source: trunk/src/uvmat.m @ 399

Last change on this file since 399 was 399, checked in by sommeria, 9 years ago

implementation of thin plate interpolation (proj on planes with mode 'filter'), rationalisation of variable formats in civ_matlab

File size: 194.5 KB
Line 
1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%%
8%
9%INPUT:
10% input: input file name (if character chain), or input image matrix to
11% visualize, or Matlab structure representing  netcdf fields (with fields
12% ListVarName....)
13%
14%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15%  Copyright Joel Sommeria,  2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%     This open is part of the toolbox UVMAT.
18%
19%     UVMAT is free software; you can redistribute it and/or modify
20%     it under the terms of the GNU General Public License as published by
21%     the Free Software Foundation; either version 2 of the License, or
22%     (at your option) any later version.
23%
24%     UVMAT is distributed in the hope that it will be useful,
25%     but WITHOUT ANY WARRANTY; without even the implied warranty of
26%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
28%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29%
30% Information stored on the interface:
31%    'Strings' of all edit boxes and menus: get(handles.Tag,'String')
32%    'Values' of all menus and toggle buttons: get(handles.Tag,'Value')
33%     Matlab structure called UvData stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
34%          It contains the following fields:
35%     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn)
36%          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
37%     - Information read in the documentation open of a series (activated by RootPath_Callback) :
38%          .XmlData, with fields:
39%               .Time: matrix of times of the images with index i and j
40%               .GeometryCalib: [1x1 struct]
41%     - Information defined from the interface:
42%           .NewSeries: =1 when the first view of a new field series is displayed, else 0
43%           .filename:(char string)
44%           .FieldName: (char string) main field selected('image', 'velocity'...)
45%           .CName: (char string)name of the scalar used for vector colors
46%          .MovieObject{1}: movie object representing an input movie
47%          .MovieObject{2}: idem for a second input series (_1)
48%          .filename_1 : last second input file name (to deal with a constant second input without reading again the file)
49%          .ZMin, .ZMax: range of the z coordinate
50%..... to complement
51%     - Information on  projection objects
52%           .Object: {[1x1 struct]}
53%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
54%     -Information on the current field (Field{i})
55%            .Txt : text information to display (e.g. error message)
56%            .NbDim: number of dimensions (=0 by default)
57%            .NbCoord: number of vector components
58%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
59%            .dt: time interval for the corresponding image pair
60%            .Mesh: estimated typical distance between vectors
61%            .ZMax:
62%            .ZMin:
63%            .X, .Y, .Z: set of vector coordinates
64%            .U,.V,.W: corresponding set of vector components
65%            .F: corresponding set of warning flags
66%            .FF: corresponding set of false flags, =0 for good vectors
67%            .C: corresponding values of the scalar used for vector color
68%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
69%                     equal to the number of vectors stored in the input open)
70%            .CName: name of the scalar .C
71%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
72%            .A image or scalar
73%            .AX: vector of dimension 2 representing the first and last values
74%              of the X coordinates for the image or scalar known on a regular grid,
75%              or vector of dimension .A for a scaler defined on irregular grid.
76%            .AY: same as .AX along the Y direction
77%            .AName: name of the scalar, ='image' for an image
78
79% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
80%
81% fields are opened and visualised by the sub-function refresh_field.m
82% (called by uvmat_opening, RUN0, runp and runm)
83% The function first reads the name of the input file from the edit boxes  of the GUI
84% A second input file can be introduced for filed comparison
85% It then reads the input file(s) with the appropriate function, read for
86% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf
87% files.
88%               Main input open   second input open(_1)        second image (pair animation)
89%            |                 |                             
90%            |                 |                                               
91%                     Field{1}         Field{2}               
92%                                                                         |
93% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
94%                                                                   Field{i}
95%                                                                    |
96% calc_field.m: calculate scalar or other derived fields (vort, div..).
97%
98% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
99%              Field{i=1->3}.X --> UvData.X                          |
100%                                                                    |
101%                                                                 UvData
102%                                                                    |
103% plot histograms of the whole  field
104% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
105%                                                                    |                                                                          |
106%                                                                ObjectData
107%                                                                    |
108% plot_field.m: plot the projected fields and store them as          |
109% UvData.axes3                                        |
110%                                                                    |
111%                                                                AxeData
112%
113%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
114% scalars are displayed either as an image or countour plot, either as a color of
115% velocity vectors. The scalar values in the first case is represented by
116% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
117% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
118% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
119% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
120% coordinates of the four image corners. The scalar name is represented by
121% the strings .AName and/or .CName.
122% If the scalar exists in an input open (image or scalar stored under its
123% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
124% Else only its name AName is recorded in Field{i}, and its field is then calculated
125%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
126     
127% Properties attached to plotting figures (standard Matlab properties):
128%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
129%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
130%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
131%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
132%    'KeyPressFcn': function called by pressing a key on the key board
133%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
134%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
135
136% Properties attached to plotting axes:
137%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
138%     AxeData:=get(gca,'UserData');
139%     AxeData.Drawing  = create: create a new object
140%                       = deform: modify an existing object by moving its defining create
141%                      = off: no current drawing action
142%                     = translate: translate an existing object
143%                    = calibration: move a calibration point
144%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
145%            .CurrentOrigin: Origin of a curently drawn edit_object
146%            .CurrentLine: currently drawn menuline (A REVOIR)
147%            .CurrentObject: handle of the currently drawn edit_object
148%            .CurrentRectZoom: current rectangle used for CheckZoom
149
150% Properties attached to projection objects (create, menuline, menuplane...):
151%    'Tag'='proj_object': for all projection objects
152%    ObjectData.Type=...: style of projection object:
153%              .ProjMode
154%              .Coord: defines the position of the object
155%              .XMin,YMin....
156%              .XMax,YMax....
157%              .DX,DY,DZ
158%              .Phi, .Theta, .Psi : Euler angles
159%              .X,.Y,.U,.V.... : field data projected on the object
160%              .IndexObj: index in the list of UvData.Object
161           %during plotting
162%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
163%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
164% To each projection object #iobj, corresponds an axis
165% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
166% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
167
168%------------------------------------------------------------------------
169%------------------------------------------------------------------------
170%  I - MAIN FUNCTION UVMAT (DO NOT MODIFY)
171%------------------------------------------------------------------------
172%------------------------------------------------------------------------
173function varargout = uvmat(varargin)
174
175% Begin initialization code - DO NOT EDIT
176gui_Singleton = 1;
177gui_State = struct('gui_Name',          mfilename, ...
178                   'gui_Singleton',     gui_Singleton, ...
179                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
180                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
181                   'gui_LayoutFcn',     [], ...
182                   'gui_Callback',      []);
183if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
184    gui_State.gui_Callback = str2func(varargin{1});
185end
186
187if nargout
188    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
189else
190    gui_mainfcn(gui_State, varargin{:});
191end
192% End initialization code - DO NOT EDIT
193
194%------------------------------------------------------------------------
195% --- Executes just before the GUI uvmat is made visible.
196function uvmat_OpeningFcn(hObject, eventdata, handles, input )
197%------------------------------------------------------------------------
198
199%% Choose default command menuline output for uvmat (standard GUI)
200handles.output = hObject;
201
202%% Update handles structure (standard GUI)
203guidata(hObject, handles);
204
205%% check the path and date of modification of all functions in uvmat
206path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
207[errormsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m
208date_str=['last modification: ' date_str];
209
210
211%% set the position of colorbar and ancillary GUIs:
212set(hObject,'Units','Normalized')
213movegui(hObject,'center')
214UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
215UvData.OpenParam.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
216UvData.OpenParam.SetObjectSize=[0.3 0.7];
217UvData.OpenParam.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
218UvData.OpenParam.CalSize=[0.28 1];
219UvData.axes3=[];%initiate the record of plotted field
220UvData.axes2=[];
221UvData.axes1=[];
222AxeData.LimEditBox=1; %initialise AxeData
223set(handles.axes3,'UserData',AxeData)
224
225%% set functions for the mouse and keyboard
226set(handles.histo_u,'NextPlot','replacechildren');
227set(handles.histo_v,'NextPlot','replacechildren');
228set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
229set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
230set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
231set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
232set(hObject,'DeleteFcn',{@closefcn})%
233
234%% refresh projection plane
235UvData.Object{1}.ProjMode='projection';%main plotting plane
236set(handles.Fields,'Value',1)
237set(handles.Fields,'string',{''})
238
239%% TRANSFORM menu: builtin fcts
240menu_str={'';'phys';'px';'phys_polar'};
241UvData.OpenParam.NbBuiltin=numel(menu_str); %number of functions
242path_uvmat=fileparts(which('uvmat'));
243addpath (path_uvmat) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
244addpath(fullfile(path_uvmat,'transform_field'))%add the path to transform functions,
245fct_handle{1,1}=[];
246testexist=zeros(size(menu_str'));%default
247testexist(1)=1;
248for ilist=2:length(menu_str)
249    if exist(menu_str{ilist},'file')
250        fct_handle{ilist,1}=str2func(menu_str{ilist});
251        testexist(ilist)=1;
252    else
253        testexist(ilist)=0;
254    end
255end
256rmpath(fullfile(path_uvmat,'transform_field'))
257
258%% load the list of previously browsed files in menus Open and Open_1
259 dir_perso=prefdir; % path to the directory .matlab for personal data
260 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
261 if exist(profil_perso,'file')
262      h=load (profil_perso);
263      if isfield(h,'MenuFile')
264          for ifile=1:min(length(h.MenuFile),5)
265              eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
266               eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
267          end
268      end
269      if isfield(h,'transform_fct') && iscell(h.transform_fct)
270         for ilist=1:length(h.transform_fct);
271             if exist(h.transform_fct{ilist},'file')
272                [path,file]=fileparts(h.transform_fct{ilist});
273                addpath(path)
274                h_func=str2func(file);
275                rmpath(path)
276                testexist=[testexist 1];
277             else
278                file='';
279                h_func=[];
280                testexist=[testexist 0];
281             end
282             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
283             menu_str=[menu_str; {file}];
284         end
285      end
286 end
287menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
288fct_handle=fct_handle(testexist==1);
289menu_str=[menu_str;{'more...'}];
290set(handles.transform_fct,'String',menu_str)
291set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
292
293%% case of an input argument for uvmat
294testinputfield=0;
295inputfile=[];
296Field=[];
297if exist('input','var')
298%     if ~isempty(errormsg)
299%         msgbox_uvmat('WARNING',errormsg)
300%     end
301    if ishandle(handles.UVMAT_title)
302        delete(handles.UVMAT_title)
303    end   
304    if isstruct(input)
305        if isfield(input,'InputFile')
306            inputfile=input.InputFile;
307        end
308        if isfield(input,'TimeIndex')
309            set(handles.i1,num2str(input.TimeIndex))
310        end
311        if isfield(input,'FieldsString')
312            UvData.FieldsString=input.FieldsString;
313        end
314    elseif ischar(input)% file name introduced as input
315           inputfile=input;
316    elseif isnumeric(input)%simple matrix introduced as input
317        sizinput=size(input);
318        if sizinput(1)<=1 || sizinput(2)<=1
319            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
320            return
321        end
322        UvData.Field.ListVarName={'A','coord_y','coord_x'};
323        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
324        UvData.Field.A=input;
325        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
326        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
327        testinputfield=1;
328    end
329else
330   if ishandle(handles.UVMAT_title)
331       set(handles.UVMAT_title,'String',...
332           [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
333           {'GNU General Public License'};...
334           {path_to_uvmat};...
335           {date_str};...
336           {['SVN revision : ' num2str(svn_info.cur_rev)]};...
337           errormsg]);
338   end
339end
340set(handles.uvmat,'UserData',UvData)
341if ~isempty(inputfile)
342    %%%%% display the input field %%%%%%%
343    display_file_name(hObject, eventdata, handles,inputfile)
344    %%%%%%%
345    testinputfield=1;
346end
347
348%% plot input field if exists
349if testinputfield
350    %delete drawn objects
351    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
352    for iobj=1:length(hother)
353        delete_object(hother(iobj))
354    end 
355    if isempty(inputfile)
356        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
357        set(handles.MenuTools,'Enable','on')
358        set(handles.OBJECT_txt,'Visible','on')
359        set(handles.edit_object,'Visible','on')
360        set(handles.ListObject,'Visible','on')
361        set(handles.frame_object,'Visible','on')
362        if ~isempty(errormsg)
363            msgbox_uvmat('ERROR',errormsg)
364        end
365    end
366end
367
368set_vec_col_bar(handles) %update the display of color code for vectors
369
370%------------------------------------------------------------------------
371% --- Outputs from this function are returned to the command menuline.
372function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
373varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
374
375%------------------------------------------------------------------------
376%------------------------------------------------------------------------
377%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
378% automatically sets the global properties when the rootfile name is introduced
379% then activate the view-field action if selected
380% it is activated either by clicking on the RootPath window or by the
381% browser
382%------------------------------------------------------------------------
383%------------------------------------------------------------------------
384% --- Executes on the menu Open/Browse...
385% search the files, recognize their type according to their name and fill the rootfile input windows
386function MenuBrowse_Callback(hObject, eventdata, handles)
387[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
388oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
389% oldfile=read_file_box,es(handles);
390if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
391         dir_perso=prefdir;
392         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
393         if exist(profil_perso,'file')
394              h=load (profil_perso);
395             if isfield(h,'MenuFile_1')
396                  oldfile=h.MenuFile_1;
397             end
398         end
399end
400[FileName, PathName] = uigetfile( ...
401       {'*.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)';
402       '*.xml',  '.xml files '; ...
403        '*.xls',  '.xls files '; ...
404        '*.civ',  '.civ files '; ...
405        '*.jpg',' jpeg image files'; ...
406        '*.png','.png image files'; ...
407        '*.tif','.tif image files'; ...
408        '*.avi;*.AVI','.avi movie files'; ...
409        '*.vol','.volume images (png)'; ...
410        '*.nc','.netcdf files'; ...
411        '*.cdf','.netcdf files'; ...
412        '*.cmx','.cmx text files ';...
413        '*.fig','.fig files (matlab fig)';...
414        '*.log','.log text files ';...
415        '*.dat','.dat text files ';...
416        '*.bat','.bat system command text files';...
417        '*.*',  'All Files (*.*)'}, ...
418        'Pick a file',oldfile);
419fileinput=[PathName FileName];%complete file name
420sizf=size(fileinput);
421if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
422
423% display the selected field and related information
424display_file_name(hObject, eventdata, handles,fileinput)
425
426% -----------------------------------------------------------------------
427% --- Open again the file whose name has been recorded in MenuFile_1
428function MenuFile_1_Callback(hObject, eventdata, handles)
429%------------------------------------------------------------------------
430fileinput=get(handles.MenuFile_1,'Label');
431display_file_name(hObject, eventdata, handles,fileinput)
432
433% -----------------------------------------------------------------------
434% --- Open again the file whose name has been recorded in MenuFile_2
435function MenuFile_2_Callback(hObject, eventdata, handles)
436%------------------------------------------------------------------------
437fileinput=get(handles.MenuFile_2,'Label');
438display_file_name(hObject, eventdata, handles,fileinput)
439
440% -----------------------------------------------------------------------
441% --- Open again the file whose name has been recorded in MenuFile_3
442function MenuFile_3_Callback(hObject, eventdata, handles)
443%------------------------------------------------------------------------
444fileinput=get(handles.MenuFile_3,'Label');
445display_file_name(hObject, eventdata, handles,fileinput)
446
447% -----------------------------------------------------------------------
448% --- Open again the file whose name has been recorded in MenuFile_4
449function MenuFile_4_Callback(hObject, eventdata, handles)
450%------------------------------------------------------------------------
451fileinput=get(handles.MenuFile_4,'Label');
452display_file_name(hObject, eventdata, handles,fileinput)
453
454% -----------------------------------------------------------------------
455% --- Open again the file whose name has been recorded in MenuFile_5
456function MenuFile_5_Callback(hObject, eventdata, handles)
457%------------------------------------------------------------------------
458fileinput=get(handles.MenuFile_5,'Label');
459display_file_name(hObject, eventdata, handles,fileinput)
460
461%------------------------------------------------------------------------
462% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
463function display_file_name(hObject, eventdata, handles,fileinput,index)
464%------------------------------------------------------------------------
465%% look for the input file existence
466if ~exist(fileinput,'file')
467    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
468    return
469end
470
471%% set the mouse pointer to 'watch'
472set(handles.uvmat,'Pointer','watch')
473set(handles.RootPath,'BackgroundColor',[1 1 0])
474drawnow
475
476%% define the relevant handles for the first fiel series (index=1) or the second file series (index=2)
477if ~exist('index','var')
478    index=1;
479end
480if index==1
481    handles_RootPath=handles.RootPath;
482    handles_SubDir=handles.SubDir;
483    handles_RootFile=handles.RootFile;
484    handles_FileIndex=handles.FileIndex;
485    handles_NomType=handles.NomType;
486    handles_FileExt=handles.FileExt;
487%     handles_Fields=handles.Fields;
488elseif index==2
489    handles_RootPath=handles.RootPath_1;
490    handles_SubDir=handles.SubDir_1;
491    handles_RootFile=handles.RootFile_1;
492    handles_FileIndex=handles.FileIndex_1;
493    handles_NomType=handles.NomType_1;
494    handles_FileExt=handles.FileExt_1;
495%     handles_Fields=handles.Fields_1;
496    set(handles.RootPath_1,'Visible','on')
497    set(handles.RootFile_1,'Visible','on')
498    set(handles.SubDir_1,'Visible','on');
499    set(handles.FileIndex_1,'Visible','on');
500    set(handles.FileExt_1,'Visible','on');
501    set(handles.NomType_1,'Visible','on');
502end
503
504%% detect root name, nomenclature and indices in the input file name:
505[FilePath,FileName,FileExt]=fileparts(fileinput);
506% detect the file type, get the movie object if relevant, and look for the corresponding file series:
507% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
508[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
509
510%% open the file or fill the GUI uvmat according to the detected file type
511switch FileType
512    case ''
513        msgbox_uvmat('ERROR','invalid input file type')
514    case 'txt'
515        edit(fileinput)
516    case 'figure'                           %display matlab figure
517        hfig=open(fileinput);
518        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
519        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
520        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
521    case {'xml','xls'}                % edit xml or Excel files
522        editxml(fileinput);
523    otherwise
524        set(handles_RootPath,'String',RootPath);
525        rootname=fullfile(RootPath,SubDir,RootFile);
526        set(handles_SubDir,'String',['/' SubDir]);
527        set(handles_RootFile,'String',['/' RootFile]); %display the separator
528        indices=fileinput(length(rootname)+1:end);
529        indices(end-length(FileExt)+1:end)=[]; %remove extension
530        set(handles_FileIndex,'String',indices);
531        set(handles_NomType,'String',NomType);
532        set(handles_FileExt,'String',FileExt);
533        if index==1
534            % fill file index counters if the first file series is opened
535            set(handles.i1,'String',num2str(i1));
536            set(handles.i2,'String',num2str(i2));
537            set(handles.j1,'String',num2stra(j1,NomType));
538            set(handles.j2,'String',num2stra(j2,NomType));
539        else %read the current field index if the second file series is opened
540            i1=str2num(get(handles.i1,'String'));
541            i2=str2num(get(handles.i2,'String'));
542            j1=stra2num(get(handles.j1,'String'));
543            j2=stra2num(get(handles.j2,'String'));
544        end
545       
546        % synchronise indices of the second  input file if it exists
547        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
548            Input=read_GUI(handles.InputFile);
549            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
550                Input.RootPath_1=Input.RootPath;
551            end
552            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
553                Input.SubDir_1=Input.SubDir;
554            end
555            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
556                Input.RootFile_1=Input.RootFile;
557            end
558            %updtate the indices of the second field series to correspond to the newly opened one
559            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1,i2,j1,j2);
560            if exist(FileName_1,'file')
561                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
562                set(handles.FileIndex_1,'String',FileIndex_1)
563            else
564                set(handles.SubField,'Value',0)
565                SubField_Callback(hObject, eventdata, handles)
566            end
567        end
568       
569        %enable other menus
570        set(handles.MenuOpen_1,'Enable','on')
571        set(handles.MenuFile_1_1,'Enable','on')
572        set(handles.MenuFile_2_1,'Enable','on')
573        set(handles.MenuFile_3_1,'Enable','on')
