source: trunk/src/uvmat.m @ 387

Last change on this file since 387 was 387, checked in by sommeria, 9 years ago

several bugs corrected: mask, color image...

File size: 194.3 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{1}: movie object representing an input movie
50%          .MovieObject{2}: idem for a second input series (_1)
51%          .filename_1 : last second input file name (to deal with a constant second input without reading again the file)
52%          .VelType_1: last velocity type (VelType, civ2...) for the second input series
53%          .FieldName_1: last field name(velocity, vorticity...) for the second input series
54%          .ZMin, .ZMax: range of the z coordinate
55%..... to complement
56%     - Information on  projection objects
57%           .Object: {[1x1 struct]}
58%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
59%     -Information on the current field (Field{i})
60%            .Txt : text information to display (e.g. error message)
61%            .NbDim: number of dimensions (=0 by default)
62%            .NbCoord: number of vector components
63%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
64%            .dt: time interval for the corresponding image pair
65%            .Mesh: estimated typical distance between vectors
66%            .ZMax:
67%            .ZMin:
68%            .X, .Y, .Z: set of vector coordinates
69%            .U,.V,.W: corresponding set of vector components
70%            .F: corresponding set of warning flags
71%            .FF: corresponding set of false flags, =0 for good vectors
72%            .C: corresponding values of the scalar used for vector color
73%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
74%                     equal to the number of vectors stored in the input open)
75%            .CName: name of the scalar .C
76%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
77%            .A image or scalar
78%            .AX: vector of dimension 2 representing the first and last values
79%              of the X coordinates for the image or scalar known on a regular grid,
80%              or vector of dimension .A for a scaler defined on irregular grid.
81%            .AY: same as .AX along the Y direction
82%            .AName: name of the scalar, ='image' for an image
83
84% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
85%
86% fields are opened and visualised by the sub-function refresh_field.m
87% (called by uvmat_opening, RUN0, runp and runm)
88% The function first reads the name of the input file from the edit boxes  of the GUI
89% A second input file can be introduced for filed comparison
90% It then reads the input file(s) with the appropriate function, read for
91% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf
92% files.
93%               Main input open   second input open(_1)        second image (pair animation)
94%            |                 |                             
95%            |                 |                                               
96%                     Field{1}         Field{2}               
97%                                                                         |
98% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
99%                                                                   Field{i}
100%                                                                    |
101% calc_field.m: calculate scalar or other derived fields (vort, div..).
102%
103% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
104%              Field{i=1->3}.X --> UvData.X                          |
105%                                                                    |
106%                                                                 UvData
107%                                                                    |
108% plot histograms of the whole  field
109% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
110%                                                                    |                                                                          |
111%                                                                ObjectData
112%                                                                    |
113% plot_field.m: plot the projected fields and store them as          |
114% UvData.axes3                                        |
115%                                                                    |
116%                                                                AxeData
117%
118%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
119% scalars are displayed either as an image or countour plot, either as a color of
120% velocity vectors. The scalar values in the first case is represented by
121% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
122% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
123% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
124% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
125% coordinates of the four image corners. The scalar name is represented by
126% the strings .AName and/or .CName.
127% If the scalar exists in an input open (image or scalar stored under its
128% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
129% Else only its name AName is recorded in Field{i}, and its field is then calculated
130%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
131     
132% Properties attached to plotting figures (standard Matlab properties):
133%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
134%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
135%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
136%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
137%    'KeyPressFcn': function called by pressing a key on the key board
138%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
139%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
140
141% Properties attached to plotting axes:
142%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
143%     AxeData:=get(gca,'UserData');
144%     AxeData.Drawing  = create: create a new object
145%                       = deform: modify an existing object by moving its defining create
146%                      = off: no current drawing action
147%                     = translate: translate an existing object
148%                    = calibration: move a calibration point
149%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
150%            .CurrentOrigin: Origin of a curently drawn edit_object
151%            .CurrentLine: currently drawn menuline (A REVOIR)
152%            .CurrentObject: handle of the currently drawn edit_object
153%            .CurrentRectZoom: current rectangle used for CheckZoom
154
155% Properties attached to projection objects (create, menuline, menuplane...):
156%    'Tag'='proj_object': for all projection objects
157%    ObjectData.Type=...: style of projection object:
158%              .ProjMode
159%              .Coord: defines the position of the object
160%              .XMin,YMin....
161%              .XMax,YMax....
162%              .DX,DY,DZ
163%              .Phi, .Theta, .Psi : Euler angles
164%              .X,.Y,.U,.V.... : field data projected on the object
165%              .IndexObj: index in the list of UvData.Object
166           %during plotting
167%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
168%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
169% To each projection object #iobj, corresponds an axis
170% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
171% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
172
173%------------------------------------------------------------------------
174%------------------------------------------------------------------------
175%  I - MAIN FUNCTION UVMAT (DO NOT MODIFY)
176%------------------------------------------------------------------------
177%------------------------------------------------------------------------
178function varargout = uvmat(varargin)
179
180% Begin initialization code - DO NOT EDIT
181gui_Singleton = 1;
182gui_State = struct('gui_Name',          mfilename, ...
183                   'gui_Singleton',     gui_Singleton, ...
184                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
185                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
186                   'gui_LayoutFcn',     [], ...
187                   'gui_Callback',      []);
188if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
189    gui_State.gui_Callback = str2func(varargin{1});
190end
191
192if nargout
193    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
194else
195    gui_mainfcn(gui_State, varargin{:});
196end
197% End initialization code - DO NOT EDIT
198
199%------------------------------------------------------------------------
200% --- Executes just before the GUI uvmat is made visible.
201function uvmat_OpeningFcn(hObject, eventdata, handles, input )
202%------------------------------------------------------------------------
203
204%% Choose default command menuline output for uvmat (standard GUI)
205handles.output = hObject;
206
207%% Update handles structure (standard GUI)
208guidata(hObject, handles);
209
210%% check the path and date of modification of all functions in uvmat
211path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
212[errormsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m
213date_str=['last modification: ' date_str];
214
215
216%% set the position of colorbar and ancillary GUIs:
217set(hObject,'Units','Normalized')
218movegui(hObject,'center')
219UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
220UvData.OpenParam.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
221UvData.OpenParam.SetObjectSize=[0.3 0.7];
222UvData.OpenParam.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
223UvData.OpenParam.CalSize=[0.28 1];
224UvData.axes3=[];%initiate the record of plotted field
225UvData.axes2=[];
226UvData.axes1=[];
227AxeData.LimEditBox=1; %initialise AxeData
228set(handles.axes3,'UserData',AxeData)
229
230%% set functions for the mouse and keyboard
231set(handles.histo_u,'NextPlot','replacechildren');
232set(handles.histo_v,'NextPlot','replacechildren');
233set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
234set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
235set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
236set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
237set(hObject,'DeleteFcn',{@closefcn})%
238
239%% refresh projection plane
240UvData.Object{1}.ProjMode='projection';%main plotting plane
241set(handles.Fields,'Value',1)
242set(handles.Fields,'string',{''})
243
244%% TRANSFORM menu: builtin fcts
245menu_str={'';'phys';'px';'phys_polar'};
246UvData.OpenParam.NbBuiltin=numel(menu_str); %number of functions
247path_uvmat=fileparts(which('uvmat'));
248addpath (path_uvmat) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
249addpath(fullfile(path_uvmat,'transform_field'))%add the path to transform functions,
250fct_handle{1,1}=[];
251testexist=zeros(size(menu_str'));%default
252testexist(1)=1;
253for ilist=2:length(menu_str)
254    if exist(menu_str{ilist},'file')
255        fct_handle{ilist,1}=str2func(menu_str{ilist});
256        testexist(ilist)=1;
257    else
258        testexist(ilist)=0;
259    end
260end
261rmpath(fullfile(path_uvmat,'transform_field'))
262
263%% load the list of previously browsed files in menus Open and Open_1
264 dir_perso=prefdir; % path to the directory .matlab for personal data
265 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
266 if exist(profil_perso,'file')
267      h=load (profil_perso);
268      if isfield(h,'MenuFile')
269          for ifile=1:min(length(h.MenuFile),5)
270              eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
271               eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
272          end
273      end
274      if isfield(h,'transform_fct') && iscell(h.transform_fct)
275         for ilist=1:length(h.transform_fct);
276             if exist(h.transform_fct{ilist},'file')
277                [path,file]=fileparts(h.transform_fct{ilist});
278                addpath(path)
279                h_func=str2func(file);
280                rmpath(path)
281                testexist=[testexist 1];
282             else
283                file='';
284                h_func=[];
285                testexist=[testexist 0];
286             end
287             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
288             menu_str=[menu_str; {file}];
289         end
290      end
291 end
292menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
293fct_handle=fct_handle(testexist==1);
294menu_str=[menu_str;{'more...'}];
295set(handles.transform_fct,'String',menu_str)
296set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
297
298%% case of an input argument for uvmat
299testinputfield=0;
300inputfile=[];
301Field=[];
302if exist('input','var')
303%     if ~isempty(errormsg)
304%         msgbox_uvmat('WARNING',errormsg)
305%     end
306    if ishandle(handles.UVMAT_title)
307        delete(handles.UVMAT_title)
308    end   
309    if isstruct(input)
310        if isfield(input,'InputFile')
311            inputfile=input.InputFile;
312        end
313        if isfield(input,'TimeIndex')
314            set(handles.i1,num2str(input.TimeIndex))
315        end
316        if isfield(input,'FieldsString')
317%             set(handles.Fields,'Value',1)
318            UvData.FieldsString=input.FieldsString;
319        end
320    elseif ischar(input)% file name introduced as input
321           inputfile=input;
322    elseif isnumeric(input)%simple matrix introduced as input
323        sizinput=size(input);
324        if sizinput(1)<=1 || sizinput(2)<=1
325            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
326            return
327        end
328        UvData.Field.ListVarName={'A','coord_y','coord_x'};
329        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
330        UvData.Field.A=input;
331        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
332        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
333        testinputfield=1;
334    end
335else
336   if ishandle(handles.UVMAT_title)
337       set(handles.UVMAT_title,'String',...
338           [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
339           {'GNU General Public License'};...
340           {path_to_uvmat};...
341           {date_str};...
342           {['SVN revision : ' num2str(svn_info.cur_rev)]};...
343           errormsg]);
344   end
345end
346set(handles.uvmat,'UserData',UvData)
347if ~isempty(inputfile)
348    %%%%% display the input field %%%%%%%
349    display_file_name(hObject, eventdata, handles,inputfile)
350    %%%%%%%
351    testinputfield=1;
352end
353
354%% plot input field if exists
355if testinputfield
356    %delete drawn objects
357    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
358    for iobj=1:length(hother)
359        delete_object(hother(iobj))
360    end 
361    if isempty(inputfile)
362        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
363        set(handles.MenuTools,'Enable','on')
364        set(handles.OBJECT_txt,'Visible','on')
365        set(handles.edit_object,'Visible','on')
366        set(handles.ListObject,'Visible','on')
367        set(handles.frame_object,'Visible','on')
368        if ~isempty(errormsg)
369            msgbox_uvmat('ERROR',errormsg)
370        end
371    end
372end
373
374set_vec_col_bar(handles) %update the display of color code for vectors
375
376%------------------------------------------------------------------------
377% --- Outputs from this function are returned to the command menuline.
378function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
379varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
380
381%------------------------------------------------------------------------
382%------------------------------------------------------------------------
383%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
384% automatically sets the global properties when the rootfile name is introduced
385% then activate the view-field action if selected
386% it is activated either by clicking on the RootPath window or by the
387% browser
388%------------------------------------------------------------------------
389%------------------------------------------------------------------------
390% --- Executes on the menu Open/Browse...
391% search the files, recognize their type according to their name and fill the rootfile input windows
392function MenuBrowse_Callback(hObject, eventdata, handles)
393[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
394oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
395% oldfile=read_file_box,es(handles);
396if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
397         dir_perso=prefdir;
398         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
399         if exist(profil_perso,'file')
400              h=load (profil_perso);
401             if isfield(h,'MenuFile_1')
402                  oldfile=h.MenuFile_1;
403             end
404         end
405end
406[FileName, PathName] = uigetfile( ...
407       {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol;*.nc;*.cmx;*.fig;*.log;*.dat;*.bat;', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.vol,*.nc,*.cmx,*.fig,*.log,*.dat,*.bat)';
408       '*.xml',  '.xml files '; ...
409        '*.xls',  '.xls files '; ...
410        '*.civ',  '.civ files '; ...
411        '*.jpg',' jpeg image files'; ...
412        '*.png','.png image files'; ...
413        '*.tif','.tif image files'; ...
414        '*.avi;*.AVI','.avi movie files'; ...
415        '*.vol','.volume images (png)'; ...
416        '*.nc','.netcdf files'; ...
417        '*.cdf','.netcdf files'; ...
418        '*.cmx','.cmx text files ';...
419        '*.fig','.fig files (matlab fig)';...
420        '*.log','.log text files ';...
421        '*.dat','.dat text files ';...
422        '*.bat','.bat system command text files';...
423        '*.*',  'All Files (*.*)'}, ...
424        'Pick a file',oldfile);
425fileinput=[PathName FileName];%complete file name
426sizf=size(fileinput);
427if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
428
429% display the selected field and related information
430display_file_name(hObject, eventdata, handles,fileinput)
431
432% -----------------------------------------------------------------------
433% --- Open again the file whose name has been recorded in MenuFile_1
434function MenuFile_1_Callback(hObject, eventdata, handles)
435%------------------------------------------------------------------------
436fileinput=get(handles.MenuFile_1,'Label');
437display_file_name(hObject, eventdata, handles,fileinput)
438
439% -----------------------------------------------------------------------
440% --- Open again the file whose name has been recorded in MenuFile_2
441function MenuFile_2_Callback(hObject, eventdata, handles)
442%------------------------------------------------------------------------
443fileinput=get(handles.MenuFile_2,'Label');
444display_file_name(hObject, eventdata, handles,fileinput)
445
446% -----------------------------------------------------------------------
447% --- Open again the file whose name has been recorded in MenuFile_3
448function MenuFile_3_Callback(hObject, eventdata, handles)
449%------------------------------------------------------------------------
450fileinput=get(handles.MenuFile_3,'Label');
451display_file_name(hObject, eventdata, handles,fileinput)
452
453% -----------------------------------------------------------------------
454% --- Open again the file whose name has been recorded in MenuFile_4
455function MenuFile_4_Callback(hObject, eventdata, handles)
456%------------------------------------------------------------------------
457fileinput=get(handles.MenuFile_4,'Label');
458display_file_name(hObject, eventdata, handles,fileinput)
459
460% -----------------------------------------------------------------------
461% --- Open again the file whose name has been recorded in MenuFile_5
462function MenuFile_5_Callback(hObject, eventdata, handles)
463%------------------------------------------------------------------------
464fileinput=get(handles.MenuFile_5,'Label');
465display_file_name(hObject, eventdata, handles,fileinput)
466
467%------------------------------------------------------------------------
468% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
469function display_file_name(hObject, eventdata, handles,fileinput,index)
470%------------------------------------------------------------------------
471%% look for the input file existence
472if ~exist(fileinput,'file')
473    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
474    return
475end
476
477%% set the mouse pointer to 'watch'
478set(handles.uvmat,'Pointer','watch')
479set(handles.RootPath,'BackgroundColor',[1 1 0])
480drawnow
481
482%% define the relevant handles for the first fiel series (index=1) or the second file series (index=2)
483if ~exist('index','var')
484    index=1;
485end
486if index==1
487    handles_RootPath=handles.RootPath;
488    handles_SubDir=handles.SubDir;
489    handles_RootFile=handles.RootFile;
490    handles_FileIndex=handles.FileIndex;
491    handles_NomType=handles.NomType;
492    handles_FileExt=handles.FileExt;
493    handles_Fields=handles.Fields;
494elseif index==2
495    handles_RootPath=handles.RootPath_1;
496    handles_SubDir=handles.SubDir_1;
497    handles_RootFile=handles.RootFile_1;
498    handles_FileIndex=handles.FileIndex_1;
499    handles_NomType=handles.NomType_1;
500    handles_FileExt=handles.FileExt_1;
501    handles_Fields=handles.Fields_1;
502    set(handles.RootPath_1,'Visible','on')
503    set(handles.RootFile_1,'Visible','on')
504    set(handles.SubDir_1,'Visible','on');
505    set(handles.FileIndex_1,'Visible','on');
506    set(handles.FileExt_1,'Visible','on');
507    set(handles.NomType_1,'Visible','on');
508end
509
510%% detect root name, nomenclature and indices in the input file name:
511[RootPath,SubDir,tild,i1,i2,j1,j2]=fileparts_uvmat(fileinput);
512[tild,FileName,FileExt]=fileparts(fileinput);
513% detect the file type, get the movie object if relevant, and look for the corresponding file series:
514[RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[FileName FileExt]);
515if strcmp(NomType,'*')% movies will be opened at the first frame
516    i1=1;
517    i2=[];
518    j1=[];
519    j2=[];
520end 
521
522%% open the file or fill the GUI uvmat according to the detected file type
523switch FileType
524    case ''
525        msgbox_uvmat('ERROR','invalid input file type')
526    case 'txt'
527        edit(fileinput)
528    case 'figure'                           %display matlab figure
529        hfig=open(fileinput);
530        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
531        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
532        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
533    case {'xml','xls'}                % edit xml or Excel files
534        editxml(fileinput);
535    otherwise
536        set(handles_RootPath,'String',RootPath);
537        rootname=fullfile(RootPath,SubDir,RootFile);
538        set(handles_SubDir,'String',['/' SubDir]);
539        set(handles_RootFile,'String',['/' RootFile]); %display the separator
540        indices=fileinput(length(rootname)+1:end);
541        indices(end-length(FileExt)+1:end)=[]; %remove extension
542        set(handles_FileIndex,'String',indices);
543        set(handles_NomType,'String',NomType);
544        set(handles_FileExt,'String',FileExt);
545        if index==1
546            % fill file index counters if the first file series is opened
547            set(handles.i1,'String',num2str(i1));
548            set(handles.i2,'String',num2str(i2));
549            set(handles.j1,'String',num2stra(j1,NomType));
550            set(handles.j2,'String',num2stra(j2,NomType));
551        else %read the current field index if the second file series is opened
552            i1=str2num(get(handles.i1,'String'));
553            i2=str2num(get(handles.i2,'String'));
554            j1=stra2num(get(handles.j1,'String'));
555            j2=stra2num(get(handles.j2,'String'));
556        end
557       
558        % synchronise indices of the second  input file if it exists
559        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
560            Input=read_GUI(handles.InputFile);
561            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
562                Input.RootPath_1=Input.RootPath;
563            end
564            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
565                Input.SubDir_1=Input.SubDir;
566            end
567            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
568                Input.RootFile_1=Input.RootFile;
569            end
570            %updtate the indices of the second field series to correspond to the newly opened one
571            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1,i2,j1,j2);
572            if exist(FileName_1,'file')
573                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
574                set(handles.FileIndex_1,'String',FileIndex_1)
575            else
576                set(handles.SubField,'Value',0)
577                SubField_Callback(hObject, eventdata, handles)
578            end
579        end
580       
581        %enable other menus
582        set(handles.MenuOpen_1,'Enable','on')
583        set(handles.MenuFile_1_1,'Enable','on')
584        set(handles.MenuFile_2_1,'Enable','on')
585        set(handles.MenuFile_3_1,'Enable','on')
586        set(handles.MenuFile_4_1,'Enable','on')
587        set(handles.MenuFile_5_1,'Enable','on')
588        set(handles.MenuExport,'Enable','on')
589        set(handles.MenuExportFigure,'Enable','on')
590        set(handles.MenuExportMovie,'Enable','on')
591        set(handles.MenuTools,'Enable','on')
592        set(handles.OBJECT_txt,'Visible','on')
593        set(handles.edit_object,'Visible','on')
594        set(handles.ListObject,'Visible','on')
595        set(handles.frame_object,'Visible','on')
596       
597        % initiate input file series and refresh the current field view:     
598        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
599
600end
601
602%% set back the mouse pointer to arrow
603set(handles.uvmat,'Pointer','arrow')
604
605%------------------------------------------------------------------------
606% --- Called by action in RootPath edit box
607function RootPath_Callback(hObject,eventdata,handles)
