source: trunk/src/uvmat.m @ 173

Last change on this file since 173 was 163, checked in by sommeria, 13 years ago

civ and uvmat modified to deal with file names containing blanks (for Windows system)

File size: 215.0 KB
Line 
1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%%
8%
9%INPUT:
10% input: input file name (if character chain), or input image matrix to
11% visualize, or Matlab structure representing  netcdf fields (with fields
12% ListVarName....)
13%
14%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15%  Copyright Joel Sommeria,  2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%     This open is part of the toolbox UVMAT.
18%
19%     UVMAT is free software; you can redistribute it and/or modify
20%     it under the terms of the GNU General Public License as published by
21%     the Free Software Foundation; either version 2 of the License, or
22%     (at your option) any later version.
23%
24%     UVMAT is distributed in the hope that it will be useful,
25%     but WITHOUT ANY WARRANTY; without even the implied warranty of
26%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
28%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29%
30% Information stored on the interface:
31%    'Strings' of all edit boxes and menus: get(handles.Tag,'String')
32%    'Values' of all menus and toggle buttons: get(handles.Tag,'Value')
33%     Matlab structure called UvData stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
34%          It contains the following fields:
35%     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn)
36%          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
37%     - Information read in the documentation open of a series (activated by RootPath_Callback) :
38%          .XmlData, with fields:
39%               .Time: matrix of times of the images with index i and j
40%               .GeometryCalib: [1x1 struct]
41%     - Information defined from the interface:
42%           .NewSeries: =1 when the first view of a new field series is displayed, else 0
43%           .filename:(char string)
44%           .VelType:(char string) type of velocity field selected
45%           .VelType_1:(char string)  REMPLACER LE CELL ACTUEL
46%           .FieldName: (char string) main field selected('image', 'velocity'...)
47%           .FieldName_1:(char string) second field selected('image', 'velocity'...)
48%           .CName: (char string)name of the scalar used for vector colors
49%          .MovieObject: movie object representing an input movie
50%          .MovieObject_1: idem for a second input series (_1)
51%          .filename_1 : last second input file name (to deal with a constant second input without reading again the file)
52%          .VelType_1: last velocity type (civ1, civ2...) for the second input series
53%          .FieldName_1: last field name(velocity, vorticity...) for the second input series
54%          .NbDim: number of space dimensions of the input field
55%          .ZMin, .ZMax: range of the z coordinate
56%..... to complement
57%     - Information on  projection objects
58%           .Object: {[1x1 struct]}
59%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
60%     -Information on the current field (Field{i})
61%            .Txt : text information to display (e.g. error message)
62%            .NbDim: number of dimensions (=0 by default)
63%            .NbCoord: number of vector components
64%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
65%            .dt: time interval for the corresponding image pair
66%            .Mesh: estimated typical distance between vectors
67%            .ZMax:
68%            .ZMin:
69%            .X, .Y, .Z: set of vector coordinates
70%            .U,.V,.W: corresponding set of vector components
71%            .F: corresponding set of warning flags
72%            .FF: corresponding set of false flags, =0 for good vectors
73%            .C: corresponding values of the scalar used for vector color
74%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
75%                     equal to the number of vectors stored in the input open)
76%            .CName: name of the scalar .C
77%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
78%            .A image or scalar
79%            .AX: vector of dimension 2 representing the first and last values
80%              of the X coordinates for the image or scalar known on a regular grid,
81%              or vector of dimension .A for a scaler defined on irregular grid.
82%            .AY: same as .AX along the Y direction
83%            .AName: name of the scalar, ='image' for an image
84
85% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
86%
87% fields are opened and visualised by the sub-function refresh_field.m
88% (called by uvmat_opening, RUN0, runp and runm)
89% The function first reads the name of the input file from the edit boxes  of the GUI
90% A second input file can be introduced for filed comparison
91% It then reads the input file(s) with the appropriate function, read for
92% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf
93% files.
94%               Main input open   second input open(_1)        second image (pair animation)
95%            |                 |                             
96%            |                 |                                               
97%                     Field{1}         Field{2}               
98%                                                                         |
99% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
100%                                                                   Field{i}
101%                                                                    |
102% calc_field.m: calculate scalar or other derived fields (vort, div..).
103%
104% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
105%              Field{i=1->3}.X --> UvData.X                          |
106%                                                                    |
107%                                                                 UvData
108%                                                                    |
109% plot histograms of the whole  field
110% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
111%                                                                    |                                                                          |
112%                                                                ObjectData
113%                                                                    |
114% plot_field.m: plot the projected fields and store them as          |
115% UvData.axes3                                        |
116%                                                                    |
117%                                                                AxeData
118%
119%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
120% scalars are displayed either as an image or countour plot, either as a color of
121% velocity vectors. The scalar values in the first case is represented by
122% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
123% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
124% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
125% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
126% coordinates of the four image corners. The scalar name is represented by
127% the strings .AName and/or .CName.
128% If the scalar exists in an input open (image or scalar stored under its
129% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
130% Else only its name AName is recorded in Field{i}, and its field is then calculated
131%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
132     
133% Properties attached to plotting figures (standard Matlab properties):
134%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
135%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
136%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
137%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
138%    'KeyPressFcn': function called by pressing a key on the key board
139%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
140%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
141
142% Properties attached to plotting axes:
143%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
144%     AxeData:=get(gca,'UserData');
145%     AxeData.Drawing  = create: create a new object
146%                       = deform: modify an existing object by moving its defining create
147%                      = off: no current drawing action
148%                     = translate: translate an existing object
149%                    = calibration: move a calibration point
150%                    = zoom: isolate a subregion for zoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
151%            .CurrentOrigin: Origin of a curently drawn edit_object
152%            .CurrentLine: currently drawn menuline (A REVOIR)
153%            .CurrentObject: handle of the currently drawn edit_object
154%            .CurrentRectZoom: current rectangle used for zoom
155
156% Properties attached to projection objects (create, menuline, menuplane...):
157%    'Tag'='proj_object': for all projection objects
158%    ObjectData.Style=...: style of projection object:
159%              .ProjMode
160%              .Coord: defines the position of the object
161%              .XMin,YMin....
162%              .XMax,YMax....
163%              .DX,DY,DZ
164%              .Phi, .Theta, .Psi : Euler angles
165%              .X,.Y,.U,.V.... : field data projected on the object
166%              .IndexObj: index in the list of UvData.Object
167           %during plotting
168%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
169%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
170% To each projection object #iobj, corresponds an axis
171% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
172% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
173
174%------------------------------------------------------------------------
175%------------------------------------------------------------------------
176%  I - MAIN FUNCTION UVMAT (DO NOT MODIFY)
177%------------------------------------------------------------------------
178%------------------------------------------------------------------------
179function varargout = uvmat(varargin)
180
181% Begin initialization code - DO NOT EDIT
182gui_Singleton = 1;
183gui_State = struct('gui_Name',          mfilename, ...
184                   'gui_Singleton',     gui_Singleton, ...
185                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
186                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
187                   'gui_LayoutFcn',     [], ...
188                   'gui_Callback',      []);
189if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
190    gui_State.gui_Callback = str2func(varargin{1});
191end
192
193if nargout
194    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
195else
196    gui_mainfcn(gui_State, varargin{:});
197end
198% End initialization code - DO NOT EDIT
199
200%------------------------------------------------------------------------
201% --- Executes just before the GUI uvmat is made visible.
202function uvmat_OpeningFcn(hObject, eventdata, handles, input )
203%------------------------------------------------------------------------
204global nb_builtin
205
206% Choose default command menuline output for uvmat
207handles.output = hObject;
208
209% Update handles structure
210guidata(hObject, handles);
211
212% set the position of colorbar and ancillary GUIs:
213set(hObject,'Units','Normalized')
214movegui(hObject,'center')
215UvData.PosColorbar=[0.805 0.022 0.019 0.445];
216UvData.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
217UvData.SetObjectSize=[0.3 0.7];
218UvData.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
219UvData.CalSize=[0.28 1];
220
221%functions for the mouse and keyboard
222set(handles.histo_u,'NextPlot','replacechildren');
223set(handles.histo_v,'NextPlot','replacechildren');
224set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
225set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
226set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
227set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
228set(hObject,'DeleteFcn',{@closefcn})%
229
230%refresh projection plane
231UvData.Object{1}.Style='plane';%main plotting plane
232UvData.Object{1}.ProjMode='projection';%main plotting plane
233if ~isfield(UvData.Object{1},'plotaxes')
234    UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
235    set(handles.list_object_1,'Value',1);
236    set(handles.list_object_1,'String',{'1-PLANE'});
237end
238
239%TRANSFORM menu: builtin fcts
240menu_str={'';'phys';'px';'phys_polar'};
241nb_builtin=numel(menu_str); %number of functions
242path_uvmat=fileparts(which('uvmat'));
243addpath(fullfile(path_uvmat,'transform_field'))
244fct_handle{1,1}=[];
245testexist=zeros(size(menu_str'));%default
246testexist(1)=1;
247for ilist=2:length(menu_str)
248    if exist(menu_str{ilist},'file')
249        fct_handle{ilist,1}=str2func(menu_str{ilist});
250        testexist(ilist)=1;
251    else
252        testexist(ilist)=0;
253    end
254end
255rmpath(fullfile(path_uvmat,'transform_field'))
256
257%load the list of previously browsed files in menus Open and Open_1
258 dir_perso=prefdir; % path to the directory .matlab for personal data
259 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
260 if exist(profil_perso,'file')
261      h=load (profil_perso);
262      if isfield(h,'MenuFile_1')
263          set(handles.MenuFile_1,'Label',h.MenuFile_1);
264          set(handles.MenuFile_1_1,'Label',h.MenuFile_1);
265      end
266      if isfield(h,'MenuFile_1')
267          set(handles.MenuFile_2,'Label',h.MenuFile_2);
268          set(handles.MenuFile_2_1,'Label',h.MenuFile_2);
269      end
270      if isfield(h,'MenuFile_1')
271          set(handles.MenuFile_3,'Label',h.MenuFile_3);
272          set(handles.MenuFile_3_1,'Label',h.MenuFile_3);
273      end
274      if isfield(h,'MenuFile_1')
275          set(handles.MenuFile_4,'Label',h.MenuFile_4);
276          set(handles.MenuFile_4_1,'Label',h.MenuFile_4);
277      end
278      if isfield(h,'MenuFile_1')
279          set(handles.MenuFile_5,'Label',h.MenuFile_5);
280          set(handles.MenuFile_5_1,'Label',h.MenuFile_5);
281      end
282      if isfield(h,'transform_fct') && iscell(h.transform_fct)
283         for ilist=1:length(h.transform_fct);
284             [path,file]=fileparts(h.transform_fct{ilist});
285             addpath(path)
286             if exist(file,'file')
287                h_func=str2func(file);
288                testexist=[testexist 1];
289             else
290                h_func=[];
291                testexist=[testexist 0];
292             end
293             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
294             rmpath(path)
295             menu_str=[menu_str; {file}];
296         end
297      end
298 end
299menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
300fct_handle=fct_handle(testexist==1);
301menu_str=[menu_str;{'more...'}];
302set(handles.transform_fct,'String',menu_str)
303set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
304 
305%initiates menu of vector colors
306list_menu=calc_field;
307%list_menu=[{'ima_cor'};{'black'};{'white'};list_menu(3:end)];
308set(handles.col_vec,'String',list_menu)
309
310%check the path and date of modification of all functions in uvmat
311path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
312[errormsg,date_str]=check_functions;%check the path of the functions called by uvmat.m
313date_str=['last modification: ' date_str];
314%case of an input argument for uvmat
315testinputfield=0;
316inputfile=[];
317Field=[];
318if exist('input','var')
319    if ~isempty(errormsg)
320        msgbox_uvmat('WARNING',errormsg)
321    end
322    if ishandle(handles.UVMAT_title)
323        delete(handles.UVMAT_title)
324    end   
325    if isstruct(input)
326        if isfield(input,'InputFile')
327            inputfile=input.InputFile;
328        end
329        Field=input;
330    elseif ischar(input)% file name introduced as input
331           inputfile=input;
332    elseif isnumeric(input)%simple matrix introduced as input
333        sizinput=size(input);
334        if sizinput(1)<=1 || sizinput(2)<=1
335            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
336            return
337        end
338        Field.ListVarName={'A','coord_y','coord_x'};
339        Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
340        Field.A=input;
341        Field.coord_x=[0.5 size(input,2)-0.5];
342        Field.coord_y=[size(input,1)-0.5 0.5];
343    end
344    if ~isempty(inputfile)
345        display_file_name(hObject, eventdata, handles,inputfile)
346        testinputfield=1;
347    else
348        UvData.TestInputFile=0;
349    end
350    if ~isempty(Field)
351        set(handles.Fields,'Value',1)
352        set(handles.Fields,'String',{'get_field...'})   
353        testinputfield=1;
354       
355        % set the colorbar position on the interface:
356        UvData.PosColorbar=[0.805 0.022 0.019 0.445];
357    elseif ischar(input)
358        scan_i_Callback(handles.scan_i, eventdata, handles);       
359    end
360else
361   if ishandle(handles.UVMAT_title)
362       fid=fopen('revision.log');
363       if fid~=-1
364         a=textscan(fid,'%s%s%s',1,'HeaderLines',1,'Delimiter','|');
365         set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG'};{'GNU General Public License'}; {path_to_uvmat}; ...
366           {['at revision ' a{1}{1}]};a{3}(1);{date_str};errormsg]);
367         fclose(fid);
368       else
369          set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG'};{'GNU General Public License'};{path_to_uvmat};...
370               {date_str};errormsg]);
371       end
372   end
373end
374UvData.NewSeries=1;
375set(hObject,'UserData',UvData)
376if testinputfield
377    %delete drawn objects
378    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
379    for iobj=1:length(hother)
380        delete_object(hother(iobj))
381    end 
382    if isempty(inputfile)
383        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
384        set(handles.MenuTools,'Enable','on')
385        set(handles.OBJECT_txt,'Visible','on')
386        set(handles.edit_object,'Visible','on')
387        set(handles.list_object_1,'Visible','on')
388        set(handles.frame_object,'Visible','on')
389        if ~isempty(errormsg)
390            msgbox_uvmat('ERROR',errormsg)
391        end
392    else
393        update_rootinfo(hObject,eventdata,handles);
394    end
395end
396set_vec_col_bar(handles) %update the display of color code for vectors
397
398%------------------------------------------------------------------------
399% --- Outputs from this function are returned to the command menuline.
400function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
401varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
402
403%------------------------------------------------------------------------
404%------------------------------------------------------------------------
405%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
406% automatically sets the global properties when the rootfile name is introduced
407% then activate the view-field action if selected
408% it is activated either by clicking on the RootPath window or by the
409% browser
410%------------------------------------------------------------------------
411%------------------------------------------------------------------------
412% --- Executes on the menu Open/Browse...
413% search the files, recognize their type according to their name and fill the rootfile input windows
414function MenuBrowse_Callback(hObject, eventdata, handles)
415oldfile=read_file_boxes(handles);
416
417if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
418         dir_perso=prefdir;
419         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
420         if exist(profil_perso,'file')
421              h=load (profil_perso);
422             if isfield(h,'MenuFile_1')
423                  oldfile=h.MenuFile_1;
424             end
425         end
426end
427[FileName, PathName] = uigetfile( ...
428       {'*.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)';
429       '*.xml',  '.xml files '; ...
430        '*.xls',  '.xls files '; ...
431        '*.civ',  '.civ files '; ...
432        '*.jpg',' jpeg image files'; ...
433        '*.png','.png image files'; ...
434        '*.tif','.tif image files'; ...
435        '*.avi;*.AVI','.avi movie files'; ...
436        '*.vol','.volume images (png)'; ...
437        '*.nc','.netcdf files'; ...
438        '*.cdf','.netcdf files'; ...
439        '*.cmx','.cmx text files';...
440        '*.cmx2','.cmx2 text files';...
441        '*.fig','.fig files (matlab fig)';...
442        '*.log','.log text files ';...
443        '*.dat','.dat text files ';...
444        '*.bat','.bat system command text files';...
445        '*.*',  'All Files (*.*)'}, ...
446        'Pick a file',oldfile);
447%global filebase
448fileinput=[PathName FileName];%complete file name
449% testblank=findstr(fileinput,' ');%look for blanks
450% if ~isempty(testblank)
451%     msgbox_uvmat('ERROR',['The input file name ' fileinput ' contains blank character : This is not allowed. Please change name'])
452%     return
453% end
454sizf=size(fileinput);
455if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
456
457% display the selected field and related information
458display_file_name(hObject, eventdata, handles,fileinput)
459
460%update list of recent files in the menubar
461MenuFile_1=fileinput;
462MenuFile_2=get(handles.MenuFile_1,'Label');
463MenuFile_3=get(handles.MenuFile_2,'Label');
464MenuFile_4=get(handles.MenuFile_3,'Label');
465MenuFile_5=get(handles.MenuFile_4,'Label');
466set(handles.MenuFile_1,'Label',MenuFile_1)
467set(handles.MenuFile_2,'Label',MenuFile_2)
468set(handles.MenuFile_3,'Label',MenuFile_3)
469set(handles.MenuFile_4,'Label',MenuFile_4)
470set(handles.MenuFile_5,'Label',MenuFile_5)
471set(handles.MenuFile_1_1,'Label',MenuFile_1)
472set(handles.MenuFile_2_1,'Label',MenuFile_2)
473set(handles.MenuFile_3_1,'Label',MenuFile_3)
474set(handles.MenuFile_4_1,'Label',MenuFile_4)
475set(handles.MenuFile_5_1,'Label',MenuFile_5)
476dir_perso=prefdir;
477profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
478if exist(profil_perso,'file')
479    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
480else
481    txt=ver('MATLAB');
482    Release=txt.Release;
483    relnumb=str2double(Release(3:4));
484    if relnumb >= 14
485        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
486    else
487        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
488    end
489end
490
491% -----------------------------------------------------------------------
492% --- Open again the file whose name has been recorded in MenuFile_1
493function MenuFile_1_Callback(hObject, eventdata, handles)
494fileinput=get(handles.MenuFile_1,'Label');
495display_file_name(hObject, eventdata, handles,fileinput)
496
497% -----------------------------------------------------------------------
498% --- Open again the file whose name has been recorded in MenuFile_2
499function MenuFile_2_Callback(hObject, eventdata, handles)
500fileinput=get(handles.MenuFile_2,'Label');
501display_file_name(hObject, eventdata, handles,fileinput)
502
503% -----------------------------------------------------------------------
504% --- Open again the file whose name has been recorded in MenuFile_3
505function MenuFile_3_Callback(hObject, eventdata, handles)
506fileinput=get(handles.MenuFile_3,'Label');
507display_file_name(hObject, eventdata, handles,fileinput)
508
509% -----------------------------------------------------------------------
510% --- Open again the file whose name has been recorded in MenuFile_4
511function MenuFile_4_Callback(hObject, eventdata, handles)
512fileinput=get(handles.MenuFile_4,'Label');
513display_file_name(hObject, eventdata, handles,fileinput)
514
515% -----------------------------------------------------------------------
516% --- Open again the file whose name has been recorded in MenuFile_5
517function MenuFile_5_Callback(hObject, eventdata, handles)
518fileinput=get(handles.MenuFile_5,'Label');
519display_file_name(hObject, eventdata, handles,fileinput)
520
521%------------------------------------------------------------------------
522% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
523function display_file_name(hObject, eventdata, handles,fileinput)
524if ~exist(fileinput,'file')
525    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
526    return
527end
528[RootPath,RootFile,i1,i2,str_a,str_b,ext,NomType,SubDir]=name2display(fileinput);
529ext_test=''; %default
530if ~isempty(ext)
531    form=imformats(ext(2:end));%test valid Matlab image formats
532    if ~isempty(form)
533        ext_test='.image';
534        imainfo=imfinfo(fileinput); 
535        if length(imainfo) >1 %case of image with multiple frames
536            i1='1'; % set the frame counter to 1 by default
537            i2='';
538            str_a='';
539            str_b='';
540            NomType='*'; %indicate a set of indexed frames within a single file
541            [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
542        end
543    elseif isequal(lower(ext),'.avi')
544        ext_test='.image';
545        i1='1'; % set the frame counter to 1 by default
546        i2='';
547        str_a='';
548        str_b='';
549        NomType='*'; %indicate a set of indexed frames within a single file
550        [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
551    else
552        ext_test=lower(ext);
553    end
554end
555switch ext_test
556    case {'.civ','.log','.cmx','.cmx2','.txt','.bat'}  %display text file
557        edit(fileinput) 
558    case '.fig'                           %display matlab figure
559        hfig=open(fileinput);
560        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
561        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
562        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
563    case {'.xml','.xls'}                % edit xml or Excel files
564       editxml(fileinput);
565    case {'.avi','.image','.vol','.nc','.cdf'}   
566        set(handles.RootPath,'String',RootPath);
567        if  isequal(SubDir,'')
568            rootname=fullfile(RootPath,RootFile);
569        else
570            rootname=fullfile(RootPath,SubDir,RootFile);
571            SubDir=['/' SubDir]; %display the separator
572        end
573        set(handles.SubDir,'String',SubDir);
574        set(handles.RootFile,'String',['/' RootFile]); %display the separator
575        indices=fileinput(length(rootname)+1:end);
576        indices(end-length(ext)+1:end)=[]; %remove extension
577        set(handles.FileIndex,'String',indices);       
578        set(handles.FileIndex,'UserData',NomType);
579        set(handles.FileExt,'String',ext);
580        % fill file index counters
581        set(handles.i1,'String',i1);   
582        set(handles.i2,'String',i2);
583        set(handles.j1,'String',str_a);
584        set(handles.j2,'String',str_b);
585       
586        % synchronise indices of the second  input file if it exists
587        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
588            [ff,rr,FileBase_1,ii,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
589            NomType_1=get(handles.FileIndex_1,'UserData');     
590            FileName_1=name_generator(FileBase_1,str2double(i1),str2double(i2),FileExt_1,NomType_1,1,stra2num(str_a),stra2num(str_b),SubDir_1);
591            if exist(FileName_1,'file')
592                FileIndex_1=name_generator('',str2double(i1),str2double(i2),'',NomType_1,1,stra2num(str_a),stra2num(str_b),'');
593                set(handles.FileIndex_1,'String',FileIndex_1)
594            else
595                set(handles.SubField,'Value',0)
596                SubField_Callback(hObject, eventdata, handles)
597            end
598        end 
599
600        %enable other menus
601        set(handles.MenuOpen_1,'Enable','on')
602        set(handles.MenuFile_1_1,'Enable','on')
603        set(handles.MenuFile_2_1,'Enable','on')
604        set(handles.MenuFile_3_1,'Enable','on')
605        set(handles.MenuFile_4_1,'Enable','on')
606        set(handles.MenuFile_5_1,'Enable','on')
607        set(handles.MenuExport,'Enable','on')
608        set(handles.MenuExportFigure,'Enable','on')
609        set(handles.MenuExportMovie,'Enable','on')
610        set(handles.MenuTools,'Enable','on')
611        set(handles.OBJECT_txt,'Visible','on')
612        set(handles.edit_object,'Visible','on')
613        set(handles.list_object_1,'Visible','on')
614        set(handles.frame_object,'Visible','on')
615         % initiate input file:
616        update_rootinfo(hObject,eventdata,handles); 
617    otherwise
618       msgbox_uvmat('ERROR',['invalid input file extension' ext])
619end
620
621%------------------------------------------------------------------------
622% --- Called by action in RootPath edit box
623function RootPath_Callback(hObject,eventdata,handles)
624%------------------------------------------------------------------------
625update_rootinfo(hObject,eventdata,handles);
626
627%------------------------------------------------------------------------
628% --- Called by action in RootFile edit box
629function SubDir_Callback(hObject, eventdata, handles)
630%------------------------------------------------------------------------
631%refresh the menu of input fields
632Fields_Callback(hObject, eventdata, handles);
633% refresh the current field
634run0_Callback(hObject, eventdata, handles);
635
636%------------------------------------------------------------------------
637% --- Called by action in RootFile edit box
638function RootFile_Callback(hObject, eventdata, handles)
639%------------------------------------------------------------------------
640update_rootinfo(hObject,eventdata,handles)
641
642%------------------------------------------------------------------------
643% --- Called by action in FileIndex edit box
644function FileIndex_Callback(hObject, eventdata, handles)
645%------------------------------------------------------------------------
646FileIndices=get(handles.FileIndex,'String');
647if isempty(str2num(FileIndices))
648    [pp,ff,str1,str2,str_a,str_b]=name2display(FileIndices);
649else
650    str1=FileIndices;
651    str2='';
652    str_a='';
653    str_b='';
654end
655set(handles.i1,'String',str1);
656set(handles.i2,'String',str2);
657set(handles.j1,'String',str_a);
658set(handles.j2,'String',str_b);
659run0_Callback(hObject, eventdata, handles)
660
661%------------------------------------------------------------------------
662% --- Update information about a new field series (indices to scan, timing,
663%     calibration from an xml file, then refresh current plots
664function update_rootinfo(hObject,eventdata,handles)
665%------------------------------------------------------------------------
666set(handles.RootPath,'BackgroundColor',[1 1 0])
667drawnow
668set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
669UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
670UvData.NewSeries=1; %flag for run0: begin a new series
671UvData.TestInputFile=1;
672set(handles.fix_pair,'Value',1) % activate by default the comp_input '-'input window
673
674[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
675if ~exist(FileName,'file')
676   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
677    return
678end
679nbfield=[];%default
680nburst=[];%default
681
682% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
683XmlData.Time=[];%default
684XmlData.GeometryCalib=[];%default
685TimeUnit=[];%default
686testima=0; %test for image input
687imainfo=[];
688ColorType='falsecolor'; %default
689hhh='';
690if isequal(lower(FileExt),'.avi') %.avi file
691    testima=1;
692    imainfo=aviinfo([FileBase FileIndices FileExt]);
693    nbfield=imainfo.NumFrames;
694    nburst=1;
695    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
696    XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
697    TimeUnit='s';
698    hhh=which('mmreader');
699    ColorType=imainfo.ImageType;%='truecolor' for color images
700elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
701    testima=1;
702    if ~isequal(SubDir,'')
703       RootFile=get(handles.RootFile,'String');
704        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
705    else
706        imainfo=imfinfo([FileBase FileIndices FileExt]);
707    end
708    ColorType=imainfo.ColorType;%='truecolor' for color images
709    if length(imainfo) >1 %case of image with multiple frames
710        nbfield=length(imainfo);
711        nburst=1;
712    end
713end
714if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
715    UvData.MovieObject=mmreader([FileBase FileIndices FileExt]);
716elseif isfield(UvData,'MovieObject')
717    UvData=rmfield(UvData,'MovieObject');
718end
719if isfield(imainfo,'Width') && isfield(imainfo,'Height')
720    set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
721    set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
722else
723    set(handles.npx,'String','');%fills nbre of pixels x box
724    set(handles.npy,'String','');%fills nbre of pixels x box
725end
726set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
727
728% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
729filexml=[FileBase '.xml'];
730fileciv=[FileBase '.civ'];
731warntext='';%default warning message
732NbSlice=1;%default
733
734if exist(filexml,'file')
735    set(handles.view_xml,'Visible','on')
736    set(handles.view_xml,'BackgroundColor',[1 1 0])
737    set(handles.RootPath,'BackgroundColor',[1 1 1])
738    set(handles.view_xml,'String','view .xml')
739    drawnow
740    [XmlData,warntext]=imadoc2struct(filexml);
741    if ~isempty(warntext)
742        msgbox_uvmat('WARNING',warntext)
743    end
744    if isfield(XmlData,'TimeUnit')
745        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
746            TimeUnit=XmlData.TimeUnit;
747        end
748    end
749    set(handles.view_xml,'BackgroundColor',[1 1 1])
750    drawnow
751    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
752        hgeometry_calib=findobj('tag','geometry_calib');
753        if ~isempty(hgeometry_calib)
754            GUserData=get(hgeometry_calib,'UserData');
755            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
756                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
757                if strcmp(answer,'Yes')
758                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
759                end
760            end
761        end
762    end 
763elseif exist(fileciv,'file')% if .civ file found
764    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
765    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
766    GeometryCalib.Tx=0;
767    GeometryCalib.Ty=0;
768    GeometryCalib.Tz=1;
769    GeometryCalib.dpx=1;
770    GeometryCalib.dpy=1;
771    GeometryCalib.sx=1;
772    GeometryCalib.Cx=0;
773    GeometryCalib.Cy=0;
774    GeometryCalib.f=1;
775    GeometryCalib.kappa1=0;
776    GeometryCalib.CoordUnit='cm';
777    XmlData.GeometryCalib=GeometryCalib;
778    if error==2, warntext=['no file ' FileBase '.civ'];
779    elseif error==1, warntext='inconsistent number of fields in the .civ file';
780    end 
781    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
782    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
783    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
784    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
785    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
786    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
787    set(handles.view_xml,'Visible','on')   
788    set(handles.view_xml,'String','view .civ')
789else
790    set(handles.view_xml,'Visible','off')
791end
792
793% store last index in handles.lat_i and .last_j
794if ~isempty(XmlData.Time)
795    nbfield=size(XmlData.Time,1);
796    nburst=size(XmlData.Time,2);
797    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
798    if isequal(nbfield,1) && ~isequal(nburst,1)% .Time is a line vector
799        NomType=get(handles.FileIndex,'UserData');
800        if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
801            XmlData.Time=(XmlData.Time)';
802            nbfield=nburst;
803            nburst=1;
804        end
805    end
806end
807last_i_cell=get(handles.last_i,'String');
808if isempty(nbfield)
809    last_i_cell{1}='';
810else
811    last_i_cell{1}=num2str(nbfield);
812end
813set(handles.last_i,'String',last_i_cell)
814last_j_cell=get(handles.last_j,'String');
815if isempty(nburst)
816     last_j_cell{1}='';
817else
818     last_j_cell{1}=num2str(nburst);
819end
820set(handles.last_j,'String',last_j_cell);
821
822% store geometric calibration in UvData
823if isfield(XmlData,'GeometryCalib')
824    GeometryCalib=XmlData.GeometryCalib;
825    if isempty(GeometryCalib)
826        set(handles.pxcm,'String','')
827        set(handles.pycm,'String','')
828        set(handles.transform_fct,'Value',1); %  no transform by default
829    else
830        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
831            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
832            set(handles.pxcm,'String','var')
833            set(handles.pycm,'String','var')
834        elseif isfield(GeometryCalib,'fx_fy')
835            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
836            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
837            set(handles.pxcm,'String',num2str(pixcmx))
838            set(handles.pycm,'String',num2str(pixcmy))
839        end
840        if ~get(handles.FixedLimits,'Value')
841            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
842        end
843        if isfield(GeometryCalib,'SliceCoord')
844           
845           siz=size(GeometryCalib.SliceCoord);
846           if siz(1)>1
847               NbSlice=siz(1);
848               set(handles.slices,'Visible','on')
849               set(handles.slices,'Value',1)
850           end
851           if isfield(GeometryCalib,'NbSlice') && isequal(GeometryCalib.NbSlice,'volume')
852               set(handles.nb_slice,'String','volume')
853           else
854               set(handles.nb_slice,'String',num2str(NbSlice))
855           end
856           slices_Callback(hObject, eventdata, handles)
857        end           
858    end
859end
860
861%update the data attached to the uvmat interface
862if ~isempty(TimeUnit)
863    set(handles.time_txt,'String',['time (' TimeUnit ')'])
864end
865UvData.TimeUnit=TimeUnit;
866UvData.XmlData=XmlData;
867UvData.NewSeries=1;
868set(handles.uvmat,'UserData',UvData)
869
870%display warning message
871if ~isequal(warntext,'')
872    msgbox_uvmat('WARNING',warntext);
873end
874
875% set default options in menu 'Fields'
876if testima
877   set(handles.Fields,'Value',1) % set menu to 'image'
878   set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'})
879elseif isequal(FileExt,'.nc')||isequal(FileExt,'.cdf')
880   Data=nc2struct(FileName,'ListGlobalAttribute','absolut_time_T0','civ');
881   col_vec=get(handles.col_vec,'String');
882   if ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0)
883       set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'})
884       set(handles.Fields,'Value',3) % set menu to 'velocity'
885       col_vec{1}='ima_cor';
886   else %general netcdf file (not civx)
887       set(handles.Fields,'Value',1) % set menu to 'get_field...
