source: trunk/src/uvmat.m @ 146

Last change on this file since 146 was 144, checked in by sommeria, 14 years ago

connection between uvmat and get_field improved, cleaning of GUI get_field

File size: 217.1 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 stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
34%          It contains the following fields:
35%     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn)
36%          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
37%     - Information read in the documentation open of a series (activated by RootPath_Callback) :
38%          .XmlData, with fields:
39%               .Time: matrix of times of the images with index i and j
40%               .GeometryCalib: [1x1 struct]
41%     - Information defined from the interface:
42%           .NewSeries: =1 when the first view of a new field series is displayed, else 0
43%           .filename:(char string)
44%           .VelType:(char string) type of velocity field selected
45%           .VelType_1:(char string)  REMPLACER LE CELL ACTUEL
46%           .FieldName: (char string) main field selected('image', 'velocity'...)
47%           .FieldName_1:(char string) second field selected('image', 'velocity'...)
48%           .CName: (char string)name of the scalar used for vector colors
49%           .CoordType: (char string) coordinate transform: e.g. 'phys' or 'px'
50%           .MouseAction: store the current effect of mouse button (create or edit objects)
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%               Main input open   second input open(_1)        second image (pair animation)
82% read_ncfield.m         |                 |                             
83% read image.m           |                 |                                               
84%                     Field{1}         Field{2}               
85%                                                                         |
86% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
87%                                                                   Field{i}
88%                                                                    |
89% calc_field.m: calculate scalar or other derived fields (vort, div..).
90%
91% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
92%              Field{i=1->3}.X --> UvData.X                          |
93%                                                                    |
94%                                                                 UvData
95%                                                                    |
96% plot histograms of the whole  field
97% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
98%                                                                    |                                                                          |
99%                                                                ObjectData
100%                                                                    |
101% plot_field.m: plot the projected fields and store them as user     |
102% data of the plotting axes                                          |
103%                                                                    |
104%                                                                AxeData
105%
106%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
107% scalars are displayed either as an image or countour plot, either as a color of
108% velocity vectors. The scalar values in the first case is represented by
109% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
110% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
111% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
112% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
113% coordinates of the four image corners. The scalar name is represented by
114% the strings .AName and/or .CName.
115% If the scalar exists in an input open (image or scalar stored under its
116% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
117% Else only its name AName is recorded in Field{i}, and its field is then calculated
118%by the fuction calc_scal after the coordinate transform or after projection on an edit
119     
120% Properties attached to plotting figures (standard Matlab properties):
121%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
122%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
123%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
124%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
125%    'KeyPressFcn': function called by pressing a key on the key board
126%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
127%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
128
129% Properties attached to plotting axes:
130%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
131%     AxeData:=get(gca,'UserData');
132%     AxeData.Drawing  = create: create a new edit
133%                       = deform: modify an existing edit by moving its defining create
134%                      = off: no current drawing action
135%                     = translate: translate an existing edit
136%                    = zoom: isolate a subregion for zoom in=1 if an edit is being currently drawn, 0 else (set to 0 by releasing mouse button)
137%            .hset_edit=handle of the set_edit interface (if a projection edit is edited);
138%            .CurrentOrigin: Origin of a curently drawn edit
139%            .CurrentLine: currently drawn menuline (A REVOIR)
140%            .CurrentObject: handle of the currently drawn edit
141%            .CurrentRectZoom: current rectangle used for zoom
142%            .zoomon : zoom state (a revoir)
143%            .X, .Y, .Z: array of coordinates defining the position of the vector: ASSOCIER AU PLAN (OBJET) PLUTOT QU'A L'AXE ?
144%            .U, .V, .W: array of components of the vector
145%            .C:
146%            .F:
147%            .FF:
148%            .A
149
150% Properties attached to projection objects (create, menuline, menuplane...):
151%    'Tag'='proj_edit': for all projection objects
152%    ObjectData.Style=...: style of projection edit:
153%              .ProjMode
154%              .Coord: defines the position of the edit
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 edit
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%------------------------------------------------------------------------
198global nb_builtin
199
200% Choose default command menuline output for uvmat
201handles.output = hObject;
202
203% Update handles structure
204guidata(hObject, handles);
205
206% set the position of colorbar and ancillary GUIs:
207set(hObject,'Units','Normalized')
208movegui(hObject,'center')
209UvData.PosColorbar=[0.805 0.022 0.019 0.445];
210UvData.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
211UvData.SetObjectSize=[0.3 0.7];
212UvData.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
213UvData.CalSize=[0.28 1];
214
215%functions for the mouse and keyboard
216set(handles.histo_u,'NextPlot','replacechildren');
217set(handles.histo_v,'NextPlot','replacechildren');
218set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
219set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
220set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
221set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
222set(hObject,'DeleteFcn',{@closefcn})%
223
224%refresh projection plane
225UvData.Object{1}.Style='plane';%main plotting plane
226UvData.Object{1}.ProjMode='projection';%main plotting plane
227if ~isfield(UvData.Object{1},'plotaxes')
228    UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
229    set(handles.list_object_1,'Value',1);
230    set(handles.list_object_1,'String',{'1-PLANE'});
231end
232
233%TRANSFORM menu: builtin fcts
234menu_str={'';'phys';'px';'phys_polar'};
235nb_builtin=numel(menu_str); %number of functions
236path_uvmat=fileparts(which('uvmat'));
237addpath(fullfile(path_uvmat,'transform_field'))
238fct_handle{1,1}=[];
239testexist=zeros(size(menu_str'));%default
240testexist(1)=1;
241for ilist=2:length(menu_str)
242    if exist(menu_str{ilist},'file')
243        fct_handle{ilist,1}=str2func(menu_str{ilist});
244        testexist(ilist)=1;
245    else
246        testexist(ilist)=0;
247    end
248end
249rmpath(fullfile(path_uvmat,'transform_field'))
250
251%load the list of previously browsed files in menus Open and Open_1
252 dir_perso=prefdir; % path to the directory .matlab for personal data
253 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
254 if exist(profil_perso,'file')
255      h=load (profil_perso);
256      if isfield(h,'MenuFile_1')
257          set(handles.MenuFile_1,'Label',h.MenuFile_1);
258          set(handles.MenuFile_1_1,'Label',h.MenuFile_1);
259      end
260      if isfield(h,'MenuFile_1')
261          set(handles.MenuFile_2,'Label',h.MenuFile_2);
262          set(handles.MenuFile_2_1,'Label',h.MenuFile_2);
263      end
264      if isfield(h,'MenuFile_1')
265          set(handles.MenuFile_3,'Label',h.MenuFile_3);
266          set(handles.MenuFile_3_1,'Label',h.MenuFile_3);
267      end
268      if isfield(h,'MenuFile_1')
269          set(handles.MenuFile_4,'Label',h.MenuFile_4);
270          set(handles.MenuFile_4_1,'Label',h.MenuFile_4);
271      end
272      if isfield(h,'MenuFile_1')
273          set(handles.MenuFile_5,'Label',h.MenuFile_5);
274          set(handles.MenuFile_5_1,'Label',h.MenuFile_5);
275      end
276      if isfield(h,'transform_fct') && iscell(h.transform_fct)
277         for ilist=1:length(h.transform_fct);
278             [path,file]=fileparts(h.transform_fct{ilist});
279             addpath(path)
280             if exist(file,'file')
281                h_func=str2func(file);
282                testexist=[testexist 1];
283             else
284                h_func=[];
285                testexist=[testexist 0];
286             end
287             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
288             rmpath(path)
289             menu_str=[menu_str; {file}];
290         end
291      end
292 end
293menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
294fct_handle=fct_handle(testexist==1);
295menu_str=[menu_str;{'more...'}];
296set(handles.transform_fct,'String',menu_str)
297set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
298 
299%initiates menu of vector colors
300list_menu=calc_field;
301%list_menu=[{'ima_cor'};{'black'};{'white'};list_menu(3:end)];
302set(handles.col_vec,'String',list_menu)
303
304%check the path and date of modification of all functions in uvmat
305path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
306[errormsg,date_str]=check_functions;%check the path of the functions called by uvmat.m
307date_str=['last modification: ' date_str];
308%case of an input argument for uvmat
309testinputfield=0;
310inputfile=[];
311Field=[];
312if exist('input','var')
313    if ~isempty(errormsg)
314        msgbox_uvmat('WARNING',errormsg)
315    end
316    if ishandle(handles.UVMAT_title)
317        delete(handles.UVMAT_title)
318    end   
319    if isstruct(input)
320        if isfield(input,'InputFile')
321            inputfile=input.InputFile;
322        end
323        Field=input;
324    elseif ischar(input)% file name introduced as input
325           inputfile=input;
326    elseif isnumeric(input)%simple matrix introduced as input
327        sizinput=size(input);
328        if sizinput(1)<=1 || sizinput(2)<=1
329            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
330            return
331        end
332        Field.ListVarName={'A','coord_y','coord_x'};
333        Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
334        Field.A=input;
335        Field.coord_x=[0.5 size(input,2)-0.5];
336        Field.coord_y=[size(input,1)-0.5 0.5];
337    end
338    if ~isempty(inputfile)
339        display_file_name(hObject, eventdata, handles,inputfile)
340        testinputfield=1;
341    else
342        UvData.TestInputFile=0;
343    end
344    if ~isempty(Field)
345        set(handles.Fields,'Value',1)
346        set(handles.Fields,'String',{'get_field...'})   
347        testinputfield=1;
348       
349        % set the colorbar position on the interface:
350        UvData.PosColorbar=[0.805 0.022 0.019 0.445];
351    elseif ischar(input)
352        scan_i_Callback(handles.scan_i, eventdata, handles);       
353    end
354else
355   if ishandle(handles.UVMAT_title)
356       fid=fopen('revision.log');
357       if fid~=-1
358         a=textscan(fid,'%s%s%s',1,'HeaderLines',1,'Delimiter','|');
359         set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG'};{'GNU General Public License'}; {path_to_uvmat}; ...
360           {['at revision ' a{1}{1}]};a{3}(1);{date_str};errormsg]);
361         fclose(fid);
362       else
363          set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG'};{'GNU General Public License'};{path_to_uvmat};...
364               {date_str};errormsg]);
365       end
366   end
367end
368UvData.NewSeries=1;
369set(hObject,'UserData',UvData)
370if testinputfield
371    %delete drawn objects
372    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
373    for iobj=1:length(hother)
374        delete_object(hother(iobj))
375    end 
376    if isempty(inputfile)
377        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
378        set(handles.MenuTools,'Enable','on')
379        set(handles.OBJECT_txt,'Visible','on')
380        set(handles.edit,'Visible','on')
381        set(handles.list_object_1,'Visible','on')
382        set(handles.frame_object,'Visible','on')
383        if ~isempty(errormsg)
384            msgbox_uvmat('ERROR',errormsg)
385        end
386    else
387        update_rootinfo(hObject,eventdata,handles);
388    end
389end
390set_vec_col_bar(handles) %update the display of color code for vectors
391
392%------------------------------------------------------------------------
393% --- Outputs from this function are returned to the command menuline.
394function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
395varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
396
397%------------------------------------------------------------------------
398%------------------------------------------------------------------------
399%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
400% automatically sets the global properties when the rootfile name is introduced
401% then activate the view-field action if selected
402% it is activated either by clicking on the RootPath window or by the
403% browser
404%------------------------------------------------------------------------
405%------------------------------------------------------------------------
406% --- Executes on the menu Open/Browse...
407% search the files, recognize their type according to their name and fill the rootfile input windows
408function MenuBrowse_Callback(hObject, eventdata, handles)
409oldfile=read_file_boxes(handles);
410
411if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
412         dir_perso=prefdir;
413         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
414         if exist(profil_perso,'file')
415              h=load (profil_perso);
416             if isfield(h,'MenuFile_1')
417                  oldfile=h.MenuFile_1;
418             end
419         end
420end
421[FileName, PathName] = uigetfile( ...
422       {'*.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)';
423       '*.xml',  '.xml files '; ...
424        '*.xls',  '.xls files '; ...
425        '*.civ',  '.civ files '; ...
426        '*.jpg',' jpeg image files'; ...
427        '*.png','.png image files'; ...
428        '*.tif','.tif image files'; ...
429        '*.avi;*.AVI','.avi movie files'; ...
430        '*.vol','.volume images (png)'; ...
431        '*.nc','.netcdf files'; ...
432        '*.cdf','.netcdf files'; ...
433        '*.cmx','.cmx text files';...
434        '*.cmx2','.cmx2 text files';...
435        '*.fig','.fig files (matlab fig)';...
436        '*.log','.log text files ';...
437        '*.dat','.dat text files ';...
438        '*.bat','.bat system command text files';...
439        '*.*',  'All Files (*.*)'}, ...
440        'Pick a file',oldfile);
441%global filebase
442fileinput=[PathName FileName];%complete file name
443testblank=findstr(fileinput,' ');%look for blanks
444if ~isempty(testblank)
445    msgbox_uvmat('ERROR',['The input file name ' fileinput ' contains blank character : This is not allowed. Please change name'])
446    return
447end
448sizf=size(fileinput);
449if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
450
451% display the selected field and related information
452display_file_name(hObject, eventdata, handles,fileinput)
453
454%update list of recent files in the menubar
455MenuFile_1=fileinput;
456MenuFile_2=get(handles.MenuFile_1,'Label');
457MenuFile_3=get(handles.MenuFile_2,'Label');
458MenuFile_4=get(handles.MenuFile_3,'Label');
459MenuFile_5=get(handles.MenuFile_4,'Label');
460set(handles.MenuFile_1,'Label',MenuFile_1)
461set(handles.MenuFile_2,'Label',MenuFile_2)
462set(handles.MenuFile_3,'Label',MenuFile_3)
463set(handles.MenuFile_4,'Label',MenuFile_4)
464set(handles.MenuFile_5,'Label',MenuFile_5)
465set(handles.MenuFile_1_1,'Label',MenuFile_1)
466set(handles.MenuFile_2_1,'Label',MenuFile_2)
467set(handles.MenuFile_3_1,'Label',MenuFile_3)
468set(handles.MenuFile_4_1,'Label',MenuFile_4)
469set(handles.MenuFile_5_1,'Label',MenuFile_5)
470dir_perso=prefdir;
471profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
472if exist(profil_perso,'file')
473    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
474else
475    txt=ver;
476    Release=txt(1).Release;
477    relnumb=str2double(Release(3:4));
478    if relnumb >= 14
479        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
480    else
481        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
482    end
483end
484
485% -----------------------------------------------------------------------
486% --- Open again the file whose name has been recorded in MenuFile_1
487function MenuFile_1_Callback(hObject, eventdata, handles)
488fileinput=get(handles.MenuFile_1,'Label');
489display_file_name(hObject, eventdata, handles,fileinput)
490
491% -----------------------------------------------------------------------
492% --- Open again the file whose name has been recorded in MenuFile_2
493function MenuFile_2_Callback(hObject, eventdata, handles)
494fileinput=get(handles.MenuFile_2,'Label');
495display_file_name(hObject, eventdata, handles,fileinput)
496
497% -----------------------------------------------------------------------
498% --- Open again the file whose name has been recorded in MenuFile_3
499function MenuFile_3_Callback(hObject, eventdata, handles)
500fileinput=get(handles.MenuFile_3,'Label');
501display_file_name(hObject, eventdata, handles,fileinput)
502
503% -----------------------------------------------------------------------
504% --- Open again the file whose name has been recorded in MenuFile_4
505function MenuFile_4_Callback(hObject, eventdata, handles)
506fileinput=get(handles.MenuFile_4,'Label');
507display_file_name(hObject, eventdata, handles,fileinput)
508
509% -----------------------------------------------------------------------
510% --- Open again the file whose name has been recorded in MenuFile_5
511function MenuFile_5_Callback(hObject, eventdata, handles)
512fileinput=get(handles.MenuFile_5,'Label');
513display_file_name(hObject, eventdata, handles,fileinput)
514
515%------------------------------------------------------------------------
516% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
517function display_file_name(hObject, eventdata, handles,fileinput)
518if ~exist(fileinput,'file')
519    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
520    return
521end
522[RootPath,RootFile,i1,i2,str_a,str_b,ext,NomType,SubDir]=name2display(fileinput);
523ext_test=''; %default
524if ~isempty(ext)
525    form=imformats(ext(2:end));%test valid Matlab image formats
526    if ~isempty(form)
527        ext_test='.image';
528        imainfo=imfinfo(fileinput); 
529        if length(imainfo) >1 %case of image with multiple frames
530            i1='1'; % set the frame counter to 1 by default
531            i2='';
532            str_a='';
533            str_b='';
534            NomType='*'; %indicate a set of indexed frames within a single file
535            [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
536        end
537    elseif isequal(lower(ext),'.avi')
538        ext_test='.image';
539        i1='1'; % set the frame counter to 1 by default
540        i2='';
541        str_a='';
542        str_b='';
543        NomType='*'; %indicate a set of indexed frames within a single file
544        [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
545    else
546        ext_test=lower(ext);
547    end
548end
549switch ext_test
550    case {'.civ','.log','.cmx','.cmx2','.txt','.bat'}  %display text file
551        edit(fileinput) 
552    case '.fig'                           %display matlab figure
553        hfig=open(fileinput);
554        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
555        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
556        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
557    case {'.xml','.xls'}                % edit xml or Excel files
558       editxml(fileinput);
559    case {'.avi','.image','.vol','.nc','.cdf'}   
560        set(handles.RootPath,'String',RootPath);
561        if  isequal(SubDir,'')
562            rootname=fullfile(RootPath,RootFile);
563        else
564            rootname=fullfile(RootPath,SubDir,RootFile);
565            SubDir=['/' SubDir]; %display the separator
566        end
567        set(handles.SubDir,'String',SubDir);
568        set(handles.RootFile,'String',['/' RootFile]); %display the separator
569        indices=fileinput(length(rootname)+1:end);
570        indices(end-length(ext)+1:end)=[]; %remove extension
571        set(handles.FileIndex,'String',indices);       
572        set(handles.FileIndex,'UserData',NomType);
573        set(handles.FileExt,'String',ext);
574        % fill file index counters
575        set(handles.i1,'String',i1);   
576        set(handles.i2,'String',i2);
577        set(handles.j1,'String',str_a);
578        set(handles.j2,'String',str_b);
579       
580        % synchronise indices of the second  input file if it exists
581        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
582            [ff,rr,FileBase_1,ii,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
583            NomType_1=get(handles.FileIndex_1,'UserData');     
584            FileName_1=name_generator(FileBase_1,str2double(i1),str2double(i2),FileExt_1,NomType_1,1,stra2num(str_a),stra2num(str_b),SubDir_1);
585            if exist(FileName_1,'file')
586                FileIndex_1=name_generator('',str2double(i1),str2double(i2),'',NomType_1,1,stra2num(str_a),stra2num(str_b),'');
587                set(handles.FileIndex_1,'String',FileIndex_1)
588            else
589                set(handles.SubField,'Value',0)
590                SubField_Callback(hObject, eventdata, handles)
591            end
592        end 
593
594        %enable other menus
595        set(handles.MenuOpen_1,'Enable','on')
596        set(handles.MenuFile_1_1,'Enable','on')
597        set(handles.MenuFile_2_1,'Enable','on')
598        set(handles.MenuFile_3_1,'Enable','on')
599        set(handles.MenuFile_4_1,'Enable','on')
600        set(handles.MenuFile_5_1,'Enable','on')
601        set(handles.MenuExport,'Enable','on')
602        set(handles.MenuExportFigure,'Enable','on')
603        set(handles.MenuExportMovie,'Enable','on')
604        set(handles.MenuTools,'Enable','on')
605        set(handles.OBJECT_txt,'Visible','on')
606        set(handles.edit,'Visible','on')
607        set(handles.list_object_1,'Visible','on')
608        set(handles.frame_object,'Visible','on')
609         % initiate input file:
610        update_rootinfo(hObject,eventdata,handles); 
611    otherwise
612       msgbox_uvmat('ERROR',['invalid input file extension' ext])
613end
614
615%------------------------------------------------------------------------
616% --- Called by action in RootPath edit box
617function RootPath_Callback(hObject,eventdata,handles)
618%------------------------------------------------------------------------
619update_rootinfo(hObject,eventdata,handles);
620
621%------------------------------------------------------------------------
622% --- Called by action in RootFile edit box
623function SubDir_Callback(hObject, eventdata, handles)
624%------------------------------------------------------------------------
625%refresh the menu of input fields
626Fields_Callback(hObject, eventdata, handles);
627% refresh the current field
628run0_Callback(hObject, eventdata, handles);
629
630%------------------------------------------------------------------------
631% --- Called by action in RootFile edit box
632function RootFile_Callback(hObject, eventdata, handles)
633%------------------------------------------------------------------------
634update_rootinfo(hObject,eventdata,handles)
635
636%------------------------------------------------------------------------
637% --- Called by action in FileIndex edit box
638function FileIndex_Callback(hObject, eventdata, handles)
639%------------------------------------------------------------------------
640FileIndices=get(handles.FileIndex,'String');
641if isempty(str2num(FileIndices))
642    [pp,ff,str1,str2,str_a,str_b]=name2display(FileIndices);
643else
644    str1=FileIndices;
645    str2='';
646    str_a='';
647    str_b='';
648end
649set(handles.i1,'String',str1);
650set(handles.i2,'String',str2);
651set(handles.j1,'String',str_a);
652set(handles.j2,'String',str_b);
653run0_Callback(hObject, eventdata, handles)
654
655%------------------------------------------------------------------------
656% --- Update information about a new field series (indices to scan, timing,
657%     calibration from an xml file, then refresh current plots
658function update_rootinfo(hObject,eventdata,handles)
659%------------------------------------------------------------------------
660set(handles.RootPath,'BackgroundColor',[1 1 0])
661drawnow
662set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
663UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
664UvData.NewSeries=1; %flag for run0: begin a new series
665UvData.TestInputFile=1;
666set(handles.fix_pair,'Value',1) % activate by default the comp_input '-'input window
667
668[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
669if ~exist(FileName,'file')
670   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
671    return
672end
673nbfield=[];%default
674nburst=[];%default
675
676% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
677XmlData.Time=[];%default
678XmlData.GeometryCalib=[];%default
679TimeUnit=[];%default
680testima=0; %test for image input
681imainfo=[];
682ColorType='falsecolor'; %default
683hhh='';
684if isequal(lower(FileExt),'.avi') %.avi file
685    testima=1;
686    imainfo=aviinfo([FileBase FileIndices FileExt]);
687    nbfield=imainfo.NumFrames;
688    nburst=1;
689    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
690    XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
691    TimeUnit='s';
692    hhh=which('mmreader');
693    ColorType=imainfo.ImageType;%='truecolor' for color images
694elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
695    testima=1;
696    if ~isequal(SubDir,'')
697       RootFile=get(handles.RootFile,'String');
698        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
699    else
700        imainfo=imfinfo([FileBase FileIndices FileExt]);
701    end
702    ColorType=imainfo.ColorType;%='truecolor' for color images
703    if length(imainfo) >1 %case of image with multiple frames
704        nbfield=length(imainfo);
705        nburst=1;
706    end
707end
708if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
709    UvData.MovieObject=mmreader([FileBase FileIndices FileExt]);
710elseif isfield(UvData,'MovieObject')
711    UvData=rmfield(UvData,'MovieObject');
712end
713if isfield(imainfo,'Width') && isfield(imainfo,'Height')
714    set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
715    set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
716else
717    set(handles.npx,'String','');%fills nbre of pixels x box
718    set(handles.npy,'String','');%fills nbre of pixels x box
719end
720set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
721
722% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
723filexml=[FileBase '.xml'];
724fileciv=[FileBase '.civ'];
725warntext='';%default warning message
726NbSlice=1;%default
727
728if exist(filexml,'file')
729    set(handles.view_xml,'Visible','on')
730    set(handles.view_xml,'BackgroundColor',[1 1 0])
731    set(handles.RootPath,'BackgroundColor',[1 1 1])
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        hgeometry_calib=findobj('tag','geometry_calib');
747        if ~isempty(hgeometry_calib)
748            GUserData=get(hgeometry_calib,'UserData');
749            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
750                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
751                if strcmp(answer,'Yes')
752                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
753                end
754            end
755        end
756    end 
757elseif exist(fileciv,'file')% if .civ file found
758    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
759    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
760    GeometryCalib.Tx=0;
761    GeometryCalib.Ty=0;
762    GeometryCalib.Tz=1;
763    GeometryCalib.dpx=1;
764    GeometryCalib.dpy=1;
765    GeometryCalib.sx=1;
766    GeometryCalib.Cx=0;
767    GeometryCalib.Cy=0;
768    GeometryCalib.f=1;
769    GeometryCalib.kappa1=0;
770    GeometryCalib.CoordUnit='cm';
771    XmlData.GeometryCalib=GeometryCalib;
772    if error==2, warntext=['no file ' FileBase '.civ'];
773    elseif error==1, warntext='inconsistent number of fields in the .civ file';
774    end 
775    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
776    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
777    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
778    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
779    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
780    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
781    set(handles.view_xml,'Visible','on')   
782    set(handles.view_xml,'String','view .civ')
783else
784    set(handles.view_xml,'Visible','off')
785end
786
787% store last index in handles.lat_i and .last_j
788if ~isempty(XmlData.Time)
789    nbfield=size(XmlData.Time,1);
790    nburst=size(XmlData.Time,2);
791    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
792    if isequal(nbfield,1) && ~isequal(nburst,1)% .Time is a line vector
793        NomType=get(handles.FileIndex,'UserData');
794        if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
795            XmlData.Time=(XmlData.Time)';
796            nbfield=nburst;
797            nburst=1;
798        end
799    end
800end
801last_i_cell=get(handles.last_i,'String');
802if isempty(nbfield)
803    last_i_cell{1}='';
804else
805    last_i_cell{1}=num2str(nbfield);
806end
807set(handles.last_i,'String',last_i_cell)
808last_j_cell=get(handles.last_j,'String');
809if isempty(nburst)
810     last_j_cell{1}='';
811else
812     last_j_cell{1}=num2str(nburst);
813end
814set(handles.last_j,'String',last_j_cell);
815
816% store geometric calibration in UvData
817if isfield(XmlData,'GeometryCalib')
818    GeometryCalib=XmlData.GeometryCalib;
819    if isempty(GeometryCalib)
820        set(handles.pxcm,'String','')
821        set(handles.pycm,'String','')
822        set(handles.transform_fct,'Value',1); %  no transform by default
823    else
824        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
825            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
826            set(handles.pxcm,'String','var')
827            set(handles.pycm,'String','var')
828        elseif isfield(GeometryCalib,'fx_fy')
829            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
830            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
831            set(handles.pxcm,'String',num2str(pixcmx))
832            set(handles.pycm,'String',num2str(pixcmy))
833        end
834        if ~get(handles.FixedLimits,'Value')
835            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
836        end
837        if isfield(GeometryCalib,'SliceCoord')
838           
839           siz=size(GeometryCalib.SliceCoord);
840           if siz(1)>1
841               NbSlice=siz(1);
842               set(handles.slices,'Visible','on')
843               set(handles.slices,'Value',1)
844           end
845           if isfield(GeometryCalib,'NbSlice') && isequal(GeometryCalib.NbSlice,'volume')
846               set(handles.nb_slice,'String','volume')
847           else
848               set(handles.nb_slice,'String',num2str(NbSlice))
849           end
850           slices_Callback(hObject, eventdata, handles)
851        end           
852    end
853end
854
855%update the data attached to the uvmat interface
856if ~isempty(TimeUnit)
857    set(handles.time_txt,'String',['time (' TimeUnit ')'])
858end
859UvData.TimeUnit=TimeUnit;
860UvData.XmlData=XmlData;
861UvData.NewSeries=1;
862set(handles.uvmat,'UserData',UvData)
863
864%display warning message
865if ~isequal(warntext,'')
866    msgbox_uvmat('WARNING',warntext);
867end
868
869% set default options in menu 'Fields'
870if testima
871   set(handles.Fields,'Value',1) % set menu to 'image'
872   set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'})
873elseif isequal(FileExt,'.nc')||isequal(FileExt,'.cdf')
874   Data=nc2struct(FileName,'ListGlobalAttribute','absolut_time_T0','civ');
875   col_vec=get(handles.col_vec,'String');
876   if ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0)
877       set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'})
878       set(handles.Fields,'Value',3) % set menu to 'velocity'
879       col_vec{1}='ima_cor';
880   else %general netcdf file (not civx)
881       set(handles.Fields,'Value',1) % set menu to 'get_field...
