source: trunk/src/uvmat.m @ 360

Last change on this file since 360 was 360, checked in by sommeria, 9 years ago

civ: bugs corrected. Iintroduction of an xm file for parameters read using the new fct fill_GUI (to test and improve)
cleaning in uvmat. Possibility of using blank increment added (go to the next available file)
fullfile_uvmat: case of two equal indices in a pair, bug repair.
find_fileseries: improved speed.

File size: 196.4 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.Style=...: 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[tild,SubDir,tild,i1,i2,j1,j2,FileExt]=fileparts_uvmat(fileinput);
512% detect the file type, get the movie object if relevant, and look for the corresponding file series:
513[RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject]=find_file_series(fileinput);
514if strcmp(NomType,'*')% movies will be opened at the first frame
515    i1=1;
516    i2=[];
517    j1=[];
518    j2=[];
519end 
520
521%% open the file or fill the GUI uvmat according to the detected file type
522switch FileType
523    case ''
524        msgbox_uvmat('ERROR','invalid input file type')
525    case 'txt'
526        edit(fileinput)
527    case 'figure'                           %display matlab figure
528        hfig=open(fileinput);
529        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
530        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
531        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
532    case {'xml','xls'}                % edit xml or Excel files
533        editxml(fileinput);
534    otherwise
535        set(handles_RootPath,'String',RootPath);
536        rootname=fullfile(RootPath,SubDir,RootFile);
537        set(handles_SubDir,'String',['/' SubDir]);
538        set(handles_RootFile,'String',['/' RootFile]); %display the separator
539        indices=fileinput(length(rootname)+1:end);
540        indices(end-length(FileExt)+1:end)=[]; %remove extension
541        set(handles_FileIndex,'String',indices);
542        set(handles_NomType,'String',NomType);
543        set(handles_FileExt,'String',FileExt);
544        if index==1
545            % fill file index counters if the first file series is opened
546            set(handles.i1,'String',num2str(i1));
547            set(handles.i2,'String',num2str(i2));
548            set(handles.j1,'String',num2stra(j1,NomType));
549            set(handles.j2,'String',num2stra(j2,NomType));
550        else %read the current field index if the second file series is opened
551            i1=str2num(get(handles.i1,'String'));
552            i2=str2num(get(handles.i2,'String'));
553            j1=stra2num(get(handles.j1,'String'));
554            j2=stra2num(get(handles.j2,'String'));
555        end
556       
557        % synchronise indices of the second  input file if it exists
558        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
559            Input=read_GUI(handles.InputFile);
560            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
561                Input.RootPath_1=Input.RootPath;
562            end
563            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
564                Input.SubDir_1=Input.SubDir;
565            end
566            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
567                Input.RootFile_1=Input.RootFile;
568            end
569            %updtate the indices of the second field series to correspond to the newly opened one
570            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1,i2,j1,j2);
571            if exist(FileName_1,'file')
572                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
573                set(handles.FileIndex_1,'String',FileIndex_1)
574            else
575                set(handles.SubField,'Value',0)
576                SubField_Callback(hObject, eventdata, handles)
577            end
578        end
579       
580        %enable other menus
581        set(handles.MenuOpen_1,'Enable','on')
582        set(handles.MenuFile_1_1,'Enable','on')
583        set(handles.MenuFile_2_1,'Enable','on')
584        set(handles.MenuFile_3_1,'Enable','on')
585        set(handles.MenuFile_4_1,'Enable','on')
586        set(handles.MenuFile_5_1,'Enable','on')
587        set(handles.MenuExport,'Enable','on')
588        set(handles.MenuExportFigure,'Enable','on')
589        set(handles.MenuExportMovie,'Enable','on')
590        set(handles.MenuTools,'Enable','on')
591        set(handles.OBJECT_txt,'Visible','on')
592        set(handles.edit_object,'Visible','on')
593        set(handles.ListObject,'Visible','on')
594        set(handles.frame_object,'Visible','on')
595       
596        % initiate input file series and refresh the current field view:     
597        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
598
599end
600
601%% set back the mouse pointer to arrow
602set(handles.uvmat,'Pointer','arrow')
603
604%------------------------------------------------------------------------
605% --- Called by action in RootPath edit box
606function RootPath_Callback(hObject,eventdata,handles)
607%------------------------------------------------------------------------
608% read the current input file name:
609[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
610fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
611% detect the file type, get the movie object if relevant, and look for the corresponding file series:
612[RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fileinput);
613% initiate the input file series and refresh the current field view:
614update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject);
615
616%------------------------------------------------------------------------
617% --- Called by action in RootFile edit box
618function SubDir_Callback(hObject, eventdata, handles)
619%------------------------------------------------------------------------
620%refresh the menu of input fields
621Fields_Callback(hObject, eventdata, handles);
622% refresh the current field view
623run0_Callback(hObject, eventdata, handles);
624
625%------------------------------------------------------------------------
626% --- Called by action in RootFile edit box
627function RootFile_Callback(hObject, eventdata, handles)
628%------------------------------------------------------------------------
629RootPath_Callback(hObject,eventdata,handles)
630
631%------------------------------------------------------------------------
632% --- Called by action in FileIndex edit box
633function FileIndex_Callback(hObject, eventdata, handles)
634%------------------------------------------------------------------------
635[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
636set(handles.i1,'String',num2str(i1));
637set(handles.i2,'String',num2str(i2));
638set(handles.j1,'String',num2str(j1));
639set(handles.j2,'String',num2str(j2));
640
641% refresh the current field view
642run0_Callback(hObject, eventdata, handles)
643
644%------------------------------------------------------------------------
645% --- Update information about a new field series (indices to scan, timing,
646%     calibration from an xml file, then refresh current plots
647function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index)
648%------------------------------------------------------------------------
649%% define the relevant handles depending on the index (1=first file series, 2= second file series)
650if ~exist('index','var')
651    index=1;
652end
653if index==1
654    handles_RootPath=handles.RootPath;
655    handles_Fields=handles.Fields;
656elseif index==2
657    handles_RootPath=handles.RootPath_1;
658    handles_Fields=handles.Fields_1;
659end
660
661set(handles_RootPath,'BackgroundColor',[1 1 0])
662drawnow
663set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
664UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
665UvData.NewSeries=1; %flag for run0: begin a new series
666UvData.TestInputFile=1;
667UvData.FileType{index}=FileType;
668UvData.i1_series{index}=i1_series;
669UvData.i2_series{index}=i2_series;
670UvData.j1_series{index}=j1_series;
671UvData.j2_series{index}=j2_series;
672% set(handles.CheckFixPair,'Value',1) % activate by default the comp_input '-'input window
673set(handles.FixVelType,'Value',0); %desactivate fixed veltype
674if index==1
675    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
676else
677    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
678end
679FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
680FileBase=fullfile(RootPath,RootFile);
681if ~exist(FileName,'file')
682   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
683    return
684end
685nbfield=[];%default
686nbfield_j=[];%default
687
688%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
689XmlData.Time=[];%default
690XmlData.GeometryCalib=[];%default
691TimeUnit=[];%default
692testima=0; %test for image input
693imainfo=[];
694ColorType='falsecolor'; %default
695hhh='';
696if isequal(lower(FileExt),'.avi') %.avi file
697    testima=1;
698    imainfo=aviinfo([FileName]);
699    nbfield=imainfo.NumFrames;
700    nbfield_j=1;
701    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
702    XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
703    TimeUnit='s';
704    hhh=which('mmreader');
705    ColorType=imainfo.ImageType;%='truecolor' for color images
706elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
707    testima=1;
708    if ~isequal(SubDir,'')
709       RootFile=get(handles.RootFile,'String');
710        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
711    else
712        imainfo=imfinfo([FileBase FileIndices FileExt]);
713    end
714    ColorType=imainfo.ColorType;%='truecolor' for color images
715    if length(imainfo) >1 %case of image with multiple frames
716        nbfield=length(imainfo);
717        nbfield_j=1;
718    end
719end
720if ~strcmp(hhh,'')% if the function mmreader is found (recent version of matlab)
721    UvData.MovieObject{index}=mmreader([FileBase FileIndices FileExt]);
722else
723    UvData.MovieObject{index}=[];
724end
725if isfield(imainfo,'Width') && isfield(imainfo,'Height')
726    if length(imainfo)>1
727        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
728        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
729    else
730        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
731        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
732    end
733else
734    set(handles.num_Npx,'String','');%fills nbre of pixels x box
735    set(handles.num_Npy,'String','');%fills nbre of pixels x box
736end
737set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
738
739%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
740filexml=[FileBase '.xml'];
741fileciv=[FileBase '.civ'];
742warntext='';%default warning message
743NbSlice=1;%default
744set(handles.RootPath,'BackgroundColor',[1 1 1])
745if exist(filexml,'file')
746    set(handles.view_xml,'Visible','on')
747    set(handles.view_xml,'BackgroundColor',[1 1 0])
748    set(handles.view_xml,'String','view .xml')
749    drawnow
750    [XmlData,warntext]=imadoc2struct(filexml);
751    if ~isempty(warntext)
752        msgbox_uvmat('WARNING',warntext)
753    end
754    if isfield(XmlData,'TimeUnit')
755        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
756            TimeUnit=XmlData.TimeUnit;
757        end
758    end
759    set(handles.view_xml,'BackgroundColor',[1 1 1])
760    drawnow
761    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
762        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
763            set (handles.nb_slice,'String','volume')
764        end
765        hgeometry_calib=findobj('tag','geometry_calib');
766        if ~isempty(hgeometry_calib)
767            GUserData=get(hgeometry_calib,'UserData');
768            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
769                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
770                if strcmp(answer,'Yes')
771                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
772                end
773            end
774        end
775    end 
776elseif exist(fileciv,'file')% if .civ file found
777    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
778    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
779    GeometryCalib.Tx=0;
780    GeometryCalib.Ty=0;
781    GeometryCalib.Tz=1;
782    GeometryCalib.dpx=1;
783    GeometryCalib.dpy=1;
784    GeometryCalib.sx=1;
785    GeometryCalib.Cx=0;
786    GeometryCalib.Cy=0;
787    GeometryCalib.f=1;
788    GeometryCalib.kappa1=0;
789    GeometryCalib.CoordUnit='cm';
790    XmlData.GeometryCalib=GeometryCalib;
791    if error==2, warntext=['no file ' FileBase '.civ'];
792    elseif error==1, warntext='inconsistent number of fields in the .civ file';
793    end 
794    set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
795    set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
796    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
797    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
798    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
799    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
800    set(handles.view_xml,'Visible','on')   
801    set(handles.view_xml,'String','view .civ')
802else
803    set(handles.view_xml,'Visible','off')
804end
805
806%% store last index in handles.lat_i and .last_j
807nbfield=max(max(i2_series));
808if isempty(nbfield)
809    nbfield=max(max(i1_series));
810end
811nbfield_j=max(max(j2_series));
812if isempty(nbfield_j)
813    nbfield_j=max(max(j1_series));
814end
815if ~isempty(XmlData.Time)
816    nbfield=size(XmlData.Time,1);
817    nbfield_j=size(XmlData.Time,2);
818    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
819    if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
820        NomType=get(handles.NomType,'String');
821        if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
822            XmlData.Time=(XmlData.Time)';
823            nbfield=nbfield_j;
824            nbfield_j=1;
825        end
826    end
827end
828last_i_cell=get(handles.last_i,'String');
829if isempty(nbfield)
830    last_i_cell{1}='';
831else
832    last_i_cell{1}=num2str(nbfield);
833end
834set(handles.last_i,'String',last_i_cell)
835last_j_cell=get(handles.last_j,'String');
836if isempty(nbfield_j)
837     last_j_cell{1}='';
838else
839     last_j_cell{1}=num2str(nbfield_j);
840end
841set(handles.last_j,'String',last_j_cell);
842
843%% store geometric calibration in UvData
844if isfield(XmlData,'GeometryCalib')
845    GeometryCalib=XmlData.GeometryCalib;
846    if isempty(GeometryCalib)
847        set(handles.pxcm,'String','')
848        set(handles.pycm,'String','')
849        set(handles.transform_fct,'Value',1); %  no transform by default
850    else
851        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
852            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
853            set(handles.pxcm,'String','var')
854            set(handles.pycm,'String','var')
855        elseif isfield(GeometryCalib,'fx_fy')
856            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
857            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
858            set(handles.pxcm,'String',num2str(pixcmx))
859            set(handles.pycm,'String',num2str(pixcmy))
860        end
861        if ~get(handles.CheckFixLimits,'Value')
862            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
863        end
864        if isfield(GeometryCalib,'SliceCoord')
865           
866           siz=size(GeometryCalib.SliceCoord);
867           if siz(1)>1
868               NbSlice=siz(1);
869               set(handles.slices,'Visible','on')
870               set(handles.slices,'Value',1)
871           end
872           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
873               set(handles.nb_slice,'String','volume')
874           else
875               set(handles.nb_slice,'String',num2str(NbSlice))
876           end
877           slices_Callback([],[], handles)
878        end           
879    end
880end
881
882%% update the data attached to the uvmat interface
883if ~isempty(TimeUnit)
884    set(handles.time_txt,'String',['time (' TimeUnit ')'])
885end
886UvData.TimeUnit=TimeUnit;
887UvData.XmlData{index}=XmlData;
888UvData.NewSeries=1;
889% UvData.MovieObject=MovieObject;
890
891%display warning message
892if ~isequal(warntext,'')
893    msgbox_uvmat('WARNING',warntext);
894end
895
896%% set default options in menu 'Fields'
897if ~testima
898    testcivx=0;
899    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
900        set(handles_Fields,'Value',1)
901        set(handles_Fields,'String',{'get_field...'})
902        UvData=rmfield(UvData,'FieldsString');
903    else
904        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
905        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
906            FieldList=calc_field;
907            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
908            set(handles_Fields,'Value',2) % set menu to 'velocity'
909            col_vec=FieldList;
910            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
911            testcivx=1;
912        end
913        if ~testcivx
914            set(handles_Fields,'Value',1) % set menu to 'get_field...
915            set(handles_Fields,'String',{'get_field...'})
916            col_vec={'get_field...'};
917        end
918        set(handles.ListColorScalar,'String',col_vec)
919    end
920end
921set(handles.uvmat,'UserData',UvData)
922
923%% set index navigation options and refresh plots
924scan_option='i';%default
925state_j='off'; %default
926if index==2
927    if get(handles.scan_j,'Value')
928        scan_option='j'; %keep the scan option for the second fiel series
929    end
930    if strcmp(get(handles.j1,'Visible'),'on')
931        state_j='on';
932    end
933end
934if ~isempty(j1_series)
935        state_j='on';
936        if isequal(nbfield,1) &&index==1
937            scan_option='j'; %scan j index by default if nbfield=1               
938        end
939end
940if isequal(scan_option,'i')
941     set(handles.scan_i,'Value',1)
942     scan_i_Callback([],[], handles);
943else
944     set(handles.scan_j,'Value',1)
945     scan_j_Callback([],[], handles);
946end
947set(handles.scan_j,'Visible',state_j)
948set(handles.j1,'Visible',state_j)
949set(handles.j2,'Visible',state_j)
950set(handles.last_j,'Visible',state_j);
951set(handles.frame_j,'Visible',state_j);
952set(handles.j_text,'Visible',state_j);
953if ~isempty(i2_series)||~isempty(j2_series)
954    set(handles.CheckFixPair,'Visible','on')
955elseif index==1
956    set(handles.CheckFixPair,'Visible','off')
957end
958
959%% view the field 
960run0_Callback([],[], handles); %view field
961mask_test=get(handles.CheckMask,'value');
962if mask_test
963    MaskData=get(handles.CheckMask,'UserData');
964    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
965          delete(MaskData.maskhandle)    %delete old mask
966    end
967    CheckMask_Callback([],[],handles)
968end
969
970%% update list of recent files in the menubar
971MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
972    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
973str_find=strcmp(FileName,MenuFile);
974if isempty(find(str_find,1))
975    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
976end
977for ifile=1:min(length(MenuFile),5)
978    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
979    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
980end
981dir_perso=prefdir;
982profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
983if exist(profil_perso,'file')
984    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
985else
986    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
987end
988
989
990%------------------------------------------------------------------------
991% --- Executes on the menu Open/Browse_1 for the second input field,
992%     search the files, recognize their type according to their name and fill the rootfile input windows
993function MenuBrowse_1_Callback(hObject, eventdata, handles)
994%------------------------------------------------------------------------
995% huvmat=get(handles.run0,'parent');
996UvData=get(handles.uvmat,'UserData');
997
998RootPath=get(handles.RootPath,'String');
999[FileName, PathName, filterindex] = uigetfile( ...
1000       {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
1001       '*.xml',  '.xml files '; ...
1002        '*.xls',  '.xls files '; ...
1003        '*.civ',  '.civ files '; ...
1004        '*.jpg','.jpg image files'; ...
1005        '*.png','.png image files'; ...
1006        '*.avi;*.AVI','.avi movie files'; ...
1007        '*.nc','.netcdf files'; ...
1008        '*.cdf','.netcdf files'; ...
1009        '*.cmx','.cmx text files';...
1010        '*.cmx2','.cmx2 text files';...
1011        '*.fig','.fig files (matlab fig)';...
1012        '*.log','.log text files ';...
1013        '*.dat','.dat text files ';...
1014        '*.*',  'All Files (*.*)'}, ...
