source: trunk/src/uvmat.m @ 34

Last change on this file since 34 was 34, checked in by sommeria, 11 years ago

get_field: list of actions put as functions in subdir get_field (like done for series), store and retrieve the latest opened files.
series: bug repair for action functions
read_get_field: bug repair for the case of vectors with unstructured coordinates

File size: 200.0 KB
Line 
1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%
8%INPUT:
9% input: input file name (if character chain), or input image matrix to
10% visualize, or Matlab structure representing  netcdf fields (with fields
11% ListVarName....)
12%
13%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14%  Copyright Joel Sommeria, Louis Gostiaux, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
15%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16%     This open is part of the toolbox UVMAT.
17%
18%     UVMAT is free software; you can redistribute it and/or modify
19%     it under the terms of the GNU General Public License as published by
20%     the Free Software Foundation; either version 2 of the License, or
21%     (at your option) any later version.
22%
23%     UVMAT is distributed in the hope that it will be useful,
24%     but WITHOUT ANY WARRANTY; without even the implied warranty of
25%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
26%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
27%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28%
29% Information stored on the interface:
30%    'Strings' of all edit boxes and menus: get(handles.Tag,'String')
31%    'Values' of all menus and toggle buttons: get(handles.Tag,'Value')
32%     Matlab structure stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
33%          It contains the following fields:
34%     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn)
35%          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
36%     - Information read in the documentation open of a series (activated by RootPath_Callback) :
37%          .XmlData, with fields:
38%               .Time: matrix of times of the images with index i and j
39%               .GeometryCalib: [1x1 struct]
40%     - Information defined from the interface:
41%           .NewSeries: =1 when the first view of a new field series is displayed, else 0
42%           .filename:(char string)
43%           .VelType:(char string) type of velocity field selected
44%           .VelType_1:(char string)  REMPLACER LE CELL ACTUEL
45%           .FieldName: (char string) main field selected('image', 'velocity'...)
46%           .FieldName_1:(char string) second field selected('image', 'velocity'...)
47%           .CName: (char string)name of the scalar used for vector colors
48%           .CoordType: (char string) coordinate transform: e.g. 'phys' or 'px'
49%           .MouseAction: store the current effect of mouse button (create or edit objects)
50%     - Information on  projection objects
51%           .Object: {[1x1 struct]}
52%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
53%     -Information on the current field (Field{i})
54%            .Txt : text information to display (e.g. error message)
55%            .NbDim: number of dimensions (=0 by default)
56%            .NbCoord: number of vector components
57%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
58%            .dt: time interval for the corresponding image pair
59%            .Mesh: estimated typical distance between vectors
60%            .ZMax:
61%            .ZMin:
62%            .X, .Y, .Z: set of vector coordinates
63%            .U,.V,.W: corresponding set of vector components
64%            .F: corresponding set of warning flags
65%            .FF: corresponding set of false flags, =0 for good vectors
66%            .C: corresponding values of the scalar used for vector color
67%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
68%                     equal to the number of vectors stored in the input open)
69%            .CName: name of the scalar .C
70%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
71%            .A image or scalar
72%            .AX: vector of dimension 2 representing the first and last values
73%              of the X coordinates for the image or scalar known on a regular grid,
74%              or vector of dimension .A for a scaler defined on irregular grid.
75%            .AY: same as .AX along the Y direction
76%            .AName: name of the scalar, ='image' for an image
77
78% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
79%
80%               Main input open   second input open(_1)        second image (pair animation)
81% read_ncfield.m         |                 |                             
82% read_image.m           |                 |                                               
83%                     Field{1}         Field{2}               
84%                                                                         |
85% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
86%                                                                   Field{i}
87%                                                                    |
88% calc_field.m: calculate scalar or other derived fields (vort, div..).
89%
90% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
91%              Field{i=1->3}.X --> UvData.X                          |
92%                                                                    |
93%                                                                 UvData
94%                                                                    |
95% plot histograms of the whole  field
96% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
97%                                                                    |                                                                          |
98%                                                                ObjectData
99%                                                                    |
100% plot_field.m: plot the projected fields and store them as user     |
101% data of the plotting axes                                          |
102%                                                                    |
103%                                                                AxeData
104%
105%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
106% scalars are displayed either as an image or countour plot, either as a color of
107% velocity vectors. The scalar values in the first case is represented by
108% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
109% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
110% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
111% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
112% coordinates of the four image corners. The scalar name is represented by
113% the strings .AName and/or .CName.
114% If the scalar exists in an input open (image or scalar stored under its
115% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
116% Else only its name AName is recorded in Field{i}, and its field is then calculated
117%by the fuction calc_scal after the coordinate transform or after projection on an edit
118     
119% Properties attached to plotting figures (standard Matlab properties):
120%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
121%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
122%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
123%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
124%    'KeyPressFcn': function called by pressing a key on the key board
125%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
126%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
127
128% Properties attached to plotting axes:
129%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
130%     AxeData:=get(gca,'UserData');
131%     AxeData.Drawing  = create: create a new edit
132%                       = deform: modify an existing edit by moving its defining create
133%                      = off: no current drawing action
134%                     = translate: translate an existing edit
135%                    = zoom: isolate a subregion for zoom in=1 if an edit is being currently drawn, 0 else (set to 0 by releasing mouse button)
136%            .hset_edit=handle of the set_edit interface (if a projection edit is edited);
137%            .CurrentOrigin: Origin of a curently drawn edit
138%            .CurrentLine: currently drawn menuline (A REVOIR)
139%            .CurrentObject: handle of the currently drawn edit
140%            .CurrentRectZoom: current rectangle used for zoom
141%            .zoomon : zoom state (a revoir)
142%            .X, .Y, .Z: array of coordinates defining the position of the vector: ASSOCIER AU PLAN (OBJET) PLUTOT QU'A L'AXE ?
143%            .U, .V, .W: array of components of the vector
144%            .C:
145%            .F:
146%            .FF:
147%            .A
148
149% Properties attached to projection objects (create, menuline, menuplane...):
150%    'Tag'='proj_edit': for all projection objects
151%    ObjectData.Style=...: style of projection edit:
152%              .ProjMode
153%              .Coord: defines the position of the edit
154%              .XMin,YMin....
155%              .XMax,YMax....
156%              .DX,DY,DZ
157%              .Phi, .Theta, .Psi : Euler angles
158%              .X,.Y,.U,.V.... : field data projected on the edit
159%              .IndexObj: index in the list of UvData.Object
160           %during plotting
161%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
162%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
163% To each projection object #iobj, corresponds an axis
164% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
165% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
166%-------------------------------------------------------------------
167%-------------------------------------------------------------------
168%  I - MAIN FUNCTION UVMAT (DO NOT MODIFY)
169%-------------------------------------------------------------------
170%-------------------------------------------------------------------
171function varargout = uvmat(varargin)
172
173% Begin initialization code - DO NOT EDIT
174gui_Singleton = 1;
175gui_State = struct('gui_Name',          mfilename, ...
176                   'gui_Singleton',     gui_Singleton, ...
177                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
178                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
179                   'gui_LayoutFcn',     [], ...
180                   'gui_Callback',      []);
181if nargin && ischar(varargin{1})
182    gui_State.gui_Callback = str2func(varargin{1});
183end
184
185if nargout
186    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
187else
188    gui_mainfcn(gui_State, varargin{:});
189end
190% End initialization code - DO NOT EDIT
191
192%-------------------------------------------------------------------
193% --- Executes just before uvmat is made visible.
194function uvmat_OpeningFcn(hObject, eventdata, handles, input )
195%-------------------------------------------------------------------
196%WARNING: avoid the second input parameter, leads to erros
197global dircur dir_opening
198% Choose default command menuline output for uvmat
199handles.output = hObject;
200
201% %group handles for input file in a structure handles.InputFile
202% handlesInputFile={handles.RootPath,handles.SubDir,handles.RootFile,handles.FileIndex,handles.FileExt};
203% TagsInputFile={'RootPath','SubDir','RootFile','FileIndex','FileExt'};
204% handles.InputFile=cell2struct(handlesInputFile,TagsInputFile,2);
205%
206% %group handles for the second input file in a structure handles.InputFile_1
207% handlesInputFile={handles.RootPath_1,handles.SubDir_1,handles.RootFile_1,handles.FileIndex_1,handles.FileExt_1};
208% TagsInputFile={'RootPath','SubDir','RootFile','FileIndex','FileExt'};
209% handles.InputFile_1=cell2struct(handlesInputFile,TagsInputFile,2);
210
211% Update handles structure
212guidata(hObject, handles);
213
214dircur=pwd; %current working directory
215dir_opening=dircur;
216
217% set the position of colorbar and ancillary GUIs:
218set(hObject,'Units','Normalized')
219movegui(hObject,'center')
220UvData.PosColorbar=[0.805 0.022 0.019 0.445];
221UvData.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
222UvData.SetObjectSize=[0.3 0.7];
223UvData.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
224UvData.CalSize=[0.28 1];
225
226%functions for the mouse and keyboard
227set(handles.histo_u,'NextPlot','replacechildren');
228set(handles.histo_v,'NextPlot','replacechildren');
229set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
230set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
231set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
232set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
233%set(hObject,'ResizeFcn',{@resize_uvmat})
234
235%load the list of previously browsed files in menus Open and Open_1
236 dir_perso=prefdir;
237 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
238 if exist(profil_perso,'file')
239      h=load (profil_perso);
240      if isfield(h,'MenuFile_1')
241          set(handles.MenuFile_1,'Label',h.MenuFile_1);
242          set(handles.MenuFile_1_1,'Label',h.MenuFile_1);
243      end
244      if isfield(h,'MenuFile_1')
245          set(handles.MenuFile_2,'Label',h.MenuFile_2);
246          set(handles.MenuFile_2_1,'Label',h.MenuFile_2);
247      end
248      if isfield(h,'MenuFile_1')
249          set(handles.MenuFile_3,'Label',h.MenuFile_3);
250          set(handles.MenuFile_3_1,'Label',h.MenuFile_3);
251      end
252      if isfield(h,'MenuFile_1')
253          set(handles.MenuFile_4,'Label',h.MenuFile_4);
254          set(handles.MenuFile_4_1,'Label',h.MenuFile_4);
255      end
256      if isfield(h,'MenuFile_1')
257          set(handles.MenuFile_5,'Label',h.MenuFile_5);
258          set(handles.MenuFile_5_1,'Label',h.MenuFile_5);
259     end
260 end
261 
262%initiates menu of vector colors
263list_menu=calc_field;
264%list_menu=[{'ima_cor'};{'black'};{'white'};list_menu(3:end)];
265set(handles.col_vec,'String',list_menu)
266
267%check the path and date of modification of all functions in uvmat
268path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
269[errormsg,date_str]=check_functions;%check the path of the functions called by uvmat.m
270
271%check the path of menu_coord transform
272%set(handles.menu_coord,'String',{'';'phys';'px';'more...'})
273path_fct{1}='';
274path_fct{2}=fileparts(path_to_uvmat);
275path_fct{3}=fileparts(path_to_uvmat);
276path_fct{4}=fileparts(path_to_uvmat);
277set(handles.menu_coord,'UserData',path_fct)
278
279%case of an input argument for uvmat
280testinputfield=0;
281inputfile=[];
282Field=[];
283if exist('input','var')
284    if ~isempty(errormsg)
285        warndlg_uvmat(errormsg,'WARNING')
286    end
287    if ishandle(handles.UVMAT_title)
288        delete(handles.UVMAT_title)
289    end   
290    if isstruct(input)
291        if isfield(input,'InputFile')
292            inputfile=input.InputFile;
293        end
294        Field=input;
295    elseif ischar(input)% file name introduced as input
296           inputfile=input;
297    elseif isnumeric(input)
298        sizinput=size(input);
299        if sizinput(1)<=1 || sizinput(2)<=1
300            warndlg_uvmat('bad input for uvmat: file name, structure or numerical matrix accepted','ERROR')
301            return
302        end
303        Field.A=input;
304        Field.AX=[0.5 size(input,2)-0.5];
305        Field.AY=[size(input,1)-0.5 0.5];
306    end
307    if ~isempty(inputfile)
308        display_file_name(hObject, eventdata, handles,inputfile)
309        testinputfield=1;
310    else
311        UvData.TestInputFile=0;
312    end
313    if ~isempty(Field)
314        set(handles.Fields,'Value',1)
315        set(handles.Fields,'String',{'get_field...'})
316%         set(handles.Fields,'Value',2)% option 'get_field...'     
