095
1096%-----------------------------------------------------------------------
1097% --- Called by action in RootPath_1 edit box
1098function RootPath_1_Callback(hObject,eventdata,handles)
1099% -----------------------------------------------------------------------
1100% update_rootinfo_1(hObject,eventdata,handles)
1101[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
1102%fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1103% detect the file type, get the movie object if relevant, and look for the corresponding file series:
1104[tild,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
1105% initiate the input file series and refresh the current field view:
1106update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
1107%-----------------------------------------------------------------------
1108% --- Called by action in RootFile_1 edit box
1109function RootFile_1_Callback(hObject, eventdata, handles)
1110% -----------------------------------------------------------------------
1111RootPath_1_Callback(hObject,eventdata,handles)
1112
1113%------------------------------------------------------------------------
1114% --- Called by action in FileIndex_1 edit box
1115function FileIndex_1_Callback(hObject, eventdata, handles)
1116%------------------------------------------------------------------------
1117run0_Callback(hObject, eventdata, handles)
1118
1119%------------------------------------------------------------------------
1120% --- switch file index scanning options scan_i and scan_j in an exclusive way
1121function scan_i_Callback(hObject, eventdata, handles)
1122%------------------------------------------------------------------------
1123if get(handles.scan_i,'Value')==1
1124    set(handles.scan_i,'BackgroundColor',[1 1 0])
1125    set(handles.scan_j,'Value',0)
1126else
1127    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1128    set(handles.scan_j,'Value',1)
1129end
1130scan_j_Callback(hObject, eventdata, handles)
1131
1132%------------------------------------------------------------------------
1133% --- switch file index scanning options scan_i and scan_j in an exclusive way
1134function scan_j_Callback(hObject, eventdata, handles)
1135%------------------------------------------------------------------------
1136if get(handles.scan_j,'Value')==1
1137    set(handles.scan_j,'BackgroundColor',[1 1 0])
1138    set(handles.scan_i,'Value',0)
1139    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1140%     NomType=get(handles.NomType,'String');
1141%     switch NomType
1142%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1143%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1144%     otherwise
1145%         set(handles.CheckFixPair,'Visible','off')
1146%     end
1147else
1148    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1149    set(handles.scan_i,'Value',1)
1150    set(handles.scan_i,'BackgroundColor',[1 1 0])
1151    set(handles.CheckFixPair,'Visible','off')
1152end
1153
1154%------------------------------------------------------------------------
1155function i1_Callback(hObject, eventdata, handles)
1156%------------------------------------------------------------------------
1157set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1158NomType=get(handles.NomType,'String');
1159i1=stra2num(get(handles.i1,'String'));
1160i2=stra2num(get(handles.i2,'String'));
1161j1=stra2num(get(handles.j1,'String'));
1162j2=stra2num(get(handles.j2,'String'));
1163indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1164%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1165set(handles.FileIndex,'String',indices)
1166set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1167if get(handles.SubField,'Value')==1
1168    NomType_1=get(handles.NomType_1,'String');
1169    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1170     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1171     set(handles.FileIndex_1,'String',indices)
1172     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1173end
1174
1175%------------------------------------------------------------------------
1176function i2_Callback(hObject, eventdata, handles)
1177%------------------------------------------------------------------------
1178set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1179i1_Callback(hObject, eventdata, handles)
1180
1181%------------------------------------------------------------------------
1182function j1_Callback(hObject, eventdata, handles)
1183%------------------------------------------------------------------------
1184set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1185i1_Callback(hObject, eventdata, handles)
1186
1187%------------------------------------------------------------------------
1188function j2_Callback(hObject, eventdata, handles)
1189%------------------------------------------------------------------------
1190set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1191i1_Callback(hObject, eventdata, handles)
1192
1193%------------------------------------------------------------------------
1194function slices_Callback(hObject, eventdata, handles)
1195%------------------------------------------------------------------------
1196if get(handles.slices,'Value')==1
1197    set(handles.slices,'BackgroundColor',[1 1 0])
1198    set(handles.nb_slice,'Visible','on')
1199    set(handles.z_text,'Visible','on')
1200    set(handles.z_index,'Visible','on')
1201    nb_slice_Callback(hObject, eventdata, handles)
1202else
1203    set(handles.nb_slice,'Visible','off')
1204    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1205    set(handles.z_text,'Visible','off')
1206    set(handles.z_index,'Visible','off')
1207    set(handles.masklevel,'Value',1)
1208    set(handles.masklevel,'String',{'1'})
1209end
1210
1211%------------------------------------------------------------------------
1212function nb_slice_Callback(hObject, eventdata, handles)
1213%------------------------------------------------------------------------
1214nb_slice_str=get(handles.nb_slice,'String');
1215if isequal(nb_slice_str,'volume')
1216    num=stra2num(get(handles.j1,'String'));
1217    last_j=get(handles.last_j,'String');
1218    nbslice=str2double(last_j{1});
1219else
1220    num=str2double(get(handles.i1,'String'));
1221    nbslice=str2double(get(handles.nb_slice,'String'));
1222end
1223z=mod(num-1,nbslice)+1;
1224set(handles.z_index,'String',num2str(z))
1225for ilist=1:nbslice
1226    list_index{ilist,1}=num2str(ilist);
1227end   
1228set(handles.masklevel,'String',list_index)
1229set(handles.masklevel,'Value',z)
1230
1231%------------------------------------------------------------------------
1232% --- Executes on button press in view_xml.
1233function view_xml_Callback(hObject, eventdata, handles)
1234%------------------------------------------------------------------------
1235%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1236 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1237FileBase=fullfile(RootPath,RootFile);
1238option=get(handles.view_xml,'String');
1239if isequal(option,'view .xml')
1240    FileXml=[FileBase '.xml'];
1241    heditxml=editxml(FileXml);
1242end
1243
1244%------------------------------------------------------------------------
1245% --- Executes on button press in CheckMask.
1246function CheckMask_Callback(hObject, eventdata, handles)
1247%------------------------------------------------------------------------
1248%case of view mask selection
1249if isequal(get(handles.CheckMask,'Value'),1)
1250   % [FF,RootPath,FileBase]=read_file_boxes(handles);
1251     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1252     FileBase=fullfile(RootPath,RootFile);
1253    num_i1=stra2num(get(handles.i1,'String'));
1254    num_j1=stra2num(get(handles.j1,'String'));
1255    currentdir=pwd; 
1256    cd(RootPath);
1257    maskfiles=dir('*_*mask_*.png');%look for a mask file
1258    cd(currentdir);%come back to the working directory
1259    mdetect=0;
1260    if ~isempty(maskfiles)
1261        for ilist=1:length(maskfiles)
1262            maskname=maskfiles(ilist).name;% take the first mask file in the list
1263            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1264%             [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1265             [tild,Name]=fileparts(maskname);
1266            Namedouble=double(Name);
1267            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1268            ind_mask=findstr('mask',Name);
1269            i=ind_mask-1;
1270            while val(i)==0 && i>0
1271                i=i-1;
1272            end
1273            nbmask_str=str2num(Name(i+1:ind_mask-1));
1274            if ~isempty(nbmask_str)
1275                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1276            end
1277        end
1278        if isequal(min(nbslice),max(nbslice))
1279            nbslice=nbslice(1);
1280        else
1281            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1282            return
1283        end
1284        if ~isempty(nbslice) && Name(i)=='_'
1285            Mask.Base=[FileBase Name(i:ind_mask+3)];
1286            Mask.NbSlice=nbslice;
1287            num_i1=mod(num_i1-1,nbslice)+1;
1288            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1289            [RootPath,RootFile]=fileparts(Mask.Base);
1290            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1291            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1292            mdetect=exist(maskname,'file');
1293            if mdetect
1294                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1295                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1296                set(handles.CheckMask,'UserData',Mask);
1297                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1298                if nbslice > 1
1299                    set(handles.slices,'value',1)
1300                    slices_Callback(hObject, eventdata, handles)
1301                end
1302            end
1303        end
1304    end
1305    errormsg=[];%default
1306    if mdetect==0
1307        [FileName, PathName, filterindex] = uigetfile( ...
1308            {'*.png', ' (*.png)';
1309            '*.png',  '.png files '; ...
1310            '*.*', 'All Files (*.*)'}, ...
1311            'Pick a mask file *.png',FileBase);
1312        maskname=fullfile(PathName,FileName);
1313        if ~exist(maskname,'file')
1314            errormsg='no file browsed';
1315        end
1316        [RootDir,tild,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1317%         [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1318        Mask.Base=fullfile(RootDir,RootFile);
1319        Mask.NbSlice=1;
1320        set(handles.CheckMask,'UserData',Mask);
1321        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1322    end
1323    if isempty(errormsg)
1324        errormsg=update_mask(handles,num_i1,num_j1);
1325    end
1326    if ~isempty(errormsg)
1327            set(handles.CheckMask,'Value',0)
1328            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1329     end
1330else % desactivate mask display
1331    MaskData=get(handles.CheckMask,'UserData');
1332    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1333          delete(MaskData.maskhandle)   
1334    end
1335    set(handles.CheckMask,'UserData',[])   
1336    UvData=get(handles.uvmat,'UserData');
1337    if isfield(UvData,'MaskName')
1338        UvData=rmfield(UvData,'MaskName');
1339        set(handles.uvmat,'UserData',UvData)
1340    end
1341    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1342end
1343
1344%------------------------------------------------------------------------
1345function errormsg=update_mask(handles,num_i1,num_j1)
1346%------------------------------------------------------------------------
1347errormsg=[];%default
1348MaskData=get(handles.CheckMask,'UserData');
1349if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1350    uistack(MaskData.maskhandle,'top');
1351end
1352num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1353[RootPath,RootFile]=fileparts(MaskData.Base);
1354MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1355%MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1356huvmat=get(handles.CheckMask,'parent');
1357UvData=get(huvmat,'UserData');
1358
1359%update mask image if the mask is new
1360if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1361    UvData.MaskName=MaskName; %update the recorded name on UvData
1362    set(huvmat,'UserData',UvData);
1363    if ~exist(MaskName,'file')
1364        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1365            delete(MaskData.maskhandle)   
1366        end
1367    else
1368        %read mask image
1369        Mask.AName='image';
1370        Mask.A=imread(MaskName);
1371        npxy=size(Mask.A);
1372        test_error=0;
1373        if length(npxy)>2
1374            errormsg=[MaskName ' is not a grey scale image'];
1375            return
1376        elseif ~isa(Mask.A,'uint8')
1377            errormsg=[MaskName ' is not a 8 bit grey level image'];
1378            return
1379        end
1380        Mask.AX=[0.5 npxy(2)-0.5];
1381        Mask.AY=[npxy(1)-0.5 0.5 ];
1382        Mask.CoordUnit='pixel';
1383        if isequal(get(handles.slices,'Value'),1)
1384           NbSlice=str2num(get(handles.nb_slice,'String'));
1385           num_i1=str2num(get(handles.i1,'String'));
1386           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1387        end
1388        %px to phys or other transform on field
1389         menu_transform=get(handles.transform_fct,'String');
1390        choice_value=get(handles.transform_fct,'Value');
1391        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1392        transform_list=get(handles.transform_fct,'UserData');
1393        transform=transform_list{choice_value};
1394        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1395            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1396                Calib=UvData.XmlData{1}.GeometryCalib;
1397                Mask=transform(Mask,UvData.XmlData{1});
1398            end
1399        end
1400        flagmask=Mask.A < 200;
1401       
1402        %make brown color image
1403        imflag(:,:,1)=0.9*flagmask;
1404        imflag(:,:,2)=0.7*flagmask;
1405        imflag(:,:,3)=zeros(size(flagmask));
1406       
1407        %update mask image
1408        hmask=[]; %default
1409        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1410            hmask=MaskData.maskhandle;
1411        end
1412        if ~isempty(hmask)
1413            set(hmask,'CData',imflag)   
1414            set(hmask,'AlphaData',flagmask*0.6)
1415            set(hmask,'XData',Mask.AX);
1416            set(hmask,'YData',Mask.AY);
1417%             uistack(hmask,'top')
1418        else
1419            axes(handles.axes3)
1420            hold on   
1421            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1422%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1423            set(handles.CheckMask,'UserData',MaskData)
1424        end
1425    end
1426end
1427
1428
1429%------------------------------------------------------------------------
1430function MenuExportFigure_Callback(hObject, eventdata, handles)
1431%------------------------------------------------------------------------
1432huvmat=get(handles.MenuExport,'parent');
1433hfig=figure;
1434copyobj(handles.axes3,hfig);
1435map=colormap(handles.axes3);
1436colormap(map);%transmit the current colormap to the zoom fig
1437colorbar
1438
1439%------------------------------------------------------------------------
1440%------------------------------------------------------------------------
1441% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1442%------------------------------------------------------------------------
1443
1444%------------------------------------------------------------------------
1445% --- Executes on button press in runplus: make one step forward and call
1446% --- run0. The step forward is along the fields series 1 or 2 depending on
1447% --- the scan_i and scan_j check box (exclusive each other)
1448function runplus_Callback(hObject, eventdata, handles)
1449%------------------------------------------------------------------------
1450set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1451drawnow
1452%TODO: introduce the option: increment ='*' to move to the next available view
1453increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1454% if isnan(increment)
1455%     set(handles.increment_scan,'String','1')%default value
1456%     increment=1;
1457% end
1458errormsg=runpm(hObject,eventdata,handles,increment);
1459if ~isempty(errormsg)
1460    msgbox_uvmat('ERROR',errormsg);
1461end
1462set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1463
1464%------------------------------------------------------------------------
1465% --- Executes on button press in runmin: make one step backward and call
1466% --- run0. The step backward is along the fields series 1 or 2 depending on
1467% --- the scan_i and scan_j check box (exclusive each other)
1468function runmin_Callback(hObject, eventdata, handles)
1469%------------------------------------------------------------------------
1470set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1471drawnow
1472increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1473% if isnan(increment)
1474%     set(handles.increment_scan,'String','1')%default value
1475%     increment=1;
1476% end
1477errormsg=runpm(hObject,eventdata,handles,increment);
1478if ~isempty(errormsg)
1479    msgbox_uvmat('ERROR',errormsg);
1480end
1481set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1482
1483%------------------------------------------------------------------------
1484% -- Executes on button press in Movie: make a series of +> steps
1485function Movie_Callback(hObject, eventdata, handles)
1486%------------------------------------------------------------------------
1487set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1488drawnow
1489increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1490% if isnan(increment)
1491%     set(handles.increment_scan,'String','1')%default value
1492%     increment=1;
1493% end
1494set(handles.STOP,'Visible','on')
1495set(handles.speed,'Visible','on')
1496set(handles.speed_txt,'Visible','on')
1497set(handles.Movie,'BusyAction','queue')
1498UvData=get(handles.uvmat,'UserData');
1499
1500while get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1501        errormsg=runpm(hObject,eventdata,handles,increment);