882       set(handles.Fields,'String',{'get_field...'})
883       col_vec{1}='get_field...';
884   end
885   set(handles.col_vec,'String',col_vec)
886else
887    msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
888    return
889end 
890
891% set index navigation options and refresh plots
892set(handles.RootPath,'BackgroundColor',[1 1 1])
893drawnow
894set_scan_options(hObject, eventdata, handles)
895
896%------------------------------------------------------------------------
897%--- Set index navigation options for new series input and refresh plot
898%------------------------------------------------------------------------
899function set_scan_options(hObject, eventdata, handles)
900
901%  set the corresponding index navigation options
902NomType=get(handles.FileIndex,'UserData');       
903NomType_1=get(handles.FileIndex_1,'UserData');
904last_i_str=get(handles.last_i,'String');
905nbfield=str2num(last_i_str{1});
906if numel(last_i_str)==2
907    nbfield=min(nbfield,str2num(last_i_str{2}));
908end 
909state_j='off'; %default
910scan_option='i';%default
911NomTypeRaw=regexprep(NomType(2:end), '-', '');
912if numel(regexp(NomTypeRaw,'\D'))>=1
913%     case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab','#A','%01dA','%02dA','%03dA','%04dA'},% two navigation indices
914        state_j='on';
915        if isequal(nbfield,1)
916            scan_option='j'; %scan j index by default if nbfield=1               
917        end
918end
919if ~isempty(NomType_1)
920    NomTypeRaw=regexprep(NomType_1(2:end), '-', '');
921    if numel(regexp(NomTypeRaw,'\D'))>=1
922%     switch NomType_1
923%         case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices
924            state_j='on';
925            if isequal(nbfield,1)
926                scan_option='j';                 
927            end           
928    end
929end
930if isequal(scan_option,'i')
931     set(handles.scan_i,'Value',1)
932     scan_i_Callback(hObject, eventdata, handles);
933else
934     set(handles.scan_j,'Value',1)
935     scan_j_Callback(hObject, eventdata, handles);
936end
937set(handles.scan_j,'Visible',state_j)
938set(handles.j1,'Visible',state_j)
939set(handles.j2,'Visible',state_j)
940set(handles.last_j,'Visible',state_j);
941set(handles.frame_j,'Visible',state_j);
942set(handles.j_text,'Visible',state_j);
943
944% view the field 
945run0_Callback(hObject, eventdata, handles); %view field
946mask_test=get(handles.mask_test,'value');
947if mask_test
948    MaskData=get(handles.mask_test,'UserData');
949    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
950          delete(MaskData.maskhandle)    %delete old mask
951    end
952    mask_test_Callback(hObject, eventdata, handles)
953end
954
955%------------------------------------------------------------------------
956% --- Executes on the menu Open/Browse_1 for the second input field,
957%     search the files, recognize their type according to their name and fill the rootfile input windows
958function MenuBrowse_1_Callback(hObject, eventdata, handles)
959%-------------------------------------------------------------------
960% huvmat=get(handles.run0,'parent');
961UvData=get(handles.uvmat,'UserData');
962
963RootPath=get(handles.RootPath,'String');
964[FileName, PathName, filterindex] = uigetfile( ...
965       {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
966       '*.xml',  '.xml files '; ...
967        '*.xls',  '.xls files '; ...
968        '*.civ',  '.civ files '; ...
969        '*.jpg','.jpg image files'; ...
970        '*.png','.png image files'; ...
971        '*.avi;*.AVI','.avi movie files'; ...
972        '*.nc','.netcdf files'; ...
973        '*.cdf','.netcdf files'; ...
974        '*.cmx','.cmx text files';...
975        '*.cmx2','.cmx2 text files';...
976        '*.fig','.fig files (matlab fig)';...
977        '*.log','.log text files ';...
978        '*.dat','.dat text files ';...
979        '*.*',  'All Files (*.*)'}, ...
980        'Pick a file',RootPath);
981fileinput_1=[PathName FileName];%complete file name
982testblank=findstr(fileinput_1,' ');%look for blanks
983if ~isempty(testblank)
984    msgbox_uvmat('ERROR',['The input file name ' fileinput_1 ' contains blank character : This is not allowed. Please change name'])
985    return
986end
987sizf=size(fileinput_1);
988if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
989
990% refresh the current displayed field
991display_file_name_1(hObject,eventdata,handles,fileinput_1)
992
993%update list of recent files in the menubar
994MenuFile_1=fileinput_1;
995MenuFile_2=get(handles.MenuFile_1,'Label');
996MenuFile_3=get(handles.MenuFile_2,'Label');
997MenuFile_4=get(handles.MenuFile_3,'Label');
998MenuFile_5=get(handles.MenuFile_4,'Label');
999set(handles.MenuFile_1,'Label',MenuFile_1)
1000set(handles.MenuFile_2,'Label',MenuFile_2)
1001set(handles.MenuFile_3,'Label',MenuFile_3)
1002set(handles.MenuFile_4,'Label',MenuFile_4)
1003set(handles.MenuFile_5,'Label',MenuFile_5)
1004set(handles.MenuFile_1_1,'Label',MenuFile_1)
1005set(handles.MenuFile_2_1,'Label',MenuFile_2)
1006set(handles.MenuFile_3_1,'Label',MenuFile_3)
1007set(handles.MenuFile_4_1,'Label',MenuFile_4)
1008set(handles.MenuFile_5_1,'Label',MenuFile_5)
1009dir_perso=prefdir;
1010profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1011if exist(profil_perso,'file')
1012    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
1013else
1014    txt=ver;
1015    Release=txt(1).Release;
1016    relnumb=str2num(Release(3:4));
1017    if relnumb >= 14
1018        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
1019    else
1020        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
1021    end
1022end
1023
1024% -----------------------------------------------------------------------
1025% --- Open again as second field the file whose name has been recorded in MenuFile_1
1026function MenuFile_1_1_Callback(hObject, eventdata, handles)
1027fileinput_1=get(handles.MenuFile_1_1,'Label');
1028display_file_name_1(hObject,eventdata,handles,fileinput_1)
1029
1030% -----------------------------------------------------------------------
1031% --- Open again as second field the file whose name has been recorded in MenuFile_2
1032function MenuFile_2_1_Callback(hObject, eventdata, handles)
1033fileinput_1=get(handles.MenuFile_2_1,'Label');
1034display_file_name_1(hObject,eventdata,handles,fileinput_1)
1035
1036% -----------------------------------------------------------------------
1037% --- Open again as second field the file whose name has been recorded in MenuFile_3
1038function MenuFile_3_1_Callback(hObject, eventdata, handles)
1039fileinput_1=get(handles.MenuFile_3_1,'Label');
1040display_file_name_1(hObject,eventdata,handles,fileinput_1)
1041
1042% -----------------------------------------------------------------------
1043% --- Open again as second field the file whose name has been recorded in MenuFile_4
1044function MenuFile_4_1_Callback(hObject, eventdata, handles)
1045fileinput_1=get(handles.MenuFile_4_1,'Label');
1046display_file_name_1(hObject,eventdata,handles,fileinput_1)
1047
1048% -----------------------------------------------------------------------
1049% --- Open again as second field the file whose name has been recorded in MenuFile_5
1050function MenuFile_5_1_Callback(hObject, eventdata, handles)
1051fileinput_1=get(handles.MenuFile_5_1,'Label');
1052display_file_name_1(hObject,eventdata,handles,fileinput_1)
1053
1054%------------------------------------------------------------------------
1055% fills the edit boxes RootPath_1, RootFile_1,NomType_1...from an input file name 'fileinput_1'
1056%------------------------------------------------------------------------
1057function display_file_name_1(hObject,eventdata,handles,fileinput_1)
1058
1059%[path,name,ext]=fileparts(fileinput_1);
1060[RootPath_1,RootFile_1,field_count,str2,str_a,str_b,FileExt_1,NomType_1,SubDir_1]=name2display(fileinput_1);
1061nbfield_1=1; %default
1062ext_test=FileExt_1;%default
1063form=imformats(FileExt_1(2:end));
1064if ~isempty(form) % if the extension corresponds to an image format recognized by Matlab
1065    imainfo=imfinfo(fileinput_1); 
1066    nbfield_1=length(imainfo);
1067    ext_test='.image';
1068elseif isequal(lower(FileExt_1),'.avi')
1069    info=aviinfo(fileinput_1);
1070    nbfield_1=info.NumFrames;
1071    ext_test='.image';
1072end
1073
1074%open directly fig or text files
1075switch ext_test
1076    case {'.civ','.log','.cmx','.cmx2','.txt'}  %display text file
1077        edit(fileinput) 
1078        return
1079    case '.fig'                           %display matlab figure
1080        hfig=open(fileinput);
1081        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
1082        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
1083        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
1084        return
1085    case {'.xml','.xls'}                % edit xml or Excel files
1086       heditxml=editxml(fileinput);
1087       return
1088    case {'.image','.nc','.cdf'}
1089%         set(handles.FileIndex,'UserData',NomType_1);
1090    otherwise
1091        msgbox_uvmat(['invalid input file extension ' FileExt_1 ' for uvmat'],'ERROR')
1092        return
1093end
1094
1095% test for image series in a single file and synchronise file indices of the two series
1096if nbfield_1 >1 %case of image with multiple frames
1097    if nbfield_1 < num_i1
1098        msgbox_uvmat('ERROR','current frame index beyond the input movie length')
1099        return
1100    else
1101        NomType_1='*'; %indicate a set of indexed frames within a single file
1102        filename_new=fileinput_1;
1103    end
1104else  % cases of data files   
1105    RootPath=get(handles.RootPath,'String');
1106    RootFile=get(handles.RootFile,'String');
1107    FileBase=fullfile(RootPath,RootFile);
1108    FileBase_1=fullfile(RootPath_1,RootFile_1);
1109    if isequal(FileBase,FileBase_1)
1110        filename_new=fileinput_1;
1111    else       
1112        num_i1=stra2num(get(handles.i1,'String'));%get the current file indices from counters
1113        num_j1=stra2num(get(handles.j1,'String'));
1114        num_i2=stra2num(get(handles.i2,'String'));
1115        num_j2=stra2num(get(handles.j2,'String'));
1116        [filename_new,idetect]=...
1117           name_generator(FileBase_1,num_i1,num_j1,FileExt_1,NomType_1,1,num_i2,num_j2,SubDir_1);%create name with indices synchronised with the first file
1118        indices=''; %default
1119        if ~idetect
1120            msgbox_uvmat('ERROR','second input file with indices corresponding to the first one does not exist')
1121            return
1122        end
1123    end
1124end
1125set(handles.FileIndex_1,'UserData',NomType_1);
1126
1127% make visible and fill the second raw of edit boxes
1128set(handles.RootPath_1,'Visible','on')
1129set(handles.RootFile_1,'Visible','on')
1130set(handles.SubDir_1,'Visible','on');
1131set(handles.FileIndex_1,'Visible','on');
1132set(handles.FileExt_1,'Visible','on');
1133[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
1134if isequal(FileBase,FileBase_1)
1135    set(handles.RootPath_1,'String','"')
1136    set(handles.RootFile_1,'String','"');
1137else
1138    set(handles.RootPath_1,'String',RootPath_1)
1139    set(handles.RootFile_1,'String',['/' RootFile_1]);
1140end
1141if  isequal(SubDir_1,'')
1142     set(handles.SubDir_1,'String','');
1143     FileBaseSub_1=FileBase_1;
1144else 
1145    set(handles.SubDir_1,'String',['/' SubDir_1]);
1146    FileBaseSub_1=fullfile(FileBase_1,SubDir_1);
1147end
1148indices=filename_new(length(FileBaseSub_1)+1:end);
1149indices(end-length(FileExt_1)+1:end)=[]; %remove extension
1150set(handles.FileIndex_1,'String',indices)
1151set(handles.FileIndex_1,'UserData',NomType_1)
1152set(handles.FileExt_1,'String',FileExt_1);
1153
1154% default choice of fields
1155if isequal(ext_test,'.image')
1156   set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1157   set(handles.Fields_1,'Value',2) % set menu to 'image'
1158elseif strcmp(FileExt_1,'.nc')||strcmp(FileExt_1,'.cdf')
1159   Data=nc2struct(fileinput_1,[]);
1160   if isfield(Data,'absolut_time_T0')
1161       set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1162       set(handles.Fields_1,'Value',4) % set menu to 'velocity'
1163   else   
1164       set(handles.Fields_1,'Value',2) % set menu to 'get_field...'
1165       set(handles.Fields_1,'String',{'';'get_field...'});
1166   end
1167end 
1168set(handles.SubField,'Visible','on')
1169set(handles.SubField,'Value',1)
1170RootPath_1_Callback(hObject,eventdata,handles); 
1171
1172%-----------------------------------------------------------------------
1173% --- Called by action in RootPath_1 edit box
1174function RootPath_1_Callback(hObject,eventdata,handles)
1175update_rootinfo_1(hObject,eventdata,handles)
1176
1177%-----------------------------------------------------------------------
1178% --- Called by action in RootFile_1 edit box
1179function RootFile_1_Callback(hObject, eventdata, handles)
1180update_rootinfo_1(hObject,eventdata,handles)
1181%-----------------------------------------------------------------------
1182
1183%------------------------------------------------------------------------
1184% --- Called by action in FileIndex_1 edit box
1185function FileIndex_1_Callback(hObject, eventdata, handles)
1186%------------------------------------------------------------------------
1187
1188run0_Callback(hObject, eventdata, handles)
1189
1190%------------------------------------------------------------------------
1191% --- Update information about a new second field series (indices to scan, timing,
1192%     calibration from an xml file, then refresh current plots
1193function update_rootinfo_1(hObject,eventdata,handles) %A REVOIR
1194
1195set(handles.RootPath_1,'BackgroundColor',[1 1 0])% indicate active program by yellow color
1196drawnow
1197UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
1198UvData.NewSeries=1; %flag for run0: begin a new series
1199
1200[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes_1(handles);
1201if ~exist(FileName,'file')
1202    msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
1203end
1204nbfield_1=[];%default
1205nburst_1=[];%default
1206XmlData.Time=[];
1207XmlData.GeometryCalib=[];%default
1208TimeUnit=[];
1209if isfield(UvData,'TimeUnit')
1210    TimeUnit=UvData.TimeUnit;
1211end
1212TimeUnit_1=[];
1213hhh='';%default, test for  movie reading with mmreader
1214imainfo=[];
1215if isequal(lower(FileExt),'.avi') %.avi file
1216    imainfo=aviinfo([FileBase FileIndices FileExt]);
1217    nbfield_1=imainfo.NumFrames;
1218    nburst_1=1;
1219    set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
1220    time=[0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond]';
1221    ColorType=imainfo.ImageType;%='truecolor' for color images
1222    hhh=which('mmreader');
1223elseif ~isempty(imformats(FileExt(2:end)))|| isequal(FileExt,'.vol')
1224    if ~isequal(SubDir,'')
1225        RootFile=get(handles.RootFile,'String');
1226        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
1227    else
1228        imainfo=imfinfo([FileBase FileIndices FileExt]);
1229    end
1230    ColorType=imainfo.ColorType;%='truecolor' for color images
1231    if length(imainfo) >1 %case of image with multiple frames
1232        nbfield_1=length(imainfo);
1233        nburst_1=1;
1234    end
1235end
1236if ~strcmp(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
1237    UvData.MovieObject_1=mmreader([FileBase FileIndices FileExt]);
1238elseif isfield(UvData,'MovieObject_1')
1239    UvData=rmfield(UvData,'MovieObject_1');
1240end
1241if ~isempty(imainfo)% (an image has been introduced as second fierld input)
1242    if strcmp(get(handles.npx,'String'),'') || strcmp(get(handles.npy,'String'),'')%update npx and npy if it is not already filled by the first input field
1243        if  isfield(imainfo,'Width') && isfield(imainfo,'Height')
1244            set(handles.npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
1245            set(handles.npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
1246        else
1247            set(handles.npx,'String','');%fills nbre of pixels x box
1248            set(handles.npy,'String','');%fills nbre of pixels x box
1249        end
1250        set(handles.BW,'Value',strcmp(ColorType,'grayscale'))% select handles.BW if grayscale image
1251    end
1252end
1253% find scaling parameters
1254filexml=[FileBase '.xml'];
1255fileciv=[FileBase '.civ'];
1256warntext='';%default warning text
1257if exist(filexml,'file')
1258    [XmlData,warntext]=imadoc2struct(filexml);
1259    if ~isempty(warntext)
1260        msgbox_uvmat('WARNING',warntext)
1261    end
1262    if isfield(XmlData,'Camera')
1263        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1264            TimeUnit=XmlData.Camera.TimeUnit;
1265        end
1266    end
1267elseif exist(fileciv,'file')% if .civ file found
1268    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
1269    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
1270    GeometryCalib.Tx=0;
1271    GeometryCalib.Ty=0;
1272    GeometryCalib.Tz=1;
1273    GeometryCalib.dpx=1;
1274    GeometryCalib.dpy=1;
1275    GeometryCalib.sx=1;
1276    GeometryCalib.Cx=0;
1277    GeometryCalib.Cy=0;
1278    GeometryCalib.f=1;
1279    GeometryCalib.kappa1=0;
1280    GeometryCalib.CoordUnit='cm';
1281    XmlData.GeometryCalib=GeometryCalib;
1282    if error==2, warntext=['no file ' FileBase '.civ'];
1283    elseif error==1, warntext='inconsistent number of fields in the .civ file';
1284    end
1285   
1286    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
1287    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
1288    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
1289    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
1290    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
1291    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
1292end   
1293if ~isempty(TimeUnit_1) && ~isequal(TimeUnit_1,TimeUnit)
1294        msgbox_uvmat('WARNING','the time units for the second series differs from the first one')
1295end
1296       
1297% store last index in handles.lat_i and .last_j
1298if ~isempty(XmlData.Time)
1299    nbfield_1=size(XmlData.Time,1);
1300    nburst_1=size(XmlData.Time,2);   
1301end
1302last_i_cell=get(handles.last_i,'String');
1303if isempty(nbfield_1)
1304    last_i_cell{2}='';
1305else
1306    last_i_cell{2}=num2str(nbfield_1);
1307end
1308set(handles.last_i,'String',last_i_cell)
1309last_j_cell=get(handles.last_j,'String');
1310if isempty(nburst_1)
1311     last_j_cell{2}='';
1312else
1313     last_j_cell{2}=num2str(nburst_1);
1314end
1315set(handles.last_j,'String',last_j_cell);
1316if ~isequal(last_i_cell{1},last_i_cell{2}) || ~isequal(last_j_cell{1},last_j_cell{2})
1317        msgbox_uvmat('WARNING','the numbers of input file of the second series differs from the first one')
1318end
1319
1320% store calibration data
1321GeometryCalib=XmlData.GeometryCalib;
1322if isempty(GeometryCalib)
1323    if isfield(UvData, 'GeometryCalib_1')
1324        UvData=rmfield(UvData,'GeometryCalib_1');
1325    end
1326else
1327    UvData.GeometryCalib_1=GeometryCalib;
1328    if (isfield(GeometryCalib,'R')& ~isequal(GeometryCalib.R(2,1),0) & ~isequal(GeometryCalib.R(1,2),0)) |...