574        set(handles.MenuFile_4_1,'Enable','on')
575        set(handles.MenuFile_5_1,'Enable','on')
576        set(handles.MenuExport,'Enable','on')
577        set(handles.MenuExportFigure,'Enable','on')
578        set(handles.MenuExportMovie,'Enable','on')
579        set(handles.MenuTools,'Enable','on')
580        set(handles.OBJECT_txt,'Visible','on')
581        set(handles.edit_object,'Visible','on')
582        set(handles.ListObject,'Visible','on')
583        set(handles.frame_object,'Visible','on')
584       
585        % initiate input file series and refresh the current field view:     
586        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
587
588end
589
590%% set back the mouse pointer to arrow
591set(handles.uvmat,'Pointer','arrow')
592
593%------------------------------------------------------------------------
594% --- Called by action in RootPath edit box
595function RootPath_Callback(hObject,eventdata,handles)
596%------------------------------------------------------------------------
597% read the current input file name:
598[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
599%fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
600% detect the file type, get the movie object if relevant, and look for the corresponding file series:
601[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
602% initiate the input file series and refresh the current field view:
603update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject);
604
605%------------------------------------------------------------------------
606% --- Called by action in RootFile edit box
607function SubDir_Callback(hObject, eventdata, handles)
608%------------------------------------------------------------------------
609%refresh the menu of input fields
610Fields_Callback(hObject, eventdata, handles);
611% refresh the current field view
612run0_Callback(hObject, eventdata, handles);
613
614%------------------------------------------------------------------------
615% --- Called by action in RootFile edit box
616function RootFile_Callback(hObject, eventdata, handles)
617%------------------------------------------------------------------------
618RootPath_Callback(hObject,eventdata,handles)
619
620%------------------------------------------------------------------------
621% --- Called by action in FileIndex edit box
622function FileIndex_Callback(hObject, eventdata, handles)
623%------------------------------------------------------------------------
624[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
625set(handles.i1,'String',num2str(i1));
626set(handles.i2,'String',num2str(i2));
627set(handles.j1,'String',num2str(j1));
628set(handles.j2,'String',num2str(j2));
629
630% refresh the current field view
631run0_Callback(hObject, eventdata, handles)
632
633%------------------------------------------------------------------------
634% --- Update information about a new field series (indices to scan, timing,
635%     calibration from an xml file, then refresh current plots
636function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
637%------------------------------------------------------------------------
638%% define the relevant handles depending on the index (1=first file series, 2= second file series)
639if ~exist('index','var')
640    index=1;
641end
642if index==1
643    handles_RootPath=handles.RootPath;
644    handles_Fields=handles.Fields;
645elseif index==2
646    handles_RootPath=handles.RootPath_1;
647    handles_Fields=handles.Fields_1;
648end
649
650set(handles_RootPath,'BackgroundColor',[1 1 0])
651drawnow
652set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
653UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
654UvData.NewSeries=1; %flag for run0: begin a new series
655UvData.TestInputFile=1;
656UvData.FileType{index}=FileType;
657UvData.i1_series{index}=i1_series;
658UvData.i2_series{index}=i2_series;
659UvData.j1_series{index}=j1_series;
660UvData.j2_series{index}=j2_series;
661% set(handles.CheckFixPair,'Value',1) % activate by default the comp_input '-'input window
662set(handles.FixVelType,'Value',0); %desactivate fixed veltype
663if index==1
664    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
665else
666    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
667end
668FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
669FileBase=fullfile(RootPath,RootFile);
670if ~exist(FileName,'file')
671   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
672    return
673end
674nbfield=[];%default
675nbfield_j=[];%default
676
677%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
678XmlData.Time=[];%default
679XmlData.GeometryCalib=[];%default
680TimeUnit=[];%default
681testima=0; %test for image input
682imainfo=[];
683ColorType='falsecolor'; %default
684hhh=[];
685UvData.MovieObject{index}=VideoObject;
686if ~isempty(VideoObject)
687    imainfo=get(VideoObject);
688    testima=1;
689    nbfield_j=1;
690    TimeUnit='s';
691    XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
692    % %         nbfield=imainfo.NumberOfFrames;
693    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
694    ColorType='truecolor';
695elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
696    testima=1;
697    if ~isequal(SubDir,'')
698        RootFile=get(handles.RootFile,'String');
699        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
700    else
701        imainfo=imfinfo([FileBase FileIndices FileExt]);
702    end
703    ColorType=imainfo.ColorType;%='truecolor' for color images
704    if length(imainfo) >1 %case of image with multiple frames
705        nbfield=length(imainfo);
706        nbfield_j=1;
707    end
708end
709if isfield(imainfo,'Width') && isfield(imainfo,'Height')
710    if length(imainfo)>1
711        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
712        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
713    else
714        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
715        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
716    end
717else
718    set(handles.num_Npx,'String','');%fills nbre of pixels x box
719    set(handles.num_Npy,'String','');%fills nbre of pixels x box
720end
721set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
722
723%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
724filexml=[FileBase '.xml'];
725fileciv=[FileBase '.civ'];
726warntext='';%default warning message
727NbSlice=1;%default
728set(handles.RootPath,'BackgroundColor',[1 1 1])
729if exist(filexml,'file')
730    set(handles.view_xml,'Visible','on')
731    set(handles.view_xml,'BackgroundColor',[1 1 0])
732    set(handles.view_xml,'String','view .xml')
733    drawnow
734    [XmlData,warntext]=imadoc2struct(filexml);
735    if ~isempty(warntext)
736        msgbox_uvmat('WARNING',warntext)
737    end
738    if isfield(XmlData,'TimeUnit')
739        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
740            TimeUnit=XmlData.TimeUnit;
741        end
742    end
743    set(handles.view_xml,'BackgroundColor',[1 1 1])
744    drawnow
745    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
746        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
747            set (handles.nb_slice,'String','volume')
748        end
749        hgeometry_calib=findobj('tag','geometry_calib');
750        if ~isempty(hgeometry_calib)
751            GUserData=get(hgeometry_calib,'UserData');
752            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
753                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
754                if strcmp(answer,'Yes')
755                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
756                end
757            end
758        end
759    end 
760elseif exist(fileciv,'file')% if .civ file found
761    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
762    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
763    GeometryCalib.Tx=0;
764    GeometryCalib.Ty=0;
765    GeometryCalib.Tz=1;
766    GeometryCalib.dpx=1;
767    GeometryCalib.dpy=1;
768    GeometryCalib.sx=1;
769    GeometryCalib.Cx=0;
770    GeometryCalib.Cy=0;
771    GeometryCalib.f=1;
772    GeometryCalib.kappa1=0;
773    GeometryCalib.CoordUnit='cm';
774    XmlData.GeometryCalib=GeometryCalib;
775    if error==2, warntext=['no file ' FileBase '.civ'];
776    elseif error==1, warntext='inconsistent number of fields in the .civ file';
777    end 
778    set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
779    set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
780    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
781    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
782    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
783    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
784    set(handles.view_xml,'Visible','on')   
785    set(handles.view_xml,'String','view .civ')
786else
787    set(handles.view_xml,'Visible','off')
788end
789
790%% store last index in handles.lat_i and .last_j
791nbfield=max(max(i2_series));
792if isempty(nbfield)
793    nbfield=max(max(i1_series));
794end
795nbfield_j=max(max(j2_series));
796if isempty(nbfield_j)
797    nbfield_j=max(max(j1_series));
798end
799if ~isempty(XmlData.Time)
800%     nbfield=size(XmlData.Time,1);
801%     nbfield_j=size(XmlData.Time,2);
802    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
803    if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
804        NomType=get(handles.NomType,'String');
805        if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
806            XmlData.Time=(XmlData.Time)';
807%             nbfield=nbfield_j;
808%             nbfield_j=1;
809        end
810    end
811end
812last_i_cell=get(handles.last_i,'String');
813if isempty(nbfield)
814    last_i_cell{1}='';
815else
816    last_i_cell{1}=num2str(nbfield);
817end
818set(handles.last_i,'String',last_i_cell)
819last_j_cell=get(handles.last_j,'String');
820if isempty(nbfield_j)
821     last_j_cell{1}='';
822else
823     last_j_cell{1}=num2str(nbfield_j);
824end
825set(handles.last_j,'String',last_j_cell);
826
827%% store geometric calibration in UvData
828if isfield(XmlData,'GeometryCalib')
829    GeometryCalib=XmlData.GeometryCalib;
830    if isempty(GeometryCalib)
831        set(handles.pxcm,'String','')
832        set(handles.pycm,'String','')
833        set(handles.transform_fct,'Value',1); %  no transform by default
834    else
835        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
836            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
837            set(handles.pxcm,'String','var')
838            set(handles.pycm,'String','var')
839        elseif isfield(GeometryCalib,'fx_fy')
840            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
841            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
842            set(handles.pxcm,'String',num2str(pixcmx))
843            set(handles.pycm,'String',num2str(pixcmy))
844        end
845        if ~get(handles.CheckFixLimits,'Value')
846            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
847        end
848        if isfield(GeometryCalib,'SliceCoord')
849           
850           siz=size(GeometryCalib.SliceCoord);
851           if siz(1)>1
852               NbSlice=siz(1);
853               set(handles.slices,'Visible','on')
854               set(handles.slices,'Value',1)
855           end
856           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
857               set(handles.nb_slice,'String','volume')
858           else
859               set(handles.nb_slice,'String',num2str(NbSlice))
860           end
861           slices_Callback([],[], handles)
862        end           
863    end
864end
865
866%% update the data attached to the uvmat interface
867if ~isempty(TimeUnit)
868    set(handles.time_txt,'String',['time (' TimeUnit ')'])
869end
870UvData.TimeUnit=TimeUnit;
871UvData.XmlData{index}=XmlData;
872UvData.NewSeries=1;
873% UvData.MovieObject=MovieObject;
874
875%display warning message
876if ~isequal(warntext,'')
877    msgbox_uvmat('WARNING',warntext);
878end
879
880%% set default options in menu 'Fields'
881if ~testima
882    testcivx=0;
883    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
884        set(handles_Fields,'Value',1)
885        set(handles_Fields,'String',{'get_field...'})
886        UvData=rmfield(UvData,'FieldsString');
887    else
888        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
889        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
890            FieldList=calc_field;
891            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
892            set(handles_Fields,'Value',2) % set menu to 'velocity'
893            col_vec=FieldList;
894            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
895            testcivx=1;
896        end
897        if ~testcivx
898            set(handles_Fields,'Value',1) % set menu to 'get_field...
899            set(handles_Fields,'String',{'get_field...'})
900            col_vec={'get_field...'};
901        end
902        set(handles.ListColorScalar,'String',col_vec)
903    end
904end
905set(handles.uvmat,'UserData',UvData)
906
907%% set index navigation options and refresh plots
908scan_option='i';%default
909state_j='off'; %default
910if index==2
911    if get(handles.scan_j,'Value')
912        scan_option='j'; %keep the scan option for the second fiel series
913    end
914    if strcmp(get(handles.j1,'Visible'),'on')
915        state_j='on';
916    end
917end
918if ~isempty(j1_series)
919        state_j='on';
920        if isequal(nbfield,1) &&index==1
921            scan_option='j'; %scan j index by default if nbfield=1               
922        end
923end
924if isequal(scan_option,'i')
925     set(handles.scan_i,'Value',1)
926     scan_i_Callback([],[], handles);
927else
928     set(handles.scan_j,'Value',1)
929     scan_j_Callback([],[], handles);
930end
931set(handles.scan_j,'Visible',state_j)
932set(handles.j1,'Visible',state_j)
933set(handles.j2,'Visible',state_j)
934set(handles.last_j,'Visible',state_j);
935set(handles.frame_j,'Visible',state_j);
936set(handles.j_text,'Visible',state_j);
937if ~isempty(i2_series)||~isempty(j2_series)
938    set(handles.CheckFixPair,'Visible','on')
939elseif index==1
940    set(handles.CheckFixPair,'Visible','off')
941end
942
943%% view the field 
944run0_Callback([],[], handles); %view field
945mask_test=get(handles.CheckMask,'value');
946if mask_test
947    MaskData=get(handles.CheckMask,'UserData');
948    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
949          delete(MaskData.maskhandle)    %delete old mask
950    end
951    CheckMask_Callback([],[],handles)
952end
953
954%% update list of recent files in the menubar
955MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
956    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
957str_find=strcmp(FileName,MenuFile);
958if isempty(find(str_find,1))
959    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
960end
961for ifile=1:min(length(MenuFile),5)
962    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
963    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
964end
965dir_perso=prefdir;
966profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
967if exist(profil_perso,'file')
968    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
969else
970    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
971end
972
973
974%------------------------------------------------------------------------
975% --- Executes on the menu Open/Browse_1 for the second input field,
976%     search the files, recognize their type according to their name and fill the rootfile input windows
977function MenuBrowse_1_Callback(hObject, eventdata, handles)
978%------------------------------------------------------------------------
979% huvmat=get(handles.run0,'parent');
980UvData=get(handles.uvmat,'UserData');
981
982RootPath=get(handles.RootPath,'String');
983[FileName, PathName, filterindex] = uigetfile( ...
984       {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
985       '*.xml',  '.xml files '; ...
986        '*.xls',  '.xls files '; ...
987        '*.civ',  '.civ files '; ...
988        '*.jpg','.jpg image files'; ...
989        '*.png','.png image files'; ...
990        '*.avi;*.AVI','.avi movie files'; ...
991        '*.nc','.netcdf files'; ...
992        '*.cdf','.netcdf files'; ...
993        '*.cmx','.cmx text files';...
994        '*.cmx2','.cmx2 text files';...
995        '*.fig','.fig files (matlab fig)';...
996        '*.log','.log text files ';...
997        '*.dat','.dat text files ';...
998        '*.*',  'All Files (*.*)'}, ...
999        'Pick a second file for comparison',RootPath);
1000fileinput_1=[PathName FileName];%complete file name
1001sizf=size(fileinput_1);
1002if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
1003
1004% refresh the current displayed field
1005set(handles.SubField,'Value',1)
1006display_file_name(hObject,eventdata,handles,fileinput_1,2)
1007
1008%update list of recent files in the menubar
1009MenuFile_1=fileinput_1;
1010MenuFile_2=get(handles.MenuFile_1,'Label');
1011MenuFile_3=get(handles.MenuFile_2,'Label');
1012MenuFile_4=get(handles.MenuFile_3,'Label');
1013MenuFile_5=get(handles.MenuFile_4,'Label');
1014set(handles.MenuFile_1,'Label',MenuFile_1)
1015set(handles.MenuFile_2,'Label',MenuFile_2)
1016set(handles.MenuFile_3,'Label',MenuFile_3)
1017set(handles.MenuFile_4,'Label',MenuFile_4)
1018set(handles.MenuFile_5,'Label',MenuFile_5)
1019set(handles.MenuFile_1_1,'Label',MenuFile_1)
1020set(handles.MenuFile_2_1,'Label',MenuFile_2)
1021set(handles.MenuFile_3_1,'Label',MenuFile_3)
1022set(handles.MenuFile_4_1,'Label',MenuFile_4)
1023set(handles.MenuFile_5_1,'Label',MenuFile_5)
1024dir_perso=prefdir;
1025profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1026if exist(profil_perso,'file')
1027    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
1028else
1029    txt=ver('MATLAB');
1030    Release=txt.Release;
1031    relnumb=str2double(Release(3:4));
1032    if relnumb >= 14
1033        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
1034    else
1035        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
1036    end
1037end
1038
1039% -----------------------------------------------------------------------
1040% --- Open again as second field the file whose name has been recorded in MenuFile_1
1041function MenuFile_1_1_Callback(hObject, eventdata, handles)
1042% -----------------------------------------------------------------------
1043fileinput_1=get(handles.MenuFile_1_1,'Label');
1044set(handles.SubField,'Value',1)
1045display_file_name(hObject,eventdata,handles,fileinput_1,2)
1046
1047% -----------------------------------------------------------------------
1048% --- Open again as second field the file whose name has been recorded in MenuFile_2
1049function MenuFile_2_1_Callback(hObject, eventdata, handles)
1050% -----------------------------------------------------------------------
1051fileinput_1=get(handles.MenuFile_2_1,'Label');
1052set(handles.SubField,'Value',1)
1053display_file_name(hObject,eventdata,handles,fileinput_1,2)
1054
1055% -----------------------------------------------------------------------
1056% --- Open again as second field the file whose name has been recorded in MenuFile_3
1057function MenuFile_3_1_Callback(hObject, eventdata, handles)
1058% -----------------------------------------------------------------------
1059fileinput_1=get(handles.MenuFile_3_1,'Label');
1060set(handles.SubField,'Value',1)
1061display_file_name(hObject,eventdata,handles,fileinput_1,2)
1062
1063% -----------------------------------------------------------------------
1064% --- Open again as second field the file whose name has been recorded in MenuFile_4
1065function MenuFile_4_1_Callback(hObject, eventdata, handles)
1066% -----------------------------------------------------------------------
1067fileinput_1=get(handles.MenuFile_4_1,'Label');
1068set(handles.SubField,'Value',1)
1069display_file_name(hObject,eventdata,handles,fileinput_1,2)
1070
1071% -----------------------------------------------------------------------
1072% --- Open again as second field the file whose name has been recorded in MenuFile_5
1073function MenuFile_5_1_Callback(hObject, eventdata, handles)
1074% -----------------------------------------------------------------------
1075fileinput_1=get(handles.MenuFile_5_1,'Label');
1076set(handles.SubField,'Value',1)
1077display_file_name(hObject,eventdata,handles,fileinput_1,2)
1078
1079%-----------------------------------------------------------------------
1080% --- Called by action in RootPath_1 edit box
1081function RootPath_1_Callback(hObject,eventdata,handles)
1082% -----------------------------------------------------------------------
1083% update_rootinfo_1(hObject,eventdata,handles)
1084[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
1085%fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1086% detect the file type, get the movie object if relevant, and look for the corresponding file series:
1087[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
1088% initiate the input file series and refresh the current field view:
1089update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
1090%-----------------------------------------------------------------------
1091% --- Called by action in RootFile_1 edit box
1092function RootFile_1_Callback(hObject, eventdata, handles)
1093% -----------------------------------------------------------------------
1094RootPath_1_Callback(hObject,eventdata,handles)
1095
1096%------------------------------------------------------------------------
1097% --- Called by action in FileIndex_1 edit box
1098function FileIndex_1_Callback(hObject, eventdata, handles)
1099%------------------------------------------------------------------------
1100run0_Callback(hObject, eventdata, handles)
1101
1102%------------------------------------------------------------------------
1103% --- switch file index scanning options scan_i and scan_j in an exclusive way
1104function scan_i_Callback(hObject, eventdata, handles)
1105%------------------------------------------------------------------------
1106if get(handles.scan_i,'Value')==1
1107    set(handles.scan_i,'BackgroundColor',[1 1 0])
1108    set(handles.scan_j,'Value',0)
1109else
1110    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1111    set(handles.scan_j,'Value',1)
1112end
1113scan_j_Callback(hObject, eventdata, handles)
1114
1115%------------------------------------------------------------------------
1116% --- switch file index scanning options scan_i and scan_j in an exclusive way
1117function scan_j_Callback(hObject, eventdata, handles)
1118%------------------------------------------------------------------------
1119if get(handles.scan_j,'Value')==1
1120    set(handles.scan_j,'BackgroundColor',[1 1 0])
1121    set(handles.scan_i,'Value',0)
1122    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1123%     NomType=get(handles.NomType,'String');
1124%     switch NomType
1125%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1126%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1127%     otherwise
1128%         set(handles.CheckFixPair,'Visible','off')
1129%     end
1130else
1131    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1132    set(handles.scan_i,'Value',1)
1133    set(handles.scan_i,'BackgroundColor',[1 1 0])
1134    set(handles.CheckFixPair,'Visible','off')
1135end
1136
1137%------------------------------------------------------------------------
1138function i1_Callback(hObject, eventdata, handles)
1139%------------------------------------------------------------------------
1140set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1141NomType=get(handles.NomType,'String');
1142i1=stra2num(get(handles.i1,'String'));
1143i2=stra2num(get(handles.i2,'String'));
1144j1=stra2num(get(handles.j1,'String'));
1145j2=stra2num(get(handles.j2,'String'));
1146indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1147%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1148set(handles.FileIndex,'String',indices)
1149set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1150if get(handles.SubField,'Value')==1
1151    NomType_1=get(handles.NomType_1,'String');
1152    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1153     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1154     set(handles.FileIndex_1,'String',indices)
1155     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1156end
1157
1158%------------------------------------------------------------------------
1159function i2_Callback(hObject, eventdata, handles)
1160%------------------------------------------------------------------------
1161set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1162i1_Callback(hObject, eventdata, handles)
1163
1164%------------------------------------------------------------------------
1165function j1_Callback(hObject, eventdata, handles)
1166%------------------------------------------------------------------------
1167set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1168i1_Callback(hObject, eventdata, handles)
1169
1170%------------------------------------------------------------------------
1171function j2_Callback(hObject, eventdata, handles)
1172%------------------------------------------------------------------------
1173set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1174i1_Callback(hObject, eventdata, handles)
1175
1176%------------------------------------------------------------------------
1177function slices_Callback(hObject, eventdata, handles)
1178%------------------------------------------------------------------------
1179if get(handles.slices,'Value')==1
1180    set(handles.slices,'BackgroundColor',[1 1 0])
1181    set(handles.nb_slice,'Visible','on')
1182    set(handles.z_text,'Visible','on')
1183    set(handles.z_index,'Visible','on')
1184    nb_slice_Callback(hObject, eventdata, handles)
1185else
1186    set(handles.nb_slice,'Visible','off')
1187    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1188    set(handles.z_text,'Visible','off')
1189    set(handles.z_index,'Visible','off')
1190    set(handles.masklevel,'Value',1)
1191    set(handles.masklevel,'String',{'1'})
1192end
1193
1194%------------------------------------------------------------------------
1195function nb_slice_Callback(hObject, eventdata, handles)
1196%------------------------------------------------------------------------
1197nb_slice_str=get(handles.nb_slice,'String');
1198if isequal(nb_slice_str,'volume')
1199    num=stra2num(get(handles.j1,'String'));
1200    last_j=get(handles.last_j,'String');
1201    nbslice=str2double(last_j{1});
1202else
1203    num=str2double(get(handles.i1,'String'));
1204    nbslice=str2double(get(handles.nb_slice,'String'));
1205end
1206z=mod(num-1,nbslice)+1;
1207set(handles.z_index,'String',num2str(z))
1208for ilist=1:nbslice
1209    list_index{ilist,1}=num2str(ilist);
1210end   
1211set(handles.masklevel,'String',list_index)
1212set(handles.masklevel,'Value',z)
1213
1214%------------------------------------------------------------------------
1215% --- Executes on button press in view_xml.