608%------------------------------------------------------------------------
609% read the current input file name:
610[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
611%fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
612% detect the file type, get the movie object if relevant, and look for the corresponding file series:
613[tild,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
614% initiate the input file series and refresh the current field view:
615update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject);
616
617%------------------------------------------------------------------------
618% --- Called by action in RootFile edit box
619function SubDir_Callback(hObject, eventdata, handles)
620%------------------------------------------------------------------------
621%refresh the menu of input fields
622Fields_Callback(hObject, eventdata, handles);
623% refresh the current field view
624run0_Callback(hObject, eventdata, handles);
625
626%------------------------------------------------------------------------
627% --- Called by action in RootFile edit box
628function RootFile_Callback(hObject, eventdata, handles)
629%------------------------------------------------------------------------
630RootPath_Callback(hObject,eventdata,handles)
631
632%------------------------------------------------------------------------
633% --- Called by action in FileIndex edit box
634function FileIndex_Callback(hObject, eventdata, handles)
635%------------------------------------------------------------------------
636[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
637set(handles.i1,'String',num2str(i1));
638set(handles.i2,'String',num2str(i2));
639set(handles.j1,'String',num2str(j1));
640set(handles.j2,'String',num2str(j2));
641
642% refresh the current field view
643run0_Callback(hObject, eventdata, handles)
644
645%------------------------------------------------------------------------
646% --- Update information about a new field series (indices to scan, timing,
647%     calibration from an xml file, then refresh current plots
648function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index)
649%------------------------------------------------------------------------
650%% define the relevant handles depending on the index (1=first file series, 2= second file series)
651if ~exist('index','var')
652    index=1;
653end
654if index==1
655    handles_RootPath=handles.RootPath;
656    handles_Fields=handles.Fields;
657elseif index==2
658    handles_RootPath=handles.RootPath_1;
659    handles_Fields=handles.Fields_1;
660end
661
662set(handles_RootPath,'BackgroundColor',[1 1 0])
663drawnow
664set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
665UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
666UvData.NewSeries=1; %flag for run0: begin a new series
667UvData.TestInputFile=1;
668UvData.FileType{index}=FileType;
669UvData.i1_series{index}=i1_series;
670UvData.i2_series{index}=i2_series;
671UvData.j1_series{index}=j1_series;
672UvData.j2_series{index}=j2_series;
673% set(handles.CheckFixPair,'Value',1) % activate by default the comp_input '-'input window
674set(handles.FixVelType,'Value',0); %desactivate fixed veltype
675if index==1
676    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
677else
678    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
679end
680FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
681FileBase=fullfile(RootPath,RootFile);
682if ~exist(FileName,'file')
683   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
684    return
685end
686nbfield=[];%default
687nbfield_j=[];%default
688
689%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
690XmlData.Time=[];%default
691XmlData.GeometryCalib=[];%default
692TimeUnit=[];%default
693testima=0; %test for image input
694imainfo=[];
695ColorType='falsecolor'; %default
696hhh='';
697if isequal(lower(FileExt),'.avi') %.avi file
698    testima=1;
699    imainfo=aviinfo([FileName]);
700    nbfield=imainfo.NumFrames;
701    nbfield_j=1;
702    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
703    XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
704    TimeUnit='s';
705    hhh=which('mmreader');
706    ColorType=imainfo.ImageType;%='truecolor' for color images
707elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
708    testima=1;
709    if ~isequal(SubDir,'')
710       RootFile=get(handles.RootFile,'String');
711        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
712    else
713        imainfo=imfinfo([FileBase FileIndices FileExt]);
714    end
715    ColorType=imainfo.ColorType;%='truecolor' for color images
716    if length(imainfo) >1 %case of image with multiple frames
717        nbfield=length(imainfo);
718        nbfield_j=1;
719    end
720end
721if ~strcmp(hhh,'')% if the function mmreader is found (recent version of matlab)
722    UvData.MovieObject{index}=mmreader([FileBase FileIndices FileExt]);
723else
724    UvData.MovieObject{index}=[];
725end
726if isfield(imainfo,'Width') && isfield(imainfo,'Height')
727    if length(imainfo)>1
728        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
729        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
730    else
731        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
732        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
733    end
734else
735    set(handles.num_Npx,'String','');%fills nbre of pixels x box
736    set(handles.num_Npy,'String','');%fills nbre of pixels x box
737end
738set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
739
740%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
741filexml=[FileBase '.xml'];
742fileciv=[FileBase '.civ'];
743warntext='';%default warning message
744NbSlice=1;%default
745set(handles.RootPath,'BackgroundColor',[1 1 1])
746if exist(filexml,'file')
747    set(handles.view_xml,'Visible','on')
748    set(handles.view_xml,'BackgroundColor',[1 1 0])
749    set(handles.view_xml,'String','view .xml')
750    drawnow
751    [XmlData,warntext]=imadoc2struct(filexml);
752    if ~isempty(warntext)
753        msgbox_uvmat('WARNING',warntext)
754    end
755    if isfield(XmlData,'TimeUnit')
756        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
757            TimeUnit=XmlData.TimeUnit;
758        end
759    end
760    set(handles.view_xml,'BackgroundColor',[1 1 1])
761    drawnow
762    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
763        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
764            set (handles.nb_slice,'String','volume')
765        end
766        hgeometry_calib=findobj('tag','geometry_calib');
767        if ~isempty(hgeometry_calib)
768            GUserData=get(hgeometry_calib,'UserData');
769            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
770                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
771                if strcmp(answer,'Yes')
772                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
773                end
774            end
775        end
776    end 
777elseif exist(fileciv,'file')% if .civ file found
778    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
779    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
780    GeometryCalib.Tx=0;
781    GeometryCalib.Ty=0;
782    GeometryCalib.Tz=1;
783    GeometryCalib.dpx=1;
784    GeometryCalib.dpy=1;
785    GeometryCalib.sx=1;
786    GeometryCalib.Cx=0;
787    GeometryCalib.Cy=0;
788    GeometryCalib.f=1;
789    GeometryCalib.kappa1=0;
790    GeometryCalib.CoordUnit='cm';
791    XmlData.GeometryCalib=GeometryCalib;
792    if error==2, warntext=['no file ' FileBase '.civ'];
793    elseif error==1, warntext='inconsistent number of fields in the .civ file';
794    end 
795    set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
796    set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
797    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
798    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
799    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
800    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
801    set(handles.view_xml,'Visible','on')   
802    set(handles.view_xml,'String','view .civ')
803else
804    set(handles.view_xml,'Visible','off')
805end
806
807%% store last index in handles.lat_i and .last_j
808nbfield=max(max(i2_series));
809if isempty(nbfield)
810    nbfield=max(max(i1_series));
811end
812nbfield_j=max(max(j2_series));
813if isempty(nbfield_j)
814    nbfield_j=max(max(j1_series));
815end
816if ~isempty(XmlData.Time)
817%     nbfield=size(XmlData.Time,1);
818%     nbfield_j=size(XmlData.Time,2);
819    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
820    if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
821        NomType=get(handles.NomType,'String');
822        if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
823            XmlData.Time=(XmlData.Time)';
824%             nbfield=nbfield_j;
825%             nbfield_j=1;
826        end
827    end
828end
829last_i_cell=get(handles.last_i,'String');
830if isempty(nbfield)
831    last_i_cell{1}='';
832else
833    last_i_cell{1}=num2str(nbfield);
834end
835set(handles.last_i,'String',last_i_cell)
836last_j_cell=get(handles.last_j,'String');
837if isempty(nbfield_j)
838     last_j_cell{1}='';
839else
840     last_j_cell{1}=num2str(nbfield_j);
841end
842set(handles.last_j,'String',last_j_cell);
843
844%% store geometric calibration in UvData
845if isfield(XmlData,'GeometryCalib')
846    GeometryCalib=XmlData.GeometryCalib;
847    if isempty(GeometryCalib)
848        set(handles.pxcm,'String','')
849        set(handles.pycm,'String','')
850        set(handles.transform_fct,'Value',1); %  no transform by default
851    else
852        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
853            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
854            set(handles.pxcm,'String','var')
855            set(handles.pycm,'String','var')
856        elseif isfield(GeometryCalib,'fx_fy')
857            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
858            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
859            set(handles.pxcm,'String',num2str(pixcmx))
860            set(handles.pycm,'String',num2str(pixcmy))
861        end
862        if ~get(handles.CheckFixLimits,'Value')
863            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
864        end
865        if isfield(GeometryCalib,'SliceCoord')
866           
867           siz=size(GeometryCalib.SliceCoord);
868           if siz(1)>1
869               NbSlice=siz(1);
870               set(handles.slices,'Visible','on')
871               set(handles.slices,'Value',1)
872           end
873           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
874               set(handles.nb_slice,'String','volume')
875           else
876               set(handles.nb_slice,'String',num2str(NbSlice))
877           end
878           slices_Callback([],[], handles)
879        end           
880    end
881end
882
883%% update the data attached to the uvmat interface
884if ~isempty(TimeUnit)
885    set(handles.time_txt,'String',['time (' TimeUnit ')'])
886end
887UvData.TimeUnit=TimeUnit;
888UvData.XmlData{index}=XmlData;
889UvData.NewSeries=1;
890% UvData.MovieObject=MovieObject;
891
892%display warning message
893if ~isequal(warntext,'')
894    msgbox_uvmat('WARNING',warntext);
895end
896
897%% set default options in menu 'Fields'
898if ~testima
899    testcivx=0;
900    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
901        set(handles_Fields,'Value',1)
902        set(handles_Fields,'String',{'get_field...'})
903        UvData=rmfield(UvData,'FieldsString');
904    else
905        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
906        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
907            FieldList=calc_field;
908            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
909            set(handles_Fields,'Value',2) % set menu to 'velocity'
910            col_vec=FieldList;
911            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
912            testcivx=1;
913        end
914        if ~testcivx
915            set(handles_Fields,'Value',1) % set menu to 'get_field...
916            set(handles_Fields,'String',{'get_field...'})
917            col_vec={'get_field...'};
918        end
919        set(handles.ListColorScalar,'String',col_vec)
920    end
921end
922set(handles.uvmat,'UserData',UvData)
923
924%% set index navigation options and refresh plots
925scan_option='i';%default
926state_j='off'; %default
927if index==2
928    if get(handles.scan_j,'Value')
929        scan_option='j'; %keep the scan option for the second fiel series
930    end
931    if strcmp(get(handles.j1,'Visible'),'on')
932        state_j='on';
933    end
934end
935if ~isempty(j1_series)
936        state_j='on';
937        if isequal(nbfield,1) &&index==1
938            scan_option='j'; %scan j index by default if nbfield=1               
939        end
940end
941if isequal(scan_option,'i')
942     set(handles.scan_i,'Value',1)
943     scan_i_Callback([],[], handles);
944else
945     set(handles.scan_j,'Value',1)
946     scan_j_Callback([],[], handles);
947end
948set(handles.scan_j,'Visible',state_j)
949set(handles.j1,'Visible',state_j)
950set(handles.j2,'Visible',state_j)
951set(handles.last_j,'Visible',state_j);
952set(handles.frame_j,'Visible',state_j);
953set(handles.j_text,'Visible',state_j);
954if ~isempty(i2_series)||~isempty(j2_series)
955    set(handles.CheckFixPair,'Visible','on')
956elseif index==1
957    set(handles.CheckFixPair,'Visible','off')
958end
959
960%% view the field 
961run0_Callback([],[], handles); %view field
962mask_test=get(handles.CheckMask,'value');
963if mask_test
964    MaskData=get(handles.CheckMask,'UserData');
965    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
966          delete(MaskData.maskhandle)    %delete old mask
967    end
968    CheckMask_Callback([],[],handles)
969end
970
971%% update list of recent files in the menubar
972MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
973    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
974str_find=strcmp(FileName,MenuFile);
975if isempty(find(str_find,1))
976    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
977end
978for ifile=1:min(length(MenuFile),5)
979    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
980    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
981end
982dir_perso=prefdir;
983profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
984if exist(profil_perso,'file')
985    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
986else
987    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
988end
989
990
991%------------------------------------------------------------------------
992% --- Executes on the menu Open/Browse_1 for the second input field,
993%     search the files, recognize their type according to their name and fill the rootfile input windows
994function MenuBrowse_1_Callback(hObject, eventdata, handles)
995%------------------------------------------------------------------------
996% huvmat=get(handles.run0,'parent');
997UvData=get(handles.uvmat,'UserData');
998
999RootPath=get(handles.RootPath,'String');
1000[FileName, PathName, filterindex] = uigetfile( ...
1001       {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
1002       '*.xml',  '.xml files '; ...
1003        '*.xls',  '.xls files '; ...
1004        '*.civ',  '.civ files '; ...
1005        '*.jpg','.jpg image files'; ...
1006        '*.png','.png image files'; ...
1007        '*.avi;*.AVI','.avi movie files'; ...
1008        '*.nc','.netcdf files'; ...
1009        '*.cdf','.netcdf files'; ...
1010        '*.cmx','.cmx text files';...
1011        '*.cmx2','.cmx2 text files';...
1012        '*.fig','.fig files (matlab fig)';...
1013        '*.log','.log text files ';...
1014        '*.dat','.dat text files ';...
1015        '*.*',  'All Files (*.*)'}, ...
1016        'Pick a second file for comparison',RootPath);
1017fileinput_1=[PathName FileName];%complete file name
1018sizf=size(fileinput_1);
1019if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
1020
1021% refresh the current displayed field
1022set(handles.SubField,'Value',1)
1023display_file_name(hObject,eventdata,handles,fileinput_1,2)
1024
1025%update list of recent files in the menubar
1026MenuFile_1=fileinput_1;
1027MenuFile_2=get(handles.MenuFile_1,'Label');
1028MenuFile_3=get(handles.MenuFile_2,'Label');
1029MenuFile_4=get(handles.MenuFile_3,'Label');
1030MenuFile_5=get(handles.MenuFile_4,'Label');
1031set(handles.MenuFile_1,'Label',MenuFile_1)
1032set(handles.MenuFile_2,'Label',MenuFile_2)
1033set(handles.MenuFile_3,'Label',MenuFile_3)
1034set(handles.MenuFile_4,'Label',MenuFile_4)
1035set(handles.MenuFile_5,'Label',MenuFile_5)
1036set(handles.MenuFile_1_1,'Label',MenuFile_1)
1037set(handles.MenuFile_2_1,'Label',MenuFile_2)
1038set(handles.MenuFile_3_1,'Label',MenuFile_3)
1039set(handles.MenuFile_4_1,'Label',MenuFile_4)
1040set(handles.MenuFile_5_1,'Label',MenuFile_5)
1041dir_perso=prefdir;
1042profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1043if exist(profil_perso,'file')
1044    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
1045else
1046    txt=ver('MATLAB');
1047    Release=txt.Release;
1048    relnumb=str2double(Release(3:4));
1049    if relnumb >= 14
1050        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
1051    else
1052        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
1053    end
1054end
1055
1056% -----------------------------------------------------------------------
1057% --- Open again as second field the file whose name has been recorded in MenuFile_1
1058function MenuFile_1_1_Callback(hObject, eventdata, handles)
1059% -----------------------------------------------------------------------
1060fileinput_1=get(handles.MenuFile_1_1,'Label');
1061set(handles.SubField,'Value',1)
1062display_file_name(hObject,eventdata,handles,fileinput_1,2)
1063
1064% -----------------------------------------------------------------------
1065% --- Open again as second field the file whose name has been recorded in MenuFile_2
1066function MenuFile_2_1_Callback(hObject, eventdata, handles)
1067% -----------------------------------------------------------------------
1068fileinput_1=get(handles.MenuFile_2_1,'Label');
1069set(handles.SubField,'Value',1)
1070display_file_name(hObject,eventdata,handles,fileinput_1,2)
1071
1072% -----------------------------------------------------------------------
1073% --- Open again as second field the file whose name has been recorded in MenuFile_3
1074function MenuFile_3_1_Callback(hObject, eventdata, handles)
1075% -----------------------------------------------------------------------
1076fileinput_1=get(handles.MenuFile_3_1,'Label');
1077set(handles.SubField,'Value',1)
1078display_file_name(hObject,eventdata,handles,fileinput_1,2)
1079
1080% -----------------------------------------------------------------------
1081% --- Open again as second field the file whose name has been recorded in MenuFile_4
1082function MenuFile_4_1_Callback(hObject, eventdata, handles)
1083% -----------------------------------------------------------------------
1084fileinput_1=get(handles.MenuFile_4_1,'Label');
1085set(handles.SubField,'Value',1)
1086display_file_name(hObject,eventdata,handles,fileinput_1,2)
1087
1088% -----------------------------------------------------------------------
1089% --- Open again as second field the file whose name has been recorded in MenuFile_5
1090function MenuFile_5_1_Callback(hObject, eventdata, handles)
1091% -----------------------------------------------------------------------
1092fileinput_1=get(handles.MenuFile_5_1,'Label');
1093set(handles.SubField,'Value',1)
1094display_file_name(hObject,eventdata,handles,fileinput_1,2)
1095
1096%-----------------------------------------------------------------------
1097% --- Called by action in RootPath_1 edit box
1098function RootPath_1_Callback(hObject,eventdata,handles)
1099% -----------------------------------------------------------------------
1100% update_rootinfo_1(hObject,eventdata,handles)
1101[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
1102%fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1103% detect the file type, get the movie object if relevant, and look for the corresponding file series:
1104[tild,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
1105% initiate the input file series and refresh the current field view:
1106update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
1107%-----------------------------------------------------------------------
1108% --- Called by action in RootFile_1 edit box
1109function RootFile_1_Callback(hObject, eventdata, handles)
1110% -----------------------------------------------------------------------
1111RootPath_1_Callback(hObject,eventdata,handles)
1112
1113%------------------------------------------------------------------------
1114% --- Called by action in FileIndex_1 edit box
1115function FileIndex_1_Callback(hObject, eventdata, handles)
1116%------------------------------------------------------------------------
1117run0_Callback(hObject, eventdata, handles)
1118
1119%------------------------------------------------------------------------
1120% --- switch file index scanning options scan_i and scan_j in an exclusive way
1121function scan_i_Callback(hObject, eventdata, handles)
1122%------------------------------------------------------------------------
1123if get(handles.scan_i,'Value')==1
1124    set(handles.scan_i,'BackgroundColor',[1 1 0])
1125    set(handles.scan_j,'Value',0)
1126else
1127    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1128    set(handles.scan_j,'Value',1)
1129end
1130scan_j_Callback(hObject, eventdata, handles)
1131
1132%------------------------------------------------------------------------
1133% --- switch file index scanning options scan_i and scan_j in an exclusive way
1134function scan_j_Callback(hObject, eventdata, handles)
1135%------------------------------------------------------------------------
1136if get(handles.scan_j,'Value')==1
1137    set(handles.scan_j,'BackgroundColor',[1 1 0])
1138    set(handles.scan_i,'Value',0)
1139    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1140%     NomType=get(handles.NomType,'String');
1141%     switch NomType
1142%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1143%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1144%     otherwise
1145%         set(handles.CheckFixPair,'Visible','off')
1146%     end
1147else
1148    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1149    set(handles.scan_i,'Value',1)
1150    set(handles.scan_i,'BackgroundColor',[1 1 0])
1151    set(handles.CheckFixPair,'Visible','off')
1152end
1153
1154%------------------------------------------------------------------------
1155function i1_Callback(hObject, eventdata, handles)
1156%------------------------------------------------------------------------
1157set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1158NomType=get(handles.NomType,'String');
1159i1=stra2num(get(handles.i1,'String'));
1160i2=stra2num(get(handles.i2,'String'));
1161j1=stra2num(get(handles.j1,'String'));
1162j2=stra2num(get(handles.j2,'String'));
1163indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1164%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1165set(handles.FileIndex,'String',indices)
1166set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1167if get(handles.SubField,'Value')==1
1168    NomType_1=get(handles.NomType_1,'String');
1169    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1170     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1171     set(handles.FileIndex_1,'String',indices)
1172     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1173end
1174
1175%------------------------------------------------------------------------
1176function i2_Callback(hObject, eventdata, handles)
1177%------------------------------------------------------------------------
1178set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1179i1_Callback(hObject, eventdata, handles)
1180
1181%------------------------------------------------------------------------
1182function j1_Callback(hObject, eventdata, handles)
1183%------------------------------------------------------------------------
1184set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1185i1_Callback(hObject, eventdata, handles)
1186
1187%------------------------------------------------------------------------
1188function j2_Callback(hObject, eventdata, handles)
1189%------------------------------------------------------------------------
1190set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1191i1_Callback(hObject, eventdata, handles)
1192
1193%------------------------------------------------------------------------
1194function slices_Callback(hObject, eventdata, handles)
1195%------------------------------------------------------------------------
1196if get(handles.slices,'Value')==1
1197    set(handles.slices,'BackgroundColor',[1 1 0])
1198    set(handles.nb_slice,'Visible','on')
1199    set(handles.z_text,'Visible','on')
1200    set(handles.z_index,'Visible','on')
1201    nb_slice_Callback(hObject, eventdata, handles)
1202else
1203    set(handles.nb_slice,'Visible','off')
1204    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1205    set(handles.z_text,'Visible','off')
1206    set(handles.z_index,'Visible','off')
1207    set(handles.masklevel,'Value',1)
1208    set(handles.masklevel,'String',{'1'})
1209end
1210
1211%------------------------------------------------------------------------
1212function nb_slice_Callback(hObject, eventdata, handles)
1213%------------------------------------------------------------------------
1214nb_slice_str=get(handles.nb_slice,'String');
1215if isequal(nb_slice_str,'volume')
1216    num=stra2num(get(handles.j1,'String'));
1217    last_j=get(handles.last_j,'String');
1218    nbslice=str2double(last_j{1});
1219else
1220    num=str2double(get(handles.i1,'String'));
1221    nbslice=str2double(get(handles.nb_slice,'String'));
1222end
1223z=mod(num-1,nbslice)+1;
1224set(handles.z_index,'String',num2str(z))
1225for ilist=1:nbslice
1226    list_index{ilist,1}=num2str(ilist);
1227end   
1228set(handles.masklevel,'String',list_index)
1229set(handles.masklevel,'Value',z)
1230
1231%------------------------------------------------------------------------
1232% --- Executes on button press in view_xml.