1329        (isfield(GeometryCalib,'kappa1')& ~isequal(GeometryCalib.kappa1,0))
1330        set(handles.pxcm,'String','var')
1331        set(handles.pycm,'String','var')
1332    else
1333        pixcmx=GeometryCalib.f*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
1334        pixcmy=GeometryCalib.f*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
1335        set(handles.pxcm,'String',num2str(pixcmx))
1336        set(handles.pycm,'String',num2str(pixcmy))
1337    end
1338end
1339UvData.XmlData_1=XmlData;
1340set(handles.uvmat,'UserData',UvData)%update the data attached to the uvmat interface
1341
1342if ~isequal(warntext,'')
1343    msgbox_uvmat('WARNING',warntext)
1344end
1345
1346set(handles.RootPath_1,'BackgroundColor',[1 1 1])% signa the end the input operation
1347drawnow
1348
1349set_scan_options(hObject, eventdata, handles)
1350
1351%---------------------------------------------------
1352% switch file index scanning options scan_i and scan_j in an exclusive way
1353function scan_i_Callback(hObject, eventdata, handles)
1354%---------------------------------------------------
1355if get(handles.scan_i,'Value')==1
1356    set(handles.scan_i,'BackgroundColor',[1 1 0])
1357    set(handles.scan_j,'Value',0)
1358%     set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1359else
1360    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1361    set(handles.scan_j,'Value',1)
1362%     set(handles.scan_j,'BackgroundColor',[1 1 0])
1363end
1364scan_j_Callback(hObject, eventdata, handles)
1365
1366%-------------------------------------------------------------------
1367% switch file index scanning options scan_i and scan_j in an exclusive way
1368function scan_j_Callback(hObject, eventdata, handles)
1369%-------------------------------------------------------------------
1370if get(handles.scan_j,'Value')==1
1371    set(handles.scan_j,'BackgroundColor',[1 1 0])
1372    set(handles.scan_i,'Value',0)
1373    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1374    NomType=get(handles.FileIndex,'UserData');
1375    switch NomType
1376    case {'_i_j1-j2','#_ab','%3dab'},% pair with j index
1377        set(handles.fix_pair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1378    otherwise
1379        set(handles.fix_pair,'Visible','off')
1380    end
1381else
1382    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1383    set(handles.scan_i,'Value',1)
1384    set(handles.scan_i,'BackgroundColor',[1 1 0])
1385    set(handles.fix_pair,'Visible','off')
1386end
1387
1388%-------------------------------------------------------------------
1389function i1_Callback(hObject, eventdata, handles)
1390%-------------------------------------------------------------------
1391set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1392NomType=get(handles.FileIndex,'UserData');
1393num1=stra2num(get(handles.i1,'String'));
1394num2=stra2num(get(handles.i2,'String'));
1395num_a=stra2num(get(handles.j1,'String'));
1396num_b=stra2num(get(handles.j2,'String'));
1397indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1398set(handles.FileIndex,'String',indices)
1399set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1400if get(handles.SubField,'Value')==1
1401    NomType_1=get(handles.FileIndex_1,'String');
1402     FileExt_1=get(handles.FileExt_1,'String');
1403    [P,F,str1,str2,str_a,str_b,Ext,NomType_1]=name2display(['xx' NomType_1 FileExt_1]);
1404     indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1405     set(handles.FileIndex_1,'String',indices)
1406     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1407end
1408%Run0_Callback(hObject, eventdata, handles)
1409
1410%-------------------------------------------------------------------
1411function i2_Callback(hObject, eventdata, handles)
1412set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1413i1_Callback(hObject, eventdata, handles)
1414%-------------------------------------------------------------------
1415
1416%-------------------------------------------------------------------
1417function j1_Callback(hObject, eventdata, handles)
1418set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1419i1_Callback(hObject, eventdata, handles)
1420%-------------------------------------------------------------------
1421
1422%-------------------------------------------------------------------
1423function j2_Callback(hObject, eventdata, handles)
1424set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1425i1_Callback(hObject, eventdata, handles)
1426%-------------------------------------------------------------------
1427
1428%-------------------------------------------------------------------
1429function slices_Callback(hObject, eventdata, handles)
1430%-------------------------------------------------------------------
1431if get(handles.slices,'Value')==1
1432    set(handles.slices,'BackgroundColor',[1 1 0])
1433    set(handles.nb_slice,'Visible','on')
1434    set(handles.z_text,'Visible','on')
1435    set(handles.z_index,'Visible','on')
1436    nb_slice_Callback(hObject, eventdata, handles)
1437else
1438    set(handles.nb_slice,'Visible','off')
1439    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1440    set(handles.z_text,'Visible','off')
1441    set(handles.z_index,'Visible','off')
1442    set(handles.masklevel,'Value',1)
1443    set(handles.masklevel,'String',{'1'})
1444end
1445
1446%-------------------------------------------------------------------
1447function nb_slice_Callback(hObject, eventdata, handles)
1448%-------------------------------------------------------------------
1449nb_slice_str=get(handles.nb_slice,'String');
1450if isequal(nb_slice_str,'volume')
1451    num=stra2num(get(handles.j1,'String'));
1452    last_j=get(handles.last_j,'String');
1453    nbslice=str2double(last_j{1});
1454else
1455    num=str2double(get(handles.i1,'String'));
1456    nbslice=str2double(get(handles.nb_slice,'String'));
1457end
1458z=mod(num-1,nbslice)+1;
1459set(handles.z_index,'String',num2str(z))
1460for ilist=1:nbslice
1461    list_index{ilist,1}=num2str(ilist);
1462end   
1463set(handles.masklevel,'String',list_index)
1464set(handles.masklevel,'Value',z)
1465
1466%-------------------------------------------------------------------
1467% --- Executes on button press in view_xml.
1468function view_xml_Callback(hObject, eventdata, handles)
1469[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1470option=get(handles.view_xml,'String');
1471if isequal(option,'view .xml')
1472    FileXml=[FileBase '.xml'];
1473    heditxml=editxml(FileXml);
1474end
1475
1476%-------------------------------------------------------------------
1477% --- Executes on button press in mask_test.
1478function mask_test_Callback(hObject, eventdata, handles)
1479%-------------------------------------------------------------------
1480%case of view mask selection
1481if isequal(get(handles.mask_test,'Value'),1)
1482    [FF,RootPath,FileBase]=read_file_boxes(handles);
1483    num_i1=stra2num(get(handles.i1,'String'));
1484    num_j1=stra2num(get(handles.j1,'String'));
1485    currentdir=pwd; 
1486    cd(RootPath);
1487    maskfiles=dir('*_*mask_*.png');%look for a mask file
1488    cd(currentdir);%come back to the working directory
1489    mdetect=0;
1490    if ~isempty(maskfiles)
1491        for ilist=1:length(maskfiles)
1492            maskname=maskfiles(ilist).name;% take the first mask file in the list
1493            [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1494            if ~strcmp(Mask_NomType{ilist},Mask_NomType{1})
1495                msgbox_uvmat('ERROR',['inconsistent mask types ' Mask_NomType{1} Mask_NomType{ilist } ' coexist in the current image directory'])
1496                return
1497            end
1498            [Path2,Name,ext]=fileparts(maskname);
1499            Namedouble=double(Name);
1500            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1501            ind_mask=findstr('mask',Name);
1502            i=ind_mask-1;
1503            while val(i)==0 && i>0
1504                i=i-1;
1505            end
1506            nbmask_str=str2num(Name(i+1:ind_mask-1));
1507            if ~isempty(nbmask_str)
1508                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1509            end
1510        end
1511        if isequal(min(nbslice),max(nbslice))
1512            nbslice=nbslice(1);
1513        else
1514            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1515            return
1516        end
1517        if ~isempty(nbslice) && Name(i)=='_'
1518            Mask.Base=[FileBase Name(i:ind_mask+3)];
1519            Mask.NbSlice=nbslice;
1520            num_i1=mod(num_i1-1,nbslice)+1;
1521            Mask.NomType=Mask_NomType{1};
1522            [maskname,mdetect]=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1523            mdetect=exist(maskname,'file');
1524            if mdetect
1525                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1526                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1527                set(handles.mask_test,'UserData',Mask);
1528                set(handles.mask_test,'BackgroundColor',[1 1 0])
1529                if nbslice > 1
1530                    set(handles.slices,'value',1)
1531                    slices_Callback(hObject, eventdata, handles)
1532                end
1533            end
1534        end
1535%         if mdetect==0
1536%             msgbox_uvmat('ERROR','no mask file detected (format ..._xxmask_ii.png needed), use the menu bar Tools/Make mask')
1537%             set(handles.mask_test,'Value',0)
1538%             return
1539%         end
1540    end
1541    errormsg=[];%default
1542    if mdetect==0
1543        [FileName, PathName, filterindex] = uigetfile( ...
1544            {'*.png', ' (*.png)';
1545            '*.png',  '.png files '; ...
1546            '*.*', 'All Files (*.*)'}, ...
1547            'Pick a mask file *.png',FileBase);
1548        maskname=fullfile(PathName,FileName);
1549        if ~exist(maskname,'file')
1550            errormsg='no file browsed';
1551        end
1552        [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1553        Mask.Base=fullfile(RootDir,RootFile);
1554        Mask.NbSlice=1;
1555        set(handles.mask_test,'UserData',Mask);
1556        set(handles.mask_test,'BackgroundColor',[1 1 0])
1557    end
1558    if isempty(errormsg)
1559        errormsg=update_mask(handles,num_i1,num_j1);
1560    end
1561    if ~isempty(errormsg)
1562            set(handles.mask_test,'Value',0)
1563            set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1564     end
1565else
1566    MaskData=get(handles.mask_test,'UserData');
1567    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1568          delete(MaskData.maskhandle)   
1569    end
1570    set(handles.mask_test,'UserData',[])   
1571    %huvmat=get(handles.mask_test,'parent');
1572    UvData=get(handles.uvmat,'UserData');
1573    if isfield(UvData,'MaskName')
1574        UvData=rmfield(UvData,'MaskName');
1575        set(handles.uvmat,'UserData',UvData)
1576    end
1577    set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1578end
1579
1580%-------------------------------------------------------------------
1581function errormsg=update_mask(handles,num_i1,num_j1)
1582%-------------------------------------------------------------------
1583errormsg=[];%default
1584MaskData=get(handles.mask_test,'UserData');
1585if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1586    uistack(MaskData.maskhandle,'top');
1587end
1588num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1589MaskData.NomType
1590MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1591huvmat=get(handles.mask_test,'parent');
1592UvData=get(huvmat,'UserData');
1593
1594%update mask image if the mask is new
1595if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1596    UvData.MaskName=MaskName; %update the recorded name on UvData
1597    set(huvmat,'UserData',UvData);
1598    if ~exist(MaskName,'file')
1599        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1600            delete(MaskData.maskhandle)   
1601        end
1602    else
1603        %read mask image
1604        Mask.AName='image';
1605        Mask.A=imread(MaskName);
1606        npxy=size(Mask.A);
1607        test_error=0;
1608        if length(npxy)>2
1609            errormsg=[MaskName ' is not a grey scale image'];
1610            return
1611        elseif ~isa(Mask.A,'uint8')
1612            errormsg=[MaskName ' is not a 8 bit grey level image'];
1613            return
1614        end
1615        Mask.AX=[0.5 npxy(2)-0.5];
1616        Mask.AY=[npxy(1)-0.5 0.5 ];
1617        Mask.CoordType='px';
1618        if isequal(get(handles.slices,'Value'),1)
1619           NbSlice=str2num(get(handles.nb_slice,'String'));
1620           num_i1=str2num(get(handles.i1,'String'));
1621           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1622        end
1623        %px to phys or other transform on field
1624         menu_transform=get(handles.transform_fct,'String');
1625        choice_value=get(handles.transform_fct,'Value');
1626        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1627        transform_list=get(handles.transform_fct,'UserData');
1628        transform=transform_list{choice_value};
1629        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1630            if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1631                Calib=UvData.XmlData.GeometryCalib;
1632                Mask=transform(Mask,UvData.XmlData);
1633            end
1634        end
1635        flagmask=Mask.A < 200;
1636       
1637        %make brown color image
1638        imflag(:,:,1)=0.9*flagmask;
1639        imflag(:,:,2)=0.7*flagmask;
1640        imflag(:,:,3)=zeros(size(flagmask));
1641       
1642        %update mask image
1643        hmask=[]; %default
1644        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1645            hmask=MaskData.maskhandle;
1646        end
1647        if ~isempty(hmask)
1648            set(hmask,'CData',imflag)   
1649            set(hmask,'AlphaData',flagmask*0.6)
1650            set(hmask,'XData',Mask.AX);
1651            set(hmask,'YData',Mask.AY);
1652%             uistack(hmask,'top')
1653        else
1654            axes(handles.axes3)
1655            hold on   
1656            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1657%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1658            set(handles.mask_test,'UserData',MaskData)
1659        end
1660    end
1661end
1662
1663
1664%-------------------------------------------------------------------
1665function MenuExportFigure_Callback(hObject, eventdata, handles)
1666%-------------------------------------------------------------------
1667huvmat=get(handles.MenuExport,'parent');
1668%UvData=get(huvmat,'UserData');
1669hfig=figure;
1670copyobj(handles.axes3,hfig);
1671map=colormap(handles.axes3);
1672colormap(map);%transmit the current colormap to the zoom fig
1673colorbar
1674
1675%-------------------------------------------------------------------
1676%-------------------------------------------------------------------
1677% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1678%-------------------------------------------------------------------
1679
1680%-------------------------------------------------------------------
1681% --- Executes on button press in runplus: make one step forward and call
1682% --- run0. The step forward is along the fields series 1 or 2 depending on
1683% --- the scan_i and scan_j check box (exclusive each other)
1684function runplus_Callback(hObject, eventdata, handles)
1685%-------------------------------------------------------------------
1686set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1687drawnow
1688%TODO: introduce the option: increment ='*' to move to the next available view
1689increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
1690if isnan(increment)
1691    set(handles.increment_scan,'String','1')%default value
1692    increment=1;
1693end
1694errormsg=runpm(hObject,eventdata,handles,increment);
1695if ~isempty(errormsg)
1696    msgbox_uvmat('ERROR',errormsg);
1697end
1698set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1699
1700%-------------------------------------------------------------------
1701% --- Executes on button press in runmin: make one step backward and call
1702% --- run0. The step backward is along the fields series 1 or 2 depending on
1703% --- the scan_i and scan_j check box (exclusive each other)
1704function runmin_Callback(hObject, eventdata, handles)
1705%-------------------------------------------------------------------
1706set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1707drawnow
1708increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
1709if isnan(increment)
1710    set(handles.increment_scan,'String','1')%default value
1711    increment=1;
1712end
1713errormsg=runpm(hObject,eventdata,handles,increment);
1714if ~isempty(errormsg)
1715    msgbox_uvmat('ERROR',errormsg);
1716end
1717set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1718
1719%-------------------------------------------------------------------
1720% -- Executes on button press in Movie: make a series of +> steps
1721function Movie_Callback(hObject, eventdata, handles)
1722%------------------------------------------------------------------
1723set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1724drawnow
1725increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
1726if isnan(increment)
1727    set(handles.increment_scan,'String','1')%default value
1728    increment=1;
1729end
1730set(handles.STOP,'Visible','on')
1731set(handles.speed,'Visible','on')
1732set(handles.speed_txt,'Visible','on')
1733set(handles.Movie,'BusyAction','queue')
1734UvData=get(handles.uvmat,'UserData');
1735
1736while get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1737        errormsg=runpm(hObject,eventdata,handles,increment);
1738        if ~isempty(errormsg)
1739            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1740            return
1741        end
1742        pause(1.02-get(handles.speed,'Value'))% wait for next image
1743end
1744if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1745    UvData.aviobj=close(UvData.aviobj);
1746   set(handles.uvmat,'UserData',UvData);
1747end
1748set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1749
1750%-------------------------------------------------------------------
1751% -- Executes on button press in Movie: make a series of <- steps
1752function MovieBackward_Callback(hObject, eventdata, handles)
1753%------------------------------------------------------------------
1754set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1755drawnow
1756increment=-str2double(get(handles.increment_scan,'String')); %get the field increment d
1757if isnan(increment)
1758    set(handles.increment_scan,'String','1')%default value
1759    increment=1;
1760end
1761set(handles.STOP,'Visible','on')
1762set(handles.speed,'Visible','on')
1763set(handles.speed_txt,'Visible','on')
1764set(handles.MovieBackward,'BusyAction','queue')
1765UvData=get(handles.uvmat,'UserData');
1766
1767while get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1768        errormsg=runpm(hObject,eventdata,handles,increment);
1769        if ~isempty(errormsg)
1770            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1771            return
1772        end
1773        pause(1.02-get(handles.speed,'Value'))% wait for next image
1774end
1775if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1776    UvData.aviobj=close(UvData.aviobj);
1777   set(handles.uvmat,'UserData',UvData);
1778end
1779set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1780
1781%-------------------------------------------------------------------
1782function STOP_Callback(hObject, eventdata, handles)
1783%-------------------------------------------------------------------
1784set(handles.movie_pair,'BusyAction','Cancel')
1785set(handles.movie_pair,'value',0)
1786set(handles.Movie,'BusyAction','Cancel')
1787set(handles.MovieBackward,'BusyAction','Cancel')
1788set(handles.MenuExportMovie,'BusyAction','Cancel')
1789set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1790set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1791set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1792
1793%------------------------------------------------------------------
1794function errormsg=runpm(hObject,eventdata,handles,increment)
1795%------------------------------------------------------------------
1796%check for mï¿œovie pair status
1797movie_status=get(handles.movie_pair,'Value');
1798if isequal(movie_status,1)
1799    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1800end
1801%read the data on the current input rootfile(s)
1802
1803[FileName,RootPath,filebase,FileIndices,FileExt,subdir]=read_file_boxes(handles);
1804NomType=get(handles.FileIndex,'UserData');
1805
1806num1=stra2num(get(handles.i1,'String'));
1807num2=stra2num(get(handles.i2,'String'));
1808num_a=stra2num(get(handles.j1,'String'));
1809num_b=stra2num(get(handles.j2,'String'));
1810
1811sub_value= get(handles.SubField,'Value');
1812if sub_value % a second input file has been entered
1813    [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1814    [pp,ff,str1,str2,str_a,str_b]=name2display(FileIndices_1);
1815    num1_1=stra2num(str1);%current set of indices for the second field (may be set different than the main indices)
1816    num2_1=stra2num(str2);
1817    num_a_1=stra2num(str_a);
1818    num_b_1=stra2num(str_b);
1819    NomType_1=get(handles.FileIndex_1,'UserData');
1820else
1821    filename_1=[];
1822end   
1823
1824comp_input=get(handles.fix_pair,'Value');
1825
1826%case of scanning along the first direction (rootfile numbers)
1827if get(handles.scan_i,'Value')==1% case of scanning along index i   
1828     num1=num1+increment;
1829     num2=num2+increment;
1830     [filename,num1,num_a,num2,num_b]=name_generator(filebase,num1,num_a,FileExt,NomType,comp_input,num2,num_b,subdir);
1831     if sub_value% set the second field name and indices
1832        num1_1=num1_1+increment;
1833        num2_1=num2_1+increment;
1834        filename_1=name_generator(filebase_1,num1_1,num_a_1,FileExt_1,NomType_1,1,num2_1,num_b_1,SubDir_1);
1835     end   
1836else % case of scanning along index j (burst numbers)
1837    num_a=num_a+increment;
1838    num_b=num_b+increment;
1839    [filename,num1,num_a,num2,num_b]=name_generator(filebase,num1,num_a,FileExt,NomType,comp_input,num2,num_b,subdir);
1840    if sub_value
1841        num_a_1=num_a_1+increment;
1842        num_b_1=num_b_1+increment;
1843        filename_1=name_generator(filebase_1,num1_1,num_a_1,FileExt_1,NomType_1,1,num2_1,num_b_1,SubDir_1);
1844    end   
1845end
1846
1847% refresh plots
1848errormsg=refresh_field(handles,filename,filename_1,num1,num2,num_a,num_b);
1849if isempty(errormsg)  %update the index counters
1850    set(handles.i1,'String',num2stra(num1,NomType,1));
1851    if isequal(num2,num1)
1852         set(handles.i2,'String','');
1853    else
1854        set(handles.i2,'String',num2stra(num2,NomType,1));
1855    end
1856    set(handles.j1,'String',num2stra(num_a,NomType,2));
1857    if isequal(num_b,num_a)
1858         set(handles.j2,'String','');
1859    else
1860        set(handles.j2,'String',num2stra(num_b,NomType,2));
1861    end
1862    [indices]=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1863    set(handles.FileIndex,'String',indices);
1864    if ~isempty(filename_1)
1865         indices_1=name_generator('',num1_1,num_a_1,'',NomType_1,1,num2_1,num_b_1,'');
1866         set(handles.FileIndex_1,'String',indices_1);
1867    end
1868    if isequal(movie_status,1)
1869        set(handles.movie_pair,'Value',1)
1870        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1871    end
1872end
1873
1874
1875%-------------------------------------------------------
1876% --- Executes on button press in movie_pair: create an alternating movie with two view
1877%-------------------------------------------------------
1878function movie_pair_Callback(hObject, eventdata, handles)
1879status=get(handles.movie_pair,'value');
1880if isequal(status,0)
1881    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1882    set(handles.i2,'String','')
1883    set(handles.j2,'String','')
1884    return
1885else
1886    set(handles.movie_pair,'BusyAction','queue')
1887end
1888%initialisation
1889set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1890drawnow
1891list_fields=get(handles.Fields,'String');% list menu fields
1892index_fields=get(handles.Fields,'Value');% selected string index
1893FieldName=list_fields{index_fields}; % selected field
1894UvData=get(handles.uvmat,'UserData');
1895if isequal(FieldName,'image')
1896    test_1=0;
1897    [ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes(handles);
1898    NomType=get(handles.FileIndex,'UserData');
1899else
1900    list_fields=get(handles.Fields_1,'String');% list menu fields
1901    index_fields=get(handles.Fields_1,'Value');% selected string index
1902    FieldName=list_fields{index_fields}; % selected field
1903    if isequal(FieldName,'image')
1904        test_1=1;
1905        [ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes_1(handles);
1906        NomType=get(handles.FileIndex_1,'UserData');
1907    else
1908        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1909        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1910        return
1911    end
1912end
1913
1914num_i1=str2double(get(handles.i1,'String'));
1915num_j1=stra2num(get(handles.j1,'String'));
1916num_i2=str2double(get(handles.i2,'String'));
1917num_j2=stra2num(get(handles.j2,'String'));
1918if isnan(num_j2)
1919    if isempty(num_i2)   
1920        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1921        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1922        return
1923    else
1924        num_j2=num_j1;%repeat the index i1 by default
1925    end
1926end
1927if isnan(num_i2)
1928    num_i2=num_i1;%repeat the index i1 by default
1929end
1930imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
1931if ~exist(imaname_1,'file')
1932      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1933      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1934      return
1935end
1936
1937%read the second image
1938Field.AName='image';
1939if test_1
1940    Field_a=UvData.Field_1;
1941else
1942    Field_a=UvData.Field;
1943end
1944Field_b.AX=Field_a.AX;
1945Field_b.AY=Field_a.AY;
1946% z index
1947nbslice=str2double(get(handles.nb_slice,'String'));
1948if ~isempty(nbslice)
1949    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1950end
1951Field_b.CoordType='px';
1952%determine the input file type
1953if (test_1 && isfield(UvData,'MovieObject_1'))||(~test_1 && isfield(UvData,'MovieObject'))
1954    FileType='movie';
1955elseif isequal(lower(Ext),'.avi')
1956    FileType='avi';
1957elseif isequal(lower(Ext),'.vol')
1958    FileType='vol';
1959else
1960   form=imformats(Ext(2:end));
1961   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1962       if isequal(NomType,'*');
1963           FileType='multimage';
1964       else
1965           FileType='image';
1966       end
1967   end
1968end
1969switch FileType
1970        case 'movie'
1971            if test_1
1972                Field_b.A=read(UvData.MovieObject_1,num_i2);
1973            else
1974                Field_b.A=read(UvData.MovieObject,num_i2);
1975            end
1976        case 'avi'
1977            mov=aviread(imaname_1,num_i2);
1978            Field_b.A=frame2im(mov(1));
1979        case 'vol'
1980            Field_b.A=imread(imaname_1);
1981        case 'multimage'
1982            Field_b.A=imread(imaname_1,num_i2);
1983        case 'image'
1984            Field_b.A=imread(imaname_1);
1985end
1986if get(handles.slices,'Value')
1987    Field.ZIndex=str2double(get(handles.z_index,'String'));
1988end
1989
1990%px to phys or other transform on field
1991menu_transform=get(handles.transform_fct,'String');
1992choice_value=get(handles.transform_fct,'Value');
1993transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1994transform_list=get(handles.transform_fct,'UserData');
1995transform=transform_list{choice_value};
1996if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1997    if test_1 && isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1998        Field_a=transform(Field_a,UvData.XmlData_1);%the first field has been stored without transform
1999        Field_b=transform(Field_b,UvData.XmlData_1);
2000    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib
2001        Field_b=transform(Field_b,UvData.XmlData);
2002    end
2003end
2004
2005 % make movie until movie speed is set to 0 or STOP is activated
2006hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
2007set(handles.STOP,'Visible','on')
2008set(handles.speed,'Visible','on')
2009set(handles.speed_txt,'Visible','on')
2010while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
2011    % read and plot the series of images in non erase mode
2012    set(hima,'CData',Field_b.A);
2013    pause(1.02-get(handles.speed,'Value'));% wait for next image
2014    set(hima,'CData',Field_a.A);
2015    pause(1.02-get(handles.speed,'Value'));% wait for next image
2016end
2017set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
2018
2019%------------------------------------------------------------------------
2020% --- Executes on button press in run0.
2021function run0_Callback(hObject, eventdata, handles)
2022%------------------------------------------------------------------------
2023set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
2024drawnow
2025filename=read_file_boxes(handles);
2026
2027filename_1=[];%default
2028if get(handles.SubField,'Value')
2029    filename_1=read_file_boxes_1(handles);
2030end
2031num_i1=stra2num(get(handles.i1,'String'));
2032num_i2=stra2num(get(handles.i2,'String'));
2033num_j1=stra2num(get(handles.j1,'String'));
2034num_j2=stra2num(get(handles.j2,'String'));
2035errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
2036if ~isempty(errormsg)
2037      msgbox_uvmat('ERROR',errormsg);
2038else
2039    set(handles.i1,'BackgroundColor',[1 1 1])
2040    set(handles.i2,'BackgroundColor',[1 1 1])
2041    set(handles.j1,'BackgroundColor',[1 1 1])
2042    set(handles.j2,'BackgroundColor',[1 1 1])
2043    set(handles.FileIndex,'BackgroundColor',[1 1 1])
2044    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
2045end   
2046set(handles.run0,'BackgroundColor',[1 0 0])
2047
2048
2049%------------------------------------------------------------------------
2050% --- read the input files and refresh all the plots, including projection.