1216function view_xml_Callback(hObject, eventdata, handles)
1217%------------------------------------------------------------------------
1218%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1219 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1220FileBase=fullfile(RootPath,RootFile);
1221option=get(handles.view_xml,'String');
1222if isequal(option,'view .xml')
1223    FileXml=[FileBase '.xml'];
1224    heditxml=editxml(FileXml);
1225end
1226
1227%------------------------------------------------------------------------
1228% --- Executes on button press in CheckMask.
1229function CheckMask_Callback(hObject, eventdata, handles)
1230%------------------------------------------------------------------------
1231%case of view mask selection
1232if isequal(get(handles.CheckMask,'Value'),1)
1233   % [FF,RootPath,FileBase]=read_file_boxes(handles);
1234     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1235     FileBase=fullfile(RootPath,RootFile);
1236    num_i1=stra2num(get(handles.i1,'String'));
1237    num_j1=stra2num(get(handles.j1,'String'));
1238    currentdir=pwd; 
1239    cd(RootPath);
1240    maskfiles=dir('*_*mask_*.png');%look for a mask file
1241    cd(currentdir);%come back to the working directory
1242    mdetect=0;
1243    if ~isempty(maskfiles)
1244        for ilist=1:length(maskfiles)
1245            maskname=maskfiles(ilist).name;% take the first mask file in the list
1246            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1247%             [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1248             [tild,Name]=fileparts(maskname);
1249            Namedouble=double(Name);
1250            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1251            ind_mask=findstr('mask',Name);
1252            i=ind_mask-1;
1253            while val(i)==0 && i>0
1254                i=i-1;
1255            end
1256            nbmask_str=str2num(Name(i+1:ind_mask-1));
1257            if ~isempty(nbmask_str)
1258                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1259            end
1260        end
1261        if isequal(min(nbslice),max(nbslice))
1262            nbslice=nbslice(1);
1263        else
1264            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1265            return
1266        end
1267        if ~isempty(nbslice) && Name(i)=='_'
1268            Mask.Base=[FileBase Name(i:ind_mask+3)];
1269            Mask.NbSlice=nbslice;
1270            num_i1=mod(num_i1-1,nbslice)+1;
1271            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1272            [RootPath,RootFile]=fileparts(Mask.Base);
1273            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1274            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1275            mdetect=exist(maskname,'file');
1276            if mdetect
1277                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1278                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1279                set(handles.CheckMask,'UserData',Mask);
1280                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1281                if nbslice > 1
1282                    set(handles.slices,'value',1)
1283                    slices_Callback(hObject, eventdata, handles)
1284                end
1285            end
1286        end
1287    end
1288    errormsg=[];%default
1289    if mdetect==0
1290        [FileName, PathName, filterindex] = uigetfile( ...
1291            {'*.png', ' (*.png)';
1292            '*.png',  '.png files '; ...
1293            '*.*', 'All Files (*.*)'}, ...
1294            'Pick a mask file *.png',FileBase);
1295        maskname=fullfile(PathName,FileName);
1296        if ~exist(maskname,'file')
1297            errormsg='no file browsed';
1298        end
1299        [RootDir,tild,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1300%         [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1301        Mask.Base=fullfile(RootDir,RootFile);
1302        Mask.NbSlice=1;
1303        set(handles.CheckMask,'UserData',Mask);
1304        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1305    end
1306    if isempty(errormsg)
1307        errormsg=update_mask(handles,num_i1,num_j1);
1308    end
1309    if ~isempty(errormsg)
1310            set(handles.CheckMask,'Value',0)
1311            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1312     end
1313else % desactivate mask display
1314    MaskData=get(handles.CheckMask,'UserData');
1315    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1316          delete(MaskData.maskhandle)   
1317    end
1318    set(handles.CheckMask,'UserData',[])   
1319    UvData=get(handles.uvmat,'UserData');
1320    if isfield(UvData,'MaskName')
1321        UvData=rmfield(UvData,'MaskName');
1322        set(handles.uvmat,'UserData',UvData)
1323    end
1324    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1325end
1326
1327%------------------------------------------------------------------------
1328function errormsg=update_mask(handles,num_i1,num_j1)
1329%------------------------------------------------------------------------
1330errormsg=[];%default
1331MaskData=get(handles.CheckMask,'UserData');
1332if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1333    uistack(MaskData.maskhandle,'top');
1334end
1335num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1336[RootPath,RootFile]=fileparts(MaskData.Base);
1337MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1338%MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1339% huvmat=get(handles.CheckMask,'parent');
1340UvData=get(handles.uvmat,'UserData');
1341%update mask image if the mask is new
1342if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1343    UvData.MaskName=MaskName; %update the recorded name on UvData
1344    set(handles.uvmat,'UserData',UvData);
1345    if ~exist(MaskName,'file')
1346        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1347            delete(MaskData.maskhandle)   
1348        end
1349    else
1350        %read mask image
1351        Mask.AName='image';
1352        Mask.A=imread(MaskName);
1353        npxy=size(Mask.A);
1354        test_error=0;
1355        if length(npxy)>2
1356            errormsg=[MaskName ' is not a grey scale image'];
1357            return
1358        elseif ~isa(Mask.A,'uint8')
1359            errormsg=[MaskName ' is not a 8 bit grey level image'];
1360            return
1361        end
1362        Mask.AX=[0.5 npxy(2)-0.5];
1363        Mask.AY=[npxy(1)-0.5 0.5 ];
1364        Mask.CoordUnit='pixel';
1365        if isequal(get(handles.slices,'Value'),1)
1366           NbSlice=str2num(get(handles.nb_slice,'String'));
1367           num_i1=str2num(get(handles.i1,'String'));
1368           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1369        end
1370        %px to phys or other transform on field
1371         menu_transform=get(handles.transform_fct,'String');
1372        choice_value=get(handles.transform_fct,'Value');
1373        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1374        transform_list=get(handles.transform_fct,'UserData');
1375        transform=transform_list{choice_value};
1376        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1377            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1378                Calib=UvData.XmlData{1}.GeometryCalib;
1379                Mask=transform(Mask,UvData.XmlData{1});
1380            end
1381        end
1382        flagmask=Mask.A < 200;
1383       
1384        %make brown color image
1385        imflag(:,:,1)=0.9*flagmask;
1386        imflag(:,:,2)=0.7*flagmask;
1387        imflag(:,:,3)=zeros(size(flagmask));
1388       
1389        %update mask image
1390        hmask=[]; %default
1391        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1392            hmask=MaskData.maskhandle;
1393        end
1394        if ~isempty(hmask)
1395            set(hmask,'CData',imflag)   
1396            set(hmask,'AlphaData',flagmask*0.6)
1397            set(hmask,'XData',Mask.AX);
1398            set(hmask,'YData',Mask.AY);
1399%             uistack(hmask,'top')
1400        else
1401            axes(handles.axes3)
1402            hold on   
1403            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1404%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1405            set(handles.CheckMask,'UserData',MaskData)
1406        end
1407    end
1408end
1409
1410
1411%------------------------------------------------------------------------
1412function MenuExportFigure_Callback(hObject, eventdata, handles)
1413%------------------------------------------------------------------------
1414% huvmat=get(handles.MenuExport,'parent');
1415hfig=figure;
1416copyobj(handles.axes3,hfig);
1417map=colormap(handles.axes3);
1418colormap(map);%transmit the current colormap to the zoom fig
1419colorbar
1420
1421%------------------------------------------------------------------------
1422%------------------------------------------------------------------------
1423% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1424%------------------------------------------------------------------------
1425
1426%------------------------------------------------------------------------
1427% --- Executes on button press in runplus: make one step forward and call
1428% --- run0. The step forward is along the fields series 1 or 2 depending on
1429% --- the scan_i and scan_j check box (exclusive each other)
1430function runplus_Callback(hObject, eventdata, handles)
1431%------------------------------------------------------------------------
1432set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1433drawnow
1434%TODO: introduce the option: increment ='*' to move to the next available view
1435increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1436% if isnan(increment)
1437%     set(handles.increment_scan,'String','1')%default value
1438%     increment=1;
1439% end
1440errormsg=runpm(hObject,eventdata,handles,increment);
1441if ~isempty(errormsg)
1442    msgbox_uvmat('ERROR',errormsg);
1443end
1444set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1445
1446%------------------------------------------------------------------------
1447% --- Executes on button press in runmin: make one step backward and call
1448% --- run0. The step backward is along the fields series 1 or 2 depending on
1449% --- the scan_i and scan_j check box (exclusive each other)
1450function runmin_Callback(hObject, eventdata, handles)
1451%------------------------------------------------------------------------
1452set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1453drawnow
1454increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1455% if isnan(increment)
1456%     set(handles.increment_scan,'String','1')%default value
1457%     increment=1;
1458% end
1459errormsg=runpm(hObject,eventdata,handles,increment);
1460if ~isempty(errormsg)
1461    msgbox_uvmat('ERROR',errormsg);
1462end
1463set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1464
1465%------------------------------------------------------------------------
1466% -- Executes on button press in Movie: make a series of +> steps
1467function Movie_Callback(hObject, eventdata, handles)
1468%------------------------------------------------------------------------
1469set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1470drawnow
1471increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1472% if isnan(increment)
1473%     set(handles.increment_scan,'String','1')%default value
1474%     increment=1;
1475% end
1476set(handles.STOP,'Visible','on')
1477set(handles.speed,'Visible','on')
1478set(handles.speed_txt,'Visible','on')
1479set(handles.Movie,'BusyAction','queue')
1480UvData=get(handles.uvmat,'UserData');
1481
1482while get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1483        errormsg=runpm(hObject,eventdata,handles,increment);
1484        if ~isempty(errormsg)
1485            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1486            return
1487        end
1488        pause(1.02-get(handles.speed,'Value'))% wait for next image
1489end
1490if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1491    UvData.aviobj=close(UvData.aviobj);
1492   set(handles.uvmat,'UserData',UvData);
1493end
1494set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1495
1496%------------------------------------------------------------------------
1497% -- Executes on button press in Movie: make a series of <- steps
1498function MovieBackward_Callback(hObject, eventdata, handles)
1499%------------------------------------------------------------------------
1500set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1501drawnow
1502increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1503set(handles.STOP,'Visible','on')
1504set(handles.speed,'Visible','on')
1505set(handles.speed_txt,'Visible','on')
1506set(handles.MovieBackward,'BusyAction','queue')
1507UvData=get(handles.uvmat,'UserData');
1508
1509while get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1510        errormsg=runpm(hObject,eventdata,handles,increment);
1511        if ~isempty(errormsg)
1512            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1513            return
1514        end
1515        pause(1.02-get(handles.speed,'Value'))% wait for next image
1516end
1517if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1518    UvData.aviobj=close(UvData.aviobj);
1519   set(handles.uvmat,'UserData',UvData);
1520end
1521set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1522
1523%------------------------------------------------------------------------
1524function STOP_Callback(hObject, eventdata, handles)
1525%------------------------------------------------------------------------
1526set(handles.movie_pair,'BusyAction','Cancel')
1527set(handles.movie_pair,'value',0)
1528set(handles.Movie,'BusyAction','Cancel')
1529set(handles.MovieBackward,'BusyAction','Cancel')
1530set(handles.MenuExportMovie,'BusyAction','Cancel')
1531set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1532set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1533set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1534
1535%------------------------------------------------------------------------
1536% --- function activated by runplus and run minus
1537function errormsg=runpm(hObject,eventdata,handles,increment)
1538%------------------------------------------------------------------------
1539errormsg='';%default
1540%% check for movie pair status
1541movie_status=get(handles.movie_pair,'Value');
1542if isequal(movie_status,1)
1543    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1544end
1545
1546%% read the current input file name(s) and field indices
1547InputFile=read_GUI(handles.InputFile);
1548InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1549InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1550FileExt=InputFile.FileExt;
1551NomType=get(handles.NomType,'String');
1552i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1553i2=[];%default
1554if strcmp(get(handles.i2,'Visible'),'on')
1555    i2=str2num(get(handles.i2,'String'));
1556end
1557j1=[];
1558if strcmp(get(handles.j1,'Visible'),'on')
1559    j1=stra2num(get(handles.j1,'String'));
1560end
1561j2=j1;
1562if strcmp(get(handles.j2,'Visible'),'on')
1563    j2=stra2num(get(handles.j2,'String'));
1564end
1565sub_value= get(handles.SubField,'Value');
1566if sub_value % a second input file has been entered
1567    [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1568    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndices_1);
1569    NomType_1=get(handles.NomType_1,'String');
1570else
1571    filename_1=[];
1572end   
1573
1574%% increment (or decrement) the field indices and update the input filename(s)
1575CheckSearch=0;
1576if isempty(increment)
1577    CheckSearch=1;% search for the next available file
1578    set(handles.CheckFixPair,'Value',0)
1579end
1580CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1581if CheckFixPair
1582    if get(handles.scan_i,'Value')==1% case of scanning along index i
1583        i1=i1+increment;
1584        i2=i2+increment;
1585        if sub_value
1586            i1_1=i1_1+increment;
1587            i2_1=i2_1+increment;
1588        end
1589    else % case of scanning along index j (burst numbers)
1590        j1=j1+increment;
1591        j2=j2+increment;
1592        if sub_value
1593            j1_1=j1_1+increment;
1594            j2_1=j2_1+increment;
1595        end
1596    end
1597else
1598    UvData=get(handles.uvmat,'UserData');
1599    ref_i=i1;
1600    if ~isempty(i2)
1601        ref_i=floor((i1+i2)/2);
1602    end
1603    ref_j=1;
1604    if ~isempty(j1)
1605        ref_j=j1;
1606        if ~isempty(j2)
1607            ref_j=floor((j1+j2)/2);
1608        end
1609    end
1610    if ~isempty(increment)
1611        if get(handles.scan_i,'Value')==1% case of scanning along index i
1612            ref_i=ref_i+increment;
1613        else % case of scanning along index j (burst numbers)
1614            ref_j=ref_j+increment;
1615        end
1616    else % free increment
1617        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
1618            step=1;
1619        else
1620            step=-1;
1621        end
1622        if get(handles.scan_i,'Value')==1% case of scanning along index i
1623            ref_i=ref_i+step;
1624            while ref_i>=0  && size(UvData.i1_series{1},1)>=ref_i+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
1625                ref_i=ref_i+step;
1626            end
1627        else % case of scanning along index j (burst numbers)
1628            ref_j=ref_j+step;
1629            while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
1630                ref_j=ref_j+step;
1631            end
1632        end
1633    end
1634    if ref_i<0
1635        errormsg='minimum i index reached';
1636    elseif ref_j<0
1637        errormsg='minimum j index reached';
1638    elseif ref_i+1>size(UvData.i1_series{1},1)
1639        errormsg='maximum i index reached';
1640    elseif ref_j+1>size(UvData.i1_series{1},2)
1641        errormsg='maximum j index reached';
1642    end
1643    if ~isempty(errormsg)
1644        return
1645    end
1646    if get(handles.scan_i,'Value')==1% case of scanning along index i
1647        i1_subseries=UvData.i1_series{1}(ref_i+1,ref_j+1,:);
1648    else
1649        i1_subseries=UvData.i1_series{1}(ref_i+1,ref_j+1,:);
1650    end
1651    i1_subseries=i1_subseries(i1_subseries>0);
1652    if isempty(i1_subseries)
1653        errormsg='no next file';
1654        return
1655    end
1656    i1=i1_subseries(end);
1657    if ~isempty(UvData.i2_series{1})
1658        if get(handles.scan_i,'Value')==1% case of scanning along index i
1659            i2_subseries=UvData.i2_series{1}(ref_i+1,ref_j+1,:);
1660        else
1661            i2_subseries=UvData.i2_series{1}(ref_i+1,ref_j+1,:);
1662        end
1663        i2_subseries=i2_subseries(i2_subseries>0);
1664        i2=i2_subseries(end);
1665    end
1666    if ~isempty(UvData.j1_series{1})
1667        if get(handles.scan_i,'Value')==1% case of scanning along index i
1668            j1_subseries=UvData.j1_series{1}(ref_i+1,ref_j+1,:);
1669        else
1670            j1_subseries=UvData.j1_series{1}(ref_i+1,ref_j+1,:);
1671        end
1672        j1_subseries=j1_subseries(j1_subseries>0);
1673        j1=j1_subseries(end);
1674    end
1675    if ~isempty(UvData.j2_series{1})
1676        if get(handles.scan_i,'Value')==1% case of scanning along index i
1677            j2_subseries=UvData.j2_series{1}(ref_i+1,ref_j+1,:);
1678        else
1679            j2_subseries=UvData.j2_series{1}(ref_i+1,ref_j+1,:);
1680        end
1681        j2_subseries=j2_subseries(j2_subseries>0);
1682        j2=j2_subseries(end);
1683    end
1684   
1685end
1686filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1687if sub_value
1688    filename_1=fullfile_uvmat(InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,FileExt_1,NomType_1,i1_1,i2_1,j1_1,j2_1);
1689end
1690
1691%% refresh plots
1692errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);
1693
1694%% update the index counters if the index move is successfull
1695if isempty(errormsg)
1696    set(handles.i1,'String',num2stra(i1,NomType,1));
1697    if isequal(i2,i1)
1698        set(handles.i2,'String','');
1699    else
1700        set(handles.i2,'String',num2stra(i2,NomType,1));
1701    end
1702    set(handles.j1,'String',num2stra(j1,NomType,2));
1703    if isequal(j2,j1)
1704        set(handles.j2,'String','');
1705    else
1706        set(handles.j2,'String',num2stra(j2,NomType,2));
1707    end
1708   % [indices]=name_generator('',i1,j1,'',NomType,1,i2,j2,'');
1709    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1710    set(handles.FileIndex,'String',indices);
1711    if ~isempty(filename_1)
1712        indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,j2_1);
1713        %indices_1=name_generator('',i1_1,j1_1,'',NomType_1,1,i2_1,j2_1,'');
1714        set(handles.FileIndex_1,'String',indices_1);
1715    end
1716    if isequal(movie_status,1)
1717        set(handles.movie_pair,'Value',1)
1718        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1719    end
1720end
1721
1722%------------------------------------------------------------------------
1723% --- Executes on button press in movie_pair: create an alternating movie with two view
1724function movie_pair_Callback(hObject, eventdata, handles)
1725%------------------------------------------------------------------------
1726%% stop movie action if the movie_pair button is off
1727if ~get(handles.movie_pair,'value')
1728    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1729    set(handles.i2,'String','')
1730    set(handles.j2,'String','')
1731    return
1732else
1733    set(handles.movie_pair,'BusyAction','queue')
1734end
1735
1736%% initialisation
1737set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1738drawnow
1739list_fields=get(handles.Fields,'String');% list menu fields
1740index_fields=get(handles.Fields,'Value');% selected string index
1741FieldName=list_fields{index_fields}; % selected field
1742UvData=get(handles.uvmat,'UserData');
1743if isequal(FieldName,'image')
1744    test_1=0;
1745    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1746    NomType=get(handles.NomType,'String');
1747else
1748    list_fields=get(handles.Fields_1,'String');% list menu fields
1749    index_fields=get(handles.Fields_1,'Value');% selected string index
1750    FieldName=list_fields{index_fields}; % selected field
1751    if isequal(FieldName,'image')
1752        test_1=1;
1753        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1754    else
1755        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1756        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1757        set(handles.movie_pair,'Value',0)
1758        return
1759    end
1760end
1761num_i1=str2num(get(handles.i1,'String'));
1762num_j1=stra2num(get(handles.j1,'String'));
1763num_i2=str2num(get(handles.i2,'String'));
1764num_j2=stra2num(get(handles.j2,'String'));
1765if isempty(num_j2)
1766    if isempty(num_i2)   
1767        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1768        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1769         set(handles.movie_pair,'Value',0)
1770        return
1771    else
1772        num_j2=num_j1;%repeat the index i1 by default
1773    end
1774end
1775if isempty(num_i2)
1776    num_i2=num_i1;%repeat the index i1 by default
1777end
1778% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1779imaname_1=fullfile_uvmat(RootPath,'',RootFile,Ext,NomType,num_i2,[],num_j2);
1780if ~exist(imaname_1,'file')
1781      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1782      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1783       set(handles.movie_pair,'Value',0)
1784      return
1785end
1786
1787%% read the second image
1788Field.AName='image';
1789if test_1
1790    Field_a=UvData.Field_1;
1791else
1792    Field_a=UvData.Field;
1793end
1794Field_b.AX=Field_a.AX;
1795Field_b.AY=Field_a.AY;
1796% z index
1797nbslice=str2double(get(handles.nb_slice,'String'));
1798if ~isempty(nbslice)
1799    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1800end
1801Field_b.CoordUnit='pixel';
1802
1803%% determine the input file type
1804if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1805    FileType='movie';
1806elseif isequal(lower(Ext),'.avi')
1807    FileType='avi';
1808elseif isequal(lower(Ext),'.vol')
1809    FileType='vol';
1810else
1811   form=imformats(Ext(2:end));
1812   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1813       if isequal(NomType,'*');
1814           FileType='multimage';
1815       else
1816           FileType='image';
1817       end
1818   end
1819end
1820switch FileType
1821        case 'movie'
1822            if test_1
1823                Field_b.A=read(UvData.MovieObject{2},num_i2);
1824            else
1825                Field_b.A=read(UvData.MovieObject{1},num_i2);
1826            end
1827        case 'avi'
1828            mov=aviread(imaname_1,num_i2);
1829            Field_b.A=frame2im(mov(1));
1830        case 'vol'
1831            Field_b.A=imread(imaname_1);
1832        case 'multimage'
1833            Field_b.A=imread(imaname_1,num_i2);
1834        case 'image'
1835            Field_b.A=imread(imaname_1);
1836end
1837if get(handles.slices,'Value')
1838    Field.ZIndex=str2double(get(handles.z_index,'String'));
1839end
1840
1841%px to phys or other transform on field
1842menu_transform=get(handles.transform_fct,'String');
1843choice_value=get(handles.transform_fct,'Value');
1844transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1845transform_list=get(handles.transform_fct,'UserData');
1846transform=transform_list{choice_value};
1847if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1848    if test_1 && isfield(UvData,'XmlData') && numel(UvData.XmlData)==2 && isfield(UvData.XmlData{2},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1849        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
1850        Field_b=transform(Field_b,UvData.XmlData{2});
1851    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
1852        Field_b=transform(Field_b,UvData.XmlData{1});
1853    end
1854end
1855
1856 % make movie until movie speed is set to 0 or STOP is activated
1857hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1858set(handles.STOP,'Visible','on')
1859set(handles.speed,'Visible','on')
1860set(handles.speed_txt,'Visible','on')
1861while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1862    % read and plot the series of images in non erase mode
1863    set(hima,'CData',Field_b.A);
1864    pause(1.02-get(handles.speed,'Value'));% wait for next image
1865    set(hima,'CData',Field_a.A);
1866    pause(1.02-get(handles.speed,'Value'));% wait for next image
1867end
1868set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1869 set(handles.movie_pair,'Value',0)
1870
1871%------------------------------------------------------------------------
1872% --- Executes on button press in run0.