1502        if ~isempty(errormsg)
1503            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1504            return
1505        end
1506        pause(1.02-get(handles.speed,'Value'))% wait for next image
1507end
1508if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1509    UvData.aviobj=close(UvData.aviobj);
1510   set(handles.uvmat,'UserData',UvData);
1511end
1512set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1513
1514%------------------------------------------------------------------------
1515% -- Executes on button press in Movie: make a series of <- steps
1516function MovieBackward_Callback(hObject, eventdata, handles)
1517%------------------------------------------------------------------------
1518set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1519drawnow
1520increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1521set(handles.STOP,'Visible','on')
1522set(handles.speed,'Visible','on')
1523set(handles.speed_txt,'Visible','on')
1524set(handles.MovieBackward,'BusyAction','queue')
1525UvData=get(handles.uvmat,'UserData');
1526
1527while get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1528        errormsg=runpm(hObject,eventdata,handles,increment);
1529        if ~isempty(errormsg)
1530            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1531            return
1532        end
1533        pause(1.02-get(handles.speed,'Value'))% wait for next image
1534end
1535if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1536    UvData.aviobj=close(UvData.aviobj);
1537   set(handles.uvmat,'UserData',UvData);
1538end
1539set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1540
1541%------------------------------------------------------------------------
1542function STOP_Callback(hObject, eventdata, handles)
1543%------------------------------------------------------------------------
1544set(handles.movie_pair,'BusyAction','Cancel')
1545set(handles.movie_pair,'value',0)
1546set(handles.Movie,'BusyAction','Cancel')
1547set(handles.MovieBackward,'BusyAction','Cancel')
1548set(handles.MenuExportMovie,'BusyAction','Cancel')
1549set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1550set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1551set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1552
1553%------------------------------------------------------------------------
1554% --- function activated by runplus and run minus
1555function errormsg=runpm(hObject,eventdata,handles,increment)
1556%------------------------------------------------------------------------
1557errormsg='';%default
1558%% check for movie pair status
1559movie_status=get(handles.movie_pair,'Value');
1560if isequal(movie_status,1)
1561    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1562end
1563
1564%% read the current input file name(s) and field indices
1565InputFile=read_GUI(handles.InputFile);
1566InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1567InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1568FileExt=InputFile.FileExt;
1569NomType=get(handles.NomType,'String');
1570i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1571i2=str2num(get(handles.i2,'String'));
1572j1=stra2num(get(handles.j1,'String'));
1573j2=stra2num(get(handles.j2,'String'));
1574sub_value= get(handles.SubField,'Value');
1575if sub_value % a second input file has been entered
1576    [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1577    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndices_1);
1578    NomType_1=get(handles.NomType_1,'String');
1579else
1580    filename_1=[];
1581end   
1582
1583%% increment (or decrement) the field indices and update the input filename(s)
1584CheckSearch=0;
1585if isempty(increment)
1586    CheckSearch=1;% search for the next available file
1587    set(handles.CheckFixPair,'Value',0)
1588end
1589CheckFixPair=get(handles.CheckFixPair,'Value');
1590if CheckFixPair
1591    if get(handles.scan_i,'Value')==1% case of scanning along index i
1592        i1=i1+increment;
1593        i2=i2+increment;
1594        if sub_value
1595            i1_1=i1_1+increment;
1596            i2_1=i2_1+increment;
1597        end
1598    else % case of scanning along index j (burst numbers)
1599        j1=j1+increment;
1600        j2=j2+increment;
1601        if sub_value
1602            j1_1=j1_1+increment;
1603            j2_1=j2_1+increment;
1604        end
1605    end
1606else
1607    UvData=get(handles.uvmat,'UserData');
1608    ref_i=i1;
1609    if ~isempty(i2)
1610        ref_i=floor((i1+i2)/2);
1611    end
1612    ref_j=1;
1613    if ~isempty(j1)
1614        ref_j=j1;
1615        if ~isempty(j2)
1616            ref_j=floor((j1+j2)/2);
1617        end
1618    end
1619    if ~isempty(increment)
1620        if get(handles.scan_i,'Value')==1% case of scanning along index i
1621            ref_i=ref_i+increment;
1622        else % case of scanning along index j (burst numbers)
1623            ref_j=ref_j+increment;
1624        end
1625    else% free increment
1626        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
1627            step=1;
1628        else
1629            step=-1;
1630        end
1631        if get(handles.scan_i,'Value')==1% case of scanning along index i
1632            ref_i=ref_i+step;
1633            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
1634                ref_i=ref_i+step;
1635            end
1636        else % case of scanning along index j (burst numbers)
1637            ref_j=ref_j+step;
1638            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
1639                ref_j=ref_j+step;
1640            end
1641        end
1642    end
1643    if ref_i<0
1644        errormsg='minimum i index reached';
1645    elseif ref_j<0
1646        errormsg='minimum j index reached';
1647    elseif ref_i+1>size(UvData.i1_series{1},1)
1648        errormsg='maximum i index reached';
1649    elseif ref_j+1>size(UvData.i1_series{1},2)
1650        errormsg='maximum j index reached';
1651    end
1652    if ~isempty(errormsg)
1653        return
1654    end
1655    if get(handles.scan_i,'Value')==1% case of scanning along index i
1656        i1_subseries=UvData.i1_series{1}(ref_i+1,:,:);
1657    else
1658        i1_subseries=UvData.i1_series{1}(:,ref_j+1,:);
1659    end
1660    i1_subseries=i1_subseries(i1_subseries>0);
1661    if isempty(i1_subseries)
1662        errormsg='no next file';
1663        return
1664    end
1665    i1=i1_subseries(end);
1666    if ~isempty(UvData.i2_series{1})
1667        if get(handles.scan_i,'Value')==1% case of scanning along index i
1668            i2_subseries=UvData.i2_series{1}(ref_i+1,:,:);
1669        else
1670            i2_subseries=UvData.i2_series{1}(:,ref_j+1,:);
1671        end
1672        i2_subseries=i2_subseries(i2_subseries>0);
1673        i2=i2_subseries(end);
1674    end
1675    if ~isempty(UvData.j1_series{1})
1676        if get(handles.scan_i,'Value')==1% case of scanning along index i
1677            j1_subseries=UvData.j1_series{1}(ref_i+1,:,:)
1678        else
1679            j1_subseries=UvData.j1_series{1}(:,ref_j+1,:)
1680        end
1681        j1_subseries=j1_subseries(j1_subseries>0);
1682        j1=j1_subseries(end);
1683    end
1684    if ~isempty(UvData.j2_series{1})
1685        if get(handles.scan_i,'Value')==1% case of scanning along index i
1686            j2_subseries=UvData.j2_series{1}(ref_i+1,:,:)
1687        else
1688            j2_subseries=UvData.j2_series{1}(:,ref_j+1,:)
1689        end
1690        j2_subseries=j2_subseries(j2_subseries>0);
1691        j2=j2_subseries(end);
1692    end
1693   
1694end
1695filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1696if sub_value
1697    filename_1=fullfile_uvmat(InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,FileExt_1,NomType_1,i1_1,i2_1,j1_1,j2_1);
1698end
1699
1700%% refresh plots
1701errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);
1702
1703%% update the index counters if the index move is successfull
1704if isempty(errormsg)
1705    set(handles.i1,'String',num2stra(i1,NomType,1));
1706    if isequal(i2,i1)
1707        set(handles.i2,'String','');
1708    else
1709        set(handles.i2,'String',num2stra(i2,NomType,1));
1710    end
1711    set(handles.j1,'String',num2stra(j1,NomType,2));
1712    if isequal(j2,j1)
1713        set(handles.j2,'String','');
1714    else
1715        set(handles.j2,'String',num2stra(j2,NomType,2));
1716    end
1717   % [indices]=name_generator('',i1,j1,'',NomType,1,i2,j2,'');
1718    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1719    set(handles.FileIndex,'String',indices);
1720    if ~isempty(filename_1)
1721        indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,j2_1);
1722        %indices_1=name_generator('',i1_1,j1_1,'',NomType_1,1,i2_1,j2_1,'');
1723        set(handles.FileIndex_1,'String',indices_1);
1724    end
1725    if isequal(movie_status,1)
1726        set(handles.movie_pair,'Value',1)
1727        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1728    end
1729end
1730
1731%------------------------------------------------------------------------
1732% --- Executes on button press in movie_pair: create an alternating movie with two view
1733function movie_pair_Callback(hObject, eventdata, handles)
1734%------------------------------------------------------------------------
1735%% stop movie action if the movie_pair button is off
1736if ~get(handles.movie_pair,'value')
1737    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1738    set(handles.i2,'String','')
1739    set(handles.j2,'String','')
1740    return
1741else
1742    set(handles.movie_pair,'BusyAction','queue')
1743end
1744
1745%% initialisation
1746set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1747drawnow
1748list_fields=get(handles.Fields,'String');% list menu fields
1749index_fields=get(handles.Fields,'Value');% selected string index
1750FieldName=list_fields{index_fields}; % selected field
1751UvData=get(handles.uvmat,'UserData');
1752if isequal(FieldName,'image')
1753    test_1=0;
1754    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1755    NomType=get(handles.NomType,'String');
1756else
1757    list_fields=get(handles.Fields_1,'String');% list menu fields
1758    index_fields=get(handles.Fields_1,'Value');% selected string index
1759    FieldName=list_fields{index_fields}; % selected field
1760    if isequal(FieldName,'image')
1761        test_1=1;
1762        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1763    else
1764        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1765        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1766        set(handles.movie_pair,'Value',0)
1767        return
1768    end
1769end
1770num_i1=str2num(get(handles.i1,'String'));
1771num_j1=stra2num(get(handles.j1,'String'));
1772num_i2=str2num(get(handles.i2,'String'));
1773num_j2=stra2num(get(handles.j2,'String'));
1774if isempty(num_j2)
1775    if isempty(num_i2)   
1776        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
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    else
1781        num_j2=num_j1;%repeat the index i1 by default
1782    end
1783end
1784if isempty(num_i2)
1785    num_i2=num_i1;%repeat the index i1 by default
1786end
1787% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1788imaname_1=fullfile_uvmat(RootPath,'',RootFile,Ext,NomType,num_i2,[],num_j2);
1789if ~exist(imaname_1,'file')
1790      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1791      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1792       set(handles.movie_pair,'Value',0)
1793      return
1794end
1795
1796%% read the second image
1797Field.AName='image';
1798if test_1
1799    Field_a=UvData.Field_1;
1800else
1801    Field_a=UvData.Field;
1802end
1803Field_b.AX=Field_a.AX;
1804Field_b.AY=Field_a.AY;
1805% z index
1806nbslice=str2double(get(handles.nb_slice,'String'));
1807if ~isempty(nbslice)
1808    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1809end
1810Field_b.CoordUnit='pixel';
1811
1812%% determine the input file type
1813if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1814    FileType='movie';
1815elseif isequal(lower(Ext),'.avi')
1816    FileType='avi';
1817elseif isequal(lower(Ext),'.vol')
1818    FileType='vol';
1819else
1820   form=imformats(Ext(2:end));
1821   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1822       if isequal(NomType,'*');
1823           FileType='multimage';
1824       else
1825           FileType='image';
1826       end
1827   end
1828end
1829switch FileType
1830        case 'movie'
1831            if test_1
1832                Field_b.A=read(UvData.MovieObject{2},num_i2);
1833            else
1834                Field_b.A=read(UvData.MovieObject{1},num_i2);
1835            end
1836        case 'avi'
1837            mov=aviread(imaname_1,num_i2);
1838            Field_b.A=frame2im(mov(1));
1839        case 'vol'
1840            Field_b.A=imread(imaname_1);
1841        case 'multimage'
1842            Field_b.A=imread(imaname_1,num_i2);
1843        case 'image'
1844            Field_b.A=imread(imaname_1);
1845end
1846if get(handles.slices,'Value')
1847    Field.ZIndex=str2double(get(handles.z_index,'String'));
1848end
1849
1850%px to phys or other transform on field
1851menu_transform=get(handles.transform_fct,'String');
1852choice_value=get(handles.transform_fct,'Value');
1853transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1854transform_list=get(handles.transform_fct,'UserData');
1855transform=transform_list{choice_value};
1856if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1857    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
1858        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
1859        Field_b=transform(Field_b,UvData.XmlData{2});
1860    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
1861        Field_b=transform(Field_b,UvData.XmlData{1});
1862    end
1863end
1864
1865 % make movie until movie speed is set to 0 or STOP is activated
1866hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1867set(handles.STOP,'Visible','on')
1868set(handles.speed,'Visible','on')
1869set(handles.speed_txt,'Visible','on')
1870while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1871    % read and plot the series of images in non erase mode
1872    set(hima,'CData',Field_b.A);
1873    pause(1.02-get(handles.speed,'Value'));% wait for next image
1874    set(hima,'CData',Field_a.A);
1875    pause(1.02-get(handles.speed,'Value'));% wait for next image
1876end
1877set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1878 set(handles.movie_pair,'Value',0)
1879
1880%------------------------------------------------------------------------
1881% --- Executes on button press in run0.
1882function run0_Callback(hObject, eventdata, handles)
1883%------------------------------------------------------------------------
1884set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1885drawnow
1886%filename=read_file_boxes(handles);
1887[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1888filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1889filename_1=[];%default
1890if get(handles.SubField,'Value')
1891    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
1892    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
1893   % filename_1=read_file_boxes_1(handles);
1894end
1895num_i1=stra2num(get(handles.i1,'String'));
1896num_i2=stra2num(get(handles.i2,'String'));
1897num_j1=stra2num(get(handles.j1,'String'));
1898num_j2=stra2num(get(handles.j2,'String'));
1899
1900errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
1901
1902if ~isempty(errormsg)
1903      msgbox_uvmat('ERROR',errormsg);
1904else
1905    set(handles.i1,'BackgroundColor',[1 1 1])
1906    set(handles.i2,'BackgroundColor',[1 1 1])
1907    set(handles.j1,'BackgroundColor',[1 1 1])
1908    set(handles.j2,'BackgroundColor',[1 1 1])
1909    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1910    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1911end   
1912set(handles.run0,'BackgroundColor',[1 0 0])
1913
1914
1915%------------------------------------------------------------------------
1916% --- read the input files and refresh all the plots, including projection.
1917% OUTPUT:
1918%  errormsg: error message char string  =[] by default
1919% INPUT:
1920% filename: first input file (=[] in the absence of input file)
1921% filename_1: second input file (=[] in the asbsenc of secodn input file)
1922% num_i1,num_i2,num_j1,num_j2; frame indices
1923% Field: structure describing an optional input field (then replace the input file)
1924function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
1925%------------------------------------------------------------------------
1926
1927%% initialisation
1928abstime=[];
1929abstime_1=[];
1930dt=[];
1931if ~exist('Field','var')
1932    Field={};
1933end
1934UvData=get(handles.uvmat,'UserData');
1935if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1936    delete(handles.UVMAT_title)
1937end
1938
1939%% determine the main input file information for action
1940FileType=[];%default
1941if ~exist(filename,'file')
1942    errormsg=['input file ' filename ' does not exist'];
1943    return
1944end
1945NomType=get(handles.NomType,'String');
1946% NomType=get(handles.FileIndex,'UserData');
1947%update the z position index
1948nbslice_str=get(handles.nb_slice,'String');
1949if isequal(nbslice_str,'volume')%NOT USED
1950    z_index=num_j1;
1951    set(handles.z_index,'String',num2str(z_index))
1952else
1953    nbslice=str2num(nbslice_str);
1954    z_index=mod(num_i1-1,nbslice)+1;
1955    set(handles.z_index,'String',num2str(z_index))
1956end
1957% refresh menu for save_mask if relevant
1958masknumber=get(handles.masklevel,'String');
1959if length(masknumber)>=z_index
1960    set(handles.masklevel,'Value',z_index)
1961end
1962
1963%% read the first input field if a filename has been introduced
1964if ~isempty(filename)
1965    ObjectName=filename;
1966    FieldName=[];%default
1967    VelType=[];%default
1968    FileExt=get(handles.FileExt,'String');
1969    FileType=UvData.FileType{1};
1970    switch FileType
1971        %     if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
1972        case {'civx','civdata','netcdf'};
1973            list_fields=get(handles.Fields,'String');% list menu fields
1974            index_fields=get(handles.Fields,'Value');% selected string index
1975            FieldName= list_fields{index_fields}; % selected field
1976            if ~strcmp(FieldName,'get_field...')