1233function view_xml_Callback(hObject, eventdata, handles)
1234%------------------------------------------------------------------------
1235%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1236 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1237FileBase=fullfile(RootPath,RootFile);
1238option=get(handles.view_xml,'String');
1239if isequal(option,'view .xml')
1240    FileXml=[FileBase '.xml'];
1241    heditxml=editxml(FileXml);
1242end
1243
1244%------------------------------------------------------------------------
1245% --- Executes on button press in CheckMask.
1246function CheckMask_Callback(hObject, eventdata, handles)
1247%------------------------------------------------------------------------
1248%case of view mask selection
1249if isequal(get(handles.CheckMask,'Value'),1)
1250   % [FF,RootPath,FileBase]=read_file_boxes(handles);
1251     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1252     FileBase=fullfile(RootPath,RootFile);
1253    num_i1=stra2num(get(handles.i1,'String'));
1254    num_j1=stra2num(get(handles.j1,'String'));
1255    currentdir=pwd; 
1256    cd(RootPath);
1257    maskfiles=dir('*_*mask_*.png');%look for a mask file
1258    cd(currentdir);%come back to the working directory
1259    mdetect=0;
1260    if ~isempty(maskfiles)
1261        for ilist=1:length(maskfiles)
1262            maskname=maskfiles(ilist).name;% take the first mask file in the list
1263            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1264%             [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1265             [tild,Name]=fileparts(maskname);
1266            Namedouble=double(Name);
1267            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1268            ind_mask=findstr('mask',Name);
1269            i=ind_mask-1;
1270            while val(i)==0 && i>0
1271                i=i-1;
1272            end
1273            nbmask_str=str2num(Name(i+1:ind_mask-1));
1274            if ~isempty(nbmask_str)
1275                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1276            end
1277        end
1278        if isequal(min(nbslice),max(nbslice))
1279            nbslice=nbslice(1);
1280        else
1281            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1282            return
1283        end
1284        if ~isempty(nbslice) && Name(i)=='_'
1285            Mask.Base=[FileBase Name(i:ind_mask+3)];
1286            Mask.NbSlice=nbslice;
1287            num_i1=mod(num_i1-1,nbslice)+1;
1288            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1289            [RootPath,RootFile]=fileparts(Mask.Base);
1290            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1291            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1292            mdetect=exist(maskname,'file');
1293            if mdetect
1294                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1295                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1296                set(handles.CheckMask,'UserData',Mask);
1297                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1298                if nbslice > 1
1299                    set(handles.slices,'value',1)
1300                    slices_Callback(hObject, eventdata, handles)
1301                end
1302            end
1303        end
1304    end
1305    errormsg=[];%default
1306    if mdetect==0
1307        [FileName, PathName, filterindex] = uigetfile( ...
1308            {'*.png', ' (*.png)';
1309            '*.png',  '.png files '; ...
1310            '*.*', 'All Files (*.*)'}, ...
1311            'Pick a mask file *.png',FileBase);
1312        maskname=fullfile(PathName,FileName);
1313        if ~exist(maskname,'file')
1314            errormsg='no file browsed';
1315        end
1316        [RootDir,tild,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1317%         [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1318        Mask.Base=fullfile(RootDir,RootFile);
1319        Mask.NbSlice=1;
1320        set(handles.CheckMask,'UserData',Mask);
1321        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1322    end
1323    if isempty(errormsg)
1324        errormsg=update_mask(handles,num_i1,num_j1);
1325    end
1326    if ~isempty(errormsg)
1327            set(handles.CheckMask,'Value',0)
1328            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1329     end
1330else % desactivate mask display
1331    MaskData=get(handles.CheckMask,'UserData');
1332    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1333          delete(MaskData.maskhandle)   
1334    end
1335    set(handles.CheckMask,'UserData',[])   
1336    UvData=get(handles.uvmat,'UserData');
1337    if isfield(UvData,'MaskName')
1338        UvData=rmfield(UvData,'MaskName');
1339        set(handles.uvmat,'UserData',UvData)
1340    end
1341    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1342end
1343
1344%------------------------------------------------------------------------
1345function errormsg=update_mask(handles,num_i1,num_j1)
1346%------------------------------------------------------------------------
1347errormsg=[];%default
1348MaskData=get(handles.CheckMask,'UserData');
1349if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1350    uistack(MaskData.maskhandle,'top');
1351end
1352num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1353[RootPath,RootFile]=fileparts(MaskData.Base);
1354MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1355%MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1356% huvmat=get(handles.CheckMask,'parent');
1357UvData=get(handles.uvmat,'UserData');
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(handles.uvmat,'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%------------------------------------------------------------------------
1431% huvmat=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=[];%default
1571if strcmp(get(handles.i2,'Visible'),'on')
1572    i2=str2num(get(handles.i2,'String'));
1573end
1574j1=[];
1575if strcmp(get(handles.j1,'Visible'),'on')
1576    j1=stra2num(get(handles.j1,'String'));
1577end
1578j2=j1;
1579if strcmp(get(handles.j2,'Visible'),'on')
1580    j2=stra2num(get(handles.j2,'String'));
1581end
1582sub_value= get(handles.SubField,'Value');
1583if sub_value % a second input file has been entered
1584    [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1585    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndices_1);
1586    NomType_1=get(handles.NomType_1,'String');
1587else
1588    filename_1=[];
1589end   
1590
1591%% increment (or decrement) the field indices and update the input filename(s)
1592CheckSearch=0;
1593if isempty(increment)
1594    CheckSearch=1;% search for the next available file
1595    set(handles.CheckFixPair,'Value',0)
1596end
1597CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1598if CheckFixPair
1599    if get(handles.scan_i,'Value')==1% case of scanning along index i
1600        i1=i1+increment;
1601        i2=i2+increment;
1602        if sub_value
1603            i1_1=i1_1+increment;
1604            i2_1=i2_1+increment;
1605        end
1606    else % case of scanning along index j (burst numbers)
1607        j1=j1+increment;
1608        j2=j2+increment;
1609        if sub_value
1610            j1_1=j1_1+increment;
1611            j2_1=j2_1+increment;
1612        end
1613    end
1614else
1615    UvData=get(handles.uvmat,'UserData');
1616    ref_i=i1;
1617    if ~isempty(i2)
1618        ref_i=floor((i1+i2)/2);
1619    end
1620    ref_j=1;
1621    if ~isempty(j1)
1622        ref_j=j1;
1623        if ~isempty(j2)
1624            ref_j=floor((j1+j2)/2);
1625        end
1626    end
1627    if ~isempty(increment)
1628        if get(handles.scan_i,'Value')==1% case of scanning along index i
1629            ref_i=ref_i+increment;
1630        else % case of scanning along index j (burst numbers)
1631            ref_j=ref_j+increment;
1632        end
1633    else% free increment
1634        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
1635            step=1;
1636        else
1637            step=-1;
1638        end
1639        if get(handles.scan_i,'Value')==1% case of scanning along index i
1640            ref_i=ref_i+step;
1641            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
1642                ref_i=ref_i+step;
1643            end
1644        else % case of scanning along index j (burst numbers)
1645            ref_j=ref_j+step;
1646            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
1647                ref_j=ref_j+step;
1648            end
1649        end
1650    end
1651    if ref_i<0
1652        errormsg='minimum i index reached';
1653    elseif ref_j<0
1654        errormsg='minimum j index reached';
1655    elseif ref_i+1>size(UvData.i1_series{1},1)
1656        errormsg='maximum i index reached';
1657    elseif ref_j+1>size(UvData.i1_series{1},2)
1658        errormsg='maximum j index reached';
1659    end
1660    if ~isempty(errormsg)
1661        return
1662    end
1663    if get(handles.scan_i,'Value')==1% case of scanning along index i
1664        i1_subseries=UvData.i1_series{1}(ref_i+1,:,:);
1665    else
1666        i1_subseries=UvData.i1_series{1}(:,ref_j+1,:);
1667    end
1668    i1_subseries=i1_subseries(i1_subseries>0);
1669    if isempty(i1_subseries)
1670        errormsg='no next file';
1671        return
1672    end
1673    i1=i1_subseries(end);
1674    if ~isempty(UvData.i2_series{1})
1675        if get(handles.scan_i,'Value')==1% case of scanning along index i
1676            i2_subseries=UvData.i2_series{1}(ref_i+1,:,:);
1677        else
1678            i2_subseries=UvData.i2_series{1}(:,ref_j+1,:);
1679        end
1680        i2_subseries=i2_subseries(i2_subseries>0);
1681        i2=i2_subseries(end);
1682    end
1683    if ~isempty(UvData.j1_series{1})
1684        if get(handles.scan_i,'Value')==1% case of scanning along index i
1685            j1_subseries=UvData.j1_series{1}(ref_i+1,:,:);
1686        else
1687            j1_subseries=UvData.j1_series{1}(:,ref_j+1,:);
1688        end
1689        j1_subseries=j1_subseries(j1_subseries>0);
1690        j1=j1_subseries(end);
1691    end
1692    if ~isempty(UvData.j2_series{1})
1693        if get(handles.scan_i,'Value')==1% case of scanning along index i
1694            j2_subseries=UvData.j2_series{1}(ref_i+1,:,:);
1695        else
1696            j2_subseries=UvData.j2_series{1}(:,ref_j+1,:);
1697        end
1698        j2_subseries=j2_subseries(j2_subseries>0);
1699        j2=j2_subseries(end);
1700    end
1701   
1702end
1703filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1704if sub_value
1705    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);
1706end
1707
1708%% refresh plots
1709errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);
1710
1711%% update the index counters if the index move is successfull
1712if isempty(errormsg)
1713    set(handles.i1,'String',num2stra(i1,NomType,1));
1714    if isequal(i2,i1)
1715        set(handles.i2,'String','');
1716    else
1717        set(handles.i2,'String',num2stra(i2,NomType,1));
1718    end
1719    set(handles.j1,'String',num2stra(j1,NomType,2));
1720    if isequal(j2,j1)
1721        set(handles.j2,'String','');
1722    else
1723        set(handles.j2,'String',num2stra(j2,NomType,2));
1724    end
1725   % [indices]=name_generator('',i1,j1,'',NomType,1,i2,j2,'');
1726    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1727    set(handles.FileIndex,'String',indices);
1728    if ~isempty(filename_1)
1729        indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,j2_1);
1730        %indices_1=name_generator('',i1_1,j1_1,'',NomType_1,1,i2_1,j2_1,'');
1731        set(handles.FileIndex_1,'String',indices_1);
1732    end
1733    if isequal(movie_status,1)
1734        set(handles.movie_pair,'Value',1)
1735        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1736    end
1737end
1738
1739%------------------------------------------------------------------------
1740% --- Executes on button press in movie_pair: create an alternating movie with two view
1741function movie_pair_Callback(hObject, eventdata, handles)
1742%------------------------------------------------------------------------
1743%% stop movie action if the movie_pair button is off
1744if ~get(handles.movie_pair,'value')
1745    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1746    set(handles.i2,'String','')
1747    set(handles.j2,'String','')
1748    return
1749else
1750    set(handles.movie_pair,'BusyAction','queue')
1751end
1752
1753%% initialisation
1754set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1755drawnow
1756list_fields=get(handles.Fields,'String');% list menu fields
1757index_fields=get(handles.Fields,'Value');% selected string index
1758FieldName=list_fields{index_fields}; % selected field
1759UvData=get(handles.uvmat,'UserData');
1760if isequal(FieldName,'image')
1761    test_1=0;
1762    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1763    NomType=get(handles.NomType,'String');
1764else
1765    list_fields=get(handles.Fields_1,'String');% list menu fields
1766    index_fields=get(handles.Fields_1,'Value');% selected string index
1767    FieldName=list_fields{index_fields}; % selected field
1768    if isequal(FieldName,'image')
1769        test_1=1;
1770        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1771    else
1772        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1773        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1774        set(handles.movie_pair,'Value',0)
1775        return
1776    end
1777end
1778num_i1=str2num(get(handles.i1,'String'));
1779num_j1=stra2num(get(handles.j1,'String'));
1780num_i2=str2num(get(handles.i2,'String'));
1781num_j2=stra2num(get(handles.j2,'String'));
1782if isempty(num_j2)
1783    if isempty(num_i2)   
1784        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1785        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1786         set(handles.movie_pair,'Value',0)
1787        return
1788    else
1789        num_j2=num_j1;%repeat the index i1 by default
1790    end
1791end
1792if isempty(num_i2)
1793    num_i2=num_i1;%repeat the index i1 by default
1794end
1795% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1796imaname_1=fullfile_uvmat(RootPath,'',RootFile,Ext,NomType,num_i2,[],num_j2);
1797if ~exist(imaname_1,'file')
1798      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1799      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1800       set(handles.movie_pair,'Value',0)
1801      return
1802end
1803
1804%% read the second image
1805Field.AName='image';
1806if test_1
1807    Field_a=UvData.Field_1;
1808else
1809    Field_a=UvData.Field;
1810end
1811Field_b.AX=Field_a.AX;
1812Field_b.AY=Field_a.AY;
1813% z index
1814nbslice=str2double(get(handles.nb_slice,'String'));
1815if ~isempty(nbslice)
1816    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1817end
1818Field_b.CoordUnit='pixel';
1819
1820%% determine the input file type
1821if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1822    FileType='movie';
1823elseif isequal(lower(Ext),'.avi')
1824    FileType='avi';
1825elseif isequal(lower(Ext),'.vol')
1826    FileType='vol';
1827else
1828   form=imformats(Ext(2:end));
1829   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1830       if isequal(NomType,'*');
1831           FileType='multimage';
1832       else
1833           FileType='image';
1834       end
1835   end
1836end
1837switch FileType
1838        case 'movie'
1839            if test_1
1840                Field_b.A=read(UvData.MovieObject{2},num_i2);
1841            else
1842                Field_b.A=read(UvData.MovieObject{1},num_i2);
1843            end
1844        case 'avi'
1845            mov=aviread(imaname_1,num_i2);
1846            Field_b.A=frame2im(mov(1));
1847        case 'vol'
1848            Field_b.A=imread(imaname_1);
1849        case 'multimage'
1850            Field_b.A=imread(imaname_1,num_i2);
1851        case 'image'
1852            Field_b.A=imread(imaname_1);
1853end
1854if get(handles.slices,'Value')
1855    Field.ZIndex=str2double(get(handles.z_index,'String'));
1856end
1857
1858%px to phys or other transform on field
1859menu_transform=get(handles.transform_fct,'String');
1860choice_value=get(handles.transform_fct,'Value');
1861transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1862transform_list=get(handles.transform_fct,'UserData');
1863transform=transform_list{choice_value};
1864if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1865    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
1866        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
1867        Field_b=transform(Field_b,UvData.XmlData{2});
1868    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
1869        Field_b=transform(Field_b,UvData.XmlData{1});
1870    end
1871end
1872
1873 % make movie until movie speed is set to 0 or STOP is activated
1874hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1875set(handles.STOP,'Visible','on')
1876set(handles.speed,'Visible','on')
1877set(handles.speed_txt,'Visible','on')
1878while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1879    % read and plot the series of images in non erase mode
1880    set(hima,'CData',Field_b.A);
1881    pause(1.02-get(handles.speed,'Value'));% wait for next image
1882    set(hima,'CData',Field_a.A);
1883    pause(1.02-get(handles.speed,'Value'));% wait for next image
1884end
1885set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1886 set(handles.movie_pair,'Value',0)
1887
1888%------------------------------------------------------------------------
1889% --- Executes on button press in run0.
1890function run0_Callback(hObject, eventdata, handles)
1891%------------------------------------------------------------------------
1892set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1893drawnow
1894%filename=read_file_boxes(handles);
1895[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1896filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1897filename_1=[];%default
1898if get(handles.SubField,'Value')
1899    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
1900    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
1901   % filename_1=read_file_boxes_1(handles);
1902end
1903num_i1=stra2num(get(handles.i1,'String'));
1904num_i2=stra2num(get(handles.i2,'String'));
1905num_j1=stra2num(get(handles.j1,'String'));
1906num_j2=stra2num(get(handles.j2,'String'));
1907
1908errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
1909
1910if ~isempty(errormsg)
1911      msgbox_uvmat('ERROR',errormsg);
1912else
1913    set(handles.i1,'BackgroundColor',[1 1 1])
1914    set(handles.i2,'BackgroundColor',[1 1 1])
1915    set(handles.j1,'BackgroundColor',[1 1 1])
1916    set(handles.j2,'BackgroundColor',[1 1 1])
1917    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1918    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1919end   
1920set(handles.run0,'BackgroundColor',[1 0 0])
1921
1922
1923%------------------------------------------------------------------------
1924% --- read the input files and refresh all the plots, including projection.