1873function run0_Callback(hObject, eventdata, handles)
1874%------------------------------------------------------------------------
1875set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1876drawnow
1877[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1878filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1879filename_1=[];%default
1880if get(handles.SubField,'Value')
1881    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
1882    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
1883end
1884num_i1=stra2num(get(handles.i1,'String'));
1885num_i2=stra2num(get(handles.i2,'String'));
1886num_j1=stra2num(get(handles.j1,'String'));
1887num_j2=stra2num(get(handles.j2,'String'));
1888
1889errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
1890
1891if ~isempty(errormsg)
1892      msgbox_uvmat('ERROR',errormsg);
1893else
1894    set(handles.i1,'BackgroundColor',[1 1 1])
1895    set(handles.i2,'BackgroundColor',[1 1 1])
1896    set(handles.j1,'BackgroundColor',[1 1 1])
1897    set(handles.j2,'BackgroundColor',[1 1 1])
1898    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1899    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1900end   
1901set(handles.run0,'BackgroundColor',[1 0 0])
1902
1903
1904%------------------------------------------------------------------------
1905% --- read the input files and refresh all the plots, including projection.
1906% OUTPUT:
1907%  errormsg: error message char string  =[] by default
1908% INPUT:
1909% filename: first input file (=[] in the absence of input file)
1910% filename_1: second input file (=[] in the asbsenc of secodn input file)
1911% num_i1,num_i2,num_j1,num_j2; frame indices
1912% Field: structure describing an optional input field (then replace the input file)
1913
1914function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
1915%------------------------------------------------------------------------
1916
1917%% initialisation
1918abstime=[];
1919abstime_1=[];
1920dt=[];
1921if ~exist('Field','var')
1922    Field={};
1923end
1924UvData=get(handles.uvmat,'UserData');
1925if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1926    delete(handles.UVMAT_title)
1927end
1928
1929%% determine the main input file information for action
1930FileType=[];%default
1931if ~exist(filename,'file')
1932    errormsg=['input file ' filename ' does not exist'];
1933    return
1934end
1935NomType=get(handles.NomType,'String');
1936% NomType=get(handles.FileIndex,'UserData');
1937%update the z position index
1938nbslice_str=get(handles.nb_slice,'String');
1939if isequal(nbslice_str,'volume')%NOT USED
1940    z_index=num_j1;
1941    set(handles.z_index,'String',num2str(z_index))
1942else
1943    nbslice=str2num(nbslice_str);
1944    z_index=mod(num_i1-1,nbslice)+1;
1945    set(handles.z_index,'String',num2str(z_index))
1946end
1947% refresh menu for save_mask if relevant
1948masknumber=get(handles.masklevel,'String');
1949if length(masknumber)>=z_index
1950    set(handles.masklevel,'Value',z_index)
1951end
1952
1953%% read the first input field if a filename has been introduced
1954if ~isempty(filename)
1955    ObjectName=filename;
1956    FieldName=[];%default
1957    VelType=[];%default
1958   % FileExt=get(handles.FileExt,'String');
1959    FileType=UvData.FileType{1};
1960    switch FileType
1961        %     if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
1962        case {'civx','civdata','netcdf'};
1963            list_fields=get(handles.Fields,'String');% list menu fields
1964            index_fields=get(handles.Fields,'Value');% selected string index
1965            FieldName= list_fields{index_fields}; % selected field
1966            if ~strcmp(FieldName,'get_field...')
1967                if get(handles.FixVelType,'Value')
1968                    VelTypeList=get(handles.VelType,'String');
1969                    VelType=VelTypeList{get(handles.VelType,'Value')};
1970%                     VelType=setfield(handles);% read the velocity type.
1971                end
1972            end
1973            if strcmp(FieldName,'velocity')
1974                list_code=get(handles.ListColorCode,'String');% list menu fields
1975                index_code=get(handles.ListColorCode,'Value');% selected string index
1976                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
1977                    list_code=get(handles.ListColorScalar,'String');% list menu fields
1978                    index_code=get(handles.ListColorScalar,'Value');% selected string index
1979                    ParamIn.ColorVar= list_code{index_code}; % selected field
1980                end
1981            end
1982        case 'video'
1983            ObjectName=UvData.MovieObject{1};         
1984        case 'vol' %TODO: update
1985            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
1986                ParamIn.Npy=UvData.XmlData.Npy;
1987                ParamIn.Npx=UvData.XmlData.Npx;
1988            else           
1989                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
1990                return
1991            end
1992    end
1993    ParamIn.FieldName=FieldName;
1994    ParamIn.VelType=VelType;
1995    ParamIn.GUIName='get_field';
1996    [Field{1},ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num_i1);
1997    if ~isempty(errormsg)
1998        errormsg=['error in reading ' filename ': ' errormsg];
1999        return
2000    end 
2001    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2002        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2003        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2004    end
2005    if isfield(ParamOut,'TimeIndex')
2006        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2007    end
2008    if isfield(ParamOut,'TimeValue')
2009        Field{1}.Time=ParamOut.TimeValue;
2010    end
2011end
2012
2013%% choose a second field filename_1 if defined
2014VelType_1=[];%default
2015FieldName_1=[];
2016ParamOut_1=[];
2017if ~isempty(filename_1)
2018    if ~exist(filename_1,'file')
2019        errormsg=['second file ' filename_1 ' does not exist'];
2020        return
2021    end
2022    Name=filename_1;
2023    FileType_1=UvData.FileType{2};
2024    switch FileType_1
2025        %     if strcmp(Ext,'.nc')||strcmp(Ext,'.cdf')
2026        case {'civx','civdata','netcdf'};
2027            list_fields=get(handles.Fields_1,'String');% list menu fields
2028            FieldName_1= list_fields{get(handles.Fields_1,'Value')}; % selected field
2029            if ~strcmp(FieldName,'get_field...')
2030                if get(handles.FixVelType,'Value')
2031                    VelTypeList=get(handles.VelType_1,'String');
2032                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2033%                     VelType_1=setfield(handles);% read the velocity type.
2034                end
2035            end
2036            if strcmp(FieldName_1,'velocity')
2037                list_code=get(handles.ListColorCode,'String');% list menu fields
2038                index_code=get(handles.ListColorCode,'Value');% selected string index
2039                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2040                    list_code=get(handles.ListColorScalar,'String');% list menu fields
2041                    index_code=get(handles.ListColorScalar,'Value');% selected string index
2042                    ParamIn.ColorVar= list_code{index_code}; % selected field
2043                end
2044            end
2045        case 'video'
2046            Name=UvData.MovieObject{2};
2047        case 'vol' %TODO: update
2048            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2049                ParamIn.Npy=UvData.XmlData.Npy;
2050                ParamIn.Npx=UvData.XmlData.Npx;
2051            else
2052                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2053                return
2054            end
2055    end
2056    NomType_1=get(handles.NomType_1,'String');
2057    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2058    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2059        if isfield(UvData,'filename_1')%&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2060            test_keepdata_1= strcmp(filename_1,UvData.filename_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
2061        end
2062    end
2063    if test_keepdata_1
2064        Field{2}=UvData.Field_1;% keep the stored field
2065    else
2066        ParamIn.FieldName=FieldName_1;
2067        ParamIn.VelType=VelType_1;
2068        ParamIn.GUIName='get_field_1';
2069        [Field{2},ParamOut_1,errormsg] = read_field(Name,FileType_1,ParamIn,num_i1);
2070        if ~isempty(errormsg)
2071            errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
2072            return
2073        end
2074        UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2075    end
2076    %     end
2077end
2078
2079%% update uvmat interface
2080if isfield(ParamOut,'Npx')
2081    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2082    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2083elseif isfield(ParamOut_1,'Npx')
2084    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2085    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2086end
2087
2088%% update the display menu for the first velocity type (first menuline)
2089test_veltype=0;
2090% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2091if (strcmp(FileType,'civx')||strcmp(FileType,'civdata'))&& ~strcmp(FieldName,'get_field...')
2092    test_veltype=1;
2093    set(handles.VelType,'Visible','on')
2094    set(handles.VelType_1,'Visible','on')
2095    set(handles.FixVelType,'Visible','on')
2096    menu=set_veltype_display(ParamOut.CivStage,FileType);
2097    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2098    index_val=find(index_menu,1);
2099    if isempty(index_val)
2100        index_val=1;
2101    end
2102    set(handles.VelType,'Value',index_val)
2103    if ~get(handles.SubField,'value')
2104        set(handles.VelType,'String',menu)
2105        set(handles.VelType_1,'Value',1)
2106        set(handles.VelType_1,'String',[{''};menu])
2107    end
2108else
2109    set(handles.VelType,'Visible','off')
2110end
2111field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2112set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2113set(handles.Fields,'Value',find(field_index,1))
2114
2115%% update the display menu for the second velocity type (second menuline)
2116test_veltype_1=0;
2117if isempty(filename_1)
2118    set(handles.Fields_1,'Value',1); %update the field menu
2119    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2120else
2121    if (~strcmp(FileType_1,'netcdf')&&~strcmp(FileType_1,'civdata')&&~strcmp(FileType_1,'civx'))|| isequal(FieldName_1,'get_field...')
2122        set(handles.VelType_1,'Visible','off')
2123    else
2124        test_veltype_1=1;
2125        set(handles.VelType_1,'Visible','on')
2126        if ~get(handles.FixVelType,'Value')
2127            menu=set_veltype_display(ParamOut_1.CivStage);
2128            index_menu=strcmp(ParamOut_1.VelType,menu);
2129            set(handles.VelType_1,'Value',1+find(index_menu,1))
2130            set(handles.VelType_1,'String',[{''};menu])
2131        end
2132    end
2133end
2134if test_veltype||test_veltype_1
2135     set(handles.FixVelType,'Visible','on')
2136else
2137     set(handles.FixVelType,'Visible','off')
2138end
2139   
2140%% introduce w as background image by default for a new series (only for nbdim=2)
2141if ~isfield(UvData,'NewSeries')
2142    UvData.NewSeries=1;
2143end
2144%put W as background image by default if NbDim=2:
2145if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2146        set(handles.SubField,'Value',1);
2147        set(handles.RootPath_1,'String','"')
2148        set(handles.RootFile_1,'String','"')
2149        set(handles.SubDir_1,'String','"');
2150         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2151        set(handles.FileIndex_1,'String',indices)
2152        set(handles.FileExt_1,'String','"');
2153        set(handles.Fields_1,'Visible','on');
2154        set(handles.Fields_1,'Visible','on');
2155        set(handles.RootPath_1,'Visible','on')
2156        set(handles.RootFile_1,'Visible','on')
2157        set(handles.SubDir_1,'Visible','on');
2158        set(handles.FileIndex_1,'Visible','on');
2159        set(handles.FileExt_1,'Visible','on');
2160        set(handles.Fields_1,'Visible','on');
2161        Field{1}.AName='w';
2162end           
2163
2164%% store the current open names, fields and vel types in uvmat interface
2165UvData.filename_1=filename_1;
2166
2167%% apply coordinate transform or other user fct
2168XmlData=[];%default
2169XmlData_1=[];%default
2170if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2171    XmlData=UvData.XmlData{1};
2172    if numel(UvData.XmlData)==2
2173        XmlData_1=UvData.XmlData{2};
2174    end
2175end
2176choice_value=get(handles.transform_fct,'Value');
2177transform_list=get(handles.transform_fct,'UserData');
2178transform=transform_list{choice_value};%selected function handles
2179% z index
2180if ~isempty(filename)
2181    Field{1}.ZIndex=z_index;
2182end
2183%px to phys or other transform on field
2184if ~isempty(transform)
2185    if length(Field)>=2
2186        Field{2}.ZIndex=z_index;
2187        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2188        if isempty(Field{2})
2189            Field(2)=[];
2190        end
2191    else
2192        Field{1}=transform(Field{1},XmlData);
2193    end
2194    %% update tps in phys coordinates if needed
2195    if (strcmp(VelType,'filter1')||strcmp(VelType,'filter2'))&& strcmp(FileType,'civdata')&&isfield(Field{1},'U')&& isfield(Field{1},'V')
2196        Field{1}.X=Field{1}.X(Field{1}.FF==0);
2197        Field{1}.Y=Field{1}.Y(Field{1}.FF==0);
2198        Field{1}.U=Field{1}.U(Field{1}.FF==0);
2199        Field{1}.V=Field{1}.V(Field{1}.FF==0);
2200        [Field{1}.SubRange,Field{1}.NbSites,Field{1}.Coord_tps,Field{1}.U_tps,Field{1}.V_tps]=filter_tps([Field{1}.X Field{1}.Y],Field{1}.U,Field{1}.V,[],Field{1}.Patch1_SubDomain,0);
2201    end
2202    if numel(Field)==2 && ~test_keepdata_1 && isequal(FileType_1(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
2203        %update tps in phys coordinates if needed
2204        if (strcmp(VelType_1,'filter1')||strcmp(VelType_1,'filter2'))&& strcmp(FileType_1,'civdata')&&isfield(Field{2},'U')&& isfield(Field{2},'V')
2205            Field{2}.X=Field{2}.X(Field{2}.FF==0);
2206            Field{2}.Y=Field{1}.Y(Field{2}.FF==0);
2207            Field{2}.U=Field{1}.U(Field{2}.FF==0);
2208            Field{2}.V=Field{1}.V(Field{2}.FF==0);
2209            [Field{2}.SubRange,Field{2}.NbSites,Field{2}.Coord_tps,Field{2}.U_tps,Field{2}.V_tps]=filter_tps([Field{2}.X Field{2}.Y],Field{2}.U,Field{2}.V,[],1500,0);
2210        end
2211    end
2212end
2213
2214%% calculate scalar
2215% if (strcmp(FileType,'civdata')||strcmp(FileType,'civx'))&&~strcmp(ParamOut.FieldName,'velocity')&& ~strcmp(ParamOut.FieldName,'get_field...');% ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
2216%     Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2217% end
2218% if numel(Field)==2 && ~test_keepdata_1 && (strcmp(FileType,'civdata')||strcmp(FileType,'civx'))  &&~strcmp(ParamOut.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2219%      Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2220% end
2221
2222%% combine the two input fields (e.g. substract velocity fields)
2223if numel(Field)==2
2224   UvData.Field=sub_field(Field{1},Field{2}); 
2225else
2226   UvData.Field=Field{1};
2227end
2228UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation
2229
2230%% get bounds and mesh (needed for mouse action and to open set_object)
2231test_x=0;
2232test_z=0;% test for unstructured z coordinate
2233[UvData.Field,errormsg]=check_field_structure(UvData.Field);
2234if ~isempty(errormsg)
2235    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];
2236    return
2237end
2238[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);
2239if ~isempty(errormsg)
2240    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];
2241    return
2242end
2243[NbDim,imax]=max(NbDim);
2244if isfield(UvData.Field,'NbDim')
2245    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2246end
2247if ~isempty(VarType{imax}.coord_x)  && ~isempty(VarType{imax}.coord_y)    %unstructured coordinates
2248    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2249    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2250    eval(['nbvec=length(UvData.Field.' XName ');'])%nbre of measurement points (e.g. vectors)
2251    test_x=1;%test for unstructured coordinates
2252    if ~isempty(VarType{imax}.coord_z)
2253        ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2254    else
2255        NbDim=2;
2256    end
2257elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0 %structured coordinate
2258    XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2259    if NbDim>1
2260        YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2261    end
2262end
2263if NbDim==3
2264    if ~test_x
2265        ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2266    end
2267    eval(['ZMax=max(UvData.Field.' ZName ');'])
2268    eval(['ZMin=min(UvData.Field.' ZName ');'])
2269    UvData.Field.ZMax=ZMax;
2270    UvData.Field.ZMin=ZMin;
2271    test_z=1;
2272    if isequal(ZMin,ZMax)%no z dependency
2273        NbDim=2;
2274        test_z=0;
2275    end
2276end
2277if exist('XName','var')
2278    eval(['XMax=max(max(UvData.Field.' XName '));'])
2279    eval(['XMin=min(min(UvData.Field.' XName '));'])
2280    UvData.Field.NbDim=NbDim;
2281    UvData.Field.XMax=XMax;
2282    UvData.Field.XMin=XMin;
2283    if NbDim >1
2284        eval(['YMax=max(max(UvData.Field.' YName '));'])
2285        eval(['YMin=min(min(UvData.Field.' YName '));'])
2286        UvData.Field.YMax=YMax;
2287        UvData.Field.YMin=YMin;
2288    end
2289    eval(['nbvec=length(UvData.Field.' XName ');'])
2290    if test_x %unstructured coordinates
2291        if test_z
2292            UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2293            UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2294        else
2295            UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2296        end
2297    else
2298        VarIndex=CellVarIndex{imax}; % list of variable indices
2299        DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2300        nbpoints_x=UvData.Field.DimValue(DimIndex(NbDim));
2301        DX=(XMax-XMin)/(nbpoints_x-1);
2302        if NbDim >1
2303            nbpoints_y=UvData.Field.DimValue(DimIndex(NbDim-1));
2304            DY=(YMax-YMin)/(nbpoints_y-1);
2305        end
2306        if NbDim==3
2307            nbpoints_z=UvData.Field.DimValue(DimIndex(1));
2308            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2309            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2310            UvData.Field.ZMax=ZMax;
2311            UvData.Field.ZMin=ZMin;
2312        else
2313            UvData.Field.Mesh=DX;%sqrt(DX*DY);
2314        end
2315    end
2316end
2317
2318%% 3D case (menuvolume)
2319if NbDim==3% && UvData.NewSeries
2320    test_set_object=1;
2321    hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2322    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2323    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2324    if ~isempty(hset_object) %if set_object is detected
2325%         hhset_object=guidata(hset_object);
2326% %         ZBounds_old(1)=get(hhset_object.z_slider,'Min');
2327% %         ZBounds_old(2)=get(hhset_object.z_slider,'Max');
2328% %         if isequal(ZBounds_old,ZBounds)
2329%             test_set_object=0;% do not refresh the GUI set_object
2330%         else
2331            delete(hset_object);% delete the GUI set_object if it does not fit
2332%         end
2333    end
2334    if test_set_object% reinitiate the GUI set_object
2335        delete_object(1);% delete the current projection object in the list UvData.Object, delete its graphic representations and update the list displayed in handles.ListObject and 2
2336        UvData.Object{1}.Type='plane';%main plotting plane
2337        UvData.Object{1}.ProjMode='projection';%main plotting plane
2338        UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2339        UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2340        UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2341        UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2342        UvData.Object{1}.Angle=[0 0 0];
2343%         UvData.Object{1}.Theta=0;
2344%         UvData.Object{1}.Psi=0;
2345        UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2346%         PlotHandles=get_plot_handles(handles);
2347        UvData.Object{1}.Name='1-PLANE';
2348        UvData.Object{1}.enable_plot=1;
2349        set_object(UvData.Object{1},handles,ZBounds);
2350        set(handles.ListObject,'Value',1);
2351        set(handles.ListObject,'String',{'1-PLANE'});
2352        set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2353        edit_object_Callback([],[], handles)
2354    end
2355    %multilevel case (single menuplane in a 3D space)
2356elseif isfield(UvData,'Z')
2357    if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2358        XmlData=UvData.XmlData{1};
2359        if isfield(XmlData,'PlanePos')
2360            UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2361        end
2362        if isfield(XmlData,'PlaneAngle')
2363            siz=size(XmlData.PlaneAngle);
2364            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2365            UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2366        end
2367    elseif isfield(UvData,'ZIndex')
2368        UvData.Object{1}.ZObject=UvData.ZIndex;
2369    end
2370else
2371%     % create a default projection
2372%     UvData.Object{1}.ProjMode='projection';%main plotting plane
2373%     UvData.Object{1}.DisplayHandle_uvmat=[]; %plane not visible in uvmat