1977                TestVelType=get(handles.FixVelType,'Value');
1978                if TestVelType
1979                    VelType=setfield(handles);% read the velocity type.
1980                end
1981            end
1982            if strcmp(FieldName,'velocity')
1983                list_code=get(handles.ListColorCode,'String');% list menu fields
1984                index_code=get(handles.ListColorCode,'Value');% selected string index
1985                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
1986                    list_code=get(handles.ListColorScalar,'String');% list menu fields
1987                    index_code=get(handles.ListColorScalar,'Value');% selected string index
1988                    ParamIn.ColorVar= list_code{index_code}; % selected field
1989                end
1990            end
1991        case 'video'
1992            ObjectName=UvData.MovieObject{1};         
1993        case 'vol' %TODO: update
1994            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
1995                ParamIn.Npy=UvData.XmlData.Npy;
1996                ParamIn.Npx=UvData.XmlData.Npx;
1997            else
1998                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
1999                return
2000            end
2001    end
2002    ParamIn.FieldName=FieldName;
2003    ParamIn.VelType=VelType;
2004    ParamIn.GUIName='get_field';
2005    [Field{1},ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num_i1);
2006    if ~isempty(errormsg)
2007        errormsg=['error in reading ' filename ': ' errormsg];
2008        return
2009    end       
2010    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2011        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2012        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2013    end
2014    if isfield(ParamOut,'TimeIndex')
2015        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2016    end
2017    if isfield(ParamOut,'TimeValue')
2018        Field{1}.Time=ParamOut.TimeValue;
2019    end
2020end
2021
2022%% choose a second field filename_1 if defined
2023VelType_1=[];%default
2024FieldName_1=[];
2025ParamOut_1=[];
2026if ~isempty(filename_1)
2027    if ~exist(filename_1,'file')
2028        errormsg=['second file ' filename_1 ' does not exist'];
2029        return
2030    end
2031    Name=filename_1;
2032    FileType_1=UvData.FileType{2};
2033    switch FileType_1
2034        %     if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
2035        case {'civx','civdata','netcdf'};
2036            list_fields=get(handles.Fields_1,'String');% list menu fields
2037            index_fields=get(handles.Fields_1,'Value');% selected string index
2038            FieldName_1= list_fields{index_fields}; % selected field
2039            if ~strcmp(FieldName,'get_field...')
2040                TestVelType=get(handles.FixVelType,'Value');
2041                if TestVelType
2042                    VelType_1=setfield(handles);% read the velocity type.
2043                end
2044            end
2045            if strcmp(FieldName_1,'velocity')
2046                list_code=get(handles.ListColorCode,'String');% list menu fields
2047                index_code=get(handles.ListColorCode,'Value');% selected string index
2048                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2049                    list_code=get(handles.ListColorScalar,'String');% list menu fields
2050                    index_code=get(handles.ListColorScalar,'Value');% selected string index
2051                    ParamIn.ColorVar= list_code{index_code}; % selected field
2052                end
2053            end
2054        case 'video'
2055            Name=UvData.MovieObject{2};
2056        case 'vol' %TODO: update
2057            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2058                ParamIn.Npy=UvData.XmlData.Npy;
2059                ParamIn.Npx=UvData.XmlData.Npx;
2060            else
2061                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2062                return
2063            end
2064    end
2065    NomType_1=get(handles.NomType_1,'String');
2066    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2067    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2068        if isfield(UvData,'filename_1')&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2069            test_keepdata_1= strcmp(filename_1,UvData.filename_1) && strcmp(VelType_1,UvData.VelType_1) && strcmp(FieldName_1,UvData.FieldName_1);
2070        end
2071    end
2072    if test_keepdata_1
2073        Field{2}=UvData.Field_1;
2074    else
2075        ParamIn.FieldName=FieldName_1;
2076        ParamIn.VelType=VelType_1;
2077        ParamIn.GUIName='get_field_1';
2078        [Field{2},ParamOut_1,errormsg] = read_field(Name,FileType_1,ParamIn,num_i1);
2079        if ~isempty(errormsg)
2080            errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
2081            return
2082        end
2083        UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2084    end
2085    %     end
2086end
2087
2088%% update uvmat interface
2089if isfield(ParamOut,'Npx')
2090    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2091    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2092elseif isfield(ParamOut_1,'Npx')
2093    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2094    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2095end
2096
2097%% update the display menu for the first velocity type (first menuline)
2098test_veltype=0;
2099% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2100if (strcmp(FileType,'civx')||strcmp(FileType,'civdata'))&& ~strcmp(FieldName,'get_field...')
2101    test_veltype=1;
2102    set(handles.VelType,'Visible','on')
2103    set(handles.VelType_1,'Visible','on')
2104    set(handles.FixVelType,'Visible','on')
2105    menu=set_veltype_display(ParamOut.CivStage);
2106    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2107    index_val=find(index_menu,1);
2108    if isempty(index_val)
2109        index_val=1;
2110    end
2111    set(handles.VelType,'Value',index_val)
2112    if ~get(handles.SubField,'value')
2113        set(handles.VelType,'String',menu)
2114        set(handles.VelType_1,'Value',1)
2115        set(handles.VelType_1,'String',[{''};menu])
2116    end
2117else
2118    set(handles.VelType,'Visible','off')
2119end
2120field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2121set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2122set(handles.Fields,'Value',find(field_index,1))
2123
2124%% update the display menu for the second velocity type (second menuline)
2125test_veltype_1=0;
2126if isempty(filename_1)
2127    set(handles.Fields_1,'Value',1); %update the field menu
2128    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2129else
2130    if ~isequal(FileType_1,'netcdf')|| isequal(FieldName_1,'get_field...')
2131        set(handles.VelType_1,'Visible','off')
2132    else
2133        test_veltype_1=1;
2134        set(handles.VelType_1,'Visible','on')
2135        if ~get(handles.FixVelType,'Value')
2136            menu=set_veltype_display(ParamOut_1.CivStage);
2137            index_menu=strcmp(ParamOut_1.VelType,menu);
2138            set(handles.VelType_1,'Value',1+find(index_menu,1))
2139            set(handles.VelType_1,'String',[{''};menu])
2140        end
2141    end
2142end
2143if test_veltype||test_veltype_1
2144     set(handles.FixVelType,'Visible','on')
2145else
2146     set(handles.FixVelType,'Visible','off')
2147end
2148   
2149%% introduce w as background image by default for a new series (only for nbdim=2)
2150if ~isfield(UvData,'NewSeries')
2151    UvData.NewSeries=1;
2152end
2153%put W as background image by default if NbDim=2:
2154if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2155        set(handles.SubField,'Value',1);
2156        %menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w'
2157        set(handles.RootPath_1,'String','"')
2158        set(handles.RootFile_1,'String','"')
2159        set(handles.SubDir_1,'String','"');
2160         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2161        %[indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,'');
2162        set(handles.FileIndex_1,'String',indices)
2163        set(handles.FileExt_1,'String','"');
2164        set(handles.Fields_1,'Visible','on');
2165        set(handles.Fields_1,'Visible','on');
2166        set(handles.RootPath_1,'Visible','on')
2167        set(handles.RootFile_1,'Visible','on')
2168        set(handles.SubDir_1,'Visible','on');
2169        set(handles.FileIndex_1,'Visible','on');
2170        set(handles.FileExt_1,'Visible','on');
2171        set(handles.Fields_1,'Visible','on');
2172        Field{1}.AName='w';
2173end           
2174
2175%% store the current open names, fields and vel types in uvmat interface
2176UvData.filename_1=filename_1;
2177UvData.VelType_1=[];%default
2178UvData.FieldName_1=[];
2179if isfield(ParamOut_1,VelType)
2180    UvData.VelType_1=ParamOut_1.VelType;
2181end
2182if isfield(ParamOut_1,FieldName)
2183    UvData.FieldName_1=ParamOut_1.FieldName;
2184end
2185
2186%% apply coordinate transform or other user fct
2187XmlData=[];%default
2188XmlData_1=[];%default
2189if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2190    XmlData=UvData.XmlData{1};
2191    if numel(UvData.XmlData)==2
2192        XmlData_1=UvData.XmlData{2};
2193    end
2194end
2195
2196% menu_transform=get(handles.transform_fct,'String');
2197choice_value=get(handles.transform_fct,'Value');
2198transform_list=get(handles.transform_fct,'UserData');
2199transform=transform_list{choice_value};%selected function handles
2200% z index
2201if ~isempty(filename)
2202    Field{1}.ZIndex=z_index;
2203end
2204%px to phys or other transform on field
2205if ~isempty(transform)
2206    if length(Field)>=2
2207        Field{2}.ZIndex=z_index;
2208        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2209        if isempty(Field{2})
2210            Field(2)=[];
2211        end
2212    else
2213        Field{1}=transform(Field{1},XmlData);
2214    end
2215end
2216
2217%% calculate scalar
2218if strcmp(FileType(1:3),'civ') && ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
2219    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2220end
2221if numel(Field)==2 && ~test_keepdata_1 && isequal(FileType_1(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2222    Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2223end
2224
2225%% combine the two input fields (e.g. substract velocity fields)
2226if numel(Field)==2
2227   UvData.Field=sub_field(Field{1},Field{2}); 
2228else
2229   UvData.Field=Field{1};
2230end
2231
2232%% get bounds and mesh (needed for mouse action and to open set_object)
2233test_x=0;
2234test_z=0;% test for unstructured z coordinate
2235[UvData.Field,errormsg]=check_field_structure(UvData.Field);
2236if ~isempty(errormsg)
2237    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];
2238    return
2239end
2240[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);
2241if ~isempty(errormsg)
2242    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];
2243    return
2244end
2245[NbDim,imax]=max(NbDim);
2246if isfield(UvData.Field,'NbDim')
2247    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2248end
2249if ~isempty(VarType{imax}.coord_x)  && ~isempty(VarType{imax}.coord_y)    %unstructured coordinates
2250    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2251    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2252    eval(['nbvec=length(UvData.Field.' XName ');'])%nbre of measurement points (e.g. vectors)
2253    test_x=1;%test for unstructured coordinates
2254    if ~isempty(VarType{imax}.coord_z)
2255        ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2256    else
2257        NbDim=2;
2258    end
2259elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0 %structured coordinate
2260    XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2261    if NbDim>1
2262        YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2263    end
2264end
2265if NbDim==3
2266    if ~test_x
2267        ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2268    end
2269    eval(['ZMax=max(UvData.Field.' ZName ');'])
2270    eval(['ZMin=min(UvData.Field.' ZName ');'])
2271    UvData.Field.ZMax=ZMax;
2272    UvData.Field.ZMin=ZMin;
2273    test_z=1;
2274    if isequal(ZMin,ZMax)%no z dependency
2275        NbDim=2;
2276        test_z=0;
2277    end
2278end
2279if exist('XName','var')
2280    eval(['XMax=max(max(UvData.Field.' XName '));'])
2281    eval(['XMin=min(min(UvData.Field.' XName '));'])
2282    UvData.Field.NbDim=NbDim;
2283    UvData.Field.XMax=XMax;
2284    UvData.Field.XMin=XMin;
2285    if NbDim >1
2286        eval(['YMax=max(max(UvData.Field.' YName '));'])
2287        eval(['YMin=min(min(UvData.Field.' YName '));'])
2288        UvData.Field.YMax=YMax;
2289        UvData.Field.YMin=YMin;
2290    end
2291    eval(['nbvec=length(UvData.Field.' XName ');'])
2292    if test_x %unstructured coordinates
2293        if test_z
2294            UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2295            UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2296        else
2297            UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2298        end
2299    else
2300        VarIndex=CellVarIndex{imax}; % list of variable indices
2301        DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2302        nbpoints_x=UvData.Field.DimValue(DimIndex(NbDim));
2303        DX=(XMax-XMin)/(nbpoints_x-1);
2304        if NbDim >1
2305            nbpoints_y=UvData.Field.DimValue(DimIndex(NbDim-1));
2306            DY=(YMax-YMin)/(nbpoints_y-1);
2307        end
2308        if NbDim==3
2309            nbpoints_z=UvData.Field.DimValue(DimIndex(1));
2310            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2311            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2312            UvData.Field.ZMax=ZMax;
2313            UvData.Field.ZMin=ZMin;
2314        else
2315            UvData.Field.Mesh=DX;%sqrt(DX*DY);
2316        end
2317    end
2318end
2319
2320%% 3D case (menuvolume)
2321if NbDim==3% && UvData.NewSeries
2322    test_set_object=1;
2323    hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2324    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2325    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2326    if ~isempty(hset_object) %if set_object is detected
2327%         hhset_object=guidata(hset_object);
2328% %         ZBounds_old(1)=get(hhset_object.z_slider,'Min');
2329% %         ZBounds_old(2)=get(hhset_object.z_slider,'Max');
2330% %         if isequal(ZBounds_old,ZBounds)
2331%             test_set_object=0;% do not refresh the GUI set_object
2332%         else
2333            delete(hset_object);% delete the GUI set_object if it does not fit
2334%         end
2335    end
2336    if test_set_object% reinitiate the GUI set_object
2337        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
2338        UvData.Object{1}.Type='plane';%main plotting plane
2339        UvData.Object{1}.ProjMode='projection';%main plotting plane
2340        UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2341        UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2342        UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2343        UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2344        UvData.Object{1}.Angle=[0 0 0];
2345%         UvData.Object{1}.Theta=0;
2346%         UvData.Object{1}.Psi=0;
2347        UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2348%         PlotHandles=get_plot_handles(handles);
2349        UvData.Object{1}.Name='1-PLANE';
2350        UvData.Object{1}.enable_plot=1;
2351        set_object(UvData.Object{1},handles,ZBounds);
2352        set(handles.ListObject,'Value',1);
2353        set(handles.ListObject,'String',{'1-PLANE'});
2354        set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2355        edit_object_Callback([],[], handles)
2356    end
2357    %multilevel case (single menuplane in a 3D space)
2358elseif isfield(UvData,'Z')
2359    if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2360        XmlData=UvData.XmlData{1};
2361        if isfield(XmlData,'PlanePos')
2362            UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2363        end
2364        if isfield(XmlData,'PlaneAngle')
2365            siz=size(XmlData.PlaneAngle);
2366            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2367            UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2368        end
2369    elseif isfield(UvData,'ZIndex')
2370        UvData.Object{1}.ZObject=UvData.ZIndex;
2371    end
2372else
2373    % create a default projection
2374    UvData.Object{1}.ProjMode='projection';%main plotting plane
2375    UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2376    set(handles.ListObject,'Value',1);
2377    list_object=get(handles.ListObject,'String');
2378    if isempty(list_object)
2379        list_object={''};
2380    elseif ~isempty(list_object{1})
2381        list_object=[{''};list_object];
2382    end
2383    set(handles.ListObject,'String',list_object);
2384%     set(handles.list_object_2,'String',list_object);
2385end
2386testnewseries=UvData.NewSeries;
2387UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2388set(handles.uvmat,'UserData',UvData)
2389
2390%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2391if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2392    set(handles.num_MinA,'String','0')
2393    set(handles.num_MaxA,'String','255')
2394end
2395
2396%% Plot the projections on the selected  projection objects
2397% main projection object (uvmat display)
2398list_object=get(handles.ListObject,'String');
2399if isequal(list_object,{''})%refresh list of objects if the menu is empty
2400    UvData.Object={[]};
2401    set(handles.ListObject,'Value',1)
2402end
2403IndexObj=get(handles.ListObject,'Value');%selected projection object for main view
2404if IndexObj(1)> numel(UvData.Object)
2405    IndexObj(1)=1;%select the first object if the selected one does not exist
2406    set(handles.ListObject,'Value',1)
2407end
2408plot_handles{1}=handles;
2409if isfield(UvData,'plotaxes')%case of movies
2410    haxes(1)=UvData.plotaxes;
2411else
2412    haxes(1)=handles.axes3;
2413end
2414%PlotParam{1}=read_plot_param(handles);%read plotting parameters on the uvmat interfac
2415PlotParam{1}=read_GUI(handles.uvmat);
2416if ~isfield(PlotParam{1},'Vectors')
2417    PlotParam{1}.Vectors.MaxVec=1;
2418    PlotParam{1}.Vectors.MinVec=0;
2419    PlotParam{1}.Vectors.CheckFixVecColor=1;
2420    PlotParam{1}.Vectors.ColCode1=0.33;
2421    PlotParam{1}.Vectors.ColCode2=0.66;
2422     PlotParam{1}.Vectors.ListColorScalar={'ima_cor'};
2423     PlotParam{1}.Vectors.ListColorCode= {'rgb'};