2051% OUTPUT:
2052%  errormsg: error message char string  =[] by default
2053% INPUT:
2054% filename: first input file (=[] in the absence of input file)
2055% filename_1: second input file (=[] in the asbsenc of secodn input file)
2056% num_i1,num_i2,num_j1,num_j2; frame indices
2057% Field: structure describing an optional input field (then replace the input file)
2058function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
2059%------------------------------------------------------------------------
2060
2061%initialisation
2062% errormsg=[]; % default error message
2063abstime=[];
2064abstime_1=[];
2065dt=[];
2066if ~exist('Field','var')
2067    Field={};
2068end
2069UvData=get(handles.uvmat,'UserData');
2070%UvData =structure containing information stored outside the uicontrol of uvmat
2071%      .NewSeries: =1 for a new series (new root fiel introduced), 0 else
2072%      .MovieObject: movie object representing an input movie
2073%      .MovieObject_1: idem for a second input series (_1)
2074%      .filename_1 : last second input file name (to deal with a constant second input without reading again the file)
2075%      .VelType_1: last velocity type (civ1, civ2...) for the second input series
2076%      .FieldName_1: last field name(velocity, vorticity...) for the second input series
2077%      .NbDim: number of space dimensions of the input field
2078%      .ZMin, .ZMax: range of the z coordinate
2079%..... to complement
2080
2081if ishandle(handles.UVMAT_title) %remove title panel on uvmat
2082    delete(handles.UVMAT_title)
2083end
2084
2085%% determine the main input file information for action
2086FileType=[];%default
2087if ~isempty(filename)
2088    if ~exist(filename,'file')
2089        errormsg=['input file ' filename ' does not exist'];
2090        return
2091    end
2092    Ext=get(handles.FileExt,'String');
2093    NomType=get(handles.FileIndex,'UserData');
2094    %update the z position index
2095    nbslice_str=get(handles.nb_slice,'String');
2096   % z_index=1;%default
2097    if isequal(nbslice_str,'volume')
2098        z_index=num_j1;
2099        set(handles.z_index,'String',num2str(z_index))
2100    else
2101        nbslice=str2num(nbslice_str);
2102        z_index=mod(num_i1-1,nbslice)+1;
2103        set(handles.z_index,'String',num2str(z_index))
2104    end
2105    % refresh menu for save_mask if relevant
2106    masknumber=get(handles.masklevel,'String');
2107    if length(masknumber)>=z_index
2108        set(handles.masklevel,'Value',z_index)
2109    end
2110
2111    % determine the input file type
2112    if isequal(Ext,'.nc')||isequal(Ext,'.cdf')
2113        FileType='netcdf';
2114    elseif isfield(UvData,'MovieObject')
2115        FileType='movie';
2116        FieldName='image';
2117    elseif isequal(lower(Ext),'.avi')
2118        FileType='avi';
2119        FieldName='image';
2120    elseif isequal(lower(Ext),'.vol')
2121        FileType='vol';
2122        FieldName='image';
2123    else
2124       form=imformats(Ext(2:end));
2125       if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2126           if isequal(NomType,'*');
2127               FileType='multimage';
2128           else
2129               FileType='image';
2130           end
2131           FieldName='image';
2132       end
2133    end
2134else
2135    FileType='netcdf';
2136    FieldName='get_field...';
2137end
2138VelType=[];%default
2139if isequal(FileType,'netcdf')
2140    list_fields=get(handles.Fields,'String');% list menu fields
2141    index_fields=get(handles.Fields,'Value');% selected string index
2142    FieldName= list_fields{index_fields}; % selected field
2143    if ~isequal(FieldName,'get_field...')% read the field names on the interface get_field...
2144       VelType=setfield(handles);
2145    end
2146end
2147%% choose a second field if Subfield option is 'on'
2148FieldName_1=[];
2149scal_color=[];
2150VelType_1=setfield_1(handles);
2151% sub_value=get(handles.SubField,'Value');
2152FileType_1='none';%default
2153if ~isempty(filename_1)
2154    % test for a constant second field (comparison with a fixed field)
2155    NomType_1=get(handles.FileIndex_1,'UserData');
2156    Ext_1=get(handles.FileExt_1,'String');
2157    % determine the input file type
2158    if isequal(Ext_1,'.nc')||isequal(Ext_1,'.cdf')
2159        FileType_1='netcdf';
2160    elseif isfield(UvData,'MovieObject_1')
2161        FileType_1='movie';
2162        FieldName_1='image';
2163    elseif isequal(lower(Ext_1),'.avi')
2164        FileType='avi';
2165        FieldName_1='image';
2166    elseif isequal(lower(Ext_1),'.vol')
2167        FileType_1='vol';
2168        FieldName_1='image';
2169    else
2170       form=imformats(Ext_1(2:end));
2171       if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2172           if isequal(NomType_1,'*');
2173               FileType_1='multimage';
2174           else
2175               FileType_1='image';
2176           end
2177           FieldName_1='image';
2178       end
2179    end
2180    if ~isequal(FieldName_1,'image')
2181        list_fields=get(handles.Fields_1,'String');% list menu fields
2182        index_fields=get(handles.Fields_1,'Value');% selected string index
2183        FieldName_1= list_fields{index_fields}; % selected field
2184        if isequal(VelType_1,'*')% free veltype choice
2185            VelType_1=[];
2186        elseif isequal(VelType_1,'"')% veltype the same as for the first field
2187            if isempty(VelType)
2188                VelType_1=[];
2189            else
2190                VelType_1=VelType;
2191            end
2192        end
2193    end
2194    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2195    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
2196        if isfield(UvData,'filename_1')&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2197            test_keepdata_1= isequal(filename_1,UvData.filename_1)&&...
2198                isequal(VelType_1,UvData.filename_1) && isequal(FieldName_1,UvData.FieldName_1);
2199        end
2200    end
2201    if test_keepdata_1
2202        Field{2}=UvData.Field_1;   
2203    elseif ~exist(filename_1,'file')
2204        errormsg=['second file ' filename_1 ' does not exist'];
2205        return
2206    end
2207end
2208
2209%% read the input field(s)
2210%read images
2211if ~isempty(filename) && isequal(FieldName,'image')
2212     switch FileType
2213        case 'movie'
2214            try
2215                A=read(UvData.MovieObject,num_i1);
2216            catch
2217                errormsg=lasterr;
2218                return
2219            end
2220        case 'avi'
2221            try
2222                mov=aviread(filename,num_i1);
2223            catch
2224                errormsg=lasterr;
2225                return
2226            end
2227            A=frame2im(mov(1));
2228        case 'vol'
2229            A=imread(filename);
2230        case 'multimage'
2231            A=imread(filename,num_i1);
2232        case 'image'
2233            A=imread(filename);
2234    end
2235    npxy=size(A);
2236    set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface
2237    set(handles.npy,'String',num2str(npxy(1)));
2238    Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
2239    Rangy=[npxy(1)-0.5 0.5]; %
2240    Field{1}.AName='image';
2241    Field{1}.ListVarName={'AY','AX','A'}; %
2242    if size(A,3)==3;%color
2243        Field{1}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
2244    else
2245        Field{1}.VarDimName={'AY','AX',{'AY','AX'}}; %
2246    end
2247    Field{1}.AY=Rangy;
2248    Field{1}.AX=Rangx;
2249    Field{1}.A=A;
2250    Field{1}.CoordType='px'; %used for mouse_motion
2251    Field{1}.CoordUnit='pixel'; %used for mouse_motion
2252end
2253
2254%read a second image
2255if  ~isempty(filename_1) && ~test_keepdata_1 && isequal(FieldName_1,'image')
2256    switch FileType_1
2257        case 'movie'
2258            A=read(UvData.MovieObject_1,num_i1);
2259        case 'avi'
2260            mov=aviread(filename_1,num_i1);
2261            A=frame2im(mov(1));
2262        case 'vol'
2263            A=imread(filename_1);
2264        case 'multimage'
2265            A=imread(filename_1,num_i1);
2266        case 'image'
2267            A=imread(filename_1);
2268        case 'netcdf'
2269        otherwise
2270            errormsg=['unknown input file type ' filename_1];
2271    end
2272    npxy=size(A);
2273    set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface
2274    set(handles.npy,'String',num2str(npxy(1)));
2275    Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
2276    Rangy=[npxy(1)-0.5 0.5]; %
2277    Field{2}.AName='image';
2278    Field{2}.ListVarName={'AY','AX','A'}; %
2279    if size(A,3)==3;%color
2280        Field{2}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
2281    else
2282        Field{2}.VarDimName={'AY','AX',{'AY','AX'}}; %
2283    end
2284    Field{2}.AY=Rangy;
2285    Field{2}.AX=Rangx;
2286    Field{2}.A=A;
2287    Field{2}.CoordType='px'; %used for mouse_motion
2288    Field{2}.CoordUnit='px'; %used for move_mou
2289end
2290
2291%read ncfile(s)
2292CivStage_1=0;%default
2293VelType_out_1=[];
2294InputField={FieldName};
2295InputField_1={FieldName_1};
2296if (~isempty(filename)&& isequal(FileType,'netcdf')) || (~isempty(filename_1)&& isequal(FileType_1,'netcdf')) ;
2297    %read the velocity field(s) from netcdf rootfile(s)
2298    list_code=get(handles.col_vec,'String');% list menu fields
2299    index_code=get(handles.col_vec,'Value');% selected string index
2300    scal_color= list_code{index_code(1)}; % selected field
2301    if isequal(FieldName,'velocity')&& ~isequal(scal_color,'black') && ~isequal(scal_color,'white')
2302        InputField=[InputField scal_color];
2303    end
2304    if isequal(FieldName_1,'velocity') && ~isequal(scal_color,'black') && ~isequal(scal_color,'white')
2305        InputField_1=[InputField_1 scal_color];
2306    end
2307    if isequal(FileType,'netcdf')  %read the first nc field
2308        if isequal(FieldName,'get_field...')% read the field names on the interface get_field.
2309            hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI
2310            if isempty(hget_field)
2311                hget_field= get_field(filename);%open the get_field GUI   
2312              %  set(hget_field,'name','get_field')
2313            elseif UvData.NewSeries% refresh the fet_field GUI for a new series
2314                delete(hget_field)
2315                hget_field= get_field(filename);%open the get_field GUI
2316                set(hget_field,'name','get_field')%rename  get_field GUI for the 'slave' mode
2317            end
2318            hhget_field=guidata(hget_field);
2319            set(hhget_field.list_fig,'Value',1)
2320            set(hhget_field.list_fig,'String',{'uvmat'})
2321            funct_list=get(hhget_field.ACTION,'UserData');
2322            funct_index=get(hhget_field.ACTION,'Value');
2323            funct=funct_list{funct_index};%select  the current action in get_field, e;g. PLOT
2324            Field{1}=funct(hget_field); %%activate the current action selected in get_field, e;g.read the names of the variables to plot
2325            CivStage=0;
2326            VelType_out=[];   
2327        else
2328            [Field{1},VelType_out]=read_civxdata(filename,InputField,VelType);
2329            if isfield(Field{1},'Txt')
2330                errormsg=Field{1}.Txt;
2331                return
2332            end
2333            CivStage=Field{1}.CivStage;
2334            UvData.NbDim=Field{1}.nb_dim;
2335        end
2336    end
2337    if ~isempty(filename_1) && ~test_keepdata_1 && isequal(FileType_1,'netcdf') %read the second file
2338        if isequal(FieldName_1,'get_field...')% read the field names on the interface get_field.
2339            hget_field_1=findobj(allchild(0),'Name','get_field_1');%find the get_field... GUI
2340            if isempty(hget_field_1)
2341                 hget_field_1= get_field(filename_1);%open the get_field GUI
2342                 set(hget_field_1,'name','get_field_1')
2343            elseif UvData.NewSeries% refresh the fet_field GUI for a new series
2344                delete(hget_field_1)
2345                hget_field_1= get_field(filename);%open the get_field GUI
2346                set(hget_field_1,'name','get_field_1')%rename  get_field GUI for the 'slave' mode
2347            end
2348            hhget_field_1=guidata(hget_field_1);%handles of GUI elements in get_field
2349            set(hhget_field_1.list_fig,'Value',1)
2350            set(hhget_field_1.list_fig,'String',{'uvmat'})
2351            funct_list=get(hhget_field_1.ACTION,'UserData');
2352            funct_index=get(hhget_field_1.ACTION,'Value');
2353            funct=funct_list{funct_index};
2354            Field{2}=funct(hget_field_1); %read the names of the variables to plot in the get_field GUI
2355        else
2356            [Field{2},VelType_out_1]=read_civxdata(filename_1,InputField_1,VelType_1);
2357            CivStage_1=Field{2}.CivStage;
2358        end
2359        if ~isequal(FileType,'netcdf')
2360            VelType_out=VelType_out_1;
2361        end
2362    end
2363end
2364
2365%store the second field for possible latter use
2366if numel(Field)==2
2367    UvData.Field_1=Field{2};
2368end
2369
2370%% update the display buttons for the first velocity type (first menuline)
2371veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2372if ~isequal(FileType,'netcdf')
2373    reset_vel_type(veltype_handles)
2374elseif isempty(VelType) && ~isequal(FieldName,'get_field...')
2375    set_veltype_display(veltype_handles,CivStage)%update the display of available velocity types for the first field
2376    if isempty(VelType_out)
2377        reset_vel_type(veltype_handles)
2378    else
2379        handle1=eval(['handles.' VelType_out]);
2380        reset_vel_type(veltype_handles,handle1)
2381    end
2382end
2383
2384%% update the display buttons for the second velocity type (second menuline)
2385veltype_handles_1=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
2386if ~isequal(FileType_1,'netcdf')
2387    reset_vel_type(veltype_handles_1)
2388elseif isempty(VelType_1) && ~isequal(FieldName_1,'get_field...')
2389    set_veltype_display(veltype_handles_1,CivStage_1)%update the display of available velocity types for the first field
2390    if isempty(VelType_out_1)
2391        reset_vel_type(veltype_handles_1)
2392    else
2393        handle1=eval(['handles.' VelType_out_1 '_1']);
2394        reset_vel_type(veltype_handles_1,handle1)
2395    end
2396end
2397
2398%% introduce w as background image by default for a new series (only for nbdim=2)
2399if ~isfield(UvData,'NewSeries')
2400    UvData.NewSeries=1;
2401end
2402%put W as background image by default if NbDim=2:
2403if ~isfield(UvData,'NbDim')||isempty(UvData.NbDim)||~isequal(UvData.NbDim,3)
2404    if UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W);
2405        set(handles.SubField,'Value',1);
2406        %menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w'
2407        set(handles.RootPath_1,'String','"')
2408        set(handles.RootFile_1,'String','"')
2409        set(handles.SubDir_1,'String','"');
2410        [indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,'');
2411        set(handles.FileIndex_1,'String',indices)
2412        set(handles.FileExt_1,'String','"');
2413        set(handles.Fields_1,'Visible','on');
2414        set(handles.Fields_1,'Visible','on');
2415        set(handles.RootPath_1,'Visible','on')
2416        set(handles.RootFile_1,'Visible','on')
2417        set(handles.SubDir_1,'Visible','on');
2418        set(handles.FileIndex_1,'Visible','on');
2419        set(handles.FileExt_1,'Visible','on');
2420        set(handles.Fields_1,'Visible','on');
2421        Field{1}.AName='w';
2422%         testscal=1;
2423    end
2424end           
2425
2426%multislice case
2427if ~isempty(filename) &&(~isfield(UvData,'NbDim') || isequal(UvData.NbDim,2))&&...%2D case
2428      isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')&& isfield(UvData.XmlData.GeometryCalib,'SliceCoord')
2429       siz=size(UvData.XmlData.GeometryCalib.SliceCoord);
2430%        if siz(1)>1
2431%            NbSlice=siz(1);
2432%        else
2433%            NbSlice=1;
2434%        end
2435end
2436
2437%store the current open names, fields and vel types in uvmat interface
2438UvData.filename=filename;
2439UvData.filename_1=filename_1;
2440UvData.VelType=VelType;
2441UvData.VelType_1=VelType_1;
2442UvData.FieldName=FieldName;
2443UvData.FieldName_1=FieldName_1;
2444if ~isempty(scal_color)
2445    UvData.CName=scal_color;
2446end
2447
2448%% coordinate transform or user fct
2449XmlData=[];%default
2450if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2451    XmlData=UvData.XmlData;
2452end
2453XmlData_1=[];%default
2454if isfield(UvData,'XmlData_1')
2455   XmlData_1=UvData.XmlData_1;
2456end
2457% menu_transform=get(handles.transform_fct,'String');
2458choice_value=get(handles.transform_fct,'Value');
2459transform_list=get(handles.transform_fct,'UserData');
2460transform=transform_list{choice_value};%selected function handles
2461% z index
2462if ~isempty(filename)
2463    Field{1}.ZIndex=z_index;
2464end
2465%px to phys or other transform on field
2466if ~isempty(transform)
2467    if length(Field)>=2
2468        Field{2}.ZIndex=z_index;
2469        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2470        if isempty(Field{2})
2471            Field(2)=[];
2472        end
2473    else
2474        Field{1}=transform(Field{1},XmlData);
2475    end
2476end
2477
2478%% calculate scalar
2479if isequal(FileType,'netcdf') && ~isequal(FieldName,'get_field...')%
2480    Field{1}=calc_field(InputField,Field{1});
2481end
2482if length(Field)==2 && ~test_keepdata_1 && isequal(FileType_1,'netcdf') && ~isequal(FieldName_1,'get_field...')
2483    Field{2}=calc_field(InputField_1,Field{2});
2484end
2485% combine the two input fields (e.g. substract velocity fields)
2486if numel(Field)==2
2487   UvData.Field=sub_field(Field{1},Field{2}); %TO UPDATE FOR MORE GENERAL INPUT 
2488else
2489   UvData.Field=Field{1};
2490end
2491
2492%% test 3D , default projection menuplane and typical mesh (needed to menuopen set_object)
2493test_x=0;
2494test_z=0;% test for unstructured z coordinate
2495UvData.ZMax=0;
2496UvData.ZMin=0;%default
2497UvData.Mesh=1; %default
2498[UvData.Field,errormsg]=check_field_structure(UvData.Field);
2499if ~isempty(errormsg)
2500    errormsg=['error in uvmat/run0_Callback/check_field_structure: ' errormsg];
2501    return
2502end
2503[CellVarIndex,NbDim,VarType]=find_field_indices(UvData.Field);
2504[NbDim,imax]=max(NbDim);
2505if isempty(imax)
2506%    DimVarIndex=0;   
2507    coord_x=[];
2508else
2509%     VarIndex=CellVarIndex{imax};
2510    coord_x=VarType{imax}.coord_x;
2511end
2512if isfield(UvData,'NbDim') && ~isempty(UvData.NbDim)
2513    NbDim=UvData.NbDim;
2514else 
2515    UvData.NbDim=NbDim;
2516end
2517if ~isempty(CellVarIndex) && ~isempty(VarType{imax}.coord_x)  && ~isempty(VarType{imax}.coord_y)    %unstructured coordinate z
2518    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2519    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2520    test_x=1;
2521elseif isfield(UvData.Field,'X') && isfield(UvData.Field,'Y')
2522    XName='X';
2523    YName='Y';
2524    test_x=1;
2525end
2526if test_x
2527    eval(['UvData.XMax=max(UvData.Field.' XName ');'])
2528    eval(['UvData.XMin=min(UvData.Field.' XName ');'])
2529    eval(['UvData.YMax=max(UvData.Field.' YName ');'])
2530    eval(['UvData.YMin=min(UvData.Field.' YName ');'])
2531    eval(['nbvec=length(UvData.Field.' XName ');'])
2532    if NbDim==3%
2533        if ~isempty(CellVarIndex) && ~isempty(VarType{imax}.coord_z)%unstructured coordinate z
2534            ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2535            eval(['UvData.ZMax=max(UvData.Field.' ZName ');'])
2536            eval(['UvData.ZMin=min(UvData.Field.' ZName ');'])
2537            test_z=1;   
2538        elseif isfield(UvData,'Z')% usual civ data
2539            UvData.ZMax=max(UvData.Z);
2540            UvData.ZMin=min(UvData.Z);
2541            test_z=1;
2542        end
2543    end
2544    if isequal(UvData.ZMin,UvData.ZMax)%no z dependency
2545        NbDim=2;
2546        test_z=0;
2547    end   
2548    if test_z
2549         UvData.Mesh=((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)*(UvData.ZMax-UvData.ZMin))/nbvec;% volume per vector
2550         UvData.Mesh=(UvData.Mesh)^(1/3);
2551    else
2552        UvData.Mesh=sqrt((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)/nbvec);%2D
2553    end
2554end
2555
2556%case of structured coordinates
2557if isfield(UvData.Field,'AX') && isfield(UvData.Field,'AY')&& isfield(UvData.Field,'A')
2558    UvData.XMax=max(UvData.Field.AX);
2559    UvData.XMin=min(UvData.Field.AX);
2560    UvData.YMax=max(UvData.Field.AY);
2561    UvData.YMin=min(UvData.Field.AY);
2562    np_A=size(UvData.Field.A);
2563    UvData.Mesh=sqrt((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)/((np_A(1)-1) * (np_A(2)-1))) ;
2564end
2565if  isempty(coord_x) && ~isempty(CellVarIndex)
2566    VarIndex=CellVarIndex{imax}; % list of variable indices
2567    DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2568    if NbDim==3
2569        nbpoints=UvData.Field.DimValue(DimIndex(1));
2570        if isfield(VarType{imax},'coord_3')&& ~isequal(VarType{imax}.coord_3,0) % z is a dimension variable
2571            ZName=UvData.Field.ListVarName{VarType{imax}.coord_3};
2572            eval(['UvData.ZMax=max(UvData.Field.' ZName ');'])
2573            eval(['UvData.ZMin=min(UvData.Field.' ZName ');'])
2574        else
2575            testcoord_z=0;
2576            if length(UvData.Field.VarAttribute)>=VarIndex(1)
2577                if isfield(UvData.Field.VarAttribute{VarIndex(1)},'Coord_1')%regular grid
2578                    Coord_z=UvData.Field.VarAttribute{VarIndex(1)}.Coord_1;
2579                    UvData.ZMax=max(Coord_z);
2580                    UvData.ZMin=min(Coord_z);
2581                    testcoord_z=1;
2582                end
2583            end
2584            if ~testcoord_z
2585                  UvData.ZMin=1;
2586                  UvData.ZMax=UvData.Field.DimValue(DimIndex(1));
2587            end
2588        end
2589        UvData.Mesh=(UvData.ZMax-UvData.ZMin)/(nbpoints-1);
2590    elseif NbDim==2
2591        nbpoints_y=UvData.Field.DimValue(DimIndex(1));       
2592        Yvar=VarType{imax}.coord_y;
2593        if Yvar~=0  % x is a dimension variable
2594            YName=UvData.Field.ListVarName{Yvar};
2595            eval(['UvData.YMax=max(UvData.Field.' YName ');'])
2596            eval(['UvData.YMin=min(UvData.Field.' YName ');'])
2597        else
2598            testcoord_y=0;
2599            if ~testcoord_y
2600                  UvData.YMin=1;
2601                  UvData.YMax=UvData.Field.DimValue(DimIndex(1));
2602            end
2603        end
2604        DY=(UvData.YMax-UvData.YMin)/(nbpoints_y-1);
2605        nbpoints_x=UvData.Field.DimValue(DimIndex(2));
2606        Xvar=VarType{imax}.coord_x;
2607        if Xvar~=0  % x is a dimension variable
2608            XName=UvData.Field.ListVarName{Xvar};
2609            eval(['UvData.XMax=max(UvData.Field.' XName ');'])
2610            eval(['UvData.XMin=min(UvData.Field.' XName ');'])
2611        else
2612            testcoord_x=0;
2613            if ~testcoord_x
2614                  UvData.XMin=1;
2615                  UvData.XMax=UvData.Field.DimValue(DimIndex(2));
2616            end
2617        end
2618        DX=(UvData.XMax-UvData.XMin)/(nbpoints_x-1);
2619        UvData.Mesh= sqrt(DX*DY);
2620    end
2621end
2622
2623%create a default projection menuplane
2624UvData.Object{1}.Style='plane';%main plotting plane
2625UvData.Object{1}.ProjMode='projection';%main plotting plane
2626if ~isfield(UvData.Object{1},'plotaxes')
2627    UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
2628    set(handles.list_object_1,'Value',1);
2629    set(handles.list_object_1,'String',{'1-PLANE'}); 
2630end
2631
2632%3D case (menuvolume)
2633if NbDim==3 && UvData.NewSeries
2634    UvData.Object{1}.NbDim=UvData.NbDim;%test for 3D objects
2635    UvData.Object{1}.RangeZ=UvData.Mesh;%main plotting plane
2636    UvData.Object{1}.Coord(1,3)=(UvData.ZMin+UvData.ZMax)/2;%section at a middle plane chosen
2637    UvData.Object{1}.Phi=0;
2638    UvData.Object{1}.Theta=0;
2639    UvData.Object{1}.Psi=0;
2640    UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR 
2641    PlotHandles=get_plot_handles(handles);
2642    ZBounds(1)=UvData.ZMin; %minimum for the Z slider
2643    ZBounds(2)=UvData.ZMax;%maximum for the Z slider
2644    UvData.Object{1}.Name='1-PLANE';
2645    UvData.Object{1}.enable_plot=1;
2646    set_object(UvData.Object{1},PlotHandles,ZBounds);
2647    set(handles.list_object_1,'Value',1);
2648%multilevel case (single menuplane in a 3D space)
2649elseif isfield(UvData,'Z')
2650    if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2651        XmlData=UvData.XmlData;
2652        if isfield(XmlData,'PlanePos')
2653             UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2654        end
2655        if isfield(XmlData,'PlaneAngle')
2656            siz=size(XmlData.PlaneAngle);
2657            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)             
2658            UvData.Object{1}.Phi=XmlData.PlaneAngle(indangle,1);
2659            UvData.Object{1}.Theta=XmlData.PlaneAngle(indangle,2);
2660            UvData.Object{1}.Psi=XmlData.PlaneAngle(indangle,3);
2661        end
2662    elseif isfield(UvData,'ZIndex')
2663        UvData.Object{1}.ZObject=UvData.ZIndex;
2664    end
2665end
2666
2667%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2668if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2669    set(handles.MinA,'String','0')
2670    set(handles.MaxA,'String','255')
2671end
2672
2673%% Plot the projections on the selected  projection objects
2674
2675% main projection object (uvmat display)
2676IndexObj(1)=get(handles.list_object_1,'Value');%selected projection object for main view
2677if IndexObj(1)> numel(UvData.Object)
2678    IndexObj(1)=1;%select the first object if the selected one does not exist
2679    set(handles.list_object_1,'Value',1)
2680end