2374%     set(handles.ListObject,'Value',1);
2375%     list_object=get(handles.ListObject,'String');
2376%     if isempty(list_object)
2377%         list_object={''};
2378%     elseif ~isempty(list_object{1})
2379%         list_object=[{''};list_object];
2380%     end
2381%     set(handles.ListObject,'String',list_object);
2382% %     set(handles.list_object_2,'String',list_object);
2383end
2384testnewseries=UvData.NewSeries;
2385UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2386set(handles.uvmat,'UserData',UvData)
2387
2388%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2389if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2390    set(handles.num_MinA,'String','0')
2391    set(handles.num_MaxA,'String','255')
2392end
2393
2394%% Plot the projections on the selected  projection objects
2395% main projection object (uvmat display)
2396list_object=get(handles.ListObject,'String');
2397if isequal(list_object,{''})%refresh list of objects if the menu is empty
2398    UvData.Object={[]};
2399    set(handles.ListObject,'Value',1)
2400end
2401IndexObj=get(handles.ListObject,'Value');%selected projection object for main view
2402if IndexObj(1)> numel(UvData.Object)
2403    IndexObj(1)=1;%select the first object if the selected one does not exist
2404    set(handles.ListObject,'Value',1)
2405end
2406plot_handles{1}=handles;
2407if isfield(UvData,'plotaxes')%case of movies
2408    haxes(1)=UvData.plotaxes;
2409else
2410    haxes(1)=handles.axes3;
2411end
2412%PlotParam{1}=read_plot_param(handles);%read plotting parameters on the uvmat interfac
2413PlotParam{1}=read_GUI(handles.uvmat);
2414if ~isfield(PlotParam{1},'Vectors')
2415    PlotParam{1}.Vectors.MaxVec=1;
2416    PlotParam{1}.Vectors.MinVec=0;
2417    PlotParam{1}.Vectors.CheckFixVecColor=1;
2418    PlotParam{1}.Vectors.ColCode1=0.33;
2419    PlotParam{1}.Vectors.ColCode2=0.66;
2420     PlotParam{1}.Vectors.ListColorScalar={'ima_cor'};
2421     PlotParam{1}.Vectors.ListColorCode= {'rgb'};
2422end
2423keeplim(1)=get(handles.CheckFixLimits,'Value');% test for fixed graph limits
2424PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2425
2426% second projection object (view_field display)
2427if length( IndexObj)>=2
2428    view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2429    if ~isempty(view_field_handle)
2430        plot_handles{2}=guidata(view_field_handle);
2431        haxes(2)=plot_handles{2}.axes3;
2432        %PlotParam{2}=read_plot_param(plot_handles{2});%read plotting parameters on the viewinterface
2433        PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2434        keeplim(2)=get(plot_handles{2}.CheckFixLimits,'Value');
2435        PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2436    end
2437end
2438
2439%loop on the projection objects: one or two
2440for imap=1:numel(IndexObj)
2441    iobj=IndexObj(imap);
2442    [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2443
2444    if ~isempty(errormsg)
2445        return
2446    end
2447    %     if testnewseries && isfield(ObjectData,'CoordUnit')&& isfield(PlotParam{imap},'Coordinates')
2448%         PlotParam{imap}.Coordinates=rmfield(PlotParam{imap}.Coordinates,'CheckFixEqual'); %set FixEqual to depend on the field (=1 if Data.CoordUnit=1 in plot_field)
2449%     end
2450    if testnewseries && isfield(ObjectData,'CoordUnit')
2451        PlotParam{imap}.Coordinates.CheckFixEqual=1;
2452    end
2453    %use of mask (TODO: check)
2454    if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2455        flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2456        AX=ObjectData.AX;%x coordiantes for the scalar field
2457        AY=ObjectData.AY;%y coordinates for the scalar field
2458        MaskX=ObjectData.MaskX;%x coordiantes for the mask
2459        MaskY=ObjectData.MaskY;%y coordiantes for the mask
2460        if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2461            nxy=size(flag_mask);
2462            sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2463            sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2464            x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2465            y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2466            %project on the positions of the scalar
2467            npxy=size(ObjectData.A);
2468            dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2469            dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2470            xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2471            yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2472            [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2473            flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2474        end
2475        AClass=class(ObjectData.A);
2476        ObjectData.A=flag_mask.*double(ObjectData.A);
2477        ObjectData.A=feval(AClass,ObjectData.A);
2478        ind_off=[];
2479        if isfield(ObjectData,'ListVarName')
2480            for ilist=1:length(ObjectData.ListVarName)
2481                if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2482                    ind_off=[ind_off ilist];
2483                end
2484            end
2485            ObjectData.ListVarName(ind_off)=[];
2486            ObjectData.VarDimIndex(ind_off)=[];
2487            ind_off=[];
2488            for ilist=1:length(ObjectData.ListDimName)
2489                if isequal(ObjectData.ListDimName{ilist},'MaskX') || isequal(ObjectData.ListDimName{ilist},'MaskY')
2490                    ind_off=[ind_off ilist];
2491                end
2492            end
2493            ObjectData.ListDimName(ind_off)=[];
2494            ObjectData.DimValue(ind_off)=[];
2495        end
2496    end   
2497    if ~isempty(ObjectData)
2498        PlotType='none'; %default
2499        if imap==2 && isempty(view_field_handle)
2500            view_field(ObjectData)
2501        else
2502            [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2503            write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2504            if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2505                ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2506            end
2507        end
2508        if isequal(PlotType,'none')
2509            hget_field=findobj(allchild(0),'name','get_field');
2510            if isempty(hget_field)
2511                get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2512            end
2513            errormsg='The field defined by get_field cannot be plotted';
2514            return
2515        end
2516    end
2517end
2518
2519%% update the mask
2520if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2521   update_mask(handles,num_i1,num_i2);
2522end
2523
2524%% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2525menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2526ind_bad=[];
2527nb_histo=1;
2528
2529% suppress coordinates from the histogram menu
2530for ivar=1:numel(menu_histo)%l loop on field variables:
2531    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2532        Role=UvData.Field.VarAttribute{ivar}.Role;
2533        switch Role
2534            case {'coord_x','coord_y','coord_z','dimvar'}
2535                ind_bad=[ind_bad ivar];
2536            case {'vector_y'}
2537                nb_histo=nb_histo+1;
2538        end
2539    end
2540    DimCell=UvData.Field.VarDimName{ivar};
2541    DimName='';
2542    if ischar(DimCell)
2543        DimName=DimCell;
2544    elseif iscell(DimCell)&& numel(DimCell)==1
2545        DimName=DimCell{1};
2546    end
2547    if strcmp(DimName,menu_histo{ivar})
2548        ind_bad=[ind_bad ivar];
2549    end
2550end
2551menu_histo(ind_bad)=[];
2552
2553%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2554% display menus and plot histograms
2555test_v=0;
2556if ~isempty(menu_histo)
2557    set(handles.histo1_menu,'Value',1)
2558    set(handles.histo1_menu,'String',menu_histo)
2559    histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2560    % case of more than one variables (eg vector components)
2561    if nb_histo > 1
2562        test_v=1;
2563        set(handles.histo2_menu,'Visible','on')
2564        set(handles.histo_v,'Visible','on')
2565        set(handles.histo2_menu,'String',menu_histo)
2566        set(handles.histo2_menu,'Value',2)
2567        histo2_menu_Callback(handles.histo2_menu,[], handles)% plot second histogram
2568    end
2569end
2570if ~test_v
2571    set(handles.histo2_menu,'Visible','off')
2572    set(handles.histo_v,'Visible','off')
2573    cla(handles.histo_v)
2574    set(handles.histo2_menu,'Value',1)
2575end
2576%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2577
2578%% display time
2579testimedoc=0;
2580TimeUnit='';
2581if isfield(UvData.Field,'Time')
2582    abstime=UvData.Field.Time;%time read from the netcdf input file
2583end
2584if isfield(UvData,'Field_1') && isfield(UvData.Field_1,'Time')
2585    abstime_1=UvData.Field_1.Time;%time read from the netcdf input file
2586end
2587if isfield(UvData.Field,'dt')
2588    dt=UvData.Field.dt;%dt read from the netcdf input file
2589    if isfield(UvData.Field,'TimeUnit')
2590       TimeUnit=UvData.Field.TimeUnit;
2591    end
2592elseif isfield(UvData,'Field_1') && isfield(UvData.Field_1,'dt')%dt obtained from the second field if not defined in the first
2593    dt=UvData.Field_1.dt;%dt read from the netcdf input file
2594    if isfield(UvData.Field_1,'TimeUnit')
2595       TimeUnit=UvData.Field_1.TimeUnit;
2596    end
2597end
2598% time from xml file overset previous result
2599if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2600    if isempty(num_i2)||isnan(num_i2)
2601        num_i2=num_i1;
2602    end
2603    if isempty(num_j1)||isnan(num_j1)
2604        num_j1=1;
2605    end
2606    if isempty(num_j2)||isnan(num_j2)
2607        num_j2=num_j1;
2608    end
2609    siz=size(UvData.XmlData{1}.Time);
2610    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2611        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2612        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2613        testimedoc=1;
2614        if isfield(UvData.XmlData{1},'TimeUnit')
2615            TimeUnit=UvData.XmlData{1}.TimeUnit;
2616        end
2617    end
2618    if numel(UvData.XmlData)==2
2619        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2620        %  [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2621        if isempty(num_i2)
2622            num_i2=num_i1;
2623        end
2624        if isempty(num_j1)
2625            num_j1=1;
2626        end
2627        if isempty(num_j2)
2628            num_j2=num_j1;
2629        end
2630        siz=size(UvData.XmlData{2}.Time);
2631        if ~isempty(num_i1) && siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2632            abstime_1=(UvData.XmlData{2}.Time(num_i1,num_j1)+UvData.XmlData{2}.Time(num_i2,num_j2))/2;%overset the time read from files
2633        end
2634    end
2635end
2636
2637if ~isequal(numel(abstime),1)
2638    abstime=[];
2639end
2640if ~isequal(numel(abstime_1),1)
2641      abstime_1=[];
2642end 
2643set(handles.abs_time,'String',num2str(abstime,4))
2644set(handles.abs_time_1,'String',num2str(abstime_1,4))
2645if testimedoc && isfield(UvData,'dt')
2646    dt=UvData.dt;
2647end
2648if isempty(dt)||isequal(dt,0)
2649    set(handles.Dt_txt,'String','')
2650else
2651    if  isempty(TimeUnit)
2652        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2653    else
2654        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2655    end
2656end
2657
2658
2659%-------------------------------------------------------------------
2660% --- translate coordinate to matrix index
2661%-------------------------------------------------------------------
2662function [indx,indy]=pos2ind(x0,rangx0,nxy)
2663indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2664indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2665
2666%-------------------------------------------------------------------
2667% --- Executes on button press in 'CheckFixLimits'.
2668%-------------------------------------------------------------------
2669function CheckFixLimits_Callback(hObject, eventdata, handles)
2670test=get(handles.CheckFixLimits,'Value');
2671if test
2672    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2673else
2674    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2675    update_plot(handles);
2676end
2677
2678%-------------------------------------------------------------------
2679% --- Executes on button press in CheckFixEqual.
2680function CheckFixEqual_Callback(hObject, eventdata, handles)
2681test=get(handles.CheckFixEqual,'Value');
2682if test
2683    set(handles.CheckFixEqual,'BackgroundColor',[1 1 0])
2684    cla(handles.axes3)
2685    update_plot(handles);
2686else
2687    set(handles.CheckFixEqual,'BackgroundColor',[0.7 0.7 0.7])
2688    update_plot(handles);
2689%     axis(handles.axes3,'image')
2690end
2691
2692%-------------------------------------------------------------------
2693
2694%-------------------------------------------------------------------
2695% --- Executes on button press in 'CheckZoom'.
2696%-------------------------------------------------------------------
2697function CheckZoom_Callback(hObject, eventdata, handles)
2698
2699if (get(handles.CheckZoom,'Value') == 1);
2700    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2701    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2702    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2703else
2704    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2705end
2706
2707%-------------------------------------------------------------------
2708%----Executes on button press in 'record': records the current flags of manual correction.
2709%-------------------------------------------------------------------
2710function record_Callback(hObject, eventdata, handles)
2711% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2712[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2713filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2714%filename=read_file_boxes(handles);
2715[erread,message]=fileattrib(filename);
2716if ~isempty(message) && ~isequal(message.UserWrite,1)
2717     msgbox_uvmat('ERROR',['no writting access to ' filename])
2718     return
2719end
2720test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2721test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2722if ~test_civ2 && ~test_civ1
2723    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2724end
2725if test_civ2
2726    nbname='nb_vectors2';
2727   flagname='vec2_FixFlag';
2728   attrname='fix2';
2729end
2730if test_civ1
2731    nbname='nb_vectors';
2732   flagname='vec_FixFlag';
2733   attrname='fix';
2734end
2735%write fix flags in the netcdf file
2736UvData=get(handles.uvmat,'UserData');
2737hhh=which('netcdf.open');% look for built-in matlab netcdf library
2738if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2739    nc=netcdf.open(filename,'NC_WRITE');
2740    netcdf.reDef(nc);
2741    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2742    dimid = netcdf.inqDimID(nc,nbname);
2743    try
2744        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2745    catch
2746        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2747    end
2748    netcdf.endDef(nc);
2749    netcdf.putVar(nc,varid,UvData.axes3.FF);
2750    netcdf.close(nc); 
2751else %old netcdf library
2752    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2753end
2754
2755%-------------------------------------------------------------------
2756%----Correct the netcdf file, using toolbox (old versions of Matlab).
2757%-------------------------------------------------------------------
2758function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2759nc=netcdf(filename,'write'); %open netcdf file
2760result=redef(nc);
2761eval(['nc.' attrname '=1;']);
2762theDim=nc(nbname) ;% get the number of velocity vectors
2763nb_vectors=size(theDim);
2764var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2765var_FixFlag(1:nb_vectors)=AxeData.FF;%
2766fin=close(nc);
2767
2768%---------------------------------------------------
2769% --- Executes on button press in SubField
2770function SubField_Callback(hObject, eventdata, handles)
2771% huvmat=get(handles.run0,'parent');
2772UvData=get(handles.uvmat,'UserData');
2773if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2774    set(handles.RootPath_1,'String','')
2775    set(handles.RootFile_1,'String','')
2776    set(handles.SubDir_1,'String','');
2777    set(handles.FileIndex_1,'String','');
2778    set(handles.FileExt_1,'String','');
2779    set(handles.RootPath_1,'Visible','off')
2780    set(handles.RootFile_1,'Visible','off')
2781    set(handles.SubDir_1,'Visible','off');
2782    set(handles.NomType_1,'Visible','off');
2783    set(handles.abs_time_1,'Visible','off')
2784    set(handles.FileIndex_1,'Visible','off');
2785    set(handles.FileExt_1,'Visible','off');
2786    set(handles.Fields_1,'Value',1);%set to blank state
2787    set(handles.VelType_1,'Value',1);%set to blank state
2788    if ~strcmp(get(handles.VelType,'Visible'),'on')
2789        set(handles.VelType_1,'Visible','off')
2790    end
2791    if isfield(UvData,'XmlData_1')
2792        UvData=rmfield(UvData,'XmlData_1');
2793    end
2794    set(handles.uvmat,'UserData',UvData);
2795    run0_Callback(hObject, eventdata, handles); %run
2796else
2797    MenuBrowse_1_Callback(hObject, eventdata, handles)
2798end
2799
2800%------------------------------------------------------------------------
2801% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
2802
2803function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
2804%------------------------------------------------------------------------
2805InputFile=read_GUI(handles.InputFile);
2806RootPath=InputFile.RootPath;
2807SubDir=regexprep(InputFile.SubDir,'/|\','');
2808RootFile=regexprep(InputFile.RootFile,'/|\','');
2809FileIndices=InputFile.FileIndex;
2810FileExt=InputFile.FileExt;
2811
2812
2813%------------------------------------------------------------------------
2814% ---- read the data displayed for the second input rootfile windows
2815function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
2816%------------------------------------------------------------------------
2817RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
2818if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
2819    RootPath_1=get(handles.RootPath,'String');
2820end;
2821SubDir_1=get(handles.SubDir_1,'String');
2822if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
2823    SubDir_1=get(handles.SubDir,'String');
2824end
2825SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2826RootFile_1=get(handles.RootFile_1,'String');
2827if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
2828    RootFile_1=get(handles.RootFile,'String');
2829end
2830RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2831FileIndex_1=get(handles.FileIndex_1,'String');
2832if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
2833    FileIndex_1=get(handles.FileIndex,'String');
2834end
2835FileExt_1=get(handles.FileExt_1,'String');
2836if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
2837    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
2838end
2839NomType_1=get(handles.NomType_1,'String');
2840if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
2841    NomType_1=get(handles.NomType,'String');%read FileExt by default
2842end
2843%------------------------------------------------------------------------
2844% --- Executes on menu selection Fields
2845function Fields_Callback(hObject, eventdata, handles)
2846%------------------------------------------------------------------------
2847list_fields=get(handles.Fields,'String');% list menu fields
2848index_fields=get(handles.Fields,'Value');% selected string index
2849field= list_fields{index_fields(1)}; % selected string
2850if isequal(field,'get_field...')
2851    set(handles.FixVelType,'visible','off')
2852    set(handles.VelType,'visible','off')
2853    set(handles.VelType_1,'visible','off')
2854    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2855    filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2856    %filename=read_file_boxes(handles);
2857    hget_field=findobj(allchild(0),'name','get_field');
2858    if ~isempty(hget_field)
2859        delete(hget_field)
2860    end
2861    hget_field=get_field(filename);
2862    set(hget_field,'Name','get_field')
2863    hhget_field=guidata(hget_field);
2864    set(hhget_field.list_fig,'Value',1)
2865    set(hhget_field.list_fig,'String',{'uvmat'})
2866    set(handles.transform_fct,'Value',1)% no transform by default
2867    set(handles.path_transform,'String','')
2868    return %no action
2869end
2870list_fields=get(handles.Fields_1,'String');% list menu fields
2871index_fields=get(handles.Fields_1,'Value');% selected string index
2872field_1= list_fields{index_fields(1)}; % selected string
2873UvData=get(handles.uvmat,'UserData');
2874
2875%read the rootfile input display
2876[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2877FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2878[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
2879% NomTypeNew=NomType;%default
2880if isequal(field,'image')
2881%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
2882%         NomTypeNew='_1_1';
2883%     elseif isequal(NomType,'#_ab')
2884%         NomTypeNew='#a';
2885%     elseif isequal(NomType,'_1-2')
2886%         NomTypeNew='_1';
2887%     end
2888    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
2889    if ~exist(imagename,'file')
2890        [FileName,PathName] = uigetfile( ...
2891            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
2892            '*.jpg',' jpeg image files'; ...
2893            '*.png','.png image files'; ...
2894            '*.tif','.tif image files'; ...
2895            '*.avi;*.AVI','.avi movie files'; ...
2896            '*.vol','.volume images (png)'; ...
2897            '*.*',  'All Files (*.*)'}, ...