888       set(handles.Fields,'String',{'get_field...'})
889       col_vec{1}='get_field...';
890   end
891   set(handles.col_vec,'String',col_vec)
892else
893    msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
894    return
895end 
896
897% set index navigation options and refresh plots
898set(handles.RootPath,'BackgroundColor',[1 1 1])
899drawnow
900set_scan_options(hObject, eventdata, handles)
901
902%------------------------------------------------------------------------
903%--- Set index navigation options for new series input and refresh plot
904%------------------------------------------------------------------------
905function set_scan_options(hObject, eventdata, handles)
906
907%  set the corresponding index navigation options
908NomType=get(handles.FileIndex,'UserData');       
909NomType_1=get(handles.FileIndex_1,'UserData');
910last_i_str=get(handles.last_i,'String');
911nbfield=str2num(last_i_str{1});
912if numel(last_i_str)==2
913    nbfield=min(nbfield,str2num(last_i_str{2}));
914end 
915state_j='off'; %default
916scan_option='i';%default
917NomTypeRaw=regexprep(NomType(2:end), '-', '');
918if numel(regexp(NomTypeRaw,'\D'))>=1
919%     case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab','#A','%01dA','%02dA','%03dA','%04dA'},% two navigation indices
920        state_j='on';
921        if isequal(nbfield,1)
922            scan_option='j'; %scan j index by default if nbfield=1               
923        end
924end
925if ~isempty(NomType_1)
926    NomTypeRaw=regexprep(NomType_1(2:end), '-', '');
927    if numel(regexp(NomTypeRaw,'\D'))>=1
928%     switch NomType_1
929%         case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices
930            state_j='on';
931            if isequal(nbfield,1)
932                scan_option='j';                 
933            end           
934    end
935end
936if isequal(scan_option,'i')
937     set(handles.scan_i,'Value',1)
938     scan_i_Callback(hObject, eventdata, handles);
939else
940     set(handles.scan_j,'Value',1)
941     scan_j_Callback(hObject, eventdata, handles);
942end
943set(handles.scan_j,'Visible',state_j)
944set(handles.j1,'Visible',state_j)
945set(handles.j2,'Visible',state_j)
946set(handles.last_j,'Visible',state_j);
947set(handles.frame_j,'Visible',state_j);
948set(handles.j_text,'Visible',state_j);
949
950% view the field 
951run0_Callback(hObject, eventdata, handles); %view field
952mask_test=get(handles.mask_test,'value');
953if mask_test
954    MaskData=get(handles.mask_test,'UserData');
955    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
956          delete(MaskData.maskhandle)    %delete old mask
957    end
958    mask_test_Callback(hObject, eventdata, handles)
959end
960
961%------------------------------------------------------------------------
962% --- Executes on the menu Open/Browse_1 for the second input field,
963%     search the files, recognize their type according to their name and fill the rootfile input windows
964function MenuBrowse_1_Callback(hObject, eventdata, handles)
965%-------------------------------------------------------------------
966% huvmat=get(handles.run0,'parent');
967UvData=get(handles.uvmat,'UserData');
968
969RootPath=get(handles.RootPath,'String');
970[FileName, PathName, filterindex] = uigetfile( ...
971       {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
972       '*.xml',  '.xml files '; ...
973        '*.xls',  '.xls files '; ...
974        '*.civ',  '.civ files '; ...
975        '*.jpg','.jpg image files'; ...
976        '*.png','.png image files'; ...
977        '*.avi;*.AVI','.avi movie files'; ...
978        '*.nc','.netcdf files'; ...
979        '*.cdf','.netcdf files'; ...
980        '*.cmx','.cmx text files';...
981        '*.cmx2','.cmx2 text files';...
982        '*.fig','.fig files (matlab fig)';...
983        '*.log','.log text files ';...
984        '*.dat','.dat text files ';...
985        '*.*',  'All Files (*.*)'}, ...
986        'Pick a file',RootPath);
987fileinput_1=[PathName FileName];%complete file name
988% testblank=findstr(fileinput_1,' ');%look for blanks
989% if ~isempty(testblank)
990%     msgbox_uvmat('ERROR',['The input file name ' fileinput_1 ' contains blank character : This is not allowed. Please change name'])
991%     return
992% end
993sizf=size(fileinput_1);
994if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
995
996% refresh the current displayed field
997display_file_name_1(hObject,eventdata,handles,fileinput_1)
998
999%update list of recent files in the menubar
1000MenuFile_1=fileinput_1;
1001MenuFile_2=get(handles.MenuFile_1,'Label');
1002MenuFile_3=get(handles.MenuFile_2,'Label');
1003MenuFile_4=get(handles.MenuFile_3,'Label');
1004MenuFile_5=get(handles.MenuFile_4,'Label');
1005set(handles.MenuFile_1,'Label',MenuFile_1)
1006set(handles.MenuFile_2,'Label',MenuFile_2)
1007set(handles.MenuFile_3,'Label',MenuFile_3)
1008set(handles.MenuFile_4,'Label',MenuFile_4)
1009set(handles.MenuFile_5,'Label',MenuFile_5)
1010set(handles.MenuFile_1_1,'Label',MenuFile_1)
1011set(handles.MenuFile_2_1,'Label',MenuFile_2)
1012set(handles.MenuFile_3_1,'Label',MenuFile_3)
1013set(handles.MenuFile_4_1,'Label',MenuFile_4)
1014set(handles.MenuFile_5_1,'Label',MenuFile_5)
1015dir_perso=prefdir;
1016profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1017if exist(profil_perso,'file')
1018    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
1019else
1020    txt=ver('MATLAB');
1021    Release=txt.Release;
1022    relnumb=str2double(Release(3:4));
1023    if relnumb >= 14
1024        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
1025    else
1026        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
1027    end
1028end
1029
1030% -----------------------------------------------------------------------
1031% --- Open again as second field the file whose name has been recorded in MenuFile_1
1032function MenuFile_1_1_Callback(hObject, eventdata, handles)
1033fileinput_1=get(handles.MenuFile_1_1,'Label');
1034display_file_name_1(hObject,eventdata,handles,fileinput_1)
1035
1036% -----------------------------------------------------------------------
1037% --- Open again as second field the file whose name has been recorded in MenuFile_2
1038function MenuFile_2_1_Callback(hObject, eventdata, handles)
1039fileinput_1=get(handles.MenuFile_2_1,'Label');
1040display_file_name_1(hObject,eventdata,handles,fileinput_1)
1041
1042% -----------------------------------------------------------------------
1043% --- Open again as second field the file whose name has been recorded in MenuFile_3
1044function MenuFile_3_1_Callback(hObject, eventdata, handles)
1045fileinput_1=get(handles.MenuFile_3_1,'Label');
1046display_file_name_1(hObject,eventdata,handles,fileinput_1)
1047
1048% -----------------------------------------------------------------------
1049% --- Open again as second field the file whose name has been recorded in MenuFile_4
1050function MenuFile_4_1_Callback(hObject, eventdata, handles)
1051fileinput_1=get(handles.MenuFile_4_1,'Label');
1052display_file_name_1(hObject,eventdata,handles,fileinput_1)
1053
1054% -----------------------------------------------------------------------
1055% --- Open again as second field the file whose name has been recorded in MenuFile_5
1056function MenuFile_5_1_Callback(hObject, eventdata, handles)
1057fileinput_1=get(handles.MenuFile_5_1,'Label');
1058display_file_name_1(hObject,eventdata,handles,fileinput_1)
1059
1060%------------------------------------------------------------------------
1061% fills the edit boxes RootPath_1, RootFile_1,NomType_1...from an input file name 'fileinput_1'
1062%------------------------------------------------------------------------
1063function display_file_name_1(hObject,eventdata,handles,fileinput_1)
1064
1065%[path,name,ext]=fileparts(fileinput_1);
1066[RootPath_1,RootFile_1,field_count,str2,str_a,str_b,FileExt_1,NomType_1,SubDir_1]=name2display(fileinput_1);
1067nbfield_1=1; %default
1068ext_test=FileExt_1;%default
1069form=imformats(FileExt_1(2:end));
1070if ~isempty(form) % if the extension corresponds to an image format recognized by Matlab
1071    imainfo=imfinfo(fileinput_1); 
1072    nbfield_1=length(imainfo);
1073    ext_test='.image';
1074elseif isequal(lower(FileExt_1),'.avi')
1075    info=aviinfo(fileinput_1);
1076    nbfield_1=info.NumFrames;
1077    ext_test='.image';
1078end
1079
1080%open directly fig or text files
1081switch ext_test
1082    case {'.civ','.log','.cmx','.cmx2','.txt'}  %display text file
1083        edit(fileinput) 
1084        return
1085    case '.fig'                           %display matlab figure
1086        hfig=open(fileinput);
1087        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
1088        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
1089        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
1090        return
1091    case {'.xml','.xls'}                % edit xml or Excel files
1092       heditxml=editxml(fileinput);
1093       return
1094    case {'.image','.nc','.cdf'}
1095%         set(handles.FileIndex,'UserData',NomType_1);
1096    otherwise
1097        msgbox_uvmat(['invalid input file extension ' FileExt_1 ' for uvmat'],'ERROR')
1098        return
1099end
1100
1101% test for image series in a single file and synchronise file indices of the two series
1102if nbfield_1 >1 %case of image with multiple frames
1103    if nbfield_1 < num_i1
1104        msgbox_uvmat('ERROR','current frame index beyond the input movie length')
1105        return
1106    else
1107        NomType_1='*'; %indicate a set of indexed frames within a single file
1108        filename_new=fileinput_1;
1109    end
1110else  % cases of data files   
1111    RootPath=get(handles.RootPath,'String');
1112    RootFile=get(handles.RootFile,'String');
1113    FileBase=fullfile(RootPath,RootFile);
1114    FileBase_1=fullfile(RootPath_1,RootFile_1);
1115    if isequal(FileBase,FileBase_1)
1116        filename_new=fileinput_1;
1117    else       
1118        num_i1=stra2num(get(handles.i1,'String'));%get the current file indices from counters
1119        num_j1=stra2num(get(handles.j1,'String'));
1120        num_i2=stra2num(get(handles.i2,'String'));
1121        num_j2=stra2num(get(handles.j2,'String'));
1122        [filename_new,idetect]=...
1123           name_generator(FileBase_1,num_i1,num_j1,FileExt_1,NomType_1,1,num_i2,num_j2,SubDir_1);%create name with indices synchronised with the first file
1124        indices=''; %default
1125        if ~idetect
1126            msgbox_uvmat('ERROR','second input file with indices corresponding to the first one does not exist')
1127            return
1128        end
1129    end
1130end
1131set(handles.FileIndex_1,'UserData',NomType_1);
1132
1133% make visible and fill the second raw of edit boxes
1134set(handles.RootPath_1,'Visible','on')
1135set(handles.RootFile_1,'Visible','on')
1136set(handles.SubDir_1,'Visible','on');
1137set(handles.FileIndex_1,'Visible','on');
1138set(handles.FileExt_1,'Visible','on');
1139[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
1140if isequal(FileBase,FileBase_1)
1141    set(handles.RootPath_1,'String','"')
1142    set(handles.RootFile_1,'String','"');
1143else
1144    set(handles.RootPath_1,'String',RootPath_1)
1145    set(handles.RootFile_1,'String',['/' RootFile_1]);
1146end
1147if  isequal(SubDir_1,'')
1148     set(handles.SubDir_1,'String','');
1149     FileBaseSub_1=FileBase_1;
1150else 
1151    set(handles.SubDir_1,'String',['/' SubDir_1]);
1152    FileBaseSub_1=fullfile(FileBase_1,SubDir_1);
1153end
1154indices=filename_new(length(FileBaseSub_1)+1:end);
1155indices(end-length(FileExt_1)+1:end)=[]; %remove extension
1156set(handles.FileIndex_1,'String',indices)
1157set(handles.FileIndex_1,'UserData',NomType_1)
1158set(handles.FileExt_1,'String',FileExt_1);
1159
1160% default choice of fields
1161if isequal(ext_test,'.image')
1162   set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1163   set(handles.Fields_1,'Value',2) % set menu to 'image'
1164elseif strcmp(FileExt_1,'.nc')||strcmp(FileExt_1,'.cdf')
1165   Data=nc2struct(fileinput_1,[]);
1166   if isfield(Data,'absolut_time_T0')
1167       set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1168       set(handles.Fields_1,'Value',4) % set menu to 'velocity'
1169   else   
1170       set(handles.Fields_1,'Value',2) % set menu to 'get_field...'
1171       set(handles.Fields_1,'String',{'';'get_field...'});
1172   end
1173end 
1174set(handles.SubField,'Visible','on')
1175set(handles.SubField,'Value',1)
1176RootPath_1_Callback(hObject,eventdata,handles); 
1177
1178%-----------------------------------------------------------------------
1179% --- Called by action in RootPath_1 edit box
1180function RootPath_1_Callback(hObject,eventdata,handles)
1181update_rootinfo_1(hObject,eventdata,handles)
1182
1183%-----------------------------------------------------------------------
1184% --- Called by action in RootFile_1 edit box
1185function RootFile_1_Callback(hObject, eventdata, handles)
1186update_rootinfo_1(hObject,eventdata,handles)
1187%-----------------------------------------------------------------------
1188
1189%------------------------------------------------------------------------
1190% --- Called by action in FileIndex_1 edit box
1191function FileIndex_1_Callback(hObject, eventdata, handles)
1192%------------------------------------------------------------------------
1193
1194run0_Callback(hObject, eventdata, handles)
1195
1196%------------------------------------------------------------------------
1197% --- Update information about a new second field series (indices to scan, timing,
1198%     calibration from an xml file, then refresh current plots
1199function update_rootinfo_1(hObject,eventdata,handles) %A REVOIR
1200
1201set(handles.RootPath_1,'BackgroundColor',[1 1 0])% indicate active program by yellow color
1202drawnow
1203UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
1204UvData.NewSeries=1; %flag for run0: begin a new series
1205
1206[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes_1(handles);
1207if ~exist(FileName,'file')
1208    msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
1209end
1210nbfield_1=[];%default
1211nburst_1=[];%default
1212XmlData.Time=[];
1213XmlData.GeometryCalib=[];%default
1214TimeUnit=[];
1215if isfield(UvData,'TimeUnit')
1216    TimeUnit=UvData.TimeUnit;
1217end
1218TimeUnit_1=[];
1219hhh='';%default, test for  movie reading with mmreader
1220imainfo=[];
1221if isequal(lower(FileExt),'.avi') %.avi file
1222    imainfo=aviinfo([FileBase FileIndices FileExt]);
1223    nbfield_1=imainfo.NumFrames;
1224    nburst_1=1;
1225    set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
1226    time=[0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond]';
1227    ColorType=imainfo.ImageType;%='truecolor' for color images
1228    hhh=which('mmreader');
1229elseif ~isempty(imformats(FileExt(2:end)))|| isequal(FileExt,'.vol')
1230    if ~isequal(SubDir,'')
1231        RootFile=get(handles.RootFile,'String');
1232        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
1233    else
1234        imainfo=imfinfo([FileBase FileIndices FileExt]);
1235    end
1236    ColorType=imainfo.ColorType;%='truecolor' for color images
1237    if length(imainfo) >1 %case of image with multiple frames
1238        nbfield_1=length(imainfo);
1239        nburst_1=1;
1240    end
1241end
1242if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
1243    UvData.MovieObject_1=mmreader([FileBase FileIndices FileExt]);
1244elseif isfield(UvData,'MovieObject_1')
1245    UvData=rmfield(UvData,'MovieObject_1');
1246end
1247if ~isempty(imainfo)% (an image has been introduced as second fierld input)
1248    if strcmp(get(handles.npx,'String'),'') || strcmp(get(handles.npy,'String'),'')%update npx and npy if it is not already filled by the first input field
1249        if  isfield(imainfo,'Width') && isfield(imainfo,'Height')
1250            set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
1251            set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
1252        else
1253            set(handles.npx,'String','');%fills nbre of pixels x box
1254            set(handles.npy,'String','');%fills nbre of pixels x box
1255        end
1256        set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
1257    end
1258end
1259% find scaling parameters
1260filexml=[FileBase '.xml'];
1261fileciv=[FileBase '.civ'];
1262warntext='';%default warning text
1263if exist(filexml,'file')
1264    [XmlData,warntext]=imadoc2struct(filexml);
1265    if ~isempty(warntext)
1266        msgbox_uvmat('WARNING',warntext)
1267    end
1268    if isfield(XmlData,'Camera')
1269        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1270            TimeUnit=XmlData.Camera.TimeUnit;
1271        end
1272    end
1273elseif exist(fileciv,'file')% if .civ file found
1274    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
1275    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
1276    GeometryCalib.Tx=0;
1277    GeometryCalib.Ty=0;
1278    GeometryCalib.Tz=1;
1279    GeometryCalib.dpx=1;
1280    GeometryCalib.dpy=1;
1281    GeometryCalib.sx=1;
1282    GeometryCalib.Cx=0;
1283    GeometryCalib.Cy=0;
1284    GeometryCalib.f=1;
1285    GeometryCalib.kappa1=0;
1286    GeometryCalib.CoordUnit='cm';
1287    XmlData.GeometryCalib=GeometryCalib;
1288    if error==2, warntext=['no file ' FileBase '.civ'];
1289    elseif error==1, warntext='inconsistent number of fields in the .civ file';
1290    end
1291   
1292    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
1293    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
1294    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
1295    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
1296    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
1297    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
1298end   
1299if ~isempty(TimeUnit_1) && ~isequal(TimeUnit_1,TimeUnit)
1300        msgbox_uvmat('WARNING','the time units for the second series differs from the first one')
1301end
1302       
1303% store last index in handles.lat_i and .last_j
1304if ~isempty(XmlData.Time)
1305    nbfield_1=size(XmlData.Time,1);
1306    nburst_1=size(XmlData.Time,2);   
1307end
1308last_i_cell=get(handles.last_i,'String');
1309if isempty(nbfield_1)
1310    last_i_cell{2}='';
1311else
1312    last_i_cell{2}=num2str(nbfield_1);
1313end
1314set(handles.last_i,'String',last_i_cell)
1315last_j_cell=get(handles.last_j,'String');
1316if isempty(nburst_1)
1317     last_j_cell{2}='';
1318else
1319     last_j_cell{2}=num2str(nburst_1);
1320end
1321set(handles.last_j,'String',last_j_cell);
1322if ~isequal(last_i_cell{1},last_i_cell{2}) || ~isequal(last_j_cell{1},last_j_cell{2})
1323        msgbox_uvmat('WARNING','the numbers of input file of the second series differs from the first one')
1324end
1325
1326% store calibration data
1327GeometryCalib=XmlData.GeometryCalib;
1328if isempty(GeometryCalib)
1329    if isfield(UvData, 'GeometryCalib_1')
1330        UvData=rmfield(UvData,'GeometryCalib_1');
1331    end
1332else
1333    UvData.GeometryCalib_1=GeometryCalib;
1334    if (isfield(GeometryCalib,'R')& ~isequal(GeometryCalib.R(2,1),0) & ~isequal(GeometryCalib.R(1,2),0)) |...