2424end
2425keeplim(1)=get(handles.CheckFixLimits,'Value');% test for fixed graph limits
2426PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2427
2428% second projection object (view_field display)
2429if length( IndexObj)>=2
2430    view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2431    if ~isempty(view_field_handle)
2432        plot_handles{2}=guidata(view_field_handle);
2433        haxes(2)=plot_handles{2}.axes3;
2434        %PlotParam{2}=read_plot_param(plot_handles{2});%read plotting parameters on the viewinterface
2435        PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2436        keeplim(2)=get(plot_handles{2}.CheckFixLimits,'Value');
2437        PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2438    end
2439end
2440
2441%loop on the projection objects: one or two
2442for imap=1:numel(IndexObj)
2443    iobj=IndexObj(imap);
2444    [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2445
2446    if ~isempty(errormsg)
2447        return
2448    end
2449    %     if testnewseries && isfield(ObjectData,'CoordUnit')&& isfield(PlotParam{imap},'Coordinates')
2450%         PlotParam{imap}.Coordinates=rmfield(PlotParam{imap}.Coordinates,'CheckFixEqual'); %set FixEqual to depend on the field (=1 if Data.CoordUnit=1 in plot_field)
2451%     end
2452    if testnewseries && isfield(ObjectData,'CoordUnit')
2453        PlotParam{imap}.Coordinates.CheckFixEqual=1;
2454    end
2455    %use of mask (TODO: check)
2456    if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2457        flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2458        AX=ObjectData.AX;%x coordiantes for the scalar field
2459        AY=ObjectData.AY;%y coordinates for the scalar field
2460        MaskX=ObjectData.MaskX;%x coordiantes for the mask
2461        MaskY=ObjectData.MaskY;%y coordiantes for the mask
2462        if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2463            nxy=size(flag_mask);
2464            sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2465            sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2466            x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2467            y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2468            %project on the positions of the scalar
2469            npxy=size(ObjectData.A);
2470            dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2471            dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2472            xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2473            yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2474            [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2475            flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2476        end
2477        AClass=class(ObjectData.A);
2478        ObjectData.A=flag_mask.*double(ObjectData.A);
2479        ObjectData.A=feval(AClass,ObjectData.A);
2480        ind_off=[];
2481        if isfield(ObjectData,'ListVarName')
2482            for ilist=1:length(ObjectData.ListVarName)
2483                if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2484                    ind_off=[ind_off ilist];
2485                end
2486            end
2487            ObjectData.ListVarName(ind_off)=[];
2488            ObjectData.VarDimIndex(ind_off)=[];
2489            ind_off=[];
2490            for ilist=1:length(ObjectData.ListDimName)
2491                if isequal(ObjectData.ListDimName{ilist},'MaskX') || isequal(ObjectData.ListDimName{ilist},'MaskY')
2492                    ind_off=[ind_off ilist];
2493                end
2494            end
2495            ObjectData.ListDimName(ind_off)=[];
2496            ObjectData.DimValue(ind_off)=[];
2497        end
2498    end   
2499    if ~isempty(ObjectData)
2500        PlotType='none'; %default
2501        if imap==2 && isempty(view_field_handle)
2502            view_field(ObjectData)
2503        else
2504            [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2505            write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2506            if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2507                ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2508            end
2509        end
2510        if isequal(PlotType,'none')
2511            hget_field=findobj(allchild(0),'name','get_field');
2512            if isempty(hget_field)
2513                get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2514            end
2515            errormsg='The field defined by get_field cannot be plotted';
2516            return
2517        end
2518    end
2519end
2520
2521%% update the mask
2522if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2523   update_mask(handles,num_i1,num_i2);
2524end
2525
2526%% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2527menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2528ind_bad=[];
2529nb_histo=1;
2530
2531% suppress coordinates from the histogram menu
2532for ivar=1:numel(menu_histo)%l loop on field variables:
2533    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2534        Role=UvData.Field.VarAttribute{ivar}.Role;
2535        switch Role
2536            case {'coord_x','coord_y','coord_z','dimvar'}
2537                ind_bad=[ind_bad ivar];
2538            case {'vector_y'}
2539                nb_histo=nb_histo+1;
2540        end
2541    end
2542    DimCell=UvData.Field.VarDimName{ivar};
2543    DimName='';
2544    if ischar(DimCell)
2545        DimName=DimCell;
2546    elseif iscell(DimCell)&& numel(DimCell)==1
2547        DimName=DimCell{1};
2548    end
2549    if strcmp(DimName,menu_histo{ivar})
2550        ind_bad=[ind_bad ivar];
2551    end
2552end
2553menu_histo(ind_bad)=[];
2554
2555%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2556% display menus and plot histograms
2557test_v=0;
2558if ~isempty(menu_histo)
2559    set(handles.histo1_menu,'Value',1)
2560    set(handles.histo1_menu,'String',menu_histo)
2561    histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2562    % case of more than one variables (eg vector components)
2563    if nb_histo > 1
2564        test_v=1;
2565        set(handles.histo2_menu,'Visible','on')
2566        set(handles.histo_v,'Visible','on')
2567        set(handles.histo2_menu,'String',menu_histo)
2568        set(handles.histo2_menu,'Value',2)
2569        histo2_menu_Callback(handles.histo2_menu,[], handles)% plot second histogram
2570    end
2571end
2572if ~test_v
2573    set(handles.histo2_menu,'Visible','off')
2574    set(handles.histo_v,'Visible','off')
2575    cla(handles.histo_v)
2576    set(handles.histo2_menu,'Value',1)
2577end
2578%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2579
2580%% display time
2581testimedoc=0;
2582TimeUnit='';
2583if isfield(UvData.Field,'Time')
2584    abstime=UvData.Field.Time;%time read from the netcdf input file
2585end
2586if isfield(UvData,'Field_1') && isfield(UvData.Field_1,'Time')
2587    abstime_1=UvData.Field_1.Time;%time read from the netcdf input file
2588end
2589if isfield(UvData.Field,'dt')
2590    dt=UvData.Field.dt;%dt read from the netcdf input file
2591    if isfield(UvData.Field,'TimeUnit')
2592       TimeUnit=UvData.Field.TimeUnit;
2593    end
2594elseif isfield(UvData,'Field_1') && isfield(UvData.Field_1,'dt')%dt obtained from the second field if not defined in the first
2595    dt=UvData.Field_1.dt;%dt read from the netcdf input file
2596    if isfield(UvData.Field_1,'TimeUnit')
2597       TimeUnit=UvData.Field_1.TimeUnit;
2598    end
2599end
2600% time from xml file overset previous result
2601if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2602    if isempty(num_i2)||isnan(num_i2)
2603        num_i2=num_i1;
2604    end
2605    if isempty(num_j1)||isnan(num_j1)
2606        num_j1=1;
2607    end
2608    if isempty(num_j2)||isnan(num_j2)
2609        num_j2=num_j1;
2610    end
2611    siz=size(UvData.XmlData{1}.Time);
2612    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2613        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2614        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2615        testimedoc=1;
2616        if isfield(UvData.XmlData{1},'TimeUnit')
2617            TimeUnit=UvData.XmlData{1}.TimeUnit;
2618        end
2619    end
2620    if numel(UvData.XmlData)==2
2621        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2622        %  [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2623        if isempty(num_i2)
2624            num_i2=num_i1;
2625        end
2626        if isempty(num_j1)
2627            num_j1=1;
2628        end
2629        if isempty(num_j2)
2630            num_j2=num_j1;
2631        end
2632        siz=size(UvData.XmlData{2}.Time);
2633        if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2634            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
2635        end
2636    end
2637end
2638
2639if ~isequal(numel(abstime),1)
2640    abstime=[];
2641end
2642if ~isequal(numel(abstime_1),1)
2643      abstime_1=[];
2644end 
2645set(handles.abs_time,'String',num2str(abstime,4))
2646set(handles.abs_time_1,'String',num2str(abstime_1,4))
2647if testimedoc && isfield(UvData,'dt')
2648    dt=UvData.dt;
2649end
2650if isempty(dt)||isequal(dt,0)
2651    set(handles.Dt_txt,'String','')
2652else
2653    if  isempty(TimeUnit)
2654        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2655    else
2656        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2657    end
2658end
2659
2660
2661%-------------------------------------------------------------------
2662% --- translate coordinate to matrix index
2663%-------------------------------------------------------------------
2664function [indx,indy]=pos2ind(x0,rangx0,nxy)
2665indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2666indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2667
2668%-------------------------------------------------------------------
2669% --- Executes on button press in 'CheckFixLimits'.
2670%-------------------------------------------------------------------
2671function CheckFixLimits_Callback(hObject, eventdata, handles)
2672test=get(handles.CheckFixLimits,'Value');
2673if test
2674    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2675else
2676    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2677    update_plot(handles);
2678end
2679
2680%-------------------------------------------------------------------
2681% --- Executes on button press in CheckFixEqual.
2682function CheckFixEqual_Callback(hObject, eventdata, handles)
2683test=get(handles.CheckFixEqual,'Value');
2684if test
2685    set(handles.CheckFixEqual,'BackgroundColor',[1 1 0])
2686    cla(handles.axes3)
2687    update_plot(handles);
2688else
2689    set(handles.CheckFixEqual,'BackgroundColor',[0.7 0.7 0.7])
2690    update_plot(handles);
2691%     axis(handles.axes3,'image')
2692end
2693
2694%-------------------------------------------------------------------
2695
2696%-------------------------------------------------------------------
2697% --- Executes on button press in 'CheckZoom'.
2698%-------------------------------------------------------------------
2699function CheckZoom_Callback(hObject, eventdata, handles)
2700
2701if (get(handles.CheckZoom,'Value') == 1);
2702    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2703    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2704    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2705else
2706    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2707end
2708
2709%-------------------------------------------------------------------
2710%----Executes on button press in 'record': records the current flags of manual correction.
2711%-------------------------------------------------------------------
2712function record_Callback(hObject, eventdata, handles)
2713% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2714[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2715filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2716%filename=read_file_boxes(handles);
2717[erread,message]=fileattrib(filename);
2718if ~isempty(message) && ~isequal(message.UserWrite,1)
2719     msgbox_uvmat('ERROR',['no writting access to ' filename])
2720     return
2721end
2722test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2723test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2724if ~test_civ2 && ~test_civ1
2725    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2726end
2727if test_civ2
2728    nbname='nb_vectors2';
2729   flagname='vec2_FixFlag';
2730   attrname='fix2';
2731end
2732if test_civ1
2733    nbname='nb_vectors';
2734   flagname='vec_FixFlag';
2735   attrname='fix';
2736end
2737%write fix flags in the netcdf file
2738UvData=get(handles.uvmat,'UserData');
2739hhh=which('netcdf.open');% look for built-in matlab netcdf library
2740if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2741    nc=netcdf.open(filename,'NC_WRITE');
2742    netcdf.reDef(nc);
2743    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2744    dimid = netcdf.inqDimID(nc,nbname);
2745    try
2746        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2747    catch
2748        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2749    end
2750    netcdf.endDef(nc);
2751    netcdf.putVar(nc,varid,UvData.axes3.FF);
2752    netcdf.close(nc); 
2753else %old netcdf library
2754    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2755end
2756
2757%-------------------------------------------------------------------
2758%----Correct the netcdf file, using toolbox (old versions of Matlab).
2759%-------------------------------------------------------------------
2760function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2761nc=netcdf(filename,'write'); %open netcdf file
2762result=redef(nc);
2763eval(['nc.' attrname '=1;']);
2764theDim=nc(nbname) ;% get the number of velocity vectors
2765nb_vectors=size(theDim);
2766var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2767var_FixFlag(1:nb_vectors)=AxeData.FF;%
2768fin=close(nc);
2769
2770%-------------------------------------------------------------------
2771%determines the fields to read from the interface
2772%------------------------------------------------------------------
2773function VelType=setfield(handles)
2774VelTypeList=get(handles.VelType,'String');
2775index=get(handles.VelType,'Value');
2776VelType=VelTypeList{index};
2777
2778%-------------------------------------------------------------------
2779%determines the veltype of the second field to read from the iinterface
2780%------------------------------------------------------------------
2781function VelType=setfield_1(handles)
2782VelTypeList=get(handles.VelType_1,'String');
2783index=get(handles.VelType_1,'Value');
2784VelType=VelTypeList{index};
2785
2786%---------------------------------------------------
2787% --- Executes on button press in SubField
2788function SubField_Callback(hObject, eventdata, handles)
2789% huvmat=get(handles.run0,'parent');
2790UvData=get(handles.uvmat,'UserData');
2791if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2792    set(handles.RootPath_1,'String','')
2793    set(handles.RootFile_1,'String','')
2794    set(handles.SubDir_1,'String','');
2795    set(handles.FileIndex_1,'String','');
2796    set(handles.FileExt_1,'String','');
2797    set(handles.RootPath_1,'Visible','off')
2798    set(handles.RootFile_1,'Visible','off')
2799    set(handles.SubDir_1,'Visible','off');
2800    set(handles.NomType_1,'Visible','off');
2801    set(handles.abs_time_1,'Visible','off')
2802    set(handles.FileIndex_1,'Visible','off');
2803    set(handles.FileExt_1,'Visible','off');
2804    set(handles.Fields_1,'Value',1);%set to blank state
2805    set(handles.VelType_1,'Value',1);%set to blank state
2806    if ~strcmp(get(handles.VelType,'Visible'),'on')
2807        set(handles.VelType_1,'Visible','off')
2808    end
2809%     set_veltype_display([handles.VelType_1 handles.interp1_1 handles.filter1_1 ...
2810%             handles.civ2_1 handles.interp2_1 handles.filter2_1],0)
2811    if isfield(UvData,'XmlData_1')
2812        UvData=rmfield(UvData,'XmlData_1');
2813    end
2814    set(handles.uvmat,'UserData',UvData);
2815    run0_Callback(hObject, eventdata, handles); %run
2816else
2817    MenuBrowse_1_Callback(hObject, eventdata, handles)
2818end
2819
2820%------------------------------------------------------------------------
2821% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
2822
2823function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
2824%------------------------------------------------------------------------
2825InputFile=read_GUI(handles.InputFile);
2826RootPath=InputFile.RootPath;
2827SubDir=regexprep(InputFile.SubDir,'/|\','');
2828RootFile=regexprep(InputFile.RootFile,'/|\','');
2829FileIndices=InputFile.FileIndex;
2830FileExt=InputFile.FileExt;
2831
2832
2833%------------------------------------------------------------------------
2834% ---- read the data displayed for the second input rootfile windows
2835function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
2836%------------------------------------------------------------------------
2837RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
2838if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
2839    RootPath_1=get(handles.RootPath,'String');
2840end;
2841SubDir_1=get(handles.SubDir_1,'String');
2842if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
2843    SubDir_1=get(handles.SubDir,'String');
2844end
2845SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2846RootFile_1=get(handles.RootFile_1,'String');
2847if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
2848    RootFile_1=get(handles.RootFile,'String');
2849end
2850RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2851FileIndex_1=get(handles.FileIndex_1,'String');
2852if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
2853    FileIndex_1=get(handles.FileIndex,'String');
2854end
2855FileExt_1=get(handles.FileExt_1,'String');
2856if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
2857    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
2858end
2859NomType_1=get(handles.NomType_1,'String');
2860if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
2861    NomType_1=get(handles.NomType,'String');%read FileExt by default
2862end
2863%------------------------------------------------------------------------
2864% --- Executes on menu selection Fields
2865function Fields_Callback(hObject, eventdata, handles)
2866%------------------------------------------------------------------------
2867list_fields=get(handles.Fields,'String');% list menu fields
2868index_fields=get(handles.Fields,'Value');% selected string index
2869field= list_fields{index_fields(1)}; % selected string
2870if isequal(field,'get_field...')