2681plot_handles{1}=handles;
2682haxes(1)=handles.axes3;
2683PlotParam{1}=read_plot_param(handles);%read plotting parameters on the uvmat interfac
2684keeplim(1)=get(handles.FixedLimits,'Value');% test for fixed graph limits
2685PosColorbar{1}=UvData.PosColorbar;%prescribe the colorbar position on the uvmat interface
2686
2687% second projection object (view_field display)
2688IndexObj_2=get(handles.list_object_2,'Value');%selected projection object for the second view
2689if isequal(get(handles.list_object_2,'Visible'),'on') && IndexObj_2 <= numel(UvData.Object)&& ~isempty(UvData.Object{IndexObj_2})
2690    IndexObj(2)=IndexObj_2;
2691    view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2692    if ~isempty(view_field_handle)
2693        plot_handles{2}=guidata(view_field_handle);
2694        haxes(2)=plot_handles{2}.axes3;
2695        PlotParam{2}=read_plot_param(plot_handles{2});%read plotting parameters on the uvmat interface
2696        keeplim(2)=get(plot_handles{2}.FixedLimits,'Value');
2697        PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2698    end
2699end
2700
2701%loop on the projection objects: one or two
2702for imap=1:numel(IndexObj)
2703    iobj=IndexObj(imap);   
2704    ObjectData=proj_field(UvData.Field,UvData.Object{iobj},iobj);% project field on the object
2705   
2706    %use of mask (TODO: check)
2707    if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2708        flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2709        AX=ObjectData.AX;%x coordiantes for the scalar field
2710        AY=ObjectData.AY;%y coordinates for the scalar field
2711        MaskX=ObjectData.MaskX;%x coordiantes for the mask
2712        MaskY=ObjectData.MaskY;%y coordiantes for the mask
2713        if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2714            nxy=size(flag_mask);
2715            sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2716            sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2717            x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2718            y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2719            %project on the positions of the scalar
2720            npxy=size(ObjectData.A);
2721            dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2722            dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2723            xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2724            yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2725            [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2726            flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2727        end
2728        AClass=class(ObjectData.A);
2729        ObjectData.A=flag_mask.*double(ObjectData.A);
2730        ObjectData.A=feval(AClass,ObjectData.A);
2731        ind_off=[];
2732        if isfield(ObjectData,'ListVarName')
2733            for ilist=1:length(ObjectData.ListVarName)
2734                if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2735                    ind_off=[ind_off ilist];
2736                end
2737            end
2738            ObjectData.ListVarName(ind_off)=[];
2739            ObjectData.VarDimIndex(ind_off)=[];
2740            ind_off=[];
2741            for ilist=1:length(ObjectData.ListDimName)
2742                if isequal(ObjectData.ListDimName{ilist},'MaskX') || isequal(ObjectData.ListDimName{ilist},'MaskY')
2743                    ind_off=[ind_off ilist];
2744                end
2745            end
2746            ObjectData.ListDimName(ind_off)=[];
2747            ObjectData.DimValue(ind_off)=[];
2748        end
2749    end
2750   
2751    if ~isempty(ObjectData)
2752        PlotType='none'; %default
2753        if imap==2 && isempty(view_field_handle)
2754            view_field(ObjectData)
2755        else
2756            [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},keeplim(imap),PosColorbar{imap});
2757            write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2758            if imap==1
2759                UvData.ProjField=ObjectData;
2760            else
2761                ViewFieldData=get(view_field_handle,'UserData');
2762                ViewFieldData.ProjField=ObjectData;
2763                set(view_field_handle,'UserData',ViewFieldData)
2764            end
2765        end
2766        if isequal(PlotType,'none')
2767            hget_field=findobj(allchild(0),'name','get_field');
2768            if isempty(hget_field)
2769                get_field([],ObjectData)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2770            else
2771                errormsg='The field defined by get_field cannot be plotted';
2772                return
2773            end
2774        end
2775    end
2776end
2777
2778%write_plot_param(handles,UvData.Object{1}.PlotParam);% update the display of the plotting parameters
2779UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2780set(handles.uvmat,'UserData',UvData)
2781
2782%% update the mask
2783if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
2784   update_mask(handles,num_i1,num_i2);
2785end
2786
2787%% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2788menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2789ind_bad=[];
2790nb_histo=1;
2791
2792% suppress coordinates from the histogram menu
2793for ivar=1:numel(menu_histo)%l loop on field variables:
2794    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2795        Role=UvData.Field.VarAttribute{ivar}.Role;
2796        switch Role
2797            case {'coord_x','coord_y','coord_z','dimvar'}
2798                ind_bad=[ind_bad ivar];
2799            case {'vector_y'}
2800                nb_histo=nb_histo+1;
2801        end
2802    end
2803    DimCell=UvData.Field.VarDimName{ivar};
2804    DimName='';
2805    if ischar(DimCell)
2806        DimName=DimCell;
2807    elseif iscell(DimCell)&& numel(DimCell)==1
2808        DimName=DimCell{1};
2809    end
2810    if strcmp(DimName,menu_histo{ivar})
2811        ind_bad=[ind_bad ivar];
2812    end
2813end
2814menu_histo(ind_bad)=[];
2815
2816%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2817% display menus and plot histograms
2818test_v=0;
2819if ~isempty(menu_histo)
2820    set(handles.histo1_menu,'Value',1)
2821    set(handles.histo1_menu,'String',menu_histo)
2822    histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2823    % case of more than one variables (eg vector components)
2824    if nb_histo > 1
2825        test_v=1;
2826        set(handles.histo2_menu,'Visible','on')
2827        set(handles.histo_v,'Visible','on')
2828        set(handles.histo2_menu,'String',menu_histo)
2829        set(handles.histo2_menu,'Value',2)
2830        histo2_menu_Callback(handles.histo2_menu,[], handles)% plot second histogram
2831    end
2832end
2833if ~test_v
2834    set(handles.histo2_menu,'Visible','off')
2835    set(handles.histo_v,'Visible','off')
2836    cla(handles.histo_v)
2837    set(handles.histo2_menu,'Value',1)
2838end
2839%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2840
2841%% display time
2842testimedoc=0;
2843if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'Time')
2844    if isempty(num_i2)||isnan(num_i2)
2845        num_i2=num_i1;
2846    end
2847    if isempty(num_j1)||isnan(num_j1)
2848        num_j1=1;
2849    end
2850    if isempty(num_j2)||isnan(num_j2)
2851        num_j2=num_j1;
2852    end
2853    siz=size(UvData.XmlData.Time);
2854    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2855        abstime=(UvData.XmlData.Time(num_i1,num_j1)+UvData.XmlData.Time(num_i2,num_j2))/2;%overset the time read from files
2856        dt=(UvData.XmlData.Time(num_i2,num_j2)-UvData.XmlData.Time(num_i1,num_j1));
2857        testimedoc=1;
2858    end
2859end
2860if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time')
2861    [P,F,str1,str2,str_a,str_b,E]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2862    num_i2=str2double(str2);
2863    if isempty(num_i2)
2864        num_i2=num_i1;
2865    end
2866    num_j1=str2double(str_a);
2867    if isempty(num_j1)
2868        num_j1=1;
2869    end
2870    num_j2=str2double(str_b);
2871    if isempty(num_j2)
2872        num_j2=num_j1;
2873    end
2874    num_i1=str2double(str1);
2875    siz=size(UvData.XmlData_1.Time);
2876    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2877        abstime_1=(UvData.XmlData_1.Time(num_i1,num_j1)+UvData.XmlData_1.Time(num_i2,num_j2))/2;%overset the time read from files
2878    end
2879end
2880set(handles.abs_time,'String',num2str(abstime,4))
2881set(handles.abs_time_1,'String',num2str(abstime_1,4))
2882if testimedoc && isfield(UvData,'dt')
2883    dt=UvData.dt;
2884end
2885if isempty(dt)||isequal(dt,0)
2886    set(handles.Dt_txt,'String','')
2887else
2888    if ~(isfield(UvData,'TimeUnit') && ~isempty(UvData.TimeUnit))
2889        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2890    else
2891        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' UvData.TimeUnit] )
2892    end
2893end
2894
2895%% update the input file name in the get_field GUI
2896if isequal(FieldName,'get_field...')
2897    set(hhget_field.inputfile,'String',filename)
2898    Tabchar={''};%default
2899    Tabcell=[];
2900    if isfield(Field{1},'ListGlobalAttribute')&& ~isempty(Field{1}.ListGlobalAttribute)
2901        for iline=1:length(Field{1}.ListGlobalAttribute)
2902            Tabcell{iline,1}=Field{1}.ListGlobalAttribute{iline};
2903            if isfield(Field{1}, Field{1}.ListGlobalAttribute{iline})
2904                eval(['val=Field{1}.' Field{1}.ListGlobalAttribute{iline} ';'])
2905                if ischar(val);
2906                    Tabcell{iline,2}=val;
2907                else
2908                    Tabcell{iline,2}=num2str(val);
2909                end
2910            end
2911        end
2912        if ~isempty(Tabcell)
2913            Tabchar=cell2tab(Tabcell,'=');
2914            Tabchar=[{''};Tabchar];
2915        end
2916    end
2917    set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field
2918end
2919if isequal(FieldName_1,'get_field...')
2920    set(hhget_field_1.inputfile,'String',filename_1)
2921    Tabchar={''};%default
2922    Tabcell=[];
2923    if isfield(Field{2},'ListGlobalAttribute')&& ~isempty(Field{2}.ListGlobalAttribute)
2924        for iline=1:length(Field{2}.ListGlobalAttribute)
2925            Tabcell{iline,1}=Field{2}.ListGlobalAttribute{iline};
2926            if isfield(Field{2}, Field{2}.ListGlobalAttribute{iline})
2927                eval(['val=Field{2}.' Field{2}.ListGlobalAttribute{iline} ';'])
2928                if ischar(val);
2929                    Tabcell{iline,2}=val;
2930                else
2931                    Tabcell{iline,2}=num2str(val);
2932                end
2933            end
2934        end
2935        if ~isempty(Tabcell)
2936            Tabchar=cell2tab(Tabcell,'=');
2937            Tabchar=[{''};Tabchar];
2938        end
2939    end
2940    set(hhget_field_1.attributes,'String',Tabchar);%update list of global attributes in get_field
2941end
2942
2943
2944%-------------------------------------------------------------------
2945% --- translate coordinate to matrix index
2946%-------------------------------------------------------------------
2947function [indx,indy]=pos2ind(x0,rangx0,nxy)
2948indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2949indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2950
2951%-------------------------------------------------------------------
2952% --- Executes on button press in 'FixedLimits'.
2953%-------------------------------------------------------------------
2954function FixedLimits_Callback(hObject, eventdata, handles)
2955test=get(handles.FixedLimits,'Value');
2956if test
2957    set(handles.FixedLimits,'BackgroundColor',[1 1 0])
2958else
2959    set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7])
2960    update_plot(handles);
2961end
2962
2963%-------------------------------------------------------------------
2964% --- Executes on button press in auto_xy.
2965function auto_xy_Callback(hObject, eventdata, handles)
2966test=get(handles.auto_xy,'Value');
2967if test
2968    set(handles.auto_xy,'BackgroundColor',[1 1 0])
2969    cla(handles.axes3)
2970    update_plot(handles);
2971else
2972    set(handles.auto_xy,'BackgroundColor',[0.7 0.7 0.7])
2973    update_plot(handles);
2974%     axis(handles.axes3,'image')
2975end
2976
2977
2978%-------------------------------------------------------------------
2979
2980%-------------------------------------------------------------------
2981% --- Executes on button press in 'zoom'.
2982%-------------------------------------------------------------------
2983function zoom_Callback(hObject, eventdata, handles)
2984
2985if (get(handles.zoom,'Value') == 1);
2986    set(handles.zoom,'BackgroundColor',[1 1 0])
2987    set(handles.FixedLimits,'Value',1)% propose by default fixed limits for the plotting axes
2988    set(handles.FixedLimits,'BackgroundColor',[1 1 0])
2989else
2990    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
2991end
2992
2993
2994%-------------------------------------------------------------------
2995%----Executes on button press in 'record': records the current flags of manual correction.
2996%-------------------------------------------------------------------
2997function record_Callback(hObject, eventdata, handles)
2998% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2999filename=read_file_boxes(handles);
3000AxeData=get(gca,'UserData');
3001[erread,message]=fileattrib(filename);
3002if ~isempty(message) && ~isequal(message.UserWrite,1)
3003     msgbox_uvmat('ERROR',['no writting access to ' filename])
3004     return
3005end
3006test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3007test_civ1=isequal(get(handles.civ1,'BackgroundColor'),[1 1 0]);
3008if ~test_civ2 && ~test_civ1
3009    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3010end
3011if test_civ2
3012    nbname='nb_vectors2';
3013   flagname='vec2_FixFlag';
3014   attrname='fix2';
3015end
3016if test_civ1
3017    nbname='nb_vectors';
3018   flagname='vec_FixFlag';
3019   attrname='fix';
3020end
3021%write fix flags in the netcdf file
3022hhh=which('netcdf.open');% look for built-in matlab netcdf library
3023if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
3024    nc=netcdf.open(filename,'NC_WRITE');
3025    netcdf.reDef(nc)
3026    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1)
3027    dimid = netcdf.inqDimID(nc,nbname);
3028    try
3029        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
3030    catch
3031        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
3032    end
3033    netcdf.endDef(nc)
3034    netcdf.putVar(nc,varid,AxeData.FF);
3035    netcdf.close(nc) 
3036else %old netcdf library
3037    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
3038end
3039
3040function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
3041nc=netcdf(filename,'write'); %open netcdf file
3042result=redef(nc);
3043eval(['nc.' attrname '=1;']);
3044theDim=nc(nbname) ;% get the number of velocity vectors
3045nb_vectors=size(theDim);
3046var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
3047var_FixFlag(1:nb_vectors)=AxeData.FF;%
3048fin=close(nc);
3049
3050
3051%-------------------------------------------------------------------
3052%determines the fields to read from the interface
3053%------------------------------------------------------------------
3054function [VelType,civ]=setfield(handles)
3055
3056VelType=[]; %default
3057if (get(handles.civ1,'Value') == 1);
3058        VelType='civ1';
3059% interp1   
3060elseif (get(handles.interp1,'Value') == 1);
3061    VelType='interp1';
3062% filter1   
3063elseif (get(handles.filter1,'Value') == 1);
3064    VelType='filter1'; 
3065% CIV2
3066elseif (get(handles.civ2,'Value') == 1);
3067    VelType='civ2';
3068% interp2   
3069elseif (get(handles.interp2,'Value') == 1);
3070    VelType='interp2';
3071% filter2   
3072elseif (get(handles.filter2,'Value') == 1); 
3073    VelType='filter2';
3074end
3075
3076if isequal(get(handles.filter2,'Visible'),'on');
3077    civ=6;
3078% interp1   
3079elseif isequal(get(handles.interp2,'Visible'),'on');
3080    civ=5;
3081% filter1   
3082elseif isequal(get(handles.civ2,'Visible'),'on');
3083    civ=4; 
3084% CIV2
3085elseif isequal(get(handles.filter1,'Visible'),'on');
3086   civ=3;
3087% interp2   
3088elseif isequal(get(handles.interp1,'Visible'),'on');
3089    civ=2;
3090% filter2   
3091elseif isequal(get(handles.civ1,'Visible'),'on'); 
3092    civ=1;
3093else
3094    civ=0;
3095end
3096
3097%-------------------------------------------------------------------
3098%determines the veltype of the second field to read from the iinterface
3099%------------------------------------------------------------------
3100function VelType=setfield_1(handles)
3101
3102VelType=[]; %default
3103if (get(handles.civ1_1,'Value') == 1);
3104    VelType='civ1';
3105% interp1   
3106elseif (get(handles.interp1_1,'Value') == 1);
3107    VelType='interp1';
3108% filter1   
3109elseif (get(handles.filter1_1,'Value') == 1);
3110    VelType='filter1'; 
3111% CIV2
3112elseif (get(handles.civ2_1,'Value') == 1);
3113    VelType='civ2';
3114% interp2   
3115elseif (get(handles.interp2_1,'Value') == 1);
3116    VelType='interp2';
3117% filter2   
3118elseif (get(handles.filter2_1,'Value') == 1); 
3119    VelType='filter2';
3120end
3121
3122
3123%---------------------------------------------------
3124% --- Executes on button press in SubField
3125function SubField_Callback(hObject, eventdata, handles)
3126huvmat=get(handles.run0,'parent');
3127UvData=get(huvmat,'UserData');
3128if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
3129    set(handles.RootPath_1,'String','')
3130    set(handles.RootFile_1,'String','')
3131    set(handles.SubDir_1,'String','');
3132    set(handles.FileIndex_1,'String','');
3133    set(handles.FileExt_1,'String','');
3134    set(handles.RootPath_1,'Visible','off')
3135    set(handles.RootFile_1,'Visible','off')
3136    set(handles.SubDir_1,'Visible','off');
3137    set(handles.FileIndex_1,'Visible','off');
3138    set(handles.FileExt_1,'Visible','off');
3139    set(handles.Fields_1,'Value',1);%set to blank state
3140    set_veltype_display([handles.civ1_1 handles.interp1_1 handles.filter1_1 ...
3141            handles.civ2_1 handles.interp2_1 handles.filter2_1],0)
3142    if isfield(UvData,'XmlData_1')
3143        UvData=rmfield(UvData,'XmlData_1');
3144    end
3145    set(huvmat,'UserData',UvData);
3146    run0_Callback(hObject, eventdata, handles); %run
3147else
3148    MenuBrowse_1_Callback(hObject, eventdata, handles)
3149end
3150
3151%------------------------------------------------------------------------
3152% --- read the data displayed for the input rootfile windows (new)
3153function [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles)
3154%------------------------------------------------------------------------
3155RootPath=get(handles.RootPath,'String');
3156FileName=RootPath; %default
3157SubDir=get(handles.SubDir,'String');
3158if ~isempty(SubDir) && ~isequal(SubDir,'')
3159    if (isequal(SubDir(1),'/')|| isequal(SubDir(1),'\'))
3160        SubDir(1)=[]; %suppress possible / or \ separator
3161    end
3162    FileName=fullfile(RootPath,SubDir);
3163end
3164RootFile=get(handles.RootFile,'String');
3165if ~isempty(RootFile) && ~isequal(RootFile,'')
3166    if (isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
3167        RootFile(1)=[]; %suppress possible / or \ separator
3168    end
3169    FileName=fullfile(FileName,RootFile);
3170end
3171FileBase=fullfile(RootPath,RootFile);
3172FileIndices=get(handles.FileIndex,'String');
3173FileExt=get(handles.FileExt,'String');
3174FileName=[FileName FileIndices FileExt];
3175
3176%------------------------------------------------------------------------
3177% ---- read the data displayed for the second input rootfile windows
3178function [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles)
3179%------------------------------------------------------------------------
3180RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3181if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3182    RootPath_1=get(handles.RootPath,'String');
3183end;
3184FileName_1=RootPath_1; %default
3185SubDir_1=get(handles.SubDir_1,'String');
3186if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3187    SubDir_1=get(handles.SubDir,'String');
3188end
3189if numel(SubDir_1)>=1
3190    if (isequal(SubDir_1(1),'/')|| isequal(SubDir_1(1),'\'))
3191        SubDir_1(1)=[]; %suppress possible / or \ separator
3192    end
3193    FileName_1=fullfile(RootPath_1,SubDir_1);
3194end
3195RootFile_1=get(handles.RootFile_1,'String');
3196if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3197    RootFile_1=get(handles.RootFile,'String');
3198end
3199if numel(RootFile_1)>=1
3200    if ~(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
3201        RootFile_1(1)=[];%suppress possible / or \ separator
3202    end
3203    FileName_1=fullfile(FileName_1,RootFile_1);
3204end
3205FileBase_1=fullfile(RootPath_1,RootFile_1);
3206if isequal(get(handles.FileIndex_1,'Visible'),'off')
3207    FileIndices_1=get(handles.FileIndex,'String');
3208else
3209    FileIndices_1=get(handles.FileIndex_1,'String');
3210end
3211FileExt_1=get(handles.FileExt_1,'String');
3212if isequal(FileExt_1,'"'),FileExt_1=get(handles.FileExt,'String'); end;
3213FileName_1=[FileName_1 FileIndices_1 FileExt_1];
3214
3215%------------------------------------------------------------------------
3216% --- Executes on menu selection Fields
3217function Fields_Callback(hObject, eventdata, handles)
3218%------------------------------------------------------------------------
3219list_fields=get(handles.Fields,'String');% list menu fields
3220index_fields=get(handles.Fields,'Value');% selected string index
3221field= list_fields{index_fields(1)}; % selected string
3222if isequal(field,'get_field...')
3223     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3224     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3225     filename=read_file_boxes(handles);
3226     hget_field=findobj(allchild(0),'name','get_field');
3227     if ~isempty(hget_field)
3228         delete(hget_field)
3229     end
3230     hget_field=get_field(filename);
3231     set(hget_field,'Name','get_field')       
3232     hhget_field=guidata(hget_field);
3233     set(hhget_field.list_fig,'Value',1)
3234     set(hhget_field.list_fig,'String',{'uvmat'})
3235     set(handles.transform_fct,'Value',1)% no transform by default
3236     set(handles.path_transform,'String','')
3237    return %no action
3238end
3239list_fields=get(handles.Fields_1,'String');% list menu fields
3240index_fields=get(handles.Fields_1,'Value');% selected string index
3241field_1= list_fields{index_fields(1)}; % selected string
3242UvData=get(handles.uvmat,'UserData');
3243
3244%read the rootfile input display
3245[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
3246[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt]);
3247NomTypeNew=NomType;%default
3248if isequal(field,'image')
3249    % transform netc type to the corresponding image type
3250%     if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')|| isequal(NomType,'#_ab')|| isequal(NomType,'_i1-i2')
3251%         UvData.SubDir=get(handles.SubDir,'String'); %preserve the subdir in memory
3252%         if ~isempty(UvData.SubDir) && (isequal(UvData.SubDir(1),'/')||isequal(UvData.SubDir(1),'/'))
3253%             UvData.SubDir(1)=[];
3254%         end
3255%         set(handles.SubDir,'String','')
3256%         set(handles.FileExt,'String','.png');
3257        if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')
3258            NomTypeNew='_i_j';
3259        elseif isequal(NomType,'#_ab')
3260            NomTypeNew='#a';
3261        elseif isequal(NomType,'_i1-i2')
3262            NomTypeNew='_i';
3263        end 
3264        imagename=name_generator(FileBase,str2double(str1),str2double(str_a),'.png',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3265        if ~exist(imagename,'file')
3266                [FileName,PathName] = uigetfile( ...
3267           {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3268            '*.jpg',' jpeg image files'; ...
3269            '*.png','.png image files'; ...
3270            '*.tif','.tif image files'; ...
3271            '*.avi;*.AVI','.avi movie files'; ...
3272            '*.vol','.volume images (png)'; ...
3273            '*.*',  'All Files (*.*)'}, ...
3274            'Pick an image',imagename);           
3275            % display the selected field and related information
3276           imagename=[PathName FileName];
3277        end
3278        display_file_name(hObject, eventdata, handles,imagename)%display the image
3279        return
3280%     end
3281%     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3282%     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3283else
3284    ext=get(handles.FileExt,'String');
3285    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3286                [FileName,PathName] = uigetfile( ...
3287           {'*.nc', ' (*.nc)';
3288            '*.nc',' netcdf files'; ...
3289            '*.*',  'All Files (*.*)'}, ...
3290            'Pick a netcdf file',FileBase);           
3291            % display the selected field and related information
3292           filename=[PathName FileName];
3293        display_file_name(hObject, eventdata, handles,filename)
3294        return
3295       %  MenuBrowse_Callback(hObject, eventdata, handles)
3296    end
3297    if isequal(field,'vort') || isequal(field,'div') || isequal(field,'strain')
3298        set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3299        set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
3300        set(handles.interp1,'BackgroundColor',[0.702 0.702 0.702])
3301        set(handles.interp2,'BackgroundColor',[0.702 0.702 0.702])
3302    elseif isequal(field,'more...');
3303        set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3304        set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
3305        str=calc_field;%get the list of available scalars by the function calc_scal
3306        [ind_answer] = listdlg('PromptString','Select a file:',...