1335        (isfield(GeometryCalib,'kappa1')& ~isequal(GeometryCalib.kappa1,0))
1336        set(handles.pxcm,'String','var')
1337        set(handles.pycm,'String','var')
1338    else
1339        if isfield(GeometryCalib,'fx_fy')
1340            pixcmx=GeometryCalib.fx_fy(1);
1341            pixcmy=GeometryCalib.fx_fy(2);
1342            set(handles.pxcm,'String',num2str(pixcmx))
1343            set(handles.pycm,'String',num2str(pixcmy))
1344        end
1345    end
1346end
1347UvData.XmlData_1=XmlData;
1348set(handles.uvmat,'UserData',UvData)%update the data attached to the uvmat interface
1349
1350if ~isequal(warntext,'')
1351    msgbox_uvmat('WARNING',warntext)
1352end
1353
1354set(handles.RootPath_1,'BackgroundColor',[1 1 1])% signa the end the input operation
1355drawnow
1356
1357set_scan_options(hObject, eventdata, handles)
1358
1359%---------------------------------------------------
1360% switch file index scanning options scan_i and scan_j in an exclusive way
1361function scan_i_Callback(hObject, eventdata, handles)
1362%---------------------------------------------------
1363if get(handles.scan_i,'Value')==1
1364    set(handles.scan_i,'BackgroundColor',[1 1 0])
1365    set(handles.scan_j,'Value',0)
1366%     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1367else
1368    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1369    set(handles.scan_j,'Value',1)
1370%     set(handles.scan_j,'BackgroundColor',[1 1 0])
1371end
1372scan_j_Callback(hObject, eventdata, handles)
1373
1374%-------------------------------------------------------------------
1375% switch file index scanning options scan_i and scan_j in an exclusive way
1376function scan_j_Callback(hObject, eventdata, handles)
1377%-------------------------------------------------------------------
1378if get(handles.scan_j,'Value')==1
1379    set(handles.scan_j,'BackgroundColor',[1 1 0])
1380    set(handles.scan_i,'Value',0)
1381    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1382    NomType=get(handles.FileIndex,'UserData');
1383    switch NomType
1384    case {'_i_j1-j2','#_ab','%3dab'},% pair with j index
1385        set(handles.fix_pair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1386    otherwise
1387        set(handles.fix_pair,'Visible','off')
1388    end
1389else
1390    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1391    set(handles.scan_i,'Value',1)
1392    set(handles.scan_i,'BackgroundColor',[1 1 0])
1393    set(handles.fix_pair,'Visible','off')
1394end
1395
1396%-------------------------------------------------------------------
1397function i1_Callback(hObject, eventdata, handles)
1398%-------------------------------------------------------------------
1399set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1400NomType=get(handles.FileIndex,'UserData');
1401num1=stra2num(get(handles.i1,'String'));
1402num2=stra2num(get(handles.i2,'String'));
1403num_a=stra2num(get(handles.j1,'String'));
1404num_b=stra2num(get(handles.j2,'String'));
1405indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1406set(handles.FileIndex,'String',indices)
1407set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1408if get(handles.SubField,'Value')==1
1409    NomType_1=get(handles.FileIndex_1,'String');
1410     FileExt_1=get(handles.FileExt_1,'String');
1411    [P,F,str1,str2,str_a,str_b,Ext,NomType_1]=name2display(['xx' NomType_1 FileExt_1]);
1412     indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1413     set(handles.FileIndex_1,'String',indices)
1414     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1415end
1416%Run0_Callback(hObject, eventdata, handles)
1417
1418%-------------------------------------------------------------------
1419function i2_Callback(hObject, eventdata, handles)
1420set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1421i1_Callback(hObject, eventdata, handles)
1422%-------------------------------------------------------------------
1423
1424%-------------------------------------------------------------------
1425function j1_Callback(hObject, eventdata, handles)
1426set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1427i1_Callback(hObject, eventdata, handles)
1428%-------------------------------------------------------------------
1429
1430%-------------------------------------------------------------------
1431function j2_Callback(hObject, eventdata, handles)
1432set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1433i1_Callback(hObject, eventdata, handles)
1434%-------------------------------------------------------------------
1435
1436%-------------------------------------------------------------------
1437function slices_Callback(hObject, eventdata, handles)
1438%-------------------------------------------------------------------
1439if get(handles.slices,'Value')==1
1440    set(handles.slices,'BackgroundColor',[1 1 0])
1441    set(handles.nb_slice,'Visible','on')
1442    set(handles.z_text,'Visible','on')
1443    set(handles.z_index,'Visible','on')
1444    nb_slice_Callback(hObject, eventdata, handles)
1445else
1446    set(handles.nb_slice,'Visible','off')
1447    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1448    set(handles.z_text,'Visible','off')
1449    set(handles.z_index,'Visible','off')
1450    set(handles.masklevel,'Value',1)
1451    set(handles.masklevel,'String',{'1'})
1452end
1453
1454%-------------------------------------------------------------------
1455function nb_slice_Callback(hObject, eventdata, handles)
1456%-------------------------------------------------------------------
1457nb_slice_str=get(handles.nb_slice,'String');
1458if isequal(nb_slice_str,'volume')
1459    num=stra2num(get(handles.j1,'String'));
1460    last_j=get(handles.last_j,'String');
1461    nbslice=str2double(last_j{1});
1462else
1463    num=str2double(get(handles.i1,'String'));
1464    nbslice=str2double(get(handles.nb_slice,'String'));
1465end
1466z=mod(num-1,nbslice)+1;
1467set(handles.z_index,'String',num2str(z))
1468for ilist=1:nbslice
1469    list_index{ilist,1}=num2str(ilist);
1470end   
1471set(handles.masklevel,'String',list_index)
1472set(handles.masklevel,'Value',z)
1473
1474%-------------------------------------------------------------------
1475% --- Executes on button press in view_xml.
1476function view_xml_Callback(hObject, eventdata, handles)
1477[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1478option=get(handles.view_xml,'String');
1479if isequal(option,'view .xml')
1480    FileXml=[FileBase '.xml'];
1481    heditxml=editxml(FileXml);
1482end
1483
1484%-------------------------------------------------------------------
1485% --- Executes on button press in mask_test.
1486function mask_test_Callback(hObject, eventdata, handles)
1487%-------------------------------------------------------------------
1488%case of view mask selection
1489if isequal(get(handles.mask_test,'Value'),1)
1490    [FF,RootPath,FileBase]=read_file_boxes(handles);
1491    num_i1=stra2num(get(handles.i1,'String'));
1492    num_j1=stra2num(get(handles.j1,'String'));
1493    currentdir=pwd; 
1494    cd(RootPath);
1495    maskfiles=dir('*_*mask_*.png');%look for a mask file
1496    cd(currentdir);%come back to the working directory
1497    mdetect=0;
1498    if ~isempty(maskfiles)
1499        for ilist=1:length(maskfiles)
1500            maskname=maskfiles(ilist).name;% take the first mask file in the list
1501            [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1502            if ~strcmp(Mask_NomType{ilist},Mask_NomType{1})
1503                msgbox_uvmat('ERROR',['inconsistent mask types ' Mask_NomType{1} Mask_NomType{ilist } ' coexist in the current image directory'])
1504                return
1505            end
1506            [Path2,Name,ext]=fileparts(maskname);
1507            Namedouble=double(Name);
1508            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1509            ind_mask=findstr('mask',Name);
1510            i=ind_mask-1;
1511            while val(i)==0 && i>0
1512                i=i-1;
1513            end
1514            nbmask_str=str2num(Name(i+1:ind_mask-1));
1515            if ~isempty(nbmask_str)
1516                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1517            end
1518        end
1519        if isequal(min(nbslice),max(nbslice))
1520            nbslice=nbslice(1);
1521        else
1522            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1523            return
1524        end
1525        if ~isempty(nbslice) && Name(i)=='_'
1526            Mask.Base=[FileBase Name(i:ind_mask+3)];
1527            Mask.NbSlice=nbslice;
1528            num_i1=mod(num_i1-1,nbslice)+1;
1529            Mask.NomType=Mask_NomType{1};
1530            [maskname,mdetect]=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1531            mdetect=exist(maskname,'file');
1532            if mdetect
1533                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1534                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1535                set(handles.mask_test,'UserData',Mask);
1536                set(handles.mask_test,'BackgroundColor',[1 1 0])
1537                if nbslice > 1
1538                    set(handles.slices,'value',1)
1539                    slices_Callback(hObject, eventdata, handles)
1540                end
1541            end
1542        end
1543    end
1544    errormsg=[];%default
1545    if mdetect==0
1546        [FileName, PathName, filterindex] = uigetfile( ...
1547            {'*.png', ' (*.png)';
1548            '*.png',  '.png files '; ...
1549            '*.*', 'All Files (*.*)'}, ...
1550            'Pick a mask file *.png',FileBase);
1551        maskname=fullfile(PathName,FileName);
1552        if ~exist(maskname,'file')
1553            errormsg='no file browsed';
1554        end
1555        [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1556        Mask.Base=fullfile(RootDir,RootFile);
1557        Mask.NbSlice=1;
1558        set(handles.mask_test,'UserData',Mask);
1559        set(handles.mask_test,'BackgroundColor',[1 1 0])
1560    end
1561    if isempty(errormsg)
1562        errormsg=update_mask(handles,num_i1,num_j1);
1563    end
1564    if ~isempty(errormsg)
1565            set(handles.mask_test,'Value',0)
1566            set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1567     end
1568else
1569    MaskData=get(handles.mask_test,'UserData');
1570    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1571          delete(MaskData.maskhandle)   
1572    end
1573    set(handles.mask_test,'UserData',[])   
1574    %huvmat=get(handles.mask_test,'parent');
1575    UvData=get(handles.uvmat,'UserData');
1576    if isfield(UvData,'MaskName')
1577        UvData=rmfield(UvData,'MaskName');
1578        set(handles.uvmat,'UserData',UvData)
1579    end
1580    set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1581end
1582
1583%-------------------------------------------------------------------
1584function errormsg=update_mask(handles,num_i1,num_j1)
1585%-------------------------------------------------------------------
1586errormsg=[];%default
1587MaskData=get(handles.mask_test,'UserData');
1588if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1589    uistack(MaskData.maskhandle,'top');
1590end
1591num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1592MaskData.NomType
1593MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1594huvmat=get(handles.mask_test,'parent');
1595UvData=get(huvmat,'UserData');
1596
1597%update mask image if the mask is new
1598if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1599    UvData.MaskName=MaskName; %update the recorded name on UvData
1600    set(huvmat,'UserData',UvData);
1601    if ~exist(MaskName,'file')
1602        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1603            delete(MaskData.maskhandle)   
1604        end
1605    else
1606        %read mask image
1607        Mask.AName='image';
1608        Mask.A=imread(MaskName);
1609        npxy=size(Mask.A);
1610        test_error=0;
1611        if length(npxy)>2
1612            errormsg=[MaskName ' is not a grey scale image'];
1613            return
1614        elseif ~isa(Mask.A,'uint8')
1615            errormsg=[MaskName ' is not a 8 bit grey level image'];
1616            return
1617        end
1618        Mask.AX=[0.5 npxy(2)-0.5];
1619        Mask.AY=[npxy(1)-0.5 0.5 ];
1620        Mask.CoordUnit='pixel';
1621        if isequal(get(handles.slices,'Value'),1)
1622           NbSlice=str2num(get(handles.nb_slice,'String'));
1623           num_i1=str2num(get(handles.i1,'String'));
1624           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1625        end
1626        %px to phys or other transform on field
1627         menu_transform=get(handles.transform_fct,'String');
1628        choice_value=get(handles.transform_fct,'Value');
1629        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1630        transform_list=get(handles.transform_fct,'UserData');
1631        transform=transform_list{choice_value};
1632        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1633            if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1634                Calib=UvData.XmlData.GeometryCalib;
1635                Mask=transform(Mask,UvData.XmlData);
1636            end
1637        end
1638        flagmask=Mask.A < 200;
1639       
1640        %make brown color image
1641        imflag(:,:,1)=0.9*flagmask;
1642        imflag(:,:,2)=0.7*flagmask;
1643        imflag(:,:,3)=zeros(size(flagmask));
1644       
1645        %update mask image
1646        hmask=[]; %default
1647        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1648            hmask=MaskData.maskhandle;
1649        end
1650        if ~isempty(hmask)
1651            set(hmask,'CData',imflag)   
1652            set(hmask,'AlphaData',flagmask*0.6)
1653            set(hmask,'XData',Mask.AX);
1654            set(hmask,'YData',Mask.AY);
1655%             uistack(hmask,'top')
1656        else
1657            axes(handles.axes3)
1658            hold on   
1659            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1660%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1661            set(handles.mask_test,'UserData',MaskData)
1662        end
1663    end
1664end
1665
1666
1667%-------------------------------------------------------------------
1668function MenuExportFigure_Callback(hObject, eventdata, handles)
1669%-------------------------------------------------------------------
1670huvmat=get(handles.MenuExport,'parent');
1671%UvData=get(huvmat,'UserData');
1672hfig=figure;
1673copyobj(handles.axes3,hfig);
1674map=colormap(handles.axes3);
1675colormap(map);%transmit the current colormap to the zoom fig
1676colorbar
1677
1678%-------------------------------------------------------------------
1679%-------------------------------------------------------------------
1680% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1681%-------------------------------------------------------------------
1682
1683%-------------------------------------------------------------------
1684% --- Executes on button press in runplus: make one step forward and call
1685% --- run0. The step forward is along the fields series 1 or 2 depending on
1686% --- the scan_i and scan_j check box (exclusive each other)
1687function runplus_Callback(hObject, eventdata, handles)
1688%-------------------------------------------------------------------
1689set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1690drawnow
1691%TODO: introduce the option: increment ='*' to move to the next available view
1692increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
1693if isnan(increment)
1694    set(handles.increment_scan,'String','1')%default value
1695    increment=1;
1696end
1697errormsg=runpm(hObject,eventdata,handles,increment);
1698if ~isempty(errormsg)
1699    msgbox_uvmat('ERROR',errormsg);
1700end
1701set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1702
1703%-------------------------------------------------------------------
1704% --- Executes on button press in runmin: make one step backward and call
1705% --- run0. The step backward is along the fields series 1 or 2 depending on
1706% --- the scan_i and scan_j check box (exclusive each other)
1707function runmin_Callback(hObject, eventdata, handles)
1708%-------------------------------------------------------------------
1709set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1710drawnow
1711increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
1712if isnan(increment)
1713    set(handles.increment_scan,'String','1')%default value
1714    increment=1;
1715end
1716errormsg=runpm(hObject,eventdata,handles,increment);
1717if ~isempty(errormsg)
1718    msgbox_uvmat('ERROR',errormsg);
1719end
1720set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1721
1722%-------------------------------------------------------------------
1723% -- Executes on button press in Movie: make a series of +> steps
1724function Movie_Callback(hObject, eventdata, handles)
1725%------------------------------------------------------------------
1726set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1727drawnow
1728increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
1729if isnan(increment)
1730    set(handles.increment_scan,'String','1')%default value
1731    increment=1;
1732end
1733set(handles.STOP,'Visible','on')
1734set(handles.speed,'Visible','on')
1735set(handles.speed_txt,'Visible','on')
1736set(handles.Movie,'BusyAction','queue')
1737UvData=get(handles.uvmat,'UserData');
1738
1739while get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1740        errormsg=runpm(hObject,eventdata,handles,increment);
1741        if ~isempty(errormsg)
1742            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1743            return
1744        end
1745        pause(1.02-get(handles.speed,'Value'))% wait for next image
1746end
1747if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1748    UvData.aviobj=close(UvData.aviobj);
1749   set(handles.uvmat,'UserData',UvData);
1750end
1751set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1752
1753%-------------------------------------------------------------------
1754% -- Executes on button press in Movie: make a series of <- steps
1755function MovieBackward_Callback(hObject, eventdata, handles)
1756%------------------------------------------------------------------
1757set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1758drawnow
1759increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
1760if isnan(increment)
1761    set(handles.increment_scan,'String','1')%default value
1762    increment=1;
1763end
1764set(handles.STOP,'Visible','on')
1765set(handles.speed,'Visible','on')
1766set(handles.speed_txt,'Visible','on')
1767set(handles.MovieBackward,'BusyAction','queue')
1768UvData=get(handles.uvmat,'UserData');
1769
1770while get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1771        errormsg=runpm(hObject,eventdata,handles,increment);
1772        if ~isempty(errormsg)
1773            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1774            return
1775        end
1776        pause(1.02-get(handles.speed,'Value'))% wait for next image
1777end
1778if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1779    UvData.aviobj=close(UvData.aviobj);
1780   set(handles.uvmat,'UserData',UvData);
1781end
1782set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1783
1784%-------------------------------------------------------------------
1785function STOP_Callback(hObject, eventdata, handles)
1786%-------------------------------------------------------------------
1787set(handles.movie_pair,'BusyAction','Cancel')
1788set(handles.movie_pair,'value',0)
1789set(handles.Movie,'BusyAction','Cancel')
1790set(handles.MovieBackward,'BusyAction','Cancel')
1791set(handles.MenuExportMovie,'BusyAction','Cancel')
1792set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1793set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1794set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1795
1796%------------------------------------------------------------------
1797function errormsg=runpm(hObject,eventdata,handles,increment)
1798%------------------------------------------------------------------
1799%check for mï¿œovie pair status
1800movie_status=get(handles.movie_pair,'Value');
1801if isequal(movie_status,1)
1802    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1803end
1804%read the data on the current input rootfile(s)
1805
1806[FileName,RootPath,filebase,FileIndices,FileExt,subdir]=read_file_boxes(handles);
1807NomType=get(handles.FileIndex,'UserData');
1808
1809num1=stra2num(get(handles.i1,'String'));
1810num2=stra2num(get(handles.i2,'String'));
1811num_a=stra2num(get(handles.j1,'String'));
1812num_b=stra2num(get(handles.j2,'String'));
1813
1814sub_value= get(handles.SubField,'Value');
1815if sub_value % a second input file has been entered
1816    [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1817    [pp,ff,str1,str2,str_a,str_b]=name2display(FileIndices_1);
1818    num1_1=stra2num(str1);%current set of indices for the second field (may be set different than the main indices)
1819    num2_1=stra2num(str2);
1820    num_a_1=stra2num(str_a);
1821    num_b_1=stra2num(str_b);
1822    NomType_1=get(handles.FileIndex_1,'UserData');
1823else
1824    filename_1=[];
1825end   
1826
1827comp_input=get(handles.fix_pair,'Value');
1828
1829%case of scanning along the first direction (rootfile numbers)
1830if get(handles.scan_i,'Value')==1% case of scanning along index i   
1831     num1=num1+increment;
1832     num2=num2+increment;
1833     [filename,num1,num_a,num2,num_b]=name_generator(filebase,num1,num_a,FileExt,NomType,comp_input,num2,num_b,subdir);
1834     if sub_value% set the second field name and indices
1835        num1_1=num1_1+increment;
1836        num2_1=num2_1+increment;
1837        filename_1=name_generator(filebase_1,num1_1,num_a_1,FileExt_1,NomType_1,1,num2_1,num_b_1,SubDir_1);
1838     end   
1839else % case of scanning along index j (burst numbers)
1840    num_a=num_a+increment;
1841    num_b=num_b+increment;
1842    [filename,num1,num_a,num2,num_b]=name_generator(filebase,num1,num_a,FileExt,NomType,comp_input,num2,num_b,subdir);
1843    if sub_value
1844        num_a_1=num_a_1+increment;
1845        num_b_1=num_b_1+increment;
1846        filename_1=name_generator(filebase_1,num1_1,num_a_1,FileExt_1,NomType_1,1,num2_1,num_b_1,SubDir_1);
1847    end   
1848end
1849
1850% refresh plots
1851errormsg=refresh_field(handles,filename,filename_1,num1,num2,num_a,num_b);
1852if isempty(errormsg)  %update the index counters
1853    set(handles.i1,'String',num2stra(num1,NomType,1));
1854    if isequal(num2,num1)
1855         set(handles.i2,'String','');
1856    else
1857        set(handles.i2,'String',num2stra(num2,NomType,1));
1858    end
1859    set(handles.j1,'String',num2stra(num_a,NomType,2));
1860    if isequal(num_b,num_a)
1861         set(handles.j2,'String','');
1862    else
1863        set(handles.j2,'String',num2stra(num_b,NomType,2));
1864    end
1865    [indices]=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1866    set(handles.FileIndex,'String',indices);
1867    if ~isempty(filename_1)
1868         indices_1=name_generator('',num1_1,num_a_1,'',NomType_1,1,num2_1,num_b_1,'');
1869         set(handles.FileIndex_1,'String',indices_1);
1870    end
1871    if isequal(movie_status,1)
1872        set(handles.movie_pair,'Value',1)
1873        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1874    end
1875end
1876
1877
1878%-------------------------------------------------------
1879% --- Executes on button press in movie_pair: create an alternating movie with two view
1880%-------------------------------------------------------
1881function movie_pair_Callback(hObject, eventdata, handles)
1882status=get(handles.movie_pair,'value');
1883if isequal(status,0)
1884    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1885    set(handles.i2,'String','')
1886    set(handles.j2,'String','')
1887    return
1888else
1889    set(handles.movie_pair,'BusyAction','queue')
1890end
1891%initialisation
1892set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1893drawnow
1894list_fields=get(handles.Fields,'String');% list menu fields
1895index_fields=get(handles.Fields,'Value');% selected string index
1896FieldName=list_fields{index_fields}; % selected field
1897UvData=get(handles.uvmat,'UserData');
1898if isequal(FieldName,'image')
1899    test_1=0;
1900    [ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes(handles);
1901    NomType=get(handles.FileIndex,'UserData');
1902else
1903    list_fields=get(handles.Fields_1,'String');% list menu fields
1904    index_fields=get(handles.Fields_1,'Value');% selected string index
1905    FieldName=list_fields{index_fields}; % selected field
1906    if isequal(FieldName,'image')
1907        test_1=1;
1908        [ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes_1(handles);
1909        NomType=get(handles.FileIndex_1,'UserData');
1910    else
1911        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1912        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1913        return
1914    end
1915end
1916
1917num_i1=str2double(get(handles.i1,'String'));
1918num_j1=stra2num(get(handles.j1,'String'));
1919num_i2=str2double(get(handles.i2,'String'));
1920num_j2=stra2num(get(handles.j2,'String'));
1921if isnan(num_j2)
1922    if isempty(num_i2)   
1923        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1924        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1925        return
1926    else
1927        num_j2=num_j1;%repeat the index i1 by default
1928    end
1929end
1930if isnan(num_i2)
1931    num_i2=num_i1;%repeat the index i1 by default
1932end
1933imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1934if ~exist(imaname_1,'file')
1935      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1936      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1937      return
1938end
1939
1940%read the second image
1941Field.AName='image';
1942if test_1
1943    Field_a=UvData.Field_1;
1944else
1945    Field_a=UvData.Field;
1946end
1947Field_b.AX=Field_a.AX;
1948Field_b.AY=Field_a.AY;
1949% z index
1950nbslice=str2double(get(handles.nb_slice,'String'));
1951if ~isempty(nbslice)
1952    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1953end
1954Field_b.CoordUnit='pixel';
1955%determine the input file type
1956if (test_1 && isfield(UvData,'MovieObject_1'))||(~test_1 && isfield(UvData,'MovieObject'))
1957    FileType='movie';
1958elseif isequal(lower(Ext),'.avi')
1959    FileType='avi';
1960elseif isequal(lower(Ext),'.vol')
1961    FileType='vol';
1962else
1963   form=imformats(Ext(2:end));
1964   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1965       if isequal(NomType,'*');
1966           FileType='multimage';
1967       else
1968           FileType='image';
1969       end
1970   end
1971end
1972switch FileType
1973        case 'movie'
1974            if test_1
1975                Field_b.A=read(UvData.MovieObject_1,num_i2);
1976            else
1977                Field_b.A=read(UvData.MovieObject,num_i2);
1978            end
1979        case 'avi'
1980            mov=aviread(imaname_1,num_i2);
1981            Field_b.A=frame2im(mov(1));
1982        case 'vol'
1983            Field_b.A=imread(imaname_1);
1984        case 'multimage'
1985            Field_b.A=imread(imaname_1,num_i2);
1986        case 'image'
1987            Field_b.A=imread(imaname_1);
1988end
1989if get(handles.slices,'Value')
1990    Field.ZIndex=str2double(get(handles.z_index,'String'));
1991end
1992
1993%px to phys or other transform on field
1994menu_transform=get(handles.transform_fct,'String');
1995choice_value=get(handles.transform_fct,'Value');
1996transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1997transform_list=get(handles.transform_fct,'UserData');
1998transform=transform_list{choice_value};
1999if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
2000    if test_1 && isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
2001        Field_a=transform(Field_a,UvData.XmlData_1);%the first field has been stored without transform
2002        Field_b=transform(Field_b,UvData.XmlData_1);
2003    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib
2004        Field_b=transform(Field_b,UvData.XmlData);
2005    end
2006end
2007
2008 % make movie until movie speed is set to 0 or STOP is activated
2009hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
2010set(handles.STOP,'Visible','on')
2011set(handles.speed,'Visible','on')
2012set(handles.speed_txt,'Visible','on')
2013while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
2014    % read and plot the series of images in non erase mode
2015    set(hima,'CData',Field_b.A);
2016    pause(1.02-get(handles.speed,'Value'));% wait for next image
2017    set(hima,'CData',Field_a.A);
2018    pause(1.02-get(handles.speed,'Value'));% wait for next image
2019end
2020set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
2021
2022%------------------------------------------------------------------------
2023% --- Executes on button press in run0.