2898            'Pick an image',imagename);   
2899        imagename=[PathName FileName];
2900    end
2901     % display the selected field and related information
2902    display_file_name(hObject, eventdata, handles,imagename)%display the image
2903    return
2904else
2905    ext=get(handles.FileExt,'String');
2906    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
2907        [FileName,PathName] = uigetfile( ...
2908            {'*.nc', ' (*.nc)';
2909            '*.nc',' netcdf files'; ...
2910            '*.*',  'All Files (*.*)'}, ...
2911            'Pick a netcdf file',FileBase);
2912        filename=[PathName FileName];
2913        % display the selected field and related information
2914        display_file_name(hObject, eventdata, handles,filename)
2915        return
2916    end
2917end
2918indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
2919set(handles.FileIndex,'String',indices)
2920% set(handles.NomType,'String',NomType)
2921
2922%common to Fields_1_Callback
2923if isequal(field,'image')||isequal(field_1,'image')
2924    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
2925    set(handles.TitleNpy,'Visible','on')
2926    set(handles.num_Npx,'Visible','on')
2927    set(handles.num_Npy,'Visible','on')
2928else
2929    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
2930    set(handles.TitleNpy,'Visible','off')
2931    set(handles.num_Npx,'Visible','off')
2932    set(handles.num_Npy,'Visible','off')
2933end
2934if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
2935    run0_Callback(hObject, eventdata, handles)
2936end
2937
2938%---------------------------------------------------
2939% --- Executes on menu selection Fields
2940function Fields_1_Callback(hObject, eventdata, handles)
2941%-------------------------------------------------
2942%% read input data
2943check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
2944UvData=get(handles.uvmat,'UserData');
2945if check_new && isfield(UvData,'XmlData')
2946    UvData.XmlData{2}=UvData.XmlData{1};
2947end
2948if isfield(UvData,'Field_1')
2949    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
2950end
2951list_fields=get(handles.Fields,'String');% list menu fields
2952index_fields=get(handles.Fields,'Value');% selected string index
2953field= list_fields{index_fields(1)}; % selected string
2954list_fields=get(handles.Fields_1,'String');% list menu fields
2955index_fields=get(handles.Fields_1,'Value');% selected string index
2956field_1= list_fields{index_fields(1)}; % selected string for the second field
2957if isequal(field_1,'')||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
2958    set(handles.SubField,'Value',0)
2959    check_new=1;
2960    SubField_Callback(hObject, eventdata, handles)
2961    if isempty(field_1)%remove second field if 'blank' field is selected
2962        return
2963    end
2964end
2965set(handles.SubField,'Value',1)%state that a second field is now entered
2966
2967%% read the rootfile input display
2968[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomTYpe_1]=read_file_boxes_1(handles);
2969filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
2970[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
2971set(handles.FileIndex_1,'Visible','on')
2972set(handles.FileExt_1,'Visible','on')
2973switch field_1
2974    case 'get_field...'
2975        set_veltype_display(0) % no veltype display
2976        hget_field=findobj(allchild(0),'name','get_field_1');
2977        if ~isempty(hget_field)
2978            delete(hget_field)
2979        end
2980        hget_field=get_field(filename_1);
2981        set(hget_field,'name','get_field_1')
2982        hhget_field=guidata(hget_field);
2983        set(hhget_field.list_fig,'Value',1)
2984        set(hhget_field.list_fig,'String',{'uvmat'})
2985        set(handles.transform_fct,'Value',1)% no transform by default
2986        set(handles.path_transform,'String','')
2987    case 'image'
2988        % transform netc type to the corresponding image type
2989        NomType=get(handles.NomType,'string');
2990        check_letter=~isempty(regexp(NomType,'[ab|AB]$'));%detect pair label by letter
2991%         NomType_1=NomType;
2992%         if check_letter
2993%             NomType_1=NomType_1(1:end-1);
2994%         else
2995%             r=regexp(NomType_1,'.-(?<num2>\d+$','names');
2996%             if ~isempty(r)
2997%                 NomType_1=regexprep(NomType_1,['-' r.num2],'');
2998%             end
2999%         end
3000        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',NomType,i1,[],j1);
3001        if ~exist(imagename,'file')
3002            [FileName,PathName] = uigetfile( ...
3003                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3004                '*.jpg',' jpeg image files'; ...
3005                '*.png','.png image files'; ...
3006                '*.tif','.tif image files'; ...
3007                '*.avi;*.AVI','.avi movie files'; ...
3008                '*.vol','.volume images (png)'; ...
3009                '*.*',  'All Files (*.*)'}, ...
3010                'Pick an image',imagename);
3011            % display the selected field and related information
3012            imagename=[PathName FileName];
3013        end
3014        set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3015        set(handles.TitleNpy,'Visible','on')
3016        set(handles.num_Npx,'Visible','on')
3017        set(handles.num_Npy,'Visible','on')
3018        display_file_name(hObject, eventdata, handles,imagename,2)%display the imag
3019    otherwise
3020        if check_new
3021            UvData.FileType{2}=UvData.FileType{1};
3022            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3023            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3024        end
3025        if ~isequal(field,'image')
3026            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3027            set(handles.TitleNpy,'Visible','off')
3028            set(handles.num_Npx,'Visible','off')
3029            set(handles.num_Npy,'Visible','off')
3030        end
3031        set(handles.uvmat,'UserData',UvData)
3032%         setfield(handles);% update the field structure ('civ1'....)
3033        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3034            run0_Callback(hObject, eventdata, handles)
3035        end
3036end
3037
3038%------------------------------------------------------------------------
3039% --- set the visibility of relevant velocity type menus:
3040function menu=set_veltype_display(Civ,FileType)
3041%------------------------------------------------------------------------
3042if ~exist('FileType','var')
3043    FileType='civx';
3044end
3045switch FileType
3046    case 'civx'
3047        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3048        if isequal(Civ,0)
3049            imax=0;
3050        elseif isequal(Civ,1) || isequal(Civ,2)
3051            imax=1;
3052        elseif isequal(Civ,3)
3053            imax=3;
3054        elseif isequal(Civ,4) || isequal(Civ,5)
3055            imax=4;
3056        elseif isequal(Civ,6) %patch2
3057            imax=6;
3058        end
3059    case 'civdata'
3060        menu={'civ1';'filter1';'civ2';'filter2'};
3061        if isequal(Civ,0)
3062            imax=0;
3063        elseif isequal(Civ,1) || isequal(Civ,2)
3064            imax=1;
3065        elseif isequal(Civ,3)
3066            imax=2;
3067        elseif isequal(Civ,4) || isequal(Civ,5)
3068            imax=3;
3069        elseif isequal(Civ,6) %patch2
3070            imax=4;
3071        end
3072end
3073
3074
3075
3076menu=menu(1:imax);
3077
3078%------------------------------------------------------------------------
3079% --- Executes on button press in VelType.
3080function VelType_Callback(hObject, eventdata, handles)
3081%------------------------------------------------------------------------
3082set(handles.FixVelType,'Value',1)
3083run0_Callback(hObject, eventdata, handles)
3084
3085%------------------------------------------------------------------------
3086% --- Executes on button press in VelType.
3087function VelType_1_Callback(hObject, eventdata, handles)
3088%------------------------------------------------------------------------
3089 
3090set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3091UvData=get(handles.uvmat,'UserData');
3092%refresh field with a second filename=first fiel name
3093set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3094drawnow   
3095InputFile=read_GUI(handles.InputFile);
3096[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3097filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3098% VelTypeList=get(handles.VelType_1,'String');
3099% VelType_1=VelTypeList{get(handles.VelType_1,'Value')};
3100if isempty(InputFile.VelType_1)
3101        filename_1='';% we plot the current field without the second field
3102        set(handles.SubField,'Value',0)
3103        SubField_Callback(hObject, eventdata, handles)
3104elseif get(handles.SubField,'Value')% if subfield is already 'on'
3105      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3106     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3107%       UvData.VelType{2}=InputFile.VelType_1;
3108else
3109     filename_1=filename;% we compare two fields in the same file
3110     UvData.FileType{2}=UvData.FileType{1};
3111%      UvData.VelType{2}=InputFile.VelType_1;
3112     set(handles.SubField,'Value',1)
3113end
3114if isfield(UvData,'Field_1')
3115    UvData=rmfield(UvData,'Field_1');% removes the stored second field if it exists
3116end
3117set(handles.uvmat,'UserData',UvData)
3118num_i1=stra2num(get(handles.i1,'String'));
3119num_i2=stra2num(get(handles.i2,'String'));
3120num_j1=stra2num(get(handles.j1,'String'));
3121num_j2=stra2num(get(handles.j2,'String'));
3122
3123errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
3124
3125if ~isempty(errormsg)
3126    msgbox_uvmat('ERROR',errormsg);
3127else
3128    set(handles.i1,'BackgroundColor',[1 1 1])
3129    set(handles.i2,'BackgroundColor',[1 1 1])
3130    set(handles.j1,'BackgroundColor',[1 1 1])
3131    set(handles.j2,'BackgroundColor',[1 1 1])
3132    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3133    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3134end
3135set(handles.run0,'BackgroundColor',[1 0 0])
3136
3137%-----------------------------------------------
3138% --- reset civ buttons
3139function reset_vel_type(handles_civ0,handle1)
3140for ibutton=1:length(handles_civ0)
3141    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3142    set(handles_civ0(ibutton),'Value',0)
3143end
3144if exist('handle1','var')%handles of selected button
3145        set(handle1,'BackgroundColor',[1 1 0]) 
3146end
3147
3148%-------------------------------------------------------
3149% --- Executes on button press in MENUVOLUME.
3150%-------------------------------------------------------
3151function VOLUME_Callback(hObject, eventdata, handles)
3152%errordlg('command VOL not implemented yet')
3153if ishandle(handles.UVMAT_title)
3154    delete(handles.UVMAT_title)
3155end
3156UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3157if isequal(get(handles.VOLUME,'Value'),1)
3158    set(handles.CheckZoom,'Value',0)
3159    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3160    set(handles.edit_vect,'Value',0)
3161    edit_vect_Callback(hObject, eventdata, handles)
3162    set(handles.edit_object,'Value',0)
3163    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3164%     set(handles.cal,'Value',0)
3165%     set(handles.cal,'BackgroundColor',[0 1 0])
3166    set(handles.edit_vect,'Value',0)
3167    edit_vect_Callback(hObject, eventdata, handles)
3168    %initiate set_object GUI
3169    data.Name='VOLUME';
3170    if isfield(UvData,'CoordType')
3171        data.CoordType=UvData.CoordType;
3172    end
3173    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3174        data.RangeY=UvData.Mesh;
3175        data.RangeX=UvData.Mesh;
3176        data.DX=UvData.Mesh;
3177        data.DY=UvData.Mesh;
3178    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3179        np=size(UvData.Field.A);
3180        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3181        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3182        data.RangeY=max(meshx,meshy);
3183        data.RangeX=max(meshx,meshy);
3184        data.DX=max(meshx,meshy);
3185    end
3186    data.ParentButton=handles.VOLUME;
3187    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3188    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3189                                                      % associate the set_object interface handle to the plotting axes
3190    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3191    pos_uvmat=get(handles.uvmat,'Position');
3192    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3193    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3194    set(hset_object,'Position',pos_set_object)
3195    end
3196    UvData.MouseAction='create_object';
3197else
3198    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3199    UvData.MouseAction='none';
3200end
3201set(handles.uvmat,'UserData',UvData)
3202
3203%-------------------------------------------------------
3204function edit_vect_Callback(hObject, eventdata, handles)
3205%-------------------------------------------------------
3206%
3207% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3208if isequal(get(handles.edit_vect,'Value'),1)
3209    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3210    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3211    if ~test_civ2 && ~test_civ1
3212        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3213    end
3214    set(handles.record,'Visible','on')
3215    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3216    set(handles.edit_object,'Value',0)
3217    set(handles.CheckZoom,'Value',0)
3218    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3219%     set(handles.create,'Value',0)
3220%     set(handles.create,'BackgroundColor',[0 1 0])
3221    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3222    set(gcf,'Pointer','arrow')
3223%     UvData.MouseAction='edit_vect';
3224else
3225    set(handles.record,'Visible','off')
3226    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3227%     UvData.MouseAction='none';
3228end
3229% set(handles.uvmat,'UserData',UvData)
3230
3231%----------------------------------------------
3232function save_mask_Callback(hObject, eventdata, handles)
3233%-----------------------------------------------------------------------
3234UvData=get(handles.uvmat,'UserData');
3235
3236flag=1;
3237npx=size(UvData.Field.A,2);
3238npy=size(UvData.Field.A,1);
3239xi=0.5:npx-0.5;
3240yi=0.5:npy-0.5;
3241[Xi,Yi]=meshgrid(xi,yi);
3242if isfield(UvData,'Object')
3243    for iobj=1:length(UvData.Object)
3244        ObjectData=UvData.Object{iobj};
3245        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3246            flagobj=1;
3247            testphys=0; %coordinates in pixels by default
3248            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3249                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3250                    Calib=UvData.XmlData{1}.GeometryCalib;
3251                    testphys=1;
3252                end
3253            end
3254            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3255                if isequal(ObjectData.Type,'polygon')
3256                    X=ObjectData.Coord(:,1);
3257                    Y=ObjectData.Coord(:,2);
3258                    if testphys
3259                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3260                    end
3261                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3262                elseif isequal(ObjectData.Type,'ellipse')
3263                    if testphys
3264                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3265                    end
3266                    RangeX=max(ObjectData.RangeX);
3267                    RangeY=max(ObjectData.RangeY);
3268                    X2Max=RangeX*RangeX;
3269                    Y2Max=RangeY*RangeY;
3270                    distX=(Xi-ObjectData.Coord(1,1));
3271                    distY=(Yi-ObjectData.Coord(1,2));
3272                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3273                elseif isequal(ObjectData.Type,'rectangle')
3274                    if testphys
3275                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3276                    end
3277                    distX=abs(Xi-ObjectData.Coord(1,1));
3278                    distY=abs(Yi-ObjectData.Coord(1,2));
3279                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3280                end
3281                if isequal(ObjectData.ProjMode,'mask_outside')
3282                    flagobj=~flagobj;
3283                end
3284                flag=flag & flagobj;
3285            end
3286        end
3287    end
3288end
3289% flag=~flag;
3290%mask name
3291RootPath=get(handles.RootPath,'String');
3292RootFile=get(handles.RootFile,'String');
3293RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3294filebase=fullfile(RootPath,RootFile);
3295list=get(handles.masklevel,'String');
3296masknumber=num2str(length(list));
3297maskindex=get(handles.masklevel,'Value');
3298mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3299%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3300imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3301imflag=flipdim(imflag,1);
3302% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3303msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3304imwrite(imflag,mask_name,'BitDepth',8);
3305
3306%display the mask
3307figure;
3308vec=linspace(0,1,256);%define a linear greyscale colormap
3309map=[vec' vec' vec'];
3310colormap(map)
3311
3312image(imflag);
3313
3314%-------------------------------------------------------------------
3315%-------------------------------------------------------------------
3316%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3317
3318%------------------------------------------------------------------
3319
3320%------------------------------------------------------------------
3321% --- Executes on selection change in ListColorScalar: choice of the color code.
3322function ListColorScalar_Callback(hObject, eventdata, handles)
3323%------------------------------------------------------------------
3324% edit the choice for color code
3325list_code=get(handles.ListColorScalar,'String');% list menu fields
3326index_code=get(handles.ListColorScalar,'Value');% selected string index
3327col_code= list_code{index_code(1)}; % selected field
3328if isequal(col_code,'black') || isequal(col_code,'white')
3329   set(handles.Slider1,'Visible','off')
3330   set(handles.Slider2,'Visible','off')
3331   set(handles.num_ColCode1,'Visible','off')
3332   set(handles.num_ColCode2,'Visible','off')
3333   set(handles.CheckFixVecColor,'Visible','off')
3334   set_vec_col_bar(handles)
3335else
3336   set(handles.Slider1,'Visible','on')
3337   set(handles.Slider2,'Visible','on')
3338   set(handles.num_ColCode1,'Visible','on')
3339   set(handles.num_ColCode2,'Visible','on')
3340   set(handles.CheckFixVecColor,'Visible','on') 
3341   if isequal(col_code,'ima_cor')
3342       set(handles.CheckFixVecColor,'Value',0)%fixed scale by default
3343       set(handles.VecColBar,'Value',0)% 3 colors r,g,b by default
3344       set(handles.Slider1,'Min',0);
3345       set(handles.Slider1,'Max',1);
3346       set(handles.Slider2,'Min',0);
3347       set(handles.Slider2,'Max',1);
3348 %      set(handles.min_title_vec,'String','0')
3349       set(handles.num_MaxVec,'String','1')
3350       set(handles.num_ColCode1,'String','0.333')
3351       num_ColCode1_Callback(hObject, eventdata, handles)
3352       set(handles.num_ColCode2,'String','0.666')
3353       num_ColCode2_Callback(hObject, eventdata, handles)
3354   else
3355       set(handles.CheckFixVecColor,'Value',1)%auto scale between min,max by default
3356       set(handles.VecColBar,'Value',1)% colormap 'jet' by default
3357       minval=get(handles.Slider1,'Min');
3358       maxval=get(handles.Slider1,'Max');
3359       set(handles.Slider1,'Value',minval)
3360       set(handles.Slider2,'Value',maxval)
3361       set_vec_col_bar(handles)
3362   end
3363%    slider_update(handles)
3364end
3365%replot the current graph
3366run0_Callback(hObject, eventdata, handles)
3367
3368
3369%----------------------------------------------------------------
3370% -- Executes on slider movement to set the color code
3371%
3372function Slider1_Callback(hObject, eventdata, handles)
3373%------------------------------------------------------------------
3374slider1=get(handles.Slider1,'Value');
3375min_val=str2num(get(handles.num_MinVec,'String'));
3376max_val=str2num(get(handles.num_MaxVec,'String'));
3377col=min_val+(max_val-min_val)*slider1;
3378set(handles.num_ColCode1,'String',num2str(col))
3379if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3380    set(handles.Slider2,'Value',col)
3381    set(handles.num_ColCode2,'String',num2str(col))
3382end
3383num_ColCode1_Callback(hObject, eventdata, handles)
3384
3385%----------------------------------------------------------------
3386% Executes on slider movement to set the color code
3387%----------------------------------------------------------------
3388function Slider2_Callback(hObject, eventdata, handles)
3389slider2=get(handles.Slider2,'Value');
3390min_val=str2num(get(handles.num_MinVec,'String'));
3391max_val=str2num(get(handles.num_MaxVec,'String'));
3392col=min_val+(max_val-min_val)*slider2;
3393set(handles.num_ColCode2,'String',num2str(col))
3394if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3395    set(handles.Slider1,'Value',col)
3396    set(handles.num_ColCode1,'String',num2str(col))
3397end
3398num_ColCode2_Callback(hObject, eventdata, handles)
3399
3400%----------------------------------------------------------------
3401% --- Execute on return carriage on the edit box corresponding to slider 1
3402%----------------------------------------------------------------
3403function num_ColCode1_Callback(hObject, eventdata, handles)
3404set_vec_col_bar(handles)
3405update_plot(handles);
3406
3407%----------------------------------------------------------------
3408% --- Execute on return carriage on the edit box corresponding to slider 2
3409%----------------------------------------------------------------
3410function num_ColCode2_Callback(hObject, eventdata, handles)
3411set_vec_col_bar(handles)
3412update_plot(handles);
3413%------------------------------------------------------------------------
3414%-------------------------------------------------------
3415% --- Executes on button press in CheckFixVecColor.
3416%-------------------------------------------------------
3417function VecColBar_Callback(hObject, eventdata, handles)
3418set_vec_col_bar(handles)
3419
3420%-------------------------------------------------------------
3421% --- Executes on selection change in transform_fct.
3422function transform_fct_Callback(hObject, eventdata, handles)
3423%-------------------------------------------------------------
3424UvData=get(handles.uvmat,'UserData');
3425menu=get(handles.transform_fct,'String');
3426ind_coord=get(handles.transform_fct,'Value');
3427coord_option=menu{ind_coord};
3428list_transform=get(handles.transform_fct,'UserData');
3429ff=functions(list_transform{end}); 
3430if isequal(coord_option,'more...');
3431    coord_fct='';
3432    prompt = {'Enter the name of the transform function'};
3433    dlg_title = 'user defined transform';
3434    num_lines= 1;
3435    [FileName, PathName] = uigetfile( ...
3436       {'*.m', ' (*.m)';
3437        '*.m',  '.m files '; ...
3438        '*.*', 'All Files (*.*)'}, ...