317        set(handles.Fields,'UserData',Field)
318        testinputfield=1;
319       
320        % set the colorbar position on the interface:
321        UvData.PosColorbar=[0.805 0.022 0.019 0.445];
322    elseif ischar(input)
323        scan_i_Callback(handles.scan_i, eventdata, handles);       
324    end
325else
326   if ishandle(handles.UVMAT_title)
327       fid=fopen('revision.log');
328       if fid~=-1
329        a=textscan(fid,'%s%s%s',1,'HeaderLines',1,'Delimiter','|');
330        set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG';'GNU General Public License'; path_to_uvmat; ['at revision ' a{1}{1}]};a{3}{1};errormsg]);
331        fclose(fid);
332       else
333           set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG';'GNU General Public License'; path_to_uvmat;date_str};errormsg]);
334       end
335   end
336end
337UvData.NewSeries=1;
338set(hObject,'UserData',UvData)
339if testinputfield
340    %delete drawn objects
341    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
342    for iobj=1:length(hother)
343        delete_object(hother(iobj))
344    end 
345    if isempty(inputfile)
346        run0_Callback(hObject, eventdata, handles)
347        set(handles.MenuTools,'Enable','on')
348        set(handles.OBJECT_txt,'Visible','on')
349        set(handles.edit,'Visible','on')
350        set(handles.list_object,'Visible','on')
351        set(handles.frame_object,'Visible','on')
352    else
353        update_rootinfo(hObject,eventdata,handles);
354    end
355end
356set_vec_col_bar(handles)
357
358%-------------------------------------------------------------------
359% --- Outputs from this function are returned to the command menuline.
360function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
361varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
362
363%-------------------------------------------------------------------
364%-------------------------------------------------------------------
365% II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
366% automatically sets the global properties when the rootfile name is introduced
367% then activate the view-field action if selected
368% it is activated either by clicking on the RootPath window or by the
369% browser
370%------------------------------------------------------------------
371%------------------------------------------------------------------
372
373% --- Executes on the menu Open/Browse...
374% search the files, recognize their type according to their name and fill the rootfile input windows
375function MenuBrowse_Callback(hObject, eventdata, handles)
376oldfile=read_file_boxes(handles);
377
378if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
379         dir_perso=prefdir;
380         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
381         if exist(profil_perso,'file')
382              h=load (profil_perso);
383             if isfield(h,'MenuFile_1')
384                  oldfile=h.MenuFile_1;
385             end
386         end
387end
388[FileName, PathName] = uigetfile( ...
389       {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
390       '*.xml',  '.xml files '; ...
391        '*.xls',  '.xls files '; ...
392        '*.civ',  '.civ files '; ...
393        '*.jpg',' jpeg image files'; ...
394        '*.png','.png image files'; ...
395        '*.tif','.tif image files'; ...
396        '*.avi;*.AVI','.avi movie files'; ...
397        '*.nc','.netcdf files'; ...
398        '*.cdf','.netcdf files'; ...
399        '*.cmx','.cmx text files';...
400        '*.cmx2','.cmx2 text files';...
401        '*.fig','.fig files (matlab fig)';...
402        '*.log','.log text files ';...
403        '*.dat','.dat text files ';...
404        '*.*',  'All Files (*.*)'}, ...
405        'Pick a file',oldfile);
406%global filebase
407fileinput=[PathName FileName];%complete file name
408testblank=findstr(fileinput,' ');%look for blanks
409if ~isempty(testblank)
410    warndlg_uvmat(['The input file name ' fileinput ' contains blank character : This is not allowed. Please change name'],'ERROR')
411    return
412end
413sizf=size(fileinput);
414if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
415
416% display the selected field and related information
417display_file_name(hObject, eventdata, handles,fileinput)
418
419%update list of recent files in the menubar
420MenuFile_1=fileinput;
421MenuFile_2=get(handles.MenuFile_1,'Label');
422MenuFile_3=get(handles.MenuFile_2,'Label');
423MenuFile_4=get(handles.MenuFile_3,'Label');
424MenuFile_5=get(handles.MenuFile_4,'Label');
425set(handles.MenuFile_1,'Label',MenuFile_1)
426set(handles.MenuFile_2,'Label',MenuFile_2)
427set(handles.MenuFile_3,'Label',MenuFile_3)
428set(handles.MenuFile_4,'Label',MenuFile_4)
429set(handles.MenuFile_5,'Label',MenuFile_5)
430set(handles.MenuFile_1_1,'Label',MenuFile_1)
431set(handles.MenuFile_2_1,'Label',MenuFile_2)
432set(handles.MenuFile_3_1,'Label',MenuFile_3)
433set(handles.MenuFile_4_1,'Label',MenuFile_4)
434set(handles.MenuFile_5_1,'Label',MenuFile_5)
435dir_perso=prefdir;
436profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
437if exist(profil_perso,'file')
438    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
439else
440    txt=ver;
441    Release=txt(1).Release;
442    relnumb=str2double(Release(3:4));
443    if relnumb >= 14
444        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
445    else
446        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
447    end
448end
449
450% --------------------------------------------------------------------
451function MenuFile_1_Callback(hObject, eventdata, handles)
452fileinput=get(handles.MenuFile_1,'Label');
453display_file_name(hObject, eventdata, handles,fileinput)
454
455% --------------------------------------------------------------------
456function MenuFile_2_Callback(hObject, eventdata, handles)
457fileinput=get(handles.MenuFile_2,'Label');
458display_file_name(hObject, eventdata, handles,fileinput)
459
460% --------------------------------------------------------------------
461function MenuFile_3_Callback(hObject, eventdata, handles)
462fileinput=get(handles.MenuFile_3,'Label');
463display_file_name(hObject, eventdata, handles,fileinput)
464
465% --------------------------------------------------------------------
466function MenuFile_4_Callback(hObject, eventdata, handles)
467fileinput=get(handles.MenuFile_4,'Label');
468display_file_name(hObject, eventdata, handles,fileinput)
469
470% --------------------------------------------------------------------
471function MenuFile_5_Callback(hObject, eventdata, handles)
472fileinput=get(handles.MenuFile_5,'Label');
473display_file_name(hObject, eventdata, handles,fileinput)
474
475%-----------------------------------------------------------------
476% fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
477%----------------------------------------------------------------
478function display_file_name(hObject, eventdata, handles,fileinput)
479if ~exist(fileinput,'file')
480    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
481    return
482end
483[RootPath,RootFile,i1,i2,str_a,str_b,ext,NomType,SubDir]=name2display(fileinput);
484ext_test=''; %default
485if ~isempty(ext)
486    form=imformats(ext(2:end));%test valid Matlab image formats
487    if ~isempty(form)
488        ext_test='.image';
489        imainfo=imfinfo(fileinput); 
490        if length(imainfo) >1 %case of image with multiple frames
491            i1='1'; % set the frame counter to 1 by default
492            i2='';
493            str_a='';
494            str_b='';
495            NomType='*'; %indicate a set of indexed frames within a single file
496            [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
497        end
498    elseif isequal(lower(ext),'.avi')
499        ext_test='.image';
500        i1='1'; % set the frame counter to 1 by default
501        i2='';
502        str_a='';
503        str_b='';
504        NomType='*'; %indicate a set of indexed frames within a single file
505        [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file
506    else
507        ext_test=lower(ext);
508    end
509end
510switch ext_test
511    case {'.civ','.log','.cmx','.cmx2','.txt'}  %display text file
512        edit(fileinput) 
513    case '.fig'                           %display matlab figure
514        hfig=open(fileinput);
515        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
516        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
517        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
518    case {'.xml','.xls'}                % edit xml or Excel files
519       editxml(fileinput);
520    case {'.avi','.image','.vol','.nc','.cdf'}   
521        set(handles.RootPath,'String',RootPath);
522        if  isequal(SubDir,'')
523            rootname=fullfile(RootPath,RootFile);
524        else
525            rootname=fullfile(RootPath,SubDir,RootFile);
526            SubDir=['/' SubDir]; %display the separator
527        end
528        set(handles.SubDir,'String',SubDir);
529        set(handles.RootFile,'String',['/' RootFile]); %display the separator
530        indices=fileinput(length(rootname)+1:end);
531        indices(end-length(ext)+1:end)=[]; %remove extension
532        set(handles.FileIndex,'String',indices);       
533        set(handles.FileIndex,'UserData',NomType);
534        set(handles.FileExt,'String',ext);
535        % fill file index counters
536        set(handles.i1,'String',i1);
537     
538        set(handles.i2,'String',i2);
539        set(handles.j1,'String',str_a);
540        set(handles.j2,'String',str_b);
541       
542        % synchronise indices of the second  input file if it exists
543        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
544            [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
545            NomType_1=get(handles.FileIndex_1,'UserData');     
546            [FileName_1,idetect]=name_generator(FileBase_1,stra2num(i1),stra2num(i2),FileExt_1,NomType_1,1,stra2num(str_a),stra2num(str_b),SubDir_1);
547            if idetect
548                FileIndex_1=name_generator('',stra2num(i1),stra2num(i2),'',NomType_1,1,stra2num(str_a),stra2num(str_b),'');
549                set(handles.FileIndex_1,'String',FileIndex_1)
550            else
551                set(handles.SubField,'Value',0)
552                SubField_Callback(hObject, eventdata, handles)
553            end
554        end 
555
556        %enable other menus