1925% OUTPUT:
1926%  errormsg: error message char string  =[] by default
1927% INPUT:
1928% filename: first input file (=[] in the absence of input file)
1929% filename_1: second input file (=[] in the asbsenc of secodn input file)
1930% num_i1,num_i2,num_j1,num_j2; frame indices
1931% Field: structure describing an optional input field (then replace the input file)
1932function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
1933%------------------------------------------------------------------------
1934
1935%% initialisation
1936abstime=[];
1937abstime_1=[];
1938dt=[];
1939if ~exist('Field','var')
1940    Field={};
1941end
1942UvData=get(handles.uvmat,'UserData');
1943if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1944    delete(handles.UVMAT_title)
1945end
1946
1947%% determine the main input file information for action
1948FileType=[];%default
1949if ~exist(filename,'file')
1950    errormsg=['input file ' filename ' does not exist'];
1951    return
1952end
1953NomType=get(handles.NomType,'String');
1954% NomType=get(handles.FileIndex,'UserData');
1955%update the z position index
1956nbslice_str=get(handles.nb_slice,'String');
1957if isequal(nbslice_str,'volume')%NOT USED
1958    z_index=num_j1;
1959    set(handles.z_index,'String',num2str(z_index))
1960else
1961    nbslice=str2num(nbslice_str);
1962    z_index=mod(num_i1-1,nbslice)+1;
1963    set(handles.z_index,'String',num2str(z_index))
1964end
1965% refresh menu for save_mask if relevant
1966masknumber=get(handles.masklevel,'String');
1967if length(masknumber)>=z_index
1968    set(handles.masklevel,'Value',z_index)
1969end
1970
1971%% read the first input field if a filename has been introduced
1972if ~isempty(filename)
1973    ObjectName=filename;
1974    FieldName=[];%default
1975    VelType=[];%default
1976    FileExt=get(handles.FileExt,'String');
1977    FileType=UvData.FileType{1};
1978    switch FileType
1979        %     if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
1980        case {'civx','civdata','netcdf'};
1981            list_fields=get(handles.Fields,'String');% list menu fields
1982            index_fields=get(handles.Fields,'Value');% selected string index
1983            FieldName= list_fields{index_fields}; % selected field
1984            if ~strcmp(FieldName,'get_field...')
1985                TestVelType=get(handles.FixVelType,'Value');
1986                if TestVelType
1987                    VelType=setfield(handles);% read the velocity type.
1988                end
1989            end
1990            if strcmp(FieldName,'velocity')
1991                list_code=get(handles.ListColorCode,'String');% list menu fields
1992                index_code=get(handles.ListColorCode,'Value');% selected string index
1993                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
1994                    list_code=get(handles.ListColorScalar,'String');% list menu fields
1995                    index_code=get(handles.ListColorScalar,'Value');% selected string index
1996                    ParamIn.ColorVar= list_code{index_code}; % selected field
1997                end
1998            end
1999        case 'video'
2000            ObjectName=UvData.MovieObject{1};         
2001        case 'vol' %TODO: update
2002            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2003                ParamIn.Npy=UvData.XmlData.Npy;
2004                ParamIn.Npx=UvData.XmlData.Npx;
2005            else           
2006                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2007                return
2008            end
2009    end
2010    ParamIn.FieldName=FieldName;
2011    ParamIn.VelType=VelType;
2012    ParamIn.GUIName='get_field';
2013    [Field{1},ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num_i1);
2014    if ~isempty(errormsg)
2015        errormsg=['error in reading ' filename ': ' errormsg];
2016        return
2017    end 
2018    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2019        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2020        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2021    end
2022    if isfield(ParamOut,'TimeIndex')
2023        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2024    end
2025    if isfield(ParamOut,'TimeValue')
2026        Field{1}.Time=ParamOut.TimeValue;
2027    end
2028end
2029
2030%% choose a second field filename_1 if defined
2031VelType_1=[];%default
2032FieldName_1=[];
2033ParamOut_1=[];
2034if ~isempty(filename_1)
2035    if ~exist(filename_1,'file')
2036        errormsg=['second file ' filename_1 ' does not exist'];
2037        return
2038    end
2039    Name=filename_1;
2040    FileType_1=UvData.FileType{2};
2041    switch FileType_1
2042        %     if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
2043        case {'civx','civdata','netcdf'};
2044            list_fields=get(handles.Fields_1,'String');% list menu fields
2045            index_fields=get(handles.Fields_1,'Value');% selected string index
2046            FieldName_1= list_fields{index_fields}; % selected field
2047            if ~strcmp(FieldName,'get_field...')
2048                TestVelType=get(handles.FixVelType,'Value');
2049                if TestVelType
2050                    VelType_1=setfield(handles);% read the velocity type.
2051                end
2052            end
2053            if strcmp(FieldName_1,'velocity')
2054                list_code=get(handles.ListColorCode,'String');% list menu fields
2055                index_code=get(handles.ListColorCode,'Value');% selected string index
2056                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2057                    list_code=get(handles.ListColorScalar,'String');% list menu fields
2058                    index_code=get(handles.ListColorScalar,'Value');% selected string index
2059                    ParamIn.ColorVar= list_code{index_code}; % selected field
2060                end
2061            end
2062        case 'video'
2063            Name=UvData.MovieObject{2};
2064        case 'vol' %TODO: update
2065            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2066                ParamIn.Npy=UvData.XmlData.Npy;
2067                ParamIn.Npx=UvData.XmlData.Npx;
2068            else
2069                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2070                return
2071            end
2072    end
2073    NomType_1=get(handles.NomType_1,'String');
2074    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2075    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2076        if isfield(UvData,'filename_1')&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2077            test_keepdata_1= strcmp(filename_1,UvData.filename_1) && strcmp(VelType_1,UvData.VelType_1) && strcmp(FieldName_1,UvData.FieldName_1);
2078        end
2079    end
2080    if test_keepdata_1
2081        Field{2}=UvData.Field_1;
2082    else
2083        ParamIn.FieldName=FieldName_1;
2084        ParamIn.VelType=VelType_1;
2085        ParamIn.GUIName='get_field_1';
2086        [Field{2},ParamOut_1,errormsg] = read_field(Name,FileType_1,ParamIn,num_i1);
2087        if ~isempty(errormsg)
2088            errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
2089            return
2090        end
2091        UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2092    end
2093    %     end
2094end
2095
2096%% update uvmat interface
2097if isfield(ParamOut,'Npx')
2098    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2099    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2100elseif isfield(ParamOut_1,'Npx')
2101    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2102    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2103end
2104
2105%% update the display menu for the first velocity type (first menuline)
2106test_veltype=0;
2107% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2108if (strcmp(FileType,'civx')||strcmp(FileType,'civdata'))&& ~strcmp(FieldName,'get_field...')
2109    test_veltype=1;
2110    set(handles.VelType,'Visible','on')
2111    set(handles.VelType_1,'Visible','on')
2112    set(handles.FixVelType,'Visible','on')
2113    menu=set_veltype_display(ParamOut.CivStage,FileType);
2114    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2115    index_val=find(index_menu,1);
2116    if isempty(index_val)
2117        index_val=1;
2118    end
2119    set(handles.VelType,'Value',index_val)
2120    if ~get(handles.SubField,'value')
2121        set(handles.VelType,'String',menu)
2122        set(handles.VelType_1,'Value',1)
2123        set(handles.VelType_1,'String',[{''};menu])
2124    end
2125else
2126    set(handles.VelType,'Visible','off')
2127end
2128field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2129set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2130set(handles.Fields,'Value',find(field_index,1))
2131
2132%% update the display menu for the second velocity type (second menuline)
2133test_veltype_1=0;
2134if isempty(filename_1)
2135    set(handles.Fields_1,'Value',1); %update the field menu
2136    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2137else
2138    if ~isequal(FileType_1,'netcdf')|| isequal(FieldName_1,'get_field...')
2139        set(handles.VelType_1,'Visible','off')
2140    else
2141        test_veltype_1=1;
2142        set(handles.VelType_1,'Visible','on')
2143        if ~get(handles.FixVelType,'Value')
2144            menu=set_veltype_display(ParamOut_1.CivStage);
2145            index_menu=strcmp(ParamOut_1.VelType,menu);
2146            set(handles.VelType_1,'Value',1+find(index_menu,1))
2147            set(handles.VelType_1,'String',[{''};menu])
2148        end
2149    end
2150end
2151if test_veltype||test_veltype_1
2152     set(handles.FixVelType,'Visible','on')
2153else
2154     set(handles.FixVelType,'Visible','off')
2155end
2156   
2157%% introduce w as background image by default for a new series (only for nbdim=2)
2158if ~isfield(UvData,'NewSeries')
2159    UvData.NewSeries=1;
2160end
2161%put W as background image by default if NbDim=2:
2162if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2163        set(handles.SubField,'Value',1);
2164        %menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w'
2165        set(handles.RootPath_1,'String','"')
2166        set(handles.RootFile_1,'String','"')
2167        set(handles.SubDir_1,'String','"');
2168         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2169        %[indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,'');
2170        set(handles.FileIndex_1,'String',indices)
2171        set(handles.FileExt_1,'String','"');
2172        set(handles.Fields_1,'Visible','on');
2173        set(handles.Fields_1,'Visible','on');
2174        set(handles.RootPath_1,'Visible','on')
2175        set(handles.RootFile_1,'Visible','on')
2176        set(handles.SubDir_1,'Visible','on');
2177        set(handles.FileIndex_1,'Visible','on');
2178        set(handles.FileExt_1,'Visible','on');
2179        set(handles.Fields_1,'Visible','on');
2180        Field{1}.AName='w';
2181end           
2182
2183%% store the current open names, fields and vel types in uvmat interface
2184UvData.filename_1=filename_1;
2185UvData.VelType_1=[];%default
2186UvData.FieldName_1=[];
2187if isfield(ParamOut_1,VelType)
2188    UvData.VelType_1=ParamOut_1.VelType;
2189end
2190if isfield(ParamOut_1,FieldName)
2191    UvData.FieldName_1=ParamOut_1.FieldName;
2192end
2193
2194%% apply coordinate transform or other user fct
2195XmlData=[];%default
2196XmlData_1=[];%default
2197if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2198    XmlData=UvData.XmlData{1};
2199    if numel(UvData.XmlData)==2
2200        XmlData_1=UvData.XmlData{2};
2201    end
2202end
2203choice_value=get(handles.transform_fct,'Value');
2204transform_list=get(handles.transform_fct,'UserData');
2205transform=transform_list{choice_value};%selected function handles
2206% z index
2207if ~isempty(filename)
2208    Field{1}.ZIndex=z_index;
2209end
2210%px to phys or other transform on field
2211if ~isempty(transform)
2212    if length(Field)>=2
2213        Field{2}.ZIndex=z_index;
2214        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2215        if isempty(Field{2})
2216            Field(2)=[];
2217        end
2218    else
2219        Field{1}=transform(Field{1},XmlData);
2220    end
2221end
2222
2223
2224%% update tps in phys coordinates if needed
2225if (strcmp(VelType,'filter1')||strcmp(VelType,'filter2'))&& strcmp(FileType,'civdata')&&isfield(Field{1},'U')&& isfield(Field{1},'V')
2226    [Field{1}.SubRange,Field{1}.NbSites,Field{1}.Coord_tps,Field{1}.U_tps,Field{1}.V_tps]=filter_tps([Field{1}.X Field{1}.Y],Field{1}.U,Field{1}.V,[],1500,0);
2227end
2228
2229%% calculate scalar
2230if strcmp(FileType(1:3),'civ') && ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
2231    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1},VelType);
2232end
2233if numel(Field)==2 && ~test_keepdata_1 && isequal(FileType_1(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2234    %update tps in phys coordinates if needed
2235    if (strcmp(VelType_1,'filter1')||strcmp(VelType_1,'filter2'))&& strcmp(FileType_1,'civdata')&&isfield(Field{2},'U')&& isfield(Field{2},'V')
2236        [Field{2}.SubRange,Field{2}.NbSites,Field{2}.Coord_tps,Field{2}.U_tps,Field{2}.V_tps]=filter_tps([Field{2}.X Field{2}.Y],Field{2}.U,Field{2}.V,[],1500,0);
2237    end
2238    Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2},VelType_1);
2239end
2240
2241%% combine the two input fields (e.g. substract velocity fields)
2242if numel(Field)==2
2243   UvData.Field=sub_field(Field{1},Field{2}); 
2244else
2245   UvData.Field=Field{1};
2246end
2247
2248%% get bounds and mesh (needed for mouse action and to open set_object)
2249test_x=0;
2250test_z=0;% test for unstructured z coordinate
2251[UvData.Field,errormsg]=check_field_structure(UvData.Field);
2252if ~isempty(errormsg)
2253    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];
2254    return
2255end
2256[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);
2257if ~isempty(errormsg)
2258    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];
2259    return
2260end
2261[NbDim,imax]=max(NbDim);
2262if isfield(UvData.Field,'NbDim')
2263    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2264end
2265if ~isempty(VarType{imax}.coord_x)  && ~isempty(VarType{imax}.coord_y)    %unstructured coordinates
2266    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2267    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2268    eval(['nbvec=length(UvData.Field.' XName ');'])%nbre of measurement points (e.g. vectors)
2269    test_x=1;%test for unstructured coordinates
2270    if ~isempty(VarType{imax}.coord_z)
2271        ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2272    else
2273        NbDim=2;
2274    end
2275elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0 %structured coordinate
2276    XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2277    if NbDim>1
2278        YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2279    end
2280end
2281if NbDim==3
2282    if ~test_x
2283        ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2284    end
2285    eval(['ZMax=max(UvData.Field.' ZName ');'])
2286    eval(['ZMin=min(UvData.Field.' ZName ');'])
2287    UvData.Field.ZMax=ZMax;
2288    UvData.Field.ZMin=ZMin;
2289    test_z=1;
2290    if isequal(ZMin,ZMax)%no z dependency
2291        NbDim=2;
2292        test_z=0;
2293    end
2294end
2295if exist('XName','var')
2296    eval(['XMax=max(max(UvData.Field.' XName '));'])
2297    eval(['XMin=min(min(UvData.Field.' XName '));'])
2298    UvData.Field.NbDim=NbDim;
2299    UvData.Field.XMax=XMax;
2300    UvData.Field.XMin=XMin;
2301    if NbDim >1
2302        eval(['YMax=max(max(UvData.Field.' YName '));'])
2303        eval(['YMin=min(min(UvData.Field.' YName '));'])
2304        UvData.Field.YMax=YMax;
2305        UvData.Field.YMin=YMin;
2306    end
2307    eval(['nbvec=length(UvData.Field.' XName ');'])
2308    if test_x %unstructured coordinates
2309        if test_z
2310            UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2311            UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2312        else
2313            UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2314        end
2315    else
2316        VarIndex=CellVarIndex{imax}; % list of variable indices
2317        DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2318        nbpoints_x=UvData.Field.DimValue(DimIndex(NbDim));
2319        DX=(XMax-XMin)/(nbpoints_x-1);
2320        if NbDim >1
2321            nbpoints_y=UvData.Field.DimValue(DimIndex(NbDim-1));
2322            DY=(YMax-YMin)/(nbpoints_y-1);
2323        end
2324        if NbDim==3
2325            nbpoints_z=UvData.Field.DimValue(DimIndex(1));
2326            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2327            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2328            UvData.Field.ZMax=ZMax;
2329            UvData.Field.ZMin=ZMin;
2330        else
2331            UvData.Field.Mesh=DX;%sqrt(DX*DY);
2332        end
2333    end
2334end
2335
2336%% 3D case (menuvolume)
2337if NbDim==3% && UvData.NewSeries
2338    test_set_object=1;
2339    hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2340    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2341    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2342    if ~isempty(hset_object) %if set_object is detected
2343%         hhset_object=guidata(hset_object);
2344% %         ZBounds_old(1)=get(hhset_object.z_slider,'Min');
2345% %         ZBounds_old(2)=get(hhset_object.z_slider,'Max');
2346% %         if isequal(ZBounds_old,ZBounds)
2347%             test_set_object=0;% do not refresh the GUI set_object
2348%         else
2349            delete(hset_object);% delete the GUI set_object if it does not fit
2350%         end
2351    end
2352    if test_set_object% reinitiate the GUI set_object
2353        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
2354        UvData.Object{1}.Type='plane';%main plotting plane
2355        UvData.Object{1}.ProjMode='projection';%main plotting plane
2356        UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2357        UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2358        UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2359        UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2360        UvData.Object{1}.Angle=[0 0 0];
2361%         UvData.Object{1}.Theta=0;
2362%         UvData.Object{1}.Psi=0;
2363        UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2364%         PlotHandles=get_plot_handles(handles);
2365        UvData.Object{1}.Name='1-PLANE';
2366        UvData.Object{1}.enable_plot=1;
2367        set_object(UvData.Object{1},handles,ZBounds);
2368        set(handles.ListObject,'Value',1);
2369        set(handles.ListObject,'String',{'1-PLANE'});
2370        set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2371        edit_object_Callback([],[], handles)
2372    end
2373    %multilevel case (single menuplane in a 3D space)
2374elseif isfield(UvData,'Z')
2375    if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2376        XmlData=UvData.XmlData{1};
2377        if isfield(XmlData,'PlanePos')
2378            UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2379        end
2380        if isfield(XmlData,'PlaneAngle')
2381            siz=size(XmlData.PlaneAngle);
2382            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2383            UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2384        end
2385    elseif isfield(UvData,'ZIndex')
2386        UvData.Object{1}.ZObject=UvData.ZIndex;
2387    end
2388else
2389    % create a default projection
2390    UvData.Object{1}.ProjMode='projection';%main plotting plane
2391    UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2392    set(handles.ListObject,'Value',1);
2393    list_object=get(handles.ListObject,'String');
2394    if isempty(list_object)
2395        list_object={''};
2396    elseif ~isempty(list_object{1})
2397        list_object=[{''};list_object];
2398    end
2399    set(handles.ListObject,'String',list_object);
2400%     set(handles.list_object_2,'String',list_object);
2401end
2402testnewseries=UvData.NewSeries;
2403UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2404set(handles.uvmat,'UserData',UvData)
2405
2406%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2407if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2408    set(handles.num_MinA,'String','0')
2409    set(handles.num_MaxA,'String','255')
2410end
2411
2412%% Plot the projections on the selected  projection objects
2413% main projection object (uvmat display)
2414list_object=get(handles.ListObject,'String');
2415if isequal(list_object,{''})%refresh list of objects if the menu is empty
2416    UvData.Object={[]};
2417    set(handles.ListObject,'Value',1)
2418end
2419IndexObj=get(handles.ListObject,'Value');%selected projection object for main view
2420if IndexObj(1)> numel(UvData.Object)
2421    IndexObj(1)=1;%select the first object if the selected one does not exist
2422    set(handles.ListObject,'Value',1)
2423end
2424plot_handles{1}=handles;
2425if isfield(UvData,'plotaxes')%case of movies
2426    haxes(1)=UvData.plotaxes;
2427else
2428    haxes(1)=handles.axes3;
2429end
2430%PlotParam{1}=read_plot_param(handles);%read plotting parameters on the uvmat interfac
2431PlotParam{1}=read_GUI(handles.uvmat);
2432if ~isfield(PlotParam{1},'Vectors')
2433    PlotParam{1}.Vectors.MaxVec=1;
2434    PlotParam{1}.Vectors.MinVec=0;
2435    PlotParam{1}.Vectors.CheckFixVecColor=1;
2436    PlotParam{1}.Vectors.ColCode1=0.33;
2437    PlotParam{1}.Vectors.ColCode2=0.66;
2438     PlotParam{1}.Vectors.ListColorScalar={'ima_cor'};
2439     PlotParam{1}.Vectors.ListColorCode= {'rgb'};
2440end
2441keeplim(1)=get(handles.CheckFixLimits,'Value');% test for fixed graph limits
2442PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2443
2444% second projection object (view_field display)
2445if length( IndexObj)>=2
2446    view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2447    if ~isempty(view_field_handle)
2448        plot_handles{2}=guidata(view_field_handle);
2449        haxes(2)=plot_handles{2}.axes3;
2450        %PlotParam{2}=read_plot_param(plot_handles{2});%read plotting parameters on the viewinterface
2451        PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2452        keeplim(2)=get(plot_handles{2}.CheckFixLimits,'Value');
2453        PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2454    end
2455end
2456
2457%loop on the projection objects: one or two
2458for imap=1:numel(IndexObj)
2459    iobj=IndexObj(imap);
2460    [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2461
2462    if ~isempty(errormsg)
2463        return
2464    end
2465    %     if testnewseries && isfield(ObjectData,'CoordUnit')&& isfield(PlotParam{imap},'Coordinates')