3307                'SelectionMode','single',...
3308                'ListString',str);
3309       % edit the choice in the field and action menu
3310        scalar=cell2mat(str(ind_answer));
3311        menu=update_menu(handles.Fields,scalar);
3312        menu=[{''};menu];
3313        set(handles.Fields_1,'String',menu);% store the selected scalar type
3314    end
3315end
3316indices=name_generator('',str2double(str1),str2double(str_a),'',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3317set(handles.FileIndex,'String',indices)
3318set(handles.FileIndex,'UserData',NomTypeNew)
3319%common to Fields_1_Callback
3320if isequal(field,'image')||isequal(field_1,'image')
3321    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3322    set(handles.npy_title,'Visible','on')
3323    set(handles.npx,'Visible','on')
3324    set(handles.npy,'Visible','on')
3325else
3326    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3327    set(handles.npy_title,'Visible','off')
3328    set(handles.npx,'Visible','off')
3329    set(handles.npy,'Visible','off')
3330end
3331setfield(handles);% update the field structure ('civ1'....)
3332
3333if ~isfield(UvData,'NewSeries')||isequal(UvData.NewSeries,0)
3334    run0_Callback(hObject, eventdata, handles)
3335end
3336
3337%---------------------------------------------------
3338% --- Executes on menu selection Fields
3339function Fields_1_Callback(hObject, eventdata, handles)
3340%-------------------------------------------------
3341list_fields=get(handles.Fields,'String');% list menu fields
3342index_fields=get(handles.Fields,'Value');% selected string index
3343field= list_fields{index_fields(1)}; % selected string
3344list_fields=get(handles.Fields_1,'String');% list menu fields
3345index_fields=get(handles.Fields_1,'Value');% selected string index
3346field_1= list_fields{index_fields(1)}; % selected string for the second field
3347if isequal(field_1,'') %remove second field if 'blank' field is selected
3348    set(handles.SubField,'Value',0)
3349    SubField_Callback(hObject, eventdata, handles)
3350    return
3351end
3352UvData=get(handles.uvmat,'UserData');
3353
3354%read the rootfile input display
3355[FileName,RootPath,FileBase,FileIndices,FileExt_prev]=read_file_boxes_1(handles);
3356[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt_prev]);
3357if isempty(FileExt_prev)|isequal(FileExt_prev,'')
3358    FileExt_1=get(handles.FileExt,'String');
3359else
3360    FileExt_1=FileExt_prev;
3361end
3362NomType_1=get(handles.FileIndex_1,'UserData');
3363if isempty(NomType_1)|isequal(NomType_1,'')
3364    NomType_1=get(handles.FileIndex,'UserData');
3365end
3366NomTypeNew=NomType_1;%default
3367
3368set(handles.SubField,'Value',1)%introduce second field
3369if isfield(UvData,'XmlData')
3370    UvData.XmlData_1=UvData.XmlData;
3371end
3372set(handles.FileIndex_1,'Visible','on')
3373set(handles.FileExt_1,'Visible','on')
3374RootPath_1=get(handles.RootPath_1,'String');
3375RootFile_1=get(handles.RootFile_1,'String');
3376if isempty(RootPath_1)||isequal(RootPath_1,'')
3377    set(handles.RootPath_1,'String','"')
3378end
3379if isempty(RootFile_1) || isequal(RootFile_1,'')
3380    set(handles.RootFile_1,'String','"')
3381end
3382if ~isempty(RootFile_1)&&(isequal(RootFile_1(1),'/')||isequal(RootFile_1(1),'\'))
3383    RootFile_1(1)=[];
3384end
3385
3386if isequal(field_1,'get_field...')
3387     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
3388     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3389     filename=read_file_boxes_1(handles);
3390     hget_field=findobj(allchild(0),'name','get_field_1');
3391     if ~isempty(hget_field)
3392         delete(hget_field)
3393     end
3394     hget_field=get_field(filename);
3395     set(hget_field,'name','get_field_1')
3396     hhget_field=guidata(hget_field);
3397     set(hhget_field.list_fig,'Value',1)
3398     set(hhget_field.list_fig,'String',{'uvmat'})
3399     set(handles.transform_fct,'Value',1)% no transform by default
3400     set(handles.path_transform,'String','')
3401    return %no action
3402end
3403if isequal(field_1,'image')
3404    % transform netc type to the corresponding image type
3405%     set(handles.FileExt_1,'String','.png');
3406    if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')| isequal(NomType_1,'#_ab')| isequal(NomType_1,'_i1-i2')
3407        UvData.SubDir_1=get(handles.SubDir_1,'String'); %preserve the subdir in memory
3408%         set(handles.SubDir_1,'String','')
3409%         set(handles.FileExt_1,'String','.png');       
3410        if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')
3411            NomTypeNew='_i_j';
3412        elseif isequal(NomType_1,'#_ab')
3413            NomTypeNew='#a';
3414        elseif isequal(NomType_1,'_i1-i2')
3415            NomTypeNew='_i';
3416        end 
3417    end
3418    imagename=name_generator(FileBase,str2double(str1),str2double(str_a),'.png',NomTypeNew,1,str2double(str2),str2double(str_b),'');
3419    if ~exist(imagename,'file')
3420        [FileName,PathName] = uigetfile( ...
3421            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3422            '*.jpg',' jpeg image files'; ...
3423            '*.png','.png image files'; ...
3424            '*.tif','.tif image files'; ...
3425            '*.avi;*.AVI','.avi movie files'; ...
3426            '*.vol','.volume images (png)'; ...
3427            '*.*',  'All Files (*.*)'}, ...
3428            'Pick an image',imagename);
3429        % display the selected field and related information
3430        imagename=[PathName FileName];
3431    end
3432    display_file_name_1(hObject, eventdata, handles,imagename)%display the image
3433    return
3434%     veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
3435%     set_veltype_display(veltype_handles,0) % unvisible civ buttons
3436else
3437    set(handles.SubDir_1,'Visible','on')
3438    if ~isequal(FileExt_prev,'.nc') %find the new NomType if the previous display was not already a netcdf file
3439        veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
3440        set_veltype_display(veltype_handles,6); % make all civ buttons visible
3441        RootPath_1=get(handles.RootPath_1,'String');
3442        RootFile_1=get(handles.RootFile_1,'String');
3443        if isempty(RootPath_1)|isequal(RootPath_1,'')
3444            set(handles.RootPath_1,'String','"')
3445        end
3446        if isempty(RootFile_1) | isequal(RootFile_1,'')
3447            set(handles.RootFile_1,'String','"')
3448        end
3449        if ~isempty(RootFile_1)&(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
3450            RootFile_1(1)=[];
3451        end
3452        filebase_1=fullfile(RootPath_1,RootFile_1);
3453        SubDir_1=get(handles.SubDir,'String');
3454        if isempty(SubDir_1)||isequal(SubDir_1,'')
3455            if isfield(UvData,'SubDir_1')
3456                SubDir_1=UvData.SubDir_1;%retrieve previous subdir
3457            else
3458                SubDir_1='?';
3459            end
3460        end
3461        str1=get(handles.i1,'String');
3462        str_a=get(handles.j1,'String');
3463        if isequal(NomType_1,'#_ab')||isequal(NomType_1,'_i1-i2_j')||isequal(NomType_1,'_i_j1-j2')||isequal(NomType_1,'_i1-i2')
3464            NomTypeNew=NomType_1;
3465        elseif isequal(NomType_1,'#a')
3466             [filename, n1,na,n2,nb,SubDir_1]=name_generator(filebase_1, str2num(str1),stra2num(str_a),'.nc','#_ab',0,[],[],SubDir_1);
3467             NomTypeNew='#_ab';
3468        elseif isequal(NomType_1,'_i_j')
3469             [filename,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),stra2num(str_a),'.nc','_i1-i2_j',0,str2num(str1),[],SubDir_1);
3470            if idetect==1
3471                NomTypeNew='_i1-i2_j';
3472            else
3473                NomTypeNew='_i_j1-j2';
3474            end
3475        else %for instance avi files or any ima_num series
3476            [filename,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),stra2num(str_a),'.nc','_i1-i2',0,str2num(str1),[],SubDir_1);
3477            NomTypeNew='_i1-i2';
3478        end           
3479        [Path,Name]=fileparts(filebase_1);
3480        set(handles.FileExt_1,'String','.nc');
3481        if ~isempty(SubDir_1) && ~strcmp(SubDir_1,'''')&& ~strcmp(SubDir_1,'"')&& ~strcmp(SubDir_1(1),'/')
3482            SubDir_1=['/' SubDir_1];
3483        end
3484        set(handles.SubDir_1,'String',SubDir_1);
3485    end
3486    if isequal(field,'vort') | isequal(field,'div') | isequal(field,'strain')
3487        set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3488        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3489        set(handles.interp1_1,'BackgroundColor',[0.702 0.702 0.702])
3490        set(handles.interp2_1,'BackgroundColor',[0.702 0.702 0.702])
3491    elseif isequal(field_1,'more...'); %add new item to the menu
3492        set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3493        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3494        str=calc_field;%get the list of available scalars by the function calc_scal
3495        [ind_answer,v] = listdlg('PromptString','Select a file:',...
3496                'SelectionMode','single',...
3497                'ListString',str);
3498       % edit the choice in the field and action menu
3499        scalar=cell2mat(str(ind_answer));
3500        menu=update_menu(handles.Fields_1,scalar);
3501        set(handles.Fields_1,'String',menu);% store the selected scalar type
3502    end
3503end
3504str1=get(handles.i1,'String');
3505str2=get(handles.i2,'String');
3506str_a=get(handles.j1,'String');
3507str_b=get(handles.j2,'String');
3508indices=name_generator('',str2num(str1),stra2num(str_a),'',NomTypeNew,1,str2num(str2),stra2num(str_b),'');
3509set(handles.FileIndex_1,'String',indices)
3510set(handles.FileIndex_1,'UserData',NomTypeNew)
3511
3512%common to Fields_Callback
3513if isequal(field,'image')|isequal(field_1,'image')
3514    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3515    set(handles.npy_title,'Visible','on')
3516    set(handles.npx,'Visible','on')
3517    set(handles.npy,'Visible','on')
3518%     set(handles.fix_pair,'Value',0)
3519else
3520    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3521    set(handles.npy_title,'Visible','off')
3522    set(handles.npx,'Visible','off')
3523    set(handles.npy,'Visible','off')
3524%     set(handles.fix_pair,'Value',1)
3525end
3526if isequal(field,'velocity')|isequal(field_1,'velocity');
3527    state_vect='on';
3528else
3529    state_vect='off';
3530end
3531if ~isequal(field,'velocity')|(~isequal(field_1,'velocity')&~isequal(field_1,''));
3532    state_scal='on';
3533else
3534    state_scal='off';
3535end
3536set(handles.uvmat,'UserData',UvData)
3537setfield(handles);% update the field structure ('civ1'....)
3538if ~isfield(UvData,'NewSeries')|isequal(UvData.NewSeries,0)
3539    run0_Callback(hObject, eventdata, handles)
3540end
3541
3542%------------------------------------------------------------------------
3543% --- set the visibility of relevant velocity type menus:
3544function set_veltype_display(handles,Civ)
3545%------------------------------------------------------------------------
3546%Civ=0; all states 'off'
3547%Civ=6; all states 'on'
3548if isequal(Civ,0)
3549    imax=0;
3550%    set(handles(1),'Visible','on')  % unvisible civ buttons
3551% else
3552%    set(handles(1),'String','civ1')
3553% end
3554elseif isequal(Civ,1) || isequal(Civ,2)
3555   imax=1;
3556elseif isequal(Civ,3)
3557    imax=3;
3558elseif isequal(Civ,4) || isequal(Civ,5)
3559    imax=4;
3560elseif isequal(Civ,6) %patch2
3561    imax=6;
3562end
3563for ibutton=1:imax;
3564    set(handles(ibutton),'Visible','on')  % unvisible civ buttons
3565end
3566% for ibutton=max(imax+1,2):6;
3567for ibutton=imax+1:6;
3568    set(handles(ibutton),'Visible','off')  % unvisible civ buttons
3569    set(handles(ibutton),'Value',0)%unactivate unvisible buttons
3570end
3571
3572%-------------------------------------------------------------------
3573% --- Executes on button press in civ1.
3574function civ1_Callback(hObject, eventdata, handles)
3575%-------------------------------------------------------------------
3576if get(handles.civ1,'Value')==1
3577    reset_vel_type([handles.interp1 handles.civ2 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ1)
3578else
3579    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3580end
3581run0_Callback(hObject, eventdata, handles)
3582
3583%-------------------------------------------------------------------
3584% --- Executes on button press in interp1.
3585function interp1_Callback(hObject, eventdata, handles)
3586%-------------------------------------------------------------------
3587if get(handles.interp1,'Value')==1
3588    reset_vel_type([handles.civ1 handles.civ2 handles.filter1 handles.interp2 handles.filter2],handles.interp1)
3589else
3590     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3591end
3592run0_Callback(hObject, eventdata, handles)
3593
3594%-------------------------------------------------------------------
3595% --- Executes on button press in filter1.
3596function filter1_Callback(hObject, eventdata, handles)
3597%-------------------------------------------------------------------
3598if get(handles.filter1,'Value')==1
3599    reset_vel_type([handles.civ1 handles.civ2 handles.interp1 handles.interp2 handles.filter2],handles.filter1)
3600else
3601     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3602end
3603run0_Callback(hObject, eventdata, handles)
3604
3605%-------------------------------------------------------------------
3606% --- Executes on button press in civ2.
3607function civ2_Callback(hObject, eventdata, handles)
3608%-------------------------------------------------------------------
3609if get(handles.civ2,'Value')==1
3610    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ2)
3611else
3612     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3613end
3614run0_Callback(hObject, eventdata, handles)
3615
3616%-----------------------------------------
3617% --- Executes on button press in interp2.
3618%-------------------------------------------
3619function interp2_Callback(hObject, eventdata, handles)
3620if get(handles.interp2,'Value')==1
3621    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.filter2],handles.interp2)
3622else
3623     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3624end
3625run0_Callback(hObject, eventdata, handles)
3626%---------------------------------------------
3627% --- Executes on button press in filter2.
3628%-------------------------------------------
3629function filter2_Callback(hObject, eventdata, handles)
3630if get(handles.filter2,'Value')==1
3631    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2],handles.filter2)
3632else
3633     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3634end
3635run0_Callback(hObject, eventdata, handles)
3636
3637%---------------------------------------------
3638function civ1_1_Callback(hObject, eventdata, handles)
3639%---------------------------------------------
3640if get(handles.civ1_1,'Value')==1
3641    reset_vel_type([handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.civ1_1)
3642else
3643     reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3644end
3645run0_Callback(hObject, eventdata, handles)
3646
3647%--------------------------------------------
3648function interp1_1_Callback(hObject, eventdata, handles)
3649%--------------------------------------------
3650if get(handles.interp1_1,'Value')==1
3651    reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.interp1_1)
3652else
3653    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3654end
3655run0_Callback(hObject, eventdata, handles)
3656
3657%--------------------------------------------
3658function filter1_1_Callback(hObject, eventdata, handles)
3659%--------------------------------------------
3660if get(handles.filter1_1,'Value')==1
3661    reset_vel_type([handles.interp1_1 handles.civ2_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.filter1_1)
3662else
3663    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3664end
3665run0_Callback(hObject, eventdata, handles)
3666
3667%--------------------------------------------
3668function civ2_1_Callback(hObject, eventdata, handles)
3669%--------------------------------------------
3670if get(handles.civ2_1,'Value')==1
3671    reset_vel_type([handles.civ1_1 handles.interp1_1  handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.civ2_1)
3672else
3673    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3674end
3675run0_Callback(hObject, eventdata, handles)
3676
3677%--------------------------------------------
3678function interp2_1_Callback(hObject, eventdata, handles)
3679%--------------------------------------------
3680if get(handles.interp2_1,'Value')==1
3681    reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.filter2_1],handles.interp2_1)
3682else
3683    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3684end
3685run0_Callback(hObject, eventdata, handles)
3686
3687%--------------------------------------------
3688function filter2_1_Callback(hObject, eventdata, handles)
3689%--------------------------------------------
3690if get(handles.filter2_1,'Value')==1
3691    reset_vel_type([handles.civ1_1 handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1],handles.filter2_1)
3692else
3693    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3694end
3695run0_Callback(hObject, eventdata, handles)
3696
3697%-----------------------------------------------
3698% --- reset civ buttons
3699function reset_vel_type(handles_civ0,handle1)
3700for ibutton=1:length(handles_civ0)
3701    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3702    set(handles_civ0(ibutton),'Value',0)
3703end
3704if exist('handle1','var')%handles of selected button
3705        set(handle1,'BackgroundColor',[1 1 0]) 
3706end
3707
3708%-------------------------------------------------------
3709% --- Executes on button press in MENUVOLUME.
3710%-------------------------------------------------------
3711function VOLUME_Callback(hObject, eventdata, handles)
3712%errordlg('command VOL not implemented yet')
3713if ishandle(handles.UVMAT_title)
3714    delete(handles.UVMAT_title)
3715end
3716UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3717if isequal(get(handles.VOLUME,'Value'),1)
3718    set(handles.zoom,'Value',0)
3719    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3720    set(handles.edit_vect,'Value',0)
3721    edit_vect_Callback(hObject, eventdata, handles)
3722    set(handles.edit,'Value',0)
3723    set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3724%     set(handles.cal,'Value',0)
3725%     set(handles.cal,'BackgroundColor',[0 1 0])
3726    set(handles.edit_vect,'Value',0)
3727    edit_vect_Callback(hObject, eventdata, handles)
3728    %initiate set_object GUI
3729    data.TITLE='VOLUME';
3730    if isfield(UvData,'CoordType')
3731        data.CoordType=UvData.CoordType;
3732    end
3733    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3734        data.RangeY=UvData.Mesh;
3735        data.RangeX=UvData.Mesh;
3736        data.DX=UvData.Mesh;
3737        data.DY=UvData.Mesh;
3738    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3739        np=size(UvData.Field.A);
3740        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3741        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3742        data.RangeY=max(meshx,meshy);
3743        data.RangeX=max(meshx,meshy);
3744        data.DX=max(meshx,meshy);
3745    end
3746    data.ParentButton=handles.VOLUME;
3747    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3748    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3749                                                      % associate the set_edit interface handle to the plotting axes
3750    if isfield(UvData,'SetObjectOrigin')                                               
3751    pos_uvmat=get(huvmat,'Position');
3752    pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3753    pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); 
3754    set(hset_object,'Position',pos_set_object)
3755    end
3756    UvData.MouseAction='create_object';
3757else
3758    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3759    UvData.MouseAction='none';
3760end
3761set(huvmat,'UserData',UvData)
3762
3763%-------------------------------------------------------
3764function edit_vect_Callback(hObject, eventdata, handles)
3765%-------------------------------------------------------
3766
3767UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3768if isequal(get(handles.edit_vect,'Value'),1)
3769    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3770    test_civ1=isequal(get(handles.civ1,'BackgroundColor'),[1 1 0]);
3771    if ~test_civ2 && ~test_civ1
3772        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3773    end
3774    set(handles.record,'Visible','on')
3775    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3776    set(handles.edit,'Value',0)
3777    set(handles.zoom,'Value',0)
3778    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3779%     set(handles.create,'Value',0)
3780%     set(handles.create,'BackgroundColor',[0 1 0])
3781    set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3782    set(gcf,'Pointer','arrow')
3783    UvData.MouseAction='edit_vect';
3784else
3785    set(handles.record,'Visible','off')
3786    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3787    UvData.MouseAction='none';
3788end
3789set(handles.uvmat,'UserData',UvData)
3790
3791%----------------------------------------------
3792function save_mask_Callback(hObject, eventdata, handles)
3793%-----------------------------------------------------------------------
3794UvData=get(handles.uvmat,'UserData');
3795
3796flag=1;
3797npx=size(UvData.Field.A,2);
3798npy=size(UvData.Field.A,1);
3799xi=[0.5:npx-0.5];
3800yi=[0.5:npy-0.5];
3801[Xi,Yi]=meshgrid(xi,yi);
3802if isfield(UvData,'Object')
3803    for iobj=1:length(UvData.Object)
3804        ObjectData=UvData.Object{iobj};
3805        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3806            flagobj=1;
3807            testphys=0; %coordinates in pixels by default
3808            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3809                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
3810                    Calib=UvData.XmlData.GeometryCalib;
3811                    testphys=1;
3812                end
3813            end
3814            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3815                if isequal(ObjectData.Style,'polygon')
3816                    X=ObjectData.Coord(:,1);
3817                    Y=ObjectData.Coord(:,2);
3818                    if testphys
3819                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3820                    end
3821                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3822                elseif isequal(ObjectData.Style,'ellipse')
3823                    if testphys
3824                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3825                    end
3826                    RangeX=max(ObjectData.RangeX);
3827                    RangeY=max(ObjectData.RangeY);
3828                    X2Max=RangeX*RangeX;
3829                    Y2Max=RangeY*RangeY;
3830                    distX=(Xi-ObjectData.Coord(1,1));
3831                    distY=(Yi-ObjectData.Coord(1,2));
3832                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3833                elseif isequal(ObjectData.Style,'rectangle')
3834                    if testphys
3835                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3836                    end
3837                    distX=abs(Xi-ObjectData.Coord(1,1));
3838                    distY=abs(Yi-ObjectData.Coord(1,2));
3839                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3840                end
3841                if isequal(ObjectData.ProjMode,'mask_outside')
3842                    flagobj=~flagobj;
3843                end
3844                flag=flag & flagobj;
3845            end
3846        end
3847    end
3848end
3849% flag=~flag;
3850%mask name
3851RootPath=get(handles.RootPath,'String');
3852RootFile=get(handles.RootFile,'String');
3853if ~isempty(RootFile)&(isequal(RootFile(1),'/')| isequal(RootFile(1),'\'))
3854        RootFile(1)=[];
3855end
3856filebase=fullfile(RootPath,RootFile);
3857list=get(handles.masklevel,'String');
3858masknumber=num2str(length(list));
3859maskindex=get(handles.masklevel,'Value');
3860mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3861imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3862imflag=flipdim(imflag,1);
3863% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3864msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3865imwrite(imflag,mask_name,'BitDepth',8);
3866
3867%display the mask
3868%update_mask(handles,num_i1,num_j1)
3869figure;
3870vec=linspace(0,1,256);%define a linear greyscale colormap
3871map=[vec' vec' vec'];
3872colormap(map)
3873
3874image(imflag);
3875
3876%-------------------------------------------------------------------
3877%-------------------------------------------------------------------
3878%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3879
3880%------------------------------------------------------------------
3881
3882
3883
3884%------------------------------------------------------------------
3885% --- Executes on selection change in col_vec: choice of the color code.