557        set(handles.MenuOpen_1,'Enable','on')
558        set(handles.MenuFile_1_1,'Enable','on')
559        set(handles.MenuFile_2_1,'Enable','on')
560        set(handles.MenuFile_3_1,'Enable','on')
561        set(handles.MenuFile_4_1,'Enable','on')
562        set(handles.MenuFile_5_1,'Enable','on')
563        set(handles.MenuExport,'Enable','on')
564        set(handles.MenuExportFigure,'Enable','on')
565        set(handles.MenuExportMovie,'Enable','on')
566        set(handles.MenuTools,'Enable','on')
567        set(handles.OBJECT_txt,'Visible','on')
568        set(handles.edit,'Visible','on')
569        set(handles.list_object,'Visible','on')
570        set(handles.frame_object,'Visible','on')
571         % initiate input file:
572        update_rootinfo(hObject,eventdata,handles); 
573    otherwise
574       msgbox_uvmat('ERROR',['invalid input file extension' ext])
575end
576
577%-------------------------------------------------------------------
578function RootPath_Callback(hObject,eventdata,handles)
579update_rootinfo(hObject,eventdata,handles);
580
581%-------------------------------------------------------------------
582%-- called by action in RootFile edit box
583%-------------------------------------------------------------------
584function SubDir_Callback(hObject, eventdata, handles)
585%refresh the menu of input fields
586Fields_Callback(hObject, eventdata, handles);
587% refresh the current field
588run0_Callback(hObject, eventdata, handles);
589
590
591%-------------------------------------------------------------------
592%-- called by action in RootFile edit box
593%-------------------------------------------------------------------
594function RootFile_Callback(hObject, eventdata, handles)
595update_rootinfo(hObject,eventdata,handles)
596
597%-------------------------------------------------------------------
598%-- called by action in FileIndex edit box
599%-------------------------------------------------------------------
600function FileIndex_Callback(hObject, eventdata, handles)
601NomType_str=get(handles.FileIndex,'String') ;
602[P,F,str1,str2,str_a,str_b]=name2display(['xx' NomType_str get(handles.FileExt,'String')]);
603% display the new index values on the counters
604set(handles.i1,'String',str1);
605set(handles.i2,'String',str2);
606set(handles.j1,'String',str_a);
607set(handles.j2,'String',str_b);
608
609%-------------------------------------------------------------------
610% -- update information about a new field series (indices to scan, timing, calibration from an xml file, then refresh current plots
611%-------------------------------------------------------------------
612function update_rootinfo(hObject,eventdata,handles)
613global dircur  dir_opening
614
615set(handles.RootPath,'BackgroundColor',[1 1 0])
616drawnow
617set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
618huvmat=get(handles.RootPath,'parent');
619UvData=get(huvmat,'UserData');%huvmat=handles of the uvmat interface
620UvData.NewSeries=1; %flag for run0: begin a new series
621UvData.TestInputFile=1;
622set(handles.fix_pair,'Value',0) % desactivate by default the comp_input '-'input window
623%FileIndex_Callback(hObject, eventdata, handles)% update field counters
624
625[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
626if ~exist(FileName,'file')
627   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
628    return
629end
630nbfield=[];%default
631nburst=[];%default
632
633% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
634XmlData.Time=[];%default
635XmlData.GeometryCalib=[];%default
636TimeUnit=[];%default
637testima=0; %test for image input
638if isequal(lower(FileExt),'.avi') %.avi file
639    testima=1;
640    info=aviinfo([FileBase FileIndices FileExt]);
641    nbfield=info.NumFrames;
642    nburst=1;
643    set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
644    XmlData.Time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]';
645    TimeUnit='s';
646    set(handles.npx,'String',num2str(info.Width));%fills nbre of pixels x box
647    set(handles.npy,'String',num2str(info.Height));%fills nbre of pixels y box
648    hhh=which('mmreader');
649    if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab)
650        UvData.MovieObject=mmreader([FileBase FileIndices FileExt]);
651    end
652elseif ~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol')%&& isequal(NomType,'*')% multi-frame image
653    testima=1;
654    if ~isequal(SubDir,'')
655       RootFile=get(handles.RootFile,'String');
656        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
657    else
658        imainfo=imfinfo([FileBase FileIndices FileExt]);
659    end
660    if length(imainfo) >1 %case of image with multiple frames
661        nbfield=length(imainfo);
662        nburst=1;
663    end
664    if isfield(UvData,'MovieObject')
665        UvData=rmfield(UvData,'MovieObject');
666    end
667else
668    %set(handles.last_i,'String','');%fills last_field box
669    set(handles.npx,'String','');%fills nbre of pixels x box
670    set(handles.npy,'String','');%fills nbre of pixels y box
671    if isfield(UvData,'MovieObject')
672        UvData=rmfield(UvData,'MovieObject');
673    end
674end
675
676% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
677filexml=[FileBase '.xml'];
678fileciv=[FileBase '.civ'];
679warntext='';%default warning message
680NbSlice=1;%default
681
682if exist(filexml,'file')
683    set(handles.view_xml,'Visible','on')
684    set(handles.view_xml,'BackgroundColor',[1 1 0])
685    set(handles.RootPath,'BackgroundColor',[1 1 1])
686    set(handles.view_xml,'String','view .xml')
687    drawnow
688    [XmlData,warntext]=imadoc2struct(filexml);
689    if ~isempty(warntext)
690        msgbox_uvmat('WARNING',warntext)
691    end
692    if isfield(XmlData,'TimeUnit')
693        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
694            TimeUnit=XmlData.TimeUnit;
695        end
696    end
697    set(handles.view_xml,'BackgroundColor',[1 1 1])
698    drawnow
699elseif exist(fileciv,'file')% if .civ file found
700    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
701    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
702    GeometryCalib.Tx=0;
703    GeometryCalib.Ty=0;
704    GeometryCalib.Tz=1;
705    GeometryCalib.dpx=1;
706    GeometryCalib.dpy=1;
707    GeometryCalib.sx=1;
708    GeometryCalib.Cx=0;
709    GeometryCalib.Cy=0;
710    GeometryCalib.f=1;
711    GeometryCalib.kappa1=0;
712    GeometryCalib.CoordUnit='cm';
713    XmlData.GeometryCalib=GeometryCalib;
714    if error==2, warntext=['no file ' FileBase '.civ'];
715    elseif error==1, warntext='inconsistent number of fields in the .civ file';
716    end 
717    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
718    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
719    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
720    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
721    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
722    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
723    set(handles.view_xml,'Visible','on')   
724    set(handles.view_xml,'String','view .civ')
725else
726    set(handles.view_xml,'Visible','off')
727end
728
729% store last index in handles.lat_i and .last_j
730if ~isempty(XmlData.Time)
731    nbfield=size(XmlData.Time,1);
732    nburst=size(XmlData.Time,2);
733end
734last_i_cell=get(handles.last_i,'String');
735if isempty(nbfield)
736    last_i_cell{1}='';
737else
738    last_i_cell{1}=num2str(nbfield);
739end
740set(handles.last_i,'String',last_i_cell)
741last_j_cell=get(handles.last_j,'String');
742if isempty(nburst)
743     last_j_cell{1}='';
744else
745     last_j_cell{1}=num2str(nburst);
746end
747set(handles.last_j,'String',last_j_cell);
748
749% store geometric calibration in UvData
750if isfield(XmlData,'GeometryCalib')
751    GeometryCalib=XmlData.GeometryCalib;
752    if isempty(GeometryCalib)
753        set(handles.pxcm,'String','')
754        set(handles.pycm,'String','')
755        set(handles.menu_coord,'Value',1); %  no transform by default
756    else
757        if (isfield(GeometryCalib,'R')& ~isequal(GeometryCalib.R(2,1),0) & ~isequal(GeometryCalib.R(1,2),0)) |...
758            (isfield(GeometryCalib,'kappa1')& ~isequal(GeometryCalib.kappa1,0))
759            set(handles.pxcm,'String','var')
760            set(handles.pycm,'String','var')
761        else
762            pixcmx=GeometryCalib.f*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
763            pixcmy=GeometryCalib.f*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
764            set(handles.pxcm,'String',num2str(pixcmx))
765            set(handles.pycm,'String',num2str(pixcmy))
766        end
767        set(handles.menu_coord,'Value',2); % phys transform by default
768        if isfield(GeometryCalib,'SliceCoord')
769           siz=size(GeometryCalib.SliceCoord);
770           if siz(1)>1
771               NbSlice=siz(1);
772               set(handles.slices,'Visible','on')
773               set(handles.slices,'Value',1)
774           end
775           set(handles.nb_slice,'String',num2str(NbSlice))
776           slices_Callback(hObject, eventdata, handles)
777    %        Coord=UvData.XmlData.GeometryCalib.SliceCoord;
778    %        ZIndex=num_i1-NbSlice*(floor((num_i1-1)/NbSlice));
779        end
780    end
781end
782
783%update the data attached to the uvmat interface
784set(handles.nb_slice,'String',num2str(NbSlice))
785if ~isempty(TimeUnit)
786    set(handles.time_txt,'String',['time (' TimeUnit ')'])
787end
788%set(handles.DtUnit,'String',['10^(-3)' TimeUnit])
789UvData.TimeUnit=TimeUnit;
790UvData.XmlData=XmlData;
791UvData.NewSeries=1;
792set(huvmat,'UserData',UvData)
793
794%display warning message
795if ~isequal(warntext,'')
796    msgbox_uvmat('WARNING',warntext);
797end
798
799% set default options in menu 'Fields'
800if testima
801   set(handles.Fields,'Value',1) % set menu to 'image'
802   set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'})
803elseif isequal(FileExt,'.nc')|isequal(FileExt,'.cdf')
804   Data=nc2struct(FileName,[]);
805   col_vec=get(handles.col_vec,'String');
806   if isfield(Data,'absolut_time_T0')&& (isfield(Data,'civ1')||isfield(Data,'civ'))
807       set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'})
808       set(handles.Fields,'Value',3) % set menu to 'velocity'
809       col_vec{1}='ima_cor';
810   else
811       set(handles.Fields,'Value',1) % set menu to 'get_field...