1015        'Pick a second file for comparison',RootPath);
1016fileinput_1=[PathName FileName];%complete file name
1017sizf=size(fileinput_1);
1018if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
1019
1020% refresh the current displayed field
1021set(handles.SubField,'Value',1)
1022display_file_name(hObject,eventdata,handles,fileinput_1,2)
1023
1024%update list of recent files in the menubar
1025MenuFile_1=fileinput_1;
1026MenuFile_2=get(handles.MenuFile_1,'Label');
1027MenuFile_3=get(handles.MenuFile_2,'Label');
1028MenuFile_4=get(handles.MenuFile_3,'Label');
1029MenuFile_5=get(handles.MenuFile_4,'Label');
1030set(handles.MenuFile_1,'Label',MenuFile_1)
1031set(handles.MenuFile_2,'Label',MenuFile_2)
1032set(handles.MenuFile_3,'Label',MenuFile_3)
1033set(handles.MenuFile_4,'Label',MenuFile_4)
1034set(handles.MenuFile_5,'Label',MenuFile_5)
1035set(handles.MenuFile_1_1,'Label',MenuFile_1)
1036set(handles.MenuFile_2_1,'Label',MenuFile_2)
1037set(handles.MenuFile_3_1,'Label',MenuFile_3)
1038set(handles.MenuFile_4_1,'Label',MenuFile_4)
1039set(handles.MenuFile_5_1,'Label',MenuFile_5)
1040dir_perso=prefdir;
1041profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1042if exist(profil_perso,'file')
1043    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
1044else
1045    txt=ver('MATLAB');
1046    Release=txt.Release;
1047    relnumb=str2double(Release(3:4));
1048    if relnumb >= 14
1049        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
1050    else
1051        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
1052    end
1053end
1054
1055% -----------------------------------------------------------------------
1056% --- Open again as second field the file whose name has been recorded in MenuFile_1
1057function MenuFile_1_1_Callback(hObject, eventdata, handles)
1058% -----------------------------------------------------------------------
1059fileinput_1=get(handles.MenuFile_1_1,'Label');
1060set(handles.SubField,'Value',1)
1061display_file_name(hObject,eventdata,handles,fileinput_1,2)
1062
1063% -----------------------------------------------------------------------
1064% --- Open again as second field the file whose name has been recorded in MenuFile_2
1065function MenuFile_2_1_Callback(hObject, eventdata, handles)
1066% -----------------------------------------------------------------------
1067fileinput_1=get(handles.MenuFile_2_1,'Label');
1068set(handles.SubField,'Value',1)
1069display_file_name(hObject,eventdata,handles,fileinput_1,2)
1070
1071% -----------------------------------------------------------------------
1072% --- Open again as second field the file whose name has been recorded in MenuFile_3
1073function MenuFile_3_1_Callback(hObject, eventdata, handles)
1074% -----------------------------------------------------------------------
1075fileinput_1=get(handles.MenuFile_3_1,'Label');
1076set(handles.SubField,'Value',1)
1077display_file_name(hObject,eventdata,handles,fileinput_1,2)
1078
1079% -----------------------------------------------------------------------
1080% --- Open again as second field the file whose name has been recorded in MenuFile_4
1081function MenuFile_4_1_Callback(hObject, eventdata, handles)
1082% -----------------------------------------------------------------------
1083fileinput_1=get(handles.MenuFile_4_1,'Label');
1084set(handles.SubField,'Value',1)
1085display_file_name(hObject,eventdata,handles,fileinput_1,2)
1086
1087% -----------------------------------------------------------------------
1088% --- Open again as second field the file whose name has been recorded in MenuFile_5
1089function MenuFile_5_1_Callback(hObject, eventdata, handles)
1090% -----------------------------------------------------------------------
1091fileinput_1=get(handles.MenuFile_5_1,'Label');
1092set(handles.SubField,'Value',1)
1093display_file_name(hObject,eventdata,handles,fileinput_1,2)
1094
1095%-----------------------------------------------------------------------
1096% --- Called by action in RootPath_1 edit box
1097function RootPath_1_Callback(hObject,eventdata,handles)
1098% -----------------------------------------------------------------------
1099% update_rootinfo_1(hObject,eventdata,handles)
1100[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
1101fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1102% detect the file type, get the movie object if relevant, and look for the corresponding file series:
1103[tild,tild,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fileinput);
1104% initiate the input file series and refresh the current field view:
1105update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
1106%-----------------------------------------------------------------------
1107% --- Called by action in RootFile_1 edit box
1108function RootFile_1_Callback(hObject, eventdata, handles)
1109% -----------------------------------------------------------------------
1110RootPath_1_Callback(hObject,eventdata,handles)
1111
1112%------------------------------------------------------------------------
1113% --- Called by action in FileIndex_1 edit box
1114function FileIndex_1_Callback(hObject, eventdata, handles)
1115%------------------------------------------------------------------------
1116run0_Callback(hObject, eventdata, handles)
1117
1118%------------------------------------------------------------------------
1119% --- switch file index scanning options scan_i and scan_j in an exclusive way
1120function scan_i_Callback(hObject, eventdata, handles)
1121%------------------------------------------------------------------------
1122if get(handles.scan_i,'Value')==1
1123    set(handles.scan_i,'BackgroundColor',[1 1 0])
1124    set(handles.scan_j,'Value',0)
1125else
1126    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1127    set(handles.scan_j,'Value',1)
1128end
1129scan_j_Callback(hObject, eventdata, handles)
1130
1131%------------------------------------------------------------------------
1132% --- switch file index scanning options scan_i and scan_j in an exclusive way
1133function scan_j_Callback(hObject, eventdata, handles)
1134%------------------------------------------------------------------------
1135if get(handles.scan_j,'Value')==1
1136    set(handles.scan_j,'BackgroundColor',[1 1 0])
1137    set(handles.scan_i,'Value',0)
1138    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1139%     NomType=get(handles.NomType,'String');
1140%     switch NomType
1141%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1142%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1143%     otherwise
1144%         set(handles.CheckFixPair,'Visible','off')
1145%     end
1146else
1147    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1148    set(handles.scan_i,'Value',1)
1149    set(handles.scan_i,'BackgroundColor',[1 1 0])
1150    set(handles.CheckFixPair,'Visible','off')
1151end
1152
1153%------------------------------------------------------------------------
1154function i1_Callback(hObject, eventdata, handles)
1155%------------------------------------------------------------------------
1156set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1157NomType=get(handles.NomType,'String');
1158i1=stra2num(get(handles.i1,'String'));
1159i2=stra2num(get(handles.i2,'String'));
1160j1=stra2num(get(handles.j1,'String'));
1161j2=stra2num(get(handles.j2,'String'));
1162indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1163%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1164set(handles.FileIndex,'String',indices)
1165set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1166if get(handles.SubField,'Value')==1
1167    NomType_1=get(handles.NomType_1,'String');
1168    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1169     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1170     set(handles.FileIndex_1,'String',indices)
1171     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1172end
1173
1174%------------------------------------------------------------------------
1175function i2_Callback(hObject, eventdata, handles)
1176%------------------------------------------------------------------------
1177set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1178i1_Callback(hObject, eventdata, handles)
1179
1180%------------------------------------------------------------------------
1181function j1_Callback(hObject, eventdata, handles)
1182%------------------------------------------------------------------------
1183set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1184i1_Callback(hObject, eventdata, handles)
1185
1186%------------------------------------------------------------------------
1187function j2_Callback(hObject, eventdata, handles)
1188%------------------------------------------------------------------------
1189set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1190i1_Callback(hObject, eventdata, handles)
1191
1192%------------------------------------------------------------------------
1193function slices_Callback(hObject, eventdata, handles)
1194%------------------------------------------------------------------------
1195if get(handles.slices,'Value')==1
1196    set(handles.slices,'BackgroundColor',[1 1 0])
1197    set(handles.nb_slice,'Visible','on')
1198    set(handles.z_text,'Visible','on')
1199    set(handles.z_index,'Visible','on')
1200    nb_slice_Callback(hObject, eventdata, handles)
1201else
1202    set(handles.nb_slice,'Visible','off')
1203    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1204    set(handles.z_text,'Visible','off')
1205    set(handles.z_index,'Visible','off')
1206    set(handles.masklevel,'Value',1)
1207    set(handles.masklevel,'String',{'1'})
1208end
1209
1210%------------------------------------------------------------------------
1211function nb_slice_Callback(hObject, eventdata, handles)
1212%------------------------------------------------------------------------
1213nb_slice_str=get(handles.nb_slice,'String');
1214if isequal(nb_slice_str,'volume')
1215    num=stra2num(get(handles.j1,'String'));
1216    last_j=get(handles.last_j,'String');
1217    nbslice=str2double(last_j{1});
1218else
1219    num=str2double(get(handles.i1,'String'));
1220    nbslice=str2double(get(handles.nb_slice,'String'));
1221end
1222z=mod(num-1,nbslice)+1;
1223set(handles.z_index,'String',num2str(z))
1224for ilist=1:nbslice
1225    list_index{ilist,1}=num2str(ilist);
1226end   
1227set(handles.masklevel,'String',list_index)
1228set(handles.masklevel,'Value',z)
1229
1230%------------------------------------------------------------------------
1231% --- Executes on button press in view_xml.
1232function view_xml_Callback(hObject, eventdata, handles)
1233%------------------------------------------------------------------------
1234%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1235 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1236FileBase=fullfile(RootPath,RootFile);
1237option=get(handles.view_xml,'String');
1238if isequal(option,'view .xml')
1239    FileXml=[FileBase '.xml'];
1240    heditxml=editxml(FileXml);
1241end
1242
1243%------------------------------------------------------------------------
1244% --- Executes on button press in CheckMask.
1245function CheckMask_Callback(hObject, eventdata, handles)
1246%------------------------------------------------------------------------
1247%case of view mask selection
1248if isequal(get(handles.CheckMask,'Value'),1)
1249   % [FF,RootPath,FileBase]=read_file_boxes(handles);
1250     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1251     FileBase=fullfile(RootPath,RootFile);
1252    num_i1=stra2num(get(handles.i1,'String'));
1253    num_j1=stra2num(get(handles.j1,'String'));
1254    currentdir=pwd; 
1255    cd(RootPath);
1256    maskfiles=dir('*_*mask_*.png');%look for a mask file
1257    cd(currentdir);%come back to the working directory
1258    mdetect=0;
1259    if ~isempty(maskfiles)
1260        for ilist=1:length(maskfiles)
1261            maskname=maskfiles(ilist).name;% take the first mask file in the list
1262            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1263%             [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1264             [tild,Name]=fileparts(maskname);
1265            Namedouble=double(Name);
1266            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1267            ind_mask=findstr('mask',Name);
1268            i=ind_mask-1;
1269            while val(i)==0 && i>0
1270                i=i-1;
1271            end
1272            nbmask_str=str2num(Name(i+1:ind_mask-1));
1273            if ~isempty(nbmask_str)
1274                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1275            end
1276        end
1277        if isequal(min(nbslice),max(nbslice))
1278            nbslice=nbslice(1);
1279        else
1280            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1281            return
1282        end
1283        if ~isempty(nbslice) && Name(i)=='_'
1284            Mask.Base=[FileBase Name(i:ind_mask+3)];
1285            Mask.NbSlice=nbslice;
1286            num_i1=mod(num_i1-1,nbslice)+1;
1287            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1288            [RootPath,RootFile]=fileparts(Mask.Base);
1289            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1290            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1291            mdetect=exist(maskname,'file');
1292            if mdetect
1293                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1294                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1295                set(handles.CheckMask,'UserData',Mask);
1296                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1297                if nbslice > 1
1298                    set(handles.slices,'value',1)
1299                    slices_Callback(hObject, eventdata, handles)
1300                end
1301            end
1302        end
1303    end
1304    errormsg=[];%default
1305    if mdetect==0
1306        [FileName, PathName, filterindex] = uigetfile( ...
1307            {'*.png', ' (*.png)';
1308            '*.png',  '.png files '; ...
1309            '*.*', 'All Files (*.*)'}, ...
1310            'Pick a mask file *.png',FileBase);
1311        maskname=fullfile(PathName,FileName);
1312        if ~exist(maskname,'file')
1313            errormsg='no file browsed';
1314        end
1315        [RootDir,tild,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1316%         [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1317        Mask.Base=fullfile(RootDir,RootFile);
1318        Mask.NbSlice=1;
1319        set(handles.CheckMask,'UserData',Mask);
1320        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1321    end
1322    if isempty(errormsg)
1323        errormsg=update_mask(handles,num_i1,num_j1);
1324    end
1325    if ~isempty(errormsg)
1326            set(handles.CheckMask,'Value',0)
1327            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1328     end
1329else % desactivate mask display
1330    MaskData=get(handles.CheckMask,'UserData');
1331    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1332          delete(MaskData.maskhandle)   
1333    end
1334    set(handles.CheckMask,'UserData',[])   
1335    UvData=get(handles.uvmat,'UserData');
1336    if isfield(UvData,'MaskName')
1337        UvData=rmfield(UvData,'MaskName');
1338        set(handles.uvmat,'UserData',UvData)
1339    end
1340    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1341end
1342
1343%------------------------------------------------------------------------
1344function errormsg=update_mask(handles,num_i1,num_j1)
1345%------------------------------------------------------------------------
1346errormsg=[];%default
1347MaskData=get(handles.CheckMask,'UserData');
1348if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1349    uistack(MaskData.maskhandle,'top');
1350end
1351num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1352[RootPath,RootFile]=fileparts(MaskData.Base);
1353MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1354%MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1355huvmat=get(handles.CheckMask,'parent');
1356UvData=get(huvmat,'UserData');
1357
1358%update mask image if the mask is new
1359if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1360    UvData.MaskName=MaskName; %update the recorded name on UvData
1361    set(huvmat,'UserData',UvData);
1362    if ~exist(MaskName,'file')
1363        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1364            delete(MaskData.maskhandle)   
1365        end
1366    else
1367        %read mask image
1368        Mask.AName='image';
1369        Mask.A=imread(MaskName);
1370        npxy=size(Mask.A);
1371        test_error=0;
1372        if length(npxy)>2
1373            errormsg=[MaskName ' is not a grey scale image'];
1374            return
1375        elseif ~isa(Mask.A,'uint8')
1376            errormsg=[MaskName ' is not a 8 bit grey level image'];
1377            return
1378        end
1379        Mask.AX=[0.5 npxy(2)-0.5];
1380        Mask.AY=[npxy(1)-0.5 0.5 ];
1381        Mask.CoordUnit='pixel';
1382        if isequal(get(handles.slices,'Value'),1)
1383           NbSlice=str2num(get(handles.nb_slice,'String'));
1384           num_i1=str2num(get(handles.i1,'String'));
1385           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1386        end
1387        %px to phys or other transform on field
1388         menu_transform=get(handles.transform_fct,'String');
1389        choice_value=get(handles.transform_fct,'Value');
1390        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1391        transform_list=get(handles.transform_fct,'UserData');
1392        transform=transform_list{choice_value};
1393        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1394            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1395                Calib=UvData.XmlData{1}.GeometryCalib;
1396                Mask=transform(Mask,UvData.XmlData{1});
1397            end
1398        end
1399        flagmask=Mask.A < 200;
1400       
1401        %make brown color image
1402        imflag(:,:,1)=0.9*flagmask;
1403        imflag(:,:,2)=0.7*flagmask;
1404        imflag(:,:,3)=zeros(size(flagmask));
1405       
1406        %update mask image
1407        hmask=[]; %default
1408        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1409            hmask=MaskData.maskhandle;
1410        end
1411        if ~isempty(hmask)
1412            set(hmask,'CData',imflag)   
1413            set(hmask,'AlphaData',flagmask*0.6)
1414            set(hmask,'XData',Mask.AX);
1415            set(hmask,'YData',Mask.AY);
1416%             uistack(hmask,'top')
1417        else
1418            axes(handles.axes3)
1419            hold on   
1420            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1421%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1422            set(handles.CheckMask,'UserData',MaskData)
1423        end
1424    end
1425end
1426
1427
1428%------------------------------------------------------------------------
1429function MenuExportFigure_Callback(hObject, eventdata, handles)
1430%------------------------------------------------------------------------
1431huvmat=get(handles.MenuExport,'parent');
1432hfig=figure;
1433copyobj(handles.axes3,hfig);
1434map=colormap(handles.axes3);
1435colormap(map);%transmit the current colormap to the zoom fig
1436colorbar
1437
1438%------------------------------------------------------------------------
1439%------------------------------------------------------------------------
1440% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1441%------------------------------------------------------------------------
1442
1443%------------------------------------------------------------------------
1444% --- Executes on button press in runplus: make one step forward and call
1445% --- run0. The step forward is along the fields series 1 or 2 depending on
1446% --- the scan_i and scan_j check box (exclusive each other)
1447function runplus_Callback(hObject, eventdata, handles)
1448%------------------------------------------------------------------------
1449set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1450drawnow
1451%TODO: introduce the option: increment ='*' to move to the next available view
1452increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1453% if isnan(increment)
1454%     set(handles.increment_scan,'String','1')%default value
1455%     increment=1;
1456% end
1457errormsg=runpm(hObject,eventdata,handles,increment);
1458if ~isempty(errormsg)
1459    msgbox_uvmat('ERROR',errormsg);
1460end
1461set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1462
1463%------------------------------------------------------------------------
1464% --- Executes on button press in runmin: make one step backward and call
1465% --- run0. The step backward is along the fields series 1 or 2 depending on
1466% --- the scan_i and scan_j check box (exclusive each other)
1467function runmin_Callback(hObject, eventdata, handles)
1468%------------------------------------------------------------------------
1469set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1470drawnow
1471increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1472% if isnan(increment)
1473%     set(handles.increment_scan,'String','1')%default value
1474%     increment=1;
1475% end
1476errormsg=runpm(hObject,eventdata,handles,increment);
1477if ~isempty(errormsg)
1478    msgbox_uvmat('ERROR',errormsg);
1479end
1480set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1481
1482%------------------------------------------------------------------------
1483% -- Executes on button press in Movie: make a series of +> steps
1484function Movie_Callback(hObject, eventdata, handles)
1485%------------------------------------------------------------------------
1486set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1487drawnow
1488increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1489% if isnan(increment)
1490%     set(handles.increment_scan,'String','1')%default value
1491%     increment=1;
1492% end
1493set(handles.STOP,'Visible','on')
1494set(handles.speed,'Visible','on')
1495set(handles.speed_txt,'Visible','on')
1496set(handles.Movie,'BusyAction','queue')
1497UvData=get(handles.uvmat,'UserData');
1498
1499while get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1500        errormsg=runpm(hObject,eventdata,handles,increment);
1501        if ~isempty(errormsg)
1502            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1503            return
1504        end
1505        pause(1.02-get(handles.speed,'Value'))% wait for next image
1506end