3439        'Pick a file', ff.file);
3440    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3441        PathName(end)=[];
3442    end
3443    transform_selected =fullfile(PathName,FileName);
3444    if ~exist(transform_selected,'file')
3445           return
3446    end
3447   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3448   if ~isequal(ext_fct,'.m')
3449        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3450        return
3451   end
3452   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3453   ind_coord=get(handles.transform_fct,'Value');
3454   addpath(PathName)
3455   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3456   set(handles.transform_fct,'UserData',list_transform)
3457   rmpath(PathName)
3458   % save the new menu in the personal file 'uvmat_perso.mat'
3459   dir_perso=prefdir;%personal Matalb directory
3460   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3461   if exist(profil_perso,'file')
3462       nb_builtin=UvData.OpenParam.NbBuiltin;
3463       for ilist=nb_builtin+1:numel(list_transform)
3464           ff=functions(list_transform{ilist});
3465           transform_fct{ilist-nb_builtin}=ff.file;
3466       end
3467        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3468   end   
3469end
3470
3471%check the current path to the selected function
3472if isa(list_transform{ind_coord},'function_handle')
3473    func=functions(list_transform{ind_coord});
3474    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3475else
3476    set(handles.path_transform,'String','')
3477end
3478
3479set(handles.CheckFixLimits,'Value',0)
3480set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3481
3482%delete drawn objects
3483hother=findobj('Tag','proj_object');%find all the proj objects
3484for iobj=1:length(hother)
3485    delete_object(hother(iobj))
3486end
3487hother=findobj('Tag','DeformPoint');%find all the proj objects
3488for iobj=1:length(hother)
3489    delete_object(hother(iobj))
3490end
3491hh=findobj('Tag','calib_points');
3492if ~isempty(hh)
3493    delete(hh)
3494end
3495hhh=findobj('Tag','calib_marker');
3496if ~isempty(hhh)
3497    delete(hhh)
3498end
3499if isfield(UvData,'Object')
3500     UvData.Object=UvData.Object(1);
3501end
3502set(handles.ListObject,'Value',1)
3503set(handles.ListObject,'String',{''})
3504
3505%delete mask if it is displayed
3506if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3507   UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3508end
3509set(handles.uvmat,'UserData',UvData)
3510run0_Callback(hObject, eventdata, handles)
3511
3512%------------------------------------------------------------------------
3513function histo1_menu_Callback(hObject, eventdata, handles)
3514%--------------------------------------------
3515%plot first histo
3516%huvmat=get(handles.histo1_menu,'parent');
3517histo_menu=get(handles.histo1_menu,'String');
3518histo_value=get(handles.histo1_menu,'Value');
3519FieldName=histo_menu{histo_value};
3520update_histo(handles.histo_u,handles.uvmat,FieldName)
3521
3522%------------------------------------------------------------------------
3523function histo2_menu_Callback(hObject, eventdata, handles)
3524%------------------------------------------------------------------------
3525%plot second histo
3526%huvmat=get(handles.histo2_menu,'parent');
3527histo_menu=get(handles.histo2_menu,'String');
3528histo_value=get(handles.histo2_menu,'Value');
3529FieldName=histo_menu{histo_value};
3530update_histo(handles.histo_v,handles.uvmat,FieldName)
3531
3532%------------------------------------------------------------------------
3533%read the field .Fieldname stored in UvData and plot its histogram
3534function update_histo(haxes,huvmat,FieldName)
3535%------------------------------------------------------------------------
3536UvData=get(huvmat,'UserData');
3537if ~isfield(UvData.Field,FieldName)
3538    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
3539    return
3540end
3541Field=UvData.Field;
3542FieldHisto=eval(['Field.' FieldName]);
3543if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
3544    indsel=find(Field.FF==0);%find values marked as false
3545    if ~isempty(indsel)
3546        FieldHisto=FieldHisto(indsel);
3547    end
3548end
3549if isempty(Field)
3550    msgbox_uvmat('ERROR',['empty field ' FieldName])
3551else
3552    nxy=size(FieldHisto);
3553    Amin=double(min(min(min(FieldHisto))));%min of image
3554    Amax=double(max(max(max(FieldHisto))));%max of image
3555    if isequal(Amin,Amax)
3556        %msgbox_uvmat('WARNING',['uniform field =' num2str(Amin)]);
3557        cla(haxes)
3558    else
3559        Histo.ListVarName={FieldName,'histo'};
3560        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
3561            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3562        else
3563            if numel(nxy)==2
3564                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
3565            else
3566                Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
3567            end
3568        end
3569        %unit
3570        units=[]; %default
3571        for ivar=1:numel(Field.ListVarName)
3572            if strcmp(Field.ListVarName{ivar},FieldName)
3573                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
3574                    units=Field.VarAttribute{ivar}.units;
3575                    break
3576                end
3577            end
3578        end
3579        if ~isempty(units)
3580            Histo.VarAttribute{1}.units=units;
3581        end
3582        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
3583        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
3584            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
3585            eval(['Histo.histo(:,1)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3586        else
3587            for col=1:size(FieldHisto,3)
3588                B=FieldHisto(:,:,col);
3589                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
3590                eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
3591            end
3592        end
3593        plot_field(Histo,haxes);
3594    end
3595end
3596
3597%------------------------------------------------
3598%CALLBACKS FOR PLOTTING PARAMETERS
3599%-------------------------------------------------
3600
3601%------------------------------------------------------------------------
3602function num_MinX_Callback(hObject, eventdata, handles)
3603%------------------------------------------------------------------------
3604set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3605set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3606update_plot(handles);
3607
3608%------------------------------------------------------------------------
3609function num_MaxX_Callback(hObject, eventdata, handles)
3610%------------------------------------------------------------------------
3611set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3612set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3613update_plot(handles);
3614
3615%------------------------------------------------------------------------
3616function num_MinY_Callback(hObject, eventdata, handles)
3617%------------------------------------------
3618set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3619set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3620update_plot(handles);
3621
3622%------------------------------------------------------------------------
3623function num_MaxY_Callback(hObject, eventdata, handles)
3624%------------------------------------------------------------------------
3625set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3626set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3627update_plot(handles);
3628
3629%------------------------------------------------------------------------
3630function num_MinA_Callback(hObject, eventdata, handles)
3631%------------------------------------------
3632set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3633set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3634MinA=str2double(get(handles.num_MinA,'String'));
3635MaxA=str2double(get(handles.num_MaxA,'String'));
3636if MinA>MaxA% switch minA and maxA in case of error
3637    MinA_old=MinA;
3638    MinA=MaxA;
3639    MaxA=MinA_old;
3640    set(handles.num_MinA,'String',num2str(MinA,5));
3641    set(handles.num_MaxA,'String',num2str(MaxA,5));
3642end
3643update_plot(handles);
3644
3645%------------------------------------------------------------------------
3646function num_MaxA_Callback(hObject, eventdata, handles)
3647%------------------------------------------------------------------------
3648set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3649set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3650MinA=str2double(get(handles.num_MinA,'String'));
3651MaxA=str2double(get(handles.num_MaxA,'String'));
3652if MinA>MaxA% switch minA and maxA in case of error
3653        MinA_old=MinA;
3654    MinA=MaxA;
3655    MaxA=MinA_old;
3656    set(handles.num_MinA,'String',num2str(MinA,5));
3657    set(handles.num_MaxA,'String',num2str(MaxA,5));
3658end
3659update_plot(handles);
3660
3661%------------------------------------------------------------------------
3662function CheckFixScalar_Callback(hObject, eventdata, handles)
3663%------------------------------------------------------------------------
3664test=get(handles.CheckFixScalar,'Value');
3665if test
3666    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3667else
3668    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3669    update_plot(handles);
3670end
3671
3672%-------------------------------------------------------------------
3673function CheckBW_Callback(hObject, eventdata, handles)
3674%-------------------------------------------------------------------
3675update_plot(handles);
3676
3677%-------------------------------------------------------------------
3678function ListContour_Callback(hObject, eventdata, handles)
3679%-------------------------------------------------------------------
3680val=get(handles.ListContour,'Value');
3681if val==2
3682    set(handles.interval_txt,'Visible','on')
3683    set(handles.num_IncrA,'Visible','on')
3684else
3685    set(handles.interval_txt,'Visible','off')
3686    set(handles.num_IncrA,'Visible','off')
3687end
3688update_plot(handles);
3689
3690%-------------------------------------------------------------------
3691function num_IncrA_Callback(hObject, eventdata, handles)
3692%-------------------------------------------------------------------
3693update_plot(handles);
3694
3695%-------------------------------------------------------------------
3696function CheckHideWarning_Callback(hObject, eventdata, handles)
3697%-------------------------------------------------------------------
3698update_plot(handles);
3699
3700%-------------------------------------------------------------------
3701function CheckHideFalse_Callback(hObject, eventdata, handles)
3702%-------------------------------------------------------------------
3703update_plot(handles);
3704
3705%-------------------------------------------------------------------
3706function num_VecScale_Callback(hObject, eventdata, handles)
3707%-------------------------------------------------------------------
3708set(handles.CheckFixVectors,'Value',1);
3709set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3710update_plot(handles);
3711
3712%-------------------------------------------------------------------
3713function CheckFixVectors_Callback(hObject, eventdata, handles)
3714%-------------------------------------------------------------------
3715test=get(handles.CheckFixVectors,'Value');
3716if test
3717    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3718else
3719    update_plot(handles);
3720    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3721    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3722end
3723
3724%------------------------------------------------------------------------
3725% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3726function CheckDecimate4_Callback(hObject, eventdata, handles)
3727%------------------------------------------------------------------------
3728update_plot(handles);
3729
3730%------------------------------------------------------------------------
3731% --- Executes on selection change in ListColorCode menu
3732function ListColorCode_Callback(hObject, eventdata, handles)
3733%------------------------------------------------------------------------
3734set_vec_col_bar(handles)
3735update_plot(handles);
3736
3737%------------------------------------------------------------------------
3738% --- Executes on button press in CheckFixVecColor.
3739function CheckFixVecColor_Callback(hObject, eventdata, handles)
3740%------------------------------------------------------------------------
3741test=get(handles.CheckFixVecColor,'Value');
3742if test
3743    set(handles.CheckFixVecColor,'BackgroundColor',[1 1 0])
3744else
3745    update_plot(handles);
3746    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3747    set(handles.CheckFixVecColor,'BackgroundColor',[0.7 0.7 0.7])
3748end
3749
3750%------------------------------------------------------------------------
3751% --- Executes on selection change in num_MaxVec.
3752function num_MinVec_Callback(hObject, eventdata, handles)
3753%------------------------------------------------------------------------
3754max_vec_Callback(hObject, eventdata, handles)
3755
3756%------------------------------------------------------------------------
3757% --- Executes on selection change in num_MaxVec.
3758function num_MaxVec_Callback(hObject, eventdata, handles)
3759%------------------------------------------------------------------------
3760set(handles.CheckFixVecColor,'Value',1)
3761CheckFixVecColor_Callback(hObject, eventdata, handles)
3762min_val=str2num(get(handles.num_MinVec,'String'));
3763max_val=str2num(get(handles.num_MaxVec,'String'));
3764slider1=get(handles.Slider1,'Value');
3765slider2=get(handles.Slider2,'Value');
3766colcode1=min_val+(max_val-min_val)*slider1;
3767colcode2=min_val+(max_val-min_val)*slider2;
3768set(handles.num_ColCode1,'String',num2str(colcode1))
3769set(handles.num_ColCode2,'String',num2str(colcode2))
3770update_plot(handles);
3771
3772%------------------------------------------------------------------------
3773% --- update the display of color code for vectors
3774function set_vec_col_bar(handles)
3775%------------------------------------------------------------------------
3776%get the image of the color display button 'VecColBar' in pixels
3777set(handles.VecColBar,'Unit','pixel');
3778pos_vert=get(handles.VecColBar,'Position');
3779set(handles.VecColBar,'Unit','Normalized');
3780width=ceil(pos_vert(3));
3781height=ceil(pos_vert(4));
3782
3783%get slider indications
3784list=get(handles.ListColorCode,'String');
3785ichoice=get(handles.ListColorCode,'Value');
3786colcode.ListColorCode=list{ichoice};
3787colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3788colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3789test3color=strcmp(colcode.ListColorCode,'rgb') || strcmp(colcode.ListColorCode,'bgr');
3790if test3color
3791    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3792    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3793end
3794% colcode.FixedCbounds=0;
3795%colcode.CheckFixVecColor=1;
3796vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3797[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3798oneheight=ones(1,height);
3799A1=colorlist(col_vec,1)*oneheight;
3800A2=colorlist(col_vec,2)*oneheight;
3801A3=colorlist(col_vec,3)*oneheight;
3802A(:,:,1)=A1';
3803A(:,:,2)=A2';
3804A(:,:,3)=A3';
3805set(handles.VecColBar,'Cdata',A)
3806
3807%-------------------------------------------------------------------
3808function update_plot(handles)
3809%-------------------------------------------------------------------
3810UvData=get(handles.uvmat,'UserData');
3811AxeData=UvData.axes3;% retrieve the current plotted data
3812PlotParam=read_GUI(handles.uvmat);
3813[tild,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
3814write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3815
3816%-------------------------------------------------------------------
3817% --- Executes on selection change in edit_object.
3818function edit_object_Callback(hObject, eventdata, handles)
3819%-------------------------------------------------------------------
3820UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3821if get(handles.edit_object,'Value')
3822    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
3823    %suppress the other options
3824    set(handles.CheckZoom,'Value',0)
3825    CheckZoom_Callback(hObject, eventdata, handles)
3826    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
3827    if ishandle(hgeometry_calib)
3828        hhgeometry_calib=guidata(hgeometry_calib);
3829        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
3830        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
3831    end
3832    hset_object=findobj(allchild(0),'Tag','set_object');
3833    if isempty(hset_object)% open the GUI set_object with data of the currently selected object
3834        ViewObject_Callback(hObject, eventdata, handles)
3835        hset_object=findobj(allchild(0),'Tag','set_object');
3836    end
3837    hhset_object=guidata(hset_object);
3838    set(hhset_object.PLOT,'enable','on');
3839else
3840    UvData.MouseAction='none';
3841    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
3842    hset_object=findobj(allchild(0),'Tag','set_object');
3843    if ~isempty(hset_object)% open the
3844        hhset_object=guidata(hset_object);
3845        set(hhset_object.PLOT,'enable','off');
3846    end
3847end
3848
3849%------------------------------------------------------------------------
3850% --- Executes on selection change in ListObject.
3851function ListObject_Callback(hObject, eventdata, handles)
3852%------------------------------------------------------------------------
3853
3854list_str=get(handles.ListObject,'String');
3855IndexObj_old=get(handles.ListObject,'UserData');%retrieve previous selection
3856IndexObj=get(handles.ListObject,'Value');%present object selection
3857
3858%% we select two objects or more at once (using the Ctrl key), keep only the last two items: the first is projected on uvmat, the second on view_field
3859if length(IndexObj)>2
3860     IndexObj=[IndexObj(end-1) IndexObj(end)];%keeps only the last two selected items at most
3861end
3862
3863%% we select one object
3864if length(IndexObj)==1%
3865    if length(IndexObj_old)>=2 && isequal(IndexObj_old(1),IndexObj)   % we select the first previously selected object->
3866        IndexObj=[1 IndexObj_old(2)];% it desactivates this object and selects the first object for uvmat
3867    elseif length(IndexObj_old)>=2 && isequal(IndexObj_old(2),IndexObj) % we select the second previously selected object->
3868        IndexObj=IndexObj_old(1);% it desactivates this object  and keeps only the first previously selected object (uvmat)
3869    else %
3870        IndexObj=[IndexObj_old(1) IndexObj];% activates a second object while keeping the first previously selected one
3871    end
3872end
3873set(handles.ListObject,'Value',IndexObj); % marks the selected objects in the list
3874set(handles.ListObject,'UserData',IndexObj)% keep the current object selection in memory for next time
3875
3876%% update the object representation
3877set(handles.edit_object,'Value',0) % desactivate the edit object mode
3878edit_object_Callback(hObject, eventdata, handles)
3879UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3880if numel(UvData.Object)<max(IndexObj);
3881    msgbox_uvmat('ERROR','invalid object list')
3882    return
3883end
3884if numel(IndexObj)>=2
3885    UvData.Object=update_obj(UvData,IndexObj(1),IndexObj(2));%update the current object graphic representation
3886    set(handles.uvmat,'UserData',UvData)
3887end
3888
3889%% project on the selected object and update the corresponding plot
3890% hview_field=findobj(allchild(0),'tag','view_field');
3891% ViewObjectAxes=[];%default
3892if ~isequal(IndexObj(1),IndexObj_old(1))
3893    update_object(handles,IndexObj(1),handles.axes3,list_str{IndexObj(1)})%plot the projection in uvmat
3894end
3895hview_field=findobj(allchild(0),'tag','view_field');
3896if length(IndexObj)==2 && (length(IndexObj_old)==1 || ~isequal(IndexObj(2),IndexObj_old(2)))
3897    if isempty(hview_field)
3898        hview_field=view_field;
3899    end
3900    PlotHandles=guidata(hview_field);
3901    update_object(handles,IndexObj(2),PlotHandles.axes3,list_str{IndexObj(2)})%plot the projection in view_field
3902    update_object_color(handles.axes3,PlotHandles.axes3,UvData.Object{IndexObj(2)}.DisplayHandle_uvmat)
3903else
3904    if ~isempty(hview_field)
3905        delete(hview_field)
3906    end
3907    hset_object=findobj(allchild(0),'tag','set_object');
3908    if ~isempty(hset_object)
3909        delete(hset_object)
3910    end
3911    update_object_color(handles.axes3,handles.axes3,[])
3912end
3913
3914%% update the color of the gfraphic object representation: the selected object in magenta, others in blue
3915% update_object_color(handles.axes3,PlotHandles.axes3,UvData.Object{IndexObj(2)}.DisplayHandle_uvmat)
3916
3917%------------------------------------------------------------------------
3918function update_object(handles,IndexObj,ViewObjectAxes,ObjectName)
3919%------------------------------------------------------------------------
3920UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3921ObjectData=UvData.Object{IndexObj};
3922ObjectData.Name=ObjectName;
3923if isequal(get(handles.edit_object,'Value'),1)
3924    ObjectData.enable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
3925end
3926ZBounds=0; % default
3927if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3928    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3929    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3930end
3931hset_object=findobj(allchild(0),'tag','set_object');
3932if ~isempty(hset_object)
3933    delete(hset_object)% delete existing version of set_object
3934end
3935    hset_object=set_object(ObjectData,[],ZBounds);
3936% end
3937edit_test=get(handles.edit_object,'Value');
3938if edit_test
3939    ObjectData.enable_plot=1;
3940else
3941    if isfield(ObjectData,'enable_plot')
3942        ObjectData=rmfield(ObjectData,'enable_plot');
3943    end
3944end
3945
3946uistack(ViewObjectAxes,'top')% display the plotting axes at the top
3947ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
3948plot_field(ProjData,ViewObjectAxes,read_GUI(get(ViewObjectAxes,'Parent')));%read plotting parameters on the uvmat interfacPlotHandles);
3949
3950%------------------------------------------------------------------------
3951%--- update the representation of objects
3952function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
3953%------------------------------------------------------------------------
3954hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object')] ;%find all the proj objects
3955hother=[hother ;findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];
3956for iobj=1:length(hother)
3957    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
3958        set(hother(iobj),'EdgeColor','b')
3959        if isequal(get(hother(iobj),'FaceColor'),'m')
3960            set(hother(iobj),'FaceColor','b')
3961        end
3962    elseif isequal(get(hother(iobj),'Type'),'image')
3963        Acolor=get(hother(iobj),'CData');
3964        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
3965        set(hother(iobj),'CData',Acolor);
3966    else
3967        set(hother(iobj),'Color','b')
3968    end
3969    set(hother(iobj),'Selected','off')
3970end
3971if ~isempty(DisplayHandle)
3972linetype=get(DisplayHandle,'Type');
3973if isequal(linetype,'line')
3974    set(DisplayHandle,'Color','m'); %set the selected object to magenta color
3975elseif isequal(linetype,'rectangle')
3976    set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
3977elseif isequal(linetype,'patch')
3978    set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
3979end
3980SubObjectData=get(DisplayHandle,'UserData');
3981if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
3982    for iobj=1:length(SubObjectData.SubObject)
3983        hsub=SubObjectData.SubObject(iobj);
3984        if isequal(get(hsub,'Type'),'rectangle')
3985            set(hsub,'EdgeColor','m'); %set the selected object to magenta color
3986        elseif isequal(get(hsub,'Type'),'image')
3987            Acolor=get(hsub,'CData');
3988            Acolor(:,:,1)=Acolor(:,:,3);
3989            set(hsub,'CData',Acolor);
3990        else
3991            set(hsub,'Color','m')
3992        end
3993    end
3994end
3995if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
3996    set(SubObjectData.DeformPoint,'Color','m')
3997end
3998end
3999
4000%------------------------------------------------------
4001% --- Executes on button press in Menu/Export/field in workspace.
4002%------------------------------------------------------
4003function MenuExportField_Callback(hObject, eventdata, handles)
4004global Data_uvmat
4005Data_uvmat=get(handles.uvmat,'UserData');
4006evalin('base','global Data_uvmat')%make CurData global in the workspace
4007display('current field :')
4008evalin('base','Data_uvmat') %display CurData in the workspace
4009commandwindow; %brings the Matlab command window to the front
4010
4011%------------------------------------------------------
4012% --- Executes on button press in Menu/Export/extract figure.