812       set(handles.Fields,'String',{'get_field...'})
813       col_vec{1}='get_field...';
814   end
815   set(handles.col_vec,'String',col_vec)
816else
817    msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
818    return
819end 
820
821% set index navigation options and refresh plots
822set(handles.RootPath,'BackgroundColor',[1 1 1])
823drawnow
824set_scan_options(hObject, eventdata, handles)
825
826
827%-------------------------------------------------------------------
828%-- set index navigation options for new series input and refresh plot
829%-------------------------------------------------------------------
830function set_scan_options(hObject, eventdata, handles)
831
832%  set the corresponding index navigation options (TO CHECK WITH THE SECOND FIELD)
833NomType=get(handles.FileIndex,'UserData');
834NomType_1=get(handles.FileIndex_1,'UserData');
835state_j='off'; %default
836scan_option='i';
837switch NomType
838    case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices
839        state_j='on';
840        if exist('nbfield','var') && isequal(nbfield,1)
841            scan_option='j';
842        else
843            scan_option='i';               
844        end
845end
846if ~isempty(NomType_1)
847    switch NomType_1
848        case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices
849            state_j='on';
850            if exist('nbfield','var') && isequal(nbfield,1)
851                scan_option='j';
852            else
853                scan_option='i';               
854            end
855    end
856end
857if isequal(scan_option,'i')
858     set(handles.scan_i,'Value',1)
859     scan_i_Callback(hObject, eventdata, handles);
860else
861     set(handles.scan_j,'Value',1)
862     scan_j_Callback(hObject, eventdata, handles);
863end
864set(handles.scan_j,'Visible',state_j)
865set(handles.j1,'Visible',state_j)
866set(handles.j2,'Visible',state_j)
867set(handles.last_j,'Visible',state_j);
868set(handles.frame_j,'Visible',state_j);
869set(handles.j_text,'Visible',state_j);
870
871% view the field 
872run0_Callback(hObject, eventdata, handles); %view field
873mask_test=get(handles.mask_test,'value');
874if mask_test
875    MaskData=get(handles.mask_test,'UserData');
876    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
877          delete(MaskData.maskhandle)    %delete old mask
878    end
879    mask_test_Callback(hObject, eventdata, handles)
880end
881%-------------------------------------------------------------------
882function MenuBrowse_1_Callback(hObject, eventdata, handles)
883%-------------------------------------------------------------------
884huvmat=get(handles.run0,'parent');
885UvData=get(huvmat,'UserData');
886
887RootPath=get(handles.RootPath,'String');
888[FileName, PathName, filterindex] = uigetfile( ...
889       {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
890       '*.xml',  '.xml files '; ...
891        '*.xls',  '.xls files '; ...
892        '*.civ',  '.civ files '; ...
893        '*.jpg','.jpg image files'; ...
894        '*.png','.png image files'; ...
895        '*.avi;*.AVI','.avi movie files'; ...
896        '*.nc','.netcdf files'; ...
897        '*.cdf','.netcdf files'; ...
898        '*.cmx','.cmx text files';...
899        '*.cmx2','.cmx2 text files';...
900        '*.fig','.fig files (matlab fig)';...
901        '*.log','.log text files ';...
902        '*.dat','.dat text files ';...
903        '*.*',  'All Files (*.*)'}, ...
904        'Pick a file',RootPath);
905fileinput_1=[PathName FileName];%complete file name
906testblank=findstr(fileinput_1,' ');%look for blanks
907if ~isempty(testblank)
908    warndlg_uvmat(['The input file name ' fileinput_1 ' contains blank character : This is not allowed. Please change name'],'ERROR')
909    return
910end
911sizf=size(fileinput_1);
912if (~ischar(fileinput_1)|~isequal(sizf(1),1)),return;end
913
914% refresh the current displayed field
915display_file_name_1(hObject,eventdata,handles,fileinput_1)
916
917%update list of recent files in the menubar
918MenuFile_1=fileinput_1;
919MenuFile_2=get(handles.MenuFile_1,'Label');
920MenuFile_3=get(handles.MenuFile_2,'Label');
921MenuFile_4=get(handles.MenuFile_3,'Label');
922MenuFile_5=get(handles.MenuFile_4,'Label');
923set(handles.MenuFile_1,'Label',MenuFile_1)
924set(handles.MenuFile_2,'Label',MenuFile_2)
925set(handles.MenuFile_3,'Label',MenuFile_3)
926set(handles.MenuFile_4,'Label',MenuFile_4)
927set(handles.MenuFile_5,'Label',MenuFile_5)
928set(handles.MenuFile_1_1,'Label',MenuFile_1)
929set(handles.MenuFile_2_1,'Label',MenuFile_2)
930set(handles.MenuFile_3_1,'Label',MenuFile_3)
931set(handles.MenuFile_4_1,'Label',MenuFile_4)
932set(handles.MenuFile_5_1,'Label',MenuFile_5)
933dir_perso=prefdir;
934profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
935if exist(profil_perso,'file')
936    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
937else
938    txt=ver;
939    Release=txt(1).Release;
940    relnumb=str2num(Release(3:4));
941    if relnumb >= 14
942        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
943    else
944        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
945    end
946end
947
948% --------------------------------------------------------------------
949function MenuFile_1_1_Callback(hObject, eventdata, handles)
950fileinput_1=get(handles.MenuFile_1_1,'Label');
951display_file_name_1(hObject,eventdata,handles,fileinput_1)
952
953% --------------------------------------------------------------------
954function MenuFile_2_1_Callback(hObject, eventdata, handles)
955fileinput_1=get(handles.MenuFile_2_1,'Label');
956display_file_name_1(hObject,eventdata,handles,fileinput_1)
957
958% --------------------------------------------------------------------
959function MenuFile_3_1_Callback(hObject, eventdata, handles)
960fileinput_1=get(handles.MenuFile_3_1,'Label');
961display_file_name_1(hObject,eventdata,handles,fileinput_1)
962
963% --------------------------------------------------------------------
964function MenuFile_4_1_Callback(hObject, eventdata, handles)
965fileinput_1=get(handles.MenuFile_4_1,'Label');
966display_file_name_1(hObject,eventdata,handles,fileinput_1)
967
968% --------------------------------------------------------------------
969function MenuFile_5_1_Callback(hObject, eventdata, handles)
970fileinput_1=get(handles.MenuFile_5_1,'Label');
971display_file_name_1(hObject,eventdata,handles,fileinput_1)
972
973%-----------------------------------------------------------------
974% fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
975%----------------------------------------------------------------
976function display_file_name_1(hObject,eventdata,handles,fileinput_1)
977
978%[path,name,ext]=fileparts(fileinput_1);
979[RootPath_1,RootFile_1,field_count,str2,str_a,str_b,FileExt_1,NomType_1,SubDir_1]=name2display(fileinput_1);
980nbfield_1=1; %default
981ext_test=FileExt_1;%default
982form=imformats(FileExt_1(2:end));
983if ~isempty(form) % if the extension corresponds to an image format recognized by Matlab
984    imainfo=imfinfo(fileinput_1); 
985    nbfield_1=length(imainfo);
986    ext_test='.image';
987elseif isequal(lower(FileExt_1),'.avi')
988    info=aviinfo(fileinput_1);
989    nbfield_1=info.NumFrames;
990    ext_test='.image';
991end
992
993%open directly fig or text files
994switch ext_test
995    case {'.civ','.log','.cmx','.cmx2','.txt'}  %display text file
996        edit(fileinput) 
997        return
998    case '.fig'                           %display matlab figure
999        hfig=open(fileinput);
1000        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
1001        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
1002        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
1003        return
1004    case {'.xml','.xls'}                % edit xml or Excel files
1005       heditxml=editxml(fileinput);
1006       return
1007    case {'.image','.nc','.cdf'}
1008%         set(handles.FileIndex,'UserData',NomType_1);
1009    otherwise
1010        warndlg_uvmat(['invalid input file extension ' FileExt_1 ' for uvmat'],'ERROR')
1011        return
1012end
1013
1014% test for image series in a single file and synchronise file indices of the two series
1015if nbfield_1 >1 %case of image with multiple frames
1016    if nbfield_1 < num_i1
1017        warndlg_uvmat('current frame index beyond the input movie length','ERROR')
1018        return
1019    else
1020        NomType_1='*'; %indicate a set of indexed frames within a single file
1021        filename_new=fileinput_1;
1022    end
1023else  % cases of data files   
1024    RootPath=get(handles.RootPath,'String');
1025    RootFile=get(handles.RootFile,'String');
1026    FileBase=fullfile(RootPath,RootFile);
1027    FileBase_1=fullfile(RootPath_1,RootFile_1);
1028    if isequal(FileBase,FileBase_1)
1029        filename_new=fileinput_1;
1030    else       
1031        num_i1=stra2num(get(handles.i1,'String'));%get the current file indices from counters
1032        num_j1=stra2num(get(handles.j1,'String'));
1033        num_i2=stra2num(get(handles.i2,'String'));
1034        num_j2=stra2num(get(handles.j2,'String'));
1035        [filename_new,idetect]=...