1507if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1508    UvData.aviobj=close(UvData.aviobj);
1509   set(handles.uvmat,'UserData',UvData);
1510end
1511set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1512
1513%------------------------------------------------------------------------
1514% -- Executes on button press in Movie: make a series of <- steps
1515function MovieBackward_Callback(hObject, eventdata, handles)
1516%------------------------------------------------------------------------
1517set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1518drawnow
1519increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1520set(handles.STOP,'Visible','on')
1521set(handles.speed,'Visible','on')
1522set(handles.speed_txt,'Visible','on')
1523set(handles.MovieBackward,'BusyAction','queue')
1524UvData=get(handles.uvmat,'UserData');
1525
1526while get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1527        errormsg=runpm(hObject,eventdata,handles,increment);
1528        if ~isempty(errormsg)
1529            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1530            return
1531        end
1532        pause(1.02-get(handles.speed,'Value'))% wait for next image
1533end
1534if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1535    UvData.aviobj=close(UvData.aviobj);
1536   set(handles.uvmat,'UserData',UvData);
1537end
1538set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1539
1540%------------------------------------------------------------------------
1541function STOP_Callback(hObject, eventdata, handles)
1542%------------------------------------------------------------------------
1543set(handles.movie_pair,'BusyAction','Cancel')
1544set(handles.movie_pair,'value',0)
1545set(handles.Movie,'BusyAction','Cancel')
1546set(handles.MovieBackward,'BusyAction','Cancel')
1547set(handles.MenuExportMovie,'BusyAction','Cancel')
1548set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1549set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1550set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1551
1552%------------------------------------------------------------------------
1553% --- function activated by runplus and run minus
1554function errormsg=runpm(hObject,eventdata,handles,increment)
1555%------------------------------------------------------------------------
1556errormsg='';%default
1557%% check for movie pair status
1558movie_status=get(handles.movie_pair,'Value');
1559if isequal(movie_status,1)
1560    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1561end
1562
1563%% read the current input file name(s) and field indices
1564InputFile=read_GUI(handles.InputFile);
1565InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1566InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1567FileExt=InputFile.FileExt;
1568NomType=get(handles.NomType,'String');
1569i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1570i2=str2num(get(handles.i2,'String'));
1571j1=stra2num(get(handles.j1,'String'));
1572j2=stra2num(get(handles.j2,'String'));
1573sub_value= get(handles.SubField,'Value');
1574if sub_value % a second input file has been entered
1575    [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1576    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndices_1);
1577    NomType_1=get(handles.NomType_1,'String');
1578else
1579    filename_1=[];
1580end   
1581
1582%% increment (or decrement) the field indices and update the input filename(s)
1583CheckSearch=0;
1584if isempty(increment)
1585    CheckSearch=1;% search for the next available file
1586    set(handles.CheckFixPair,'Value',0)
1587end
1588CheckFixPair=get(handles.CheckFixPair,'Value');
1589if CheckFixPair
1590    if get(handles.scan_i,'Value')==1% case of scanning along index i
1591        i1=i1+increment;
1592        i2=i2+increment;
1593        if sub_value
1594            i1_1=i1_1+increment;
1595            i2_1=i2_1+increment;
1596        end
1597    else % case of scanning along index j (burst numbers)
1598        j1=j1+increment;
1599        j2=j2+increment;
1600        if sub_value
1601            j1_1=j1_1+increment;
1602            j2_1=j2_1+increment;
1603        end
1604    end
1605else
1606    UvData=get(handles.uvmat,'UserData');
1607    ref_i=i1;
1608    if ~isempty(i2)
1609        ref_i=floor((i1+i2)/2);
1610    end
1611    ref_j=1;
1612    if ~isempty(j1)
1613        ref_j=j1;
1614        if ~isempty(j2)
1615            ref_j=floor((j1+j2)/2);
1616        end
1617    end
1618    if ~isempty(increment)
1619        if get(handles.scan_i,'Value')==1% case of scanning along index i
1620            ref_i=ref_i+increment;
1621        else % case of scanning along index j (burst numbers)
1622            ref_j=ref_j+increment;
1623        end
1624    else% free increment
1625        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
1626            step=1;
1627        else
1628            step=-1;
1629        end
1630        if get(handles.scan_i,'Value')==1% case of scanning along index i
1631            ref_i=ref_i+step;
1632            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
1633                ref_i=ref_i+step;
1634            end
1635        else % case of scanning along index j (burst numbers)
1636            ref_j=ref_j+step;
1637            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
1638                ref_j=ref_j+step;
1639            end
1640        end
1641    end
1642    if ref_i<0
1643        errormsg='minimum i index reached';
1644    elseif ref_j<0
1645        errormsg='minimum j index reached';
1646    elseif ref_i+1>size(UvData.i1_series{1},1)
1647        errormsg='maximum i index reached';
1648    elseif ref_j+1>size(UvData.i1_series{1},2)
1649        errormsg='maximum j index reached';
1650    end
1651    if ~isempty(errormsg)
1652        return
1653    end
1654    i1=UvData.i1_series{1}(ref_i+1,ref_j+1,1);
1655    if ~isempty(UvData.i2_series{1})
1656        i2=UvData.i2_series{1}(ref_i+1,ref_j+1,1);
1657    end
1658    if ~isempty(UvData.j1_series{1})
1659        j1=UvData.j1_series{1}(ref_i+1,ref_j+1,1);
1660    end
1661    if ~isempty(UvData.j2_series{1})
1662        j2=UvData.j2_series{1}(ref_i+1,ref_j+1,1);
1663    end
1664end
1665filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1666if sub_value
1667    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);
1668end
1669
1670%% refresh plots
1671errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);
1672
1673%% update the index counters if the index move is successfull
1674if isempty(errormsg)
1675    set(handles.i1,'String',num2stra(i1,NomType,1));
1676    if isequal(i2,i1)
1677        set(handles.i2,'String','');
1678    else
1679        set(handles.i2,'String',num2stra(i2,NomType,1));
1680    end
1681    set(handles.j1,'String',num2stra(j1,NomType,2));
1682    if isequal(j2,j1)
1683        set(handles.j2,'String','');
1684    else
1685        set(handles.j2,'String',num2stra(j2,NomType,2));
1686    end
1687   % [indices]=name_generator('',i1,j1,'',NomType,1,i2,j2,'');
1688    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1689    set(handles.FileIndex,'String',indices);
1690    if ~isempty(filename_1)
1691        indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,j2_1);
1692        %indices_1=name_generator('',i1_1,j1_1,'',NomType_1,1,i2_1,j2_1,'');
1693        set(handles.FileIndex_1,'String',indices_1);
1694    end
1695    if isequal(movie_status,1)
1696        set(handles.movie_pair,'Value',1)
1697        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1698    end
1699end
1700
1701%------------------------------------------------------------------------
1702% --- Executes on button press in movie_pair: create an alternating movie with two view
1703function movie_pair_Callback(hObject, eventdata, handles)
1704%------------------------------------------------------------------------
1705%% stop movie action if the movie_pair button is off
1706if ~get(handles.movie_pair,'value')
1707    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1708    set(handles.i2,'String','')
1709    set(handles.j2,'String','')
1710    return
1711else
1712    set(handles.movie_pair,'BusyAction','queue')
1713end
1714
1715%% initialisation
1716set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1717drawnow
1718list_fields=get(handles.Fields,'String');% list menu fields
1719index_fields=get(handles.Fields,'Value');% selected string index
1720FieldName=list_fields{index_fields}; % selected field
1721UvData=get(handles.uvmat,'UserData');
1722if isequal(FieldName,'image')
1723    test_1=0;
1724    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1725    NomType=get(handles.NomType,'String');
1726else
1727    list_fields=get(handles.Fields_1,'String');% list menu fields
1728    index_fields=get(handles.Fields_1,'Value');% selected string index
1729    FieldName=list_fields{index_fields}; % selected field
1730    if isequal(FieldName,'image')
1731        test_1=1;
1732        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1733    else
1734        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1735        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1736        set(handles.movie_pair,'Value',0)
1737        return
1738    end
1739end
1740num_i1=str2num(get(handles.i1,'String'));
1741num_j1=stra2num(get(handles.j1,'String'));
1742num_i2=str2num(get(handles.i2,'String'));
1743num_j2=stra2num(get(handles.j2,'String'));
1744if isempty(num_j2)
1745    if isempty(num_i2)   
1746        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1747        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1748         set(handles.movie_pair,'Value',0)
1749        return
1750    else
1751        num_j2=num_j1;%repeat the index i1 by default
1752    end
1753end
1754if isempty(num_i2)
1755    num_i2=num_i1;%repeat the index i1 by default
1756end
1757% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1758imaname_1=fullfile_uvmat(RootPath,'',RootFile,Ext,NomType,num_i2,[],num_j2);
1759if ~exist(imaname_1,'file')
1760      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1761      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1762       set(handles.movie_pair,'Value',0)
1763      return
1764end
1765
1766%% read the second image
1767Field.AName='image';
1768if test_1
1769    Field_a=UvData.Field_1;
1770else
1771    Field_a=UvData.Field;
1772end
1773Field_b.AX=Field_a.AX;
1774Field_b.AY=Field_a.AY;
1775% z index
1776nbslice=str2double(get(handles.nb_slice,'String'));
1777if ~isempty(nbslice)
1778    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1779end
1780Field_b.CoordUnit='pixel';
1781
1782%% determine the input file type
1783if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1784    FileType='movie';
1785elseif isequal(lower(Ext),'.avi')
1786    FileType='avi';
1787elseif isequal(lower(Ext),'.vol')
1788    FileType='vol';
1789else
1790   form=imformats(Ext(2:end));
1791   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1792       if isequal(NomType,'*');
1793           FileType='multimage';
1794       else
1795           FileType='image';
1796       end
1797   end
1798end
1799switch FileType
1800        case 'movie'
1801            if test_1
1802                Field_b.A=read(UvData.MovieObject{2},num_i2);
1803            else
1804                Field_b.A=read(UvData.MovieObject{1},num_i2);
1805            end
1806        case 'avi'
1807            mov=aviread(imaname_1,num_i2);
1808            Field_b.A=frame2im(mov(1));
1809        case 'vol'
1810            Field_b.A=imread(imaname_1);
1811        case 'multimage'
1812            Field_b.A=imread(imaname_1,num_i2);
1813        case 'image'
1814            Field_b.A=imread(imaname_1);
1815end
1816if get(handles.slices,'Value')
1817    Field.ZIndex=str2double(get(handles.z_index,'String'));
1818end
1819
1820%px to phys or other transform on field
1821menu_transform=get(handles.transform_fct,'String');
1822choice_value=get(handles.transform_fct,'Value');
1823transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1824transform_list=get(handles.transform_fct,'UserData');
1825transform=transform_list{choice_value};
1826if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1827    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
1828        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
1829        Field_b=transform(Field_b,UvData.XmlData{2});
1830    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
1831        Field_b=transform(Field_b,UvData.XmlData{1});
1832    end
1833end
1834
1835 % make movie until movie speed is set to 0 or STOP is activated
1836hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1837set(handles.STOP,'Visible','on')
1838set(handles.speed,'Visible','on')
1839set(handles.speed_txt,'Visible','on')
1840while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1841    % read and plot the series of images in non erase mode
1842    set(hima,'CData',Field_b.A);
1843    pause(1.02-get(handles.speed,'Value'));% wait for next image
1844    set(hima,'CData',Field_a.A);
1845    pause(1.02-get(handles.speed,'Value'));% wait for next image
1846end
1847set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1848 set(handles.movie_pair,'Value',0)
1849
1850%------------------------------------------------------------------------
1851% --- Executes on button press in run0.
1852function run0_Callback(hObject, eventdata, handles)
1853%------------------------------------------------------------------------
1854set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1855drawnow
1856%filename=read_file_boxes(handles);
1857[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1858filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1859filename_1=[];%default
1860if get(handles.SubField,'Value')
1861    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
1862    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
1863   % filename_1=read_file_boxes_1(handles);
1864end
1865num_i1=stra2num(get(handles.i1,'String'));
1866num_i2=stra2num(get(handles.i2,'String'));
1867num_j1=stra2num(get(handles.j1,'String'));
1868num_j2=stra2num(get(handles.j2,'String'));
1869
1870errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
1871
1872if ~isempty(errormsg)
1873      msgbox_uvmat('ERROR',errormsg);
1874else
1875    set(handles.i1,'BackgroundColor',[1 1 1])
1876    set(handles.i2,'BackgroundColor',[1 1 1])
1877    set(handles.j1,'BackgroundColor',[1 1 1])
1878    set(handles.j2,'BackgroundColor',[1 1 1])
1879    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1880    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1881end   
1882set(handles.run0,'BackgroundColor',[1 0 0])
1883
1884
1885%------------------------------------------------------------------------
1886% --- read the input files and refresh all the plots, including projection.
1887% OUTPUT:
1888%  errormsg: error message char string  =[] by default
1889% INPUT:
1890% filename: first input file (=[] in the absence of input file)
1891% filename_1: second input file (=[] in the asbsenc of secodn input file)
1892% num_i1,num_i2,num_j1,num_j2; frame indices
1893% Field: structure describing an optional input field (then replace the input file)
1894function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
1895%------------------------------------------------------------------------
1896
1897%% initialisation
1898abstime=[];
1899abstime_1=[];
1900dt=[];
1901if ~exist('Field','var')
1902    Field={};
1903end
1904UvData=get(handles.uvmat,'UserData');
1905if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1906    delete(handles.UVMAT_title)
1907end
1908
1909%% determine the main input file information for action
1910FileType=[];%default
1911if ~exist(filename,'file')
1912    errormsg=['input file ' filename ' does not exist'];
1913    return
1914end
1915NomType=get(handles.NomType,'String');
1916% NomType=get(handles.FileIndex,'UserData');
1917%update the z position index
1918nbslice_str=get(handles.nb_slice,'String');
1919if isequal(nbslice_str,'volume')%NOT USED
1920    z_index=num_j1;
1921    set(handles.z_index,'String',num2str(z_index))
1922else
1923    nbslice=str2num(nbslice_str);
1924    z_index=mod(num_i1-1,nbslice)+1;
1925    set(handles.z_index,'String',num2str(z_index))
1926end
1927% refresh menu for save_mask if relevant
1928masknumber=get(handles.masklevel,'String');
1929if length(masknumber)>=z_index
1930    set(handles.masklevel,'Value',z_index)
1931end
1932
1933%% read the first input field if a filename has been introduced
1934if ~isempty(filename)
1935    ObjectName=filename;
1936    FieldName=[];%default
1937    VelType=[];%default
1938    FileExt=get(handles.FileExt,'String');
1939    FileType=UvData.FileType{1};
1940    switch FileType
1941        %     if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
1942        case {'civx','civdata','netcdf'};
1943            list_fields=get(handles.Fields,'String');% list menu fields
1944            index_fields=get(handles.Fields,'Value');% selected string index
1945            FieldName= list_fields{index_fields}; % selected field
1946            if ~strcmp(FieldName,'get_field...')
1947                TestVelType=get(handles.FixVelType,'Value');
1948                if TestVelType
1949                    VelType=setfield(handles);% read the velocity type.
1950                end
1951            end
1952            if strcmp(FieldName,'velocity')
1953                list_code=get(handles.ListColorCode,'String');% list menu fields
1954                index_code=get(handles.ListColorCode,'Value');% selected string index
1955                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
1956                    list_code=get(handles.ListColorScalar,'String');% list menu fields
1957                    index_code=get(handles.ListColorScalar,'Value');% selected string index
1958                    ParamIn.ColorVar= list_code{index_code}; % selected field
1959                end
1960            end
1961        case 'video'
1962            ObjectName=UvData.MovieObject{1};         
1963        case 'vol' %TODO: update
1964            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
1965                ParamIn.Npy=UvData.XmlData.Npy;
1966                ParamIn.Npx=UvData.XmlData.Npx;
1967            else
1968                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
1969                return
1970            end
1971    end
1972    ParamIn.FieldName=FieldName;
1973    ParamIn.VelType=VelType;
1974    ParamIn.GUIName='get_field';
1975    [Field{1},ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num_i1);
1976    if ~isempty(errormsg)
1977        errormsg=['error in reading ' filename ': ' errormsg];
1978        return
1979    end       
1980    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
1981        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
1982        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
1983    end
1984    if isfield(ParamOut,'TimeIndex')
1985        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
1986    end
1987    if isfield(ParamOut,'TimeValue')
1988        Field{1}.Time=ParamOut.TimeValue;
1989    end
1990end
1991
1992%% choose a second field filename_1 if defined
1993VelType_1=[];%default
1994FieldName_1=[];
1995ParamOut_1=[];
1996if ~isempty(filename_1)
1997    if ~exist(filename_1,'file')
1998        errormsg=['second file ' filename_1 ' does not exist'];
1999        return
2000    end
2001    Name=filename_1;
2002    FileType_1=UvData.FileType{2};
2003    switch FileType_1
2004        %     if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
2005        case {'civx','civdata','netcdf'};
2006            list_fields=get(handles.Fields_1,'String');% list menu fields
2007            index_fields=get(handles.Fields_1,'Value');% selected string index
2008            FieldName_1= list_fields{index_fields}; % selected field
2009            if ~strcmp(FieldName,'get_field...')
2010                TestVelType=get(handles.FixVelType,'Value');
2011                if TestVelType
2012                    VelType_1=setfield(handles);% read the velocity type.
2013                end
2014            end
2015            if strcmp(FieldName_1,'velocity')
2016                list_code=get(handles.ListColorCode,'String');% list menu fields
2017                index_code=get(handles.ListColorCode,'Value');% selected string index
2018                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2019                    list_code=get(handles.ListColorScalar,'String');% list menu fields
2020                    index_code=get(handles.ListColorScalar,'Value');% selected string index
2021                    ParamIn.ColorVar= list_code{index_code}; % selected field
2022                end
2023            end
2024        case 'video'
2025            Name=UvData.MovieObject{2};
2026        case 'vol' %TODO: update
2027            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2028                ParamIn.Npy=UvData.XmlData.Npy;
2029                ParamIn.Npx=UvData.XmlData.Npx;
2030            else
2031                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2032                return
2033            end
2034    end
2035    NomType_1=get(handles.NomType_1,'String');
2036    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2037    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2038        if isfield(UvData,'filename_1')&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2039            test_keepdata_1= strcmp(filename_1,UvData.filename_1) && strcmp(VelType_1,UvData.VelType_1) && strcmp(FieldName_1,UvData.FieldName_1);
2040        end
2041    end
2042    if test_keepdata_1
2043        Field{2}=UvData.Field_1;
2044    else
2045        ParamIn.FieldName=FieldName_1;
2046        ParamIn.VelType=VelType_1;
2047        ParamIn.GUIName='get_field_1';
2048        [Field{2},ParamOut_1,errormsg] = read_field(Name,FileType_1,ParamIn,num_i1);
2049        if ~isempty(errormsg)
2050            errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
2051            return
2052        end
2053        UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2054    end
2055    %     end
2056end
2057
2058%% update uvmat interface
2059if isfield(ParamOut,'Npx')
2060    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2061    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2062elseif isfield(ParamOut_1,'Npx')
2063    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2064    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2065end
2066
2067%% update the display menu for the first velocity type (first menuline)
2068test_veltype=0;
2069% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2070if (strcmp(FileType,'civx')||strcmp(FileType,'civdata'))&& ~strcmp(FieldName,'get_field...')