2871    set(handles.FixVelType,'visible','off')
2872    set(handles.VelType,'visible','off')
2873    set(handles.VelType_1,'visible','off')
2874    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2875    filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2876    %filename=read_file_boxes(handles);
2877    hget_field=findobj(allchild(0),'name','get_field');
2878    if ~isempty(hget_field)
2879        delete(hget_field)
2880    end
2881    hget_field=get_field(filename);
2882    set(hget_field,'Name','get_field')
2883    hhget_field=guidata(hget_field);
2884    set(hhget_field.list_fig,'Value',1)
2885    set(hhget_field.list_fig,'String',{'uvmat'})
2886    set(handles.transform_fct,'Value',1)% no transform by default
2887    set(handles.path_transform,'String','')
2888    return %no action
2889end
2890list_fields=get(handles.Fields_1,'String');% list menu fields
2891index_fields=get(handles.Fields_1,'Value');% selected string index
2892field_1= list_fields{index_fields(1)}; % selected string
2893UvData=get(handles.uvmat,'UserData');
2894
2895%read the rootfile input display
2896[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2897FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2898[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
2899% NomTypeNew=NomType;%default
2900if isequal(field,'image')
2901%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
2902%         NomTypeNew='_1_1';
2903%     elseif isequal(NomType,'#_ab')
2904%         NomTypeNew='#a';
2905%     elseif isequal(NomType,'_1-2')
2906%         NomTypeNew='_1';
2907%     end
2908    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
2909    if ~exist(imagename,'file')
2910        [FileName,PathName] = uigetfile( ...
2911            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
2912            '*.jpg',' jpeg image files'; ...
2913            '*.png','.png image files'; ...
2914            '*.tif','.tif image files'; ...
2915            '*.avi;*.AVI','.avi movie files'; ...
2916            '*.vol','.volume images (png)'; ...
2917            '*.*',  'All Files (*.*)'}, ...
2918            'Pick an image',imagename);   
2919        imagename=[PathName FileName];
2920    end
2921     % display the selected field and related information
2922    display_file_name(hObject, eventdata, handles,imagename)%display the image
2923    return
2924else
2925    ext=get(handles.FileExt,'String');
2926    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
2927        [FileName,PathName] = uigetfile( ...
2928            {'*.nc', ' (*.nc)';
2929            '*.nc',' netcdf files'; ...
2930            '*.*',  'All Files (*.*)'}, ...
2931            'Pick a netcdf file',FileBase);
2932        filename=[PathName FileName];
2933        % display the selected field and related information
2934        display_file_name(hObject, eventdata, handles,filename)
2935        return
2936    end
2937end
2938indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
2939set(handles.FileIndex,'String',indices)
2940% set(handles.NomType,'String',NomType)
2941
2942%common to Fields_1_Callback
2943if isequal(field,'image')||isequal(field_1,'image')
2944    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
2945    set(handles.TitleNpy,'Visible','on')
2946    set(handles.num_Npx,'Visible','on')
2947    set(handles.num_Npy,'Visible','on')
2948else
2949    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
2950    set(handles.TitleNpy,'Visible','off')
2951    set(handles.num_Npx,'Visible','off')
2952    set(handles.num_Npy,'Visible','off')
2953end
2954setfield(handles);% update the field structure ('civ1'....)
2955if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
2956    run0_Callback(hObject, eventdata, handles)
2957end
2958
2959%---------------------------------------------------
2960% --- Executes on menu selection Fields
2961function Fields_1_Callback(hObject, eventdata, handles)
2962%-------------------------------------------------
2963%% read input data
2964check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
2965UvData=get(handles.uvmat,'UserData');
2966if check_new && isfield(UvData,'XmlData')
2967    UvData.XmlData{2}=UvData.XmlData{1};
2968end
2969list_fields=get(handles.Fields,'String');% list menu fields
2970index_fields=get(handles.Fields,'Value');% selected string index
2971field= list_fields{index_fields(1)}; % selected string
2972list_fields=get(handles.Fields_1,'String');% list menu fields
2973index_fields=get(handles.Fields_1,'Value');% selected string index
2974field_1= list_fields{index_fields(1)}; % selected string for the second field
2975if isequal(field_1,'')||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
2976    set(handles.SubField,'Value',0)
2977    check_new=1;
2978    SubField_Callback(hObject, eventdata, handles)
2979    if isempty(field_1)%remove second field if 'blank' field is selected
2980        return
2981    end
2982end
2983set(handles.SubField,'Value',1)%state that a second field is now entered
2984
2985%% read the rootfile input display
2986[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomTYpe_1]=read_file_boxes_1(handles);
2987filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
2988[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
2989set(handles.FileIndex_1,'Visible','on')
2990set(handles.FileExt_1,'Visible','on')
2991switch field_1
2992    case 'get_field...'
2993        set_veltype_display(0) % no veltype display
2994        hget_field=findobj(allchild(0),'name','get_field_1');
2995        if ~isempty(hget_field)
2996            delete(hget_field)
2997        end
2998        hget_field=get_field(filename_1);
2999        set(hget_field,'name','get_field_1')
3000        hhget_field=guidata(hget_field);
3001        set(hhget_field.list_fig,'Value',1)
3002        set(hhget_field.list_fig,'String',{'uvmat'})
3003        set(handles.transform_fct,'Value',1)% no transform by default
3004        set(handles.path_transform,'String','')
3005    case 'image'
3006        % transform netc type to the corresponding image type
3007        NomType=get(handles.NomType,'string');
3008        check_letter=~isempty(regexp(NomType,'[ab|AB]$'));%detect pair label by letter
3009%         NomType_1=NomType;
3010%         if check_letter
3011%             NomType_1=NomType_1(1:end-1);
3012%         else
3013%             r=regexp(NomType_1,'.-(?<num2>\d+$','names');
3014%             if ~isempty(r)
3015%                 NomType_1=regexprep(NomType_1,['-' r.num2],'');
3016%             end
3017%         end
3018        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',NomType,i1,[],j1);
3019        if ~exist(imagename,'file')
3020            [FileName,PathName] = uigetfile( ...
3021                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3022                '*.jpg',' jpeg image files'; ...
3023                '*.png','.png image files'; ...
3024                '*.tif','.tif image files'; ...
3025                '*.avi;*.AVI','.avi movie files'; ...
3026                '*.vol','.volume images (png)'; ...
3027                '*.*',  'All Files (*.*)'}, ...
3028                'Pick an image',imagename);
3029            % display the selected field and related information
3030            imagename=[PathName FileName];
3031        end
3032        set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3033        set(handles.TitleNpy,'Visible','on')
3034        set(handles.num_Npx,'Visible','on')
3035        set(handles.num_Npy,'Visible','on')
3036        display_file_name(hObject, eventdata, handles,imagename,2)%display the imag
3037    otherwise
3038        if check_new
3039            UvData.FileType{2}=UvData.FileType{1};
3040            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3041            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3042        end
3043        if ~isequal(field,'image')
3044            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3045            set(handles.TitleNpy,'Visible','off')
3046            set(handles.num_Npx,'Visible','off')
3047            set(handles.num_Npy,'Visible','off')
3048        end
3049        set(handles.uvmat,'UserData',UvData)
3050        setfield(handles);% update the field structure ('civ1'....)
3051        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3052            run0_Callback(hObject, eventdata, handles)
3053        end
3054end
3055
3056%------------------------------------------------------------------------
3057% --- set the visibility of relevant velocity type menus:
3058function menu=set_veltype_display(Civ)
3059%------------------------------------------------------------------------
3060if isequal(Civ,0)
3061    imax=0;
3062elseif isequal(Civ,1) || isequal(Civ,2)
3063   imax=1;
3064elseif isequal(Civ,3)
3065    imax=3;
3066elseif isequal(Civ,4) || isequal(Civ,5)
3067    imax=4;
3068elseif isequal(Civ,6) %patch2
3069    imax=6;
3070end
3071menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3072menu=menu(1:imax);
3073
3074%------------------------------------------------------------------------
3075% --- Executes on button press in VelType.
3076function VelType_Callback(hObject, eventdata, handles)
3077%------------------------------------------------------------------------
3078set(handles.FixVelType,'Value',1)
3079run0_Callback(hObject, eventdata, handles)
3080
3081%------------------------------------------------------------------------
3082% --- Executes on button press in VelType.
3083function VelType_1_Callback(hObject, eventdata, handles)
3084%------------------------------------------------------------------------
3085 
3086set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3087%refresh field with a second filename=first fiel name
3088set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3089drawnow   
3090InputFile=read_GUI(handles.InputFile);
3091[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3092filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3093%filename=read_file_boxes(handles);
3094
3095index=get(handles.VelType_1,'Value');
3096if index==1
3097        filename_1='';% we plot the current field without the second field
3098        set(handles.SubField,'Value',0)
3099        SubField_Callback(hObject, eventdata, handles)
3100elseif get(handles.SubField,'Value')% if subfield is already 'on'
3101      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3102     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3103    %filename_1=read_file_boxes_1(handles); %read the current second field
3104else
3105     filename_1=filename;% we compare two fields in the same file
3106     set(handles.SubField,'Value',1)
3107end
3108
3109num_i1=stra2num(get(handles.i1,'String'));
3110num_i2=stra2num(get(handles.i2,'String'));
3111num_j1=stra2num(get(handles.j1,'String'));
3112num_j2=stra2num(get(handles.j2,'String'));
3113
3114errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
3115
3116if ~isempty(errormsg)
3117    msgbox_uvmat('ERROR',errormsg);
3118else
3119    set(handles.i1,'BackgroundColor',[1 1 1])
3120    set(handles.i2,'BackgroundColor',[1 1 1])
3121    set(handles.j1,'BackgroundColor',[1 1 1])
3122    set(handles.j2,'BackgroundColor',[1 1 1])
3123    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3124    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3125end
3126set(handles.run0,'BackgroundColor',[1 0 0])
3127
3128%-----------------------------------------------
3129% --- reset civ buttons
3130function reset_vel_type(handles_civ0,handle1)
3131for ibutton=1:length(handles_civ0)
3132    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3133    set(handles_civ0(ibutton),'Value',0)
3134end
3135if exist('handle1','var')%handles of selected button
3136        set(handle1,'BackgroundColor',[1 1 0]) 
3137end
3138
3139%-------------------------------------------------------
3140% --- Executes on button press in MENUVOLUME.
3141%-------------------------------------------------------
3142function VOLUME_Callback(hObject, eventdata, handles)
3143%errordlg('command VOL not implemented yet')
3144if ishandle(handles.UVMAT_title)
3145    delete(handles.UVMAT_title)
3146end
3147UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3148if isequal(get(handles.VOLUME,'Value'),1)
3149    set(handles.CheckZoom,'Value',0)
3150    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3151    set(handles.edit_vect,'Value',0)
3152    edit_vect_Callback(hObject, eventdata, handles)
3153    set(handles.edit_object,'Value',0)
3154    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3155%     set(handles.cal,'Value',0)
3156%     set(handles.cal,'BackgroundColor',[0 1 0])
3157    set(handles.edit_vect,'Value',0)
3158    edit_vect_Callback(hObject, eventdata, handles)
3159    %initiate set_object GUI
3160    data.Name='VOLUME';
3161    if isfield(UvData,'CoordType')
3162        data.CoordType=UvData.CoordType;
3163    end
3164    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3165        data.RangeY=UvData.Mesh;
3166        data.RangeX=UvData.Mesh;
3167        data.DX=UvData.Mesh;
3168        data.DY=UvData.Mesh;
3169    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3170        np=size(UvData.Field.A);
3171        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3172        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3173        data.RangeY=max(meshx,meshy);
3174        data.RangeX=max(meshx,meshy);
3175        data.DX=max(meshx,meshy);
3176    end
3177    data.ParentButton=handles.VOLUME;
3178    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3179    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3180                                                      % associate the set_object interface handle to the plotting axes
3181    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3182    pos_uvmat=get(huvmat,'Position');
3183    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3184    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3185    set(hset_object,'Position',pos_set_object)
3186    end
3187    UvData.MouseAction='create_object';
3188else
3189    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3190    UvData.MouseAction='none';
3191end
3192set(huvmat,'UserData',UvData)
3193
3194%-------------------------------------------------------
3195function edit_vect_Callback(hObject, eventdata, handles)
3196%-------------------------------------------------------
3197%
3198% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3199if isequal(get(handles.edit_vect,'Value'),1)
3200    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3201    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3202    if ~test_civ2 && ~test_civ1
3203        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3204    end
3205    set(handles.record,'Visible','on')
3206    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3207    set(handles.edit_object,'Value',0)
3208    set(handles.CheckZoom,'Value',0)
3209    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3210%     set(handles.create,'Value',0)
3211%     set(handles.create,'BackgroundColor',[0 1 0])
3212    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3213    set(gcf,'Pointer','arrow')
3214%     UvData.MouseAction='edit_vect';
3215else
3216    set(handles.record,'Visible','off')
3217    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3218%     UvData.MouseAction='none';
3219end
3220% set(handles.uvmat,'UserData',UvData)
3221
3222%----------------------------------------------
3223function save_mask_Callback(hObject, eventdata, handles)
3224%-----------------------------------------------------------------------
3225UvData=get(handles.uvmat,'UserData');
3226
3227flag=1;
3228npx=size(UvData.Field.A,2);
3229npy=size(UvData.Field.A,1);
3230xi=0.5:npx-0.5;
3231yi=0.5:npy-0.5;
3232[Xi,Yi]=meshgrid(xi,yi);
3233if isfield(UvData,'Object')
3234    for iobj=1:length(UvData.Object)
3235        ObjectData=UvData.Object{iobj};
3236        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3237            flagobj=1;
3238            testphys=0; %coordinates in pixels by default
3239            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3240                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3241                    Calib=UvData.XmlData{1}.GeometryCalib;
3242                    testphys=1;
3243                end
3244            end
3245            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3246                if isequal(ObjectData.Type,'polygon')
3247                    X=ObjectData.Coord(:,1);
3248                    Y=ObjectData.Coord(:,2);
3249                    if testphys
3250                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3251                    end
3252                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3253                elseif isequal(ObjectData.Type,'ellipse')
3254                    if testphys
3255                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3256                    end
3257                    RangeX=max(ObjectData.RangeX);
3258                    RangeY=max(ObjectData.RangeY);
3259                    X2Max=RangeX*RangeX;
3260                    Y2Max=RangeY*RangeY;
3261                    distX=(Xi-ObjectData.Coord(1,1));
3262                    distY=(Yi-ObjectData.Coord(1,2));
3263                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3264                elseif isequal(ObjectData.Type,'rectangle')
3265                    if testphys
3266                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3267                    end
3268                    distX=abs(Xi-ObjectData.Coord(1,1));
3269                    distY=abs(Yi-ObjectData.Coord(1,2));
3270                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3271                end
3272                if isequal(ObjectData.ProjMode,'mask_outside')
3273                    flagobj=~flagobj;
3274                end
3275                flag=flag & flagobj;
3276            end
3277        end
3278    end
3279end
3280% flag=~flag;
3281%mask name
3282RootPath=get(handles.RootPath,'String');
3283RootFile=get(handles.RootFile,'String');
3284RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3285filebase=fullfile(RootPath,RootFile);
3286list=get(handles.masklevel,'String');
3287masknumber=num2str(length(list));
3288maskindex=get(handles.masklevel,'Value');
3289mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3290%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3291imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3292imflag=flipdim(imflag,1);
3293% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3294msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3295imwrite(imflag,mask_name,'BitDepth',8);
3296
3297%display the mask
3298figure;
3299vec=linspace(0,1,256);%define a linear greyscale colormap
3300map=[vec' vec' vec'];
3301colormap(map)
3302
3303image(imflag);
3304
3305%-------------------------------------------------------------------
3306%-------------------------------------------------------------------
3307%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3308
3309%------------------------------------------------------------------
3310
3311%------------------------------------------------------------------
3312% --- Executes on selection change in ListColorScalar: choice of the color code.