4013%------------------------------------------------------
4014function MenuExport_plot_Callback(hObject, eventdata, handles)
4015huvmat=get(handles.MenuExport_plot,'parent');
4016UvData=get(huvmat,'UserData');
4017hfig=figure;
4018newaxes=copyobj(handles.axes3,hfig);
4019map=colormap(handles.axes3);
4020colormap(map);%transmit the current colormap to the zoom fig
4021colorbar
4022
4023
4024% --------------------------------------------------------------------
4025function Insert_Callback(hObject, eventdata, handles)
4026
4027
4028% --------------------------------------------------------------------
4029function MenuHelp_Callback(hObject, eventdata, handles)
4030% --------------------------------------------------------------------
4031path_to_uvmat=which ('uvmat');% check the path of uvmat
4032pathelp=fileparts(path_to_uvmat);
4033helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4034if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4035else
4036    addpath (fullfile(pathelp,'uvmat_doc'))
4037    web(helpfile);
4038end
4039
4040%------------------------------------------------------------------------
4041% --------------------------------------------------------------------
4042function MenuExportMovie_Callback(hObject, eventdata, handles)
4043% --------------------------------------------------------------------
4044set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4045huvmat=get(handles.run0,'parent');
4046UvData=get(huvmat,'UserData');
4047%[xx,xx,FileBase]=read_file_boxes(handles);
4048[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4049FileBase=fullfile(RootPath,RootFile);
4050 %read the current input file name
4051prompt = {'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)'};
4052dlg_title = 'select properties of the output avi movie';
4053num_lines= 1;
4054% nbfield_cell=get(handles.last_i,'String');
4055def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4056answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4057aviname=answer{1};
4058fps=str2double(answer{2});
4059% check for existing file with output name aviname
4060if exist(aviname,'file')
4061    backup=aviname;
4062    testexist=2;
4063    while testexist==2
4064        backup=[backup '~'];
4065        testexist=exist(backup,'file');     
4066    end
4067    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4068    if isequal(success,1)
4069        delete(aviname)%delete existing file
4070    else
4071        msgbox_uvmat('ERROR',message)
4072        return
4073    end
4074end
4075%create avi open
4076aviobj=avifile(aviname,'Compression','None','fps',fps);
4077
4078%display first view for tests
4079newfig=figure;
4080newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4081set(newaxes,'Tag','movieaxes')
4082nbpix=[512 384]*str2double(answer{3});
4083set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4084set(newaxes,'Position',eval(answer{4}));
4085map=colormap(handles.axes3);
4086colormap(map);%transmit the current colormap to the zoom fig
4087msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4088        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4089UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4090set(huvmat,'UserData',UvData);
4091increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4092set(handles.STOP,'Visible','on')
4093set(handles.speed,'Visible','on')
4094set(handles.speed_txt,'Visible','on')
4095set(handles.Movie,'BusyAction','queue')
4096
4097%imin=str2double(get(handles.i1,'String'));
4098imax=str2double(answer{5});
4099% if isfield(UvData,'Time')
4100htitle=get(newaxes,'Title');
4101xlim=get(newaxes,'XLim');
4102ylim=get(newaxes,'YLim');
4103set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4104time_str=get(handles.abs_time,'String');
4105set(htitle,'String',['t=' time_str])
4106set(handles.speed,'Value',1)
4107for i=1:imax
4108    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4109            runpm(hObject,eventdata,handles,increment)% run plus
4110            drawnow
4111            time_str=get(handles.abs_time,'String');
4112            if ishandle(htitle)
4113             set(htitle,'String',['t=' time_str])
4114            end
4115            mov=getframe(newfig);
4116            aviobj=addframe(aviobj,mov);
4117    end
4118end
4119aviobj=close(aviobj);
4120UvData=rmfield(UvData,'plotaxes');
4121%UvData.Object{1}.plotaxes=handles.axes3;
4122set(huvmat,'UserData',UvData);
4123msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4124
4125%------------------------------------------------------------------------
4126function MenuCalib_Callback(hObject, eventdata, handles)
4127%------------------------------------------------------------------------
4128
4129UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4130
4131%suppress competing options
4132set(handles.CheckZoom,'Value',0)
4133set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4134set(handles.ListObject,'Value',1)     
4135% initiate display of GUI geometry_calib
4136data=[]; %default
4137if isfield(UvData,'CoordType')
4138    data.CoordType=UvData.CoordType;
4139end
4140pos=get(handles.uvmat,'Position');
4141pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4142pos(2)=pos(2)-0.02;
4143%[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
4144[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4145FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4146set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4147if isfield(UvData.OpenParam,'CalOrigin')
4148    pos_uvmat=get(handles.uvmat,'Position');
4149    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4150    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4151    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4152end
4153geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4154set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4155set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4156
4157%------------------------------------------------------------------------
4158function MenuMask_Callback(hObject, eventdata, handles)
4159%------------------------------------------------------------------------
4160UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4161ListObj=UvData.Object;
4162select=zeros(1,numel(ListObj));
4163for iobj=1:numel(ListObj);
4164    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4165        select(iobj)=1;
4166    end
4167end
4168val=find(select);
4169if isempty(val)
4170    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4171    return
4172else
4173    set(handles.ListObject,'Max',2);%allow multiple selection
4174    set(handles.ListObject,'Value',val);
4175    flag=1;
4176    npx=size(UvData.Field.A,2);
4177    npy=size(UvData.Field.A,1);
4178    xi=0.5:npx-0.5;
4179    yi=0.5:npy-0.5;
4180    [Xi,Yi]=meshgrid(xi,yi);
4181    if isfield(UvData,'Object')
4182        for iobj=1:length(UvData.Object)
4183            ObjectData=UvData.Object{iobj};
4184            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4185                flagobj=1;
4186                testphys=0; %coordinates in pixels by default
4187                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4188                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4189                        Calib=UvData.XmlData{1}.GeometryCalib;
4190                        testphys=1;
4191                    end
4192                end
4193                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4194                    if isequal(ObjectData.Type,'polygon')
4195                        X=ObjectData.Coord(:,1);
4196                        Y=ObjectData.Coord(:,2);
4197                        if testphys
4198                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4199                        end
4200                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4201                    elseif isequal(ObjectData.Type,'ellipse')
4202                        if testphys
4203                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4204                        end
4205                        RangeX=max(ObjectData.RangeX);
4206                        RangeY=max(ObjectData.RangeY);
4207                        X2Max=RangeX*RangeX;
4208                        Y2Max=RangeY*RangeY;
4209                        distX=(Xi-ObjectData.Coord(1,1));
4210                        distY=(Yi-ObjectData.Coord(1,2));
4211                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4212                    elseif isequal(ObjectData.Type,'rectangle')
4213                        if testphys
4214                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4215                        end
4216                        distX=abs(Xi-ObjectData.Coord(1,1));
4217                        distY=abs(Yi-ObjectData.Coord(1,2));
4218                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4219                    end
4220                    if isequal(ObjectData.ProjMode,'mask_outside')
4221                        flagobj=~flagobj;
4222                    end
4223                    flag=flag & flagobj;
4224                end
4225            end
4226        end
4227    end
4228    %mask name
4229    RootPath=get(handles.RootPath,'String');
4230    RootFile=get(handles.RootFile,'String');
4231    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4232        RootFile(1)=[];
4233    end
4234    filebase=fullfile(RootPath,RootFile);
4235    list=get(handles.masklevel,'String');
4236    masknumber=num2str(length(list));
4237    maskindex=get(handles.masklevel,'Value');
4238    mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4239    %mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4240    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4241    imflag=flipdim(imflag,1);
4242
4243    %display the mask
4244    hfigmask=figure;
4245    set(hfigmask,'Name','mask image')
4246    vec=linspace(0,1,256);%define a linear greyscale colormap
4247    map=[vec' vec' vec'];
4248    colormap(map)
4249    image(imflag);
4250    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4251    if ~strcmp(answer,'Cancel')
4252        mask_dir=fileparts(answer);
4253        if ~exist(mask_dir,'dir')
4254            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4255            return
4256        end
4257        imwrite(imflag,answer,'BitDepth',8);
4258    end
4259    set(handles.ListObject,'Value',1)
4260%     set(handles.ListObject,'Max',1)
4261end
4262
4263%------------------------------------------------------------------------
4264%-- open the GUI set_grid.fig to create grid
4265function MenuGrid_Callback(hObject, eventdata, handles)
4266%------------------------------------------------------------------------
4267%suppress the other options if grid is chosen
4268set(handles.edit_vect,'Value',0)
4269edit_vect_Callback(hObject, eventdata, handles)
4270set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4271set(handles.ListObject,'Value',1)     
4272
4273%prepare display of the set_grid GUI
4274[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4275FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4276CoordList=get(handles.transform_fct,'String');
4277val=get(handles.transform_fct,'Value');
4278set_grid(FileName,CoordList{val});% call the set_object interface
4279
4280%------------------------------------------------------------------------
4281% open the GUI 'series'
4282function MenuSeries_Callback(hObject, eventdata, handles)
4283%------------------------------------------------------------------------
4284series; %first display of the GUI to fill waiting time
4285[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4286param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4287if isequal(get(handles.SubField,'Value'),1)
4288    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
4289    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
4290    %FileName_1=read_file_boxes_1(handles);%
4291    if ~isequal(FileName_1,param.FileName)
4292        param.FileName_1=FileName_1;
4293    end
4294end
4295param.NomType=get(handles.NomType,'String');
4296% param.NomType=get(handles.FileIndex,'UserData');
4297param.NomType_1=get(handles.NomType_1,'String');
4298% param.NomType_1=get(handles.FileIndex_1,'UserData');
4299param.CheckFixPair=get(handles.CheckFixPair,'Value');
4300huvmat=get(handles.MenuSeries,'parent');
4301UvData=get(huvmat,'UserData');
4302if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4303    param.Time=UvData.XmlData{1}.Time;
4304end
4305if isequal(get(handles.scan_i,'Value'),1)
4306    param.incr_i=str2num(get(handles.increment_scan,'String'));
4307elseif isequal(get(handles.scan_j,'Value'),1)
4308    param.incr_j=str2num(get(handles.increment_scan,'String'));
4309end
4310param.list_fields=get(handles.Fields,'String');% list menu fields
4311param.list_fields(1)=[]; %suppress  'image' option
4312param.index_fields=get(handles.Fields,'Value');% selected string index
4313if param.index_fields>1
4314    param.index_fields=param.index_fields-1;
4315end
4316param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4317param.list_fields_1(1)=[]; %suppress  'image' option
4318param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4319if param.index_fields_1>1
4320    param.index_fields_1=param.index_fields_1-1;
4321end
4322param.menu_coord_str=get(handles.transform_fct,'String');
4323param.menu_coord_val=get(handles.transform_fct,'Value');
4324series(param); %run the series interface
4325
4326%------------------------------------------------------------------------
4327% -- open the GUI civ.fig for civx (PIV)
4328function MenuPIV_Callback(hObject, eventdata, handles)
4329%------------------------------------------------------------------------
4330 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4331 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4332civ(FileName);% interface de civ(not in the uvmat file)
4333
4334%------------------------------------------------------------------------
4335function MenuTools_Callback(hObject, eventdata, handles)
4336%------------------------------------------------------------------------
4337
4338%------------------------------------------------------------------------
4339function MenuEditObject_Callback(hObject, eventdata, handles)
4340%------------------------------------------------------------------------
4341set(handles.edit_object,'Value',1)
4342edit_Callback(hObject, eventdata, handles)
4343
4344%------------------------------------------------------------------------
4345function enable_transform(handles,state)
4346%------------------------------------------------------------------------
4347set(handles.transform_fct,'Visible',state)
4348set(handles.TRANSFORM_txt,'Visible',state)   
4349set(handles.transform_fct,'Visible',state) 
4350set(handles.path_transform,'Visible',state)
4351set(handles.pxcmx_txt,'Visible',state)
4352set(handles.pxcmy_txt,'Visible',state)
4353set(handles.pxcm,'Visible',state)
4354set(handles.pycm,'Visible',state)
4355
4356%------------------------------------------------------------------------
4357function MenuEditVectors_Callback(hObject, eventdata, handles)
4358%------------------------------------------------------------------------
4359set(handles.edit_vect,'Visible','on')
4360set(handles.edit_vect,'Value',1)
4361edit_vect_Callback(hObject, eventdata, handles)
4362
4363% -----------------------------------------------------------------------
4364function Menupoints_Callback(hObject, eventdata, handles)
4365%------------------------------------------------------------------------
4366data.Type='points';
4367data.ProjMode='projection';%default
4368create_object(data,handles)
4369
4370% -----------------------------------------------------------------------
4371function Menuline_Callback(hObject, eventdata, handles)
4372%------------------------------------------------------------------------
4373data.Type='line';
4374data.ProjMode='projection';%default
4375create_object(data,handles)
4376
4377%------------------------------------------------------------------------
4378function Menupolyline_Callback(hObject, eventdata, handles)
4379%------------------------------------------------------------------------
4380data.Type='polyline';
4381data.ProjMode='projection';%default
4382create_object(data,handles)
4383
4384%------------------------------------------------------------------------
4385function Menupolygon_Callback(hObject, eventdata, handles)
4386%------------------------------------------------------------------------
4387data.Type='polygon';
4388data.ProjMode='inside';%default
4389create_object(data,handles)
4390
4391%------------------------------------------------------------------------
4392function Menurectangle_Callback(hObject, eventdata, handles)
4393%------------------------------------------------------------------------
4394data.Type='rectangle';
4395data.ProjMode='inside';%default
4396create_object(data,handles)
4397
4398%------------------------------------------------------------------------
4399function Menuellipse_Callback(hObject, eventdata, handles)
4400%------------------------------------------------------------------------
4401data.Type='ellipse';
4402data.ProjMode='inside';%default
4403create_object(data,handles)
4404
4405%------------------------------------------------------------------------
4406function MenuMaskObject_Callback(hObject, eventdata, handles)
4407%------------------------------------------------------------------------
4408data.Type='polygon';
4409data.TypeMenu={'polygon'};
4410data.ProjMode='mask_inside';%default
4411data.ProjModeMenu={'mask_inside';'mask_outside'};
4412create_object(data,handles)
4413
4414%------------------------------------------------------------------------
4415function Menuplane_Callback(hObject, eventdata, handles)
4416%------------------------------------------------------------------------
4417data.Type='plane';
4418data.ProjMode='projection';%default
4419
4420create_object(data,handles)
4421
4422%------------------------------------------------------------------------
4423function Menuvolume_Callback(hObject, eventdata, handles)
4424%------------------------------------------------------------------------
4425data.Type='volume';
4426data.ProjMode='interp';%default
4427% set(handles.create,'Visible','on')
4428% set(handles.create,'Value',1)
4429% VOLUME_Callback(hObject,eventdata,handles)
4430create_object(data,handles)
4431
4432%------------------------------------------------------------------------
4433function MenuBrowseObject_Callback(hObject, eventdata, handles)
4434%------------------------------------------------------------------------
4435%get the object file
4436[FileName, PathName, filterindex] = uigetfile( ...
4437       {'*.xml;*.mat', ' (*.xml,*.mat)';
4438       '*.xml',  '.xml files '; ...
4439        '*.mat',  '.mat matlab files '}, ...
4440        'Pick an xml Object file',get(handles.RootPath,'String'));
4441fileinput=[PathName FileName];%complete file name
4442sizf=size(fileinput);
4443if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4444
4445%read the file
4446data=xml2struct(fileinput);
4447data.enable_plot=1;
4448[tild,data.Name]=fileparts(FileName);
4449hset_object=findobj(allchild(0),'tag','set_object');
4450if ~isempty(hset_object)
4451    delete(hset_object)% delete existing version of set_object
4452end
4453set_object(data);% call the set_object interface
4454set(handles.edit_object,'Value',0); %suppress the object edit mode
4455set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4456set(handles.MenuObject,'checked','on')
4457set(handles.delete_object,'Visible','on')
4458
4459%------------------------------------------------------------------------
4460% --- generic function used for the creation of a projection object
4461function create_object(data,handles)
4462%------------------------------------------------------------------------
4463hset_object=findobj(allchild(0),'tag','set_object');
4464if ~isempty(hset_object)
4465    delete(hset_object)% delete existing version of set_object
4466end
4467hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4468if ishandle(hgeometry_calib)
4469    hhgeometry_calib=guidata(hgeometry_calib);
4470    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4471    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4472end
4473UvData=get(handles.uvmat,'UserData');
4474set(handles.edit_object,'Value',0); %suppress the object edit mode
4475set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4476data.enable_plot=1;
4477data.Coord=[0 0]; %default
4478if isfield(UvData,'Field')
4479    Field=UvData.Field;
4480    if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
4481        ord=10^(floor(log10(Field.Mesh)));%order of magnitude
4482        if Field.Mesh/ord>=5
4483            mesh=5*ord;
4484        elseif Field.Mesh/ord>=2
4485            mesh=2*ord;
4486        else
4487            mesh=ord;
4488        end
4489        data.RangeX=mesh;
4490        data.RangeY=mesh;
4491        data.DX=mesh;
4492        data.DY=mesh;
4493    elseif isfield(Field,'AX')&& isfield(Field,'AY')&& isfield(Field,'A')%only image
4494        np=size(Field.A);
4495        meshx=(Field.AX(end)-Field.AX(1))/np(2);
4496        meshy=abs(Field.AY(end)-Field.AY(1))/np(1);
4497        data.RangeY=max(meshx,meshy);
4498        data.RangeX=max(meshx,meshy);
4499        data.DX=max(meshx,meshy);
4500    end
4501    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4502         data.Coord=[0 0 0]; %default
4503    end
4504    if isfield(Field,'CoordUnit')
4505        data.CoordUnit=Field.CoordUnit;
4506    end
4507end
4508if ishandle(handles.UVMAT_title)
4509    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4510end
4511set_object(data,handles);% call the set_object interface
4512set(handles.MenuObject,'checked','on')
4513set(handles.uvmat,'UserData',UvData)
4514set(handles.CheckZoom,'Value',0)
4515CheckZoom_Callback(handles.uvmat, [], handles)
4516set(handles.delete_object,'Visible','on')
4517
4518%------------------------------------------------------------------------
4519function MenuRuler_Callback(hObject, eventdata, handles)
4520%------------------------------------------------------------------------
4521set(handles.CheckZoom,'Value',0)
4522CheckZoom_Callback(handles.uvmat, [], handles)
4523set(handles.MenuRuler,'checked','on')
4524UvData=get(handles.uvmat,'UserData');
4525UvData.MouseAction='ruler';
4526set(handles.uvmat,'UserData',UvData);
4527
4528%------------------------------------------------------------------------
4529% --- executed when closing: set the parent interface button to value 0
4530function closefcn(gcbo,eventdata)
4531%------------------------------------------------------------------------
4532%delete all the associated figures if exist
4533hh=findobj(allchild(0),'tag','view_field');
4534if ~isempty(hh)
4535    delete(hh)
4536end
4537hh=findobj(allchild(0),'tag','geometry_calib');
4538if ~isempty(hh)
4539    delete(hh)
4540end
4541hh=findobj(allchild(0),'tag','set_object');
4542if ~isempty(hh)
4543    hhh=findobj(hh,'tag','PLOT');
4544    set(hhh,'enable','off')
4545end
4546
4547%------------------------------------------------------------------------
4548% --- Executes on button press in delete_object.
4549function delete_object_Callback(hObject, eventdata, handles)
4550%------------------------------------------------------------------------
4551IndexObj=get(handles.ListObject,'Value');
4552if IndexObj(end)>1
4553    delete_object(IndexObj(end))
4554end
4555
4556% --- Executes on button press in FixVelType.
4557function FixVelType_Callback(hObject, eventdata, handles)
4558val=get(handles.FixVelType,'Value');
4559if ~val
4560    run0_Callback(hObject, eventdata, handles)
4561end
4562
4563%------------------------------------------------------------------------
4564% --- Executes on button press in ViewObject.
4565function ViewObject_Callback(hObject, eventdata, handles)
4566%------------------------------------------------------------------------
4567IndexObj=get(handles.ListObject,'Value');
4568IndexObj=IndexObj(end); %keeps only the secodn value
4569UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4570if numel(UvData.Object)<IndexObj;% error in UvData
4571    msgbox_uvmat('ERROR','invalid object list')
4572    return
4573end
4574ObjectData=UvData.Object{IndexObj};
4575ZBounds=0; % default
4576if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4577    ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4578    ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4579end
4580hset_object=findobj(allchild(0),'tag','set_object');
4581if ~isempty(hset_object)
4582    delete(hset_object)% delete existing version of set_object
4583end
4584if ~isfield(ObjectData,'Type')% default plane
4585    ObjectData.Type='plane';
4586end
4587hset_object=set_object(ObjectData,[],ZBounds);
4588if get(handles.edit_object,'Value')% edit mode
4589    hhset_object=guidata(hset_object);
4590    set(hhset_object.PLOT,'Enable','on')
4591end
4592
4593
4594function NomType_Callback(hObject, eventdata, handles)
4595
4596
4597function NomType_1_Callback(hObject, eventdata, handles)
4598
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