2071    test_veltype=1;
2072    set(handles.VelType,'Visible','on')
2073    set(handles.VelType_1,'Visible','on')
2074    set(handles.FixVelType,'Visible','on')
2075    menu=set_veltype_display(ParamOut.CivStage);
2076    index_menu=strcmp(ParamOut.VelType,menu);
2077    set(handles.VelType,'Value',find(index_menu,1))
2078    if ~get(handles.SubField,'value')
2079    set(handles.VelType,'String',menu)
2080     set(handles.VelType_1,'Value',1)
2081     set(handles.VelType_1,'String',[{''};menu])
2082    end
2083else
2084    set(handles.VelType,'Visible','off')
2085end
2086field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2087set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2088set(handles.Fields,'Value',find(field_index,1))
2089
2090%% update the display menu for the second velocity type (second menuline)
2091test_veltype_1=0;
2092if isempty(filename_1)
2093    set(handles.Fields_1,'Value',1); %update the field menu
2094    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2095else
2096    if ~isequal(FileType_1,'netcdf')|| isequal(FieldName_1,'get_field...')
2097        set(handles.VelType_1,'Visible','off')
2098    else
2099        test_veltype_1=1;
2100        set(handles.VelType_1,'Visible','on')
2101        if ~get(handles.FixVelType,'Value')
2102            menu=set_veltype_display(ParamOut_1.CivStage);
2103            index_menu=strcmp(ParamOut_1.VelType,menu);
2104            set(handles.VelType_1,'Value',1+find(index_menu,1))
2105            set(handles.VelType_1,'String',[{''};menu])
2106        end
2107    end
2108end
2109if test_veltype||test_veltype_1
2110     set(handles.FixVelType,'Visible','on')
2111else
2112     set(handles.FixVelType,'Visible','off')
2113end
2114   
2115%% introduce w as background image by default for a new series (only for nbdim=2)
2116if ~isfield(UvData,'NewSeries')
2117    UvData.NewSeries=1;
2118end
2119%put W as background image by default if NbDim=2:
2120if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2121        set(handles.SubField,'Value',1);
2122        %menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w'
2123        set(handles.RootPath_1,'String','"')
2124        set(handles.RootFile_1,'String','"')
2125        set(handles.SubDir_1,'String','"');
2126         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2127        %[indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,'');
2128        set(handles.FileIndex_1,'String',indices)
2129        set(handles.FileExt_1,'String','"');
2130        set(handles.Fields_1,'Visible','on');
2131        set(handles.Fields_1,'Visible','on');
2132        set(handles.RootPath_1,'Visible','on')
2133        set(handles.RootFile_1,'Visible','on')
2134        set(handles.SubDir_1,'Visible','on');
2135        set(handles.FileIndex_1,'Visible','on');
2136        set(handles.FileExt_1,'Visible','on');
2137        set(handles.Fields_1,'Visible','on');
2138        Field{1}.AName='w';
2139end           
2140
2141%% store the current open names, fields and vel types in uvmat interface
2142UvData.filename_1=filename_1;
2143UvData.VelType_1=[];%default
2144UvData.FieldName_1=[];
2145if isfield(ParamOut_1,VelType)
2146    UvData.VelType_1=ParamOut_1.VelType;
2147end
2148if isfield(ParamOut_1,FieldName)
2149    UvData.FieldName_1=ParamOut_1.FieldName;
2150end
2151
2152%% apply coordinate transform or other user fct
2153XmlData=[];%default
2154XmlData_1=[];%default
2155if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2156    XmlData=UvData.XmlData{1};
2157    if numel(UvData.XmlData)==2
2158        XmlData_1=UvData.XmlData{2};
2159    end
2160end
2161
2162% menu_transform=get(handles.transform_fct,'String');
2163choice_value=get(handles.transform_fct,'Value');
2164transform_list=get(handles.transform_fct,'UserData');
2165transform=transform_list{choice_value};%selected function handles
2166% z index
2167if ~isempty(filename)
2168    Field{1}.ZIndex=z_index;
2169end
2170%px to phys or other transform on field
2171if ~isempty(transform)
2172    if length(Field)>=2
2173        Field{2}.ZIndex=z_index;
2174        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2175        if isempty(Field{2})
2176            Field(2)=[];
2177        end
2178    else
2179        Field{1}=transform(Field{1},XmlData);
2180    end
2181end
2182
2183%% calculate scalar
2184if strcmp(FileType(1:3),'civ') && ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
2185    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2186end
2187if numel(Field)==2 && ~test_keepdata_1 && isequal(FileType_1(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2188    Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2189end
2190
2191%% combine the two input fields (e.g. substract velocity fields)
2192if numel(Field)==2
2193   UvData.Field=sub_field(Field{1},Field{2}); 
2194else
2195   UvData.Field=Field{1};
2196end
2197
2198%% get bounds and mesh (needed for mouse action and to open set_object)
2199test_x=0;
2200test_z=0;% test for unstructured z coordinate
2201[UvData.Field,errormsg]=check_field_structure(UvData.Field);
2202if ~isempty(errormsg)
2203    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];
2204    return
2205end
2206[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);
2207if ~isempty(errormsg)
2208    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];
2209    return
2210end
2211[NbDim,imax]=max(NbDim);
2212if isfield(UvData.Field,'NbDim')
2213    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2214end
2215if ~isempty(VarType{imax}.coord_x)  && ~isempty(VarType{imax}.coord_y)    %unstructured coordinates
2216    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2217    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2218    eval(['nbvec=length(UvData.Field.' XName ');'])%nbre of measurement points (e.g. vectors)
2219    test_x=1;%test for unstructured coordinates
2220    if ~isempty(VarType{imax}.coord_z)
2221        ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2222    else
2223        NbDim=2;
2224    end
2225elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0 %structured coordinate
2226    XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2227    if NbDim>1
2228        YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2229    end
2230end
2231if NbDim==3
2232    if ~test_x
2233        ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2234    end
2235    eval(['ZMax=max(UvData.Field.' ZName ');'])
2236    eval(['ZMin=min(UvData.Field.' ZName ');'])
2237    UvData.Field.ZMax=ZMax;
2238    UvData.Field.ZMin=ZMin;
2239    test_z=1;
2240    if isequal(ZMin,ZMax)%no z dependency
2241        NbDim=2;
2242        test_z=0;
2243    end
2244end
2245if exist('XName','var')
2246    eval(['XMax=max(max(UvData.Field.' XName '));'])
2247    eval(['XMin=min(min(UvData.Field.' XName '));'])
2248    UvData.Field.NbDim=NbDim;
2249    UvData.Field.XMax=XMax;
2250    UvData.Field.XMin=XMin;
2251    if NbDim >1
2252        eval(['YMax=max(max(UvData.Field.' YName '));'])
2253        eval(['YMin=min(min(UvData.Field.' YName '));'])
2254        UvData.Field.YMax=YMax;
2255        UvData.Field.YMin=YMin;
2256    end
2257    eval(['nbvec=length(UvData.Field.' XName ');'])
2258    if test_x %unstructured coordinates
2259        if test_z
2260            UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2261            UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2262        else
2263            UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2264        end
2265    else
2266        VarIndex=CellVarIndex{imax}; % list of variable indices
2267        DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2268        nbpoints_x=UvData.Field.DimValue(DimIndex(NbDim));
2269        DX=(XMax-XMin)/(nbpoints_x-1);
2270        if NbDim >1
2271            nbpoints_y=UvData.Field.DimValue(DimIndex(NbDim-1));
2272            DY=(YMax-YMin)/(nbpoints_y-1);
2273        end
2274        if NbDim==3
2275            nbpoints_z=UvData.Field.DimValue(DimIndex(1));
2276            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2277            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2278            UvData.Field.ZMax=ZMax;
2279            UvData.Field.ZMin=ZMin;
2280        else
2281            UvData.Field.Mesh=DX;%sqrt(DX*DY);
2282        end
2283    end
2284end
2285
2286%% 3D case (menuvolume)
2287if NbDim==3% && UvData.NewSeries
2288    test_set_object=1;
2289    hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2290    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2291    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2292    if ~isempty(hset_object) %if set_object is detected
2293%         hhset_object=guidata(hset_object);
2294% %         ZBounds_old(1)=get(hhset_object.z_slider,'Min');
2295% %         ZBounds_old(2)=get(hhset_object.z_slider,'Max');
2296% %         if isequal(ZBounds_old,ZBounds)
2297%             test_set_object=0;% do not refresh the GUI set_object
2298%         else
2299            delete(hset_object);% delete the GUI set_object if it does not fit
2300%         end
2301    end
2302    if test_set_object% reinitiate the GUI set_object
2303        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
2304        UvData.Object{1}.Style='plane';%main plotting plane
2305        UvData.Object{1}.ProjMode='projection';%main plotting plane
2306        UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2307        UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2308        UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2309        UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2310        UvData.Object{1}.Angle=[0 0 0];
2311%         UvData.Object{1}.Theta=0;
2312%         UvData.Object{1}.Psi=0;
2313        UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2314%         PlotHandles=get_plot_handles(handles);
2315        UvData.Object{1}.Name='1-PLANE';
2316        UvData.Object{1}.enable_plot=1;
2317        set_object(UvData.Object{1},handles,ZBounds);
2318        set(handles.ListObject,'Value',1);
2319        set(handles.ListObject,'String',{'1-PLANE'});
2320        set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2321        edit_object_Callback([],[], handles)
2322    end
2323    %multilevel case (single menuplane in a 3D space)
2324elseif isfield(UvData,'Z')
2325    if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2326        XmlData=UvData.XmlData{1};
2327        if isfield(XmlData,'PlanePos')
2328            UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2329        end
2330        if isfield(XmlData,'PlaneAngle')
2331            siz=size(XmlData.PlaneAngle);
2332            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2333            UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2334        end
2335    elseif isfield(UvData,'ZIndex')
2336        UvData.Object{1}.ZObject=UvData.ZIndex;
2337    end
2338else
2339    % create a default projection
2340    UvData.Object{1}.ProjMode='projection';%main plotting plane
2341    UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2342    set(handles.ListObject,'Value',1);
2343    list_object=get(handles.ListObject,'String');
2344    if isempty(list_object)
2345        list_object={''};
2346    elseif ~isempty(list_object{1})
2347        list_object=[{''};list_object];
2348    end
2349    set(handles.ListObject,'String',list_object);
2350%     set(handles.list_object_2,'String',list_object);
2351end
2352testnewseries=UvData.NewSeries;
2353UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2354set(handles.uvmat,'UserData',UvData)
2355
2356%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2357if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2358    set(handles.num_MinA,'String','0')
2359    set(handles.num_MaxA,'String','255')
2360end
2361
2362%% Plot the projections on the selected  projection objects
2363% main projection object (uvmat display)
2364list_object=get(handles.ListObject,'String');
2365if isequal(list_object,{''})%refresh list of objects if the menu is empty
2366    UvData.Object={[]};
2367    set(handles.ListObject,'Value',1)
2368end
2369IndexObj=get(handles.ListObject,'Value');%selected projection object for main view
2370if IndexObj(1)> numel(UvData.Object)
2371    IndexObj(1)=1;%select the first object if the selected one does not exist
2372    set(handles.ListObject,'Value',1)
2373end
2374plot_handles{1}=handles;
2375if isfield(UvData,'plotaxes')%case of movies
2376    haxes(1)=UvData.plotaxes;
2377else
2378    haxes(1)=handles.axes3;
2379end
2380%PlotParam{1}=read_plot_param(handles);%read plotting parameters on the uvmat interfac
2381PlotParam{1}=read_GUI(handles.uvmat);
2382if ~isfield(PlotParam{1},'Vectors')
2383    PlotParam{1}.Vectors.MaxVec=1;
2384    PlotParam{1}.Vectors.MinVec=0;
2385    PlotParam{1}.Vectors.CheckFixVecColor=1;
2386    PlotParam{1}.Vectors.ColCode1=0.33;
2387    PlotParam{1}.Vectors.ColCode2=0.66;
2388     PlotParam{1}.Vectors.ListColorScalar={'ima_cor'};
2389     PlotParam{1}.Vectors.ListColorCode= {'rgb'};
2390end
2391keeplim(1)=get(handles.CheckFixLimits,'Value');% test for fixed graph limits
2392PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2393
2394% second projection object (view_field display)
2395if length( IndexObj)>=2
2396    view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2397    if ~isempty(view_field_handle)
2398        plot_handles{2}=guidata(view_field_handle);
2399        haxes(2)=plot_handles{2}.axes3;
2400        %PlotParam{2}=read_plot_param(plot_handles{2});%read plotting parameters on the viewinterface
2401        PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2402        keeplim(2)=get(plot_handles{2}.CheckFixLimits,'Value');
2403        PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2404    end
2405end
2406
2407%loop on the projection objects: one or two
2408for imap=1:numel(IndexObj)
2409    iobj=IndexObj(imap);
2410    [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2411
2412    if ~isempty(errormsg)
2413        return
2414    end
2415    %     if testnewseries && isfield(ObjectData,'CoordUnit')&& isfield(PlotParam{imap},'Coordinates')
2416%         PlotParam{imap}.Coordinates=rmfield(PlotParam{imap}.Coordinates,'CheckFixEqual'); %set FixEqual to depend on the field (=1 if Data.CoordUnit=1 in plot_field)
2417%     end
2418    if testnewseries && isfield(ObjectData,'CoordUnit')
2419        PlotParam{imap}.Coordinates.CheckFixEqual=1;
2420    end
2421    %use of mask (TODO: check)
2422    if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2423        flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2424        AX=ObjectData.AX;%x coordiantes for the scalar field
2425        AY=ObjectData.AY;%y coordinates for the scalar field
2426        MaskX=ObjectData.MaskX;%x coordiantes for the mask
2427        MaskY=ObjectData.MaskY;%y coordiantes for the mask
2428        if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2429            nxy=size(flag_mask);
2430            sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2431            sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2432            x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2433            y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2434            %project on the positions of the scalar
2435            npxy=size(ObjectData.A);
2436            dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2437            dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2438            xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2439            yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2440            [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2441            flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2442        end
2443        AClass=class(ObjectData.A);
2444        ObjectData.A=flag_mask.*double(ObjectData.A);
2445        ObjectData.A=feval(AClass,ObjectData.A);
2446        ind_off=[];
2447        if isfield(ObjectData,'ListVarName')
2448            for ilist=1:length(ObjectData.ListVarName)
2449                if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2450                    ind_off=[ind_off ilist];
2451                end
2452            end
2453            ObjectData.ListVarName(ind_off)=[];
2454            ObjectData.VarDimIndex(ind_off)=[];
2455            ind_off=[];
2456            for ilist=1:length(ObjectData.ListDimName)
2457                if isequal(ObjectData.ListDimName{ilist},'MaskX') || isequal(ObjectData.ListDimName{ilist},'MaskY')
2458                    ind_off=[ind_off ilist];
2459                end
2460            end
2461            ObjectData.ListDimName(ind_off)=[];
2462            ObjectData.DimValue(ind_off)=[];
2463        end
2464    end   
2465    if ~isempty(ObjectData)
2466        PlotType='none'; %default
2467        if imap==2 && isempty(view_field_handle)
2468            view_field(ObjectData)
2469        else
2470            [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2471            write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2472            if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2473                ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2474            end
2475        end
2476        if isequal(PlotType,'none')
2477            hget_field=findobj(allchild(0),'name','get_field');
2478            if isempty(hget_field)
2479                get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2480            end
2481            errormsg='The field defined by get_field cannot be plotted';
2482            return
2483        end
2484    end
2485end
2486
2487%% update the mask
2488if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2489   update_mask(handles,num_i1,num_i2);
2490end
2491
2492%% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2493menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2494ind_bad=[];
2495nb_histo=1;
2496
2497% suppress coordinates from the histogram menu
2498for ivar=1:numel(menu_histo)%l loop on field variables:
2499    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2500        Role=UvData.Field.VarAttribute{ivar}.Role;
2501        switch Role
2502            case {'coord_x','coord_y','coord_z','dimvar'}
2503                ind_bad=[ind_bad ivar];
2504            case {'vector_y'}
2505                nb_histo=nb_histo+1;
2506        end
2507    end
2508    DimCell=UvData.Field.VarDimName{ivar};
2509    DimName='';
2510    if ischar(DimCell)
2511        DimName=DimCell;
2512    elseif iscell(DimCell)&& numel(DimCell)==1
2513        DimName=DimCell{1};
2514    end
2515    if strcmp(DimName,menu_histo{ivar})
2516        ind_bad=[ind_bad ivar];
2517    end
2518end
2519menu_histo(ind_bad)=[];
2520
2521%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2522% display menus and plot histograms
2523test_v=0;
2524if ~isempty(menu_histo)
2525    set(handles.histo1_menu,'Value',1)
2526    set(handles.histo1_menu,'String',menu_histo)
2527    histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2528    % case of more than one variables (eg vector components)
2529    if nb_histo > 1
2530        test_v=1;
2531        set(handles.histo2_menu,'Visible','on')
2532        set(handles.histo_v,'Visible','on')
2533        set(handles.histo2_menu,'String',menu_histo)
2534        set(handles.histo2_menu,'Value',2)
2535        histo2_menu_Callback(handles.histo2_menu,[], handles)% plot second histogram
2536    end
2537end
2538if ~test_v
2539    set(handles.histo2_menu,'Visible','off')
2540    set(handles.histo_v,'Visible','off')
2541    cla(handles.histo_v)
2542    set(handles.histo2_menu,'Value',1)
2543end
2544%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2545
2546%% display time
2547testimedoc=0;
2548TimeUnit='';
2549if isfield(UvData.Field,'Time')
2550    abstime=UvData.Field.Time;%time read from the netcdf input file
2551end
2552if isfield(UvData,'Field_1') && isfield(UvData.Field_1,'Time')
2553    abstime_1=UvData.Field_1.Time;%time read from the netcdf input file
2554end
2555if isfield(UvData.Field,'dt')
2556    dt=UvData.Field.dt;%dt read from the netcdf input file
2557    if isfield(UvData.Field,'TimeUnit')
2558       TimeUnit=UvData.Field.TimeUnit;
2559    end
2560elseif isfield(UvData,'Field_1') && isfield(UvData.Field_1,'dt')%dt obtained from the second field if not defined in the first
2561    dt=UvData.Field_1.dt;%dt read from the netcdf input file
2562    if isfield(UvData.Field_1,'TimeUnit')
2563       TimeUnit=UvData.Field_1.TimeUnit;
2564    end
2565end
2566% time from xml file overset previous result
2567if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2568    if isempty(num_i2)||isnan(num_i2)
2569        num_i2=num_i1;
2570    end
2571    if isempty(num_j1)||isnan(num_j1)
2572        num_j1=1;
2573    end
2574    if isempty(num_j2)||isnan(num_j2)
2575        num_j2=num_j1;
2576    end
2577    siz=size(UvData.XmlData{1}.Time);
2578    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2579        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2580        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2581        testimedoc=1;
2582        if isfield(UvData.XmlData{1},'TimeUnit')
2583            TimeUnit=UvData.XmlData{1}.TimeUnit;
2584        end
2585    end
2586    if numel(UvData.XmlData)==2
2587        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2588        %  [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2589        if isempty(num_i2)
2590            num_i2=num_i1;
2591        end
2592        if isempty(num_j1)
2593            num_j1=1;
2594        end
2595        if isempty(num_j2)
2596            num_j2=num_j1;
2597        end
2598        siz=size(UvData.XmlData{2}.Time);
2599        if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2600            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
2601        end
2602    end
2603end
2604
2605if ~isequal(numel(abstime),1)
2606    abstime=[];
2607end
2608if ~isequal(numel(abstime_1),1)
2609      abstime_1=[];
2610end 
2611set(handles.abs_time,'String',num2str(abstime,4))
2612set(handles.abs_time_1,'String',num2str(abstime_1,4))
2613if testimedoc && isfield(UvData,'dt')
2614    dt=UvData.dt;
2615end
2616if isempty(dt)||isequal(dt,0)
2617    set(handles.Dt_txt,'String','')
2618else
2619    if  isempty(TimeUnit)
2620        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2621    else
2622        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2623    end
2624end
2625
2626
2627%-------------------------------------------------------------------
2628% --- translate coordinate to matrix index
2629%-------------------------------------------------------------------
2630function [indx,indy]=pos2ind(x0,rangx0,nxy)
2631indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2632indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2633
2634%-------------------------------------------------------------------
2635% --- Executes on button press in 'CheckFixLimits'.