3313function ListColorScalar_Callback(hObject, eventdata, handles)
3314%------------------------------------------------------------------
3315% edit the choice for color code
3316list_code=get(handles.ListColorScalar,'String');% list menu fields
3317index_code=get(handles.ListColorScalar,'Value');% selected string index
3318col_code= list_code{index_code(1)}; % selected field
3319if isequal(col_code,'black') || isequal(col_code,'white')
3320   set(handles.Slider1,'Visible','off')
3321   set(handles.Slider2,'Visible','off')
3322   set(handles.num_ColCode1,'Visible','off')
3323   set(handles.num_ColCode2,'Visible','off')
3324   set(handles.CheckFixVecColor,'Visible','off')
3325   set_vec_col_bar(handles)
3326else
3327   set(handles.Slider1,'Visible','on')
3328   set(handles.Slider2,'Visible','on')
3329   set(handles.num_ColCode1,'Visible','on')
3330   set(handles.num_ColCode2,'Visible','on')
3331   set(handles.CheckFixVecColor,'Visible','on') 
3332   if isequal(col_code,'ima_cor')
3333       set(handles.CheckFixVecColor,'Value',0)%fixed scale by default
3334       set(handles.VecColBar,'Value',0)% 3 colors r,g,b by default
3335       set(handles.Slider1,'Min',0);
3336       set(handles.Slider1,'Max',1);
3337       set(handles.Slider2,'Min',0);
3338       set(handles.Slider2,'Max',1);
3339 %      set(handles.min_title_vec,'String','0')
3340       set(handles.num_MaxVec,'String','1')
3341       set(handles.num_ColCode1,'String','0.333')
3342       num_ColCode1_Callback(hObject, eventdata, handles)
3343       set(handles.num_ColCode2,'String','0.666')
3344       num_ColCode2_Callback(hObject, eventdata, handles)
3345   else
3346       set(handles.CheckFixVecColor,'Value',1)%auto scale between min,max by default
3347       set(handles.VecColBar,'Value',1)% colormap 'jet' by default
3348       minval=get(handles.Slider1,'Min');
3349       maxval=get(handles.Slider1,'Max');
3350       set(handles.Slider1,'Value',minval)
3351       set(handles.Slider2,'Value',maxval)
3352       set_vec_col_bar(handles)
3353   end
3354%    slider_update(handles)
3355end
3356%replot the current graph
3357run0_Callback(hObject, eventdata, handles)
3358
3359
3360%----------------------------------------------------------------
3361% -- Executes on slider movement to set the color code
3362%
3363function Slider1_Callback(hObject, eventdata, handles)
3364%------------------------------------------------------------------
3365slider1=get(handles.Slider1,'Value');
3366min_val=str2num(get(handles.num_MinVec,'String'));
3367max_val=str2num(get(handles.num_MaxVec,'String'));
3368col=min_val+(max_val-min_val)*slider1;
3369set(handles.num_ColCode1,'String',num2str(col))
3370if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3371    set(handles.Slider2,'Value',col)
3372    set(handles.num_ColCode2,'String',num2str(col))
3373end
3374num_ColCode1_Callback(hObject, eventdata, handles)
3375
3376%----------------------------------------------------------------
3377% Executes on slider movement to set the color code
3378%----------------------------------------------------------------
3379function Slider2_Callback(hObject, eventdata, handles)
3380slider2=get(handles.Slider2,'Value');
3381min_val=str2num(get(handles.num_MinVec,'String'));
3382max_val=str2num(get(handles.num_MaxVec,'String'));
3383col=min_val+(max_val-min_val)*slider2;
3384set(handles.num_ColCode2,'String',num2str(col))
3385if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3386    set(handles.Slider1,'Value',col)
3387    set(handles.num_ColCode1,'String',num2str(col))
3388end
3389num_ColCode2_Callback(hObject, eventdata, handles)
3390
3391%----------------------------------------------------------------
3392% --- Execute on return carriage on the edit box corresponding to slider 1
3393%----------------------------------------------------------------
3394function num_ColCode1_Callback(hObject, eventdata, handles)
3395set_vec_col_bar(handles)
3396update_plot(handles);
3397
3398%----------------------------------------------------------------
3399% --- Execute on return carriage on the edit box corresponding to slider 2
3400%----------------------------------------------------------------
3401function num_ColCode2_Callback(hObject, eventdata, handles)
3402set_vec_col_bar(handles)
3403update_plot(handles);
3404%------------------------------------------------------------------------
3405%-------------------------------------------------------
3406% --- Executes on button press in CheckFixVecColor.
3407%-------------------------------------------------------
3408function VecColBar_Callback(hObject, eventdata, handles)
3409set_vec_col_bar(handles)
3410
3411%-------------------------------------------------------------
3412% --- Executes on selection change in transform_fct.
3413function transform_fct_Callback(hObject, eventdata, handles)
3414%-------------------------------------------------------------
3415UvData=get(handles.uvmat,'UserData');
3416menu=get(handles.transform_fct,'String');
3417ind_coord=get(handles.transform_fct,'Value');
3418coord_option=menu{ind_coord};
3419list_transform=get(handles.transform_fct,'UserData');
3420ff=functions(list_transform{end}); 
3421if isequal(coord_option,'more...');
3422    coord_fct='';
3423    prompt = {'Enter the name of the transform function'};
3424    dlg_title = 'user defined transform';
3425    num_lines= 1;
3426    [FileName, PathName] = uigetfile( ...
3427       {'*.m', ' (*.m)';
3428        '*.m',  '.m files '; ...
3429        '*.*', 'All Files (*.*)'}, ...
3430        'Pick a file', ff.file);
3431    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3432        PathName(end)=[];
3433    end
3434    transform_selected =fullfile(PathName,FileName);
3435    if ~exist(transform_selected,'file')
3436           return
3437    end
3438   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3439   if ~isequal(ext_fct,'.m')
3440        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3441        return
3442   end
3443   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3444   ind_coord=get(handles.transform_fct,'Value');
3445   addpath(PathName)
3446   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3447   set(handles.transform_fct,'UserData',list_transform)
3448   rmpath(PathName)
3449   % save the new menu in the personal file 'uvmat_perso.mat'
3450   dir_perso=prefdir;%personal Matalb directory
3451   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3452   if exist(profil_perso,'file')
3453       nb_builtin=UvData.OpenParam.NbBuiltin;
3454       for ilist=nb_builtin+1:numel(list_transform)
3455           ff=functions(list_transform{ilist});
3456           transform_fct{ilist-nb_builtin}=ff.file;
3457       end
3458        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3459   end   
3460end
3461
3462%check the current path to the selected function
3463if isa(list_transform{ind_coord},'function_handle')
3464    func=functions(list_transform{ind_coord});
3465    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3466else
3467    set(handles.path_transform,'String','')
3468end
3469
3470set(handles.CheckFixLimits,'Value',0)
3471set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3472
3473%delete drawn objects
3474hother=findobj('Tag','proj_object');%find all the proj objects
3475for iobj=1:length(hother)
3476    delete_object(hother(iobj))
3477end
3478hother=findobj('Tag','DeformPoint');%find all the proj objects
3479for iobj=1:length(hother)
3480    delete_object(hother(iobj))
3481end
3482hh=findobj('Tag','calib_points');
3483if ~isempty(hh)
3484    delete(hh)
3485end
3486hhh=findobj('Tag','calib_marker');
3487if ~isempty(hhh)
3488    delete(hhh)
3489end
3490if isfield(UvData,'Object')
3491     UvData.Object=UvData.Object(1);
3492end
3493set(handles.ListObject,'Value',1)
3494set(handles.ListObject,'String',{''})
3495
3496%delete mask if it is displayed
3497if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3498   UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3499end
3500set(handles.uvmat,'UserData',UvData)
3501run0_Callback(hObject, eventdata, handles)
3502
3503%------------------------------------------------------------------------
3504function histo1_menu_Callback(hObject, eventdata, handles)
3505%--------------------------------------------
3506%plot first histo
3507huvmat=get(handles.histo1_menu,'parent');
3508histo_menu=get(handles.histo1_menu,'String');
3509histo_value=get(handles.histo1_menu,'Value');
3510FieldName=histo_menu{histo_value};
3511update_histo(handles.histo_u,huvmat,FieldName)
3512
3513%------------------------------------------------------------------------
3514function histo2_menu_Callback(hObject, eventdata, handles)
3515%------------------------------------------------------------------------
3516%plot second histo
3517huvmat=get(handles.histo2_menu,'parent');
3518histo_menu=get(handles.histo2_menu,'String');
3519histo_value=get(handles.histo2_menu,'Value');
3520FieldName=histo_menu{histo_value};
3521update_histo(handles.histo_v,huvmat,FieldName)
3522
3523%------------------------------------------------------------------------
3524%read the field .Fieldname stored in UvData and plot its histogram
3525function update_histo(haxes,huvmat,FieldName)
3526%------------------------------------------------------------------------
3527UvData=get(huvmat,'UserData');
3528if ~isfield(UvData.Field,FieldName)
3529    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
3530    return
3531end
3532Field=UvData.Field;
3533FieldHisto=eval(['Field.' FieldName]);
3534if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
3535    indsel=find(Field.FF==0);%find values marked as false
3536    if ~isempty(indsel)
3537        FieldHisto=FieldHisto(indsel);
3538    end
3539end
3540if isempty(Field)
3541    msgbox_uvmat('ERROR',['empty field ' FieldName])
3542else
3543    nxy=size(FieldHisto);
3544    Amin=double(min(min(min(FieldHisto))));%min of image
3545    Amax=double(max(max(max(FieldHisto))));%max of image
3546    if isequal(Amin,Amax)
3547        %msgbox_uvmat('WARNING',['uniform field =' num2str(Amin)]);
3548        cla(haxes)
3549    else
3550        Histo.ListVarName={FieldName,'histo'};
3551        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
3552            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3553        else
3554            if numel(nxy)==2
3555                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3556            else
3557                Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
3558            end
3559        end
3560        %unit
3561        units=[]; %default
3562        for ivar=1:numel(Field.ListVarName)
3563            if strcmp(Field.ListVarName{ivar},FieldName)
3564                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
3565                    units=Field.VarAttribute{ivar}.units;
3566                    break
3567                end
3568            end
3569        end
3570        if ~isempty(units)
3571            Histo.VarAttribute{1}.units=units;
3572        end
3573        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
3574        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
3575            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
3576            eval(['Histo.histo(:,1)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3577        else
3578            for col=1:size(FieldHisto,3)
3579                B=FieldHisto(:,:,col);
3580                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
3581                eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3582            end
3583        end
3584        plot_field(Histo,haxes);
3585    end
3586end
3587
3588%------------------------------------------------
3589%CALLBACKS FOR PLOTTING PARAMETERS
3590%-------------------------------------------------
3591
3592%------------------------------------------------------------------------
3593function num_MinX_Callback(hObject, eventdata, handles)
3594%------------------------------------------------------------------------
3595set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3596set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3597update_plot(handles);
3598
3599%------------------------------------------------------------------------
3600function num_MaxX_Callback(hObject, eventdata, handles)
3601%------------------------------------------------------------------------
3602set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3603set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3604update_plot(handles);
3605
3606%------------------------------------------------------------------------
3607function num_MinY_Callback(hObject, eventdata, handles)
3608%------------------------------------------
3609set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3610set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3611update_plot(handles);
3612
3613%------------------------------------------------------------------------
3614function num_MaxY_Callback(hObject, eventdata, handles)
3615%------------------------------------------------------------------------
3616set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3617set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3618update_plot(handles);
3619
3620%------------------------------------------------------------------------
3621function num_MinA_Callback(hObject, eventdata, handles)
3622%------------------------------------------
3623set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3624set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3625MinA=str2double(get(handles.num_MinA,'String'));
3626MaxA=str2double(get(handles.num_MaxA,'String'));
3627if MinA>MaxA% switch minA and maxA in case of error
3628    MinA_old=MinA;
3629    MinA=MaxA;
3630    MaxA=MinA_old;
3631    set(handles.num_MinA,'String',num2str(MinA,5));
3632    set(handles.num_MaxA,'String',num2str(MaxA,5));
3633end
3634update_plot(handles);
3635
3636%------------------------------------------------------------------------
3637function num_MaxA_Callback(hObject, eventdata, handles)
3638%------------------------------------------------------------------------
3639set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3640set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3641MinA=str2double(get(handles.num_MinA,'String'));
3642MaxA=str2double(get(handles.num_MaxA,'String'));
3643if MinA>MaxA% switch minA and maxA in case of error
3644        MinA_old=MinA;
3645    MinA=MaxA;
3646    MaxA=MinA_old;
3647    set(handles.num_MinA,'String',num2str(MinA,5));
3648    set(handles.num_MaxA,'String',num2str(MaxA,5));
3649end
3650update_plot(handles);
3651
3652%------------------------------------------------------------------------
3653function CheckFixScalar_Callback(hObject, eventdata, handles)
3654%------------------------------------------------------------------------
3655test=get(handles.CheckFixScalar,'Value');
3656if test
3657    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3658else
3659    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3660    update_plot(handles);
3661end
3662
3663%-------------------------------------------------------------------
3664function CheckBW_Callback(hObject, eventdata, handles)
3665%-------------------------------------------------------------------
3666update_plot(handles);
3667
3668%-------------------------------------------------------------------
3669function ListContour_Callback(hObject, eventdata, handles)
3670%-------------------------------------------------------------------
3671val=get(handles.ListContour,'Value');
3672if val==2
3673    set(handles.interval_txt,'Visible','on')
3674    set(handles.num_IncrA,'Visible','on')
3675else
3676    set(handles.interval_txt,'Visible','off')
3677    set(handles.num_IncrA,'Visible','off')
3678end
3679update_plot(handles);
3680
3681%-------------------------------------------------------------------
3682function num_IncrA_Callback(hObject, eventdata, handles)
3683%-------------------------------------------------------------------
3684update_plot(handles);
3685
3686%-------------------------------------------------------------------
3687function CheckHideWarning_Callback(hObject, eventdata, handles)
3688%-------------------------------------------------------------------
3689update_plot(handles);
3690
3691%-------------------------------------------------------------------
3692function CheckHideFalse_Callback(hObject, eventdata, handles)
3693%-------------------------------------------------------------------
3694update_plot(handles);
3695
3696%-------------------------------------------------------------------
3697function num_VecScale_Callback(hObject, eventdata, handles)
3698%-------------------------------------------------------------------
3699set(handles.CheckFixVectors,'Value',1);
3700set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3701update_plot(handles);
3702
3703%-------------------------------------------------------------------
3704function CheckFixVectors_Callback(hObject, eventdata, handles)
3705%-------------------------------------------------------------------
3706test=get(handles.CheckFixVectors,'Value');
3707if test
3708    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3709else
3710    update_plot(handles);
3711    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3712    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3713end
3714
3715%------------------------------------------------------------------------
3716% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3717function CheckDecimate4_Callback(hObject, eventdata, handles)
3718%------------------------------------------------------------------------
3719update_plot(handles);
3720
3721%------------------------------------------------------------------------
3722% --- Executes on selection change in ListColorCode menu
3723function ListColorCode_Callback(hObject, eventdata, handles)
3724%------------------------------------------------------------------------
3725set_vec_col_bar(handles)
3726update_plot(handles);
3727
3728%------------------------------------------------------------------------
3729% --- Executes on button press in CheckFixVecColor.
3730function CheckFixVecColor_Callback(hObject, eventdata, handles)
3731%------------------------------------------------------------------------
3732test=get(handles.CheckFixVecColor,'Value');
3733if test
3734    set(handles.CheckFixVecColor,'BackgroundColor',[1 1 0])
3735else
3736    update_plot(handles);
3737    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3738    set(handles.CheckFixVecColor,'BackgroundColor',[0.7 0.7 0.7])
3739end
3740
3741%------------------------------------------------------------------------
3742% --- Executes on selection change in num_MaxVec.
3743function num_MinVec_Callback(hObject, eventdata, handles)
3744%------------------------------------------------------------------------
3745max_vec_Callback(hObject, eventdata, handles)
3746
3747%------------------------------------------------------------------------
3748% --- Executes on selection change in num_MaxVec.