3886%
3887function col_vec_Callback(hObject, eventdata, handles)
3888%------------------------------------------------------------------
3889% edit the choice for color code
3890list_code=get(handles.col_vec,'String');% list menu fields
3891index_code=get(handles.col_vec,'Value');% selected string index
3892col_code= list_code{index_code(1)}; % selected field
3893if isequal(col_code,'black') || isequal(col_code,'white')
3894   set(handles.slider1,'Visible','off')
3895   set(handles.slider2,'Visible','off')
3896   set(handles.colcode1,'Visible','off')
3897   set(handles.colcode2,'Visible','off')
3898   set(handles.AutoVecColor,'Visible','off')
3899   set_vec_col_bar(handles)
3900else
3901   set(handles.slider1,'Visible','on')
3902   set(handles.slider2,'Visible','on')
3903   set(handles.colcode1,'Visible','on')
3904   set(handles.colcode2,'Visible','on')
3905   set(handles.AutoVecColor,'Visible','on') 
3906   if isequal(col_code,'ima_cor')
3907       set(handles.AutoVecColor,'Value',0)%fixed scale by default
3908       set(handles.vec_col_bar,'Value',0)% 3 colors r,g,b by default
3909       set(handles.slider1,'Min',0);
3910       set(handles.slider1,'Max',1);
3911       set(handles.slider2,'Min',0);
3912       set(handles.slider2,'Max',1);
3913 %      set(handles.min_title_vec,'String','0')
3914       set(handles.max_vec,'String','1')
3915       set(handles.colcode1,'String','0.333')
3916       colcode1_Callback(hObject, eventdata, handles)
3917       set(handles.colcode2,'String','0.666')
3918       colcode2_Callback(hObject, eventdata, handles)
3919   else
3920       set(handles.AutoVecColor,'Value',1)%auto scale between min,max by default
3921       set(handles.vec_col_bar,'Value',1)% colormap 'jet' by default
3922       minval=get(handles.slider1,'Min');
3923       maxval=get(handles.slider1,'Max');
3924       set(handles.slider1,'Value',minval)
3925       set(handles.slider2,'Value',maxval)
3926       set_vec_col_bar(handles)
3927   end
3928%    slider_update(handles)
3929end
3930%replot the current graph
3931run0_Callback(hObject, eventdata, handles)
3932
3933
3934%----------------------------------------------------------------
3935% -- Executes on slider movement to set the color code
3936%
3937function slider1_Callback(hObject, eventdata, handles)
3938%------------------------------------------------------------------
3939slider1=get(handles.slider1,'Value');
3940min_val=str2num(get(handles.min_vec,'String'));
3941max_val=str2num(get(handles.max_vec,'String'));
3942col=min_val+(max_val-min_val)*slider1;
3943set(handles.colcode1,'String',num2str(col))
3944if(get(handles.slider2,'Value') < col)%move also the second slider at the same value if needed
3945    set(handles.slider2,'Value',col)
3946    set(handles.colcode2,'String',num2str(col))
3947end
3948colcode1_Callback(hObject, eventdata, handles)
3949
3950%----------------------------------------------------------------
3951% Executes on slider movement to set the color code
3952%----------------------------------------------------------------
3953function slider2_Callback(hObject, eventdata, handles)
3954slider2=get(handles.slider2,'Value');
3955min_val=str2num(get(handles.min_vec,'String'));
3956max_val=str2num(get(handles.max_vec,'String'));
3957col=min_val+(max_val-min_val)*slider2;
3958set(handles.colcode2,'String',num2str(col))
3959if(get(handles.slider1,'Value') > col)%move also the first slider at the same value if needed
3960    set(handles.slider1,'Value',col)
3961    set(handles.colcode1,'String',num2str(col))
3962end
3963colcode2_Callback(hObject, eventdata, handles)
3964
3965%----------------------------------------------------------------
3966%execute on return carriage on the edit box corresponding to slider 1
3967%----------------------------------------------------------------
3968function colcode1_Callback(hObject, eventdata, handles)
3969% col=str2num(get(handles.colcode1,'String'));
3970% set(handles.slider1,'Value',col)
3971set_vec_col_bar(handles)
3972update_plot(handles);
3973
3974%----------------------------------------------------------------
3975%execute on return carriage on the edit box corresponding to slider 2
3976%----------------------------------------------------------------
3977function colcode2_Callback(hObject, eventdata, handles)
3978% col=str2num(get(handles.colcode2,'String'));
3979% set(handles.slider2,'Value',col)
3980% slider2_Callback(hObject, eventdata, handles)
3981set_vec_col_bar(handles)
3982update_plot(handles);
3983%------------------------------------------------------------
3984%update the slider values after displaying vectors
3985%--------------------------------------------------------
3986% function slider_update(handles,auto,minC,colcode1,colcode2,maxC)
3987% set(handles.slider1,'Min',minC)
3988% set(handles.slider1,'Max',maxC)
3989% set(handles.slider2,'Min',minC)
3990% set(handles.slider2,'Max',maxC)
3991% set(handles.min_title_vec,'String',num2str(minC))
3992% set(handles.max_vec,'String',num2str(maxC))
3993% if auto
3994%         set(handles.colcode1,'String',num2str(colcode1,3))%update display
3995%         set(handles.colcode2,'String',num2str(colcode2,3))
3996% end
3997% set(handles.slider1,'Value',colcode1)%update slider with constant display
3998% set(handles.slider2,'Value',colcode2)
3999% set_vec_col_bar(handles)
4000
4001
4002%-------------------------------------------------------
4003% --- Executes on button press in AutoVecColor.
4004%-------------------------------------------------------
4005function vec_col_bar_Callback(hObject, eventdata, handles)
4006set_vec_col_bar(handles)
4007
4008%-------------------------------------------------------------
4009% --- Executes on selection change in transform_fct.
4010function transform_fct_Callback(hObject, eventdata, handles)
4011%-------------------------------------------------------------
4012global nb_builtin
4013
4014huvmat=get(handles.transform_fct,'parent');
4015menu=get(handles.transform_fct,'String');
4016ind_coord=get(handles.transform_fct,'Value');
4017coord_option=menu{ind_coord};
4018list_transform=get(handles.transform_fct,'UserData');
4019ff=functions(list_transform{end}); 
4020if isequal(coord_option,'more...');
4021    coord_fct='';
4022    prompt = {'Enter the name of the transform function'};
4023    dlg_title = 'user defined transform';
4024    num_lines= 1;
4025    [FileName, PathName] = uigetfile( ...
4026       {'*.m', ' (*.m)';
4027        '*.m',  '.m files '; ...
4028        '*.*', 'All Files (*.*)'}, ...
4029        'Pick a file', ff.file);
4030    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
4031        PathName(end)=[];
4032    end
4033    transform_selected =fullfile(PathName,FileName);
4034    if ~exist(transform_selected,'file')
4035           return
4036    end
4037   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
4038   if ~isequal(ext_fct,'.m')
4039        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
4040        return
4041   end
4042   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
4043   ind_coord=get(handles.transform_fct,'Value');
4044   addpath(PathName)
4045   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
4046   set(handles.transform_fct,'UserData',list_transform)
4047   rmpath(PathName)
4048   % save the new menu in the personal file 'uvmat_perso.mat'
4049   dir_perso=prefdir;%personal Matalb directory
4050   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
4051   if exist(profil_perso,'file')
4052       for ilist=nb_builtin+1:numel(list_transform)
4053           ff=functions(list_transform{ilist});
4054           transform_fct{ilist-nb_builtin}=ff.file;
4055       end
4056        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
4057   end   
4058end
4059
4060%check the current path to the selected function
4061if isa(list_transform{ind_coord},'function_handle')
4062    func=functions(list_transform{ind_coord});
4063    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
4064else
4065    set(handles.path_transform,'String','')
4066end
4067
4068set(handles.FixedLimits,'Value',0)
4069set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7])
4070
4071UvData=get(huvmat,'UserData');
4072
4073%delete drawn objects
4074hother=findobj('Tag','proj_object');%find all the proj objects
4075for iobj=1:length(hother)
4076    delete_object(hother(iobj))
4077end
4078hother=findobj('Tag','DeformPoint');%find all the proj objects
4079for iobj=1:length(hother)
4080    delete_object(hother(iobj))
4081end
4082hh=findobj('Tag','calib_points');
4083if ~isempty(hh)
4084    delete(hh)
4085end
4086hhh=findobj('Tag','calib_marker');
4087if ~isempty(hhh)
4088    delete(hhh)
4089end
4090if isfield(UvData,'Object')
4091     UvData.Object=UvData.Object(1);
4092end
4093list_object=get(handles.list_object_1,'String');
4094set(handles.list_object_1,'Value',1)
4095set(handles.list_object_1,'String',list_object(1))
4096set(handles.list_object_2,'Value',2)
4097set(handles.list_object_2,'String',[list_object(1);{'...'}])
4098list_object_2_Callback(hObject, eventdata, handles)
4099
4100%delete mask if it is displayed
4101if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
4102   UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
4103end
4104set(huvmat,'UserData',UvData)
4105run0_Callback(hObject, eventdata, handles)
4106
4107%--------------------------------------------
4108function histo1_menu_Callback(hObject, eventdata, handles)
4109%--------------------------------------------
4110%plot first histo
4111huvmat=get(handles.histo1_menu,'parent');
4112histo_menu=get(handles.histo1_menu,'String');
4113histo_value=get(handles.histo1_menu,'Value');
4114FieldName=histo_menu{histo_value};
4115% UvData=get(huvmat,'UserData');
4116update_histo(handles.histo_u,huvmat,FieldName)
4117
4118%----------------------------------------------
4119function histo2_menu_Callback(hObject, eventdata, handles)
4120%----------------------------------------------
4121%plot second histo
4122huvmat=get(handles.histo2_menu,'parent');
4123histo_menu=get(handles.histo2_menu,'String');
4124histo_value=get(handles.histo2_menu,'Value');
4125FieldName=histo_menu{histo_value};
4126% UvData=get(huvmat,'UserData');
4127update_histo(handles.histo_v,huvmat,FieldName)
4128
4129
4130%--------------------------------------------
4131%read the field .Fieldname stored in UvData and plot its histogram
4132function update_histo(haxes,huvmat,FieldName)
4133UvData=get(huvmat,'UserData');
4134if ~isfield(UvData.Field,FieldName)
4135    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
4136    return
4137end
4138Field=UvData.Field;
4139FieldHisto=eval(['Field.' FieldName]);
4140if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
4141    indsel=find(Field.FF==0);%find values marked as false
4142    if ~isempty(indsel)
4143        FieldHisto=FieldHisto(indsel);
4144    end
4145end
4146if isempty(Field)
4147    msgbox_uvmat('ERROR',['empty field ' FieldName])
4148else
4149    nxy=size(FieldHisto);
4150    Amin=double(min(min(min(FieldHisto))));%min of image
4151    Amax=double(max(max(max(FieldHisto))));%max of image
4152    if isequal(Amin,Amax)
4153       Histo.Txt=['uniform field =' num2str(Amin)];
4154    else
4155    Histo.ListVarName={FieldName,'histo'};
4156    if numel(nxy)==2
4157        Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
4158    else %color images
4159        Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
4160    end
4161    %unit
4162    units=[]; %default
4163    for ivar=1:numel(Field.ListVarName)   
4164        if strcmp(Field.ListVarName{ivar},FieldName)
4165            if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
4166                units=Field.VarAttribute{ivar}.units;
4167                break
4168            end
4169        end
4170    end
4171    if ~isempty(units)
4172        Histo.VarAttribute{1}.units=units;
4173    end
4174    eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
4175    for col=1:size(FieldHisto,3)
4176        B=FieldHisto(:,:,col);
4177        C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
4178       eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
4179    end
4180    set(haxes,'XLimMode','auto')%reset auto mode (after zoom effect)
4181    set(haxes,'YLimMode','auto')
4182    plot_field(Histo,haxes);
4183    end
4184end
4185
4186
4187
4188%------------------------------------------------
4189%CALLBACKS FOR PLOTTING PARAMETERS
4190%-------------------------------------------------
4191
4192%-----------------------------------------------------------------
4193function MinA_Callback(hObject, eventdata, handles)
4194%------------------------------------------
4195set(handles.AutoScal,'Value',1) %suppress auto mode
4196set(handles.AutoScal,'BackgroundColor',[1 1 0])
4197update_plot(handles);
4198
4199%-----------------------------------------------------------------
4200function MaxA_Callback(hObject, eventdata, handles)
4201%--------------------------------------------
4202set(handles.AutoScal,'Value',1) %suppress auto mode
4203set(handles.AutoScal,'BackgroundColor',[1 1 0])
4204update_plot(handles);
4205
4206%-----------------------------------------------
4207function AutoScal_Callback(hObject, eventdata, handles)
4208%--------------------------------------------
4209test=get(handles.AutoScal,'Value');
4210if test
4211    set(handles.AutoScal,'BackgroundColor',[1 1 0])
4212else
4213    set(handles.AutoScal,'BackgroundColor',[0.7 0.7 0.7])
4214    update_plot(handles);
4215end
4216
4217%-------------------------------------------------------------------
4218function BW_Callback(hObject, eventdata, handles)
4219%-------------------------------------------------------------------
4220update_plot(handles);
4221
4222%-------------------------------------------------------------------
4223function Contours_Callback(hObject, eventdata, handles)
4224%-------------------------------------------------------------------
4225val=get(handles.Contours,'Value');
4226if val==2
4227    set(handles.interval_txt,'Visible','on')
4228    set(handles.IncrA,'Visible','on')
4229else
4230    set(handles.interval_txt,'Visible','off')
4231    set(handles.IncrA,'Visible','off')
4232end
4233update_plot(handles);
4234
4235%-------------------------------------------------------------------
4236function IncrA_Callback(hObject, eventdata, handles)
4237%-------------------------------------------------------------------
4238update_plot(handles);
4239
4240%-------------------------------------------------------------------
4241function HideWarning_Callback(hObject, eventdata, handles)
4242%-------------------------------------------------------------------
4243update_plot(handles);
4244
4245%-------------------------------------------------------------------
4246function HideFalse_Callback(hObject, eventdata, handles)
4247%-------------------------------------------------------------------
4248update_plot(handles);
4249
4250%-------------------------------------------------------------------
4251function VecScale_Callback(hObject, eventdata, handles)
4252%-------------------------------------------------------------------
4253set(handles.AutoVec,'Value',1);
4254set(handles.AutoVec,'BackgroundColor',[1 1 0])
4255update_plot(handles);
4256
4257%-------------------------------------------------------------------
4258function AutoVec_Callback(hObject, eventdata, handles)
4259%-------------------------------------------------------------------
4260test=get(handles.AutoVec,'Value');
4261if test
4262    set(handles.AutoVec,'BackgroundColor',[1 1 0])
4263else
4264    update_plot(handles);
4265    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4266    set(handles.AutoVec,'BackgroundColor',[0.7 0.7 0.7])
4267end
4268
4269%------------------------------------------------------------------------
4270% --- Executes on selection change in decimate4 (nb_vec/4).
4271function decimate4_Callback(hObject, eventdata, handles)
4272%------------------------------------------------------------------------
4273update_plot(handles);
4274
4275%------------------------------------------------------------------------
4276% --- Executes on selection change in color_code menu
4277function color_code_Callback(hObject, eventdata, handles)
4278%------------------------------------------------------------------------
4279set_vec_col_bar(handles)
4280update_plot(handles);
4281
4282%------------------------------------------------------------------------
4283% --- Executes on button press in AutoVecColor.
4284function AutoVecColor_Callback(hObject, eventdata, handles)
4285%------------------------------------------------------------------------
4286test=get(handles.AutoVecColor,'Value');
4287if test
4288    set(handles.AutoVecColor,'BackgroundColor',[1 1 0])
4289else
4290    update_plot(handles);
4291    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4292    set(handles.AutoVecColor,'BackgroundColor',[0.7 0.7 0.7])
4293end
4294
4295%------------------------------------------------------------------------
4296% --- Executes on selection change in max_vec.
4297function min_vec_Callback(hObject, eventdata, handles)
4298%------------------------------------------------------------------------
4299max_vec_Callback(hObject, eventdata, handles)
4300
4301%------------------------------------------------------------------------
4302% --- Executes on selection change in max_vec.
4303function max_vec_Callback(hObject, eventdata, handles)
4304%------------------------------------------------------------------------
4305set(handles.AutoVecColor,'Value',1)
4306AutoVecColor_Callback(hObject, eventdata, handles)
4307min_val=str2num(get(handles.min_vec,'String'));
4308max_val=str2num(get(handles.max_vec,'String'));
4309slider1=get(handles.slider1,'Value');
4310slider2=get(handles.slider2,'Value');
4311colcode1=min_val+(max_val-min_val)*slider1;
4312colcode2=min_val+(max_val-min_val)*slider2;
4313set(handles.colcode1,'String',num2str(colcode1))
4314set(handles.colcode2,'String',num2str(colcode2))
4315update_plot(handles);
4316
4317%------------------------------------------------------------------------
4318% --- update the display of color code for vectors
4319function set_vec_col_bar(handles)
4320%------------------------------------------------------------------------
4321%get the image of the color display button 'vec_col_bar' in pixels
4322set(handles.vec_col_bar,'Unit','pixel');
4323pos_vert=get(handles.vec_col_bar,'Position');
4324set(handles.vec_col_bar,'Unit','Normalized');
4325width=ceil(pos_vert(3));
4326height=ceil(pos_vert(4));
4327
4328%get slider indications
4329list=get(handles.color_code,'String');
4330ichoice=get(handles.color_code,'Value');
4331colcode.ColorCode=list{ichoice};
4332colcode.MinC=str2num(get(handles.min_vec,'String'));
4333colcode.MaxC=str2num(get(handles.max_vec,'String'));
4334test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4335if test3color
4336    colcode.colcode1=str2num(get(handles.colcode1,'String'));
4337    colcode.colcode2=str2num(get(handles.colcode2,'String'));
4338end
4339% colcode.option=get(handles.vec_col_bar,'Value');
4340colcode.FixedCbounds=0;
4341% list_code=get(handles.col_vec,'String');% list menu fields
4342% index_code=get(handles.col_vec,'Value');% selected string index
4343% colcode.CName= list_code{index_code(1)}; % selected field used for vector color
4344colcode.FixedCbounds=1;
4345vec_C=colcode.MinC+(colcode.MaxC-colcode.MinC)*[0.5:width-0.5]/width;%sample of vec_C values from min to max
4346[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4347oneheight=ones(1,height);
4348A1=colorlist(col_vec,1)*oneheight;
4349A2=colorlist(col_vec,2)*oneheight;
4350A3=colorlist(col_vec,3)*oneheight;
4351A(:,:,1)=A1';
4352A(:,:,2)=A2';
4353A(:,:,3)=A3';
4354set(handles.vec_col_bar,'Cdata',A)
4355
4356
4357%-------------------------------------------------------------------
4358function update_plot(handles)
4359%-------------------------------------------------------------------
4360haxes= handles.axes3;
4361AxeData=get(haxes,'UserData');
4362PlotParam=read_plot_param(handles);
4363[PlotType,PlotParamOut]= plot_field(AxeData,haxes,PlotParam,1);
4364write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4365
4366%-------------------------------------------------------------------
4367% --- Executes on button press in grid.
4368function grid_Callback(hObject, eventdata, handles)
4369
4370
4371
4372%-------------------------------------------------------------------
4373% --- Executes on selection change in edit.
4374function edit_Callback(hObject, eventdata, handles)
4375%-------------------------------------------------------------------
4376UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4377test=get(handles.edit,'Value');
4378if test
4379    UvData.MouseAction='edit_object';
4380    set(handles.edit,'BackgroundColor',[1,1,0]) 
4381    %suppress the other options
4382    set(handles.zoom,'Value',0)
4383    zoom_Callback(hObject, eventdata, handles)
4384    set(handles.edit_vect,'Value',0)
4385    edit_vect_Callback(hObject, eventdata, handles) 
4386    %list_object_Callback(hObject, eventdata, handles)
4387else
4388    UvData.MouseAction='none';
4389    set(handles.edit,'BackgroundColor',[0.7,0.7,0.7])   
4390end
4391set(handles.uvmat,'UserData',UvData);
4392hset_object=findobj(allchild(0),'Tag','set_object');
4393if ~isempty(hset_object)
4394    hhset_object=guidata(hset_object);
4395    if test
4396        set(hhset_object.PLOT,'enable','on');
4397    else
4398       set(hhset_object.PLOT,'enable','off');
4399    end
4400end
4401
4402%------------------------------------------------------------------------
4403% --- Executes on selection change in list_object_1.
4404function list_object_1_Callback(hObject, eventdata, handles)
4405%------------------------------------------------------------------------
4406list_str=get(handles.list_object_1,'String');
4407IndexObj=get(handles.list_object_1,'Value');
4408str_1=list_str{IndexObj};
4409val_2=get(handles.list_object_2,'Value');
4410str_2=get(handles.list_object_2,'String');
4411if isequal(val_2,IndexObj)% if the first selection is equal to the second, it will suppress the second
4412    set(handles.list_object_2,'Value',numel(str_2))%select the end of the list ('...')
4413    list_object_2_Callback(hObject, eventdata, handles)
4414end
4415update_object(handles,IndexObj,1,str_1)
4416
4417%------------------------------------------------------------------------
4418% --- Executes on selection change in list_object_1.
4419function list_object_2_Callback(hObject, eventdata, handles)
4420%------------------------------------------------------------------------
4421list_str=get(handles.list_object_2,'String');
4422IndexObj=get(handles.list_object_2,'Value');
4423if isequal(list_str{IndexObj},'...')
4424    hview_field=findobj(allchild(0),'Tag','view_field');
4425    if ~isempty(hview_field)
4426        delete(hview_field)
4427    end
4428else
4429    update_object(handles,IndexObj,2,list_str{IndexObj})
4430end
4431
4432%------------------------------------------------------------------------
4433function update_object(handles,IndexObj,option,ObjectName)
4434%------------------------------------------------------------------------
4435UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4436if ~(length(UvData.Object)>=IndexObj);
4437    return
4438end
4439ObjectData=UvData.Object{IndexObj};
4440ObjectData.Name=ObjectName;
4441if isequal(get(handles.edit,'Value'),1)
4442    ObjectData.enable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
4443end
4444PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4445ZBounds=0; % default
4446    if isfield(UvData,'ZMin') && isfield(UvData,'ZMax')
4447        ZBounds(1)=UvData.ZMin; %minimum for the Z slider
4448        ZBounds(2)=UvData.ZMax;%maximum for the Z slider
4449    end
4450hset_object=findobj(allchild(0),'tag','set_object');
4451if ~isempty(hset_object)
4452    delete(hset_object)% delete existing version of set_object
4453end
4454hset_object=set_object(ObjectData,PlotHandles,ZBounds);% call the set_object interface,
4455%set(hset_object,'name',ObjectName)
4456
4457% %project the current field on the object and plot it
4458% ProjData= proj_field(UvData.Field,ObjectData,IndexObj);%project the current interface field on ObjectData
4459% if option==1%length(UvData.Object)>= IndexObj && isfield(UvData.Object{IndexObj},'plotaxes')&& ishandle(UvData.Object{IndexObj}.plotaxes)
4460%     plot_field(ProjData,handles.axes3,PlotHandles);
4461%     UvData.Object{IndexObj}.plotaxes=handles.axes3;
4462% else
4463%     UvData.Object{IndexObj}.plotaxes=view_field(ProjData);
4464% end
4465% set(handles.uvmat,'UserData',UvData)
4466hother=findobj('Tag','proj_object');%find all the proj objects
4467for iobj=1:length(hother)
4468    if isequal(get(hother(iobj),'Type'),'rectangle')|isequal(get(hother(iobj),'Type'),'patch')
4469        set(hother(iobj),'EdgeColor','b')
4470        if isequal(get(hother(iobj),'FaceColor'),'m')
4471            set(hother(iobj),'FaceColor','b')
4472        end
4473    elseif isequal(get(hother(iobj),'Type'),'image')
4474           Acolor=get(hother(iobj),'CData');
4475           Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4476           set(hother(iobj),'CData',Acolor);
4477    else
4478         set(hother(iobj),'Color','b')
4479    end
4480    set(hother(iobj),'Selected','off')
4481end
4482hother=findobj('Tag','DeformPoint');
4483set(hother,'Color','b');
4484set(hother,'Selected','off')   
4485if isfield(ObjectData,'HandlesDisplay')
4486    for iview=1:length(ObjectData.HandlesDisplay)
4487        if ishandle(ObjectData.HandlesDisplay(iview))
4488            uistack(ObjectData.HandlesDisplay(iview),'top')
4489            linetype=get(ObjectData.HandlesDisplay(iview),'Type');
4490            if isequal(linetype,'line')
4491                set(ObjectData.HandlesDisplay(iview),'Color','m'); %set the selected object to magenta color
4492            elseif isequal(linetype,'rectangle')
4493                set(ObjectData.HandlesDisplay(iview),'EdgeColor','m'); %set the selected object to magenta color
4494            elseif isequal(linetype,'patch')
4495                set(ObjectData.HandlesDisplay(iview),'FaceColor','m'); %set the selected object to magenta color
4496            end
4497            SubObjectData=get(ObjectData.HandlesDisplay(iview),'UserData');
4498            if isfield(SubObjectData,'SubObject')& ishandle(SubObjectData.SubObject)
4499                uistack(SubObjectData.SubObject,'top')
4500                for iobj=1:length(SubObjectData.SubObject)
4501                    hsub=SubObjectData.SubObject(iobj);
4502                    if isequal(get(hsub,'Type'),'rectangle')
4503                        set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4504                    elseif isequal(get(hsub,'Type'),'image')
4505                       Acolor=get(hsub,'CData');
4506                       Acolor(:,:,1)=Acolor(:,:,3);
4507                       set(hsub,'CData',Acolor);
4508                    else
4509                        set(hsub,'Color','m')
4510                    end
4511                end
4512            end
4513            if isfield(SubObjectData,'DeformPoint')& ishandle(SubObjectData.DeformPoint)
4514                set(SubObjectData.DeformPoint,'Color','m')
4515            end
4516        end
4517    end
4518end
4519pause(0.1)
4520figure(hset_object)%put set_object in front
4521
4522%------------------------------------------------------
4523% --- Executes on button press in Menu/Export/field in workspace.
4524%------------------------------------------------------
4525function MenuExportField_Callback(hObject, eventdata, handles)
4526global Data_uvmat
4527Data_uvmat=get(handles.uvmat,'UserData');
4528evalin('base','global Data_uvmat')%make CurData global in the workspace
4529display('current field :')
4530evalin('base','Data_uvmat') %display CurData in the workspace
4531commandwindow; %brings the Matlab command window to the front
4532
4533%------------------------------------------------------
4534% --- Executes on button press in Menu/Export/extract figure.