2636%-------------------------------------------------------------------
2637function CheckFixLimits_Callback(hObject, eventdata, handles)
2638test=get(handles.CheckFixLimits,'Value');
2639if test
2640    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2641else
2642    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2643    update_plot(handles);
2644end
2645
2646%-------------------------------------------------------------------
2647% --- Executes on button press in CheckFixEqual.
2648function CheckFixEqual_Callback(hObject, eventdata, handles)
2649test=get(handles.CheckFixEqual,'Value');
2650if test
2651    set(handles.CheckFixEqual,'BackgroundColor',[1 1 0])
2652    cla(handles.axes3)
2653    update_plot(handles);
2654else
2655    set(handles.CheckFixEqual,'BackgroundColor',[0.7 0.7 0.7])
2656    update_plot(handles);
2657%     axis(handles.axes3,'image')
2658end
2659
2660%-------------------------------------------------------------------
2661
2662%-------------------------------------------------------------------
2663% --- Executes on button press in 'CheckZoom'.
2664%-------------------------------------------------------------------
2665function CheckZoom_Callback(hObject, eventdata, handles)
2666
2667if (get(handles.CheckZoom,'Value') == 1);
2668    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2669    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2670    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2671else
2672    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2673end
2674
2675%-------------------------------------------------------------------
2676%----Executes on button press in 'record': records the current flags of manual correction.
2677%-------------------------------------------------------------------
2678function record_Callback(hObject, eventdata, handles)
2679% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2680[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2681filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2682%filename=read_file_boxes(handles);
2683[erread,message]=fileattrib(filename);
2684if ~isempty(message) && ~isequal(message.UserWrite,1)
2685     msgbox_uvmat('ERROR',['no writting access to ' filename])
2686     return
2687end
2688test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2689test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2690if ~test_civ2 && ~test_civ1
2691    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2692end
2693if test_civ2
2694    nbname='nb_vectors2';
2695   flagname='vec2_FixFlag';
2696   attrname='fix2';
2697end
2698if test_civ1
2699    nbname='nb_vectors';
2700   flagname='vec_FixFlag';
2701   attrname='fix';
2702end
2703%write fix flags in the netcdf file
2704UvData=get(handles.uvmat,'UserData');
2705hhh=which('netcdf.open');% look for built-in matlab netcdf library
2706if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2707    nc=netcdf.open(filename,'NC_WRITE');
2708    netcdf.reDef(nc);
2709    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2710    dimid = netcdf.inqDimID(nc,nbname);
2711    try
2712        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2713    catch
2714        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2715    end
2716    netcdf.endDef(nc);
2717    netcdf.putVar(nc,varid,UvData.axes3.FF);
2718    netcdf.close(nc); 
2719else %old netcdf library
2720    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2721end
2722
2723%-------------------------------------------------------------------
2724%----Correct the netcdf file, using toolbox (old versions of Matlab).
2725%-------------------------------------------------------------------
2726function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2727nc=netcdf(filename,'write'); %open netcdf file
2728result=redef(nc);
2729eval(['nc.' attrname '=1;']);
2730theDim=nc(nbname) ;% get the number of velocity vectors
2731nb_vectors=size(theDim);
2732var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2733var_FixFlag(1:nb_vectors)=AxeData.FF;%
2734fin=close(nc);
2735
2736%-------------------------------------------------------------------
2737%determines the fields to read from the interface
2738%------------------------------------------------------------------
2739function VelType=setfield(handles)
2740VelTypeList=get(handles.VelType,'String');
2741index=get(handles.VelType,'Value');
2742VelType=VelTypeList{index};
2743
2744%-------------------------------------------------------------------
2745%determines the veltype of the second field to read from the iinterface
2746%------------------------------------------------------------------
2747function VelType=setfield_1(handles)
2748VelTypeList=get(handles.VelType_1,'String');
2749index=get(handles.VelType_1,'Value');
2750VelType=VelTypeList{index};
2751
2752%---------------------------------------------------
2753% --- Executes on button press in SubField
2754function SubField_Callback(hObject, eventdata, handles)
2755% huvmat=get(handles.run0,'parent');
2756UvData=get(handles.uvmat,'UserData');
2757if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2758    set(handles.RootPath_1,'String','')
2759    set(handles.RootFile_1,'String','')
2760    set(handles.SubDir_1,'String','');
2761    set(handles.FileIndex_1,'String','');
2762    set(handles.FileExt_1,'String','');
2763    set(handles.RootPath_1,'Visible','off')
2764    set(handles.RootFile_1,'Visible','off')
2765    set(handles.SubDir_1,'Visible','off');
2766    set(handles.NomType_1,'Visible','off');
2767    set(handles.abs_time_1,'Visible','off')
2768    set(handles.FileIndex_1,'Visible','off');
2769    set(handles.FileExt_1,'Visible','off');
2770    set(handles.Fields_1,'Value',1);%set to blank state
2771    set(handles.VelType_1,'Value',1);%set to blank state
2772    if ~strcmp(get(handles.VelType,'Visible'),'on')
2773        set(handles.VelType_1,'Visible','off')
2774    end
2775%     set_veltype_display([handles.VelType_1 handles.interp1_1 handles.filter1_1 ...
2776%             handles.civ2_1 handles.interp2_1 handles.filter2_1],0)
2777    if isfield(UvData,'XmlData_1')
2778        UvData=rmfield(UvData,'XmlData_1');
2779    end
2780    set(handles.uvmat,'UserData',UvData);
2781    run0_Callback(hObject, eventdata, handles); %run
2782else
2783    MenuBrowse_1_Callback(hObject, eventdata, handles)
2784end
2785
2786%------------------------------------------------------------------------
2787% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
2788
2789function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
2790%------------------------------------------------------------------------
2791InputFile=read_GUI(handles.InputFile);
2792RootPath=InputFile.RootPath;
2793SubDir=regexprep(InputFile.SubDir,'/|\','');
2794RootFile=regexprep(InputFile.RootFile,'/|\','');
2795FileIndices=InputFile.FileIndex;
2796FileExt=InputFile.FileExt;
2797
2798
2799%------------------------------------------------------------------------
2800% ---- read the data displayed for the second input rootfile windows
2801function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
2802%------------------------------------------------------------------------
2803RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
2804if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
2805    RootPath_1=get(handles.RootPath,'String');
2806end;
2807SubDir_1=get(handles.SubDir_1,'String');
2808if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
2809    SubDir_1=get(handles.SubDir,'String');
2810end
2811SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2812RootFile_1=get(handles.RootFile_1,'String');
2813if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
2814    RootFile_1=get(handles.RootFile,'String');
2815end
2816RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2817FileIndex_1=get(handles.FileIndex_1,'String');
2818if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
2819    FileIndex_1=get(handles.FileIndex,'String');
2820end
2821FileExt_1=get(handles.FileExt_1,'String');
2822if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
2823    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
2824end
2825NomType_1=get(handles.NomType_1,'String');
2826if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
2827    NomType_1=get(handles.NomType,'String');%read FileExt by default
2828end
2829%------------------------------------------------------------------------
2830% --- Executes on menu selection Fields
2831function Fields_Callback(hObject, eventdata, handles)
2832%------------------------------------------------------------------------
2833list_fields=get(handles.Fields,'String');% list menu fields
2834index_fields=get(handles.Fields,'Value');% selected string index
2835field= list_fields{index_fields(1)}; % selected string
2836if isequal(field,'get_field...')
2837    set(handles.FixVelType,'visible','off')
2838    set(handles.VelType,'visible','off')
2839    set(handles.VelType_1,'visible','off')
2840    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2841    filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2842    %filename=read_file_boxes(handles);
2843    hget_field=findobj(allchild(0),'name','get_field');
2844    if ~isempty(hget_field)
2845        delete(hget_field)
2846    end
2847    hget_field=get_field(filename);
2848    set(hget_field,'Name','get_field')
2849    hhget_field=guidata(hget_field);
2850    set(hhget_field.list_fig,'Value',1)
2851    set(hhget_field.list_fig,'String',{'uvmat'})
2852    set(handles.transform_fct,'Value',1)% no transform by default
2853    set(handles.path_transform,'String','')
2854    return %no action
2855end
2856list_fields=get(handles.Fields_1,'String');% list menu fields
2857index_fields=get(handles.Fields_1,'Value');% selected string index
2858field_1= list_fields{index_fields(1)}; % selected string
2859UvData=get(handles.uvmat,'UserData');
2860
2861%read the rootfile input display
2862[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2863FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2864[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
2865% NomTypeNew=NomType;%default
2866if isequal(field,'image')
2867%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
2868%         NomTypeNew='_1_1';
2869%     elseif isequal(NomType,'#_ab')
2870%         NomTypeNew='#a';
2871%     elseif isequal(NomType,'_1-2')
2872%         NomTypeNew='_1';
2873%     end
2874    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
2875    if ~exist(imagename,'file')
2876        [FileName,PathName] = uigetfile( ...
2877            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
2878            '*.jpg',' jpeg image files'; ...
2879            '*.png','.png image files'; ...
2880            '*.tif','.tif image files'; ...
2881            '*.avi;*.AVI','.avi movie files'; ...
2882            '*.vol','.volume images (png)'; ...
2883            '*.*',  'All Files (*.*)'}, ...
2884            'Pick an image',imagename);   
2885        imagename=[PathName FileName];
2886    end
2887     % display the selected field and related information
2888    display_file_name(hObject, eventdata, handles,imagename)%display the image
2889    return
2890else
2891    ext=get(handles.FileExt,'String');
2892    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
2893        [FileName,PathName] = uigetfile( ...
2894            {'*.nc', ' (*.nc)';
2895            '*.nc',' netcdf files'; ...
2896            '*.*',  'All Files (*.*)'}, ...
2897            'Pick a netcdf file',FileBase);
2898        filename=[PathName FileName];
2899        % display the selected field and related information
2900        display_file_name(hObject, eventdata, handles,filename)
2901        return
2902    end
2903end
2904indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
2905set(handles.FileIndex,'String',indices)
2906% set(handles.NomType,'String',NomType)
2907
2908%common to Fields_1_Callback
2909if isequal(field,'image')||isequal(field_1,'image')
2910    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
2911    set(handles.TitleNpy,'Visible','on')
2912    set(handles.num_Npx,'Visible','on')
2913    set(handles.num_Npy,'Visible','on')
2914else
2915    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
2916    set(handles.TitleNpy,'Visible','off')
2917    set(handles.num_Npx,'Visible','off')
2918    set(handles.num_Npy,'Visible','off')
2919end
2920setfield(handles);% update the field structure ('civ1'....)
2921if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
2922    run0_Callback(hObject, eventdata, handles)
2923end
2924
2925%---------------------------------------------------
2926% --- Executes on menu selection Fields
2927function Fields_1_Callback(hObject, eventdata, handles)
2928%-------------------------------------------------
2929%% read input data
2930check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
2931UvData=get(handles.uvmat,'UserData');
2932if check_new && isfield(UvData,'XmlData')
2933    UvData.XmlData{2}=UvData.XmlData{1};
2934end
2935list_fields=get(handles.Fields,'String');% list menu fields
2936index_fields=get(handles.Fields,'Value');% selected string index
2937field= list_fields{index_fields(1)}; % selected string
2938list_fields=get(handles.Fields_1,'String');% list menu fields
2939index_fields=get(handles.Fields_1,'Value');% selected string index
2940field_1= list_fields{index_fields(1)}; % selected string for the second field
2941if isequal(field_1,'')||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
2942    set(handles.SubField,'Value',0)
2943    check_new=1;
2944    SubField_Callback(hObject, eventdata, handles)
2945    if isempty(field_1)%remove second field if 'blank' field is selected
2946        return
2947    end
2948end
2949set(handles.SubField,'Value',1)%state that a second field is now entered
2950
2951%% read the rootfile input display
2952[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomTYpe_1]=read_file_boxes_1(handles);
2953filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
2954[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
2955set(handles.FileIndex_1,'Visible','on')
2956set(handles.FileExt_1,'Visible','on')
2957switch field_1
2958    case 'get_field...'
2959        set_veltype_display(0) % no veltype display
2960        hget_field=findobj(allchild(0),'name','get_field_1');
2961        if ~isempty(hget_field)
2962            delete(hget_field)
2963        end
2964        hget_field=get_field(filename_1);
2965        set(hget_field,'name','get_field_1')
2966        hhget_field=guidata(hget_field);
2967        set(hhget_field.list_fig,'Value',1)
2968        set(hhget_field.list_fig,'String',{'uvmat'})
2969        set(handles.transform_fct,'Value',1)% no transform by default
2970        set(handles.path_transform,'String','')
2971    case 'image'
2972        % transform netc type to the corresponding image type
2973        NomType=get(handles.NomType,'string');
2974        check_letter=~isempty(regexp(NomType,'[ab|AB]$'));%detect pair label by letter
2975%         NomType_1=NomType;
2976%         if check_letter
2977%             NomType_1=NomType_1(1:end-1);
2978%         else
2979%             r=regexp(NomType_1,'.-(?<num2>\d+$','names');
2980%             if ~isempty(r)
2981%                 NomType_1=regexprep(NomType_1,['-' r.num2],'');
2982%             end
2983%         end
2984        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',NomType,i1,[],j1);
2985        if ~exist(imagename,'file')
2986            [FileName,PathName] = uigetfile( ...
2987                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
2988                '*.jpg',' jpeg image files'; ...
2989                '*.png','.png image files'; ...
2990                '*.tif','.tif image files'; ...
2991                '*.avi;*.AVI','.avi movie files'; ...
2992                '*.vol','.volume images (png)'; ...
2993                '*.*',  'All Files (*.*)'}, ...
2994                'Pick an image',imagename);
2995            % display the selected field and related information
2996            imagename=[PathName FileName];
2997        end
2998        set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
2999        set(handles.TitleNpy,'Visible','on')
3000        set(handles.num_Npx,'Visible','on')
3001        set(handles.num_Npy,'Visible','on')
3002        display_file_name(hObject, eventdata, handles,imagename,2)%display the imag
3003    otherwise
3004        if check_new
3005            UvData.FileType{2}=UvData.FileType{1};
3006            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3007            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3008        end
3009        if ~isequal(field,'image')
3010            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3011            set(handles.TitleNpy,'Visible','off')
3012            set(handles.num_Npx,'Visible','off')
3013            set(handles.num_Npy,'Visible','off')
3014        end
3015        set(handles.uvmat,'UserData',UvData)
3016        setfield(handles);% update the field structure ('civ1'....)
3017        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3018            run0_Callback(hObject, eventdata, handles)
3019        end
3020end
3021
3022%------------------------------------------------------------------------
3023% --- set the visibility of relevant velocity type menus:
3024function menu=set_veltype_display(Civ)
3025%------------------------------------------------------------------------
3026if isequal(Civ,0)
3027    imax=0;
3028elseif isequal(Civ,1) || isequal(Civ,2)
3029   imax=1;
3030elseif isequal(Civ,3)
3031    imax=3;
3032elseif isequal(Civ,4) || isequal(Civ,5)
3033    imax=4;
3034elseif isequal(Civ,6) %patch2
3035    imax=6;
3036end
3037menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3038menu=menu(1:imax);
3039
3040%------------------------------------------------------------------------
3041% --- Executes on button press in VelType.
3042function VelType_Callback(hObject, eventdata, handles)
3043%------------------------------------------------------------------------
3044set(handles.FixVelType,'Value',1)
3045run0_Callback(hObject, eventdata, handles)
3046
3047%------------------------------------------------------------------------
3048% --- Executes on button press in VelType.