2466%         PlotParam{imap}.Coordinates=rmfield(PlotParam{imap}.Coordinates,'CheckFixEqual'); %set FixEqual to depend on the field (=1 if Data.CoordUnit=1 in plot_field)
2467%     end
2468    if testnewseries && isfield(ObjectData,'CoordUnit')
2469        PlotParam{imap}.Coordinates.CheckFixEqual=1;
2470    end
2471    %use of mask (TODO: check)
2472    if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2473        flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2474        AX=ObjectData.AX;%x coordiantes for the scalar field
2475        AY=ObjectData.AY;%y coordinates for the scalar field
2476        MaskX=ObjectData.MaskX;%x coordiantes for the mask
2477        MaskY=ObjectData.MaskY;%y coordiantes for the mask
2478        if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2479            nxy=size(flag_mask);
2480            sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2481            sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2482            x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2483            y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2484            %project on the positions of the scalar
2485            npxy=size(ObjectData.A);
2486            dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2487            dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2488            xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2489            yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2490            [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2491            flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2492        end
2493        AClass=class(ObjectData.A);
2494        ObjectData.A=flag_mask.*double(ObjectData.A);
2495        ObjectData.A=feval(AClass,ObjectData.A);
2496        ind_off=[];
2497        if isfield(ObjectData,'ListVarName')
2498            for ilist=1:length(ObjectData.ListVarName)
2499                if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2500                    ind_off=[ind_off ilist];
2501                end
2502            end
2503            ObjectData.ListVarName(ind_off)=[];
2504            ObjectData.VarDimIndex(ind_off)=[];
2505            ind_off=[];
2506            for ilist=1:length(ObjectData.ListDimName)
2507                if isequal(ObjectData.ListDimName{ilist},'MaskX') || isequal(ObjectData.ListDimName{ilist},'MaskY')
2508                    ind_off=[ind_off ilist];
2509                end
2510            end
2511            ObjectData.ListDimName(ind_off)=[];
2512            ObjectData.DimValue(ind_off)=[];
2513        end
2514    end   
2515    if ~isempty(ObjectData)
2516        PlotType='none'; %default
2517        if imap==2 && isempty(view_field_handle)
2518            view_field(ObjectData)
2519        else
2520            [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2521            write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2522            if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2523                ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2524            end
2525        end
2526        if isequal(PlotType,'none')
2527            hget_field=findobj(allchild(0),'name','get_field');
2528            if isempty(hget_field)
2529                get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2530            end
2531            errormsg='The field defined by get_field cannot be plotted';
2532            return
2533        end
2534    end
2535end
2536
2537%% update the mask
2538if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2539   update_mask(handles,num_i1,num_i2);
2540end
2541
2542%% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2543menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2544ind_bad=[];
2545nb_histo=1;
2546
2547% suppress coordinates from the histogram menu
2548for ivar=1:numel(menu_histo)%l loop on field variables:
2549    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2550        Role=UvData.Field.VarAttribute{ivar}.Role;
2551        switch Role
2552            case {'coord_x','coord_y','coord_z','dimvar'}
2553                ind_bad=[ind_bad ivar];
2554            case {'vector_y'}
2555                nb_histo=nb_histo+1;
2556        end
2557    end
2558    DimCell=UvData.Field.VarDimName{ivar};
2559    DimName='';
2560    if ischar(DimCell)
2561        DimName=DimCell;
2562    elseif iscell(DimCell)&& numel(DimCell)==1
2563        DimName=DimCell{1};
2564    end
2565    if strcmp(DimName,menu_histo{ivar})
2566        ind_bad=[ind_bad ivar];
2567    end
2568end
2569menu_histo(ind_bad)=[];
2570
2571%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2572% display menus and plot histograms
2573test_v=0;
2574if ~isempty(menu_histo)
2575    set(handles.histo1_menu,'Value',1)
2576    set(handles.histo1_menu,'String',menu_histo)
2577    histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2578    % case of more than one variables (eg vector components)
2579    if nb_histo > 1
2580        test_v=1;
2581        set(handles.histo2_menu,'Visible','on')
2582        set(handles.histo_v,'Visible','on')
2583        set(handles.histo2_menu,'String',menu_histo)
2584        set(handles.histo2_menu,'Value',2)
2585        histo2_menu_Callback(handles.histo2_menu,[], handles)% plot second histogram
2586    end
2587end
2588if ~test_v
2589    set(handles.histo2_menu,'Visible','off')
2590    set(handles.histo_v,'Visible','off')
2591    cla(handles.histo_v)
2592    set(handles.histo2_menu,'Value',1)
2593end
2594%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2595
2596%% display time
2597testimedoc=0;
2598TimeUnit='';
2599if isfield(UvData.Field,'Time')
2600    abstime=UvData.Field.Time;%time read from the netcdf input file
2601end
2602if isfield(UvData,'Field_1') && isfield(UvData.Field_1,'Time')
2603    abstime_1=UvData.Field_1.Time;%time read from the netcdf input file
2604end
2605if isfield(UvData.Field,'dt')
2606    dt=UvData.Field.dt;%dt read from the netcdf input file
2607    if isfield(UvData.Field,'TimeUnit')
2608       TimeUnit=UvData.Field.TimeUnit;
2609    end
2610elseif isfield(UvData,'Field_1') && isfield(UvData.Field_1,'dt')%dt obtained from the second field if not defined in the first
2611    dt=UvData.Field_1.dt;%dt read from the netcdf input file
2612    if isfield(UvData.Field_1,'TimeUnit')
2613       TimeUnit=UvData.Field_1.TimeUnit;
2614    end
2615end
2616% time from xml file overset previous result
2617if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2618    if isempty(num_i2)||isnan(num_i2)
2619        num_i2=num_i1;
2620    end
2621    if isempty(num_j1)||isnan(num_j1)
2622        num_j1=1;
2623    end
2624    if isempty(num_j2)||isnan(num_j2)
2625        num_j2=num_j1;
2626    end
2627    siz=size(UvData.XmlData{1}.Time);
2628    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2629        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2630        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2631        testimedoc=1;
2632        if isfield(UvData.XmlData{1},'TimeUnit')
2633            TimeUnit=UvData.XmlData{1}.TimeUnit;
2634        end
2635    end
2636    if numel(UvData.XmlData)==2
2637        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2638        %  [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2639        if isempty(num_i2)
2640            num_i2=num_i1;
2641        end
2642        if isempty(num_j1)
2643            num_j1=1;
2644        end
2645        if isempty(num_j2)
2646            num_j2=num_j1;
2647        end
2648        siz=size(UvData.XmlData{2}.Time);
2649        if ~isempty(num_i1) && siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2650            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
2651        end
2652    end
2653end
2654
2655if ~isequal(numel(abstime),1)
2656    abstime=[];
2657end
2658if ~isequal(numel(abstime_1),1)
2659      abstime_1=[];
2660end 
2661set(handles.abs_time,'String',num2str(abstime,4))
2662set(handles.abs_time_1,'String',num2str(abstime_1,4))
2663if testimedoc && isfield(UvData,'dt')
2664    dt=UvData.dt;
2665end
2666if isempty(dt)||isequal(dt,0)
2667    set(handles.Dt_txt,'String','')
2668else
2669    if  isempty(TimeUnit)
2670        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2671    else
2672        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2673    end
2674end
2675
2676
2677%-------------------------------------------------------------------
2678% --- translate coordinate to matrix index
2679%-------------------------------------------------------------------
2680function [indx,indy]=pos2ind(x0,rangx0,nxy)
2681indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2682indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2683
2684%-------------------------------------------------------------------
2685% --- Executes on button press in 'CheckFixLimits'.
2686%-------------------------------------------------------------------
2687function CheckFixLimits_Callback(hObject, eventdata, handles)
2688test=get(handles.CheckFixLimits,'Value');
2689if test
2690    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2691else
2692    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2693    update_plot(handles);
2694end
2695
2696%-------------------------------------------------------------------
2697% --- Executes on button press in CheckFixEqual.
2698function CheckFixEqual_Callback(hObject, eventdata, handles)
2699test=get(handles.CheckFixEqual,'Value');
2700if test
2701    set(handles.CheckFixEqual,'BackgroundColor',[1 1 0])
2702    cla(handles.axes3)
2703    update_plot(handles);
2704else
2705    set(handles.CheckFixEqual,'BackgroundColor',[0.7 0.7 0.7])
2706    update_plot(handles);
2707%     axis(handles.axes3,'image')
2708end
2709
2710%-------------------------------------------------------------------
2711
2712%-------------------------------------------------------------------
2713% --- Executes on button press in 'CheckZoom'.
2714%-------------------------------------------------------------------
2715function CheckZoom_Callback(hObject, eventdata, handles)
2716
2717if (get(handles.CheckZoom,'Value') == 1);
2718    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2719    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2720    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2721else
2722    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2723end
2724
2725%-------------------------------------------------------------------
2726%----Executes on button press in 'record': records the current flags of manual correction.
2727%-------------------------------------------------------------------
2728function record_Callback(hObject, eventdata, handles)
2729% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2730[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2731filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2732%filename=read_file_boxes(handles);
2733[erread,message]=fileattrib(filename);
2734if ~isempty(message) && ~isequal(message.UserWrite,1)
2735     msgbox_uvmat('ERROR',['no writting access to ' filename])
2736     return
2737end
2738test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2739test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2740if ~test_civ2 && ~test_civ1
2741    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2742end
2743if test_civ2
2744    nbname='nb_vectors2';
2745   flagname='vec2_FixFlag';
2746   attrname='fix2';
2747end
2748if test_civ1
2749    nbname='nb_vectors';
2750   flagname='vec_FixFlag';
2751   attrname='fix';
2752end
2753%write fix flags in the netcdf file
2754UvData=get(handles.uvmat,'UserData');
2755hhh=which('netcdf.open');% look for built-in matlab netcdf library
2756if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2757    nc=netcdf.open(filename,'NC_WRITE');
2758    netcdf.reDef(nc);
2759    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2760    dimid = netcdf.inqDimID(nc,nbname);
2761    try
2762        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2763    catch
2764        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2765    end
2766    netcdf.endDef(nc);
2767    netcdf.putVar(nc,varid,UvData.axes3.FF);
2768    netcdf.close(nc); 
2769else %old netcdf library
2770    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2771end
2772
2773%-------------------------------------------------------------------
2774%----Correct the netcdf file, using toolbox (old versions of Matlab).
2775%-------------------------------------------------------------------
2776function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2777nc=netcdf(filename,'write'); %open netcdf file
2778result=redef(nc);
2779eval(['nc.' attrname '=1;']);
2780theDim=nc(nbname) ;% get the number of velocity vectors
2781nb_vectors=size(theDim);
2782var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2783var_FixFlag(1:nb_vectors)=AxeData.FF;%
2784fin=close(nc);
2785
2786%-------------------------------------------------------------------
2787%determines the fields to read from the interface
2788%------------------------------------------------------------------
2789function VelType=setfield(handles)
2790VelTypeList=get(handles.VelType,'String');
2791index=get(handles.VelType,'Value');
2792VelType=VelTypeList{index};
2793
2794%-------------------------------------------------------------------
2795%determines the veltype of the second field to read from the iinterface
2796%------------------------------------------------------------------
2797function VelType=setfield_1(handles)
2798VelTypeList=get(handles.VelType_1,'String');
2799index=get(handles.VelType_1,'Value');
2800VelType=VelTypeList{index};
2801
2802%---------------------------------------------------
2803% --- Executes on button press in SubField
2804function SubField_Callback(hObject, eventdata, handles)
2805% huvmat=get(handles.run0,'parent');
2806UvData=get(handles.uvmat,'UserData');
2807if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2808    set(handles.RootPath_1,'String','')
2809    set(handles.RootFile_1,'String','')
2810    set(handles.SubDir_1,'String','');
2811    set(handles.FileIndex_1,'String','');
2812    set(handles.FileExt_1,'String','');
2813    set(handles.RootPath_1,'Visible','off')
2814    set(handles.RootFile_1,'Visible','off')
2815    set(handles.SubDir_1,'Visible','off');
2816    set(handles.NomType_1,'Visible','off');
2817    set(handles.abs_time_1,'Visible','off')
2818    set(handles.FileIndex_1,'Visible','off');
2819    set(handles.FileExt_1,'Visible','off');
2820    set(handles.Fields_1,'Value',1);%set to blank state
2821    set(handles.VelType_1,'Value',1);%set to blank state
2822    if ~strcmp(get(handles.VelType,'Visible'),'on')
2823        set(handles.VelType_1,'Visible','off')
2824    end
2825    if isfield(UvData,'XmlData_1')
2826        UvData=rmfield(UvData,'XmlData_1');
2827    end
2828    set(handles.uvmat,'UserData',UvData);
2829    run0_Callback(hObject, eventdata, handles); %run
2830else
2831    MenuBrowse_1_Callback(hObject, eventdata, handles)
2832end
2833
2834%------------------------------------------------------------------------
2835% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
2836
2837function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
2838%------------------------------------------------------------------------
2839InputFile=read_GUI(handles.InputFile);
2840RootPath=InputFile.RootPath;
2841SubDir=regexprep(InputFile.SubDir,'/|\','');
2842RootFile=regexprep(InputFile.RootFile,'/|\','');
2843FileIndices=InputFile.FileIndex;
2844FileExt=InputFile.FileExt;
2845
2846
2847%------------------------------------------------------------------------
2848% ---- read the data displayed for the second input rootfile windows
2849function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
2850%------------------------------------------------------------------------
2851RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
2852if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
2853    RootPath_1=get(handles.RootPath,'String');
2854end;
2855SubDir_1=get(handles.SubDir_1,'String');
2856if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
2857    SubDir_1=get(handles.SubDir,'String');
2858end
2859SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2860RootFile_1=get(handles.RootFile_1,'String');
2861if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
2862    RootFile_1=get(handles.RootFile,'String');
2863end
2864RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2865FileIndex_1=get(handles.FileIndex_1,'String');
2866if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
2867    FileIndex_1=get(handles.FileIndex,'String');
2868end
2869FileExt_1=get(handles.FileExt_1,'String');
2870if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
2871    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
2872end
2873NomType_1=get(handles.NomType_1,'String');
2874if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
2875    NomType_1=get(handles.NomType,'String');%read FileExt by default
2876end
2877%------------------------------------------------------------------------
2878% --- Executes on menu selection Fields
2879function Fields_Callback(hObject, eventdata, handles)
2880%------------------------------------------------------------------------
2881list_fields=get(handles.Fields,'String');% list menu fields
2882index_fields=get(handles.Fields,'Value');% selected string index
2883field= list_fields{index_fields(1)}; % selected string
2884if isequal(field,'get_field...')
2885    set(handles.FixVelType,'visible','off')
2886    set(handles.VelType,'visible','off')
2887    set(handles.VelType_1,'visible','off')
2888    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2889    filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2890    %filename=read_file_boxes(handles);
2891    hget_field=findobj(allchild(0),'name','get_field');
2892    if ~isempty(hget_field)
2893        delete(hget_field)
2894    end
2895    hget_field=get_field(filename);
2896    set(hget_field,'Name','get_field')
2897    hhget_field=guidata(hget_field);
2898    set(hhget_field.list_fig,'Value',1)
2899    set(hhget_field.list_fig,'String',{'uvmat'})
2900    set(handles.transform_fct,'Value',1)% no transform by default
2901    set(handles.path_transform,'String','')
2902    return %no action
2903end
2904list_fields=get(handles.Fields_1,'String');% list menu fields
2905index_fields=get(handles.Fields_1,'Value');% selected string index
2906field_1= list_fields{index_fields(1)}; % selected string
2907UvData=get(handles.uvmat,'UserData');
2908
2909%read the rootfile input display
2910[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2911FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2912[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
2913% NomTypeNew=NomType;%default
2914if isequal(field,'image')
2915%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
2916%         NomTypeNew='_1_1';
2917%     elseif isequal(NomType,'#_ab')
2918%         NomTypeNew='#a';
2919%     elseif isequal(NomType,'_1-2')
2920%         NomTypeNew='_1';
2921%     end
2922    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
2923    if ~exist(imagename,'file')
2924        [FileName,PathName] = uigetfile( ...
2925            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
2926            '*.jpg',' jpeg image files'; ...
2927            '*.png','.png image files'; ...
2928            '*.tif','.tif image files'; ...
2929            '*.avi;*.AVI','.avi movie files'; ...
2930            '*.vol','.volume images (png)'; ...
2931            '*.*',  'All Files (*.*)'}, ...
2932            'Pick an image',imagename);   
2933        imagename=[PathName FileName];
2934    end
2935     % display the selected field and related information
2936    display_file_name(hObject, eventdata, handles,imagename)%display the image
2937    return
2938else
2939    ext=get(handles.FileExt,'String');
2940    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
2941        [FileName,PathName] = uigetfile( ...
2942            {'*.nc', ' (*.nc)';
2943            '*.nc',' netcdf files'; ...
2944            '*.*',  'All Files (*.*)'}, ...
2945            'Pick a netcdf file',FileBase);
2946        filename=[PathName FileName];
2947        % display the selected field and related information
2948        display_file_name(hObject, eventdata, handles,filename)
2949        return
2950    end
2951end
2952indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
2953set(handles.FileIndex,'String',indices)
2954% set(handles.NomType,'String',NomType)
2955
2956%common to Fields_1_Callback
2957if isequal(field,'image')||isequal(field_1,'image')
2958    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
2959    set(handles.TitleNpy,'Visible','on')
2960    set(handles.num_Npx,'Visible','on')
2961    set(handles.num_Npy,'Visible','on')
2962else
2963    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
2964    set(handles.TitleNpy,'Visible','off')
2965    set(handles.num_Npx,'Visible','off')
2966    set(handles.num_Npy,'Visible','off')
2967end
2968setfield(handles);% update the field structure ('civ1'....)
2969if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
2970    run0_Callback(hObject, eventdata, handles)
2971end
2972
2973%---------------------------------------------------
2974% --- Executes on menu selection Fields
2975function Fields_1_Callback(hObject, eventdata, handles)
2976%-------------------------------------------------
2977%% read input data
2978check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
2979UvData=get(handles.uvmat,'UserData');
2980if check_new && isfield(UvData,'XmlData')
2981    UvData.XmlData{2}=UvData.XmlData{1};
2982end
2983list_fields=get(handles.Fields,'String');% list menu fields
2984index_fields=get(handles.Fields,'Value');% selected string index
2985field= list_fields{index_fields(1)}; % selected string
2986list_fields=get(handles.Fields_1,'String');% list menu fields
2987index_fields=get(handles.Fields_1,'Value');% selected string index
2988field_1= list_fields{index_fields(1)}; % selected string for the second field
2989if isequal(field_1,'')||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
2990    set(handles.SubField,'Value',0)
2991    check_new=1;
2992    SubField_Callback(hObject, eventdata, handles)
2993    if isempty(field_1)%remove second field if 'blank' field is selected
2994        return
2995    end
2996end
2997set(handles.SubField,'Value',1)%state that a second field is now entered
2998
2999%% read the rootfile input display
3000[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomTYpe_1]=read_file_boxes_1(handles);
3001filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3002[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3003set(handles.FileIndex_1,'Visible','on')
3004set(handles.FileExt_1,'Visible','on')
3005switch field_1
3006    case 'get_field...'