1036           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
1037        indices=''; %default
1038        if ~idetect
1039            warndlg_uvmat('second input file with indices corresponding to the first one does not exist','ERROR')
1040            return
1041        end
1042    end
1043end
1044set(handles.FileIndex,'UserData',NomType_1);
1045
1046% make visible and fill the second raw of edit boxes
1047set(handles.RootPath_1,'Visible','on')
1048set(handles.RootFile_1,'Visible','on')
1049set(handles.SubDir_1,'Visible','on');
1050set(handles.FileIndex_1,'Visible','on');
1051set(handles.FileExt_1,'Visible','on');
1052[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
1053if isequal(FileBase,FileBase_1)
1054    set(handles.RootPath_1,'String','"')
1055    set(handles.RootFile_1,'String','"');
1056else
1057    set(handles.RootPath_1,'String',RootPath_1)
1058    set(handles.RootFile_1,'String',['/' RootFile_1]);
1059end
1060if  isequal(SubDir_1,'')
1061     set(handles.SubDir_1,'String','');
1062     FileBaseSub_1=FileBase_1;
1063else 
1064    set(handles.SubDir_1,'String',['/' SubDir_1]);
1065    FileBaseSub_1=fullfile(FileBase_1,SubDir_1);
1066end
1067indices=filename_new(length(FileBaseSub_1)+1:end);
1068indices(end-length(FileExt_1)+1:end)=[]; %remove extension
1069set(handles.FileIndex_1,'String',indices)
1070set(handles.FileIndex_1,'UserData',NomType_1)
1071set(handles.FileExt_1,'String',FileExt_1);
1072
1073% default choice of fields
1074if isequal(ext_test,'.image')
1075   set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1076   set(handles.Fields_1,'Value',2) % set menu to 'image'
1077elseif isequal(FileExt_1,'.nc')|isequal(FileExt_1,'.cdf')
1078   Data=nc2struct(fileinput_1,[]);
1079   if isfield(Data,'absolut_time_T0')
1080       set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'})
1081       set(handles.Fields_1,'Value',4) % set menu to 'velocity'
1082   else   
1083       set(handles.Fields_1,'Value',2) % set menu to 'get_field...'
1084       set(handles.Fields_1,'String',{'';'get_field...'});
1085   end
1086end 
1087set(handles.SubField,'Visible','on')
1088set(handles.SubField,'Value',1)
1089RootPath_1_Callback(hObject,eventdata,handles); 
1090
1091
1092%-----------------------------------------------------
1093function RootPath_1_Callback(hObject,eventdata,handles)
1094update_rootinfo_1(hObject,eventdata,handles)
1095
1096%-------------------------------------------------------------------
1097function RootFile_1_Callback(hObject, eventdata, handles)
1098update_rootinfo_1(hObject,eventdata,handles)
1099%-------------------------------------------------------------------
1100
1101%-------------------------------------------------------------------
1102function update_rootinfo_1(hObject,eventdata,handles) %A REVOIR
1103
1104set(handles.RootPath_1,'BackgroundColor',[1 1 0])% indicate active program by yellow color
1105drawnow
1106huvmat=get(handles.RootPath,'parent');
1107UvData=get(huvmat,'UserData');%huvmat=handles of the uvmat interface
1108UvData.NewSeries=1; %flag for run0: begin a new series
1109
1110[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes_1(handles);
1111if ~exist(FileName,'file')
1112    msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
1113end
1114nbfield_1=[];%default
1115nburst_1=[];%default
1116XmlData.Time=[];
1117XmlData.GeometryCalib=[];%default
1118TimeUnit=[];
1119if isfield(UvData,'TimeUnit')
1120    TimeUnit=UvData.TimeUnit;
1121end
1122TimeUnit_1=[];
1123testima=0; %test for image input
1124if isequal(lower(FileExt),'.avi') %.avi file
1125    testima=1;
1126    info=aviinfo([FileBase FileIndices FileExt]);
1127    nbfield_1=info.NumFrames;
1128    nburst_1=1;
1129    %set(handles.last_i,'String',num2str(info.NumFrames));%fills last_field box
1130    set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
1131%     set(handles.dt,'UserData',info.FramesPerSecond);
1132    time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]';
1133    npx=get(handles.npx,'String');
1134    npy=get(handles.npy,'String');
1135    if isequal(npx,'') || isequal(npy,'')
1136        set(handles.npx,'String',num2str(info.Width));%fills nbre of pixels x box
1137        set(handles.npy,'String',num2str(info.Height));%fills nbre of pixels y box
1138    end
1139elseif ~isempty(imformats(FileExt(2:end))) %&& isequal(NomType,'*')% multi-frame image
1140    testima=1;
1141    imainfo=imfinfo([FileBase FileIndices FileExt]); 
1142    if length(imainfo) >1 %case of image with multiple frames
1143        nbfield_1=length(imainfo);
1144        nburst_1=1;
1145        %set(handles.last_i,'String',num2str(length(imainfo)));%fills last_field box
1146    end       
1147else
1148    %set(handles.last_i,'String','');%fills last_field box
1149    set(handles.npx,'String','');%fills nbre of pixels x box
1150    set(handles.npy,'String','');%fills nbre of pixels y box
1151end
1152
1153% find scaling parameters
1154filexml=[FileBase '.xml'];
1155fileciv=[FileBase '.civ'];
1156warntext='';%default warning text
1157if exist(filexml,'file')
1158    [XmlData,warntext]=imadoc2struct(filexml);
1159    if ~isempty(warntext)
1160        msgbox_uvmat('WARNING',warntext)
1161    end
1162    if isfield(XmlData,'Camera')
1163%         if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
1164%             NbSlice=XmlData.Camera.NbSlice;
1165%         end
1166        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1167            TimeUnit=XmlData.Camera.TimeUnit;
1168        end
1169    end
1170elseif exist(fileciv,'file')% if .civ file found
1171    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
1172    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
1173    GeometryCalib.Tx=0;
1174    GeometryCalib.Ty=0;
1175    GeometryCalib.Tz=1;
1176    GeometryCalib.dpx=1;
1177    GeometryCalib.dpy=1;
1178    GeometryCalib.sx=1;
1179    GeometryCalib.Cx=0;
1180    GeometryCalib.Cy=0;
1181    GeometryCalib.f=1;
1182    GeometryCalib.kappa1=0;
1183    GeometryCalib.CoordUnit='cm';
1184    XmlData.GeometryCalib=GeometryCalib;
1185    if error==2, warntext=['no file ' FileBase '.civ'];
1186    elseif error==1, warntext='inconsistent number of fields in the .civ file';
1187    end
1188   
1189    set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
1190    set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
1191    set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
1192    set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
1193    set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
1194    set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
1195end   
1196if ~isempty(TimeUnit_1) && ~isequal(TimeUnit_1,TimeUnit)
1197        warndlg_uvmat('the time units for the second series differs from the first one','WARNING')
1198end
1199       
1200% store last index in handles.lat_i and .last_j
1201if ~isempty(XmlData.Time)
1202    nbfield_1=size(XmlData.Time,1);
1203    nburst_1=size(XmlData.Time,2);   
1204end
1205last_i_cell=get(handles.last_i,'String');
1206if isempty(nbfield_1)
1207    last_i_cell{2}='';
1208else
1209    last_i_cell{2}=num2str(nbfield_1);
1210end
1211set(handles.last_i,'String',last_i_cell)
1212last_j_cell=get(handles.last_j,'String');
1213if isempty(nburst_1)
1214     last_j_cell{2}='';
1215else
1216     last_j_cell{2}=num2str(nburst_1);
1217end
1218set(handles.last_j,'String',last_j_cell);
1219if ~isequal(last_i_cell{1},last_i_cell{2}) || ~isequal(last_j_cell{1},last_j_cell{2})
1220        warndlg_uvmat('the numbers of input file of the second series differs from the first one','WARNING')
1221end
1222
1223% store calibration data
1224GeometryCalib=XmlData.GeometryCalib;
1225if isempty(GeometryCalib)
1226    if isfield(UvData, 'GeometryCalib_1')
1227        UvData=rmfield(UvData,'GeometryCalib_1');
1228    end
1229else
1230    UvData.GeometryCalib_1=GeometryCalib;
1231    if (isfield(GeometryCalib,'R')& ~isequal(GeometryCalib.R(2,1),0) & ~isequal(GeometryCalib.R(1,2),0)) |...