3049function VelType_1_Callback(hObject, eventdata, handles)
3050%------------------------------------------------------------------------
3051 
3052set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3053%refresh field with a second filename=first fiel name
3054set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3055drawnow   
3056InputFile=read_GUI(handles.InputFile);
3057[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3058filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3059%filename=read_file_boxes(handles);
3060
3061index=get(handles.VelType_1,'Value');
3062if index==1
3063        filename_1='';% we plot the current field without the second field
3064        set(handles.SubField,'Value',0)
3065        SubField_Callback(hObject, eventdata, handles)
3066elseif get(handles.SubField,'Value')% if subfield is already 'on'
3067      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3068     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3069    %filename_1=read_file_boxes_1(handles); %read the current second field
3070else
3071     filename_1=filename;% we compare two fields in the same file
3072     set(handles.SubField,'Value',1)
3073end
3074
3075num_i1=stra2num(get(handles.i1,'String'));
3076num_i2=stra2num(get(handles.i2,'String'));
3077num_j1=stra2num(get(handles.j1,'String'));
3078num_j2=stra2num(get(handles.j2,'String'));
3079
3080errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
3081
3082if ~isempty(errormsg)
3083    msgbox_uvmat('ERROR',errormsg);
3084else
3085    set(handles.i1,'BackgroundColor',[1 1 1])
3086    set(handles.i2,'BackgroundColor',[1 1 1])
3087    set(handles.j1,'BackgroundColor',[1 1 1])
3088    set(handles.j2,'BackgroundColor',[1 1 1])
3089    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3090    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3091end
3092set(handles.run0,'BackgroundColor',[1 0 0])
3093
3094%-----------------------------------------------
3095% --- reset civ buttons
3096function reset_vel_type(handles_civ0,handle1)
3097for ibutton=1:length(handles_civ0)
3098    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3099    set(handles_civ0(ibutton),'Value',0)
3100end
3101if exist('handle1','var')%handles of selected button
3102        set(handle1,'BackgroundColor',[1 1 0]) 
3103end
3104
3105%-------------------------------------------------------
3106% --- Executes on button press in MENUVOLUME.
3107%-------------------------------------------------------
3108function VOLUME_Callback(hObject, eventdata, handles)
3109%errordlg('command VOL not implemented yet')
3110if ishandle(handles.UVMAT_title)
3111    delete(handles.UVMAT_title)
3112end
3113UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3114if isequal(get(handles.VOLUME,'Value'),1)
3115    set(handles.CheckZoom,'Value',0)
3116    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3117    set(handles.edit_vect,'Value',0)
3118    edit_vect_Callback(hObject, eventdata, handles)
3119    set(handles.edit_object,'Value',0)
3120    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3121%     set(handles.cal,'Value',0)
3122%     set(handles.cal,'BackgroundColor',[0 1 0])
3123    set(handles.edit_vect,'Value',0)
3124    edit_vect_Callback(hObject, eventdata, handles)
3125    %initiate set_object GUI
3126    data.TITLE='VOLUME';
3127    if isfield(UvData,'CoordType')
3128        data.CoordType=UvData.CoordType;
3129    end
3130    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3131        data.RangeY=UvData.Mesh;
3132        data.RangeX=UvData.Mesh;
3133        data.DX=UvData.Mesh;
3134        data.DY=UvData.Mesh;
3135    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3136        np=size(UvData.Field.A);
3137        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3138        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3139        data.RangeY=max(meshx,meshy);
3140        data.RangeX=max(meshx,meshy);
3141        data.DX=max(meshx,meshy);
3142    end
3143    data.ParentButton=handles.VOLUME;
3144    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3145    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3146                                                      % associate the set_object interface handle to the plotting axes
3147    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3148    pos_uvmat=get(huvmat,'Position');
3149    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3150    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3151    set(hset_object,'Position',pos_set_object)
3152    end
3153    UvData.MouseAction='create_object';
3154else
3155    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3156    UvData.MouseAction='none';
3157end
3158set(huvmat,'UserData',UvData)
3159
3160%-------------------------------------------------------
3161function edit_vect_Callback(hObject, eventdata, handles)
3162%-------------------------------------------------------
3163%
3164% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3165if isequal(get(handles.edit_vect,'Value'),1)
3166    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3167    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3168    if ~test_civ2 && ~test_civ1
3169        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3170    end
3171    set(handles.record,'Visible','on')
3172    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3173    set(handles.edit_object,'Value',0)
3174    set(handles.CheckZoom,'Value',0)
3175    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3176%     set(handles.create,'Value',0)
3177%     set(handles.create,'BackgroundColor',[0 1 0])
3178    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3179    set(gcf,'Pointer','arrow')
3180%     UvData.MouseAction='edit_vect';
3181else
3182    set(handles.record,'Visible','off')
3183    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3184%     UvData.MouseAction='none';
3185end
3186% set(handles.uvmat,'UserData',UvData)
3187
3188%----------------------------------------------
3189function save_mask_Callback(hObject, eventdata, handles)
3190%-----------------------------------------------------------------------
3191UvData=get(handles.uvmat,'UserData');
3192
3193flag=1;
3194npx=size(UvData.Field.A,2);
3195npy=size(UvData.Field.A,1);
3196xi=0.5:npx-0.5;
3197yi=0.5:npy-0.5;
3198[Xi,Yi]=meshgrid(xi,yi);
3199if isfield(UvData,'Object')
3200    for iobj=1:length(UvData.Object)
3201        ObjectData=UvData.Object{iobj};
3202        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3203            flagobj=1;
3204            testphys=0; %coordinates in pixels by default
3205            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3206                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3207                    Calib=UvData.XmlData{1}.GeometryCalib;
3208                    testphys=1;
3209                end
3210            end
3211            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3212                if isequal(ObjectData.Style,'polygon')
3213                    X=ObjectData.Coord(:,1);
3214                    Y=ObjectData.Coord(:,2);
3215                    if testphys
3216                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3217                    end
3218                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3219                elseif isequal(ObjectData.Style,'ellipse')
3220                    if testphys
3221                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3222                    end
3223                    RangeX=max(ObjectData.RangeX);
3224                    RangeY=max(ObjectData.RangeY);
3225                    X2Max=RangeX*RangeX;
3226                    Y2Max=RangeY*RangeY;
3227                    distX=(Xi-ObjectData.Coord(1,1));
3228                    distY=(Yi-ObjectData.Coord(1,2));
3229                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3230                elseif isequal(ObjectData.Style,'rectangle')
3231                    if testphys
3232                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3233                    end
3234                    distX=abs(Xi-ObjectData.Coord(1,1));
3235                    distY=abs(Yi-ObjectData.Coord(1,2));
3236                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3237                end
3238                if isequal(ObjectData.ProjMode,'mask_outside')
3239                    flagobj=~flagobj;
3240                end
3241                flag=flag & flagobj;
3242            end
3243        end
3244    end
3245end
3246% flag=~flag;
3247%mask name
3248RootPath=get(handles.RootPath,'String');
3249RootFile=get(handles.RootFile,'String');
3250RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3251filebase=fullfile(RootPath,RootFile);
3252list=get(handles.masklevel,'String');
3253masknumber=num2str(length(list));
3254maskindex=get(handles.masklevel,'Value');
3255mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3256%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3257imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3258imflag=flipdim(imflag,1);
3259% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3260msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3261imwrite(imflag,mask_name,'BitDepth',8);
3262
3263%display the mask
3264figure;
3265vec=linspace(0,1,256);%define a linear greyscale colormap
3266map=[vec' vec' vec'];
3267colormap(map)
3268
3269image(imflag);
3270
3271%-------------------------------------------------------------------
3272%-------------------------------------------------------------------
3273%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3274
3275%------------------------------------------------------------------
3276
3277%------------------------------------------------------------------
3278% --- Executes on selection change in ListColorScalar: choice of the color code.
3279function ListColorScalar_Callback(hObject, eventdata, handles)
3280%------------------------------------------------------------------
3281% edit the choice for color code
3282list_code=get(handles.ListColorScalar,'String');% list menu fields
3283index_code=get(handles.ListColorScalar,'Value');% selected string index
3284col_code= list_code{index_code(1)}; % selected field
3285if isequal(col_code,'black') || isequal(col_code,'white')
3286   set(handles.Slider1,'Visible','off')
3287   set(handles.Slider2,'Visible','off')
3288   set(handles.num_ColCode1,'Visible','off')
3289   set(handles.num_ColCode2,'Visible','off')
3290   set(handles.CheckFixVecColor,'Visible','off')
3291   set_vec_col_bar(handles)
3292else
3293   set(handles.Slider1,'Visible','on')
3294   set(handles.Slider2,'Visible','on')
3295   set(handles.num_ColCode1,'Visible','on')
3296   set(handles.num_ColCode2,'Visible','on')
3297   set(handles.CheckFixVecColor,'Visible','on') 
3298   if isequal(col_code,'ima_cor')
3299       set(handles.CheckFixVecColor,'Value',0)%fixed scale by default
3300       set(handles.VecColBar,'Value',0)% 3 colors r,g,b by default
3301       set(handles.Slider1,'Min',0);
3302       set(handles.Slider1,'Max',1);
3303       set(handles.Slider2,'Min',0);
3304       set(handles.Slider2,'Max',1);
3305 %      set(handles.min_title_vec,'String','0')
3306       set(handles.num_MaxVec,'String','1')
3307       set(handles.num_ColCode1,'String','0.333')
3308       num_ColCode1_Callback(hObject, eventdata, handles)
3309       set(handles.num_ColCode2,'String','0.666')
3310       num_ColCode2_Callback(hObject, eventdata, handles)
3311   else
3312       set(handles.CheckFixVecColor,'Value',1)%auto scale between min,max by default
3313       set(handles.VecColBar,'Value',1)% colormap 'jet' by default
3314       minval=get(handles.Slider1,'Min');
3315       maxval=get(handles.Slider1,'Max');
3316       set(handles.Slider1,'Value',minval)
3317       set(handles.Slider2,'Value',maxval)
3318       set_vec_col_bar(handles)
3319   end
3320%    slider_update(handles)
3321end
3322%replot the current graph
3323run0_Callback(hObject, eventdata, handles)
3324
3325
3326%----------------------------------------------------------------
3327% -- Executes on slider movement to set the color code
3328%
3329function Slider1_Callback(hObject, eventdata, handles)
3330%------------------------------------------------------------------
3331slider1=get(handles.Slider1,'Value');
3332min_val=str2num(get(handles.num_MinVec,'String'));
3333max_val=str2num(get(handles.num_MaxVec,'String'));
3334col=min_val+(max_val-min_val)*slider1;
3335set(handles.num_ColCode1,'String',num2str(col))
3336if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3337    set(handles.Slider2,'Value',col)
3338    set(handles.num_ColCode2,'String',num2str(col))
3339end
3340num_ColCode1_Callback(hObject, eventdata, handles)
3341
3342%----------------------------------------------------------------
3343% Executes on slider movement to set the color code
3344%----------------------------------------------------------------
3345function Slider2_Callback(hObject, eventdata, handles)
3346slider2=get(handles.Slider2,'Value');
3347min_val=str2num(get(handles.num_MinVec,'String'));
3348max_val=str2num(get(handles.num_MaxVec,'String'));
3349col=min_val+(max_val-min_val)*slider2;
3350set(handles.num_ColCode2,'String',num2str(col))
3351if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3352    set(handles.Slider1,'Value',col)
3353    set(handles.num_ColCode1,'String',num2str(col))
3354end
3355num_ColCode2_Callback(hObject, eventdata, handles)
3356
3357%----------------------------------------------------------------
3358% --- Execute on return carriage on the edit box corresponding to slider 1
3359%----------------------------------------------------------------
3360function num_ColCode1_Callback(hObject, eventdata, handles)
3361set_vec_col_bar(handles)
3362update_plot(handles);
3363
3364%----------------------------------------------------------------
3365% --- Execute on return carriage on the edit box corresponding to slider 2
3366%----------------------------------------------------------------
3367function num_ColCode2_Callback(hObject, eventdata, handles)
3368set_vec_col_bar(handles)
3369update_plot(handles);
3370%------------------------------------------------------------------------
3371%-------------------------------------------------------
3372% --- Executes on button press in CheckFixVecColor.
3373%-------------------------------------------------------
3374function VecColBar_Callback(hObject, eventdata, handles)
3375set_vec_col_bar(handles)
3376
3377%-------------------------------------------------------------
3378% --- Executes on selection change in transform_fct.
3379function transform_fct_Callback(hObject, eventdata, handles)
3380%-------------------------------------------------------------
3381UvData=get(handles.uvmat,'UserData');
3382menu=get(handles.transform_fct,'String');
3383ind_coord=get(handles.transform_fct,'Value');
3384coord_option=menu{ind_coord};
3385list_transform=get(handles.transform_fct,'UserData');
3386ff=functions(list_transform{end}); 
3387if isequal(coord_option,'more...');
3388    coord_fct='';
3389    prompt = {'Enter the name of the transform function'};
3390    dlg_title = 'user defined transform';
3391    num_lines= 1;
3392    [FileName, PathName] = uigetfile( ...
3393       {'*.m', ' (*.m)';
3394        '*.m',  '.m files '; ...
3395        '*.*', 'All Files (*.*)'}, ...
3396        'Pick a file', ff.file);
3397    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3398        PathName(end)=[];
3399    end
3400    transform_selected =fullfile(PathName,FileName);
3401    if ~exist(transform_selected,'file')
3402           return
3403    end
3404   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3405   if ~isequal(ext_fct,'.m')
3406        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3407        return
3408   end
3409   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3410   ind_coord=get(handles.transform_fct,'Value');
3411   addpath(PathName)
3412   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3413   set(handles.transform_fct,'UserData',list_transform)
3414   rmpath(PathName)
3415   % save the new menu in the personal file 'uvmat_perso.mat'
3416   dir_perso=prefdir;%personal Matalb directory
3417   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3418   if exist(profil_perso,'file')
3419       nb_builtin=UvData.OpenParam.NbBuiltin;
3420       for ilist=nb_builtin+1:numel(list_transform)
3421           ff=functions(list_transform{ilist});
3422           transform_fct{ilist-nb_builtin}=ff.file;
3423       end
3424        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3425   end   
3426end
3427
3428%check the current path to the selected function
3429if isa(list_transform{ind_coord},'function_handle')
3430    func=functions(list_transform{ind_coord});
3431    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3432else
3433    set(handles.path_transform,'String','')
3434end
3435
3436set(handles.CheckFixLimits,'Value',0)
3437set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3438
3439%delete drawn objects
3440hother=findobj('Tag','proj_object');%find all the proj objects
3441for iobj=1:length(hother)
3442    delete_object(hother(iobj))
3443end
3444hother=findobj('Tag','DeformPoint');%find all the proj objects
3445for iobj=1:length(hother)
3446    delete_object(hother(iobj))
3447end
3448hh=findobj('Tag','calib_points');
3449if ~isempty(hh)
3450    delete(hh)
3451end
3452hhh=findobj('Tag','calib_marker');
3453if ~isempty(hhh)
3454    delete(hhh)
3455end
3456if isfield(UvData,'Object')
3457     UvData.Object=UvData.Object(1);
3458end
3459set(handles.ListObject,'Value',1)
3460set(handles.ListObject,'String',{''})
3461
3462%delete mask if it is displayed
3463if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3464   UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3465end
3466set(handles.uvmat,'UserData',UvData)
3467run0_Callback(hObject, eventdata, handles)
3468
3469%------------------------------------------------------------------------
3470function histo1_menu_Callback(hObject, eventdata, handles)
3471%--------------------------------------------
3472%plot first histo
3473huvmat=get(handles.histo1_menu,'parent');
3474histo_menu=get(handles.histo1_menu,'String');
3475histo_value=get(handles.histo1_menu,'Value');
3476FieldName=histo_menu{histo_value};
3477update_histo(handles.histo_u,huvmat,FieldName)
3478
3479%------------------------------------------------------------------------
3480function histo2_menu_Callback(hObject, eventdata, handles)
3481%------------------------------------------------------------------------
3482%plot second histo
3483huvmat=get(handles.histo2_menu,'parent');
3484histo_menu=get(handles.histo2_menu,'String');
3485histo_value=get(handles.histo2_menu,'Value');
3486FieldName=histo_menu{histo_value};
3487update_histo(handles.histo_v,huvmat,FieldName)
3488
3489%------------------------------------------------------------------------
3490%read the field .Fieldname stored in UvData and plot its histogram
3491function update_histo(haxes,huvmat,FieldName)
3492%------------------------------------------------------------------------
3493UvData=get(huvmat,'UserData');
3494if ~isfield(UvData.Field,FieldName)
3495    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
3496    return
3497end
3498Field=UvData.Field;
3499FieldHisto=eval(['Field.' FieldName]);
3500if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
3501    indsel=find(Field.FF==0);%find values marked as false
3502    if ~isempty(indsel)
3503        FieldHisto=FieldHisto(indsel);
3504    end
3505end
3506if isempty(Field)
3507    msgbox_uvmat('ERROR',['empty field ' FieldName])
3508else
3509    nxy=size(FieldHisto);
3510    Amin=double(min(min(min(FieldHisto))));%min of image
3511    Amax=double(max(max(max(FieldHisto))));%max of image
3512    if isequal(Amin,Amax)
3513        %msgbox_uvmat('WARNING',['uniform field =' num2str(Amin)]);
3514        cla(haxes)
3515    else
3516        Histo.ListVarName={FieldName,'histo'};
3517        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
3518            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3519        else
3520            if numel(nxy)==2
3521                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3522            else
3523                Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
3524            end
3525        end
3526        %unit
3527        units=[]; %default
3528        for ivar=1:numel(Field.ListVarName)
3529            if strcmp(Field.ListVarName{ivar},FieldName)
3530                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
3531                    units=Field.VarAttribute{ivar}.units;
3532                    break
3533                end
3534            end
3535        end
3536        if ~isempty(units)
3537            Histo.VarAttribute{1}.units=units;
3538        end
3539        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
3540        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
3541            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
3542            eval(['Histo.histo(:,1)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3543        else
3544            for col=1:size(FieldHisto,3)
3545                B=FieldHisto(:,:,col);
3546                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
3547                eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3548            end
3549        end
3550        plot_field(Histo,haxes);
3551    end
3552end
3553
3554%------------------------------------------------
3555%CALLBACKS FOR PLOTTING PARAMETERS
3556%-------------------------------------------------
3557
3558%------------------------------------------------------------------------
3559function num_MinX_Callback(hObject, eventdata, handles)
3560%------------------------------------------------------------------------
3561set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3562set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3563update_plot(handles);
3564
3565%------------------------------------------------------------------------
3566function num_MaxX_Callback(hObject, eventdata, handles)
3567%------------------------------------------------------------------------
3568set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3569set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3570update_plot(handles);
3571
3572%------------------------------------------------------------------------
3573function num_MinY_Callback(hObject, eventdata, handles)
3574%------------------------------------------
3575set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3576set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3577update_plot(handles);
3578
3579%------------------------------------------------------------------------
3580function num_MaxY_Callback(hObject, eventdata, handles)
3581%------------------------------------------------------------------------
3582set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3583set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3584update_plot(handles);
3585
3586%------------------------------------------------------------------------
3587function num_MinA_Callback(hObject, eventdata, handles)
3588%------------------------------------------
3589set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3590set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3591MinA=str2double(get(handles.num_MinA,'String'));
3592MaxA=str2double(get(handles.num_MaxA,'String'));
3593if MinA>MaxA% switch minA and maxA in case of error
3594    MinA_old=MinA;
3595    MinA=MaxA;
3596    MaxA=MinA_old;
3597    set(handles.num_MinA,'String',num2str(MinA,5));
3598    set(handles.num_MaxA,'String',num2str(MaxA,5));
3599end
3600update_plot(handles);
3601
3602%------------------------------------------------------------------------
3603function num_MaxA_Callback(hObject, eventdata, handles)
3604%------------------------------------------------------------------------
3605set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3606set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3607MinA=str2double(get(handles.num_MinA,'String'));
3608MaxA=str2double(get(handles.num_MaxA,'String'));
3609if MinA>MaxA% switch minA and maxA in case of error
3610        MinA_old=MinA;
3611    MinA=MaxA;
3612    MaxA=MinA_old;
3613    set(handles.num_MinA,'String',num2str(MinA,5));
3614    set(handles.num_MaxA,'String',num2str(MaxA,5));
3615end
3616update_plot(handles);
3617
3618%------------------------------------------------------------------------
3619function CheckFixScalar_Callback(hObject, eventdata, handles)
3620%------------------------------------------------------------------------
3621test=get(handles.CheckFixScalar,'Value');
3622if test
3623    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3624else
3625    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3626    update_plot(handles);
3627end
3628
3629%-------------------------------------------------------------------
3630function CheckBW_Callback(hObject, eventdata, handles)
3631%-------------------------------------------------------------------
3632update_plot(handles);
3633
3634%-------------------------------------------------------------------
3635function ListContour_Callback(hObject, eventdata, handles)
3636%-------------------------------------------------------------------
3637val=get(handles.ListContour,'Value');
3638if val==2
3639    set(handles.interval_txt,'Visible','on')
3640    set(handles.num_IncrA,'Visible','on')
3641else
3642    set(handles.interval_txt,'Visible','off')
3643    set(handles.num_IncrA,'Visible','off')
3644end
3645update_plot(handles);
3646
3647%-------------------------------------------------------------------
3648function num_IncrA_Callback(hObject, eventdata, handles)
3649%-------------------------------------------------------------------
3650update_plot(handles);
3651
3652%-------------------------------------------------------------------
3653function CheckHideWarning_Callback(hObject, eventdata, handles)
3654%-------------------------------------------------------------------
3655update_plot(handles);
3656
3657%-------------------------------------------------------------------
3658function CheckHideFalse_Callback(hObject, eventdata, handles)
3659%-------------------------------------------------------------------
3660update_plot(handles);
3661
3662%-------------------------------------------------------------------
3663function num_VecScale_Callback(hObject, eventdata, handles)
3664%-------------------------------------------------------------------
3665set(handles.CheckFixVectors,'Value',1);
3666set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3667update_plot(handles);
3668
3669%-------------------------------------------------------------------
3670function CheckFixVectors_Callback(hObject, eventdata, handles)
3671%-------------------------------------------------------------------
3672test=get(handles.CheckFixVectors,'Value');
3673if test
3674    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3675else
3676    update_plot(handles);
3677    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3678    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3679end
3680
3681%------------------------------------------------------------------------
3682% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3683function CheckDecimate4_Callback(hObject, eventdata, handles)
3684%------------------------------------------------------------------------
3685update_plot(handles);
3686
3687%------------------------------------------------------------------------
3688% --- Executes on selection change in ListColorCode menu
3689function ListColorCode_Callback(hObject, eventdata, handles)
3690%------------------------------------------------------------------------
3691set_vec_col_bar(handles)
3692update_plot(handles);
3693
3694%------------------------------------------------------------------------
3695% --- Executes on button press in CheckFixVecColor.