3007        set_veltype_display(0) % no veltype display
3008        hget_field=findobj(allchild(0),'name','get_field_1');
3009        if ~isempty(hget_field)
3010            delete(hget_field)
3011        end
3012        hget_field=get_field(filename_1);
3013        set(hget_field,'name','get_field_1')
3014        hhget_field=guidata(hget_field);
3015        set(hhget_field.list_fig,'Value',1)
3016        set(hhget_field.list_fig,'String',{'uvmat'})
3017        set(handles.transform_fct,'Value',1)% no transform by default
3018        set(handles.path_transform,'String','')
3019    case 'image'
3020        % transform netc type to the corresponding image type
3021        NomType=get(handles.NomType,'string');
3022        check_letter=~isempty(regexp(NomType,'[ab|AB]$'));%detect pair label by letter
3023%         NomType_1=NomType;
3024%         if check_letter
3025%             NomType_1=NomType_1(1:end-1);
3026%         else
3027%             r=regexp(NomType_1,'.-(?<num2>\d+$','names');
3028%             if ~isempty(r)
3029%                 NomType_1=regexprep(NomType_1,['-' r.num2],'');
3030%             end
3031%         end
3032        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',NomType,i1,[],j1);
3033        if ~exist(imagename,'file')
3034            [FileName,PathName] = uigetfile( ...
3035                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3036                '*.jpg',' jpeg image files'; ...
3037                '*.png','.png image files'; ...
3038                '*.tif','.tif image files'; ...
3039                '*.avi;*.AVI','.avi movie files'; ...
3040                '*.vol','.volume images (png)'; ...
3041                '*.*',  'All Files (*.*)'}, ...
3042                'Pick an image',imagename);
3043            % display the selected field and related information
3044            imagename=[PathName FileName];
3045        end
3046        set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3047        set(handles.TitleNpy,'Visible','on')
3048        set(handles.num_Npx,'Visible','on')
3049        set(handles.num_Npy,'Visible','on')
3050        display_file_name(hObject, eventdata, handles,imagename,2)%display the imag
3051    otherwise
3052        if check_new
3053            UvData.FileType{2}=UvData.FileType{1};
3054            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3055            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3056        end
3057        if ~isequal(field,'image')
3058            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3059            set(handles.TitleNpy,'Visible','off')
3060            set(handles.num_Npx,'Visible','off')
3061            set(handles.num_Npy,'Visible','off')
3062        end
3063        set(handles.uvmat,'UserData',UvData)
3064        setfield(handles);% update the field structure ('civ1'....)
3065        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3066            run0_Callback(hObject, eventdata, handles)
3067        end
3068end
3069
3070%------------------------------------------------------------------------
3071% --- set the visibility of relevant velocity type menus:
3072function menu=set_veltype_display(Civ,FileType)
3073%------------------------------------------------------------------------
3074if isequal(Civ,0)
3075    imax=0;
3076elseif isequal(Civ,1) || isequal(Civ,2)
3077   imax=1;
3078elseif isequal(Civ,3)
3079    imax=3;
3080elseif isequal(Civ,4) || isequal(Civ,5)
3081    imax=4;
3082elseif isequal(Civ,6) %patch2
3083    imax=6;
3084end
3085if ~exist('FileType','var')
3086    FileType='civx';
3087end
3088switch FileType
3089    case 'civx'
3090menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3091    case 'civdata'
3092    menu={'civ1';'civ-filter1';'filter1';'civ2';'civ-filter2';'filter2'};   
3093end
3094menu=menu(1:imax);
3095
3096%------------------------------------------------------------------------
3097% --- Executes on button press in VelType.
3098function VelType_Callback(hObject, eventdata, handles)
3099%------------------------------------------------------------------------
3100set(handles.FixVelType,'Value',1)
3101run0_Callback(hObject, eventdata, handles)
3102
3103%------------------------------------------------------------------------
3104% --- Executes on button press in VelType.
3105function VelType_1_Callback(hObject, eventdata, handles)
3106%------------------------------------------------------------------------
3107 
3108set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3109%refresh field with a second filename=first fiel name
3110set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3111drawnow   
3112InputFile=read_GUI(handles.InputFile);
3113[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3114filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3115%filename=read_file_boxes(handles);
3116
3117index=get(handles.VelType_1,'Value');
3118if index==1
3119        filename_1='';% we plot the current field without the second field
3120        set(handles.SubField,'Value',0)
3121        SubField_Callback(hObject, eventdata, handles)
3122elseif get(handles.SubField,'Value')% if subfield is already 'on'
3123      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3124     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3125    %filename_1=read_file_boxes_1(handles); %read the current second field
3126else
3127     filename_1=filename;% we compare two fields in the same file
3128     set(handles.SubField,'Value',1)
3129end
3130
3131num_i1=stra2num(get(handles.i1,'String'));
3132num_i2=stra2num(get(handles.i2,'String'));
3133num_j1=stra2num(get(handles.j1,'String'));
3134num_j2=stra2num(get(handles.j2,'String'));
3135
3136errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
3137
3138if ~isempty(errormsg)
3139    msgbox_uvmat('ERROR',errormsg);
3140else
3141    set(handles.i1,'BackgroundColor',[1 1 1])
3142    set(handles.i2,'BackgroundColor',[1 1 1])
3143    set(handles.j1,'BackgroundColor',[1 1 1])
3144    set(handles.j2,'BackgroundColor',[1 1 1])
3145    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3146    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3147end
3148set(handles.run0,'BackgroundColor',[1 0 0])
3149
3150%-----------------------------------------------
3151% --- reset civ buttons
3152function reset_vel_type(handles_civ0,handle1)
3153for ibutton=1:length(handles_civ0)
3154    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3155    set(handles_civ0(ibutton),'Value',0)
3156end
3157if exist('handle1','var')%handles of selected button
3158        set(handle1,'BackgroundColor',[1 1 0]) 
3159end
3160
3161%-------------------------------------------------------
3162% --- Executes on button press in MENUVOLUME.
3163%-------------------------------------------------------
3164function VOLUME_Callback(hObject, eventdata, handles)
3165%errordlg('command VOL not implemented yet')
3166if ishandle(handles.UVMAT_title)
3167    delete(handles.UVMAT_title)
3168end
3169UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3170if isequal(get(handles.VOLUME,'Value'),1)
3171    set(handles.CheckZoom,'Value',0)
3172    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3173    set(handles.edit_vect,'Value',0)
3174    edit_vect_Callback(hObject, eventdata, handles)
3175    set(handles.edit_object,'Value',0)
3176    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3177%     set(handles.cal,'Value',0)
3178%     set(handles.cal,'BackgroundColor',[0 1 0])
3179    set(handles.edit_vect,'Value',0)
3180    edit_vect_Callback(hObject, eventdata, handles)
3181    %initiate set_object GUI
3182    data.Name='VOLUME';
3183    if isfield(UvData,'CoordType')
3184        data.CoordType=UvData.CoordType;
3185    end
3186    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3187        data.RangeY=UvData.Mesh;
3188        data.RangeX=UvData.Mesh;
3189        data.DX=UvData.Mesh;
3190        data.DY=UvData.Mesh;
3191    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3192        np=size(UvData.Field.A);
3193        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3194        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3195        data.RangeY=max(meshx,meshy);
3196        data.RangeX=max(meshx,meshy);
3197        data.DX=max(meshx,meshy);
3198    end
3199    data.ParentButton=handles.VOLUME;
3200    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3201    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3202                                                      % associate the set_object interface handle to the plotting axes
3203    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3204    pos_uvmat=get(handles.uvmat,'Position');
3205    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3206    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3207    set(hset_object,'Position',pos_set_object)
3208    end
3209    UvData.MouseAction='create_object';
3210else
3211    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3212    UvData.MouseAction='none';
3213end
3214set(handles.uvmat,'UserData',UvData)
3215
3216%-------------------------------------------------------
3217function edit_vect_Callback(hObject, eventdata, handles)
3218%-------------------------------------------------------
3219%
3220% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3221if isequal(get(handles.edit_vect,'Value'),1)
3222    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3223    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3224    if ~test_civ2 && ~test_civ1
3225        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3226    end
3227    set(handles.record,'Visible','on')
3228    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3229    set(handles.edit_object,'Value',0)
3230    set(handles.CheckZoom,'Value',0)
3231    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3232%     set(handles.create,'Value',0)
3233%     set(handles.create,'BackgroundColor',[0 1 0])
3234    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3235    set(gcf,'Pointer','arrow')
3236%     UvData.MouseAction='edit_vect';
3237else
3238    set(handles.record,'Visible','off')
3239    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3240%     UvData.MouseAction='none';
3241end
3242% set(handles.uvmat,'UserData',UvData)
3243
3244%----------------------------------------------
3245function save_mask_Callback(hObject, eventdata, handles)
3246%-----------------------------------------------------------------------
3247UvData=get(handles.uvmat,'UserData');
3248
3249flag=1;
3250npx=size(UvData.Field.A,2);
3251npy=size(UvData.Field.A,1);
3252xi=0.5:npx-0.5;
3253yi=0.5:npy-0.5;
3254[Xi,Yi]=meshgrid(xi,yi);
3255if isfield(UvData,'Object')
3256    for iobj=1:length(UvData.Object)
3257        ObjectData=UvData.Object{iobj};
3258        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3259            flagobj=1;
3260            testphys=0; %coordinates in pixels by default
3261            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3262                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3263                    Calib=UvData.XmlData{1}.GeometryCalib;
3264                    testphys=1;
3265                end
3266            end
3267            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3268                if isequal(ObjectData.Type,'polygon')
3269                    X=ObjectData.Coord(:,1);
3270                    Y=ObjectData.Coord(:,2);
3271                    if testphys
3272                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3273                    end
3274                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3275                elseif isequal(ObjectData.Type,'ellipse')
3276                    if testphys
3277                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3278                    end
3279                    RangeX=max(ObjectData.RangeX);
3280                    RangeY=max(ObjectData.RangeY);
3281                    X2Max=RangeX*RangeX;
3282                    Y2Max=RangeY*RangeY;
3283                    distX=(Xi-ObjectData.Coord(1,1));
3284                    distY=(Yi-ObjectData.Coord(1,2));
3285                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3286                elseif isequal(ObjectData.Type,'rectangle')
3287                    if testphys
3288                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3289                    end
3290                    distX=abs(Xi-ObjectData.Coord(1,1));
3291                    distY=abs(Yi-ObjectData.Coord(1,2));
3292                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3293                end
3294                if isequal(ObjectData.ProjMode,'mask_outside')
3295                    flagobj=~flagobj;
3296                end
3297                flag=flag & flagobj;
3298            end
3299        end
3300    end
3301end
3302% flag=~flag;
3303%mask name
3304RootPath=get(handles.RootPath,'String');
3305RootFile=get(handles.RootFile,'String');
3306RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3307filebase=fullfile(RootPath,RootFile);
3308list=get(handles.masklevel,'String');
3309masknumber=num2str(length(list));
3310maskindex=get(handles.masklevel,'Value');
3311mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3312%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3313imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3314imflag=flipdim(imflag,1);
3315% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3316msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3317imwrite(imflag,mask_name,'BitDepth',8);
3318
3319%display the mask
3320figure;
3321vec=linspace(0,1,256);%define a linear greyscale colormap
3322map=[vec' vec' vec'];
3323colormap(map)
3324
3325image(imflag);
3326
3327%-------------------------------------------------------------------
3328%-------------------------------------------------------------------
3329%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3330
3331%------------------------------------------------------------------
3332
3333%------------------------------------------------------------------
3334% --- Executes on selection change in ListColorScalar: choice of the color code.
3335function ListColorScalar_Callback(hObject, eventdata, handles)
3336%------------------------------------------------------------------
3337% edit the choice for color code
3338list_code=get(handles.ListColorScalar,'String');% list menu fields
3339index_code=get(handles.ListColorScalar,'Value');% selected string index
3340col_code= list_code{index_code(1)}; % selected field
3341if isequal(col_code,'black') || isequal(col_code,'white')
3342   set(handles.Slider1,'Visible','off')
3343   set(handles.Slider2,'Visible','off')
3344   set(handles.num_ColCode1,'Visible','off')
3345   set(handles.num_ColCode2,'Visible','off')
3346   set(handles.CheckFixVecColor,'Visible','off')
3347   set_vec_col_bar(handles)
3348else
3349   set(handles.Slider1,'Visible','on')
3350   set(handles.Slider2,'Visible','on')
3351   set(handles.num_ColCode1,'Visible','on')
3352   set(handles.num_ColCode2,'Visible','on')
3353   set(handles.CheckFixVecColor,'Visible','on') 
3354   if isequal(col_code,'ima_cor')
3355       set(handles.CheckFixVecColor,'Value',0)%fixed scale by default
3356       set(handles.VecColBar,'Value',0)% 3 colors r,g,b by default
3357       set(handles.Slider1,'Min',0);
3358       set(handles.Slider1,'Max',1);
3359       set(handles.Slider2,'Min',0);
3360       set(handles.Slider2,'Max',1);
3361 %      set(handles.min_title_vec,'String','0')
3362       set(handles.num_MaxVec,'String','1')
3363       set(handles.num_ColCode1,'String','0.333')
3364       num_ColCode1_Callback(hObject, eventdata, handles)
3365       set(handles.num_ColCode2,'String','0.666')
3366       num_ColCode2_Callback(hObject, eventdata, handles)
3367   else
3368       set(handles.CheckFixVecColor,'Value',1)%auto scale between min,max by default
3369       set(handles.VecColBar,'Value',1)% colormap 'jet' by default
3370       minval=get(handles.Slider1,'Min');
3371       maxval=get(handles.Slider1,'Max');
3372       set(handles.Slider1,'Value',minval)
3373       set(handles.Slider2,'Value',maxval)
3374       set_vec_col_bar(handles)
3375   end
3376%    slider_update(handles)
3377end
3378%replot the current graph
3379run0_Callback(hObject, eventdata, handles)
3380
3381
3382%----------------------------------------------------------------
3383% -- Executes on slider movement to set the color code
3384%
3385function Slider1_Callback(hObject, eventdata, handles)
3386%------------------------------------------------------------------
3387slider1=get(handles.Slider1,'Value');
3388min_val=str2num(get(handles.num_MinVec,'String'));
3389max_val=str2num(get(handles.num_MaxVec,'String'));
3390col=min_val+(max_val-min_val)*slider1;
3391set(handles.num_ColCode1,'String',num2str(col))
3392if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3393    set(handles.Slider2,'Value',col)
3394    set(handles.num_ColCode2,'String',num2str(col))
3395end
3396num_ColCode1_Callback(hObject, eventdata, handles)
3397
3398%----------------------------------------------------------------
3399% Executes on slider movement to set the color code
3400%----------------------------------------------------------------
3401function Slider2_Callback(hObject, eventdata, handles)
3402slider2=get(handles.Slider2,'Value');
3403min_val=str2num(get(handles.num_MinVec,'String'));
3404max_val=str2num(get(handles.num_MaxVec,'String'));
3405col=min_val+(max_val-min_val)*slider2;
3406set(handles.num_ColCode2,'String',num2str(col))
3407if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3408    set(handles.Slider1,'Value',col)
3409    set(handles.num_ColCode1,'String',num2str(col))
3410end
3411num_ColCode2_Callback(hObject, eventdata, handles)
3412
3413%----------------------------------------------------------------
3414% --- Execute on return carriage on the edit box corresponding to slider 1
3415%----------------------------------------------------------------
3416function num_ColCode1_Callback(hObject, eventdata, handles)
3417set_vec_col_bar(handles)
3418update_plot(handles);
3419
3420%----------------------------------------------------------------
3421% --- Execute on return carriage on the edit box corresponding to slider 2
3422%----------------------------------------------------------------
3423function num_ColCode2_Callback(hObject, eventdata, handles)
3424set_vec_col_bar(handles)
3425update_plot(handles);
3426%------------------------------------------------------------------------
3427%-------------------------------------------------------
3428% --- Executes on button press in CheckFixVecColor.
3429%-------------------------------------------------------
3430function VecColBar_Callback(hObject, eventdata, handles)
3431set_vec_col_bar(handles)
3432
3433%-------------------------------------------------------------
3434% --- Executes on selection change in transform_fct.
3435function transform_fct_Callback(hObject, eventdata, handles)
3436%-------------------------------------------------------------
3437UvData=get(handles.uvmat,'UserData');
3438menu=get(handles.transform_fct,'String');
3439ind_coord=get(handles.transform_fct,'Value');
3440coord_option=menu{ind_coord};
3441list_transform=get(handles.transform_fct,'UserData');
3442ff=functions(list_transform{end}); 
3443if isequal(coord_option,'more...');
3444    coord_fct='';
3445    prompt = {'Enter the name of the transform function'};
3446    dlg_title = 'user defined transform';
3447    num_lines= 1;
3448    [FileName, PathName] = uigetfile( ...
3449       {'*.m', ' (*.m)';
3450        '*.m',  '.m files '; ...
3451        '*.*', 'All Files (*.*)'}, ...