1232        (isfield(GeometryCalib,'kappa1')& ~isequal(GeometryCalib.kappa1,0))
1233        set(handles.pxcm,'String','var')
1234        set(handles.pycm,'String','var')
1235    else
1236        pixcmx=GeometryCalib.f*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
1237        pixcmy=GeometryCalib.f*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
1238        set(handles.pxcm,'String',num2str(pixcmx))
1239        set(handles.pycm,'String',num2str(pixcmy))
1240    end
1241end
1242UvData.XmlData_1=XmlData;
1243set(huvmat,'UserData',UvData)%update the data attached to the uvmat interface
1244
1245if ~isequal(warntext,'')
1246    warndlg_uvmat(warntext,'WARNING')
1247end
1248
1249set(handles.RootPath_1,'BackgroundColor',[1 1 1])% signa the end the input operation
1250drawnow
1251
1252set_scan_options(hObject, eventdata, handles)
1253
1254
1255%---------------------------------------------------
1256% switch file index scanning options scan_i and scan_j in an exclusive way
1257function scan_i_Callback(hObject, eventdata, handles)
1258%---------------------------------------------------
1259if get(handles.scan_i,'Value')==1
1260    set(handles.scan_i,'BackgroundColor',[1 1 0])
1261    set(handles.scan_j,'Value',0)
1262    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1263else
1264    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1265    set(handles.scan_j,'Value',1)
1266    set(handles.scan_j,'BackgroundColor',[1 1 0])
1267end
1268%-------------------------------------------------------------------
1269%---------------------------------------------------
1270% switch file index scanning options scan_i and scan_j in an exclusive way
1271function scan_j_Callback(hObject, eventdata, handles)
1272%---------------------------------------------------
1273%-------------------------------------------------------------------
1274if get(handles.scan_j,'Value')==1
1275    set(handles.scan_j,'BackgroundColor',[1 1 0])
1276    set(handles.scan_i,'Value',0)
1277    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1278else
1279    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1280    set(handles.scan_i,'Value',1)
1281    set(handles.scan_i,'BackgroundColor',[1 1 0])
1282end
1283
1284%-------------------------------------------------------------------
1285function i1_Callback(hObject, eventdata, handles)
1286%-------------------------------------------------------------------
1287% [filebase,num1,num_a,num2,num_b,ext,NomType,subdir]=read_input_file(handles);
1288[FileName,RootPath,filebase,xx,FileExt]=read_file_boxes(handles);
1289NomType=get(handles.FileIndex,'UserData');
1290num1=stra2num(get(handles.i1,'String'));
1291num2=stra2num(get(handles.i2,'String'));
1292num_a=stra2num(get(handles.j1,'String'));
1293num_b=stra2num(get(handles.j2,'String'));
1294indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1295set(handles.FileIndex,'String',indices)
1296if get(handles.SubField,'Value')==1
1297    NomType_1=get(handles.FileIndex_1,'String');
1298     FileExt_1=get(handles.FileExt_1,'String');
1299    [P,F,str1,str2,str_a,str_b,Ext,NomType_1]=name2display(['xx' NomType_1 FileExt_1]);
1300     indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1301     set(handles.FileIndex_1,'String',indices)
1302end
1303run0_Callback(hObject, eventdata, handles)
1304
1305%-------------------------------------------------------------------
1306function i2_Callback(hObject, eventdata, handles)
1307i1_Callback(hObject, eventdata, handles)
1308%-------------------------------------------------------------------
1309
1310%-------------------------------------------------------------------
1311function j1_Callback(hObject, eventdata, handles)
1312i1_Callback(hObject, eventdata, handles)
1313%-------------------------------------------------------------------
1314
1315%-------------------------------------------------------------------
1316function j2_Callback(hObject, eventdata, handles)
1317i1_Callback(hObject, eventdata, handles)
1318%-------------------------------------------------------------------
1319
1320%-------------------------------------------------------------------
1321function slices_Callback(hObject, eventdata, handles)
1322%-------------------------------------------------------------------
1323if get(handles.slices,'Value')==1
1324    set(handles.slices,'BackgroundColor',[1 1 0])
1325    set(handles.nb_slice,'Visible','on')
1326    set(handles.z_text,'Visible','on')
1327    set(handles.z_index,'Visible','on')
1328    nb_slice_Callback(hObject, eventdata, handles)
1329%      z=mod(num_i1-1,nbslice)+1;
1330%         set(handles.z_index,'String',num2str(z))
1331else
1332    set(handles.nb_slice,'Visible','off')
1333    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1334    set(handles.z_text,'Visible','off')
1335    set(handles.z_index,'Visible','off')
1336    set(handles.masklevel,'Value',1)
1337    set(handles.masklevel,'String',{'1'})
1338end
1339
1340%-------------------------------------------------------------------
1341function nb_slice_Callback(hObject, eventdata, handles)
1342%-------------------------------------------------------------------
1343num_i1=str2num(get(handles.i1,'String'));
1344nbslice=str2num(get(handles.nb_slice,'String'));
1345z=mod(num_i1-1,nbslice)+1;
1346set(handles.z_index,'String',num2str(z))
1347for ilist=1:nbslice
1348    list_index{ilist,1}=num2str(ilist);
1349end   
1350set(handles.masklevel,'String',list_index)
1351set(handles.masklevel,'Value',z)
1352
1353
1354%-------------------------------------------------------------------
1355% --- Executes on button press in view_xml.
1356function view_xml_Callback(hObject, eventdata, handles)
1357[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1358option=get(handles.view_xml,'String');
1359if isequal(option,'view .xml')
1360    FileXml=[FileBase '.xml'];
1361    heditxml=editxml(FileXml);
1362end
1363
1364%-------------------------------------------------------------------
1365% --- Executes on button press in mask_test.
1366function mask_test_Callback(hObject, eventdata, handles)
1367%-------------------------------------------------------------------
1368if isequal(get(handles.mask_test,'Value'),1)
1369    [FF,RootPath,FileBase]=read_file_boxes(handles);
1370    num_i1=stra2num(get(handles.i1,'String'));
1371    num_j1=stra2num(get(handles.j1,'String'));
1372    currentdir=pwd; 
1373    cd(RootPath);
1374    maskfiles=dir('*_*mask_*.png');%look for a mask file
1375    cd(currentdir);%come back to the working directory
1376    mdetect=0;
1377    if isempty(maskfiles)
1378         msgbox_uvmat('ERROR','no mask file detected (format ..._xxmask_ii.png needed), use the menu bar Tools/Make mask')
1379         return
1380    end
1381    for ilist=1:length(maskfiles)
1382        maskname=maskfiles(ilist).name;% take the first mask file in the list
1383        [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1384        if ~strcmp(Mask_NomType{ilist},Mask_NomType{1})
1385            msgbox_uvmat('ERROR',['inconsistent mask types ' Mask_NomType{1} Mask_NomType{ilist } ' coexist in the current image directory'])
1386            return
1387        end
1388        [Path2,Name,ext]=fileparts(maskname);
1389        Namedouble=double(Name);
1390        val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1391        ind_mask=findstr('mask',Name);
1392        i=ind_mask-1;
1393        while val(i)==0 & i>0
1394            i=i-1;
1395        end
1396        nbmask_str=str2num(Name(i+1:ind_mask-1));
1397        if ~isempty(nbmask_str)
1398            nbslice(ilist)=nbmask_str; % number of different masks (slices)
1399        end
1400    end
1401    if isequal(min(nbslice),max(nbslice))
1402        nbslice=nbslice(1);
1403    else
1404        msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1405         return
1406    end
1407    if ~isempty(nbslice) && Name(i)=='_'
1408        Mask.Base=[FileBase Name(i:ind_mask+3)];
1409        Mask.NbSlice=nbslice;
1410        num_i1=mod(num_i1-1,nbslice)+1
1411        Mask.NomType=Mask_NomType{1};
1412        [maskname,mdetect]=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType)%
1413        mdetect=exist(maskname,'file')
1414        if mdetect
1415            set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1416            set(handles.nb_slice,'BackgroundColor',[1 1 0])
1417            set(handles.mask_test,'UserData',Mask); 
1418            set(handles.mask_test,'BackgroundColor',[1 1 0])
1419            if nbslice > 1
1420                set(handles.slices,'value',1)
1421                slices_Callback(hObject, eventdata, handles)
1422            end
1423        end
1424    end
1425    if mdetect==0
1426         msgbox_uvmat('ERROR','no mask file detected (format ..._xxmask_ii.png needed), use the menu bar Tools/Make mask')
1427         set(handles.mask_test,'Value',0)
1428         return
1429    end   
1430    update_mask(handles,num_i1,num_j1);
1431else
1432    MaskData=get(handles.mask_test,'UserData');
1433    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1434          delete(MaskData.maskhandle)   
1435    end
1436    set(handles.mask_test,'UserData',[])   
1437    huvmat=get(handles.mask_test,'parent');
1438    UvData=get(huvmat,'UserData');
1439    if isfield(UvData,'MaskName')
1440        UvData=rmfield(UvData,'MaskName');
1441        set(huvmat,'UserData',UvData)
1442    end
1443    set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7])
1444end
1445
1446%-------------------------------------------------------------------
1447function update_mask(handles,num_i1,num_j1)
1448%-------------------------------------------------------------------
1449
1450MaskData=get(handles.mask_test,'UserData');
1451if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1452    uistack(MaskData.maskhandle,'top');
1453end
1454num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1455[MaskName,mdetect]=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1456huvmat=get(handles.mask_test,'parent');
1457UvData=get(huvmat,'UserData');
1458
1459%update mask image if the mask is new
1460if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1461    UvData.MaskName=MaskName; %update the recorded name on UvData
1462    set(huvmat,'UserData',UvData);
1463    if mdetect==0
1464        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1465            delete(MaskData.maskhandle)   
1466        end
1467    else
1468        %read mask image
1469        Mask.AName='image';
1470        Mask.A=imread(MaskName);
1471        npxy=size(Mask.A);
1472        Mask.AX=[0.5 npxy(2)-0.5];
1473        Mask.AY=[npxy(1)-0.5 0.5 ];
1474        Mask.CoordType='px';
1475        if isequal(get(handles.slices,'Value'),1)
1476           NbSlice=str2num(get(handles.nb_slice,'String'));
1477           num_i1=str2num(get(handles.i1,'String'));
1478           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1479        end
1480        %px to phys or other transform on field
1481        menu_transform=get(handles.menu_coord,'String');
1482        choice_value=get(handles.menu_coord,'Value');
1483        transform=menu_transform{choice_value};%name of the transform fct  given by the menu 'menu_coord'
1484        if  ~isequal(transform,'') && ~isequal(transform,'px')
1485            if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1486                Calib=UvData.XmlData.GeometryCalib;
1487                Mask=feval(transform,Mask,UvData.XmlData);
1488            end
1489        end
1490        flagmask=Mask.A < 200;
1491       
1492        %make brown color image
1493        imflag(:,:,1)=0.9*flagmask;
1494        imflag(:,:,2)=0.7*flagmask;
1495        imflag(:,:,3)=zeros(size(flagmask));
1496       
1497        %update mask image
1498        hmask=[]; %default
1499        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1500            hmask=MaskData.maskhandle;
1501        end
1502        if ~isempty(hmask)
1503            set(hmask,'CData',imflag)   
1504            set(hmask,'AlphaData',flagmask*0.6)
1505            set(hmask,'XData',Mask.AX);
1506            set(hmask,'YData',Mask.AY);
1507%             uistack(hmask,'top')
1508        else
1509            axes(handles.axes3)
1510            hold on   
1511            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1512%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1513            set(handles.mask_test,'UserData',MaskData)
1514        end
1515    end
1516end
1517
1518
1519%-------------------------------------------------------------------