2024function run0_Callback(hObject, eventdata, handles)
2025%------------------------------------------------------------------------
2026set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
2027drawnow
2028filename=read_file_boxes(handles);
2029
2030filename_1=[];%default
2031if get(handles.SubField,'Value')
2032    filename_1=read_file_boxes_1(handles);
2033end
2034num_i1=stra2num(get(handles.i1,'String'));
2035num_i2=stra2num(get(handles.i2,'String'));
2036num_j1=stra2num(get(handles.j1,'String'));
2037num_j2=stra2num(get(handles.j2,'String'));
2038errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
2039if ~isempty(errormsg)
2040      msgbox_uvmat('ERROR',errormsg);
2041else
2042    set(handles.i1,'BackgroundColor',[1 1 1])
2043    set(handles.i2,'BackgroundColor',[1 1 1])
2044    set(handles.j1,'BackgroundColor',[1 1 1])
2045    set(handles.j2,'BackgroundColor',[1 1 1])
2046    set(handles.FileIndex,'BackgroundColor',[1 1 1])
2047    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
2048end   
2049set(handles.run0,'BackgroundColor',[1 0 0])
2050
2051
2052%------------------------------------------------------------------------
2053% --- read the input files and refresh all the plots, including projection.
2054% OUTPUT:
2055%  errormsg: error message char string  =[] by default
2056% INPUT:
2057% filename: first input file (=[] in the absence of input file)
2058% filename_1: second input file (=[] in the asbsenc of secodn input file)
2059% num_i1,num_i2,num_j1,num_j2; frame indices
2060% Field: structure describing an optional input field (then replace the input file)
2061function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
2062%------------------------------------------------------------------------
2063
2064%initialisation
2065% errormsg=[]; % default error message
2066abstime=[];
2067abstime_1=[];
2068dt=[];
2069if ~exist('Field','var')
2070    Field={};
2071end
2072UvData=get(handles.uvmat,'UserData');
2073
2074
2075if ishandle(handles.UVMAT_title) %remove title panel on uvmat
2076    delete(handles.UVMAT_title)
2077end
2078
2079%% determine the main input file information for action
2080FileType=[];%default
2081if ~isempty(filename)
2082    if ~exist(filename,'file')
2083        errormsg=['input file ' filename ' does not exist'];
2084        return
2085    end
2086    Ext=get(handles.FileExt,'String');
2087    NomType=get(handles.FileIndex,'UserData');
2088    %update the z position index
2089    nbslice_str=get(handles.nb_slice,'String');
2090   % z_index=1;%default
2091    if isequal(nbslice_str,'volume')
2092        z_index=num_j1;
2093        set(handles.z_index,'String',num2str(z_index))
2094    else
2095        nbslice=str2num(nbslice_str);
2096        z_index=mod(num_i1-1,nbslice)+1;
2097        set(handles.z_index,'String',num2str(z_index))
2098    end
2099    % refresh menu for save_mask if relevant
2100    masknumber=get(handles.masklevel,'String');
2101    if length(masknumber)>=z_index
2102        set(handles.masklevel,'Value',z_index)
2103    end
2104
2105    % determine the input file type
2106    if isequal(Ext,'.nc')||isequal(Ext,'.cdf')
2107        FileType='netcdf';
2108    elseif isfield(UvData,'MovieObject')
2109        FileType='movie';
2110        FieldName='image';
2111    elseif isequal(lower(Ext),'.avi')
2112        FileType='avi';
2113        FieldName='image';
2114    elseif isequal(lower(Ext),'.vol')
2115        FileType='vol';
2116        FieldName='image';
2117    else
2118       form=imformats(Ext(2:end));
2119       if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2120           if isequal(NomType,'*');
2121               FileType='multimage';
2122           else
2123               FileType='image';
2124           end
2125           FieldName='image';
2126       end
2127    end
2128else
2129    FileType='netcdf';
2130    FieldName='get_field...';
2131end
2132VelType=[];%default
2133if isequal(FileType,'netcdf')
2134    list_fields=get(handles.Fields,'String');% list menu fields
2135    index_fields=get(handles.Fields,'Value');% selected string index
2136    FieldName= list_fields{index_fields}; % selected field
2137    if ~isequal(FieldName,'get_field...')% read the field names on the interface get_field...
2138       VelType=setfield(handles);
2139    end
2140end
2141
2142%% choose a second field if Subfield option is 'on'
2143FieldName_1=[];
2144scal_color=[];
2145VelType_1=setfield_1(handles);
2146% sub_value=get(handles.SubField,'Value');
2147FileType_1='none';%default
2148if ~isempty(filename_1)
2149    % test for a constant second field (comparison with a fixed field)
2150    NomType_1=get(handles.FileIndex_1,'UserData');
2151    Ext_1=get(handles.FileExt_1,'String');
2152    % determine the input file type
2153    if isequal(Ext_1,'.nc')||isequal(Ext_1,'.cdf')
2154        FileType_1='netcdf';
2155    elseif isfield(UvData,'MovieObject_1')
2156        FileType_1='movie';
2157        FieldName_1='image';
2158    elseif isequal(lower(Ext_1),'.avi')
2159        FileType='avi';
2160        FieldName_1='image';
2161    elseif isequal(lower(Ext_1),'.vol')
2162        FileType_1='vol';
2163        FieldName_1='image';
2164    elseif length(Ext_1)>1
2165       form=imformats(Ext_1(2:end));
2166       if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2167           if isequal(NomType_1,'*');
2168               FileType_1='multimage';
2169           else
2170               FileType_1='image';
2171           end
2172           FieldName_1='image';
2173       end
2174    end
2175    if ~isequal(FieldName_1,'image')
2176        list_fields=get(handles.Fields_1,'String');% list menu fields
2177        index_fields=get(handles.Fields_1,'Value');% selected string index
2178        FieldName_1= list_fields{index_fields}; % selected field
2179        if isequal(VelType_1,'*')% free veltype choice
2180            VelType_1=[];
2181        elseif isequal(VelType_1,'"')% veltype the same as for the first field
2182            if isempty(VelType)
2183                VelType_1=[];
2184            else
2185                VelType_1=VelType;
2186            end
2187        end
2188    end
2189    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2190    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2191        if isfield(UvData,'filename_1')&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2192            test_keepdata_1= isequal(filename_1,UvData.filename_1)&&...
2193                isequal(VelType_1,UvData.filename_1) && isequal(FieldName_1,UvData.FieldName_1);
2194        end
2195    end
2196    if test_keepdata_1
2197        Field{2}=UvData.Field_1;   
2198    elseif ~exist(filename_1,'file')
2199        errormsg=['second file ' filename_1 ' does not exist'];
2200        return
2201    end
2202end
2203
2204%% read the input field(s)
2205%read images
2206if ~isempty(filename) && isequal(FieldName,'image')
2207     switch FileType
2208        case 'movie'
2209            try
2210                A=read(UvData.MovieObject,num_i1);
2211            catch
2212                errormsg=lasterr;
2213                return
2214            end
2215        case 'avi'
2216            try
2217                mov=aviread(filename,num_i1);
2218            catch
2219                errormsg=lasterr;
2220                return
2221            end
2222            A=frame2im(mov(1));
2223        case 'vol'
2224            A=imread(filename);
2225        case 'multimage'
2226            A=imread(filename,num_i1);
2227        case 'image'
2228            A=imread(filename);
2229    end
2230    npxy=size(A);
2231    set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface
2232    set(handles.npy,'String',num2str(npxy(1)));
2233    Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
2234    Rangy=[npxy(1)-0.5 0.5]; %
2235    Field{1}.AName='image';
2236    Field{1}.ListVarName={'AY','AX','A'}; %
2237    if size(A,3)==3;%color
2238        Field{1}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
2239    else
2240        Field{1}.VarDimName={'AY','AX',{'AY','AX'}}; %
2241    end
2242    Field{1}.AY=Rangy;
2243    Field{1}.AX=Rangx;
2244    Field{1}.A=A;
2245   % Field{1}.CoordType='px'; %used for mouse_motion
2246    Field{1}.CoordUnit='pixel'; %used for mouse_motion
2247end
2248
2249%read a second image
2250if  ~isempty(filename_1) && ~test_keepdata_1 && isequal(FieldName_1,'image')
2251    switch FileType_1
2252        case 'movie'
2253            A=read(UvData.MovieObject_1,num_i1);
2254        case 'avi'
2255            mov=aviread(filename_1,num_i1);
2256            A=frame2im(mov(1));
2257        case 'vol'
2258            A=imread(filename_1);
2259        case 'multimage'
2260            A=imread(filename_1,num_i1);
2261        case 'image'
2262            A=imread(filename_1);
2263        case 'netcdf'
2264        otherwise
2265            errormsg=['unknown input file type ' filename_1];
2266    end
2267    npxy=size(A);
2268    set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface
2269    set(handles.npy,'String',num2str(npxy(1)));
2270    Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
2271    Rangy=[npxy(1)-0.5 0.5]; %
2272    Field{2}.AName='image';
2273    Field{2}.ListVarName={'AY','AX','A'}; %
2274    if size(A,3)==3;%color
2275        Field{2}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
2276    else
2277        Field{2}.VarDimName={'AY','AX',{'AY','AX'}}; %
2278    end
2279    Field{2}.AY=Rangy;
2280    Field{2}.AX=Rangx;
2281    Field{2}.A=A;
2282    Field{2}.CoordType='px'; %used for mouse_motion
2283    Field{2}.CoordUnit='px'; %used for move_mou
2284end
2285
2286%read ncfile(s)
2287CivStage_1=0;%default
2288VelType_out_1=[];
2289InputField={FieldName};
2290InputField_1={FieldName_1};
2291if (~isempty(filename)&& isequal(FileType,'netcdf')) || (~isempty(filename_1)&& isequal(FileType_1,'netcdf')) ;
2292    %read the velocity field(s) from netcdf rootfile(s)
2293    list_code=get(handles.col_vec,'String');% list menu fields
2294    index_code=get(handles.col_vec,'Value');% selected string index
2295    scal_color= list_code{index_code(1)}; % selected field
2296    if isequal(FieldName,'velocity')&& ~isequal(scal_color,'black') && ~isequal(scal_color,'white')
2297        InputField=[InputField scal_color];
2298    end
2299    if isequal(FieldName_1,'velocity') && ~isequal(scal_color,'black') && ~isequal(scal_color,'white')
2300        InputField_1=[InputField_1 scal_color];
2301    end
2302    if isequal(FileType,'netcdf')  %read the first nc field
2303        if isequal(FieldName,'get_field...')% read the field names on the interface get_field.
2304            hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI
2305            if isempty(hget_field)
2306                hget_field= get_field(filename);%open the get_field GUI   
2307              %  set(hget_field,'name','get_field')
2308            elseif UvData.NewSeries% refresh the fet_field GUI for a new series
2309                delete(hget_field)
2310                hget_field= get_field(filename);%open the get_field GUI
2311                set(hget_field,'name','get_field')%rename  get_field GUI for the 'slave' mode
2312            end
2313            hhget_field=guidata(hget_field);
2314            set(hhget_field.list_fig,'Value',1)
2315            set(hhget_field.list_fig,'String',{'uvmat'})
2316            funct_list=get(hhget_field.ACTION,'UserData');
2317            funct_index=get(hhget_field.ACTION,'Value');
2318            funct=funct_list{funct_index};%select  the current action in get_field, e;g. PLOT
2319            Field{1}=funct(hget_field); %%activate the current action selected in get_field, e;g.read the names of the variables to plot
2320            CivStage=0;
2321            VelType_out=[];   
2322        else
2323            [Field{1},VelType_out]=read_civxdata(filename,InputField,VelType);
2324            if isfield(Field{1},'Txt')
2325                errormsg=Field{1}.Txt;
2326                return
2327            end
2328            CivStage=Field{1}.CivStage;
2329            UvData.NbDim=Field{1}.nb_dim;
2330        end
2331    end
2332    if ~isempty(filename_1) && ~test_keepdata_1 && isequal(FileType_1,'netcdf') %read the second file
2333        if isequal(FieldName_1,'get_field...')% read the field names on the interface get_field.
2334            hget_field_1=findobj(allchild(0),'Name','get_field_1');%find the get_field... GUI
2335            if isempty(hget_field_1)
2336                 hget_field_1= get_field(filename_1);%open the get_field GUI
2337                 set(hget_field_1,'name','get_field_1')
2338            elseif UvData.NewSeries% refresh the fet_field GUI for a new series
2339                delete(hget_field_1)
2340                hget_field_1= get_field(filename);%open the get_field GUI
2341                set(hget_field_1,'name','get_field_1')%rename  get_field GUI for the 'slave' mode
2342            end
2343            hhget_field_1=guidata(hget_field_1);%handles of GUI elements in get_field
2344            set(hhget_field_1.list_fig,'Value',1)
2345            set(hhget_field_1.list_fig,'String',{'uvmat'})
2346            funct_list=get(hhget_field_1.ACTION,'UserData');
2347            funct_index=get(hhget_field_1.ACTION,'Value');
2348            funct=funct_list{funct_index};
2349            Field{2}=funct(hget_field_1); %read the names of the variables to plot in the get_field GUI
2350        else
2351            [Field{2},VelType_out_1]=read_civxdata(filename_1,InputField_1,VelType_1);
2352            CivStage_1=Field{2}.CivStage;
2353        end
2354        if ~isequal(FileType,'netcdf')
2355            VelType_out=VelType_out_1;
2356        end
2357    end
2358end
2359
2360%store the second field for possible latter use
2361if numel(Field)==2
2362    UvData.Field_1=Field{2};
2363end
2364
2365%% update the display buttons for the first velocity type (first menuline)
2366veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2367if ~isequal(FileType,'netcdf')
2368    reset_vel_type(veltype_handles)
2369elseif isempty(VelType) && ~isequal(FieldName,'get_field...')
2370    set_veltype_display(veltype_handles,CivStage)%update the display of available velocity types for the first field
2371    if isempty(VelType_out)
2372        reset_vel_type(veltype_handles)
2373    else
2374        handle1=eval(['handles.' VelType_out]);
2375        reset_vel_type(veltype_handles,handle1)
2376    end
2377end
2378
2379%% update the display buttons for the second velocity type (second menuline)
2380veltype_handles_1=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
2381if ~isequal(FileType_1,'netcdf')
2382    reset_vel_type(veltype_handles_1)
2383elseif isempty(VelType_1) && ~isequal(FieldName_1,'get_field...')
2384    set_veltype_display(veltype_handles_1,CivStage_1)%update the display of available velocity types for the first field
2385    if isempty(VelType_out_1)
2386        reset_vel_type(veltype_handles_1)
2387    else
2388        handle1=eval(['handles.' VelType_out_1 '_1']);
2389        reset_vel_type(veltype_handles_1,handle1)
2390    end
2391end
2392
2393%% introduce w as background image by default for a new series (only for nbdim=2)
2394if ~isfield(UvData,'NewSeries')
2395    UvData.NewSeries=1;
2396end
2397%put W as background image by default if NbDim=2:
2398if ~isfield(UvData,'NbDim')||isempty(UvData.NbDim)||~isequal(UvData.NbDim,3)
2399    if UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W);
2400        set(handles.SubField,'Value',1);
2401        %menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w'
2402        set(handles.RootPath_1,'String','"')
2403        set(handles.RootFile_1,'String','"')
2404        set(handles.SubDir_1,'String','"');
2405        [indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,'');
2406        set(handles.FileIndex_1,'String',indices)
2407        set(handles.FileExt_1,'String','"');
2408        set(handles.Fields_1,'Visible','on');
2409        set(handles.Fields_1,'Visible','on');
2410        set(handles.RootPath_1,'Visible','on')
2411        set(handles.RootFile_1,'Visible','on')
2412        set(handles.SubDir_1,'Visible','on');
2413        set(handles.FileIndex_1,'Visible','on');
2414        set(handles.FileExt_1,'Visible','on');
2415        set(handles.Fields_1,'Visible','on');
2416        Field{1}.AName='w';
2417%         testscal=1;
2418    end
2419end           
2420
2421%multislice case
2422if ~isempty(filename) &&(~isfield(UvData,'NbDim') || isequal(UvData.NbDim,2))&&...%2D case
2423      isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')&& isfield(UvData.XmlData.GeometryCalib,'SliceCoord')
2424       siz=size(UvData.XmlData.GeometryCalib.SliceCoord);
2425%        if siz(1)>1
2426%            NbSlice=siz(1);
2427%        else
2428%            NbSlice=1;
2429%        end
2430end
2431
2432%store the current open names, fields and vel types in uvmat interface
2433UvData.filename=filename;
2434UvData.filename_1=filename_1;
2435UvData.VelType=VelType;
2436UvData.VelType_1=VelType_1;
2437UvData.FieldName=FieldName;
2438UvData.FieldName_1=FieldName_1;
2439if ~isempty(scal_color)
2440    UvData.CName=scal_color;
2441end
2442
2443%% coordinate transform or user fct
2444XmlData=[];%default
2445if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2446    XmlData=UvData.XmlData;
2447end
2448XmlData_1=[];%default
2449if isfield(UvData,'XmlData_1')
2450   XmlData_1=UvData.XmlData_1;
2451end
2452% menu_transform=get(handles.transform_fct,'String');
2453choice_value=get(handles.transform_fct,'Value');
2454transform_list=get(handles.transform_fct,'UserData');
2455transform=transform_list{choice_value};%selected function handles
2456% z index
2457if ~isempty(filename)
2458    Field{1}.ZIndex=z_index;
2459end
2460%px to phys or other transform on field
2461if ~isempty(transform)
2462    if length(Field)>=2
2463        Field{2}.ZIndex=z_index;
2464        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2465        if isempty(Field{2})
2466            Field(2)=[];
2467        end
2468    else
2469        Field{1}=transform(Field{1},XmlData);
2470    end
2471end
2472
2473%% calculate scalar
2474if isequal(FileType,'netcdf') && ~isequal(FieldName,'get_field...')%
2475    Field{1}=calc_field(InputField,Field{1});
2476end
2477if length(Field)==2 && ~test_keepdata_1 && isequal(FileType_1,'netcdf') && ~isequal(FieldName_1,'get_field...')