3696function CheckFixVecColor_Callback(hObject, eventdata, handles)
3697%------------------------------------------------------------------------
3698test=get(handles.CheckFixVecColor,'Value');
3699if test
3700    set(handles.CheckFixVecColor,'BackgroundColor',[1 1 0])
3701else
3702    update_plot(handles);
3703    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3704    set(handles.CheckFixVecColor,'BackgroundColor',[0.7 0.7 0.7])
3705end
3706
3707%------------------------------------------------------------------------
3708% --- Executes on selection change in num_MaxVec.
3709function num_MinVec_Callback(hObject, eventdata, handles)
3710%------------------------------------------------------------------------
3711max_vec_Callback(hObject, eventdata, handles)
3712
3713%------------------------------------------------------------------------
3714% --- Executes on selection change in num_MaxVec.
3715function num_MaxVec_Callback(hObject, eventdata, handles)
3716%------------------------------------------------------------------------
3717set(handles.CheckFixVecColor,'Value',1)
3718CheckFixVecColor_Callback(hObject, eventdata, handles)
3719min_val=str2num(get(handles.num_MinVec,'String'));
3720max_val=str2num(get(handles.num_MaxVec,'String'));
3721slider1=get(handles.Slider1,'Value');
3722slider2=get(handles.Slider2,'Value');
3723colcode1=min_val+(max_val-min_val)*slider1;
3724colcode2=min_val+(max_val-min_val)*slider2;
3725set(handles.num_ColCode1,'String',num2str(colcode1))
3726set(handles.num_ColCode2,'String',num2str(colcode2))
3727update_plot(handles);
3728
3729%------------------------------------------------------------------------
3730% --- update the display of color code for vectors
3731function set_vec_col_bar(handles)
3732%------------------------------------------------------------------------
3733%get the image of the color display button 'VecColBar' in pixels
3734set(handles.VecColBar,'Unit','pixel');
3735pos_vert=get(handles.VecColBar,'Position');
3736set(handles.VecColBar,'Unit','Normalized');
3737width=ceil(pos_vert(3));
3738height=ceil(pos_vert(4));
3739
3740%get slider indications
3741list=get(handles.ListColorCode,'String');
3742ichoice=get(handles.ListColorCode,'Value');
3743colcode.ListColorCode=list{ichoice};
3744colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3745colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3746test3color=strcmp(colcode.ListColorCode,'rgb') || strcmp(colcode.ListColorCode,'bgr');
3747if test3color
3748    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3749    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3750end
3751% colcode.FixedCbounds=0;
3752%colcode.CheckFixVecColor=1;
3753vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3754[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3755oneheight=ones(1,height);
3756A1=colorlist(col_vec,1)*oneheight;
3757A2=colorlist(col_vec,2)*oneheight;
3758A3=colorlist(col_vec,3)*oneheight;
3759A(:,:,1)=A1';
3760A(:,:,2)=A2';
3761A(:,:,3)=A3';
3762set(handles.VecColBar,'Cdata',A)
3763
3764%-------------------------------------------------------------------
3765function update_plot(handles)
3766%-------------------------------------------------------------------
3767UvData=get(handles.uvmat,'UserData');
3768AxeData=UvData.axes3;% retrieve the current plotted data
3769PlotParam=read_GUI(handles.uvmat);
3770[PP,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
3771write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3772
3773%-------------------------------------------------------------------
3774% --- Executes on selection change in edit_object.
3775function edit_object_Callback(hObject, eventdata, handles)
3776%-------------------------------------------------------------------
3777UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3778test=get(handles.edit_object,'Value');
3779if test
3780    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
3781    %suppress the other options
3782    set(handles.CheckZoom,'Value',0)
3783    CheckZoom_Callback(hObject, eventdata, handles)
3784    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
3785    if ishandle(hgeometry_calib)
3786        hhgeometry_calib=guidata(hgeometry_calib);
3787        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
3788        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
3789    end
3790else
3791    UvData.MouseAction='none';
3792    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])   
3793end
3794set(handles.uvmat,'UserData',UvData);
3795hset_object=findobj(allchild(0),'Tag','set_object');
3796if ~isempty(hset_object)
3797    hhset_object=guidata(hset_object);
3798    if test
3799        set(hhset_object.PLOT,'enable','on');
3800    else
3801       set(hhset_object.PLOT,'enable','off');
3802    end
3803end
3804
3805%------------------------------------------------------------------------
3806% --- Executes on selection change in ListObject.
3807function ListObject_Callback(hObject, eventdata, handles)
3808%------------------------------------------------------------------------
3809
3810list_str=get(handles.ListObject,'String');
3811IndexObj_old=get(handles.ListObject,'UserData');%retrieve previous selection
3812IndexObj=get(handles.ListObject,'Value');%present object selection
3813
3814%% 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
3815if length(IndexObj)>2
3816     IndexObj=[IndexObj(end-1) IndexObj(end)];%keeps only the last two selected items at most
3817end
3818
3819%% we select one object
3820if length(IndexObj)==1%
3821    if length(IndexObj_old)>=2 && isequal(IndexObj_old(1),IndexObj)   % we select the first previously selected object->
3822        IndexObj=[1 IndexObj_old(2)];% it desactivates this object and selects the first object for uvmat
3823    elseif length(IndexObj_old)>=2 && isequal(IndexObj_old(2),IndexObj) % we select the second previously selected object->
3824        IndexObj=IndexObj_old(1);% it desactivates this object  and keeps only the first previously selected object (uvmat)
3825    else %
3826        IndexObj=[IndexObj_old(1) IndexObj];% activates a second object while keeping the first previously selected one
3827    end
3828end
3829set(handles.ListObject,'Value',IndexObj); % marks the selected objects in the list
3830set(handles.ListObject,'UserData',IndexObj)% keep the current object selection in memory for next time
3831
3832%% update the object representation
3833set(handles.edit_object,'Value',0) % desactivate the edit object mode
3834edit_object_Callback(hObject, eventdata, handles)
3835UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3836if numel(UvData.Object)<max(IndexObj);
3837    msgbox_uvmat('ERROR','invalid object list')
3838    return
3839end
3840if numel(IndexObj)>=2
3841    UvData.Object=update_obj(UvData,IndexObj(1),IndexObj(2));%update the current object graphic representation
3842    set(handles.uvmat,'UserData',UvData)
3843end
3844
3845%% project on the selected object and update the corresponding plot
3846% hview_field=findobj(allchild(0),'tag','view_field');
3847% ViewObjectAxes=[];%default
3848if ~isequal(IndexObj(1),IndexObj_old(1))
3849    update_object(handles,IndexObj(1),handles.axes3,list_str{IndexObj(1)})%plot the projection in uvmat
3850end
3851hview_field=findobj(allchild(0),'tag','view_field');
3852if length(IndexObj)==2 && (length(IndexObj_old)==1 || ~isequal(IndexObj(2),IndexObj_old(2)))
3853    if isempty(hview_field)
3854        hview_field=view_field;
3855    end
3856    PlotHandles=guidata(hview_field);
3857    update_object(handles,IndexObj(2),PlotHandles.axes3,list_str{IndexObj(2)})%plot the projection in view_field
3858    update_object_color(handles.axes3,PlotHandles.axes3,UvData.Object{IndexObj(2)}.DisplayHandle_uvmat)
3859else
3860    if ~isempty(hview_field)
3861        delete(hview_field)
3862    end
3863    hset_object=findobj(allchild(0),'tag','set_object');
3864    if ~isempty(hset_object)
3865        delete(hset_object)
3866    end
3867    update_object_color(handles.axes3,handles.axes3,[])
3868end
3869
3870%% update the color of the gfraphic object representation: the selected object in magenta, others in blue
3871% update_object_color(handles.axes3,PlotHandles.axes3,UvData.Object{IndexObj(2)}.DisplayHandle_uvmat)
3872
3873%------------------------------------------------------------------------
3874function update_object(handles,IndexObj,ViewObjectAxes,ObjectName)
3875%------------------------------------------------------------------------
3876UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3877ObjectData=UvData.Object{IndexObj};
3878ObjectData.Name=ObjectName;
3879if isequal(get(handles.edit_object,'Value'),1)
3880    ObjectData.enable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
3881end
3882ZBounds=0; % default
3883if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3884    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3885    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3886end
3887hset_object=findobj(allchild(0),'tag','set_object');
3888if ~isempty(hset_object)
3889    delete(hset_object)% delete existing version of set_object
3890end
3891    hset_object=set_object(ObjectData,[],ZBounds);
3892% end
3893edit_test=get(handles.edit_object,'Value');
3894if edit_test
3895    ObjectData.enable_plot=1;
3896else
3897    if isfield(ObjectData,'enable_plot')
3898        ObjectData=rmfield(ObjectData,'enable_plot');
3899    end
3900end
3901
3902uistack(ViewObjectAxes,'top')% display the plotting axes at the top
3903ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
3904plot_field(ProjData,ViewObjectAxes,read_GUI(get(ViewObjectAxes,'Parent')));%read plotting parameters on the uvmat interfacPlotHandles);
3905
3906%------------------------------------------------------------------------
3907%--- update the representation of objects
3908function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
3909%------------------------------------------------------------------------
3910hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object')] ;%find all the proj objects
3911hother=[hother ;findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];
3912for iobj=1:length(hother)
3913    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
3914        set(hother(iobj),'EdgeColor','b')
3915        if isequal(get(hother(iobj),'FaceColor'),'m')
3916            set(hother(iobj),'FaceColor','b')
3917        end
3918    elseif isequal(get(hother(iobj),'Type'),'image')
3919        Acolor=get(hother(iobj),'CData');
3920        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
3921        set(hother(iobj),'CData',Acolor);
3922    else
3923        set(hother(iobj),'Color','b')
3924    end
3925    set(hother(iobj),'Selected','off')
3926end
3927if ~isempty(DisplayHandle)
3928linetype=get(DisplayHandle,'Type');
3929if isequal(linetype,'line')
3930    set(DisplayHandle,'Color','m'); %set the selected object to magenta color
3931elseif isequal(linetype,'rectangle')
3932    set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
3933elseif isequal(linetype,'patch')
3934    set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
3935end
3936SubObjectData=get(DisplayHandle,'UserData');
3937if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
3938    for iobj=1:length(SubObjectData.SubObject)
3939        hsub=SubObjectData.SubObject(iobj);
3940        if isequal(get(hsub,'Type'),'rectangle')
3941            set(hsub,'EdgeColor','m'); %set the selected object to magenta color
3942        elseif isequal(get(hsub,'Type'),'image')
3943            Acolor=get(hsub,'CData');
3944            Acolor(:,:,1)=Acolor(:,:,3);
3945            set(hsub,'CData',Acolor);
3946        else
3947            set(hsub,'Color','m')
3948        end
3949    end
3950end
3951if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
3952    set(SubObjectData.DeformPoint,'Color','m')
3953end
3954end
3955
3956%------------------------------------------------------
3957% --- Executes on button press in Menu/Export/field in workspace.
3958%------------------------------------------------------
3959function MenuExportField_Callback(hObject, eventdata, handles)
3960global Data_uvmat
3961Data_uvmat=get(handles.uvmat,'UserData');
3962evalin('base','global Data_uvmat')%make CurData global in the workspace
3963display('current field :')
3964evalin('base','Data_uvmat') %display CurData in the workspace
3965commandwindow; %brings the Matlab command window to the front
3966
3967%------------------------------------------------------
3968% --- Executes on button press in Menu/Export/extract figure.