3452        'Pick a file', ff.file);
3453    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3454        PathName(end)=[];
3455    end
3456    transform_selected =fullfile(PathName,FileName);
3457    if ~exist(transform_selected,'file')
3458           return
3459    end
3460   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3461   if ~isequal(ext_fct,'.m')
3462        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3463        return
3464   end
3465   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3466   ind_coord=get(handles.transform_fct,'Value');
3467   addpath(PathName)
3468   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3469   set(handles.transform_fct,'UserData',list_transform)
3470   rmpath(PathName)
3471   % save the new menu in the personal file 'uvmat_perso.mat'
3472   dir_perso=prefdir;%personal Matalb directory
3473   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3474   if exist(profil_perso,'file')
3475       nb_builtin=UvData.OpenParam.NbBuiltin;
3476       for ilist=nb_builtin+1:numel(list_transform)
3477           ff=functions(list_transform{ilist});
3478           transform_fct{ilist-nb_builtin}=ff.file;
3479       end
3480        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3481   end   
3482end
3483
3484%check the current path to the selected function
3485if isa(list_transform{ind_coord},'function_handle')
3486    func=functions(list_transform{ind_coord});
3487    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3488else
3489    set(handles.path_transform,'String','')
3490end
3491
3492set(handles.CheckFixLimits,'Value',0)
3493set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3494
3495%delete drawn objects
3496hother=findobj('Tag','proj_object');%find all the proj objects
3497for iobj=1:length(hother)
3498    delete_object(hother(iobj))
3499end
3500hother=findobj('Tag','DeformPoint');%find all the proj objects
3501for iobj=1:length(hother)
3502    delete_object(hother(iobj))
3503end
3504hh=findobj('Tag','calib_points');
3505if ~isempty(hh)
3506    delete(hh)
3507end
3508hhh=findobj('Tag','calib_marker');
3509if ~isempty(hhh)
3510    delete(hhh)
3511end
3512if isfield(UvData,'Object')
3513     UvData.Object=UvData.Object(1);
3514end
3515set(handles.ListObject,'Value',1)
3516set(handles.ListObject,'String',{''})
3517
3518%delete mask if it is displayed
3519if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3520   UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3521end
3522set(handles.uvmat,'UserData',UvData)
3523run0_Callback(hObject, eventdata, handles)
3524
3525%------------------------------------------------------------------------
3526function histo1_menu_Callback(hObject, eventdata, handles)
3527%--------------------------------------------
3528%plot first histo
3529%huvmat=get(handles.histo1_menu,'parent');
3530histo_menu=get(handles.histo1_menu,'String');
3531histo_value=get(handles.histo1_menu,'Value');
3532FieldName=histo_menu{histo_value};
3533update_histo(handles.histo_u,handles.uvmat,FieldName)
3534
3535%------------------------------------------------------------------------
3536function histo2_menu_Callback(hObject, eventdata, handles)
3537%------------------------------------------------------------------------
3538%plot second histo
3539%huvmat=get(handles.histo2_menu,'parent');
3540histo_menu=get(handles.histo2_menu,'String');
3541histo_value=get(handles.histo2_menu,'Value');
3542FieldName=histo_menu{histo_value};
3543update_histo(handles.histo_v,handles.uvmat,FieldName)
3544
3545%------------------------------------------------------------------------
3546%read the field .Fieldname stored in UvData and plot its histogram
3547function update_histo(haxes,huvmat,FieldName)
3548%------------------------------------------------------------------------
3549UvData=get(huvmat,'UserData');
3550if ~isfield(UvData.Field,FieldName)
3551    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
3552    return
3553end
3554Field=UvData.Field;
3555FieldHisto=eval(['Field.' FieldName]);
3556if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
3557    indsel=find(Field.FF==0);%find values marked as false
3558    if ~isempty(indsel)
3559        FieldHisto=FieldHisto(indsel);
3560    end
3561end
3562if isempty(Field)
3563    msgbox_uvmat('ERROR',['empty field ' FieldName])
3564else
3565    nxy=size(FieldHisto);
3566    Amin=double(min(min(min(FieldHisto))));%min of image
3567    Amax=double(max(max(max(FieldHisto))));%max of image
3568    if isequal(Amin,Amax)
3569        %msgbox_uvmat('WARNING',['uniform field =' num2str(Amin)]);
3570        cla(haxes)
3571    else
3572        Histo.ListVarName={FieldName,'histo'};
3573        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
3574            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3575        else
3576            if numel(nxy)==2
3577                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3578            else
3579                Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
3580            end
3581        end
3582        %unit
3583        units=[]; %default
3584        for ivar=1:numel(Field.ListVarName)
3585            if strcmp(Field.ListVarName{ivar},FieldName)
3586                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
3587                    units=Field.VarAttribute{ivar}.units;
3588                    break
3589                end
3590            end
3591        end
3592        if ~isempty(units)
3593            Histo.VarAttribute{1}.units=units;
3594        end
3595        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
3596        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
3597            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
3598            eval(['Histo.histo(:,1)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3599        else
3600            for col=1:size(FieldHisto,3)
3601                B=FieldHisto(:,:,col);
3602                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
3603                eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3604            end
3605        end
3606        plot_field(Histo,haxes);
3607    end
3608end
3609
3610%------------------------------------------------
3611%CALLBACKS FOR PLOTTING PARAMETERS
3612%-------------------------------------------------
3613
3614%------------------------------------------------------------------------
3615function num_MinX_Callback(hObject, eventdata, handles)
3616%------------------------------------------------------------------------
3617set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3618set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3619update_plot(handles);
3620
3621%------------------------------------------------------------------------
3622function num_MaxX_Callback(hObject, eventdata, handles)
3623%------------------------------------------------------------------------
3624set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3625set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3626update_plot(handles);
3627
3628%------------------------------------------------------------------------
3629function num_MinY_Callback(hObject, eventdata, handles)
3630%------------------------------------------
3631set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3632set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3633update_plot(handles);
3634
3635%------------------------------------------------------------------------
3636function num_MaxY_Callback(hObject, eventdata, handles)
3637%------------------------------------------------------------------------
3638set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3639set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3640update_plot(handles);
3641
3642%------------------------------------------------------------------------
3643function num_MinA_Callback(hObject, eventdata, handles)
3644%------------------------------------------
3645set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3646set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3647MinA=str2double(get(handles.num_MinA,'String'));
3648MaxA=str2double(get(handles.num_MaxA,'String'));
3649if MinA>MaxA% switch minA and maxA in case of error
3650    MinA_old=MinA;
3651    MinA=MaxA;
3652    MaxA=MinA_old;
3653    set(handles.num_MinA,'String',num2str(MinA,5));
3654    set(handles.num_MaxA,'String',num2str(MaxA,5));
3655end
3656update_plot(handles);
3657
3658%------------------------------------------------------------------------
3659function num_MaxA_Callback(hObject, eventdata, handles)
3660%------------------------------------------------------------------------
3661set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3662set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3663MinA=str2double(get(handles.num_MinA,'String'));
3664MaxA=str2double(get(handles.num_MaxA,'String'));
3665if MinA>MaxA% switch minA and maxA in case of error
3666        MinA_old=MinA;
3667    MinA=MaxA;
3668    MaxA=MinA_old;
3669    set(handles.num_MinA,'String',num2str(MinA,5));
3670    set(handles.num_MaxA,'String',num2str(MaxA,5));
3671end
3672update_plot(handles);
3673
3674%------------------------------------------------------------------------
3675function CheckFixScalar_Callback(hObject, eventdata, handles)
3676%------------------------------------------------------------------------
3677test=get(handles.CheckFixScalar,'Value');
3678if test
3679    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3680else
3681    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3682    update_plot(handles);
3683end
3684
3685%-------------------------------------------------------------------
3686function CheckBW_Callback(hObject, eventdata, handles)
3687%-------------------------------------------------------------------
3688update_plot(handles);
3689
3690%-------------------------------------------------------------------
3691function ListContour_Callback(hObject, eventdata, handles)
3692%-------------------------------------------------------------------
3693val=get(handles.ListContour,'Value');
3694if val==2
3695    set(handles.interval_txt,'Visible','on')
3696    set(handles.num_IncrA,'Visible','on')
3697else
3698    set(handles.interval_txt,'Visible','off')
3699    set(handles.num_IncrA,'Visible','off')
3700end
3701update_plot(handles);
3702
3703%-------------------------------------------------------------------
3704function num_IncrA_Callback(hObject, eventdata, handles)
3705%-------------------------------------------------------------------
3706update_plot(handles);
3707
3708%-------------------------------------------------------------------
3709function CheckHideWarning_Callback(hObject, eventdata, handles)
3710%-------------------------------------------------------------------
3711update_plot(handles);
3712
3713%-------------------------------------------------------------------
3714function CheckHideFalse_Callback(hObject, eventdata, handles)
3715%-------------------------------------------------------------------
3716update_plot(handles);
3717
3718%-------------------------------------------------------------------
3719function num_VecScale_Callback(hObject, eventdata, handles)
3720%-------------------------------------------------------------------
3721set(handles.CheckFixVectors,'Value',1);
3722set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3723update_plot(handles);
3724
3725%-------------------------------------------------------------------
3726function CheckFixVectors_Callback(hObject, eventdata, handles)
3727%-------------------------------------------------------------------
3728test=get(handles.CheckFixVectors,'Value');
3729if test
3730    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3731else
3732    update_plot(handles);
3733    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3734    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3735end
3736
3737%------------------------------------------------------------------------
3738% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3739function CheckDecimate4_Callback(hObject, eventdata, handles)
3740%------------------------------------------------------------------------
3741update_plot(handles);
3742
3743%------------------------------------------------------------------------
3744% --- Executes on selection change in ListColorCode menu
3745function ListColorCode_Callback(hObject, eventdata, handles)
3746%------------------------------------------------------------------------
3747set_vec_col_bar(handles)
3748update_plot(handles);
3749
3750%------------------------------------------------------------------------
3751% --- Executes on button press in CheckFixVecColor.
3752function CheckFixVecColor_Callback(hObject, eventdata, handles)
3753%------------------------------------------------------------------------
3754test=get(handles.CheckFixVecColor,'Value');
3755if test
3756    set(handles.CheckFixVecColor,'BackgroundColor',[1 1 0])
3757else
3758    update_plot(handles);
3759    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3760    set(handles.CheckFixVecColor,'BackgroundColor',[0.7 0.7 0.7])
3761end
3762
3763%------------------------------------------------------------------------
3764% --- Executes on selection change in num_MaxVec.
3765function num_MinVec_Callback(hObject, eventdata, handles)
3766%------------------------------------------------------------------------
3767max_vec_Callback(hObject, eventdata, handles)
3768
3769%------------------------------------------------------------------------
3770% --- Executes on selection change in num_MaxVec.
3771function num_MaxVec_Callback(hObject, eventdata, handles)
3772%------------------------------------------------------------------------
3773set(handles.CheckFixVecColor,'Value',1)
3774CheckFixVecColor_Callback(hObject, eventdata, handles)
3775min_val=str2num(get(handles.num_MinVec,'String'));
3776max_val=str2num(get(handles.num_MaxVec,'String'));
3777slider1=get(handles.Slider1,'Value');
3778slider2=get(handles.Slider2,'Value');
3779colcode1=min_val+(max_val-min_val)*slider1;
3780colcode2=min_val+(max_val-min_val)*slider2;
3781set(handles.num_ColCode1,'String',num2str(colcode1))
3782set(handles.num_ColCode2,'String',num2str(colcode2))
3783update_plot(handles);
3784
3785%------------------------------------------------------------------------
3786% --- update the display of color code for vectors
3787function set_vec_col_bar(handles)
3788%------------------------------------------------------------------------
3789%get the image of the color display button 'VecColBar' in pixels
3790set(handles.VecColBar,'Unit','pixel');
3791pos_vert=get(handles.VecColBar,'Position');
3792set(handles.VecColBar,'Unit','Normalized');
3793width=ceil(pos_vert(3));
3794height=ceil(pos_vert(4));
3795
3796%get slider indications
3797list=get(handles.ListColorCode,'String');
3798ichoice=get(handles.ListColorCode,'Value');
3799colcode.ListColorCode=list{ichoice};
3800colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3801colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3802test3color=strcmp(colcode.ListColorCode,'rgb') || strcmp(colcode.ListColorCode,'bgr');
3803if test3color
3804    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3805    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3806end
3807% colcode.FixedCbounds=0;
3808%colcode.CheckFixVecColor=1;
3809vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3810[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3811oneheight=ones(1,height);
3812A1=colorlist(col_vec,1)*oneheight;
3813A2=colorlist(col_vec,2)*oneheight;
3814A3=colorlist(col_vec,3)*oneheight;
3815A(:,:,1)=A1';
3816A(:,:,2)=A2';
3817A(:,:,3)=A3';
3818set(handles.VecColBar,'Cdata',A)
3819
3820%-------------------------------------------------------------------
3821function update_plot(handles)
3822%-------------------------------------------------------------------
3823UvData=get(handles.uvmat,'UserData');
3824AxeData=UvData.axes3;% retrieve the current plotted data
3825PlotParam=read_GUI(handles.uvmat);
3826[PP,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
3827write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3828
3829%-------------------------------------------------------------------
3830% --- Executes on selection change in edit_object.
3831function edit_object_Callback(hObject, eventdata, handles)
3832%-------------------------------------------------------------------
3833UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3834test=get(handles.edit_object,'Value');
3835if test
3836    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
3837    %suppress the other options
3838    set(handles.CheckZoom,'Value',0)
3839    CheckZoom_Callback(hObject, eventdata, handles)
3840    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
3841    if ishandle(hgeometry_calib)
3842        hhgeometry_calib=guidata(hgeometry_calib);
3843        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
3844        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
3845    end
3846else
3847    UvData.MouseAction='none';
3848    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])   
3849end
3850set(handles.uvmat,'UserData',UvData);
3851hset_object=findobj(allchild(0),'Tag','set_object');
3852if ~isempty(hset_object)
3853    hhset_object=guidata(hset_object);
3854    if test
3855        set(hhset_object.PLOT,'enable','on');
3856    else
3857       set(hhset_object.PLOT,'enable','off');
3858    end
3859end
3860
3861%------------------------------------------------------------------------
3862% --- Executes on selection change in ListObject.
3863function ListObject_Callback(hObject, eventdata, handles)
3864%------------------------------------------------------------------------
3865
3866list_str=get(handles.ListObject,'String');
3867IndexObj_old=get(handles.ListObject,'UserData');%retrieve previous selection
3868IndexObj=get(handles.ListObject,'Value');%present object selection
3869
3870%% 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
3871if length(IndexObj)>2
3872     IndexObj=[IndexObj(end-1) IndexObj(end)];%keeps only the last two selected items at most
3873end
3874
3875%% we select one object
3876if length(IndexObj)==1%
3877    if length(IndexObj_old)>=2 && isequal(IndexObj_old(1),IndexObj)   % we select the first previously selected object->
3878        IndexObj=[1 IndexObj_old(2)];% it desactivates this object and selects the first object for uvmat
3879    elseif length(IndexObj_old)>=2 && isequal(IndexObj_old(2),IndexObj) % we select the second previously selected object->
3880        IndexObj=IndexObj_old(1);% it desactivates this object  and keeps only the first previously selected object (uvmat)
3881    else %
3882        IndexObj=[IndexObj_old(1) IndexObj];% activates a second object while keeping the first previously selected one
3883    end
3884end
3885set(handles.ListObject,'Value',IndexObj); % marks the selected objects in the list
3886set(handles.ListObject,'UserData',IndexObj)% keep the current object selection in memory for next time
3887
3888%% update the object representation
3889set(handles.edit_object,'Value',0) % desactivate the edit object mode
3890edit_object_Callback(hObject, eventdata, handles)
3891UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3892if numel(UvData.Object)<max(IndexObj);
3893    msgbox_uvmat('ERROR','invalid object list')
3894    return
3895end
3896if numel(IndexObj)>=2
3897    UvData.Object=update_obj(UvData,IndexObj(1),IndexObj(2));%update the current object graphic representation
3898    set(handles.uvmat,'UserData',UvData)
3899end
3900
3901%% project on the selected object and update the corresponding plot
3902% hview_field=findobj(allchild(0),'tag','view_field');
3903% ViewObjectAxes=[];%default
3904if ~isequal(IndexObj(1),IndexObj_old(1))
3905    update_object(handles,IndexObj(1),handles.axes3,list_str{IndexObj(1)})%plot the projection in uvmat
3906end
3907hview_field=findobj(allchild(0),'tag','view_field');
3908if length(IndexObj)==2 && (length(IndexObj_old)==1 || ~isequal(IndexObj(2),IndexObj_old(2)))
3909    if isempty(hview_field)
3910        hview_field=view_field;
3911    end
3912    PlotHandles=guidata(hview_field);
3913    update_object(handles,IndexObj(2),PlotHandles.axes3,list_str{IndexObj(2)})%plot the projection in view_field
3914    update_object_color(handles.axes3,PlotHandles.axes3,UvData.Object{IndexObj(2)}.DisplayHandle_uvmat)
3915else
3916    if ~isempty(hview_field)
3917        delete(hview_field)
3918    end
3919    hset_object=findobj(allchild(0),'tag','set_object');
3920    if ~isempty(hset_object)
3921        delete(hset_object)
3922    end
3923    update_object_color(handles.axes3,handles.axes3,[])
3924end
3925
3926%% update the color of the gfraphic object representation: the selected object in magenta, others in blue
3927% update_object_color(handles.axes3,PlotHandles.axes3,UvData.Object{IndexObj(2)}.DisplayHandle_uvmat)
3928
3929%------------------------------------------------------------------------
3930function update_object(handles,IndexObj,ViewObjectAxes,ObjectName)
3931%------------------------------------------------------------------------
3932UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3933ObjectData=UvData.Object{IndexObj};
3934ObjectData.Name=ObjectName;
3935if isequal(get(handles.edit_object,'Value'),1)
3936    ObjectData.enable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
3937end
3938ZBounds=0; % default
3939if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3940    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3941    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3942end
3943hset_object=findobj(allchild(0),'tag','set_object');
3944if ~isempty(hset_object)
3945    delete(hset_object)% delete existing version of set_object
3946end
3947    hset_object=set_object(ObjectData,[],ZBounds);
3948% end
3949edit_test=get(handles.edit_object,'Value');
3950if edit_test
3951    ObjectData.enable_plot=1;
3952else
3953    if isfield(ObjectData,'enable_plot')
3954        ObjectData=rmfield(ObjectData,'enable_plot');
3955    end
3956end
3957
3958uistack(ViewObjectAxes,'top')% display the plotting axes at the top
3959ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
3960plot_field(ProjData,ViewObjectAxes,read_GUI(get(ViewObjectAxes,'Parent')));%read plotting parameters on the uvmat interfacPlotHandles);
3961
3962%------------------------------------------------------------------------
3963%--- update the representation of objects
3964function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
3965%------------------------------------------------------------------------
3966hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object')] ;%find all the proj objects
3967hother=[hother ;findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];
3968for iobj=1:length(hother)
3969    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
3970        set(hother(iobj),'EdgeColor','b')
3971        if isequal(get(hother(iobj),'FaceColor'),'m')
3972            set(hother(iobj),'FaceColor','b')
3973        end
3974    elseif isequal(get(hother(iobj),'Type'),'image')
3975        Acolor=get(hother(iobj),'CData');
3976        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
3977        set(hother(iobj),'CData',Acolor);
3978    else
3979        set(hother(iobj),'Color','b')
3980    end
3981    set(hother(iobj),'Selected','off')
3982end
3983if ~isempty(DisplayHandle)
3984linetype=get(DisplayHandle,'Type');
3985if isequal(linetype,'line')
3986    set(DisplayHandle,'Color','m'); %set the selected object to magenta color
3987elseif isequal(linetype,'rectangle')
3988    set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
3989elseif isequal(linetype,'patch')
3990    set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
3991end
3992SubObjectData=get(DisplayHandle,'UserData');
3993if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
3994    for iobj=1:length(SubObjectData.SubObject)
3995        hsub=SubObjectData.SubObject(iobj);
3996        if isequal(get(hsub,'Type'),'rectangle')
3997            set(hsub,'EdgeColor','m'); %set the selected object to magenta color
3998        elseif isequal(get(hsub,'Type'),'image')
3999            Acolor=get(hsub,'CData');
4000            Acolor(:,:,1)=Acolor(:,:,3);
4001            set(hsub,'CData',Acolor);
4002        else
4003            set(hsub,'Color','m')
4004        end
4005    end
4006end
4007if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4008    set(SubObjectData.DeformPoint,'Color','m')
4009end
4010end
4011
4012%------------------------------------------------------
4013% --- Executes on button press in Menu/Export/field in workspace.
4014%------------------------------------------------------
4015function MenuExportField_Callback(hObject, eventdata, handles)
4016global Data_uvmat
4017Data_uvmat=get(handles.uvmat,'UserData');
4018evalin('base','global Data_uvmat')%make CurData global in the workspace
4019display('current field :')
4020evalin('base','Data_uvmat') %display CurData in the workspace
4021commandwindow; %brings the Matlab command window to the front
4022
4023%------------------------------------------------------
4024% --- Executes on button press in Menu/Export/extract figure.