2478    Field{2}=calc_field(InputField_1,Field{2});
2479end
2480% combine the two input fields (e.g. substract velocity fields)
2481if numel(Field)==2
2482   UvData.Field=sub_field(Field{1},Field{2}); %TO UPDATE FOR MORE GENERAL INPUT 
2483else
2484   UvData.Field=Field{1};
2485end
2486
2487%% test 3D , default projection menuplane and typical mesh (needed to menuopen set_object)
2488test_x=0;
2489test_z=0;% test for unstructured z coordinate
2490UvData.ZMax=0;
2491UvData.ZMin=0;%default
2492%UvData.Mesh=1; %default
2493[UvData.Field,errormsg]=check_field_structure(UvData.Field);
2494if ~isempty(errormsg)
2495    errormsg=['error in uvmat/run0_Callback/check_field_structure: ' errormsg];
2496    return
2497end
2498[CellVarIndex,NbDim,VarType]=find_field_indices(UvData.Field);
2499[NbDim,imax]=max(NbDim);
2500% if isempty(imax)
2501% %    DimVarIndex=0;   
2502%     coord_x=[];
2503% else
2504% %     VarIndex=CellVarIndex{imax};
2505%     coord_x=VarType{imax}.coord_x;
2506% end
2507% if isfield(UvData,'NbDim') && ~isempty(UvData.NbDim)
2508%     NbDim=UvData.NbDim;
2509% else 
2510UvData.NbDim=NbDim;
2511% end
2512if ~isempty(VarType{imax}.coord_x)  && ~isempty(VarType{imax}.coord_y)    %unstructured coordinates
2513    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2514    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2515    eval(['nbvec=length(UvData.Field.' XName ');'])%nbre of measurement points (e.g. vectors)
2516    test_x=1;%test for unstructured coordinates
2517elseif NbDim==2
2518    YName=UvData.Field.ListVarName{VarType{imax}.coord(1)}; %structured coordinates
2519    XName=UvData.Field.ListVarName{VarType{imax}.coord(2)};
2520elseif NbDim==3
2521    ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2522    YName=UvData.Field.ListVarName{VarType{imax}.coord(2)};
2523    XName=UvData.Field.ListVarName{VarType{imax}.coord(3)};
2524end
2525
2526eval(['XMax=max(UvData.Field.' XName ');'])
2527eval(['XMin=min(UvData.Field.' XName ');'])
2528eval(['YMax=max(UvData.Field.' YName ');'])
2529eval(['YMin=min(UvData.Field.' YName ');'])
2530eval(['nbvec=length(UvData.Field.' XName ');'])
2531if NbDim==3%
2532    if ~isempty(CellVarIndex) && ~isempty(VarType{imax}.coord_z)%unstructured coordinate z
2533%         ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2534        eval(['ZMax=max(UvData.Field.' ZName ');'])
2535        eval(['ZMin=min(UvData.Field.' ZName ');'])
2536        test_z=1;   
2537    elseif isfield(UvData,'Z')% usual civ data
2538        ZMax=max(UvData.Z);
2539        ZMin=min(UvData.Z);
2540        test_z=1;
2541    end
2542    if isequal(ZMin,ZMax)%no z dependency
2543        NbDim=2;
2544        test_z=0;
2545    end
2546end
2547if test_x
2548    if test_z
2549        UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2550        UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2551    else
2552        UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2553    end
2554else
2555    VarIndex=CellVarIndex{imax}; % list of variable indices
2556    DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2557    nbpoints_y=UvData.Field.DimValue(DimIndex(1));
2558    nbpoints_x=UvData.Field.DimValue(DimIndex(2));
2559    DX=(XMax-XMin)/nbpoints_x;
2560    DY=(YMax-YMin)/nbpoints_y;
2561    UvData.Field.Mesh=sqrt(DX*DY);
2562end
2563UvData.Field.XMax=XMax;
2564UvData.Field.XMin=XMin;
2565UvData.Field.YMax=XMax;
2566UvData.Field.YMin=XMin;
2567if test_z
2568    UvData.Field.ZMax=ZMax;
2569    UvData.Field.ZMin=ZMin;
2570end
2571
2572%case of structured coordinates
2573
2574% if  isempty(coord_x) && ~isempty(CellVarIndex)
2575%     VarIndex=CellVarIndex{imax}; % list of variable indices
2576%     DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2577%     if NbDim==3
2578%         nbpoints=UvData.Field.DimValue(DimIndex(1));
2579%         if isfield(VarType{imax},'coord_3')&& ~isequal(VarType{imax}.coord_3,0) % z is a dimension variable
2580%             ZName=UvData.Field.ListVarName{VarType{imax}.coord_3};
2581%             eval(['UvData.ZMax=max(UvData.Field.' ZName ');'])
2582%             eval(['UvData.ZMin=min(UvData.Field.' ZName ');'])
2583%         else
2584%             testcoord_z=0;
2585%             if length(UvData.Field.VarAttribute)>=VarIndex(1)
2586%                 if isfield(UvData.Field.VarAttribute{VarIndex(1)},'Coord_1')%regular grid
2587%                     Coord_z=UvData.Field.VarAttribute{VarIndex(1)}.Coord_1;
2588%                     UvData.ZMax=max(Coord_z);
2589%                     UvData.ZMin=min(Coord_z);
2590%                     testcoord_z=1;
2591%                 end
2592%             end
2593%             if ~testcoord_z
2594%                   UvData.ZMin=1;
2595%                   UvData.ZMax=UvData.Field.DimValue(DimIndex(1));
2596%             end
2597%         end
2598%         Field.Mesh=(UvData.ZMax-UvData.ZMin)/(nbpoints-1);
2599%     elseif NbDim==2
2600%         nbpoints_y=UvData.Field.DimValue(DimIndex(1));       
2601%         Yvar=VarType{imax}.coord_y;
2602%         if Yvar~=0  % x is a dimension variable
2603%             YName=UvData.Field.ListVarName{Yvar};
2604%             eval(['UvData.YMax=max(UvData.Field.' YName ');'])
2605%             eval(['UvData.YMin=min(UvData.Field.' YName ');'])
2606%         else
2607%             testcoord_y=0;
2608%             if ~testcoord_y
2609%                   UvData.YMin=1;
2610%                   UvData.YMax=UvData.Field.DimValue(DimIndex(1));
2611%             end
2612%         end
2613%         DY=(UvData.YMax-UvData.YMin)/(nbpoints_y-1);
2614%         nbpoints_x=UvData.Field.DimValue(DimIndex(2));
2615%         Xvar=VarType{imax}.coord_x;
2616%         if Xvar~=0  % x is a dimension variable
2617%             XName=UvData.Field.ListVarName{Xvar};
2618%             eval(['UvData.XMax=max(UvData.Field.' XName ');'])
2619%             eval(['UvData.XMin=min(UvData.Field.' XName ');'])
2620%         else
2621%             testcoord_x=0;
2622%             if ~testcoord_x
2623%                   UvData.XMin=1;
2624%                   UvData.XMax=UvData.Field.DimValue(DimIndex(2));
2625%             end
2626%         end
2627%         DX=(UvData.XMax-UvData.XMin)/(nbpoints_x-1);
2628%         Field.Mesh= sqrt(DX*DY);
2629%     end
2630% end
2631
2632%create a default projection menuplane
2633UvData.Object{1}.Style='plane';%main plotting plane
2634UvData.Object{1}.ProjMode='projection';%main plotting plane
2635if ~isfield(UvData.Object{1},'plotaxes')
2636    UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
2637    set(handles.list_object_1,'Value',1);
2638    set(handles.list_object_1,'String',{'1-PLANE'}); 
2639end
2640
2641%3D case (menuvolume)
2642if NbDim==3 && UvData.NewSeries
2643    UvData.Object{1}.NbDim=UvData.NbDim;%test for 3D objects
2644    UvData.Object{1}.RangeZ=Field.Mesh;%main plotting plane
2645    UvData.Object{1}.Coord(1,3)=(UvData.ZMin+UvData.ZMax)/2;%section at a middle plane chosen
2646    UvData.Object{1}.Phi=0;
2647    UvData.Object{1}.Theta=0;
2648    UvData.Object{1}.Psi=0;
2649    UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR 
2650    PlotHandles=get_plot_handles(handles);
2651    ZBounds(1)=UvData.ZMin; %minimum for the Z slider
2652    ZBounds(2)=UvData.ZMax;%maximum for the Z slider
2653    UvData.Object{1}.Name='1-PLANE';
2654    UvData.Object{1}.enable_plot=1;
2655    set_object(UvData.Object{1},PlotHandles,ZBounds);
2656    set(handles.list_object_1,'Value',1);
2657%multilevel case (single menuplane in a 3D space)
2658elseif isfield(UvData,'Z')
2659    if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2660        XmlData=UvData.XmlData;
2661        if isfield(XmlData,'PlanePos')
2662             UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2663        end
2664        if isfield(XmlData,'PlaneAngle')
2665            siz=size(XmlData.PlaneAngle);
2666            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)             
2667            UvData.Object{1}.Phi=XmlData.PlaneAngle(indangle,1);
2668            UvData.Object{1}.Theta=XmlData.PlaneAngle(indangle,2);
2669            UvData.Object{1}.Psi=XmlData.PlaneAngle(indangle,3);
2670        end
2671    elseif isfield(UvData,'ZIndex')
2672        UvData.Object{1}.ZObject=UvData.ZIndex;
2673    end
2674end
2675
2676%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2677if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2678    set(handles.MinA,'String','0')
2679    set(handles.MaxA,'String','255')
2680end
2681
2682%% Plot the projections on the selected  projection objects
2683
2684% main projection object (uvmat display)
2685IndexObj(1)=get(handles.list_object_1,'Value');%selected projection object for main view
2686if IndexObj(1)> numel(UvData.Object)
2687    IndexObj(1)=1;%select the first object if the selected one does not exist
2688    set(handles.list_object_1,'Value',1)
2689end
2690plot_handles{1}=handles;
2691haxes(1)=handles.axes3;
2692PlotParam{1}=read_plot_param(handles);%read plotting parameters on the uvmat interfac
2693keeplim(1)=get(handles.FixedLimits,'Value');% test for fixed graph limits
2694PosColorbar{1}=UvData.PosColorbar;%prescribe the colorbar position on the uvmat interface
2695
2696% second projection object (view_field display)
2697IndexObj_2=get(handles.list_object_2,'Value');%selected projection object for the second view
2698if isequal(get(handles.list_object_2,'Visible'),'on') && IndexObj_2 <= numel(UvData.Object)&& ~isempty(UvData.Object{IndexObj_2})
2699    IndexObj(2)=IndexObj_2;
2700    view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2701    if ~isempty(view_field_handle)
2702        plot_handles{2}=guidata(view_field_handle);
2703        haxes(2)=plot_handles{2}.axes3;
2704        PlotParam{2}=read_plot_param(plot_handles{2});%read plotting parameters on the uvmat interface
2705        keeplim(2)=get(plot_handles{2}.FixedLimits,'Value');
2706        PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2707    end
2708end
2709
2710%loop on the projection objects: one or two
2711for imap=1:numel(IndexObj)
2712    iobj=IndexObj(imap);   
2713    [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2714    if ~isempty(errormsg)
2715        return
2716    end
2717    %use of mask (TODO: check)
2718    if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2719        flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2720        AX=ObjectData.AX;%x coordiantes for the scalar field
2721        AY=ObjectData.AY;%y coordinates for the scalar field
2722        MaskX=ObjectData.MaskX;%x coordiantes for the mask
2723        MaskY=ObjectData.MaskY;%y coordiantes for the mask
2724        if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2725            nxy=size(flag_mask);
2726            sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2727            sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2728            x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2729            y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2730            %project on the positions of the scalar
2731            npxy=size(ObjectData.A);
2732            dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2733            dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2734            xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2735            yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2736            [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2737            flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2738        end
2739        AClass=class(ObjectData.A);
2740        ObjectData.A=flag_mask.*double(ObjectData.A);
2741        ObjectData.A=feval(AClass,ObjectData.A);
2742        ind_off=[];
2743        if isfield(ObjectData,'ListVarName')
2744            for ilist=1:length(ObjectData.ListVarName)
2745                if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2746                    ind_off=[ind_off ilist];
2747                end
2748            end
2749            ObjectData.ListVarName(ind_off)=[];
2750            ObjectData.VarDimIndex(ind_off)=[];
2751            ind_off=[];
2752            for ilist=1:length(ObjectData.ListDimName)
2753                if isequal(ObjectData.ListDimName{ilist},'MaskX') || isequal(ObjectData.ListDimName{ilist},'MaskY')
2754                    ind_off=[ind_off ilist];
2755                end
2756            end
2757            ObjectData.ListDimName(ind_off)=[];
2758            ObjectData.DimValue(ind_off)=[];
2759        end
2760    end
2761   
2762    if ~isempty(ObjectData)
2763        PlotType='none'; %default
2764        if imap==2 && isempty(view_field_handle)
2765            view_field(ObjectData)
2766        else
2767            [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},keeplim(imap),PosColorbar{imap});
2768            write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2769            if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2770                ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2771            end
2772            if imap==1           
2773                UvData.axes3=ObjectData;
2774            else
2775                ViewFieldData=get(view_field_handle,'UserData');
2776                ViewFieldData.axes3=ObjectData;
2777                set(view_field_handle,'UserData',ViewFieldData)
2778            end
2779        end
2780        if isequal(PlotType,'none')
2781            hget_field=findobj(allchild(0),'name','get_field');
2782            if isempty(hget_field)
2783                get_field([],ObjectData)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2784            else
2785                errormsg='The field defined by get_field cannot be plotted';
2786                return
2787            end
2788        end
2789    end
2790end
2791
2792%write_plot_param(handles,UvData.Object{1}.PlotParam);% update the display of the plotting parameters
2793UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2794set(handles.uvmat,'UserData',UvData)
2795
2796%% update the mask
2797if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
2798   update_mask(handles,num_i1,num_i2);
2799end
2800
2801%% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2802menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2803ind_bad=[];
2804nb_histo=1;
2805
2806% suppress coordinates from the histogram menu
2807for ivar=1:numel(menu_histo)%l loop on field variables:
2808    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2809        Role=UvData.Field.VarAttribute{ivar}.Role;
2810        switch Role
2811            case {'coord_x','coord_y','coord_z','dimvar'}
2812                ind_bad=[ind_bad ivar];
2813            case {'vector_y'}
2814                nb_histo=nb_histo+1;
2815        end
2816    end
2817    DimCell=UvData.Field.VarDimName{ivar};
2818    DimName='';
2819    if ischar(DimCell)
2820        DimName=DimCell;
2821    elseif iscell(DimCell)&& numel(DimCell)==1
2822        DimName=DimCell{1};
2823    end
2824    if strcmp(DimName,menu_histo{ivar})
2825        ind_bad=[ind_bad ivar];
2826    end
2827end
2828menu_histo(ind_bad)=[];
2829
2830%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2831% display menus and plot histograms
2832test_v=0;
2833if ~isempty(menu_histo)
2834    set(handles.histo1_menu,'Value',1)
2835    set(handles.histo1_menu,'String',menu_histo)
2836    histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2837    % case of more than one variables (eg vector components)
2838    if nb_histo > 1
2839        test_v=1;
2840        set(handles.histo2_menu,'Visible','on')
2841        set(handles.histo_v,'Visible','on')
2842        set(handles.histo2_menu,'String',menu_histo)
2843        set(handles.histo2_menu,'Value',2)
2844        histo2_menu_Callback(handles.histo2_menu,[], handles)% plot second histogram
2845    end
2846end
2847if ~test_v
2848    set(handles.histo2_menu,'Visible','off')
2849    set(handles.histo_v,'Visible','off')
2850    cla(handles.histo_v)
2851    set(handles.histo2_menu,'Value',1)
2852end
2853%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2854
2855%% display time
2856testimedoc=0;
2857if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'Time')
2858    if isempty(num_i2)||isnan(num_i2)
2859        num_i2=num_i1;
2860    end
2861    if isempty(num_j1)||isnan(num_j1)
2862        num_j1=1;
2863    end
2864    if isempty(num_j2)||isnan(num_j2)
2865        num_j2=num_j1;
2866    end
2867    siz=size(UvData.XmlData.Time);
2868    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2869        abstime=(UvData.XmlData.Time(num_i1,num_j1)+UvData.XmlData.Time(num_i2,num_j2))/2;%overset the time read from files
2870        dt=(UvData.XmlData.Time(num_i2,num_j2)-UvData.XmlData.Time(num_i1,num_j1));
2871        testimedoc=1;
2872    end
2873end
2874if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time')
2875    [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2876    num_i2=str2double(str2);
2877    if isnan(num_i2)
2878        num_i2=num_i1;
2879    end
2880    num_j1=str2double(str_a);
2881    if isnan(num_j1)
2882        num_j1=1;
2883    end
2884    num_j2=str2double(str_b);
2885    if isnan(num_j2)
2886        num_j2=num_j1;
2887    end
2888    num_i1=str2double(str1);
2889    siz=size(UvData.XmlData_1.Time);
2890    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2891        abstime_1=(UvData.XmlData_1.Time(num_i1,num_j1)+UvData.XmlData_1.Time(num_i2,num_j2))/2;%overset the time read from files
2892    end
2893end
2894set(handles.abs_time,'String',num2str(abstime,4))
2895set(handles.abs_time_1,'String',num2str(abstime_1,4))
2896if testimedoc && isfield(UvData,'dt')
2897    dt=UvData.dt;
2898end
2899if isempty(dt)||isequal(dt,0)
2900    set(handles.Dt_txt,'String','')
2901else
2902    if ~(isfield(UvData,'TimeUnit') && ~isempty(UvData.TimeUnit))
2903        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2904    else
2905        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' UvData.TimeUnit] )
2906    end
2907end
2908
2909%% update the input file name in the get_field GUI
2910if isequal(FieldName,'get_field...')
2911    set(hhget_field.inputfile,'String',filename)
2912    Tabchar={''};%default
2913    Tabcell=[];
2914    if isfield(Field{1},'ListGlobalAttribute')&& ~isempty(Field{1}.ListGlobalAttribute)
2915        for iline=1:length(Field{1}.ListGlobalAttribute)
2916            Tabcell{iline,1}=Field{1}.ListGlobalAttribute{iline};
2917            if isfield(Field{1}, Field{1}.ListGlobalAttribute{iline})
2918                eval(['val=Field{1}.' Field{1}.ListGlobalAttribute{iline} ';'])
2919                if ischar(val);
2920                    Tabcell{iline,2}=val;
2921                else
2922                    Tabcell{iline,2}=num2str(val);
2923                end
2924            end
2925        end
2926        if ~isempty(Tabcell)
2927            Tabchar=cell2tab(Tabcell,'=');
2928            Tabchar=[{''};Tabchar];
2929        end
2930    end
2931    set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field
2932end
2933if isequal(FieldName_1,'get_field...')
2934    set(hhget_field_1.inputfile,'String',filename_1)
2935    Tabchar={''};%default
2936    Tabcell=[];
2937    if isfield(Field{2},'ListGlobalAttribute')&& ~isempty(Field{2}.ListGlobalAttribute)
2938        for iline=1:length(Field{2}.ListGlobalAttribute)
2939            Tabcell{iline,1}=Field{2}.ListGlobalAttribute{iline};
2940            if isfield(Field{2}, Field{2}.ListGlobalAttribute{iline})
2941                eval(['val=Field{2}.' Field{2}.ListGlobalAttribute{iline} ';'])
2942                if ischar(val);
2943                    Tabcell{iline,2}=val;
2944                else
2945                    Tabcell{iline,2}=num2str(val);
2946                end
2947            end
2948        end
2949        if ~isempty(Tabcell)
2950            Tabchar=cell2tab(Tabcell,'=');
2951            Tabchar=[{''};Tabchar];
2952        end
2953    end
2954    set(hhget_field_1.attributes,'String',Tabchar);%update list of global attributes in get_field
2955end
2956
2957
2958%-------------------------------------------------------------------
2959% --- translate coordinate to matrix index
2960%-------------------------------------------------------------------
2961function [indx,indy]=pos2ind(x0,rangx0,nxy)
2962indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2963indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2964
2965%-------------------------------------------------------------------
2966% --- Executes on button press in 'FixedLimits'.
2967%-------------------------------------------------------------------
2968function FixedLimits_Callback(hObject, eventdata, handles)
2969test=get(handles.FixedLimits,'Value');
2970if test
2971    set(handles.FixedLimits,'BackgroundColor',[1 1 0])
2972else
2973    set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7])
2974    update_plot(handles);
2975end
2976
2977%-------------------------------------------------------------------
2978% --- Executes on button press in auto_xy.
2979function auto_xy_Callback(hObject, eventdata, handles)
2980test=get(handles.auto_xy,'Value');
2981if test
2982    set(handles.auto_xy,'BackgroundColor',[1 1 0])
2983    cla(handles.axes3)
2984    update_plot(handles);
2985else
2986    set(handles.auto_xy,'BackgroundColor',[0.7 0.7 0.7])
2987    update_plot(handles);
2988%     axis(handles.axes3,'image')
2989end
2990
2991
2992%-------------------------------------------------------------------
2993
2994%-------------------------------------------------------------------
2995% --- Executes on button press in 'zoom'.
2996%-------------------------------------------------------------------
2997function zoom_Callback(hObject, eventdata, handles)
2998
2999if (get(handles.zoom,'Value') == 1);
3000    set(handles.zoom,'BackgroundColor',[1 1 0])
3001    set(handles.FixedLimits,'Value',1)% propose by default fixed limits for the plotting axes
3002    set(handles.FixedLimits,'BackgroundColor',[1 1 0])
3003else
3004    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3005end
3006
3007
3008%-------------------------------------------------------------------
3009%----Executes on button press in 'record': records the current flags of manual correction.
3010%-------------------------------------------------------------------
3011function record_Callback(hObject, eventdata, handles)
3012% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
3013filename=read_file_boxes(handles);
3014[erread,message]=fileattrib(filename);
3015if ~isempty(message) && ~isequal(message.UserWrite,1)
3016     msgbox_uvmat('ERROR',['no writting access to ' filename])
3017     return
3018end
3019test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3020test_civ1=isequal(get(handles.civ1,'BackgroundColor'),[1 1 0]);
3021if ~test_civ2 && ~test_civ1
3022    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3023end
3024if test_civ2
3025    nbname='nb_vectors2';
3026   flagname='vec2_FixFlag';
3027   attrname='fix2';
3028end
3029if test_civ1
3030    nbname='nb_vectors';
3031   flagname='vec_FixFlag';
3032   attrname='fix';
3033end
3034%write fix flags in the netcdf file
3035UvData=get(handles.uvmat,'UserData');
3036hhh=which('netcdf.open');% look for built-in matlab netcdf library
3037if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
3038    nc=netcdf.open(filename,'NC_WRITE');
3039    netcdf.reDef(nc)
3040    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1)
3041    dimid = netcdf.inqDimID(nc,nbname);
3042    try
3043        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
3044    catch
3045        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
3046    end
3047    netcdf.endDef(nc)
3048    netcdf.putVar(nc,varid,UvData.axes3.FF);
3049    netcdf.close(nc) 
3050else %old netcdf library
3051    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
3052end
3053
3054%-------------------------------------------------------------------
3055%----Correct the netcdf file, using toolbox (old versions of Matlab).
3056%-------------------------------------------------------------------
3057function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
3058nc=netcdf(filename,'write'); %open netcdf file
3059result=redef(nc);
3060eval(['nc.' attrname '=1;']);
3061theDim=nc(nbname) ;% get the number of velocity vectors
3062nb_vectors=size(theDim);
3063var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
3064var_FixFlag(1:nb_vectors)=AxeData.FF;%
3065fin=close(nc);
3066
3067
3068%-------------------------------------------------------------------
3069%determines the fields to read from the interface
3070%------------------------------------------------------------------
3071function [VelType,civ]=setfield(handles)
3072
3073VelType=[]; %default
3074if (get(handles.civ1,'Value') == 1);
3075        VelType='civ1';
3076% interp1   
3077elseif (get(handles.interp1,'Value') == 1);
3078    VelType='interp1';
3079% filter1   
3080elseif (get(handles.filter1,'Value') == 1);
3081    VelType='filter1'; 
3082% CIV2
3083elseif (get(handles.civ2,'Value') == 1);
3084    VelType='civ2';
3085% interp2   
3086elseif (get(handles.interp2,'Value') == 1);
3087    VelType='interp2';
3088% filter2   
3089elseif (get(handles.filter2,'Value') == 1); 
3090    VelType='filter2';
3091end
3092
3093if isequal(get(handles.filter2,'Visible'),'on');
3094    civ=6;
3095% interp1   
3096elseif isequal(get(handles.interp2,'Visible'),'on');
3097    civ=5;
3098% filter1   
3099elseif isequal(get(handles.civ2,'Visible'),'on');
3100    civ=4; 
3101% CIV2
3102elseif isequal(get(handles.filter1,'Visible'),'on');
3103   civ=3;
3104% interp2   
3105elseif isequal(get(handles.interp1,'Visible'),'on');
3106    civ=2;
3107% filter2   
3108elseif isequal(get(handles.civ1,'Visible'),'on'); 
3109    civ=1;
3110else
3111    civ=0;
3112end
3113
3114%-------------------------------------------------------------------
3115%determines the veltype of the second field to read from the iinterface
3116%------------------------------------------------------------------
3117function VelType=setfield_1(handles)
3118
3119VelType=[]; %default
3120if (get(handles.civ1_1,'Value') == 1);
3121    VelType='civ1';
3122% interp1   
3123elseif (get(handles.interp1_1,'Value') == 1);
3124    VelType='interp1';
3125% filter1   
3126elseif (get(handles.filter1_1,'Value') == 1);
3127    VelType='filter1'; 
3128% CIV2
3129elseif (get(handles.civ2_1,'Value') == 1);
3130    VelType='civ2';
3131% interp2   
3132elseif (get(handles.interp2_1,'Value') == 1);
3133    VelType='interp2';
3134% filter2   
3135elseif (get(handles.filter2_1,'Value') == 1); 
3136    VelType='filter2';
3137end
3138
3139
3140%---------------------------------------------------
3141% --- Executes on button press in SubField
3142function SubField_Callback(hObject, eventdata, handles)
3143huvmat=get(handles.run0,'parent');
3144UvData=get(huvmat,'UserData');
3145if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
3146    set(handles.RootPath_1,'String','')
3147    set(handles.RootFile_1,'String','')
3148    set(handles.SubDir_1,'String','');
3149    set(handles.FileIndex_1,'String','');
3150    set(handles.FileExt_1,'String','');
3151    set(handles.RootPath_1,'Visible','off')
3152    set(handles.RootFile_1,'Visible','off')
3153    set(handles.SubDir_1,'Visible','off');
3154    set(handles.FileIndex_1,'Visible','off');
3155    set(handles.FileExt_1,'Visible','off');
3156    set(handles.Fields_1,'Value',1);%set to blank state
3157    set_veltype_display([handles.civ1_1 handles.interp1_1 handles.filter1_1 ...
3158            handles.civ2_1 handles.interp2_1 handles.filter2_1],0)
3159    if isfield(UvData,'XmlData_1')
3160        UvData=rmfield(UvData,'XmlData_1');
3161    end
3162    set(huvmat,'UserData',UvData);
3163    run0_Callback(hObject, eventdata, handles); %run
3164else
3165    MenuBrowse_1_Callback(hObject, eventdata, handles)
3166end
3167
3168%------------------------------------------------------------------------
3169% --- read the data displayed for the input rootfile windows (new)
3170function [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles)
3171%------------------------------------------------------------------------
3172RootPath=get(handles.RootPath,'String');
3173FileName=RootPath; %default
3174SubDir=get(handles.SubDir,'String');
3175if ~isempty(SubDir) && ~isequal(SubDir,'')
3176    if (isequal(SubDir(1),'/')|| isequal(SubDir(1),'\'))
3177        SubDir(1)=[]; %suppress possible / or \ separator
3178    end
3179    FileName=fullfile(RootPath,SubDir);
3180end
3181RootFile=get(handles.RootFile,'String');
3182if ~isempty(RootFile) && ~isequal(RootFile,'')
3183    if (isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
3184        RootFile(1)=[]; %suppress possible / or \ separator
3185    end
3186    FileName=fullfile(FileName,RootFile);
3187end
3188FileBase=fullfile(RootPath,RootFile);
3189FileIndices=get(handles.FileIndex,'String');
3190FileExt=get(handles.FileExt,'String');
3191FileName=[FileName FileIndices FileExt];
3192
3193%------------------------------------------------------------------------
3194% ---- read the data displayed for the second input rootfile windows
3195function [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles)
3196%------------------------------------------------------------------------
3197RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3198if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3199    RootPath_1=get(handles.RootPath,'String');
3200end;
3201FileName_1=RootPath_1; %default
3202SubDir_1=get(handles.SubDir_1,'String');
3203if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3204    SubDir_1=get(handles.SubDir,'String');
3205end
3206if numel(SubDir_1)>=1
3207    if (isequal(SubDir_1(1),'/')|| isequal(SubDir_1(1),'\'))
3208        SubDir_1(1)=[]; %suppress possible / or \ separator
3209    end
3210    FileName_1=fullfile(RootPath_1,SubDir_1);
3211end
3212RootFile_1=get(handles.RootFile_1,'String');
3213if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3214    RootFile_1=get(handles.RootFile,'String');
3215end
3216if numel(RootFile_1)>=1
3217    if ~(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
3218        RootFile_1(1)=[];%suppress possible / or \ separator
3219    end
3220    FileName_1=fullfile(FileName_1,RootFile_1);
3221end
3222FileBase_1=fullfile(RootPath_1,RootFile_1);
3223if isequal(get(handles.FileIndex_1,'Visible'),'off')
3224    FileIndices_1=get(handles.FileIndex,'String');
3225else
3226    FileIndices_1=get(handles.FileIndex_1,'String');
3227end
3228FileExt_1=get(handles.FileExt_1,'String');
3229if isequal(FileExt_1,'"'),FileExt_1=get(handles.FileExt,'String'); end;
3230FileName_1=[FileName_1 FileIndices_1 FileExt_1];
3231
3232%------------------------------------------------------------------------
3233% --- Executes on menu selection Fields
3234function Fields_Callback(hObject, eventdata, handles)
3235%------------------------------------------------------------------------
3236list_fields=get(handles.Fields,'String');% list menu fields
3237index_fields=get(handles.Fields,'Value');% selected string index
3238field= list_fields{index_fields(1)}; % selected string
3239if isequal(field,'get_field...')