1520function MenuExportFigure_Callback(hObject, eventdata, handles)
1521%-------------------------------------------------------------------
1522huvmat=get(handles.MenuExport,'parent');
1523UvData=get(huvmat,'UserData');
1524hfig=figure;
1525newaxes=copyobj(handles.axes3,hfig);
1526map=colormap(handles.axes3);
1527colormap(map);%transmit the current colormap to the zoom fig
1528colorbar
1529
1530%-------------------------------------------------------------------
1531%-------------------------------------------------------------------
1532% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1533%-------------------------------------------------------------------
1534%-------------------------------------------------------------------
1535
1536%Executes on button press in runplus: make one step forward and call
1537%run0. The step forward is along the fields series 1 or 2 depending on
1538%the scan_i and scan_j check box (exclusive each other)
1539%-------------------------------------------------------------------
1540function runplus_Callback(hObject, eventdata, handles)
1541increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1542runpm(hObject,eventdata,handles,increment)
1543
1544%-------------------------------------------------------------------
1545%Executes on button press in runmin: make one step backward and call
1546%run0. The step backward is along the fields series 1 or 2 depending on
1547%the scan_i and scan_j check box (exclusive each other)
1548%-------------------------------------------------------------------
1549function runmin_Callback(hObject, eventdata, handles)
1550increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1551runpm(hObject,eventdata,handles,increment)
1552
1553%-------------------------------------------------------------------
1554%Executes on button press in runmin: make one step backward and call
1555%run0. The step backward is along the fields series 1 or 2 depending on
1556%the scan_i and scan_j check box (exclusive each other)
1557%-------------------------------------------------------------------
1558function RunMovie_Callback(hObject, eventdata, handles)
1559%------------------------------------------------------------------
1560set(handles.RunMovie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1561drawnow
1562increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1563set(handles.STOP,'Visible','on')
1564set(handles.speed,'Visible','on')
1565set(handles.speed_txt,'Visible','on')
1566set(handles.RunMovie,'BusyAction','queue')
1567testavi=0;
1568huvmat=get(handles.RunMovie,'parent');
1569UvData=get(huvmat,'UserData');
1570
1571while get(handles.speed,'Value')~=0 & isequal(get(handles.RunMovie,'BusyAction'),'queue') % enable STOP command
1572        runpm(hObject,eventdata,handles,increment)
1573        pause(1.02-get(handles.speed,'Value'))% wait for next image
1574end
1575if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1576    UvData.aviobj=close(UvData.aviobj);
1577   set(huvmat,'UserData',UvData);
1578end
1579set(handles.RunMovie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1580
1581%-------------------------------------------------------------------
1582function STOP_Callback(hObject, eventdata, handles)
1583%-------------------------------------------------------------------
1584set(handles.run0,'BusyAction','Cancel')
1585set(handles.RunMovie,'BusyAction','Cancel')
1586set(handles.MenuExportMovie,'BusyAction','Cancel')
1587
1588
1589%------------------------------------------------------------------
1590function runpm(hObject,eventdata,handles,increment)
1591%------------------------------------------------------------------
1592%read the data on the current input rootfile(s)
1593
1594[FileName,RootPath,filebase,FileIndices,FileExt,subdir]=read_file_boxes(handles);
1595NomType=get(handles.FileIndex,'UserData');
1596
1597num1=stra2num(get(handles.i1,'String'));
1598num2=stra2num(get(handles.i2,'String'));
1599num_a=stra2num(get(handles.j1,'String'));
1600num_b=stra2num(get(handles.j2,'String'));
1601
1602sub_value= get(handles.SubField,'Value');
1603if sub_value ==1
1604    [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles);
1605end   
1606
1607comp_input=get(handles.fix_pair,'Value');
1608if isequal(NomType,'_i1-i2')|isequal(NomType,'_i1-i2_j')
1609    comp_input=1; %impose a fixed pair interval
1610    set(handles.fix_pair,'Value',1)
1611end
1612
1613%case of scanning along the first direction (rootfile numbers)
1614if get(handles.scan_i,'Value')==1% case of scanning along field numbers   
1615     num1=num1+increment;
1616     num2=num2+increment;
1617    if comp_input==0% find a free pair
1618        [filename,num_i1_out,num_j1_out,num_i2_out,num_j2_out]=...
1619           name_generator(filebase,num1,num_a,FileExt,NomType,0,num2,num_b,subdir);
1620        if exist(filename,'file')
1621            num_a=num_j1_out;
1622            num_b=num_j2_out;
1623        end
1624    end
1625    if sub_value>=2
1626        num_i1=num_i1+increment;
1627        num_i2=num_i2+increment;
1628    end   
1629else % case of scanning along the second direction (burst numbers)
1630    lastfield_cell=get(handles.last_j,'String'); % get the last field number
1631    lastfield=str2num(lastfield_cell{1});
1632    num_a=num_a+increment;
1633    num_b=num_b+increment;
1634    if sub_value >=2
1635      num_j1=num_j1+increment;
1636      num_j2=num_j2+increment;
1637    elseif ~isempty(lastfield) && num_a>lastfield
1638        num_a=1;
1639        num1=num1+1;
1640        num2=num2+1;
1641    end
1642end
1643
1644% display the new open numbers
1645set(handles.i1,'String',num2stra(num1,NomType,1));
1646set(handles.i2,'String',num2stra(num2,NomType,1));
1647set(handles.j1,'String',num2stra(num_a,NomType,2));
1648set(handles.j2,'String',num2stra(num_b,NomType,2));
1649[indices]=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1650set(handles.FileIndex,'String',indices);
1651if sub_value ==1
1652    NomType_1=get(handles.FileIndex_1,'UserData');
1653     [indices]=...
1654           name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1655     set(handles.FileIndex_1,'String',indices);
1656end
1657
1658% refresh plots
1659run0_Callback(hObject, eventdata, handles); %run
1660
1661
1662%-------------------------------------------------------
1663% --- Executes on button press in movie_pair.
1664%-------------------------------------------------------
1665function movie_pair_Callback(hObject, eventdata, handles)
1666%initialisation
1667set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1668drawnow
1669list_fields=get(handles.Fields,'String');% list menu fields
1670index_fields=get(handles.Fields,'Value');% selected string index
1671FieldName=list_fields{index_fields}; % selected field
1672huvmat=get(handles.movie_pair,'parent');
1673if isequal(FieldName,'image')
1674    run0_Callback(hObject, eventdata, handles)%display the first image
1675    UvData=get(huvmat,'UserData');
1676else
1677    warndlg_uvmat('an image or movie must be first introduced as input','ERROR')
1678    return
1679end
1680[ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes(handles);
1681NomType=get(handles.FileIndex,'UserData');
1682num_i2=str2num(get(handles.i2,'String'));
1683num_j2=str2num(get(handles.j2,'String'));
1684if ~isempty(num_j2)
1685    num_i1=str2num(get(handles.i1,'String'));
1686    [imaname_1,idetect]=name_generator(filebase,num_i1,num_j2,Ext,NomType);
1687    if idetect==0
1688        warndlg_uvmat(['second input open (-)  ' imaname_1 ' not found'],'ERROR');
1689        return
1690    end
1691    set(handles.i2,'String',''); % indicates that the second index i2 is not used
1692elseif ~isempty(num_i2)
1693    num_j1=str2num(get(handles.j1,'String'));
1694    [imaname_1,idetect]=name_generator(filebase,num_i2,num_j1,Ext,NomType);
1695    if idetect==0
1696        warndlg_uvmat(['second input open (-)  ' imaname_1 ' not found'],'ERROR');
1697        return
1698    end
1699else   
1700    warndlg_uvmat('a second image index i2 or j2 is needed to show the pair as a movie','ERROR')
1701    return
1702end
1703
1704%read the second image
1705Field.AName='image';
1706% Field.ListDimName={'AY','AX'}; %A FAIRE
1707% Field.DimValue=[];
1708% Field.ListVarName={'A'};
1709Field.AX=UvData.Field.AX;
1710Field.AY=UvData.Field.AY;
1711Field.CoordType='px';
1712[Field.A,error]=read_image(imaname_1,NomType,num_i2);
1713
1714
1715%px to phys or other transform on field
1716menu_transform=get(handles.menu_coord,'String');
1717choice_value=get(handles.menu_coord,'Value');
1718transform=menu_transform{choice_value};%name of the transform fct  given by the menu 'menu_coord'
1719if  ~isequal(transform,'') && ~isequal(transform,'px')
1720    if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1721        Field=feval(transform,Field,UvData.XmlData);
1722    end
1723end
1724
1725 % make movie until movie speed is set to 0 or STOP is activated
1726hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1727set(handles.STOP,'Visible','on')
1728set(handles.speed,'Visible','on')
1729set(handles.speed_txt,'Visible','on')
1730while get(handles.speed,'Value')~=0 & isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1731    % read and plot the series of images in non erase mode
1732    set(hima,'CData',Field.A);
1733    pause(1.02-get(handles.speed,'Value'));% wait for next image
1734    set(hima,'CData',UvData.Field.A);
1735    pause(1.02-get(handles.speed,'Value'));% wait for next image
1736end
1737set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1738
1739%run0_Callback(hObject, eventdata, handles)
1740
1741%-------------------------------------------------------
1742% --- Executes on button press in run0.
1743%-------------------------------------------------
1744function run0_Callback(hObject, eventdata, handles)
1745
1746%initialisation
1747set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1748drawnow
1749abstime=[];
1750abstime_1=[];
1751dt=[];
1752CalibCell={};%default
1753Field={};
1754huvmat=get(handles.run0,'parent');
1755UvData=get(huvmat,'UserData');
1756if isfield(UvData,'Txt')
1757    UvData=rmfield(UvData,'Txt');%erase previous error message
1758end
1759set(handles.run0,'BusyAction','queue');
1760if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1761    delete(handles.UVMAT_title)
1762end
1763
1764% determine the main input file information for action
1765TestInputFile=1;%default
1766if isfield(UvData,'TestInputFile')&& isequal(UvData.TestInputFile,0),
1767    TestInputFile=0;
1768end
1769num_i1=[];%default
1770if TestInputFile
1771    [filename,RootPath,filebase,xx,Ext,SubDir]=read_file_boxes(handles);
1772    if ~exist(filename,'file')
1773        msgbox_uvmat('ERROR',['input file ' filename ' does not exist'])
1774        return
1775    end
1776    num_i1=stra2num(get(handles.i1,'String'));
1777    num_i2=stra2num(get(handles.i2,'String'));
1778    num_j1=stra2num(get(handles.j1,'String'));
1779    num_j2=stra2num(get(handles.j2,'String'));
1780    NomType=get(handles.FileIndex,'UserData');
1781    %update the z position index
1782%     if isequal(get(handles.nb_slice,'String'),'vol.')%case of volume
1783%         set(handles.z_index,'String',get(handles.j1,'String'));
1784%     else
1785    nbslice=str2num(get(handles.nb_slice,'String'));
1786    z_index=mod(num_i1-1,nbslice)+1;
1787    if ~isempty(nbslice)
1788        z_index=mod(num_i1-1,nbslice)+1;
1789        set(handles.z_index,'String',num2str(z_index))
1790        % refresh menu for save_mask if relevant
1791        masknumber=get(handles.masklevel,'String');
1792        if length(masknumber)>=z_index
1793            set(handles.masklevel,'Value',z_index)
1794        end
1795    end
1796%     end
1797    % choose the main field
1798    testima=0;
1799    if isequal(lower(Ext),'.avi')||isequal(lower(Ext),'.vol')
1800       testima=1;
1801       FieldName='image';
1802    else
1803       form=imformats(Ext([2:end]));
1804       if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1805           testima=1;
1806           FieldName='image';
1807       end
1808    end
1809else
1810    filename=[];
1811    FieldName='get_field...';
1812    testima=0;
1813end
1814VelType=[];%default
1815
1816if ~testima
1817    list_fields=get(handles.Fields,'String');% list menu fields
1818    index_fields=get(handles.Fields,'Value');% selected string index
1819    FieldName= list_fields{index_fields}; % selected field
1820    if isequal(FieldName,'get_field...')% read the field names on the interface get_field...