4025%------------------------------------------------------
4026function MenuExport_plot_Callback(hObject, eventdata, handles)
4027huvmat=get(handles.MenuExport_plot,'parent');
4028UvData=get(huvmat,'UserData');
4029hfig=figure;
4030newaxes=copyobj(handles.axes3,hfig);
4031map=colormap(handles.axes3);
4032colormap(map);%transmit the current colormap to the zoom fig
4033colorbar
4034
4035
4036% --------------------------------------------------------------------
4037function Insert_Callback(hObject, eventdata, handles)
4038
4039
4040% --------------------------------------------------------------------
4041function MenuHelp_Callback(hObject, eventdata, handles)
4042% --------------------------------------------------------------------
4043path_to_uvmat=which ('uvmat');% check the path of uvmat
4044pathelp=fileparts(path_to_uvmat);
4045helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4046if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4047else
4048    addpath (fullfile(pathelp,'uvmat_doc'))
4049    web(helpfile);
4050end
4051
4052%------------------------------------------------------------------------
4053% --------------------------------------------------------------------
4054function MenuExportMovie_Callback(hObject, eventdata, handles)
4055% --------------------------------------------------------------------
4056set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4057huvmat=get(handles.run0,'parent');
4058UvData=get(huvmat,'UserData');
4059%[xx,xx,FileBase]=read_file_boxes(handles);
4060[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4061FileBase=fullfile(RootPath,RootFile);
4062 %read the current input file name
4063prompt = {'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)'};
4064dlg_title = 'select properties of the output avi movie';
4065num_lines= 1;
4066% nbfield_cell=get(handles.last_i,'String');
4067def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4068answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4069aviname=answer{1};
4070fps=str2double(answer{2});
4071% check for existing file with output name aviname
4072if exist(aviname,'file')
4073    backup=aviname;
4074    testexist=2;
4075    while testexist==2
4076        backup=[backup '~'];
4077        testexist=exist(backup,'file');     
4078    end
4079    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4080    if isequal(success,1)
4081        delete(aviname)%delete existing file
4082    else
4083        msgbox_uvmat('ERROR',message)
4084        return
4085    end
4086end
4087%create avi open
4088aviobj=avifile(aviname,'Compression','None','fps',fps);
4089
4090%display first view for tests
4091newfig=figure;
4092newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4093set(newaxes,'Tag','movieaxes')
4094nbpix=[512 384]*str2double(answer{3});
4095set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4096set(newaxes,'Position',eval(answer{4}));
4097map=colormap(handles.axes3);
4098colormap(map);%transmit the current colormap to the zoom fig
4099msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4100        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4101UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4102set(huvmat,'UserData',UvData);
4103increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4104set(handles.STOP,'Visible','on')
4105set(handles.speed,'Visible','on')
4106set(handles.speed_txt,'Visible','on')
4107set(handles.Movie,'BusyAction','queue')
4108
4109%imin=str2double(get(handles.i1,'String'));
4110imax=str2double(answer{5});
4111% if isfield(UvData,'Time')
4112htitle=get(newaxes,'Title');
4113xlim=get(newaxes,'XLim');
4114ylim=get(newaxes,'YLim');
4115set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4116time_str=get(handles.abs_time,'String');
4117set(htitle,'String',['t=' time_str])
4118set(handles.speed,'Value',1)
4119for i=1:imax
4120    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4121            runpm(hObject,eventdata,handles,increment)% run plus
4122            drawnow
4123            time_str=get(handles.abs_time,'String');
4124            if ishandle(htitle)
4125             set(htitle,'String',['t=' time_str])
4126            end
4127            mov=getframe(newfig);
4128            aviobj=addframe(aviobj,mov);
4129    end
4130end
4131aviobj=close(aviobj);
4132UvData=rmfield(UvData,'plotaxes');
4133%UvData.Object{1}.plotaxes=handles.axes3;
4134set(huvmat,'UserData',UvData);
4135msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4136
4137%------------------------------------------------------------------------
4138function MenuCalib_Callback(hObject, eventdata, handles)
4139%------------------------------------------------------------------------
4140
4141UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4142
4143%suppress competing options
4144set(handles.CheckZoom,'Value',0)
4145set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4146set(handles.ListObject,'Value',1)     
4147% initiate display of GUI geometry_calib
4148data=[]; %default
4149if isfield(UvData,'CoordType')
4150    data.CoordType=UvData.CoordType;
4151end
4152pos=get(handles.uvmat,'Position');
4153pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4154pos(2)=pos(2)-0.02;
4155%[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
4156[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4157FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4158set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4159if isfield(UvData.OpenParam,'CalOrigin')
4160    pos_uvmat=get(handles.uvmat,'Position');
4161    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4162    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4163    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4164end
4165geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4166set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4167set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4168
4169%------------------------------------------------------------------------
4170function MenuMask_Callback(hObject, eventdata, handles)
4171%------------------------------------------------------------------------
4172UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4173ListObj=UvData.Object;
4174select=zeros(1,numel(ListObj));
4175for iobj=1:numel(ListObj);
4176    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4177        select(iobj)=1;
4178    end
4179end
4180val=find(select);
4181if isempty(val)
4182    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4183    return
4184else
4185    set(handles.ListObject,'Max',2);%allow multiple selection
4186    set(handles.ListObject,'Value',val);
4187    flag=1;
4188    npx=size(UvData.Field.A,2);
4189    npy=size(UvData.Field.A,1);
4190    xi=0.5:npx-0.5;
4191    yi=0.5:npy-0.5;
4192    [Xi,Yi]=meshgrid(xi,yi);
4193    if isfield(UvData,'Object')
4194        for iobj=1:length(UvData.Object)
4195            ObjectData=UvData.Object{iobj};
4196            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4197                flagobj=1;
4198                testphys=0; %coordinates in pixels by default
4199                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4200                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4201                        Calib=UvData.XmlData{1}.GeometryCalib;
4202                        testphys=1;
4203                    end
4204                end
4205                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4206                    if isequal(ObjectData.Type,'polygon')
4207                        X=ObjectData.Coord(:,1);
4208                        Y=ObjectData.Coord(:,2);
4209                        if testphys
4210                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4211                        end
4212                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4213                    elseif isequal(ObjectData.Type,'ellipse')
4214                        if testphys
4215                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4216                        end
4217                        RangeX=max(ObjectData.RangeX);
4218                        RangeY=max(ObjectData.RangeY);
4219                        X2Max=RangeX*RangeX;
4220                        Y2Max=RangeY*RangeY;
4221                        distX=(Xi-ObjectData.Coord(1,1));
4222                        distY=(Yi-ObjectData.Coord(1,2));
4223                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4224                    elseif isequal(ObjectData.Type,'rectangle')
4225                        if testphys
4226                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4227                        end
4228                        distX=abs(Xi-ObjectData.Coord(1,1));
4229                        distY=abs(Yi-ObjectData.Coord(1,2));
4230                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4231                    end
4232                    if isequal(ObjectData.ProjMode,'mask_outside')
4233                        flagobj=~flagobj;
4234                    end
4235                    flag=flag & flagobj;
4236                end
4237            end
4238        end
4239    end
4240    %mask name
4241    RootPath=get(handles.RootPath,'String');
4242    RootFile=get(handles.RootFile,'String');
4243    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4244        RootFile(1)=[];
4245    end
4246    filebase=fullfile(RootPath,RootFile);
4247    list=get(handles.masklevel,'String');
4248    masknumber=num2str(length(list));
4249    maskindex=get(handles.masklevel,'Value');
4250    mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4251    %mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4252    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4253    imflag=flipdim(imflag,1);
4254
4255    %display the mask
4256    hfigmask=figure;
4257    set(hfigmask,'Name','mask image')
4258    vec=linspace(0,1,256);%define a linear greyscale colormap
4259    map=[vec' vec' vec'];
4260    colormap(map)
4261    image(imflag);
4262    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4263    if ~strcmp(answer,'Cancel')
4264        mask_dir=fileparts(answer);
4265        if ~exist(mask_dir,'dir')
4266            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4267            return
4268        end
4269        imwrite(imflag,answer,'BitDepth',8);
4270    end
4271    set(handles.ListObject,'Value',1)
4272%     set(handles.ListObject,'Max',1)
4273end
4274
4275%------------------------------------------------------------------------
4276%-- open the GUI set_grid.fig to create grid
4277function MenuGrid_Callback(hObject, eventdata, handles)
4278%------------------------------------------------------------------------
4279%suppress the other options if grid is chosen
4280set(handles.edit_vect,'Value',0)
4281edit_vect_Callback(hObject, eventdata, handles)
4282set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4283set(handles.ListObject,'Value',1)     
4284
4285%prepare display of the set_grid GUI
4286[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4287FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4288CoordList=get(handles.transform_fct,'String');
4289val=get(handles.transform_fct,'Value');
4290set_grid(FileName,CoordList{val});% call the set_object interface
4291
4292%------------------------------------------------------------------------
4293% open the GUI 'series'
4294function MenuSeries_Callback(hObject, eventdata, handles)
4295%------------------------------------------------------------------------
4296series; %first display of the GUI to fill waiting time
4297[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4298param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4299if isequal(get(handles.SubField,'Value'),1)
4300    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
4301    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
4302    %FileName_1=read_file_boxes_1(handles);%
4303    if ~isequal(FileName_1,param.FileName)
4304        param.FileName_1=FileName_1;
4305    end
4306end
4307param.NomType=get(handles.NomType,'String');
4308% param.NomType=get(handles.FileIndex,'UserData');
4309param.NomType_1=get(handles.NomType_1,'String');
4310% param.NomType_1=get(handles.FileIndex_1,'UserData');
4311param.CheckFixPair=get(handles.CheckFixPair,'Value');
4312huvmat=get(handles.MenuSeries,'parent');
4313UvData=get(huvmat,'UserData');
4314if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4315    param.Time=UvData.XmlData{1}.Time;
4316end
4317if isequal(get(handles.scan_i,'Value'),1)
4318    param.incr_i=str2num(get(handles.increment_scan,'String'));
4319elseif isequal(get(handles.scan_j,'Value'),1)
4320    param.incr_j=str2num(get(handles.increment_scan,'String'));
4321end
4322param.list_fields=get(handles.Fields,'String');% list menu fields
4323param.list_fields(1)=[]; %suppress  'image' option
4324param.index_fields=get(handles.Fields,'Value');% selected string index
4325if param.index_fields>1
4326    param.index_fields=param.index_fields-1;
4327end
4328param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4329param.list_fields_1(1)=[]; %suppress  'image' option
4330param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4331if param.index_fields_1>1
4332    param.index_fields_1=param.index_fields_1-1;
4333end
4334param.menu_coord_str=get(handles.transform_fct,'String');
4335param.menu_coord_val=get(handles.transform_fct,'Value');
4336series(param); %run the series interface
4337
4338%------------------------------------------------------------------------
4339% -- open the GUI civ.fig for civx (PIV)
4340function MenuPIV_Callback(hObject, eventdata, handles)
4341%------------------------------------------------------------------------
4342 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4343 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4344civ(FileName);% interface de civ(not in the uvmat file)
4345
4346%------------------------------------------------------------------------
4347function MenuTools_Callback(hObject, eventdata, handles)
4348%------------------------------------------------------------------------
4349
4350%------------------------------------------------------------------------
4351function MenuEditObject_Callback(hObject, eventdata, handles)
4352%------------------------------------------------------------------------
4353set(handles.edit_object,'Value',1)
4354edit_Callback(hObject, eventdata, handles)
4355
4356%------------------------------------------------------------------------
4357function enable_transform(handles,state)
4358%------------------------------------------------------------------------
4359set(handles.transform_fct,'Visible',state)
4360set(handles.TRANSFORM_txt,'Visible',state)   
4361set(handles.transform_fct,'Visible',state) 
4362set(handles.path_transform,'Visible',state)
4363set(handles.pxcmx_txt,'Visible',state)
4364set(handles.pxcmy_txt,'Visible',state)
4365set(handles.pxcm,'Visible',state)
4366set(handles.pycm,'Visible',state)
4367
4368%------------------------------------------------------------------------
4369function MenuEditVectors_Callback(hObject, eventdata, handles)
4370%------------------------------------------------------------------------
4371set(handles.edit_vect,'Visible','on')
4372set(handles.edit_vect,'Value',1)
4373edit_vect_Callback(hObject, eventdata, handles)
4374
4375% -----------------------------------------------------------------------
4376function Menupoints_Callback(hObject, eventdata, handles)
4377%------------------------------------------------------------------------
4378data.Type='points';
4379data.ProjMode='projection';%default
4380create_object(data,handles)
4381
4382% -----------------------------------------------------------------------
4383function Menuline_Callback(hObject, eventdata, handles)
4384%------------------------------------------------------------------------
4385data.Type='line';
4386data.ProjMode='projection';%default
4387create_object(data,handles)
4388
4389%------------------------------------------------------------------------
4390function Menupolyline_Callback(hObject, eventdata, handles)
4391%------------------------------------------------------------------------
4392data.Type='polyline';
4393data.ProjMode='projection';%default
4394create_object(data,handles)
4395
4396%------------------------------------------------------------------------
4397function Menupolygon_Callback(hObject, eventdata, handles)
4398%------------------------------------------------------------------------
4399data.Type='polygon';
4400data.ProjMode='inside';%default
4401create_object(data,handles)
4402
4403%------------------------------------------------------------------------
4404function Menurectangle_Callback(hObject, eventdata, handles)
4405%------------------------------------------------------------------------
4406data.Type='rectangle';
4407data.ProjMode='inside';%default
4408create_object(data,handles)
4409
4410%------------------------------------------------------------------------
4411function Menuellipse_Callback(hObject, eventdata, handles)
4412%------------------------------------------------------------------------
4413data.Type='ellipse';
4414data.ProjMode='inside';%default
4415create_object(data,handles)
4416
4417%------------------------------------------------------------------------
4418function MenuMaskObject_Callback(hObject, eventdata, handles)
4419%------------------------------------------------------------------------
4420data.Type='polygon';
4421data.TypeMenu={'polygon'};
4422data.ProjMode='mask_inside';%default
4423data.ProjModeMenu={'mask_inside';'mask_outside'};
4424create_object(data,handles)
4425
4426%------------------------------------------------------------------------
4427function Menuplane_Callback(hObject, eventdata, handles)
4428%------------------------------------------------------------------------
4429data.Type='plane';
4430data.ProjMode='projection';%default
4431
4432create_object(data,handles)
4433
4434%------------------------------------------------------------------------
4435function Menuvolume_Callback(hObject, eventdata, handles)
4436%------------------------------------------------------------------------
4437data.Type='volume';
4438data.ProjMode='interp';%default
4439% set(handles.create,'Visible','on')
4440% set(handles.create,'Value',1)
4441% VOLUME_Callback(hObject,eventdata,handles)
4442create_object(data,handles)
4443
4444%------------------------------------------------------------------------
4445function MenuBrowseObject_Callback(hObject, eventdata, handles)
4446%------------------------------------------------------------------------
4447%get the object file
4448[FileName, PathName, filterindex] = uigetfile( ...
4449       {'*.xml;*.mat', ' (*.xml,*.mat)';
4450       '*.xml',  '.xml files '; ...
4451        '*.mat',  '.mat matlab files '}, ...
4452        'Pick an xml Object file',get(handles.RootPath,'String'));
4453fileinput=[PathName FileName];%complete file name
4454sizf=size(fileinput);
4455if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4456
4457%read the file
4458% t=xmltree(fileinput);
4459% data=convert(t);
4460data=xml2struct(fileinput);
4461data.enable_plot=1;
4462[pp,data.Name]=fileparts(FileName);
4463%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4464hset_object=findobj(allchild(0),'tag','set_object');
4465if ~isempty(hset_object)
4466    delete(hset_object)% delete existing version of set_object
4467end
4468set_object(data);% call the set_object interface
4469set(handles.edit_object,'Value',0); %suppress the object edit mode
4470set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4471set(handles.MenuObject,'checked','on')
4472set(handles.delete_object,'Visible','on')
4473
4474%------------------------------------------------------------------------
4475% --- generic function used for the creation of a projection object
4476function create_object(data,handles)
4477%------------------------------------------------------------------------
4478hset_object=findobj(allchild(0),'tag','set_object');
4479if ~isempty(hset_object)
4480    delete(hset_object)% delete existing version of set_object
4481end
4482hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4483if ishandle(hgeometry_calib)
4484    hhgeometry_calib=guidata(hgeometry_calib);
4485    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4486    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4487end
4488UvData=get(handles.uvmat,'UserData');
4489set(handles.edit_object,'Value',0); %suppress the object edit mode
4490set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4491data.enable_plot=1;
4492transform_list=get(handles.transform_fct,'String');
4493val=get(handles.transform_fct,'Value');
4494%data.CoordType=transform_list{val};
4495data.Coord=[0 0]; %default
4496if isfield(UvData,'Field')
4497    Field=UvData.Field;
4498    if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
4499        data.RangeX=Field.Mesh;
4500        data.RangeY=Field.Mesh;
4501        data.DX=Field.Mesh;
4502        data.DY=Field.Mesh;
4503    elseif isfield(Field,'AX')&& isfield(Field,'AY')&& isfield(Field,'A')%only image
4504        np=size(Field.A);
4505        meshx=(Field.AX(end)-Field.AX(1))/np(2);
4506        meshy=abs(Field.AY(end)-Field.AY(1))/np(1);
4507        data.RangeY=max(meshx,meshy);
4508        data.RangeX=max(meshx,meshy);
4509        data.DX=max(meshx,meshy);
4510    end
4511    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4512         data.Coord=[0 0 0]; %default
4513    end
4514    if isfield(Field,'CoordUnit')
4515        data.CoordUnit=Field.CoordUnit;
4516    end
4517end
4518% if isfield(data,'Type') && isequal(data.Type,'line')
4519%     if isfield(data,'DX')
4520%         data.Coord=[[0 0 0];[data.DX 0 0]]; %default
4521%     else
4522%         data.Coord=[[0 0 0];[1 0 0]]; %default
4523%     end
4524% end
4525if ishandle(handles.UVMAT_title)
4526    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4527end
4528%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4529set_object(data,handles);% call the set_object interface
4530set(handles.MenuObject,'checked','on')
4531set(handles.uvmat,'UserData',UvData)
4532set(handles.CheckZoom,'Value',0)
4533CheckZoom_Callback(handles.uvmat, [], handles)
4534set(handles.delete_object,'Visible','on')
4535% set(handles._title,'Visible','on')
4536% set(handles.view_field_title,'Visible','on')
4537
4538%------------------------------------------------------------------------
4539function MenuRuler_Callback(hObject, eventdata, handles)
4540%------------------------------------------------------------------------
4541set(handles.CheckZoom,'Value',0)
4542CheckZoom_Callback(handles.uvmat, [], handles)
4543set(handles.MenuRuler,'checked','on')
4544UvData=get(handles.uvmat,'UserData');
4545UvData.MouseAction='ruler';
4546set(handles.uvmat,'UserData',UvData);
4547
4548%------------------------------------------------------------------------
4549% --- executed when closing: set the parent interface button to value 0
4550function closefcn(gcbo,eventdata)
4551%------------------------------------------------------------------------
4552%delete all the associated figures if exist
4553hh=findobj(allchild(0),'tag','view_field');
4554if ~isempty(hh)
4555    delete(hh)
4556end
4557hh=findobj(allchild(0),'tag','geometry_calib');
4558if ~isempty(hh)
4559    delete(hh)
4560end
4561hh=findobj(allchild(0),'tag','set_object');
4562if ~isempty(hh)
4563    hhh=findobj(hh,'tag','PLOT');
4564    set(hhh,'enable','off')
4565end
4566
4567%------------------------------------------------------------------------
4568% --- Executes on button press in delete_object.
4569function delete_object_Callback(hObject, eventdata, handles)
4570%------------------------------------------------------------------------
4571IndexObj=get(handles.ListObject,'Value');
4572if IndexObj(end)>1
4573    delete_object(IndexObj(end))
4574end
4575
4576% --- Executes on button press in FixVelType.
4577function FixVelType_Callback(hObject, eventdata, handles)
4578val=get(handles.FixVelType,'Value');
4579if ~val
4580    run0_Callback(hObject, eventdata, handles)
4581end
4582
4583% --- Executes on button press in ViewObject.
4584function ViewObject_Callback(hObject, eventdata, handles)
4585IndexObj=get(handles.ListObject,'Value');
4586IndexObj=IndexObj(end); %keeps only the secodn value
4587UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4588if numel(UvData.Object)<IndexObj;% error in UvData
4589    msgbox_uvmat('ERROR','invalid object list')
4590    return
4591end
4592ObjectData=UvData.Object{IndexObj};
4593ZBounds=0; % default
4594if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4595    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4596    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4597end
4598hset_object=findobj(allchild(0),'tag','set_object');
4599if ~isempty(hset_object)
4600    delete(hset_object)% delete existing version of set_object
4601end
4602hset_object=set_object(ObjectData,[],ZBounds);
4603
4604
4605function NomType_Callback(hObject, eventdata, handles)
4606
4607
4608function NomType_1_Callback(hObject, eventdata, handles)
4609
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