3240     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3241     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3242     filename=read_file_boxes(handles);
3243     hget_field=findobj(allchild(0),'name','get_field');
3244     if ~isempty(hget_field)
3245         delete(hget_field)
3246     end
3247     hget_field=get_field(filename);
3248     set(hget_field,'Name','get_field')       
3249     hhget_field=guidata(hget_field);
3250     set(hhget_field.list_fig,'Value',1)
3251     set(hhget_field.list_fig,'String',{'uvmat'})
3252     set(handles.transform_fct,'Value',1)% no transform by default
3253     set(handles.path_transform,'String','')
3254    return %no action
3255end
3256list_fields=get(handles.Fields_1,'String');% list menu fields
3257index_fields=get(handles.Fields_1,'Value');% selected string index
3258field_1= list_fields{index_fields(1)}; % selected string
3259UvData=get(handles.uvmat,'UserData');
3260
3261%read the rootfile input display
3262[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
3263[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt]);
3264NomTypeNew=NomType;%default
3265if isequal(field,'image')
3266    % transform netc type to the corresponding image type
3267%     if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')|| isequal(NomType,'#_ab')|| isequal(NomType,'_i1-i2')
3268%         UvData.SubDir=get(handles.SubDir,'String'); %preserve the subdir in memory
3269%         if ~isempty(UvData.SubDir) && (isequal(UvData.SubDir(1),'/')||isequal(UvData.SubDir(1),'/'))
3270%             UvData.SubDir(1)=[];
3271%         end
3272%         set(handles.SubDir,'String','')
3273%         set(handles.FileExt,'String','.png');
3274        if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')
3275            NomTypeNew='_i_j';
3276        elseif isequal(NomType,'#_ab')
3277            NomTypeNew='#a';
3278        elseif isequal(NomType,'_i1-i2')
3279            NomTypeNew='_i';
3280        end 
3281        imagename=name_generator(FileBase,str2double(str1),str2double(str_a),'.png',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3282        if ~exist(imagename,'file')
3283                [FileName,PathName] = uigetfile( ...
3284           {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3285            '*.jpg',' jpeg image files'; ...
3286            '*.png','.png image files'; ...
3287            '*.tif','.tif image files'; ...
3288            '*.avi;*.AVI','.avi movie files'; ...
3289            '*.vol','.volume images (png)'; ...
3290            '*.*',  'All Files (*.*)'}, ...
3291            'Pick an image',imagename);           
3292            % display the selected field and related information
3293           imagename=[PathName FileName];
3294        end
3295        display_file_name(hObject, eventdata, handles,imagename)%display the image
3296        return
3297%     end
3298%     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3299%     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3300else
3301    ext=get(handles.FileExt,'String');
3302    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3303                [FileName,PathName] = uigetfile( ...
3304           {'*.nc', ' (*.nc)';
3305            '*.nc',' netcdf files'; ...
3306            '*.*',  'All Files (*.*)'}, ...
3307            'Pick a netcdf file',FileBase);           
3308            % display the selected field and related information
3309           filename=[PathName FileName];
3310        display_file_name(hObject, eventdata, handles,filename)
3311        return
3312       %  MenuBrowse_Callback(hObject, eventdata, handles)
3313    end
3314    if isequal(field,'vort') || isequal(field,'div') || isequal(field,'strain')
3315        set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3316        set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
3317        set(handles.interp1,'BackgroundColor',[0.702 0.702 0.702])
3318        set(handles.interp2,'BackgroundColor',[0.702 0.702 0.702])
3319    elseif isequal(field,'more...');
3320        set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3321        set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
3322        str=calc_field;%get the list of available scalars by the function calc_scal
3323        [ind_answer] = listdlg('PromptString','Select a file:',...
3324                'SelectionMode','single',...
3325                'ListString',str);
3326       % edit the choice in the field and action menu
3327        scalar=cell2mat(str(ind_answer));
3328        menu=update_menu(handles.Fields,scalar);
3329        menu=[{''};menu];
3330        set(handles.Fields_1,'String',menu);% store the selected scalar type
3331    end
3332end
3333indices=name_generator('',str2double(str1),str2double(str_a),'',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3334set(handles.FileIndex,'String',indices)
3335set(handles.FileIndex,'UserData',NomTypeNew)
3336%common to Fields_1_Callback
3337if isequal(field,'image')||isequal(field_1,'image')
3338    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3339    set(handles.npy_title,'Visible','on')
3340    set(handles.npx,'Visible','on')
3341    set(handles.npy,'Visible','on')
3342else
3343    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3344    set(handles.npy_title,'Visible','off')
3345    set(handles.npx,'Visible','off')
3346    set(handles.npy,'Visible','off')
3347end
3348setfield(handles);% update the field structure ('civ1'....)
3349
3350if ~isfield(UvData,'NewSeries')||isequal(UvData.NewSeries,0)
3351    run0_Callback(hObject, eventdata, handles)
3352end
3353
3354%---------------------------------------------------
3355% --- Executes on menu selection Fields
3356function Fields_1_Callback(hObject, eventdata, handles)
3357%-------------------------------------------------
3358list_fields=get(handles.Fields,'String');% list menu fields
3359index_fields=get(handles.Fields,'Value');% selected string index
3360field= list_fields{index_fields(1)}; % selected string
3361list_fields=get(handles.Fields_1,'String');% list menu fields
3362index_fields=get(handles.Fields_1,'Value');% selected string index
3363field_1= list_fields{index_fields(1)}; % selected string for the second field
3364if isequal(field_1,'') %remove second field if 'blank' field is selected
3365    set(handles.SubField,'Value',0)
3366    SubField_Callback(hObject, eventdata, handles)
3367    return
3368end
3369UvData=get(handles.uvmat,'UserData');
3370
3371%read the rootfile input display
3372[FileName,RootPath,FileBase,FileIndices,FileExt_prev]=read_file_boxes_1(handles);
3373[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt_prev]);
3374if isempty(FileExt_prev)|isequal(FileExt_prev,'')
3375    FileExt_1=get(handles.FileExt,'String');
3376else
3377    FileExt_1=FileExt_prev;
3378end
3379NomType_1=get(handles.FileIndex_1,'UserData');
3380if isempty(NomType_1)|isequal(NomType_1,'')
3381    NomType_1=get(handles.FileIndex,'UserData');
3382end
3383NomTypeNew=NomType_1;%default
3384
3385set(handles.SubField,'Value',1)%introduce second field
3386if isfield(UvData,'XmlData')
3387    UvData.XmlData_1=UvData.XmlData;
3388end
3389set(handles.FileIndex_1,'Visible','on')
3390set(handles.FileExt_1,'Visible','on')
3391RootPath_1=get(handles.RootPath_1,'String');
3392RootFile_1=get(handles.RootFile_1,'String');
3393if isempty(RootPath_1)||isequal(RootPath_1,'')
3394    set(handles.RootPath_1,'String','"')
3395end
3396if isempty(RootFile_1) || isequal(RootFile_1,'')
3397    set(handles.RootFile_1,'String','"')
3398end
3399if ~isempty(RootFile_1)&&(isequal(RootFile_1(1),'/')||isequal(RootFile_1(1),'\'))
3400    RootFile_1(1)=[];
3401end
3402
3403if isequal(field_1,'get_field...')
3404     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3405     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3406     filename=read_file_boxes_1(handles);
3407     hget_field=findobj(allchild(0),'name','get_field_1');
3408     if ~isempty(hget_field)
3409         delete(hget_field)
3410     end
3411     hget_field=get_field(filename);
3412     set(hget_field,'name','get_field_1')
3413     hhget_field=guidata(hget_field);
3414     set(hhget_field.list_fig,'Value',1)
3415     set(hhget_field.list_fig,'String',{'uvmat'})
3416     set(handles.transform_fct,'Value',1)% no transform by default
3417     set(handles.path_transform,'String','')
3418    return %no action
3419end
3420if isequal(field_1,'image')
3421    % transform netc type to the corresponding image type
3422%     set(handles.FileExt_1,'String','.png');
3423    if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')| isequal(NomType_1,'#_ab')| isequal(NomType_1,'_i1-i2')
3424        UvData.SubDir_1=get(handles.SubDir_1,'String'); %preserve the subdir in memory
3425%         set(handles.SubDir_1,'String','')
3426%         set(handles.FileExt_1,'String','.png');       
3427        if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')
3428            NomTypeNew='_i_j';
3429        elseif isequal(NomType_1,'#_ab')
3430            NomTypeNew='#a';
3431        elseif isequal(NomType_1,'_i1-i2')
3432            NomTypeNew='_i';
3433        end 
3434    end
3435    imagename=name_generator(FileBase,str2double(str1),str2double(str_a),'.png',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3436    if ~exist(imagename,'file')
3437        [FileName,PathName] = uigetfile( ...
3438            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3439            '*.jpg',' jpeg image files'; ...
3440            '*.png','.png image files'; ...
3441            '*.tif','.tif image files'; ...
3442            '*.avi;*.AVI','.avi movie files'; ...
3443            '*.vol','.volume images (png)'; ...
3444            '*.*',  'All Files (*.*)'}, ...
3445            'Pick an image',imagename);
3446        % display the selected field and related information
3447        imagename=[PathName FileName];
3448    end
3449    display_file_name_1(hObject, eventdata, handles,imagename)%display the image
3450    return
3451%     veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
3452%     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3453else
3454    set(handles.SubDir_1,'Visible','on')
3455    if ~isequal(FileExt_prev,'.nc') %find the new NomType if the previous display was not already a netcdf file
3456        veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
3457        set_veltype_display(veltype_handles,6); % make all civ buttons visible
3458        RootPath_1=get(handles.RootPath_1,'String');
3459        RootFile_1=get(handles.RootFile_1,'String');
3460        if isempty(RootPath_1)|isequal(RootPath_1,'')
3461            set(handles.RootPath_1,'String','"')
3462        end
3463        if isempty(RootFile_1) | isequal(RootFile_1,'')
3464            set(handles.RootFile_1,'String','"')
3465        end
3466        if ~isempty(RootFile_1)&(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
3467            RootFile_1(1)=[];
3468        end
3469        filebase_1=fullfile(RootPath_1,RootFile_1);
3470        SubDir_1=get(handles.SubDir,'String');
3471        if isempty(SubDir_1)||isequal(SubDir_1,'')
3472            if isfield(UvData,'SubDir_1')
3473                SubDir_1=UvData.SubDir_1;%retrieve previous subdir
3474            else
3475                SubDir_1='?';
3476            end
3477        end
3478        str1=get(handles.i1,'String');
3479        str_a=get(handles.j1,'String');
3480        if isequal(NomType_1,'#_ab')||isequal(NomType_1,'_i1-i2_j')||isequal(NomType_1,'_i_j1-j2')||isequal(NomType_1,'_i1-i2')
3481            NomTypeNew=NomType_1;
3482        elseif isequal(NomType_1,'#a')
3483             [filename, n1,na,n2,nb,SubDir_1]=name_generator(filebase_1, str2num(str1),stra2num(str_a),'.nc','#_ab',0,[],[],SubDir_1);
3484             NomTypeNew='#_ab';
3485        elseif isequal(NomType_1,'_i_j')
3486             [filename,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),stra2num(str_a),'.nc','_i1-i2_j',0,str2num(str1),[],SubDir_1);
3487            if idetect==1
3488                NomTypeNew='_i1-i2_j';
3489            else
3490                NomTypeNew='_i_j1-j2';
3491            end
3492        else %for instance avi files or any ima_num series
3493            [filename,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),stra2num(str_a),'.nc','_i1-i2',0,str2num(str1),[],SubDir_1);
3494            NomTypeNew='_i1-i2';
3495        end           
3496        [Path,Name]=fileparts(filebase_1);
3497        set(handles.FileExt_1,'String','.nc');
3498        if ~isempty(SubDir_1) && ~strcmp(SubDir_1,'''')&& ~strcmp(SubDir_1,'"')&& ~strcmp(SubDir_1(1),'/')
3499            SubDir_1=['/' SubDir_1];
3500        end
3501        set(handles.SubDir_1,'String',SubDir_1);
3502    end
3503    if isequal(field,'vort') | isequal(field,'div') | isequal(field,'strain')
3504        set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3505        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3506        set(handles.interp1_1,'BackgroundColor',[0.702 0.702 0.702])
3507        set(handles.interp2_1,'BackgroundColor',[0.702 0.702 0.702])
3508    elseif isequal(field_1,'more...'); %add new item to the menu
3509        set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3510        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3511        str=calc_field;%get the list of available scalars by the function calc_scal
3512        [ind_answer,v] = listdlg('PromptString','Select a file:',...
3513                'SelectionMode','single',...
3514                'ListString',str);
3515       % edit the choice in the field and action menu
3516        scalar=cell2mat(str(ind_answer));
3517        menu=update_menu(handles.Fields_1,scalar);
3518        set(handles.Fields_1,'String',menu);% store the selected scalar type
3519    end
3520end
3521str1=get(handles.i1,'String');
3522str2=get(handles.i2,'String');
3523str_a=get(handles.j1,'String');
3524str_b=get(handles.j2,'String');
3525indices=name_generator('',str2num(str1),stra2num(str_a),'',NomTypeNew,1,str2num(str2),stra2num(str_b),'');
3526set(handles.FileIndex_1,'String',indices)
3527set(handles.FileIndex_1,'UserData',NomTypeNew)
3528
3529%common to Fields_Callback
3530if isequal(field,'image')|isequal(field_1,'image')
3531    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3532    set(handles.npy_title,'Visible','on')
3533    set(handles.npx,'Visible','on')
3534    set(handles.npy,'Visible','on')
3535%     set(handles.fix_pair,'Value',0)
3536else
3537    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3538    set(handles.npy_title,'Visible','off')
3539    set(handles.npx,'Visible','off')
3540    set(handles.npy,'Visible','off')
3541%     set(handles.fix_pair,'Value',1)
3542end
3543if isequal(field,'velocity')|isequal(field_1,'velocity');
3544    state_vect='on';
3545else
3546    state_vect='off';
3547end
3548if ~isequal(field,'velocity')|(~isequal(field_1,'velocity')&~isequal(field_1,''));
3549    state_scal='on';
3550else
3551    state_scal='off';
3552end
3553set(handles.uvmat,'UserData',UvData)
3554setfield(handles);% update the field structure ('civ1'....)
3555if ~isfield(UvData,'NewSeries')|isequal(UvData.NewSeries,0)
3556    run0_Callback(hObject, eventdata, handles)
3557end
3558
3559%------------------------------------------------------------------------
3560% --- set the visibility of relevant velocity type menus:
3561function set_veltype_display(handles,Civ)
3562%------------------------------------------------------------------------
3563%Civ=0; all states 'off'
3564%Civ=6; all states 'on'
3565if isequal(Civ,0)
3566    imax=0;
3567%    set(handles(1),'Visible','on')  % unvisible civ buttons
3568% else
3569%    set(handles(1),'String','civ1')
3570% end
3571elseif isequal(Civ,1) || isequal(Civ,2)
3572   imax=1;
3573elseif isequal(Civ,3)
3574    imax=3;
3575elseif isequal(Civ,4) || isequal(Civ,5)
3576    imax=4;
3577elseif isequal(Civ,6) %patch2
3578    imax=6;
3579end
3580for ibutton=1:imax;
3581    set(handles(ibutton),'Visible','on')  % unvisible civ buttons
3582end
3583% for ibutton=max(imax+1,2):6;
3584for ibutton=imax+1:6;
3585    set(handles(ibutton),'Visible','off')  % unvisible civ buttons
3586    set(handles(ibutton),'Value',0)%unactivate unvisible buttons
3587end
3588
3589%-------------------------------------------------------------------
3590% --- Executes on button press in civ1.
3591function civ1_Callback(hObject, eventdata, handles)
3592%-------------------------------------------------------------------
3593if get(handles.civ1,'Value')==1
3594    reset_vel_type([handles.interp1 handles.civ2 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ1)
3595else
3596    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3597end
3598run0_Callback(hObject, eventdata, handles)
3599
3600%-------------------------------------------------------------------
3601% --- Executes on button press in interp1.
3602function interp1_Callback(hObject, eventdata, handles)
3603%-------------------------------------------------------------------
3604if get(handles.interp1,'Value')==1
3605    reset_vel_type([handles.civ1 handles.civ2 handles.filter1 handles.interp2 handles.filter2],handles.interp1)
3606else
3607     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3608end
3609run0_Callback(hObject, eventdata, handles)
3610
3611%-------------------------------------------------------------------
3612% --- Executes on button press in filter1.
3613function filter1_Callback(hObject, eventdata, handles)
3614%-------------------------------------------------------------------
3615if get(handles.filter1,'Value')==1
3616    reset_vel_type([handles.civ1 handles.civ2 handles.interp1 handles.interp2 handles.filter2],handles.filter1)
3617else
3618     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3619end
3620run0_Callback(hObject, eventdata, handles)
3621
3622%-------------------------------------------------------------------
3623% --- Executes on button press in civ2.
3624function civ2_Callback(hObject, eventdata, handles)
3625%-------------------------------------------------------------------
3626if get(handles.civ2,'Value')==1
3627    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ2)
3628else
3629     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3630end
3631run0_Callback(hObject, eventdata, handles)
3632
3633%-----------------------------------------
3634% --- Executes on button press in interp2.
3635%-------------------------------------------
3636function interp2_Callback(hObject, eventdata, handles)
3637if get(handles.interp2,'Value')==1
3638    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.filter2],handles.interp2)
3639else
3640     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3641end
3642run0_Callback(hObject, eventdata, handles)
3643%---------------------------------------------
3644% --- Executes on button press in filter2.
3645%-------------------------------------------
3646function filter2_Callback(hObject, eventdata, handles)
3647if get(handles.filter2,'Value')==1
3648    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2],handles.filter2)
3649else
3650     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3651end
3652run0_Callback(hObject, eventdata, handles)
3653
3654%---------------------------------------------
3655function civ1_1_Callback(hObject, eventdata, handles)
3656%---------------------------------------------
3657if get(handles.civ1_1,'Value')==1
3658    reset_vel_type([handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.civ1_1)
3659else
3660     reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3661end
3662run0_Callback(hObject, eventdata, handles)
3663
3664%--------------------------------------------
3665function interp1_1_Callback(hObject, eventdata, handles)
3666%--------------------------------------------
3667if get(handles.interp1_1,'Value')==1
3668    reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.interp1_1)
3669else
3670    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3671end
3672run0_Callback(hObject, eventdata, handles)
3673
3674%--------------------------------------------
3675function filter1_1_Callback(hObject, eventdata, handles)
3676%--------------------------------------------
3677if get(handles.filter1_1,'Value')==1
3678    reset_vel_type([handles.interp1_1 handles.civ2_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.filter1_1)
3679else
3680    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3681end
3682run0_Callback(hObject, eventdata, handles)
3683
3684%--------------------------------------------
3685function civ2_1_Callback(hObject, eventdata, handles)
3686%--------------------------------------------
3687if get(handles.civ2_1,'Value')==1
3688    reset_vel_type([handles.civ1_1 handles.interp1_1  handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.civ2_1)
3689else
3690    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3691end
3692run0_Callback(hObject, eventdata, handles)
3693
3694%--------------------------------------------
3695function interp2_1_Callback(hObject, eventdata, handles)
3696%--------------------------------------------
3697if get(handles.interp2_1,'Value')==1
3698    reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.filter2_1],handles.interp2_1)
3699else
3700    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3701end
3702run0_Callback(hObject, eventdata, handles)
3703
3704%--------------------------------------------
3705function filter2_1_Callback(hObject, eventdata, handles)
3706%--------------------------------------------
3707if get(handles.filter2_1,'Value')==1
3708    reset_vel_type([handles.civ1_1 handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1],handles.filter2_1)
3709else
3710    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3711end
3712run0_Callback(hObject, eventdata, handles)
3713
3714%-----------------------------------------------
3715% --- reset civ buttons
3716function reset_vel_type(handles_civ0,handle1)
3717for ibutton=1:length(handles_civ0)
3718    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3719    set(handles_civ0(ibutton),'Value',0)
3720end
3721if exist('handle1','var')%handles of selected button
3722        set(handle1,'BackgroundColor',[1 1 0]) 
3723end
3724
3725%-------------------------------------------------------
3726% --- Executes on button press in MENUVOLUME.
3727%-------------------------------------------------------
3728function VOLUME_Callback(hObject, eventdata, handles)
3729%errordlg('command VOL not implemented yet')
3730if ishandle(handles.UVMAT_title)
3731    delete(handles.UVMAT_title)
3732end
3733UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3734if isequal(get(handles.VOLUME,'Value'),1)
3735    set(handles.zoom,'Value',0)
3736    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3737    set(handles.edit_vect,'Value',0)
3738    edit_vect_Callback(hObject, eventdata, handles)
3739    set(handles.edit_object,'Value',0)
3740    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3741%     set(handles.cal,'Value',0)
3742%     set(handles.cal,'BackgroundColor',[0 1 0])
3743    set(handles.edit_vect,'Value',0)
3744    edit_vect_Callback(hObject, eventdata, handles)
3745    %initiate set_object GUI
3746    data.TITLE='VOLUME';
3747    if isfield(UvData,'CoordType')
3748        data.CoordType=UvData.CoordType;
3749    end
3750    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3751        data.RangeY=UvData.Mesh;
3752        data.RangeX=UvData.Mesh;
3753        data.DX=UvData.Mesh;
3754        data.DY=UvData.Mesh;
3755    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3756        np=size(UvData.Field.A);
3757        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3758        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3759        data.RangeY=max(meshx,meshy);
3760        data.RangeX=max(meshx,meshy);
3761        data.DX=max(meshx,meshy);
3762    end
3763    data.ParentButton=handles.VOLUME;
3764    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3765    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3766                                                      % associate the set_object interface handle to the plotting axes
3767    if isfield(UvData,'SetObjectOrigin')                                               
3768    pos_uvmat=get(huvmat,'Position');
3769    pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3770    pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); 
3771    set(hset_object,'Position',pos_set_object)
3772    end
3773    UvData.MouseAction='create_object';
3774else
3775    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3776    UvData.MouseAction='none';
3777end
3778set(huvmat,'UserData',UvData)
3779
3780%-------------------------------------------------------
3781function edit_vect_Callback(hObject, eventdata, handles)
3782%-------------------------------------------------------
3783%
3784% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3785if isequal(get(handles.edit_vect,'Value'),1)
3786    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3787    test_civ1=isequal(get(handles.civ1,'BackgroundColor'),[1 1 0]);
3788    if ~test_civ2 && ~test_civ1
3789        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3790    end
3791    set(handles.record,'Visible','on')
3792    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3793    set(handles.edit_object,'Value',0)
3794    set(handles.zoom,'Value',0)
3795    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3796%     set(handles.create,'Value',0)
3797%     set(handles.create,'BackgroundColor',[0 1 0])
3798    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3799    set(gcf,'Pointer','arrow')
3800%     UvData.MouseAction='edit_vect';
3801else
3802    set(handles.record,'Visible','off')
3803    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3804%     UvData.MouseAction='none';
3805end
3806% set(handles.uvmat,'UserData',UvData)
3807
3808%----------------------------------------------
3809function save_mask_Callback(hObject, eventdata, handles)
3810%-----------------------------------------------------------------------
3811UvData=get(handles.uvmat,'UserData');
3812
3813flag=1;
3814npx=size(UvData.Field.A,2);
3815npy=size(UvData.Field.A,1);
3816xi=[0.5:npx-0.5];
3817yi=[0.5:npy-0.5];
3818[Xi,Yi]=meshgrid(xi,yi);
3819if isfield(UvData,'Object')
3820    for iobj=1:length(UvData.Object)
3821        ObjectData=UvData.Object{iobj};
3822        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3823            flagobj=1;
3824            testphys=0; %coordinates in pixels by default
3825            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3826                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
3827                    Calib=UvData.XmlData.GeometryCalib;
3828                    testphys=1;
3829                end
3830            end
3831            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3832                if isequal(ObjectData.Style,'polygon')
3833                    X=ObjectData.Coord(:,1);
3834                    Y=ObjectData.Coord(:,2);
3835                    if testphys
3836                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3837                    end
3838                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3839                elseif isequal(ObjectData.Style,'ellipse')
3840                    if testphys
3841                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3842                    end
3843                    RangeX=max(ObjectData.RangeX);
3844                    RangeY=max(ObjectData.RangeY);
3845                    X2Max=RangeX*RangeX;
3846                    Y2Max=RangeY*RangeY;
3847                    distX=(Xi-ObjectData.Coord(1,1));
3848                    distY=(Yi-ObjectData.Coord(1,2));
3849                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3850                elseif isequal(ObjectData.Style,'rectangle')
3851                    if testphys
3852                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3853                    end
3854                    distX=abs(Xi-ObjectData.Coord(1,1));
3855                    distY=abs(Yi-ObjectData.Coord(1,2));
3856                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3857                end
3858                if isequal(ObjectData.ProjMode,'mask_outside')
3859                    flagobj=~flagobj;
3860                end
3861                flag=flag & flagobj;
3862            end
3863        end
3864    end
3865end
3866% flag=~flag;
3867%mask name
3868RootPath=get(handles.RootPath,'String');
3869RootFile=get(handles.RootFile,'String');
3870if ~isempty(RootFile)&(isequal(RootFile(1),'/')| isequal(RootFile(1),'\'))
3871        RootFile(1)=[];
3872end
3873filebase=fullfile(RootPath,RootFile);
3874list=get(handles.masklevel,'String');
3875masknumber=num2str(length(list));
3876maskindex=get(handles.masklevel,'Value');
3877mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3878imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3879imflag=flipdim(imflag,1);
3880% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3881msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3882imwrite(imflag,mask_name,'BitDepth',8);
3883
3884%display the mask
3885%update_mask(handles,num_i1,num_j1)
3886figure;
3887vec=linspace(0,1,256);%define a linear greyscale colormap
3888map=[vec' vec' vec'];
3889colormap(map)
3890
3891image(imflag);
3892
3893%-------------------------------------------------------------------
3894%-------------------------------------------------------------------
3895%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3896
3897%------------------------------------------------------------------
3898
3899
3900
3901%------------------------------------------------------------------
3902% --- Executes on selection change in col_vec: choice of the color code.