3749function num_MaxVec_Callback(hObject, eventdata, handles)
3750%------------------------------------------------------------------------
3751set(handles.CheckFixVecColor,'Value',1)
3752CheckFixVecColor_Callback(hObject, eventdata, handles)
3753min_val=str2num(get(handles.num_MinVec,'String'));
3754max_val=str2num(get(handles.num_MaxVec,'String'));
3755slider1=get(handles.Slider1,'Value');
3756slider2=get(handles.Slider2,'Value');
3757colcode1=min_val+(max_val-min_val)*slider1;
3758colcode2=min_val+(max_val-min_val)*slider2;
3759set(handles.num_ColCode1,'String',num2str(colcode1))
3760set(handles.num_ColCode2,'String',num2str(colcode2))
3761update_plot(handles);
3762
3763%------------------------------------------------------------------------
3764% --- update the display of color code for vectors
3765function set_vec_col_bar(handles)
3766%------------------------------------------------------------------------
3767%get the image of the color display button 'VecColBar' in pixels
3768set(handles.VecColBar,'Unit','pixel');
3769pos_vert=get(handles.VecColBar,'Position');
3770set(handles.VecColBar,'Unit','Normalized');
3771width=ceil(pos_vert(3));
3772height=ceil(pos_vert(4));
3773
3774%get slider indications
3775list=get(handles.ListColorCode,'String');
3776ichoice=get(handles.ListColorCode,'Value');
3777colcode.ListColorCode=list{ichoice};
3778colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3779colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3780test3color=strcmp(colcode.ListColorCode,'rgb') || strcmp(colcode.ListColorCode,'bgr');
3781if test3color
3782    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3783    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3784end
3785% colcode.FixedCbounds=0;
3786%colcode.CheckFixVecColor=1;
3787vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3788[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3789oneheight=ones(1,height);
3790A1=colorlist(col_vec,1)*oneheight;
3791A2=colorlist(col_vec,2)*oneheight;
3792A3=colorlist(col_vec,3)*oneheight;
3793A(:,:,1)=A1';
3794A(:,:,2)=A2';
3795A(:,:,3)=A3';
3796set(handles.VecColBar,'Cdata',A)
3797
3798%-------------------------------------------------------------------
3799function update_plot(handles)
3800%-------------------------------------------------------------------
3801UvData=get(handles.uvmat,'UserData');
3802AxeData=UvData.axes3;% retrieve the current plotted data
3803PlotParam=read_GUI(handles.uvmat);
3804[PP,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
3805write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3806
3807%-------------------------------------------------------------------
3808% --- Executes on selection change in edit_object.
3809function edit_object_Callback(hObject, eventdata, handles)
3810%-------------------------------------------------------------------
3811UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3812test=get(handles.edit_object,'Value');
3813if test
3814    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
3815    %suppress the other options
3816    set(handles.CheckZoom,'Value',0)
3817    CheckZoom_Callback(hObject, eventdata, handles)
3818    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
3819    if ishandle(hgeometry_calib)
3820        hhgeometry_calib=guidata(hgeometry_calib);
3821        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
3822        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
3823    end
3824else
3825    UvData.MouseAction='none';
3826    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])   
3827end
3828set(handles.uvmat,'UserData',UvData);
3829hset_object=findobj(allchild(0),'Tag','set_object');
3830if ~isempty(hset_object)
3831    hhset_object=guidata(hset_object);
3832    if test
3833        set(hhset_object.PLOT,'enable','on');
3834    else
3835       set(hhset_object.PLOT,'enable','off');
3836    end
3837end
3838
3839%------------------------------------------------------------------------
3840% --- Executes on selection change in ListObject.
3841function ListObject_Callback(hObject, eventdata, handles)
3842%------------------------------------------------------------------------
3843
3844list_str=get(handles.ListObject,'String');
3845IndexObj_old=get(handles.ListObject,'UserData');%retrieve previous selection
3846IndexObj=get(handles.ListObject,'Value');%present object selection
3847
3848%% we select two objects or more at once (using the Ctrl key), keep only the last two items: the first is projected on uvmat, the second on view_field
3849if length(IndexObj)>2
3850     IndexObj=[IndexObj(end-1) IndexObj(end)];%keeps only the last two selected items at most
3851end
3852
3853%% we select one object
3854if length(IndexObj)==1%
3855    if length(IndexObj_old)>=2 && isequal(IndexObj_old(1),IndexObj)   % we select the first previously selected object->
3856        IndexObj=[1 IndexObj_old(2)];% it desactivates this object and selects the first object for uvmat
3857    elseif length(IndexObj_old)>=2 && isequal(IndexObj_old(2),IndexObj) % we select the second previously selected object->
3858        IndexObj=IndexObj_old(1);% it desactivates this object  and keeps only the first previously selected object (uvmat)
3859    else %
3860        IndexObj=[IndexObj_old(1) IndexObj];% activates a second object while keeping the first previously selected one
3861    end
3862end
3863set(handles.ListObject,'Value',IndexObj); % marks the selected objects in the list
3864set(handles.ListObject,'UserData',IndexObj)% keep the current object selection in memory for next time
3865
3866%% update the object representation
3867set(handles.edit_object,'Value',0) % desactivate the edit object mode
3868edit_object_Callback(hObject, eventdata, handles)
3869UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3870if numel(UvData.Object)<max(IndexObj);
3871    msgbox_uvmat('ERROR','invalid object list')
3872    return
3873end
3874if numel(IndexObj)>=2
3875    UvData.Object=update_obj(UvData,IndexObj(1),IndexObj(2));%update the current object graphic representation
3876    set(handles.uvmat,'UserData',UvData)
3877end
3878
3879%% project on the selected object and update the corresponding plot
3880% hview_field=findobj(allchild(0),'tag','view_field');
3881% ViewObjectAxes=[];%default
3882if ~isequal(IndexObj(1),IndexObj_old(1))
3883    update_object(handles,IndexObj(1),handles.axes3,list_str{IndexObj(1)})%plot the projection in uvmat
3884end
3885hview_field=findobj(allchild(0),'tag','view_field');
3886if length(IndexObj)==2 && (length(IndexObj_old)==1 || ~isequal(IndexObj(2),IndexObj_old(2)))
3887    if isempty(hview_field)
3888        hview_field=view_field;
3889    end
3890    PlotHandles=guidata(hview_field);
3891    update_object(handles,IndexObj(2),PlotHandles.axes3,list_str{IndexObj(2)})%plot the projection in view_field
3892    update_object_color(handles.axes3,PlotHandles.axes3,UvData.Object{IndexObj(2)}.DisplayHandle_uvmat)
3893else
3894    if ~isempty(hview_field)
3895        delete(hview_field)
3896    end
3897    hset_object=findobj(allchild(0),'tag','set_object');
3898    if ~isempty(hset_object)
3899        delete(hset_object)
3900    end
3901    update_object_color(handles.axes3,handles.axes3,[])
3902end
3903
3904%% update the color of the gfraphic object representation: the selected object in magenta, others in blue
3905% update_object_color(handles.axes3,PlotHandles.axes3,UvData.Object{IndexObj(2)}.DisplayHandle_uvmat)
3906
3907%------------------------------------------------------------------------
3908function update_object(handles,IndexObj,ViewObjectAxes,ObjectName)
3909%------------------------------------------------------------------------
3910UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3911ObjectData=UvData.Object{IndexObj};
3912ObjectData.Name=ObjectName;
3913if isequal(get(handles.edit_object,'Value'),1)
3914    ObjectData.enable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
3915end
3916ZBounds=0; % default
3917if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3918    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3919    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3920end
3921hset_object=findobj(allchild(0),'tag','set_object');
3922if ~isempty(hset_object)
3923    delete(hset_object)% delete existing version of set_object
3924end
3925    hset_object=set_object(ObjectData,[],ZBounds);
3926% end
3927edit_test=get(handles.edit_object,'Value');
3928if edit_test
3929    ObjectData.enable_plot=1;
3930else
3931    if isfield(ObjectData,'enable_plot')
3932        ObjectData=rmfield(ObjectData,'enable_plot');
3933    end
3934end
3935
3936uistack(ViewObjectAxes,'top')% display the plotting axes at the top
3937ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
3938plot_field(ProjData,ViewObjectAxes,read_GUI(get(ViewObjectAxes,'Parent')));%read plotting parameters on the uvmat interfacPlotHandles);
3939
3940%------------------------------------------------------------------------
3941%--- update the representation of objects
3942function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
3943%------------------------------------------------------------------------
3944hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object')] ;%find all the proj objects
3945hother=[hother ;findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];
3946for iobj=1:length(hother)
3947    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
3948        set(hother(iobj),'EdgeColor','b')
3949        if isequal(get(hother(iobj),'FaceColor'),'m')
3950            set(hother(iobj),'FaceColor','b')
3951        end
3952    elseif isequal(get(hother(iobj),'Type'),'image')
3953        Acolor=get(hother(iobj),'CData');
3954        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
3955        set(hother(iobj),'CData',Acolor);
3956    else
3957        set(hother(iobj),'Color','b')
3958    end
3959    set(hother(iobj),'Selected','off')
3960end
3961if ~isempty(DisplayHandle)
3962linetype=get(DisplayHandle,'Type');
3963if isequal(linetype,'line')
3964    set(DisplayHandle,'Color','m'); %set the selected object to magenta color
3965elseif isequal(linetype,'rectangle')
3966    set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
3967elseif isequal(linetype,'patch')
3968    set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
3969end
3970SubObjectData=get(DisplayHandle,'UserData');
3971if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
3972    for iobj=1:length(SubObjectData.SubObject)
3973        hsub=SubObjectData.SubObject(iobj);
3974        if isequal(get(hsub,'Type'),'rectangle')
3975            set(hsub,'EdgeColor','m'); %set the selected object to magenta color
3976        elseif isequal(get(hsub,'Type'),'image')
3977            Acolor=get(hsub,'CData');
3978            Acolor(:,:,1)=Acolor(:,:,3);
3979            set(hsub,'CData',Acolor);
3980        else
3981            set(hsub,'Color','m')
3982        end
3983    end
3984end
3985if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
3986    set(SubObjectData.DeformPoint,'Color','m')
3987end
3988end
3989
3990%------------------------------------------------------
3991% --- Executes on button press in Menu/Export/field in workspace.
3992%------------------------------------------------------
3993function MenuExportField_Callback(hObject, eventdata, handles)
3994global Data_uvmat
3995Data_uvmat=get(handles.uvmat,'UserData');
3996evalin('base','global Data_uvmat')%make CurData global in the workspace
3997display('current field :')
3998evalin('base','Data_uvmat') %display CurData in the workspace
3999commandwindow; %brings the Matlab command window to the front
4000
4001%------------------------------------------------------
4002% --- Executes on button press in Menu/Export/extract figure.
4003%------------------------------------------------------
4004function MenuExport_plot_Callback(hObject, eventdata, handles)
4005huvmat=get(handles.MenuExport_plot,'parent');
4006UvData=get(huvmat,'UserData');
4007hfig=figure;
4008newaxes=copyobj(handles.axes3,hfig);
4009map=colormap(handles.axes3);
4010colormap(map);%transmit the current colormap to the zoom fig
4011colorbar
4012
4013
4014% --------------------------------------------------------------------
4015function Insert_Callback(hObject, eventdata, handles)
4016
4017
4018% --------------------------------------------------------------------
4019function MenuHelp_Callback(hObject, eventdata, handles)
4020% --------------------------------------------------------------------
4021path_to_uvmat=which ('uvmat');% check the path of uvmat
4022pathelp=fileparts(path_to_uvmat);
4023helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4024if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4025else
4026    addpath (fullfile(pathelp,'uvmat_doc'))
4027    web(helpfile);
4028end
4029
4030%------------------------------------------------------------------------
4031% --------------------------------------------------------------------
4032function MenuExportMovie_Callback(hObject, eventdata, handles)
4033% --------------------------------------------------------------------
4034set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4035huvmat=get(handles.run0,'parent');
4036UvData=get(huvmat,'UserData');
4037%[xx,xx,FileBase]=read_file_boxes(handles);
4038[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4039FileBase=fullfile(RootPath,RootFile);
4040 %read the current input file name
4041prompt = {'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)'};
4042dlg_title = 'select properties of the output avi movie';
4043num_lines= 1;
4044% nbfield_cell=get(handles.last_i,'String');
4045def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4046answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4047aviname=answer{1};
4048fps=str2double(answer{2});
4049% check for existing file with output name aviname
4050if exist(aviname,'file')
4051    backup=aviname;
4052    testexist=2;
4053    while testexist==2
4054        backup=[backup '~'];
4055        testexist=exist(backup,'file');     
4056    end
4057    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4058    if isequal(success,1)
4059        delete(aviname)%delete existing file
4060    else
4061        msgbox_uvmat('ERROR',message)
4062        return
4063    end
4064end
4065%create avi open
4066aviobj=avifile(aviname,'Compression','None','fps',fps);
4067
4068%display first view for tests
4069newfig=figure;
4070newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4071set(newaxes,'Tag','movieaxes')
4072nbpix=[512 384]*str2double(answer{3});
4073set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4074set(newaxes,'Position',eval(answer{4}));
4075map=colormap(handles.axes3);
4076colormap(map);%transmit the current colormap to the zoom fig
4077msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4078        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4079UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4080set(huvmat,'UserData',UvData);
4081increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4082set(handles.STOP,'Visible','on')
4083set(handles.speed,'Visible','on')
4084set(handles.speed_txt,'Visible','on')
4085set(handles.Movie,'BusyAction','queue')
4086
4087%imin=str2double(get(handles.i1,'String'));
4088imax=str2double(answer{5});
4089% if isfield(UvData,'Time')
4090htitle=get(newaxes,'Title');
4091xlim=get(newaxes,'XLim');
4092ylim=get(newaxes,'YLim');
4093set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4094time_str=get(handles.abs_time,'String');
4095set(htitle,'String',['t=' time_str])
4096set(handles.speed,'Value',1)
4097for i=1:imax
4098    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4099            runpm(hObject,eventdata,handles,increment)% run plus
4100            drawnow
4101            time_str=get(handles.abs_time,'String');
4102            if ishandle(htitle)
4103             set(htitle,'String',['t=' time_str])
4104            end
4105            mov=getframe(newfig);
4106            aviobj=addframe(aviobj,mov);
4107    end
4108end
4109aviobj=close(aviobj);
4110UvData=rmfield(UvData,'plotaxes');
4111%UvData.Object{1}.plotaxes=handles.axes3;
4112set(huvmat,'UserData',UvData);
4113msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4114
4115%------------------------------------------------------------------------
4116function MenuCalib_Callback(hObject, eventdata, handles)
4117%------------------------------------------------------------------------
4118
4119UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4120
4121%suppress competing options
4122set(handles.CheckZoom,'Value',0)
4123set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4124set(handles.ListObject,'Value',1)     
4125% initiate display of GUI geometry_calib
4126data=[]; %default
4127if isfield(UvData,'CoordType')
4128    data.CoordType=UvData.CoordType;
4129end
4130pos=get(handles.uvmat,'Position');
4131pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4132pos(2)=pos(2)-0.02;
4133%[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
4134[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4135FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4136set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4137if isfield(UvData.OpenParam,'CalOrigin')
4138    pos_uvmat=get(handles.uvmat,'Position');
4139    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4140    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4141    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4142end
4143geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4144set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4145set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4146
4147%------------------------------------------------------------------------
4148function MenuMask_Callback(hObject, eventdata, handles)
4149%------------------------------------------------------------------------
4150UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4151ListObj=UvData.Object;
4152select=zeros(1,numel(ListObj));
4153for iobj=1:numel(ListObj);
4154    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4155        select(iobj)=1;
4156    end
4157end
4158val=find(select);
4159if isempty(val)
4160    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4161    return
4162else
4163    set(handles.ListObject,'Max',2);%allow multiple selection
4164    set(handles.ListObject,'Value',val);
4165    flag=1;
4166    npx=size(UvData.Field.A,2);
4167    npy=size(UvData.Field.A,1);
4168    xi=0.5:npx-0.5;
4169    yi=0.5:npy-0.5;