3969%------------------------------------------------------
3970function MenuExport_plot_Callback(hObject, eventdata, handles)
3971huvmat=get(handles.MenuExport_plot,'parent');
3972UvData=get(huvmat,'UserData');
3973hfig=figure;
3974newaxes=copyobj(handles.axes3,hfig);
3975map=colormap(handles.axes3);
3976colormap(map);%transmit the current colormap to the zoom fig
3977colorbar
3978
3979
3980% --------------------------------------------------------------------
3981function Insert_Callback(hObject, eventdata, handles)
3982
3983
3984% --------------------------------------------------------------------
3985function MenuHelp_Callback(hObject, eventdata, handles)
3986% --------------------------------------------------------------------
3987path_to_uvmat=which ('uvmat');% check the path of uvmat
3988pathelp=fileparts(path_to_uvmat);
3989helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3990if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
3991else
3992    addpath (fullfile(pathelp,'uvmat_doc'))
3993    web(helpfile);
3994end
3995
3996%------------------------------------------------------------------------
3997% --------------------------------------------------------------------
3998function MenuExportMovie_Callback(hObject, eventdata, handles)
3999% --------------------------------------------------------------------
4000set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4001huvmat=get(handles.run0,'parent');
4002UvData=get(huvmat,'UserData');
4003%[xx,xx,FileBase]=read_file_boxes(handles);
4004[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4005FileBase=fullfile(RootPath,RootFile);
4006 %read the current input file name
4007prompt = {'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)'};
4008dlg_title = 'select properties of the output avi movie';
4009num_lines= 1;
4010% nbfield_cell=get(handles.last_i,'String');
4011def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4012answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4013aviname=answer{1};
4014fps=str2double(answer{2});
4015% check for existing file with output name aviname
4016if exist(aviname,'file')
4017    backup=aviname;
4018    testexist=2;
4019    while testexist==2
4020        backup=[backup '~'];
4021        testexist=exist(backup,'file');     
4022    end
4023    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4024    if isequal(success,1)
4025        delete(aviname)%delete existing file
4026    else
4027        msgbox_uvmat('ERROR',message)
4028        return
4029    end
4030end
4031%create avi open
4032aviobj=avifile(aviname,'Compression','None','fps',fps);
4033
4034%display first view for tests
4035newfig=figure;
4036newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4037set(newaxes,'Tag','movieaxes')
4038nbpix=[512 384]*str2double(answer{3});
4039set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4040set(newaxes,'Position',eval(answer{4}));
4041map=colormap(handles.axes3);
4042colormap(map);%transmit the current colormap to the zoom fig
4043msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4044        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4045UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4046set(huvmat,'UserData',UvData);
4047increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4048set(handles.STOP,'Visible','on')
4049set(handles.speed,'Visible','on')
4050set(handles.speed_txt,'Visible','on')
4051set(handles.Movie,'BusyAction','queue')
4052
4053%imin=str2double(get(handles.i1,'String'));
4054imax=str2double(answer{5});
4055% if isfield(UvData,'Time')
4056htitle=get(newaxes,'Title');
4057xlim=get(newaxes,'XLim');
4058ylim=get(newaxes,'YLim');
4059set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4060time_str=get(handles.abs_time,'String');
4061set(htitle,'String',['t=' time_str])
4062set(handles.speed,'Value',1)
4063for i=1:imax
4064    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4065            runpm(hObject,eventdata,handles,increment)% run plus
4066            drawnow
4067            time_str=get(handles.abs_time,'String');
4068            if ishandle(htitle)
4069             set(htitle,'String',['t=' time_str])
4070            end
4071            mov=getframe(newfig);
4072            aviobj=addframe(aviobj,mov);
4073    end
4074end
4075aviobj=close(aviobj);
4076UvData=rmfield(UvData,'plotaxes');
4077%UvData.Object{1}.plotaxes=handles.axes3;
4078set(huvmat,'UserData',UvData);
4079msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4080
4081%------------------------------------------------------------------------
4082function MenuCalib_Callback(hObject, eventdata, handles)
4083%------------------------------------------------------------------------
4084
4085UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4086
4087%suppress competing options
4088set(handles.CheckZoom,'Value',0)
4089set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4090set(handles.ListObject,'Value',1)     
4091% initiate display of GUI geometry_calib
4092data=[]; %default
4093if isfield(UvData,'CoordType')
4094    data.CoordType=UvData.CoordType;
4095end
4096pos=get(handles.uvmat,'Position');
4097pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4098pos(2)=pos(2)-0.02;
4099%[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
4100[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4101FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4102set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4103if isfield(UvData.OpenParam,'CalOrigin')
4104    pos_uvmat=get(handles.uvmat,'Position');
4105    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4106    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4107    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4108end
4109geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4110set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4111set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4112
4113%------------------------------------------------------------------------
4114function MenuMask_Callback(hObject, eventdata, handles)
4115%------------------------------------------------------------------------
4116UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4117ListObj=UvData.Object;
4118select=zeros(1,numel(ListObj));
4119for iobj=1:numel(ListObj);
4120    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4121        select(iobj)=1;
4122    end
4123end
4124val=find(select);
4125if isempty(val)
4126    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4127    return
4128else
4129    set(handles.ListObject,'Max',2);%allow multiple selection
4130    set(handles.ListObject,'Value',val);
4131    flag=1;
4132    npx=size(UvData.Field.A,2);
4133    npy=size(UvData.Field.A,1);
4134    xi=0.5:npx-0.5;
4135    yi=0.5:npy-0.5;
4136    [Xi,Yi]=meshgrid(xi,yi);
4137    if isfield(UvData,'Object')
4138        for iobj=1:length(UvData.Object)
4139            ObjectData=UvData.Object{iobj};
4140            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4141                flagobj=1;
4142                testphys=0; %coordinates in pixels by default
4143                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4144                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4145                        Calib=UvData.XmlData{1}.GeometryCalib;
4146                        testphys=1;
4147                    end
4148                end
4149                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Style')
4150                    if isequal(ObjectData.Style,'polygon')
4151                        X=ObjectData.Coord(:,1);
4152                        Y=ObjectData.Coord(:,2);
4153                        if testphys
4154                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4155                        end
4156                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4157                    elseif isequal(ObjectData.Style,'ellipse')
4158                        if testphys
4159                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4160                        end
4161                        RangeX=max(ObjectData.RangeX);
4162                        RangeY=max(ObjectData.RangeY);
4163                        X2Max=RangeX*RangeX;
4164                        Y2Max=RangeY*RangeY;
4165                        distX=(Xi-ObjectData.Coord(1,1));
4166                        distY=(Yi-ObjectData.Coord(1,2));
4167                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4168                    elseif isequal(ObjectData.Style,'rectangle')
4169                        if testphys
4170                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4171                        end
4172                        distX=abs(Xi-ObjectData.Coord(1,1));
4173                        distY=abs(Yi-ObjectData.Coord(1,2));
4174                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4175                    end
4176                    if isequal(ObjectData.ProjMode,'mask_outside')
4177                        flagobj=~flagobj;
4178                    end
4179                    flag=flag & flagobj;
4180                end
4181            end
4182        end
4183    end
4184    %mask name
4185    RootPath=get(handles.RootPath,'String');
4186    RootFile=get(handles.RootFile,'String');
4187    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4188        RootFile(1)=[];
4189    end
4190    filebase=fullfile(RootPath,RootFile);
4191    list=get(handles.masklevel,'String');
4192    masknumber=num2str(length(list));
4193    maskindex=get(handles.masklevel,'Value');
4194    mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4195    %mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4196    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4197    imflag=flipdim(imflag,1);
4198
4199    %display the mask
4200    hfigmask=figure;
4201    set(hfigmask,'Name','mask image')
4202    vec=linspace(0,1,256);%define a linear greyscale colormap
4203    map=[vec' vec' vec'];
4204    colormap(map)
4205    image(imflag);
4206    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4207    if ~strcmp(answer,'Cancel')
4208        mask_dir=fileparts(answer);
4209        if ~exist(mask_dir,'dir')
4210            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4211            return
4212        end
4213        imwrite(imflag,answer,'BitDepth',8);
4214    end
4215    set(handles.ListObject,'Value',1)
4216    set(handles.ListObject,'Max',1)
4217end
4218
4219%------------------------------------------------------------------------
4220%-- open the GUI set_grid.fig to create grid
4221function MenuGrid_Callback(hObject, eventdata, handles)
4222%------------------------------------------------------------------------
4223%suppress the other options if grid is chosen
4224set(handles.edit_vect,'Value',0)
4225edit_vect_Callback(hObject, eventdata, handles)
4226set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4227set(handles.ListObject,'Value',1)     
4228
4229%prepare display of the set_grid GUI
4230[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4231FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4232CoordList=get(handles.transform_fct,'String');
4233val=get(handles.transform_fct,'Value');
4234set_grid(FileName,CoordList{val});% call the set_object interface
4235
4236%------------------------------------------------------------------------
4237% open the GUI 'series'
4238function MenuSeries_Callback(hObject, eventdata, handles)
4239%------------------------------------------------------------------------
4240series; %first display of the GUI to fill waiting time
4241[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4242param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4243if isequal(get(handles.SubField,'Value'),1)
4244    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
4245    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
4246    %FileName_1=read_file_boxes_1(handles);%
4247    if ~isequal(FileName_1,param.FileName)
4248        param.FileName_1=FileName_1;
4249    end
4250end
4251param.NomType=get(handles.NomType,'String');
4252% param.NomType=get(handles.FileIndex,'UserData');
4253param.NomType_1=get(handles.NomType_1,'String');
4254% param.NomType_1=get(handles.FileIndex_1,'UserData');
4255param.CheckFixPair=get(handles.CheckFixPair,'Value');
4256huvmat=get(handles.MenuSeries,'parent');
4257UvData=get(huvmat,'UserData');
4258if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4259    param.Time=UvData.XmlData{1}.Time;
4260end
4261if isequal(get(handles.scan_i,'Value'),1)
4262    param.incr_i=str2num(get(handles.increment_scan,'String'));
4263elseif isequal(get(handles.scan_j,'Value'),1)
4264    param.incr_j=str2num(get(handles.increment_scan,'String'));
4265end
4266param.list_fields=get(handles.Fields,'String');% list menu fields
4267param.list_fields(1)=[]; %suppress  'image' option
4268param.index_fields=get(handles.Fields,'Value');% selected string index
4269if param.index_fields>1
4270    param.index_fields=param.index_fields-1;
4271end
4272param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4273param.list_fields_1(1)=[]; %suppress  'image' option
4274param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4275if param.index_fields_1>1
4276    param.index_fields_1=param.index_fields_1-1;
4277end
4278param.menu_coord_str=get(handles.transform_fct,'String');
4279param.menu_coord_val=get(handles.transform_fct,'Value');
4280series(param); %run the series interface
4281
4282%------------------------------------------------------------------------
4283% -- open the GUI civ.fig for civx (PIV)
4284function MenuPIV_Callback(hObject, eventdata, handles)
4285%------------------------------------------------------------------------
4286 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4287 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4288civ(FileName);% interface de civ(not in the uvmat file)
4289
4290%------------------------------------------------------------------------
4291function MenuTools_Callback(hObject, eventdata, handles)
4292%------------------------------------------------------------------------
4293
4294%------------------------------------------------------------------------
4295function MenuEditObject_Callback(hObject, eventdata, handles)
4296%------------------------------------------------------------------------
4297set(handles.edit_object,'Value',1)
4298edit_Callback(hObject, eventdata, handles)
4299
4300%------------------------------------------------------------------------
4301function enable_transform(handles,state)
4302%------------------------------------------------------------------------
4303set(handles.transform_fct,'Visible',state)
4304set(handles.TRANSFORM_txt,'Visible',state)   
4305set(handles.transform_fct,'Visible',state) 
4306set(handles.path_transform,'Visible',state)
4307set(handles.pxcmx_txt,'Visible',state)
4308set(handles.pxcmy_txt,'Visible',state)
4309set(handles.pxcm,'Visible',state)
4310set(handles.pycm,'Visible',state)
4311
4312%------------------------------------------------------------------------
4313function MenuEditVectors_Callback(hObject, eventdata, handles)
4314%------------------------------------------------------------------------
4315set(handles.edit_vect,'Visible','on')
4316set(handles.edit_vect,'Value',1)
4317edit_vect_Callback(hObject, eventdata, handles)
4318
4319% -----------------------------------------------------------------------
4320function Menupoints_Callback(hObject, eventdata, handles)
4321%------------------------------------------------------------------------
4322data.Style='points';
4323data.ProjMode='projection';%default
4324create_object(data,handles)
4325
4326% -----------------------------------------------------------------------
4327function Menuline_Callback(hObject, eventdata, handles)
4328%------------------------------------------------------------------------
4329data.Style='line';
4330data.ProjMode='projection';%default
4331create_object(data,handles)
4332
4333%------------------------------------------------------------------------
4334function Menupolyline_Callback(hObject, eventdata, handles)
4335%------------------------------------------------------------------------
4336data.Style='polyline';
4337data.ProjMode='projection';%default
4338create_object(data,handles)
4339
4340%------------------------------------------------------------------------
4341function Menupolygon_Callback(hObject, eventdata, handles)
4342%------------------------------------------------------------------------
4343data.Style='polygon';
4344data.ProjMode='inside';%default
4345create_object(data,handles)
4346
4347%------------------------------------------------------------------------
4348function Menurectangle_Callback(hObject, eventdata, handles)
4349%------------------------------------------------------------------------
4350data.Style='rectangle';
4351data.ProjMode='inside';%default
4352create_object(data,handles)
4353
4354%------------------------------------------------------------------------
4355function Menuellipse_Callback(hObject, eventdata, handles)
4356%------------------------------------------------------------------------
4357data.Style='ellipse';
4358data.ProjMode='inside';%default
4359create_object(data,handles)
4360
4361%------------------------------------------------------------------------
4362function MenuMaskObject_Callback(hObject, eventdata, handles)
4363%------------------------------------------------------------------------
4364data.Style='polygon';
4365data.StyleMenu={'polygon'};
4366data.ProjMode='mask_inside';%default
4367data.ProjMenu={'mask_inside';'mask_outside'};
4368create_object(data,handles)
4369
4370%------------------------------------------------------------------------
4371function Menuplane_Callback(hObject, eventdata, handles)
4372%------------------------------------------------------------------------
4373data.Style='plane';
4374data.ProjMode='projection';%default
4375
4376create_object(data,handles)
4377
4378%------------------------------------------------------------------------
4379function Menuvolume_Callback(hObject, eventdata, handles)
4380%------------------------------------------------------------------------
4381data.Style='volume';
4382data.ProjMode='interp';%default
4383% set(handles.create,'Visible','on')
4384% set(handles.create,'Value',1)
4385% VOLUME_Callback(hObject,eventdata,handles)
4386create_object(data,handles)
4387
4388%------------------------------------------------------------------------
4389function MenuBrowseObject_Callback(hObject, eventdata, handles)
4390%------------------------------------------------------------------------
4391%get the object file
4392[FileName, PathName, filterindex] = uigetfile( ...
4393       {'*.xml;*.mat', ' (*.xml,*.mat)';
4394       '*.xml',  '.xml files '; ...
4395        '*.mat',  '.mat matlab files '}, ...
4396        'Pick an xml Object file',get(handles.RootPath,'String'));
4397fileinput=[PathName FileName];%complete file name
4398sizf=size(fileinput);
4399if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4400
4401%read the file
4402t=xmltree(fileinput);
4403data=convert(t);
4404data.enable_plot=1;
4405[pp,data.Name]=fileparts(FileName);
4406%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4407hset_object=findobj(allchild(0),'tag','set_object');
4408if ~isempty(hset_object)
4409    delete(hset_object)% delete existing version of set_object
4410end
4411set_object(data);% call the set_object interface
4412set(handles.edit_object,'Value',0); %suppress the object edit mode
4413set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4414set(handles.MenuObject,'checked','on')
4415set(handles.delete_object,'Visible','on')
4416
4417%------------------------------------------------------------------------
4418% --- generic function used for the creation of a projection object
4419function create_object(data,handles)
4420%------------------------------------------------------------------------
4421hset_object=findobj(allchild(0),'tag','set_object');
4422if ~isempty(hset_object)
4423    delete(hset_object)% delete existing version of set_object
4424end
4425hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4426if ishandle(hgeometry_calib)
4427    hhgeometry_calib=guidata(hgeometry_calib);
4428    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4429    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4430end
4431UvData=get(handles.uvmat,'UserData');
4432set(handles.edit_object,'Value',0); %suppress the object edit mode
4433set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4434data.enable_plot=1;
4435transform_list=get(handles.transform_fct,'String');
4436val=get(handles.transform_fct,'Value');
4437%data.CoordType=transform_list{val};
4438if isfield(UvData,'Field')
4439    Field=UvData.Field;
4440    if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
4441        data.RangeX=Field.Mesh;
4442        data.RangeY=Field.Mesh;
4443        data.DX=Field.Mesh;
4444        data.DY=Field.Mesh;
4445    elseif isfield(Field,'AX')&& isfield(Field,'AY')&& isfield(Field,'A')%only image
4446        np=size(Field.A);
4447        meshx=(Field.AX(end)-Field.AX(1))/np(2);
4448        meshy=abs(Field.AY(end)-Field.AY(1))/np(1);
4449        data.RangeY=max(meshx,meshy);
4450        data.RangeX=max(meshx,meshy);
4451        data.DX=max(meshx,meshy);
4452    end
4453    if isfield(Field,'NbDim')
4454        data.NbDim=Field.NbDim;
4455    end
4456    if isfield(Field,'CoordUnit')
4457        data.CoordUnit=Field.CoordUnit;
4458    end
4459end
4460data.Coord=[0 0 0]; %default
4461if isfield(data,'Style') && isequal(data.Style,'line')
4462    if isfield(data,'DX')
4463        data.Coord=[[0 0 0];[data.DX 0 0]]; %default
4464    else
4465        data.Coord=[[0 0 0];[1 0 0]]; %default
4466    end
4467end
4468if ishandle(handles.UVMAT_title)
4469    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4470end
4471%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4472set_object(data,handles);% call the set_object interface
4473set(handles.MenuObject,'checked','on')
4474set(handles.uvmat,'UserData',UvData)
4475set(handles.CheckZoom,'Value',0)
4476CheckZoom_Callback(handles.uvmat, [], handles)
4477set(handles.delete_object,'Visible','on')
4478% set(handles._title,'Visible','on')
4479% set(handles.view_field_title,'Visible','on')
4480
4481%------------------------------------------------------------------------
4482function MenuRuler_Callback(hObject, eventdata, handles)
4483%------------------------------------------------------------------------
4484set(handles.CheckZoom,'Value',0)
4485CheckZoom_Callback(handles.uvmat, [], handles)
4486set(handles.MenuRuler,'checked','on')
4487UvData=get(handles.uvmat,'UserData');
4488UvData.MouseAction='ruler';
4489set(handles.uvmat,'UserData',UvData);
4490
4491%------------------------------------------------------------------------
4492% --- executed when closing: set the parent interface button to value 0
4493function closefcn(gcbo,eventdata)
4494%------------------------------------------------------------------------
4495%delete all the associated figures if exist
4496hh=findobj(allchild(0),'tag','view_field');
4497if ~isempty(hh)
4498    delete(hh)
4499end
4500hh=findobj(allchild(0),'tag','geometry_calib');
4501if ~isempty(hh)
4502    delete(hh)
4503end
4504hh=findobj(allchild(0),'tag','set_object');
4505if ~isempty(hh)
4506    hhh=findobj(hh,'tag','PLOT');
4507    set(hhh,'enable','off')
4508end
4509
4510%------------------------------------------------------------------------
4511% --- Executes on button press in delete_object.
4512function delete_object_Callback(hObject, eventdata, handles)
4513%------------------------------------------------------------------------
4514IndexObj=get(handles.ListObject,'Value');
4515if IndexObj(end)>1
4516    delete_object(IndexObj(end))
4517end
4518
4519% --- Executes on button press in FixVelType.
4520function FixVelType_Callback(hObject, eventdata, handles)
4521val=get(handles.FixVelType,'Value');
4522if ~val
4523    run0_Callback(hObject, eventdata, handles)
4524end
4525
4526% --- Executes on button press in ViewObject.
4527function ViewObject_Callback(hObject, eventdata, handles)
4528IndexObj=get(handles.ListObject,'Value');
4529IndexObj=IndexObj(end); %keeps only the secodn value
4530UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4531if numel(UvData.Object)<IndexObj;% error in UvData
4532    msgbox_uvmat('ERROR','invalid object list')
4533    return
4534end
4535ObjectData=UvData.Object{IndexObj};
4536ZBounds=0; % default
4537if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4538    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4539    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4540end
4541hset_object=findobj(allchild(0),'tag','set_object');
4542if ~isempty(hset_object)
4543    delete(hset_object)% delete existing version of set_object
4544end
4545hset_object=set_object(ObjectData,[],ZBounds);
4546
4547
4548function NomType_Callback(hObject, eventdata, handles)
4549
4550
4551function NomType_1_Callback(hObject, eventdata, handles)
4552
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