3903%
3904function col_vec_Callback(hObject, eventdata, handles)
3905%------------------------------------------------------------------
3906% edit the choice for color code
3907list_code=get(handles.col_vec,'String');% list menu fields
3908index_code=get(handles.col_vec,'Value');% selected string index
3909col_code= list_code{index_code(1)}; % selected field
3910if isequal(col_code,'black') || isequal(col_code,'white')
3911   set(handles.slider1,'Visible','off')
3912   set(handles.slider2,'Visible','off')
3913   set(handles.colcode1,'Visible','off')
3914   set(handles.colcode2,'Visible','off')
3915   set(handles.AutoVecColor,'Visible','off')
3916   set_vec_col_bar(handles)
3917else
3918   set(handles.slider1,'Visible','on')
3919   set(handles.slider2,'Visible','on')
3920   set(handles.colcode1,'Visible','on')
3921   set(handles.colcode2,'Visible','on')
3922   set(handles.AutoVecColor,'Visible','on') 
3923   if isequal(col_code,'ima_cor')
3924       set(handles.AutoVecColor,'Value',0)%fixed scale by default
3925       set(handles.vec_col_bar,'Value',0)% 3 colors r,g,b by default
3926       set(handles.slider1,'Min',0);
3927       set(handles.slider1,'Max',1);
3928       set(handles.slider2,'Min',0);
3929       set(handles.slider2,'Max',1);
3930 %      set(handles.min_title_vec,'String','0')
3931       set(handles.max_vec,'String','1')
3932       set(handles.colcode1,'String','0.333')
3933       colcode1_Callback(hObject, eventdata, handles)
3934       set(handles.colcode2,'String','0.666')
3935       colcode2_Callback(hObject, eventdata, handles)
3936   else
3937       set(handles.AutoVecColor,'Value',1)%auto scale between min,max by default
3938       set(handles.vec_col_bar,'Value',1)% colormap 'jet' by default
3939       minval=get(handles.slider1,'Min');
3940       maxval=get(handles.slider1,'Max');
3941       set(handles.slider1,'Value',minval)
3942       set(handles.slider2,'Value',maxval)
3943       set_vec_col_bar(handles)
3944   end
3945%    slider_update(handles)
3946end
3947%replot the current graph
3948run0_Callback(hObject, eventdata, handles)
3949
3950
3951%----------------------------------------------------------------
3952% -- Executes on slider movement to set the color code
3953%
3954function slider1_Callback(hObject, eventdata, handles)
3955%------------------------------------------------------------------
3956slider1=get(handles.slider1,'Value');
3957min_val=str2num(get(handles.min_vec,'String'));
3958max_val=str2num(get(handles.max_vec,'String'));
3959col=min_val+(max_val-min_val)*slider1;
3960set(handles.colcode1,'String',num2str(col))
3961if(get(handles.slider2,'Value') < col)%move also the second slider at the same value if needed
3962    set(handles.slider2,'Value',col)
3963    set(handles.colcode2,'String',num2str(col))
3964end
3965colcode1_Callback(hObject, eventdata, handles)
3966
3967%----------------------------------------------------------------
3968% Executes on slider movement to set the color code
3969%----------------------------------------------------------------
3970function slider2_Callback(hObject, eventdata, handles)
3971slider2=get(handles.slider2,'Value');
3972min_val=str2num(get(handles.min_vec,'String'));
3973max_val=str2num(get(handles.max_vec,'String'));
3974col=min_val+(max_val-min_val)*slider2;
3975set(handles.colcode2,'String',num2str(col))
3976if(get(handles.slider1,'Value') > col)%move also the first slider at the same value if needed
3977    set(handles.slider1,'Value',col)
3978    set(handles.colcode1,'String',num2str(col))
3979end
3980colcode2_Callback(hObject, eventdata, handles)
3981
3982%----------------------------------------------------------------
3983%execute on return carriage on the edit box corresponding to slider 1
3984%----------------------------------------------------------------
3985function colcode1_Callback(hObject, eventdata, handles)
3986% col=str2num(get(handles.colcode1,'String'));
3987% set(handles.slider1,'Value',col)
3988set_vec_col_bar(handles)
3989update_plot(handles);
3990
3991%----------------------------------------------------------------
3992%execute on return carriage on the edit box corresponding to slider 2
3993%----------------------------------------------------------------
3994function colcode2_Callback(hObject, eventdata, handles)
3995% col=str2num(get(handles.colcode2,'String'));
3996% set(handles.slider2,'Value',col)
3997% slider2_Callback(hObject, eventdata, handles)
3998set_vec_col_bar(handles)
3999update_plot(handles);
4000%------------------------------------------------------------
4001%update the slider values after displaying vectors
4002%--------------------------------------------------------
4003% function slider_update(handles,auto,minC,colcode1,colcode2,maxC)
4004% set(handles.slider1,'Min',minC)
4005% set(handles.slider1,'Max',maxC)
4006% set(handles.slider2,'Min',minC)
4007% set(handles.slider2,'Max',maxC)
4008% set(handles.min_title_vec,'String',num2str(minC))
4009% set(handles.max_vec,'String',num2str(maxC))
4010% if auto
4011%         set(handles.colcode1,'String',num2str(colcode1,3))%update display
4012%         set(handles.colcode2,'String',num2str(colcode2,3))
4013% end
4014% set(handles.slider1,'Value',colcode1)%update slider with constant display
4015% set(handles.slider2,'Value',colcode2)
4016% set_vec_col_bar(handles)
4017
4018
4019%-------------------------------------------------------
4020% --- Executes on button press in AutoVecColor.
4021%-------------------------------------------------------
4022function vec_col_bar_Callback(hObject, eventdata, handles)
4023set_vec_col_bar(handles)
4024
4025%-------------------------------------------------------------
4026% --- Executes on selection change in transform_fct.
4027function transform_fct_Callback(hObject, eventdata, handles)
4028%-------------------------------------------------------------
4029global nb_builtin
4030
4031huvmat=get(handles.transform_fct,'parent');
4032menu=get(handles.transform_fct,'String');
4033ind_coord=get(handles.transform_fct,'Value');
4034coord_option=menu{ind_coord};
4035list_transform=get(handles.transform_fct,'UserData');
4036ff=functions(list_transform{end}); 
4037if isequal(coord_option,'more...');
4038    coord_fct='';
4039    prompt = {'Enter the name of the transform function'};
4040    dlg_title = 'user defined transform';
4041    num_lines= 1;
4042    [FileName, PathName] = uigetfile( ...
4043       {'*.m', ' (*.m)';
4044        '*.m',  '.m files '; ...
4045        '*.*', 'All Files (*.*)'}, ...
4046        'Pick a file', ff.file);
4047    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
4048        PathName(end)=[];
4049    end
4050    transform_selected =fullfile(PathName,FileName);
4051    if ~exist(transform_selected,'file')
4052           return
4053    end
4054   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
4055   if ~isequal(ext_fct,'.m')
4056        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
4057        return
4058   end
4059   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
4060   ind_coord=get(handles.transform_fct,'Value');
4061   addpath(PathName)
4062   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
4063   set(handles.transform_fct,'UserData',list_transform)
4064   rmpath(PathName)
4065   % save the new menu in the personal file 'uvmat_perso.mat'
4066   dir_perso=prefdir;%personal Matalb directory
4067   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
4068   if exist(profil_perso,'file')
4069       for ilist=nb_builtin+1:numel(list_transform)
4070           ff=functions(list_transform{ilist});
4071           transform_fct{ilist-nb_builtin}=ff.file;
4072       end
4073        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
4074   end   
4075end
4076
4077%check the current path to the selected function
4078if isa(list_transform{ind_coord},'function_handle')
4079    func=functions(list_transform{ind_coord});
4080    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
4081else
4082    set(handles.path_transform,'String','')
4083end
4084
4085set(handles.FixedLimits,'Value',0)
4086set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7])
4087
4088UvData=get(huvmat,'UserData');
4089
4090%delete drawn objects
4091hother=findobj('Tag','proj_object');%find all the proj objects
4092for iobj=1:length(hother)
4093    delete_object(hother(iobj))
4094end
4095hother=findobj('Tag','DeformPoint');%find all the proj objects
4096for iobj=1:length(hother)
4097    delete_object(hother(iobj))
4098end
4099hh=findobj('Tag','calib_points');
4100if ~isempty(hh)
4101    delete(hh)
4102end
4103hhh=findobj('Tag','calib_marker');
4104if ~isempty(hhh)
4105    delete(hhh)
4106end
4107if isfield(UvData,'Object')
4108     UvData.Object=UvData.Object(1);
4109end
4110list_object=get(handles.list_object_1,'String');
4111set(handles.list_object_1,'Value',1)
4112set(handles.list_object_1,'String',list_object(1))
4113set(handles.list_object_2,'Value',2)
4114set(handles.list_object_2,'String',[list_object(1);{'...'}])
4115list_object_2_Callback(hObject, eventdata, handles)
4116
4117%delete mask if it is displayed
4118if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
4119   UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
4120end
4121set(huvmat,'UserData',UvData)
4122run0_Callback(hObject, eventdata, handles)
4123
4124%--------------------------------------------
4125function histo1_menu_Callback(hObject, eventdata, handles)
4126%--------------------------------------------
4127%plot first histo
4128huvmat=get(handles.histo1_menu,'parent');
4129histo_menu=get(handles.histo1_menu,'String');
4130histo_value=get(handles.histo1_menu,'Value');
4131FieldName=histo_menu{histo_value};
4132% UvData=get(huvmat,'UserData');
4133update_histo(handles.histo_u,huvmat,FieldName)
4134
4135%----------------------------------------------
4136function histo2_menu_Callback(hObject, eventdata, handles)
4137%----------------------------------------------
4138%plot second histo
4139huvmat=get(handles.histo2_menu,'parent');
4140histo_menu=get(handles.histo2_menu,'String');
4141histo_value=get(handles.histo2_menu,'Value');
4142FieldName=histo_menu{histo_value};
4143% UvData=get(huvmat,'UserData');
4144update_histo(handles.histo_v,huvmat,FieldName)
4145
4146
4147%--------------------------------------------
4148%read the field .Fieldname stored in UvData and plot its histogram
4149function update_histo(haxes,huvmat,FieldName)
4150UvData=get(huvmat,'UserData');
4151if ~isfield(UvData.Field,FieldName)
4152    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
4153    return
4154end
4155Field=UvData.Field;
4156FieldHisto=eval(['Field.' FieldName]);
4157if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
4158    indsel=find(Field.FF==0);%find values marked as false
4159    if ~isempty(indsel)
4160        FieldHisto=FieldHisto(indsel);
4161    end
4162end
4163if isempty(Field)
4164    msgbox_uvmat('ERROR',['empty field ' FieldName])
4165else
4166    nxy=size(FieldHisto);
4167    Amin=double(min(min(min(FieldHisto))));%min of image
4168    Amax=double(max(max(max(FieldHisto))));%max of image
4169    if isequal(Amin,Amax)
4170       Histo.Txt=['uniform field =' num2str(Amin)];
4171    else
4172    Histo.ListVarName={FieldName,'histo'};
4173    if numel(nxy)==2
4174        Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
4175    else %color images
4176        Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
4177    end
4178    %unit
4179    units=[]; %default
4180    for ivar=1:numel(Field.ListVarName)   
4181        if strcmp(Field.ListVarName{ivar},FieldName)
4182            if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
4183                units=Field.VarAttribute{ivar}.units;
4184                break
4185            end
4186        end
4187    end
4188    if ~isempty(units)
4189        Histo.VarAttribute{1}.units=units;
4190    end
4191    eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
4192    for col=1:size(FieldHisto,3)
4193        B=FieldHisto(:,:,col);
4194        C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
4195       eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
4196    end
4197    set(haxes,'XLimMode','auto')%reset auto mode (after zoom effect)
4198    set(haxes,'YLimMode','auto')
4199    plot_field(Histo,haxes);
4200    end
4201end
4202
4203
4204
4205%------------------------------------------------
4206%CALLBACKS FOR PLOTTING PARAMETERS
4207%-------------------------------------------------
4208
4209%-----------------------------------------------------------------
4210function MinA_Callback(hObject, eventdata, handles)
4211%------------------------------------------
4212set(handles.AutoScal,'Value',1) %suppress auto mode
4213set(handles.AutoScal,'BackgroundColor',[1 1 0])
4214update_plot(handles);
4215
4216%-----------------------------------------------------------------
4217function MaxA_Callback(hObject, eventdata, handles)
4218%--------------------------------------------
4219set(handles.AutoScal,'Value',1) %suppress auto mode
4220set(handles.AutoScal,'BackgroundColor',[1 1 0])
4221update_plot(handles);
4222
4223%-----------------------------------------------
4224function AutoScal_Callback(hObject, eventdata, handles)
4225%--------------------------------------------
4226test=get(handles.AutoScal,'Value');
4227if test
4228    set(handles.AutoScal,'BackgroundColor',[1 1 0])
4229else
4230    set(handles.AutoScal,'BackgroundColor',[0.7 0.7 0.7])
4231    update_plot(handles);
4232end
4233
4234%-------------------------------------------------------------------
4235function BW_Callback(hObject, eventdata, handles)
4236%-------------------------------------------------------------------
4237update_plot(handles);
4238
4239%-------------------------------------------------------------------
4240function Contours_Callback(hObject, eventdata, handles)
4241%-------------------------------------------------------------------
4242val=get(handles.Contours,'Value');
4243if val==2
4244    set(handles.interval_txt,'Visible','on')
4245    set(handles.IncrA,'Visible','on')
4246else
4247    set(handles.interval_txt,'Visible','off')
4248    set(handles.IncrA,'Visible','off')
4249end
4250update_plot(handles);
4251
4252%-------------------------------------------------------------------
4253function IncrA_Callback(hObject, eventdata, handles)
4254%-------------------------------------------------------------------
4255update_plot(handles);
4256
4257%-------------------------------------------------------------------
4258function HideWarning_Callback(hObject, eventdata, handles)
4259%-------------------------------------------------------------------
4260update_plot(handles);
4261
4262%-------------------------------------------------------------------
4263function HideFalse_Callback(hObject, eventdata, handles)
4264%-------------------------------------------------------------------
4265update_plot(handles);
4266
4267%-------------------------------------------------------------------
4268function VecScale_Callback(hObject, eventdata, handles)
4269%-------------------------------------------------------------------
4270set(handles.AutoVec,'Value',1);
4271set(handles.AutoVec,'BackgroundColor',[1 1 0])
4272update_plot(handles);
4273
4274%-------------------------------------------------------------------
4275function AutoVec_Callback(hObject, eventdata, handles)
4276%-------------------------------------------------------------------
4277test=get(handles.AutoVec,'Value');
4278if test
4279    set(handles.AutoVec,'BackgroundColor',[1 1 0])
4280else
4281    update_plot(handles);
4282    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4283    set(handles.AutoVec,'BackgroundColor',[0.7 0.7 0.7])
4284end
4285
4286%------------------------------------------------------------------------
4287% --- Executes on selection change in decimate4 (nb_vec/4).
4288function decimate4_Callback(hObject, eventdata, handles)
4289%------------------------------------------------------------------------
4290update_plot(handles);
4291
4292%------------------------------------------------------------------------
4293% --- Executes on selection change in color_code menu
4294function color_code_Callback(hObject, eventdata, handles)
4295%------------------------------------------------------------------------
4296set_vec_col_bar(handles)
4297update_plot(handles);
4298
4299%------------------------------------------------------------------------
4300% --- Executes on button press in AutoVecColor.
4301function AutoVecColor_Callback(hObject, eventdata, handles)
4302%------------------------------------------------------------------------
4303test=get(handles.AutoVecColor,'Value');
4304if test
4305    set(handles.AutoVecColor,'BackgroundColor',[1 1 0])
4306else
4307    update_plot(handles);
4308    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4309    set(handles.AutoVecColor,'BackgroundColor',[0.7 0.7 0.7])
4310end
4311
4312%------------------------------------------------------------------------
4313% --- Executes on selection change in max_vec.
4314function min_vec_Callback(hObject, eventdata, handles)
4315%------------------------------------------------------------------------
4316max_vec_Callback(hObject, eventdata, handles)
4317
4318%------------------------------------------------------------------------
4319% --- Executes on selection change in max_vec.
4320function max_vec_Callback(hObject, eventdata, handles)
4321%------------------------------------------------------------------------
4322set(handles.AutoVecColor,'Value',1)
4323AutoVecColor_Callback(hObject, eventdata, handles)
4324min_val=str2num(get(handles.min_vec,'String'));
4325max_val=str2num(get(handles.max_vec,'String'));
4326slider1=get(handles.slider1,'Value');
4327slider2=get(handles.slider2,'Value');
4328colcode1=min_val+(max_val-min_val)*slider1;
4329colcode2=min_val+(max_val-min_val)*slider2;
4330set(handles.colcode1,'String',num2str(colcode1))
4331set(handles.colcode2,'String',num2str(colcode2))
4332update_plot(handles);
4333
4334%------------------------------------------------------------------------
4335% --- update the display of color code for vectors
4336function set_vec_col_bar(handles)
4337%------------------------------------------------------------------------
4338%get the image of the color display button 'vec_col_bar' in pixels
4339set(handles.vec_col_bar,'Unit','pixel');
4340pos_vert=get(handles.vec_col_bar,'Position');
4341set(handles.vec_col_bar,'Unit','Normalized');
4342width=ceil(pos_vert(3));
4343height=ceil(pos_vert(4));
4344
4345%get slider indications
4346list=get(handles.color_code,'String');
4347ichoice=get(handles.color_code,'Value');
4348colcode.ColorCode=list{ichoice};
4349colcode.MinC=str2num(get(handles.min_vec,'String'));
4350colcode.MaxC=str2num(get(handles.max_vec,'String'));
4351test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4352if test3color
4353    colcode.colcode1=str2num(get(handles.colcode1,'String'));
4354    colcode.colcode2=str2num(get(handles.colcode2,'String'));
4355end
4356% colcode.option=get(handles.vec_col_bar,'Value');
4357colcode.FixedCbounds=0;
4358% list_code=get(handles.col_vec,'String');% list menu fields
4359% index_code=get(handles.col_vec,'Value');% selected string index
4360% colcode.CName= list_code{index_code(1)}; % selected field used for vector color
4361colcode.FixedCbounds=1;
4362vec_C=colcode.MinC+(colcode.MaxC-colcode.MinC)*[0.5:width-0.5]/width;%sample of vec_C values from min to max
4363[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4364oneheight=ones(1,height);
4365A1=colorlist(col_vec,1)*oneheight;
4366A2=colorlist(col_vec,2)*oneheight;
4367A3=colorlist(col_vec,3)*oneheight;
4368A(:,:,1)=A1';
4369A(:,:,2)=A2';
4370A(:,:,3)=A3';
4371set(handles.vec_col_bar,'Cdata',A)
4372
4373
4374%-------------------------------------------------------------------
4375function update_plot(handles)
4376%-------------------------------------------------------------------
4377haxes= handles.axes3;
4378UvData=get(handles.uvmat,'UserData');
4379AxeData=UvData.axes3;
4380PlotParam=read_plot_param(handles);
4381[PlotType,PlotParamOut]= plot_field(AxeData,haxes,PlotParam,1);
4382write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4383
4384%-------------------------------------------------------------------
4385% --- Executes on button press in grid.
4386function grid_Callback(hObject, eventdata, handles)
4387
4388
4389
4390%-------------------------------------------------------------------
4391% --- Executes on selection change in edit_object.
4392function edit_object_Callback(hObject, eventdata, handles)
4393%-------------------------------------------------------------------
4394UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4395test=get(handles.edit_object,'Value');
4396if test
4397    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4398    %suppress the other options
4399    set(handles.zoom,'Value',0)
4400    zoom_Callback(hObject, eventdata, handles)
4401else
4402    UvData.MouseAction='none';
4403    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])   
4404end
4405set(handles.uvmat,'UserData',UvData);
4406hset_object=findobj(allchild(0),'Tag','set_object');
4407if ~isempty(hset_object)
4408    hhset_object=guidata(hset_object);
4409    if test
4410        set(hhset_object.PLOT,'enable','on');
4411    else
4412       set(hhset_object.PLOT,'enable','off');
4413    end
4414end
4415
4416%------------------------------------------------------------------------
4417% --- Executes on selection change in list_object_1.
4418function list_object_1_Callback(hObject, eventdata, handles)
4419%------------------------------------------------------------------------
4420list_str=get(handles.list_object_1,'String');
4421IndexObj=get(handles.list_object_1,'Value');
4422str_1=list_str{IndexObj};
4423val_2=get(handles.list_object_2,'Value');
4424str_2=get(handles.list_object_2,'String');
4425if isequal(val_2,IndexObj)% if the first selection is equal to the second, it will suppress the second
4426    set(handles.list_object_2,'Value',numel(str_2))%select the end of the list ('...')
4427    list_object_2_Callback(hObject, eventdata, handles)
4428end
4429update_object(handles,IndexObj,1,str_1)
4430
4431%------------------------------------------------------------------------
4432% --- Executes on selection change in list_object_1.
4433function list_object_2_Callback(hObject, eventdata, handles)
4434%------------------------------------------------------------------------
4435list_str=get(handles.list_object_2,'String');
4436IndexObj=get(handles.list_object_2,'Value');
4437if ischar(list_str) || strcmp(list_str{IndexObj},'...')
4438    hview_field=findobj(allchild(0),'Tag','view_field');
4439    if ~isempty(hview_field)
4440        delete(hview_field)
4441    end
4442else
4443    update_object(handles,IndexObj,2,list_str{IndexObj})
4444end
4445
4446%------------------------------------------------------------------------
4447function update_object(handles,IndexObj,option,ObjectName)
4448%------------------------------------------------------------------------
4449UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4450if numel(UvData.Object)<IndexObj;
4451    return
4452end
4453ObjectData=UvData.Object{IndexObj};
4454ObjectData.Name=ObjectName;
4455if isequal(get(handles.edit_object,'Value'),1)
4456    ObjectData.enable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
4457end
4458ZBounds=0; % default
4459    if isfield(UvData,'ZMin') && isfield(UvData,'ZMax')
4460        ZBounds(1)=UvData.ZMin; %minimum for the Z slider
4461        ZBounds(2)=UvData.ZMax;%maximum for the Z slider
4462    end
4463hset_object=findobj(allchild(0),'tag','set_object');
4464if ~isempty(hset_object)
4465    delete(hset_object)% delete existing version of set_object
4466end
4467hset_object=set_object(ObjectData,[],ZBounds);% call the set_object interface,
4468
4469% %project the current field on the object and plot it
4470ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4471if option==1%length(UvData.Object)>= IndexObj && isfield(UvData.Object{IndexObj},'plotaxes')&& ishandle(UvData.Object{IndexObj}.plotaxes)
4472    PlotHandles=handles;
4473%     UvData.Object{IndexObj}.plotaxes=handles.axes3;
4474else
4475    hview_field=findobj(allchild(0),'tag','view_field');
4476    if isempty(hview_field)
4477        hview_field=view_field;
4478    end
4479    PlotHandles=guidata(hview_field);
4480%     hview_field=view_field(ProjData);
4481%     hhviewfield=guidata(hviewfield);
4482   % UvData.Object{IndexObj}.plotaxes=hhviewfield.axes3;
4483end
4484if ~isempty(ProjData)
4485plot_field(ProjData,PlotHandles.axes3,PlotHandles);
4486end
4487set(handles.uvmat,'UserData',UvData)
4488hother=findobj('Tag','proj_object');%find all the proj objects
4489for iobj=1:length(hother)
4490    if isequal(get(hother(iobj),'Type'),'rectangle')|isequal(get(hother(iobj),'Type'),'patch')
4491        set(hother(iobj),'EdgeColor','b')
4492        if isequal(get(hother(iobj),'FaceColor'),'m')
4493            set(hother(iobj),'FaceColor','b')
4494        end
4495    elseif isequal(get(hother(iobj),'Type'),'image')
4496           Acolor=get(hother(iobj),'CData');
4497           Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4498           set(hother(iobj),'CData',Acolor);
4499    else
4500         set(hother(iobj),'Color','b')
4501    end
4502    set(hother(iobj),'Selected','off')
4503end
4504hother=findobj('Tag','DeformPoint');
4505set(hother,'Color','b');
4506set(hother,'Selected','off')   
4507if isfield(ObjectData,'DisplayHandle_uvmat')
4508%     for iview=1:length(ObjectData.HandlesDisplay)
4509        if ishandle(ObjectData.DisplayHandle_uvmat)
4510            uistack(ObjectData.DisplayHandle_uvmat,'top')
4511            linetype=get(ObjectData.DisplayHandle_uvmat,'Type');
4512            if isequal(linetype,'line')
4513                set(ObjectData.DisplayHandle_uvmat,'Color','m'); %set the selected object to magenta color
4514            elseif isequal(linetype,'rectangle')
4515                set(ObjectData.DisplayHandle_uvmat,'EdgeColor','m'); %set the selected object to magenta color
4516            elseif isequal(linetype,'patch')
4517                set(ObjectData.DisplayHandle_uvmat,'FaceColor','m'); %set the selected object to magenta color
4518            end
4519            SubObjectData=get(ObjectData.DisplayHandle_uvmat,'UserData');
4520            if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4521                uistack(SubObjectData.SubObject,'top')
4522                for iobj=1:length(SubObjectData.SubObject)
4523                    hsub=SubObjectData.SubObject(iobj);
4524                    if isequal(get(hsub,'Type'),'rectangle')
4525                        set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4526                    elseif isequal(get(hsub,'Type'),'image')
4527                       Acolor=get(hsub,'CData');
4528                       Acolor(:,:,1)=Acolor(:,:,3);
4529                       set(hsub,'CData',Acolor);
4530                    else
4531                        set(hsub,'Color','m')
4532                    end
4533                end
4534            end
4535            if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4536                set(SubObjectData.DeformPoint,'Color','m')
4537            end
4538        end
4539%     end
4540end
4541pause(0.1)
4542figure(hset_object)%put set_object in front
4543
4544%------------------------------------------------------
4545% --- Executes on button press in Menu/Export/field in workspace.