4170    [Xi,Yi]=meshgrid(xi,yi);
4171    if isfield(UvData,'Object')
4172        for iobj=1:length(UvData.Object)
4173            ObjectData=UvData.Object{iobj};
4174            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4175                flagobj=1;
4176                testphys=0; %coordinates in pixels by default
4177                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4178                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4179                        Calib=UvData.XmlData{1}.GeometryCalib;
4180                        testphys=1;
4181                    end
4182                end
4183                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Style')
4184                    if isequal(ObjectData.Type,'polygon')
4185                        X=ObjectData.Coord(:,1);
4186                        Y=ObjectData.Coord(:,2);
4187                        if testphys
4188                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4189                        end
4190                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4191                    elseif isequal(ObjectData.Type,'ellipse')
4192                        if testphys
4193                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4194                        end
4195                        RangeX=max(ObjectData.RangeX);
4196                        RangeY=max(ObjectData.RangeY);
4197                        X2Max=RangeX*RangeX;
4198                        Y2Max=RangeY*RangeY;
4199                        distX=(Xi-ObjectData.Coord(1,1));
4200                        distY=(Yi-ObjectData.Coord(1,2));
4201                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4202                    elseif isequal(ObjectData.Type,'rectangle')
4203                        if testphys
4204                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4205                        end
4206                        distX=abs(Xi-ObjectData.Coord(1,1));
4207                        distY=abs(Yi-ObjectData.Coord(1,2));
4208                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4209                    end
4210                    if isequal(ObjectData.ProjMode,'mask_outside')
4211                        flagobj=~flagobj;
4212                    end
4213                    flag=flag & flagobj;
4214                end
4215            end
4216        end
4217    end
4218    %mask name
4219    RootPath=get(handles.RootPath,'String');
4220    RootFile=get(handles.RootFile,'String');
4221    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4222        RootFile(1)=[];
4223    end
4224    filebase=fullfile(RootPath,RootFile);
4225    list=get(handles.masklevel,'String');
4226    masknumber=num2str(length(list));
4227    maskindex=get(handles.masklevel,'Value');
4228    mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4229    %mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4230    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4231    imflag=flipdim(imflag,1);
4232
4233    %display the mask
4234    hfigmask=figure;
4235    set(hfigmask,'Name','mask image')
4236    vec=linspace(0,1,256);%define a linear greyscale colormap
4237    map=[vec' vec' vec'];
4238    colormap(map)
4239    image(imflag);
4240    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4241    if ~strcmp(answer,'Cancel')
4242        mask_dir=fileparts(answer);
4243        if ~exist(mask_dir,'dir')
4244            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4245            return
4246        end
4247        imwrite(imflag,answer,'BitDepth',8);
4248    end
4249    set(handles.ListObject,'Value',1)
4250    set(handles.ListObject,'Max',1)
4251end
4252
4253%------------------------------------------------------------------------
4254%-- open the GUI set_grid.fig to create grid
4255function MenuGrid_Callback(hObject, eventdata, handles)
4256%------------------------------------------------------------------------
4257%suppress the other options if grid is chosen
4258set(handles.edit_vect,'Value',0)
4259edit_vect_Callback(hObject, eventdata, handles)
4260set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4261set(handles.ListObject,'Value',1)     
4262
4263%prepare display of the set_grid GUI
4264[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4265FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4266CoordList=get(handles.transform_fct,'String');
4267val=get(handles.transform_fct,'Value');
4268set_grid(FileName,CoordList{val});% call the set_object interface
4269
4270%------------------------------------------------------------------------
4271% open the GUI 'series'
4272function MenuSeries_Callback(hObject, eventdata, handles)
4273%------------------------------------------------------------------------
4274series; %first display of the GUI to fill waiting time
4275[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4276param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4277if isequal(get(handles.SubField,'Value'),1)
4278    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
4279    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
4280    %FileName_1=read_file_boxes_1(handles);%
4281    if ~isequal(FileName_1,param.FileName)
4282        param.FileName_1=FileName_1;
4283    end
4284end
4285param.NomType=get(handles.NomType,'String');
4286% param.NomType=get(handles.FileIndex,'UserData');
4287param.NomType_1=get(handles.NomType_1,'String');
4288% param.NomType_1=get(handles.FileIndex_1,'UserData');
4289param.CheckFixPair=get(handles.CheckFixPair,'Value');
4290huvmat=get(handles.MenuSeries,'parent');
4291UvData=get(huvmat,'UserData');
4292if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4293    param.Time=UvData.XmlData{1}.Time;
4294end
4295if isequal(get(handles.scan_i,'Value'),1)
4296    param.incr_i=str2num(get(handles.increment_scan,'String'));
4297elseif isequal(get(handles.scan_j,'Value'),1)
4298    param.incr_j=str2num(get(handles.increment_scan,'String'));
4299end
4300param.list_fields=get(handles.Fields,'String');% list menu fields
4301param.list_fields(1)=[]; %suppress  'image' option
4302param.index_fields=get(handles.Fields,'Value');% selected string index
4303if param.index_fields>1
4304    param.index_fields=param.index_fields-1;
4305end
4306param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4307param.list_fields_1(1)=[]; %suppress  'image' option
4308param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4309if param.index_fields_1>1
4310    param.index_fields_1=param.index_fields_1-1;
4311end
4312param.menu_coord_str=get(handles.transform_fct,'String');
4313param.menu_coord_val=get(handles.transform_fct,'Value');
4314series(param); %run the series interface
4315
4316%------------------------------------------------------------------------
4317% -- open the GUI civ.fig for civx (PIV)
4318function MenuPIV_Callback(hObject, eventdata, handles)
4319%------------------------------------------------------------------------
4320 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4321 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4322civ(FileName);% interface de civ(not in the uvmat file)
4323
4324%------------------------------------------------------------------------
4325function MenuTools_Callback(hObject, eventdata, handles)
4326%------------------------------------------------------------------------
4327
4328%------------------------------------------------------------------------
4329function MenuEditObject_Callback(hObject, eventdata, handles)
4330%------------------------------------------------------------------------
4331set(handles.edit_object,'Value',1)
4332edit_Callback(hObject, eventdata, handles)
4333
4334%------------------------------------------------------------------------
4335function enable_transform(handles,state)
4336%------------------------------------------------------------------------
4337set(handles.transform_fct,'Visible',state)
4338set(handles.TRANSFORM_txt,'Visible',state)   
4339set(handles.transform_fct,'Visible',state) 
4340set(handles.path_transform,'Visible',state)
4341set(handles.pxcmx_txt,'Visible',state)
4342set(handles.pxcmy_txt,'Visible',state)
4343set(handles.pxcm,'Visible',state)
4344set(handles.pycm,'Visible',state)
4345
4346%------------------------------------------------------------------------
4347function MenuEditVectors_Callback(hObject, eventdata, handles)
4348%------------------------------------------------------------------------
4349set(handles.edit_vect,'Visible','on')
4350set(handles.edit_vect,'Value',1)
4351edit_vect_Callback(hObject, eventdata, handles)
4352
4353% -----------------------------------------------------------------------
4354function Menupoints_Callback(hObject, eventdata, handles)
4355%------------------------------------------------------------------------
4356data.Type='points';
4357data.ProjMode='projection';%default
4358create_object(data,handles)
4359
4360% -----------------------------------------------------------------------
4361function Menuline_Callback(hObject, eventdata, handles)
4362%------------------------------------------------------------------------
4363data.Type='line';
4364data.ProjMode='projection';%default
4365create_object(data,handles)
4366
4367%------------------------------------------------------------------------
4368function Menupolyline_Callback(hObject, eventdata, handles)
4369%------------------------------------------------------------------------
4370data.Type='polyline';
4371data.ProjMode='projection';%default
4372create_object(data,handles)
4373
4374%------------------------------------------------------------------------
4375function Menupolygon_Callback(hObject, eventdata, handles)
4376%------------------------------------------------------------------------
4377data.Type='polygon';
4378data.ProjMode='inside';%default
4379create_object(data,handles)
4380
4381%------------------------------------------------------------------------
4382function Menurectangle_Callback(hObject, eventdata, handles)
4383%------------------------------------------------------------------------
4384data.Type='rectangle';
4385data.ProjMode='inside';%default
4386create_object(data,handles)
4387
4388%------------------------------------------------------------------------
4389function Menuellipse_Callback(hObject, eventdata, handles)
4390%------------------------------------------------------------------------
4391data.Type='ellipse';
4392data.ProjMode='inside';%default
4393create_object(data,handles)
4394
4395%------------------------------------------------------------------------
4396function MenuMaskObject_Callback(hObject, eventdata, handles)
4397%------------------------------------------------------------------------
4398data.Type='polygon';
4399data.TypeMenu={'polygon'};
4400data.ProjMode='mask_inside';%default
4401data.ProjMenu={'mask_inside';'mask_outside'};
4402create_object(data,handles)
4403
4404%------------------------------------------------------------------------
4405function Menuplane_Callback(hObject, eventdata, handles)
4406%------------------------------------------------------------------------
4407data.Type='plane';
4408data.ProjMode='projection';%default
4409
4410create_object(data,handles)
4411
4412%------------------------------------------------------------------------
4413function Menuvolume_Callback(hObject, eventdata, handles)
4414%------------------------------------------------------------------------
4415data.Type='volume';
4416data.ProjMode='interp';%default
4417% set(handles.create,'Visible','on')
4418% set(handles.create,'Value',1)
4419% VOLUME_Callback(hObject,eventdata,handles)
4420create_object(data,handles)
4421
4422%------------------------------------------------------------------------
4423function MenuBrowseObject_Callback(hObject, eventdata, handles)
4424%------------------------------------------------------------------------
4425%get the object file
4426[FileName, PathName, filterindex] = uigetfile( ...
4427       {'*.xml;*.mat', ' (*.xml,*.mat)';
4428       '*.xml',  '.xml files '; ...
4429        '*.mat',  '.mat matlab files '}, ...
4430        'Pick an xml Object file',get(handles.RootPath,'String'));
4431fileinput=[PathName FileName];%complete file name
4432sizf=size(fileinput);
4433if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4434
4435%read the file
4436% t=xmltree(fileinput);
4437% data=convert(t);
4438data=xml2struct(fileinput);
4439data.enable_plot=1;
4440[pp,data.Name]=fileparts(FileName);
4441%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4442hset_object=findobj(allchild(0),'tag','set_object');
4443if ~isempty(hset_object)
4444    delete(hset_object)% delete existing version of set_object
4445end
4446set_object(data);% call the set_object interface
4447set(handles.edit_object,'Value',0); %suppress the object edit mode
4448set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4449set(handles.MenuObject,'checked','on')
4450set(handles.delete_object,'Visible','on')
4451
4452%------------------------------------------------------------------------
4453% --- generic function used for the creation of a projection object
4454function create_object(data,handles)
4455%------------------------------------------------------------------------
4456hset_object=findobj(allchild(0),'tag','set_object');
4457if ~isempty(hset_object)
4458    delete(hset_object)% delete existing version of set_object
4459end
4460hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4461if ishandle(hgeometry_calib)
4462    hhgeometry_calib=guidata(hgeometry_calib);
4463    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4464    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4465end
4466UvData=get(handles.uvmat,'UserData');
4467set(handles.edit_object,'Value',0); %suppress the object edit mode
4468set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4469data.enable_plot=1;
4470transform_list=get(handles.transform_fct,'String');
4471val=get(handles.transform_fct,'Value');
4472%data.CoordType=transform_list{val};
4473data.Coord=[0 0]; %default
4474if isfield(UvData,'Field')
4475    Field=UvData.Field;
4476    if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
4477        data.RangeX=Field.Mesh;
4478        data.RangeY=Field.Mesh;
4479        data.DX=Field.Mesh;
4480        data.DY=Field.Mesh;
4481    elseif isfield(Field,'AX')&& isfield(Field,'AY')&& isfield(Field,'A')%only image
4482        np=size(Field.A);
4483        meshx=(Field.AX(end)-Field.AX(1))/np(2);
4484        meshy=abs(Field.AY(end)-Field.AY(1))/np(1);
4485        data.RangeY=max(meshx,meshy);
4486        data.RangeX=max(meshx,meshy);
4487        data.DX=max(meshx,meshy);
4488    end
4489    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4490         data.Coord=[0 0 0]; %default
4491    end
4492    if isfield(Field,'CoordUnit')
4493        data.CoordUnit=Field.CoordUnit;
4494    end
4495end
4496% if isfield(data,'Type') && isequal(data.Type,'line')
4497%     if isfield(data,'DX')
4498%         data.Coord=[[0 0 0];[data.DX 0 0]]; %default
4499%     else
4500%         data.Coord=[[0 0 0];[1 0 0]]; %default
4501%     end
4502% end
4503if ishandle(handles.UVMAT_title)
4504    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4505end
4506%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4507set_object(data,handles);% call the set_object interface
4508set(handles.MenuObject,'checked','on')
4509set(handles.uvmat,'UserData',UvData)
4510set(handles.CheckZoom,'Value',0)
4511CheckZoom_Callback(handles.uvmat, [], handles)
4512set(handles.delete_object,'Visible','on')
4513% set(handles._title,'Visible','on')
4514% set(handles.view_field_title,'Visible','on')
4515
4516%------------------------------------------------------------------------
4517function MenuRuler_Callback(hObject, eventdata, handles)
4518%------------------------------------------------------------------------
4519set(handles.CheckZoom,'Value',0)
4520CheckZoom_Callback(handles.uvmat, [], handles)
4521set(handles.MenuRuler,'checked','on')
4522UvData=get(handles.uvmat,'UserData');
4523UvData.MouseAction='ruler';
4524set(handles.uvmat,'UserData',UvData);
4525
4526%------------------------------------------------------------------------
4527% --- executed when closing: set the parent interface button to value 0
4528function closefcn(gcbo,eventdata)
4529%------------------------------------------------------------------------
4530%delete all the associated figures if exist
4531hh=findobj(allchild(0),'tag','view_field');
4532if ~isempty(hh)
4533    delete(hh)
4534end
4535hh=findobj(allchild(0),'tag','geometry_calib');
4536if ~isempty(hh)
4537    delete(hh)
4538end
4539hh=findobj(allchild(0),'tag','set_object');
4540if ~isempty(hh)
4541    hhh=findobj(hh,'tag','PLOT');
4542    set(hhh,'enable','off')
4543end
4544
4545%------------------------------------------------------------------------
4546% --- Executes on button press in delete_object.
4547function delete_object_Callback(hObject, eventdata, handles)
4548%------------------------------------------------------------------------
4549IndexObj=get(handles.ListObject,'Value');
4550if IndexObj(end)>1
4551    delete_object(IndexObj(end))
4552end
4553
4554% --- Executes on button press in FixVelType.
4555function FixVelType_Callback(hObject, eventdata, handles)
4556val=get(handles.FixVelType,'Value');
4557if ~val
4558    run0_Callback(hObject, eventdata, handles)
4559end
4560
4561% --- Executes on button press in ViewObject.
4562function ViewObject_Callback(hObject, eventdata, handles)
4563IndexObj=get(handles.ListObject,'Value');
4564IndexObj=IndexObj(end); %keeps only the secodn value
4565UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4566if numel(UvData.Object)<IndexObj;% error in UvData
4567    msgbox_uvmat('ERROR','invalid object list')
4568    return
4569end
4570ObjectData=UvData.Object{IndexObj};
4571ZBounds=0; % default
4572if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4573    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4574    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4575end
4576hset_object=findobj(allchild(0),'tag','set_object');
4577if ~isempty(hset_object)
4578    delete(hset_object)% delete existing version of set_object
4579end
4580hset_object=set_object(ObjectData,[],ZBounds);
4581
4582
4583function NomType_Callback(hObject, eventdata, handles)
4584
4585
4586function NomType_1_Callback(hObject, eventdata, handles)
4587
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