4535%------------------------------------------------------
4536function MenuExport_plot_Callback(hObject, eventdata, handles)
4537huvmat=get(handles.MenuExport_plot,'parent');
4538UvData=get(huvmat,'UserData');
4539hfig=figure;
4540newaxes=copyobj(handles.axes3,hfig);
4541map=colormap(handles.axes3);
4542colormap(map);%transmit the current colormap to the zoom fig
4543colorbar
4544
4545
4546% --------------------------------------------------------------------
4547function Insert_Callback(hObject, eventdata, handles)
4548
4549
4550% --------------------------------------------------------------------
4551function MenuHelp_Callback(hObject, eventdata, handles)
4552% --------------------------------------------------------------------
4553path_to_uvmat=which ('uvmat');% check the path of uvmat
4554pathelp=fileparts(path_to_uvmat);
4555helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4556if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4557else
4558    addpath (fullfile(pathelp,'uvmat_doc'))
4559    web(helpfile);
4560end
4561
4562
4563% --------------------------------------------------------------------
4564function MenuExportMovie_Callback(hObject, eventdata, handles)
4565% --------------------------------------------------------------------
4566set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4567huvmat=get(handles.run0,'parent');
4568UvData=get(huvmat,'UserData');
4569[xx,xx,FileBase]=read_file_boxes(handles);
4570 %read the current input file name
4571prompt = {'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)'};
4572dlg_title = 'select properties of the output avi movie';
4573num_lines= 1;
4574% nbfield_cell=get(handles.last_i,'String');
4575def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4576answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4577aviname=answer{1};
4578fps=str2double(answer{2});
4579% check for existing file with output name aviname
4580if exist(aviname,'file')
4581    backup=aviname;
4582    testexist=2;
4583    while testexist==2
4584        backup=[backup '~'];
4585        testexist=exist(backup,'file');     
4586    end
4587    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4588    if isequal(success,1)
4589        delete(aviname)%delete existing file
4590    else
4591        msgbox_uvmat('ERROR',message)
4592        return
4593    end
4594end
4595%create avi open
4596aviobj=avifile(aviname,'Compression','None','fps',fps);
4597
4598%display first view for tests
4599newfig=figure;
4600newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4601set(newaxes,'Tag','movieaxes')
4602nbpix=[512 384]*str2double(answer{3});
4603set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4604set(newaxes,'Position',eval(answer{4}));
4605map=colormap(handles.axes3);
4606colormap(map);%transmit the current colormap to the zoom fig
4607msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4608        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4609UvData.Object{1}.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4610set(huvmat,'UserData',UvData);
4611increment=str2double(get(handles.increment_scan,'String')); %get the field increment d
4612if isnan(increment)
4613    set(handles.increment_scan,'String','1')%default value
4614    increment=1;
4615end
4616set(handles.STOP,'Visible','on')
4617set(handles.speed,'Visible','on')
4618set(handles.speed_txt,'Visible','on')
4619set(handles.Movie,'BusyAction','queue')
4620
4621%imin=str2double(get(handles.i1,'String'));
4622imax=str2double(answer{5});
4623% if isfield(UvData,'Time')
4624htitle=get(newaxes,'Title');
4625xlim=get(newaxes,'XLim');
4626ylim=get(newaxes,'YLim');
4627set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4628time_str=get(handles.abs_time,'String');
4629set(htitle,'String',['t=' time_str])
4630set(handles.speed,'Value',1)
4631for i=1:imax
4632    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4633            runpm(hObject,eventdata,handles,increment)% run plus
4634            drawnow
4635            time_str=get(handles.abs_time,'String');
4636            if ishandle(htitle)
4637             set(htitle,'String',['t=' time_str])
4638            end
4639            mov=getframe(newfig);
4640            aviobj=addframe(aviobj,mov);
4641    end
4642end
4643close(aviobj);
4644UvData.Object{1}.plotaxes=handles.axes3;
4645set(huvmat,'UserData',UvData);
4646msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4647
4648
4649% ------------------------------------------------------------------
4650function MenuCalib_Callback(hObject, eventdata, handles)
4651
4652UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4653
4654%suppress competing options
4655set(handles.zoom,'Value',0)
4656set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
4657set(handles.MenuMask,'enable','off')
4658set(handles.MenuGrid,'enable','off')
4659set(handles.MenuObject,'enable','off')
4660set(handles.MenuEdit,'enable','off')
4661set(handles.list_object_1,'Value',1)     
4662% initiate display of GUI geometry_calib
4663data=[]; %default
4664if isfield(UvData,'CoordType')
4665    data.CoordType=UvData.CoordType;
4666end
4667pos=get(handles.uvmat,'Position');
4668pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4669pos(2)=pos(2)-0.02;
4670[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
4671[UvData.hset_object,UvData.sethandles]=geometry_calib(FileName,pos);% call the geometry_calib interface
4672pos_uvmat=get(handles.uvmat,'Position');
4673
4674if isfield(UvData,'CalOrigin')
4675    pos_cal(1)=pos_uvmat(1)+UvData.CalOrigin(1)*pos_uvmat(3);
4676    pos_cal(2)=pos_uvmat(2)+UvData.CalOrigin(2)*pos_uvmat(4);
4677    pos_cal(3:4)=UvData.CalSize .* pos_uvmat(3:4);
4678    set(UvData.hset_object,'Position',pos_cal)
4679end
4680UvData.MouseAction='calib';
4681set(handles.uvmat,'UserData',UvData);
4682
4683
4684% ------------------------------------------------------------------
4685function MenuMask_Callback(hObject, eventdata, handles)
4686% set(handles.TOOLS_txt,'Visible','on')
4687% set(handles.frame_tools,'Visible','on')
4688% % set(handles.create,'Visible','on')
4689% % set(handles.create,'Value',1)
4690% % set(handles.create,'BackgroundColor',[1 1 0]) %visualise in yellow
4691% set(handles.save_mask,'Visible','on')
4692% set(handles.masklevel,'Visible','on')
4693% if isequal(get(handles.z_index,'Visible'),'on')
4694%     nb_slice=str2num(get(handles.nb_slice,'String'));
4695%     for ilist=1:nb_slice
4696%         list_index{ilist,1}=num2str(ilist);
4697%     end   
4698%     set(handles.masklevel,'String',list_index)
4699%     val=str2num(get(handles.z_index,'String'));
4700%     if val<=nb_slice
4701%         set(handles.masklevel,'Value',val)
4702%     end
4703% else
4704%     set(handles.masklevel,'String',{'1'})
4705%     set(handles.masklevel,'Value',1)
4706% end
4707% if ishandle(handles.UVMAT_title)
4708%     delete(handles.UVMAT_title)
4709% end
4710UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4711% set(handles.zoom,'Value',0)
4712% set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
4713% set(handles.edit_vect,'Value',0)
4714% edit_vect_Callback(hObject, eventdata, handles)
4715% set(handles.edit,'Value',0)
4716% set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
4717% set(handles.edit_vect,'Value',0) 
4718% edit_vect_Callback(hObject, eventdata, handles)
4719% set(handles.cal,'Value',0)
4720% set(handles.cal,'BackgroundColor',[0 1 0])
4721
4722%initiate the GUI set_object
4723% data.TITLE='MASK';
4724% if isfield(UvData,'CoordType')
4725%     data.CoordType=UvData.CoordType;
4726% end
4727% if isfield(UvData,'Mesh')&&~isempty(UvData.Mesh)
4728%     data.YMax=UvData.Mesh;
4729% elseif isfield(UvData.Field,'AX')&&isfield(UvData.Field,'AY')&& isfield(UvData.Field,'A')%only image
4730%     np=size(UvData.Field.A);
4731%     meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1);
4732%     meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1);
4733%     data.YMax=max(meshx,meshy);
4734%     data.DX=max(meshx,meshy);
4735% end
4736% data.Coord=[0 0 0]; %default
4737% PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters
4738% [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface
4739% pos_uvmat=get(handles.uvmat,'Position');
4740% if isfield(UvData,'SetObjectOrigin')
4741%     pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
4742%     pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
4743%     set(hset_object,'Position',pos_set_object)
4744% end
4745ListObj=UvData.Object;
4746select=zeros(1,numel(ListObj));
4747for iobj=1:numel(ListObj);
4748    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4749        select(iobj)=1;
4750    end
4751end
4752val=find(select);
4753if isempty(val)
4754    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4755    return
4756else
4757    set(handles.list_object_1,'Max',2);%allow multiple selection
4758    set(handles.list_object_1,'Value',val);
4759%     answer=msgbox_uvmat('INPUT_Y-N',['make the mask image from ' num2str(numel(val)) ' polygons']);
4760%     if ~isempty(answer)
4761        flag=1;
4762        npx=size(UvData.Field.A,2);
4763        npy=size(UvData.Field.A,1);
4764        xi=0.5:npx-0.5;
4765        yi=0.5:npy-0.5;
4766        [Xi,Yi]=meshgrid(xi,yi);
4767        if isfield(UvData,'Object')
4768            for iobj=1:length(UvData.Object)
4769                ObjectData=UvData.Object{iobj};
4770                if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4771                    flagobj=1;
4772                    testphys=0; %coordinates in pixels by default
4773                    if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
4774                        if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
4775                            Calib=UvData.XmlData.GeometryCalib;
4776                            testphys=1;
4777                        end
4778                    end
4779                    if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
4780                        if isequal(ObjectData.Style,'polygon')
4781                            X=ObjectData.Coord(:,1);
4782                            Y=ObjectData.Coord(:,2);
4783                            if testphys
4784                                [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4785                            end
4786                            flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4787                        elseif isequal(ObjectData.Style,'ellipse')
4788                            if testphys
4789                                %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4790                            end
4791                            RangeX=max(ObjectData.RangeX);
4792                            RangeY=max(ObjectData.RangeY);
4793                            X2Max=RangeX*RangeX;
4794                            Y2Max=RangeY*RangeY;
4795                            distX=(Xi-ObjectData.Coord(1,1));
4796                            distY=(Yi-ObjectData.Coord(1,2));
4797                            flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4798                        elseif isequal(ObjectData.Style,'rectangle')
4799                            if testphys
4800                                %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4801                            end
4802                            distX=abs(Xi-ObjectData.Coord(1,1));
4803                            distY=abs(Yi-ObjectData.Coord(1,2));
4804                            flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4805                        end
4806                        if isequal(ObjectData.ProjMode,'mask_outside')
4807                            flagobj=~flagobj;
4808                        end
4809                        flag=flag & flagobj;
4810                    end
4811                end
4812            end
4813        end
4814        % flag=~flag;
4815        %mask name
4816        RootPath=get(handles.RootPath,'String');
4817        RootFile=get(handles.RootFile,'String');
4818        if ~isempty(RootFile)&(isequal(RootFile(1),'/')| isequal(RootFile(1),'\'))
4819            RootFile(1)=[];
4820        end
4821        filebase=fullfile(RootPath,RootFile);
4822        list=get(handles.masklevel,'String');
4823        masknumber=num2str(length(list));
4824        maskindex=get(handles.masklevel,'Value');
4825        mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4826        imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4827        imflag=flipdim(imflag,1);
4828        % imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when
4829        % 20<imflag<200)
4830
4831        %display the mask
4832        %update_mask(handles,num_i1,num_j1)
4833        figure;
4834        vec=linspace(0,1,256);%define a linear greyscale colormap
4835        map=[vec' vec' vec'];
4836        colormap(map)
4837        image(imflag);
4838        answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4839        if ~strcmp(answer,'Cancel')
4840            mask_dir=fileparts(answer);
4841            if ~exist(mask_dir,'dir')
4842                msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4843                return
4844            end
4845            imwrite(imflag,answer,'BitDepth',8);
4846        end
4847        set(handles.list_object_1,'Value',1)
4848        set(handles.list_object_1,'Max',1)
4849%     end
4850end       
4851     
4852
4853% UvData.MouseAction='create_object';
4854set(handles.uvmat,'UserData',UvData);
4855
4856% ------------------------------------------------------------------
4857%-- open the GUI set_grid.fig to create grid
4858function MenuGrid_Callback(hObject, eventdata, handles)
4859%UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4860
4861%suppress the other options if grid is chosen
4862set(handles.edit_vect,'Value',0)
4863edit_vect_Callback(hObject, eventdata, handles)
4864set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
4865set(handles.list_object_1,'Value',1)     
4866
4867%prepare display of the set_grid GUI
4868FileName=read_file_boxes(handles);
4869CoordList=get(handles.transform_fct,'String');
4870val=get(handles.transform_fct,'Value');
4871set_grid(FileName,CoordList{val});% call the set_object interface
4872%set(handles.uvmat,'UserData',UvData);
4873
4874%----------------------------------------------------------------
4875% open the GUI 'series'
4876%----------------------------------------------------------------
4877function MenuSeries_Callback(hObject, eventdata, handles)
4878%-------------------------------------------------------------------
4879
4880[param.FileName]=read_file_boxes(handles);
4881if isequal(get(handles.SubField,'Value'),1)
4882    FileName_1=read_file_boxes_1(handles);%
4883    if ~isequal(FileName_1,param.FileName)
4884        param.FileName_1=FileName_1;
4885    end
4886end
4887param.NomType=get(handles.FileIndex,'UserData');
4888param.NomType_1=get(handles.FileIndex_1,'UserData');
4889param.comp_input=get(handles.fix_pair,'Value');
4890huvmat=get(handles.MenuSeries,'parent');
4891UvData=get(huvmat,'UserData');
4892if isfield(UvData,'Time')
4893    param.Time=UvData.XmlData.Time;
4894end
4895if isequal(get(handles.scan_i,'Value'),1)
4896    param.incr_i=str2double(get(handles.increment_scan,'String'));
4897elseif isequal(get(handles.scan_j,'Value'),1)
4898    param.incr_j=str2double(get(handles.increment_scan,'String'));
4899end
4900param.list_fields=get(handles.Fields,'String');% list menu fields
4901param.list_fields(1)=[]; %suppress  'image' option
4902param.index_fields=get(handles.Fields,'Value');% selected string index
4903if param.index_fields>1
4904    param.index_fields=param.index_fields-1;
4905end
4906param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4907param.list_fields_1(1)=[]; %suppress  'image' option
4908param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4909if param.index_fields_1>1
4910    param.index_fields_1=param.index_fields_1-1;
4911end
4912param.civ1=get(handles.civ1,'Value');
4913param.civ2=get(handles.civ2,'Value');
4914param.interp1=get(handles.interp1,'Value');
4915param.interp2=get(handles.interp2,'Value');
4916param.filter1=get(handles.filter1,'Value');
4917param.filter2=get(handles.filter2,'Value');
4918param.menu_coord_str=get(handles.transform_fct,'String');
4919param.menu_coord_val=get(handles.transform_fct,'Value');
4920
4921series(param); %run the series interface
4922
4923% ------------------------------------------------------------------
4924% -- open the GUI civ.fig for civx (PIV)
4925% ------------------------------------------------------------------
4926function MenuPIV_Callback(hObject, eventdata, handles)
4927 
4928[FileName,RootPath,filebase,FileIndices,ext,SubDir]=read_file_boxes(handles);
4929num1=stra2num(get(handles.i1,'String'));
4930num2=stra2num(get(handles.i2,'String'));
4931num_a=stra2num(get(handles.j1,'String'));
4932num_b=stra2num(get(handles.j2,'String'));
4933NomType=get(handles.FileIndex,'UserData');
4934ind_opening=1; % default (images): will advice civ1 option by default in the civ interface
4935if isequal(ext,'.nc') ||  isequal(ext,'.cdf')% netcdf files
4936    ind_opening=2;% propose 'fix' as the default option
4937% +read the current netcdf rootfile
4938    Data=nc2struct(FileName,[]);
4939    if isfield(Data,'fix') & isequal(Data.fix,1)
4940        ind_opening=3;
4941    end
4942    if isfield(Data,'patch') & isequal(Data.patch,1)
4943        ind_opening=4;
4944    end
4945    if isfield(Data,'civ2') & isequal(Data.civ2,1)
4946        ind_opening=5;
4947    end
4948    if isfield(Data,'fix2') & isequal(Data.fix2,1)
4949        ind_opening=6;
4950    end
4951end     
4952param.RootName=filebase;
4953param.NomType=NomType;
4954param.num1=num1;
4955param.num2=num2;
4956param.num_a=num_a;
4957param.num_b=num_b;
4958param.SubDir=SubDir;
4959param.IndOpening=ind_opening;% A REVOIR +TRANSMETTRE IMADOC INFO
4960param.ImaExt=ext;
4961civ(param);% interface de civ(not in the uvmat file)
4962
4963% ------------------------------------------------------------------
4964function MenuTools_Callback(hObject, eventdata, handles)
4965
4966% ------------------------------------------------------------------
4967function MenuEditObject_Callback(hObject, eventdata, handles)
4968set(handles.edit,'Value',1)
4969edit_Callback(hObject, eventdata, handles)
4970
4971%--------------------------------------------------------------------------
4972function enable_transform(handles,state)
4973set(handles.transform_fct,'Visible',state)
4974set(handles.TRANSFORM_txt,'Visible',state)   
4975set(handles.transform_fct,'Visible',state) 
4976set(handles.path_transform,'Visible',state)
4977set(handles.pxcmx_txt,'Visible',state)
4978set(handles.pxcmy_txt,'Visible',state)
4979set(handles.pxcm,'Visible',state)
4980set(handles.pycm,'Visible',state)
4981
4982%------------------------------------------------------------------------
4983function MenuEditVectors_Callback(hObject, eventdata, handles)
4984%------------------------------------------------------------------------
4985set(handles.edit_vect,'Visible','on')
4986set(handles.edit_vect,'Value',1)
4987edit_vect_Callback(hObject, eventdata, handles)
4988
4989% --------------------------------------------------------------------
4990function Menupoints_Callback(hObject, eventdata, handles)
4991data.Style='points';
4992data.ProjMode='projection';%default
4993create_object(data,handles)
4994
4995% --------------------------------------------------------------------
4996function Menuline_Callback(hObject, eventdata, handles)
4997% set(handles.create,'Visible','on')
4998% set(handles.create,'Value',1)
4999% LINE_Callback(hObject,eventdata,handles)
5000data.Style='line';
5001data.ProjMode='projection';%default
5002create_object(data,handles)
5003
5004%------------------------------------------------------------------------
5005function Menupolyline_Callback(hObject, eventdata, handles)
5006%------------------------------------------------------------------------
5007data.Style='polyline';
5008data.ProjMode='projection';%default
5009create_object(data,handles)
5010
5011%------------------------------------------------------------------------
5012function Menupolygon_Callback(hObject, eventdata, handles)
5013%------------------------------------------------------------------------
5014data.Style='polygon';
5015data.ProjMode='inside';%default
5016create_object(data,handles)
5017
5018%------------------------------------------------------------------------
5019function Menurectangle_Callback(hObject, eventdata, handles)
5020%------------------------------------------------------------------------
5021data.Style='rectangle';
5022data.ProjMode='inside';%default
5023create_object(data,handles)
5024
5025%------------------------------------------------------------------------
5026function Menuellipse_Callback(hObject, eventdata, handles)
5027%------------------------------------------------------------------------
5028data.Style='ellipse';
5029data.ProjMode='inside';%default
5030create_object(data,handles)
5031
5032%------------------------------------------------------------------------
5033function MenuMaskObject_Callback(hObject, eventdata, handles)
5034%------------------------------------------------------------------------
5035data.Style='polygon';
5036data.StyleMenu={'polygon'};
5037data.ProjMode='mask_inside';%default
5038data.ProjMenu={'mask_inside';'mask_outside'};
5039create_object(data,handles)
5040
5041% ------------------------------------------------------------------
5042function Menuplane_Callback(hObject, eventdata, handles)
5043data.Style='plane';
5044data.ProjMode='projection';%default
5045
5046create_object(data,handles)
5047
5048% ------------------------------------------------------------------
5049function Menuvolume_Callback(hObject, eventdata, handles)
5050data.Style='volume';
5051data.ProjMode='interp';%default
5052% set(handles.create,'Visible','on')
5053% set(handles.create,'Value',1)
5054% VOLUME_Callback(hObject,eventdata,handles)
5055create_object(data,handles)
5056
5057%------------------------------------------------------------------------
5058function MenuBrowseObject_Callback(hObject, eventdata, handles)
5059%------------------------------------------------------------------------
5060%get the object file
5061[FileName, PathName, filterindex] = uigetfile( ...
5062       {'*.xml;*.mat', ' (*.xml,*.mat)';
5063       '*.xml',  '.xml files '; ...
5064        '*.mat',  '.mat matlab files '}, ...
5065        'Pick an xml Object file',get(handles.RootPath,'String'));
5066fileinput=[PathName FileName];%complete file name
5067testblank=findstr(fileinput,' ');%look for blanks
5068if ~isempty(testblank)
5069    msgbox_uvmat('ERROR','forbidden input file name: contain blanks')
5070    return
5071end
5072sizf=size(fileinput);
5073if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
5074
5075%read the file
5076t=xmltree(fileinput);
5077data=convert(t);
5078data.enable_plot=1;
5079[pp,data.Name]=fileparts(FileName);
5080%PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
5081hset_object=findobj(allchild(0),'tag','set_object');
5082if ~isempty(hset_object)
5083    delete(hset_object)% delete existing version of set_object
5084end
5085UvData=get(handles.uvmat,'UserData');
5086[hset_object,UvData.sethandles]=set_object(data);% call the set_object interface
5087% %position the set_object GUI with respect to uvmat
5088% pos_uvmat=get(handles.uvmat,'Position');
5089% if isfield(UvData,'SetObjectOrigin')
5090%     pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
5091%     pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
5092%     set(hset_object,'Position',pos_set_object)
5093% end
5094set(handles.edit,'Value',0); %suppress the object edit mode
5095set(handles.edit,'BackgroundColor',[0.7,0.7,0.7]) 
5096UvData.MouseAction='create_object';
5097set(handles.uvmat,'UserData',UvData)
5098set(handles.delete_object,'Visible','on')
5099set(handles.uvmat_title,'Visible','on')
5100set(handles.view_field_title,'Visible','on')
5101
5102%------------------------------------------------------------------------
5103% --- generic function used for the creation of a projection object
5104function create_object(data,handles)
5105%------------------------------------------------------------------------
5106hset_object=findobj(allchild(0),'tag','set_object');
5107if ~isempty(hset_object)
5108    delete(hset_object)% delete existing version of set_object
5109end
5110UvData=get(handles.uvmat,'UserData');
5111set(handles.edit,'Value',0); %suppress the object edit mode
5112set(handles.edit,'BackgroundColor',[0.7,0.7,0.7]) 
5113data.enable_plot=1;
5114transform_list=get(handles.transform_fct,'String');
5115val=get(handles.transform_fct,'Value');
5116data.CoordType=transform_list{val};
5117% if isfield(UvData,'CoordType')
5118%     data.CoordType=UvData.CoordType;
5119% end
5120if isfield(UvData,'Mesh')&&~isempty(UvData.Mesh)
5121    data.RangeX=UvData.Mesh;
5122    data.RangeY=UvData.Mesh;
5123    data.DX=UvData.Mesh;
5124    data.DY=UvData.Mesh;
5125elseif isfield(UvData.Field,'AX')&& isfield(UvData.Field,'AY')&& isfield(UvData.Field,'A')%only image
5126    np=size(UvData.Field.A);
5127    meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
5128    meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
5129    data.RangeY=max(meshx,meshy);
5130    data.RangeX=max(meshx,meshy);
5131    data.DX=max(meshx,meshy);
5132end
5133if isfield(UvData,'NbDim')
5134    data.NbDim=UvData.NbDim;
5135end
5136data.Coord=[0 0 0]; %default
5137if isfield(data,'Style') && isequal(data.Style,'line')
5138    if isfield(data,'DX')
5139        data.Coord=[[0 0 0];[data.DX 0 0]]; %default
5140    else
5141        data.Coord=[[0 0 0];[1 0 0]]; %default
5142    end
5143end
5144%data.ParentButton=handles.create;
5145if ishandle(handles.UVMAT_title)
5146    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
5147end
5148PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
5149[hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface
5150
5151UvData.MouseAction='create_object';
5152set(handles.uvmat,'UserData',UvData)
5153set(handles.zoom,'Value',0)
5154zoom_Callback(handles.uvmat, [], handles)
5155set(handles.delete_object,'Visible','on')
5156set(handles.uvmat_title,'Visible','on')
5157set(handles.view_field_title,'Visible','on')
5158
5159%------------------------------------------------------------------------
5160function MenuRuler_Callback(hObject, eventdata, handles)
5161%------------------------------------------------------------------------
5162set(handles.zoom,'Value',0)
5163zoom_Callback(handles.uvmat, [], handles)
5164UvData=get(handles.uvmat,'UserData');
5165UvData.MouseAction='ruler';
5166set(handles.uvmat,'UserData',UvData);
5167
5168%------------------------------------------------------------------------
5169% --- executed when closing: set the parent interface button to value 0
5170function closefcn(gcbo,eventdata)
5171%------------------------------------------------------------------------
5172%delete all the associated figures if exist
5173hh=findobj(allchild(0),'tag','view_field');
5174if ~isempty(hh)
5175    delete(hh)
5176end
5177hh=findobj(allchild(0),'tag','geometry_calib');
5178if ~isempty(hh)
5179    delete(hh)
5180end
5181hh=findobj(allchild(0),'tag','set_object');
5182if ~isempty(hh)
5183    hhh=findobj(hh,'tag','PLOT');
5184    set(hhh,'enable','off')
5185end
5186
5187
5188% --- Executes on button press in delete_object.
5189function delete_object_Callback(hObject, eventdata, handles)
5190IndexObj=get(handles.list_object_2,'Value');
5191    if IndexObj>1
5192        delete_object(IndexObj)
5193    end
5194   
5195
5196
5197
5198
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