4546%------------------------------------------------------
4547function MenuExportField_Callback(hObject, eventdata, handles)
4548global Data_uvmat
4549Data_uvmat=get(handles.uvmat,'UserData');
4550evalin('base','global Data_uvmat')%make CurData global in the workspace
4551display('current field :')
4552evalin('base','Data_uvmat') %display CurData in the workspace
4553commandwindow; %brings the Matlab command window to the front
4554
4555%------------------------------------------------------
4556% --- Executes on button press in Menu/Export/extract figure.
4557%------------------------------------------------------
4558function MenuExport_plot_Callback(hObject, eventdata, handles)
4559huvmat=get(handles.MenuExport_plot,'parent');
4560UvData=get(huvmat,'UserData');
4561hfig=figure;
4562newaxes=copyobj(handles.axes3,hfig);
4563map=colormap(handles.axes3);
4564colormap(map);%transmit the current colormap to the zoom fig
4565colorbar
4566
4567
4568% --------------------------------------------------------------------
4569function Insert_Callback(hObject, eventdata, handles)
4570
4571
4572% --------------------------------------------------------------------
4573function MenuHelp_Callback(hObject, eventdata, handles)
4574% --------------------------------------------------------------------
4575path_to_uvmat=which ('uvmat');% check the path of uvmat
4576pathelp=fileparts(path_to_uvmat);
4577helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4578if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4579else
4580    addpath (fullfile(pathelp,'uvmat_doc'))
4581    web(helpfile);
4582end
4583
4584
4585% --------------------------------------------------------------------
4586function MenuExportMovie_Callback(hObject, eventdata, handles)
4587% --------------------------------------------------------------------
4588set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4589huvmat=get(handles.run0,'parent');
4590UvData=get(huvmat,'UserData');
4591[xx,xx,FileBase]=read_file_boxes(handles);
4592 %read the current input file name
4593prompt = {'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)'};
4594dlg_title = 'select properties of the output avi movie';
4595num_lines= 1;
4596% nbfield_cell=get(handles.last_i,'String');
4597def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4598answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4599aviname=answer{1};
4600fps=str2double(answer{2});
4601% check for existing file with output name aviname
4602if exist(aviname,'file')
4603    backup=aviname;
4604    testexist=2;
4605    while testexist==2
4606        backup=[backup '~'];
4607        testexist=exist(backup,'file');     
4608    end
4609    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4610    if isequal(success,1)
4611        delete(aviname)%delete existing file
4612    else
4613        msgbox_uvmat('ERROR',message)
4614        return
4615    end
4616end
4617%create avi open
4618aviobj=avifile(aviname,'Compression','None','fps',fps);
4619
4620%display first view for tests
4621newfig=figure;
4622newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4623set(newaxes,'Tag','movieaxes')
4624nbpix=[512 384]*str2double(answer{3});
4625set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4626set(newaxes,'Position',eval(answer{4}));
4627map=colormap(handles.axes3);
4628colormap(map);%transmit the current colormap to the zoom fig
4629msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4630        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4631UvData.Object{1}.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4632set(huvmat,'UserData',UvData);
4633increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
4634if isnan(increment)
4635    set(handles.increment_scan,'String','1')%default value
4636    increment=1;
4637end
4638set(handles.STOP,'Visible','on')
4639set(handles.speed,'Visible','on')
4640set(handles.speed_txt,'Visible','on')
4641set(handles.Movie,'BusyAction','queue')
4642
4643%imin=str2double(get(handles.i1,'String'));
4644imax=str2double(answer{5});
4645% if isfield(UvData,'Time')
4646htitle=get(newaxes,'Title');
4647xlim=get(newaxes,'XLim');
4648ylim=get(newaxes,'YLim');
4649set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4650time_str=get(handles.abs_time,'String');
4651set(htitle,'String',['t=' time_str])
4652set(handles.speed,'Value',1)
4653for i=1:imax
4654    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4655            runpm(hObject,eventdata,handles,increment)% run plus
4656            drawnow
4657            time_str=get(handles.abs_time,'String');
4658            if ishandle(htitle)
4659             set(htitle,'String',['t=' time_str])
4660            end
4661            mov=getframe(newfig);
4662            aviobj=addframe(aviobj,mov);
4663    end
4664end
4665close(aviobj);
4666UvData.Object{1}.plotaxes=handles.axes3;
4667set(huvmat,'UserData',UvData);
4668msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4669
4670
4671% ------------------------------------------------------------------
4672function MenuCalib_Callback(hObject, eventdata, handles)
4673
4674UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4675
4676%suppress competing options
4677set(handles.zoom,'Value',0)
4678set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
4679set(handles.list_object_1,'Value',1)     
4680% initiate display of GUI geometry_calib
4681data=[]; %default
4682if isfield(UvData,'CoordType')
4683    data.CoordType=UvData.CoordType;
4684end
4685pos=get(handles.uvmat,'Position');
4686pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4687pos(2)=pos(2)-0.02;
4688[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
4689set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4690if isfield(UvData,'CalOrigin')
4691    pos_uvmat=get(handles.uvmat,'Position');
4692    pos_cal(1)=pos_uvmat(1)+UvData.CalOrigin(1)*pos_uvmat(3);
4693    pos_cal(2)=pos_uvmat(2)+UvData.CalOrigin(2)*pos_uvmat(4);
4694    pos_cal(3:4)=UvData.CalSize .* pos_uvmat(3:4);
4695end
4696geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4697set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4698set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4699
4700
4701% ------------------------------------------------------------------
4702function MenuMask_Callback(hObject, eventdata, handles)
4703UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4704ListObj=UvData.Object;
4705select=zeros(1,numel(ListObj));
4706for iobj=1:numel(ListObj);
4707    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4708        select(iobj)=1;
4709    end
4710end
4711val=find(select);
4712if isempty(val)
4713    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4714    return
4715else
4716    set(handles.list_object_1,'Max',2);%allow multiple selection
4717    set(handles.list_object_1,'Value',val);
4718    flag=1;
4719    npx=size(UvData.Field.A,2);
4720    npy=size(UvData.Field.A,1);
4721    xi=0.5:npx-0.5;
4722    yi=0.5:npy-0.5;
4723    [Xi,Yi]=meshgrid(xi,yi);
4724    if isfield(UvData,'Object')
4725        for iobj=1:length(UvData.Object)
4726            ObjectData=UvData.Object{iobj};
4727            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4728                flagobj=1;
4729                testphys=0; %coordinates in pixels by default
4730                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4731                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
4732                        Calib=UvData.XmlData.GeometryCalib;
4733                        testphys=1;
4734                    end
4735                end
4736                if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
4737                    if isequal(ObjectData.Style,'polygon')
4738                        X=ObjectData.Coord(:,1);
4739                        Y=ObjectData.Coord(:,2);
4740                        if testphys
4741                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4742                        end
4743                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4744                    elseif isequal(ObjectData.Style,'ellipse')
4745                        if testphys
4746                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4747                        end
4748                        RangeX=max(ObjectData.RangeX);
4749                        RangeY=max(ObjectData.RangeY);
4750                        X2Max=RangeX*RangeX;
4751                        Y2Max=RangeY*RangeY;
4752                        distX=(Xi-ObjectData.Coord(1,1));
4753                        distY=(Yi-ObjectData.Coord(1,2));
4754                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4755                    elseif isequal(ObjectData.Style,'rectangle')
4756                        if testphys
4757                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4758                        end
4759                        distX=abs(Xi-ObjectData.Coord(1,1));
4760                        distY=abs(Yi-ObjectData.Coord(1,2));
4761                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4762                    end
4763                    if isequal(ObjectData.ProjMode,'mask_outside')
4764                        flagobj=~flagobj;
4765                    end
4766                    flag=flag & flagobj;
4767                end
4768            end
4769        end
4770    end
4771    % flag=~flag;
4772    %mask name
4773    RootPath=get(handles.RootPath,'String');
4774    RootFile=get(handles.RootFile,'String');
4775    if ~isempty(RootFile)&(isequal(RootFile(1),'/')| isequal(RootFile(1),'\'))
4776        RootFile(1)=[];
4777    end
4778    filebase=fullfile(RootPath,RootFile);
4779    list=get(handles.masklevel,'String');
4780    masknumber=num2str(length(list));
4781    maskindex=get(handles.masklevel,'Value');
4782    mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4783    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4784    imflag=flipdim(imflag,1);
4785
4786    %display the mask
4787    figure;
4788    vec=linspace(0,1,256);%define a linear greyscale colormap
4789    map=[vec' vec' vec'];
4790    colormap(map)
4791    image(imflag);
4792    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4793    if ~strcmp(answer,'Cancel')
4794        mask_dir=fileparts(answer);
4795        if ~exist(mask_dir,'dir')
4796            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4797            return
4798        end
4799        imwrite(imflag,answer,'BitDepth',8);
4800    end
4801    set(handles.list_object_1,'Value',1)
4802    set(handles.list_object_1,'Max',1)
4803end
4804
4805%set(handles.uvmat,'UserData',UvData);
4806
4807% ------------------------------------------------------------------
4808%-- open the GUI set_grid.fig to create grid
4809function MenuGrid_Callback(hObject, eventdata, handles)
4810%UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4811
4812%suppress the other options if grid is chosen
4813set(handles.edit_vect,'Value',0)
4814edit_vect_Callback(hObject, eventdata, handles)
4815set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4816set(handles.list_object_1,'Value',1)     
4817
4818%prepare display of the set_grid GUI
4819FileName=read_file_boxes(handles);
4820CoordList=get(handles.transform_fct,'String');
4821val=get(handles.transform_fct,'Value');
4822set_grid(FileName,CoordList{val});% call the set_object interface
4823%set(handles.uvmat,'UserData',UvData);
4824
4825%----------------------------------------------------------------
4826% open the GUI 'series'
4827%----------------------------------------------------------------
4828function MenuSeries_Callback(hObject, eventdata, handles)
4829%-------------------------------------------------------------------
4830series; %first display of the GUI to fill waiting time
4831[param.FileName]=read_file_boxes(handles);
4832if isequal(get(handles.SubField,'Value'),1)
4833    FileName_1=read_file_boxes_1(handles);%
4834    if ~isequal(FileName_1,param.FileName)
4835        param.FileName_1=FileName_1;
4836    end
4837end
4838param.NomType=get(handles.FileIndex,'UserData');
4839param.NomType_1=get(handles.FileIndex_1,'UserData');
4840param.comp_input=get(handles.fix_pair,'Value');
4841huvmat=get(handles.MenuSeries,'parent');
4842UvData=get(huvmat,'UserData');
4843if isfield(UvData,'Time')
4844    param.Time=UvData.XmlData.Time;
4845end
4846if isequal(get(handles.scan_i,'Value'),1)
4847    param.incr_i=str2double(get(handles.increment_scan,'String'));
4848elseif isequal(get(handles.scan_j,'Value'),1)
4849    param.incr_j=str2double(get(handles.increment_scan,'String'));
4850end
4851param.list_fields=get(handles.Fields,'String');% list menu fields
4852param.list_fields(1)=[]; %suppress  'image' option
4853param.index_fields=get(handles.Fields,'Value');% selected string index
4854if param.index_fields>1
4855    param.index_fields=param.index_fields-1;
4856end
4857param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4858param.list_fields_1(1)=[]; %suppress  'image' option
4859param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4860if param.index_fields_1>1
4861    param.index_fields_1=param.index_fields_1-1;
4862end
4863param.civ1=get(handles.civ1,'Value');
4864param.civ2=get(handles.civ2,'Value');
4865param.interp1=get(handles.interp1,'Value');
4866param.interp2=get(handles.interp2,'Value');
4867param.filter1=get(handles.filter1,'Value');
4868param.filter2=get(handles.filter2,'Value');
4869param.menu_coord_str=get(handles.transform_fct,'String');
4870param.menu_coord_val=get(handles.transform_fct,'Value');
4871
4872series(param); %run the series interface
4873
4874% ------------------------------------------------------------------
4875% -- open the GUI civ.fig for civx (PIV)
4876% ------------------------------------------------------------------
4877function MenuPIV_Callback(hObject, eventdata, handles)
4878 
4879[FileName,RootPath,filebase,FileIndices,ext,SubDir]=read_file_boxes(handles);
4880num1=stra2num(get(handles.i1,'String'));
4881num2=stra2num(get(handles.i2,'String'));
4882num_a=stra2num(get(handles.j1,'String'));
4883num_b=stra2num(get(handles.j2,'String'));
4884NomType=get(handles.FileIndex,'UserData');
4885ind_opening=1; % default (images): will advice civ1 option by default in the civ interface
4886if isequal(ext,'.nc') ||  isequal(ext,'.cdf')% netcdf files
4887    ind_opening=2;% propose 'fix' as the default option
4888% +read the current netcdf rootfile
4889    Data=nc2struct(FileName,'ListGlobalAttribute','fix','patch','civ2','fix2');
4890    if isfield(Data,'fix') && isequal(Data.fix,1)
4891        ind_opening=3;
4892    end
4893    if isfield(Data,'patch') && isequal(Data.patch,1)
4894        ind_opening=4;
4895    end
4896    if isfield(Data,'civ2') && isequal(Data.civ2,1)
4897        ind_opening=5;
4898    end
4899    if isfield(Data,'fix2') && isequal(Data.fix2,1)
4900        ind_opening=6;
4901    end
4902end     
4903param.RootName=filebase;
4904param.NomType=NomType;
4905param.num1=num1;
4906param.num2=num2;
4907param.num_a=num_a;
4908param.num_b=num_b;
4909param.SubDir=SubDir;
4910param.IndOpening=ind_opening;% A REVOIR +TRANSMETTRE IMADOC INFO
4911param.ImaExt=ext;
4912civ(param);% interface de civ(not in the uvmat file)
4913   
4914% ------------------------------------------------------------------
4915function MenuTools_Callback(hObject, eventdata, handles)
4916
4917% ------------------------------------------------------------------
4918function MenuEditObject_Callback(hObject, eventdata, handles)
4919set(handles.edit_object,'Value',1)
4920edit_Callback(hObject, eventdata, handles)
4921
4922%--------------------------------------------------------------------------
4923function enable_transform(handles,state)
4924set(handles.transform_fct,'Visible',state)
4925set(handles.TRANSFORM_txt,'Visible',state)   
4926set(handles.transform_fct,'Visible',state) 
4927set(handles.path_transform,'Visible',state)
4928set(handles.pxcmx_txt,'Visible',state)
4929set(handles.pxcmy_txt,'Visible',state)
4930set(handles.pxcm,'Visible',state)
4931set(handles.pycm,'Visible',state)
4932
4933%------------------------------------------------------------------------
4934function MenuEditVectors_Callback(hObject, eventdata, handles)
4935%------------------------------------------------------------------------
4936% set(handles.MenuEditVectors,'checked','on')
4937set(handles.edit_vect,'Visible','on')
4938set(handles.edit_vect,'Value',1)
4939edit_vect_Callback(hObject, eventdata, handles)
4940
4941% --------------------------------------------------------------------
4942function Menupoints_Callback(hObject, eventdata, handles)
4943data.Style='points';
4944data.ProjMode='projection';%default
4945create_object(data,handles)
4946
4947% --------------------------------------------------------------------
4948function Menuline_Callback(hObject, eventdata, handles)
4949% set(handles.create,'Visible','on')
4950% set(handles.create,'Value',1)
4951% LINE_Callback(hObject,eventdata,handles)
4952data.Style='line';
4953data.ProjMode='projection';%default
4954create_object(data,handles)
4955
4956%------------------------------------------------------------------------
4957function Menupolyline_Callback(hObject, eventdata, handles)
4958%------------------------------------------------------------------------
4959data.Style='polyline';
4960data.ProjMode='projection';%default
4961create_object(data,handles)
4962
4963%------------------------------------------------------------------------
4964function Menupolygon_Callback(hObject, eventdata, handles)
4965%------------------------------------------------------------------------
4966data.Style='polygon';
4967data.ProjMode='inside';%default
4968create_object(data,handles)
4969
4970%------------------------------------------------------------------------
4971function Menurectangle_Callback(hObject, eventdata, handles)
4972%------------------------------------------------------------------------
4973data.Style='rectangle';
4974data.ProjMode='inside';%default
4975create_object(data,handles)
4976
4977%------------------------------------------------------------------------
4978function Menuellipse_Callback(hObject, eventdata, handles)
4979%------------------------------------------------------------------------
4980data.Style='ellipse';
4981data.ProjMode='inside';%default
4982create_object(data,handles)
4983
4984%------------------------------------------------------------------------
4985function MenuMaskObject_Callback(hObject, eventdata, handles)
4986%------------------------------------------------------------------------
4987data.Style='polygon';
4988data.StyleMenu={'polygon'};
4989data.ProjMode='mask_inside';%default
4990data.ProjMenu={'mask_inside';'mask_outside'};
4991create_object(data,handles)
4992
4993% ------------------------------------------------------------------
4994function Menuplane_Callback(hObject, eventdata, handles)
4995data.Style='plane';
4996data.ProjMode='projection';%default
4997
4998create_object(data,handles)
4999
5000% ------------------------------------------------------------------
5001function Menuvolume_Callback(hObject, eventdata, handles)
5002data.Style='volume';
5003data.ProjMode='interp';%default
5004% set(handles.create,'Visible','on')
5005% set(handles.create,'Value',1)
5006% VOLUME_Callback(hObject,eventdata,handles)
5007create_object(data,handles)
5008
5009%------------------------------------------------------------------------
5010function MenuBrowseObject_Callback(hObject, eventdata, handles)
5011%------------------------------------------------------------------------
5012%get the object file
5013[FileName, PathName, filterindex] = uigetfile( ...
5014       {'*.xml;*.mat', ' (*.xml,*.mat)';
5015       '*.xml',  '.xml files '; ...
5016        '*.mat',  '.mat matlab files '}, ...
5017        'Pick an xml Object file',get(handles.RootPath,'String'));
5018fileinput=[PathName FileName];%complete file name
5019% testblank=findstr(fileinput,' ');%look for blanks
5020% if ~isempty(testblank)
5021%     msgbox_uvmat('ERROR','forbidden input file name: contain blanks')
5022%     return
5023% end
5024sizf=size(fileinput);
5025if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
5026
5027%read the file
5028t=xmltree(fileinput);
5029data=convert(t);
5030data.enable_plot=1;
5031[pp,data.Name]=fileparts(FileName);
5032%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
5033hset_object=findobj(allchild(0),'tag','set_object');
5034if ~isempty(hset_object)
5035    delete(hset_object)% delete existing version of set_object
5036end
5037% UvData=get(handles.uvmat,'UserData');
5038set_object(data);% call the set_object interface
5039% %position the set_object GUI with respect to uvmat
5040% pos_uvmat=get(handles.uvmat,'Position');
5041% if isfield(UvData,'SetObjectOrigin')
5042%     pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
5043%     pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
5044%     set(hset_object,'Position',pos_set_object)
5045% end
5046set(handles.edit_object,'Value',0); %suppress the object edit mode
5047set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
5048set(handles.MenuObject,'checked','on')
5049%UvData.MouseAction='create_object';
5050% set(handles.uvmat,'UserData',UvData)
5051set(handles.delete_object,'Visible','on')
5052set(handles.uvmat_title,'Visible','on')
5053set(handles.view_field_title,'Visible','on')
5054
5055%------------------------------------------------------------------------
5056% --- generic function used for the creation of a projection object
5057function create_object(data,handles)
5058%------------------------------------------------------------------------
5059hset_object=findobj(allchild(0),'tag','set_object');
5060if ~isempty(hset_object)
5061    delete(hset_object)% delete existing version of set_object
5062end
5063UvData=get(handles.uvmat,'UserData');
5064set(handles.edit_object,'Value',0); %suppress the object edit mode
5065set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
5066data.enable_plot=1;
5067transform_list=get(handles.transform_fct,'String');
5068val=get(handles.transform_fct,'Value');
5069%data.CoordType=transform_list{val};
5070if isfield(UvData,'Field')
5071    Field=UvData.Field;
5072    if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
5073        data.RangeX=Field.Mesh;
5074        data.RangeY=Field.Mesh;
5075        data.DX=Field.Mesh;
5076        data.DY=Field.Mesh;
5077    elseif isfield(Field,'AX')&& isfield(Field,'AY')&& isfield(Field,'A')%only image
5078        np=size(Field.A);
5079        meshx=(Field.AX(end)-Field.AX(1))/np(2);
5080        meshy=abs(Field.AY(end)-Field.AY(1))/np(1);
5081        data.RangeY=max(meshx,meshy);
5082        data.RangeX=max(meshx,meshy);
5083        data.DX=max(meshx,meshy);
5084    end
5085    if isfield(Field,'NbDim')
5086        data.NbDim=Field.NbDim;
5087    end
5088    if isfield(Field,'CoordUnit')
5089        data.CoordUnit=Field.CoordUnit;
5090    end
5091end
5092data.Coord=[0 0 0]; %default
5093if isfield(data,'Style') && isequal(data.Style,'line')
5094    if isfield(data,'DX')
5095        data.Coord=[[0 0 0];[data.DX 0 0]]; %default
5096    else
5097        data.Coord=[[0 0 0];[1 0 0]]; %default
5098    end
5099end
5100if ishandle(handles.UVMAT_title)
5101    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
5102end
5103PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
5104set_object(data,PlotHandles);% call the set_object interface
5105set(handles.MenuObject,'checked','on')
5106set(handles.uvmat,'UserData',UvData)
5107set(handles.zoom,'Value',0)
5108zoom_Callback(handles.uvmat, [], handles)
5109set(handles.delete_object,'Visible','on')
5110set(handles.uvmat_title,'Visible','on')
5111set(handles.view_field_title,'Visible','on')
5112
5113%------------------------------------------------------------------------
5114function MenuRuler_Callback(hObject, eventdata, handles)
5115%------------------------------------------------------------------------
5116set(handles.zoom,'Value',0)
5117zoom_Callback(handles.uvmat, [], handles)
5118set(handles.MenuRuler,'checked','on')
5119UvData=get(handles.uvmat,'UserData');
5120UvData.MouseAction='ruler';
5121set(handles.uvmat,'UserData',UvData);
5122
5123%------------------------------------------------------------------------
5124% --- executed when closing: set the parent interface button to value 0
5125function closefcn(gcbo,eventdata)
5126%------------------------------------------------------------------------
5127%delete all the associated figures if exist
5128hh=findobj(allchild(0),'tag','view_field');
5129if ~isempty(hh)
5130    delete(hh)
5131end
5132hh=findobj(allchild(0),'tag','geometry_calib');
5133if ~isempty(hh)
5134    delete(hh)
5135end
5136hh=findobj(allchild(0),'tag','set_object');
5137if ~isempty(hh)
5138    hhh=findobj(hh,'tag','PLOT');
5139    set(hhh,'enable','off')
5140end
5141
5142
5143% --- Executes on button press in delete_object.
5144function delete_object_Callback(hObject, eventdata, handles)
5145IndexObj=get(handles.list_object_2,'Value');
5146    if IndexObj>1
5147        delete_object(IndexObj)
5148    end
5149   
5150
5151
5152
5153
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