1821        VelType=get(handles.Fields,'UserData');
1822        Field{1}=get(handles.Fields,'UserData');
1823    else
1824       VelType=setfield(handles);
1825       %enable_transform(handles,'on')% no field transform (possible transform in the GUI get_field)
1826    end
1827end
1828
1829% choose a second field if Subfield option is 'on'
1830filename_1=[];
1831VelType_1=[];%default
1832FieldName_1=[];
1833scal_color=[];
1834testvel=0;
1835testX=0;%default
1836VelType_1=setfield_1(handles);
1837sub_value=get(handles.SubField,'Value');
1838if sub_value==1
1839    filename_1=read_file_boxes_1(handles);
1840    if ~exist(filename_1,'file')
1841        msgbox_uvmat('ERROR',['second file ' filename_1 ' does not exist'])
1842        return
1843    end
1844    NomType_1=get(handles.FileIndex_1,'UserData');
1845    list_fields=get(handles.Fields_1,'String');% list menu fields
1846    index_fields=get(handles.Fields_1,'Value');% selected string index
1847    FieldName_1= list_fields{index_fields}; % selected field
1848    if isequal(VelType_1,'*')% free veltype choice
1849        VelType_1=[];
1850    elseif isequal(VelType_1,'"')% veltype the same as for the first field
1851        if isempty(VelType)
1852            VelType_1=[];
1853        else
1854            VelType_1=VelType;
1855        end
1856    end
1857end
1858
1859% test for keeping the previous stored data if the input files are unchanged
1860test_keepdata_1=0;%defautl
1861test_keepdata=0;
1862if sub_value>=2
1863    if ~isequal(NomType_1,'*')%in cas of a series of files (not avi movie)
1864        if isfield(UvData,'filename_1')& isfield(UvData,'VelType_1') & isfield(UvData,'FieldName_1')
1865            test_keepdata_1= isequal(filename_1,UvData.filename_1)&...
1866                isequal(VelType_1,UvData.filename_1) & isequal(FieldName_1,UvData.FieldName_1);
1867
1868        end
1869    end
1870end
1871
1872%read the input field(s)
1873testima_1=isequal(FieldName_1,'image');
1874%read images
1875if  ~isempty(filename) && testima
1876    if isfield(UvData,'MovieObject')
1877        A=read(UvData.MovieObject,num_i1);
1878    else
1879        [A,error]=read_image(filename,NomType,num_i1);
1880        if ~isequal(error,0)
1881            msgbox_uvmat('ERROR',error)
1882            return
1883        end
1884    end
1885    npxy=size(A);
1886    set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface
1887    set(handles.npy,'String',num2str(npxy(1)));
1888    Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
1889    Rangy=[npxy(1)-0.5 0.5]; %
1890    npx=str2num(get(handles.npx,'String'));
1891    npy=str2num(get(handles.npy,'String'));
1892    if isfield(UvData.XmlData,'Time')
1893        abs_time=UvData.XmlData.Time;
1894    end
1895    Field{1}.AName='image';
1896    Field{1}.ListVarName={'AY','AX','A'}; %
1897    if size(A,3)==3;%color
1898        Field{1}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
1899    else
1900        Field{1}.VarDimName={'AY','AX',{'AY','AX'}}; %
1901    end
1902    Field{1}.AY=Rangy;
1903    Field{1}.AX=Rangx;
1904    Field{1}.A=A;
1905    Field{1}.CoordType='px'; %used for mouse_motion
1906    Field{1}.CoordUnit='pixel'; %used for mouse_motion
1907end
1908if ~isfield(UvData,'Txt')& ~isempty(filename_1) & testima_1
1909    [A,error]=read_image(filename_1,NomType_1,num_i1);
1910    if ~isequal(error,0)
1911        msgbox_uvmat('ERROR',error)
1912        return
1913    end
1914    npxy=size(A);
1915    set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface
1916    set(handles.npy,'String',num2str(npxy(1)));
1917    Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
1918    Rangy=[npxy(1)-0.5 0.5]; %
1919    npx=str2num(get(handles.npx,'String'));
1920    npy=str2num(get(handles.npy,'String'));
1921    if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time')
1922        abs_time=UvData.XmlData_1.Time;
1923    end
1924    Field{2}.AName='image';
1925    Field{2}.ListVarName={'AY','AX','A'}; %
1926    if size(A,3)==3;%color
1927        Field{2}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
1928    else
1929        Field{2}.VarDimName={'AY','AX',{'AY','AX'}}; %
1930    end
1931    Field{2}.AY=Rangy;
1932    Field{2}.AX=Rangx;
1933    Field{2}.A=A;
1934    Field{2}.CoordType='px'; %used for mouse_motion
1935    Field{2}.CoordUnit='px'; %used for move_mou
1936end
1937
1938%read ncfile(s)
1939CivStage_1=0;%default
1940VelType_out_1=[];
1941InputField={FieldName};
1942InputField_1={FieldName_1};
1943if ~isfield(UvData,'Txt') && ((~isempty(filename)&~testima) || (~isempty(filename_1)&~testima_1)) ;
1944    %read the velocity field(s) from netcdf rootfile(s)
1945    list_code=get(handles.col_vec,'String');% list menu fields
1946    index_code=get(handles.col_vec,'Value');% selected string index
1947    scal_color= list_code{index_code(1)}; % selected field
1948    if isequal(FieldName,'velocity')&& ~isequal(scal_color,'black') && ~isequal(scal_color,'white')
1949        InputField=[InputField scal_color];
1950    end
1951    if isequal(FieldName_1,'velocity') && ~isequal(scal_color,'black') && ~isequal(scal_color,'white')
1952        InputField_1=[InputField_1 scal_color];
1953    end
1954    if ~testima  %read the first nc field
1955        if isequal(FieldName,'get_field...')% read the field names on the interface get_field.
1956            test_detect=0;%default
1957            VelType=get(handles.Fields,'UserData');
1958            hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI
1959            if isempty(hget_field)
1960                hget_field= get_field(filename);%open the get_field GUI   
1961            end
1962            test_detect=1;
1963            hhget_field=guidata(hget_field);
1964            set(hhget_field.inputfile,'String',filename)% update the list of input fields in get_field
1965            set(hhget_field.ACTION,'Value',1)% PLOT option selected
1966            set(hhget_field.list_fig,'Value',2)% plotting axes =uvmat selected
1967            [Field{1},errormsg]=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI
1968            if ~isempty(errormsg)
1969                msgbox_uvmat('ERROR',['error in uvmat/run0_Callback/read_get_field: ' errormsg])
1970                return
1971            end
1972            CivStage=0;
1973            VelType_out=[];         
1974        else
1975            [Field{1},VelType_out]=read_civxdata(filename,InputField,VelType);
1976            if isfield(Field{1},'Txt')
1977                msgbox_uvmat('ERROR',Field{1}.Txt)
1978                return
1979            end
1980            CivStage=Field{1}.CivStage;
1981            UvData.NbDim=Field{1}.nb_dim;
1982        end
1983    end
1984    if ~isempty(filename_1) && ~testima_1 %read the second file
1985        if isequal(FieldName_1,'get_field...')% read the field names on the interface get_field.
1986            test_detect=0;%default
1987            hget_field=findobj(allchild(0),'Name','get_field_1');%find the get_field... GUI
1988             if isempty(hget_field)
1989                 hget_field= get_field(filename_1);%open the get_field GUI
1990                 set(hget_field,'name','get_field_1')
1991%                 enable_transform(handles,'off')% no field transform (possible transform in the GUI get_field)
1992             end
1993            test_detect=1;
1994            hhget_field=guidata(hget_field);%handles of GUI elements in get_field
1995            SubField=get_field('read_var_names',hObject,eventdata,hhget_field); %read the names of the variables to plot in the get_field GUI
1996            [Field{2},var_detect]=nc2struct(filename_1,SubField.ListVarName); %read the corresponding input data               
1997            Field{2}.VarAttribute=SubField.VarAttribute;
1998            if isequal(get(hhget_field.menu_coord,'Visible'),'on')
1999                list_transform=get(hhget_field.menu_coord,'String');
2000                val_list=get(hhget_field.menu_coord,'Value');
2001                transf=list_transform{val_list};
2002                if ~isempty(transf)
2003                    Field{2}=feval(transf,Field{2});
2004                end
2005            end
2006
2007            %update the display on get_field
2008            set(hhget_field.inputfile,'String',filename_1)
2009            set(hhget_field.variables,'Value',1)
2010            Tabchar={''};%default
2011            Tabcell=[];
2012            if isfield(Field{2},'ListGlobalAttribute')& ~isempty(Field{2}.ListGlobalAttribute)
2013                for iline=1:length(Field{2}.ListGlobalAttribute)
2014                    Tabcell{iline,1}=Field{2}.ListGlobalAttribute{iline};
2015                    if isfield(Field{2}, Field{2}.ListGlobalAttribute{iline})
2016                        eval(['val=Field{2}.' Field{2}.ListGlobalAttribute{iline} ';'])
2017                        if ischar(val);
2018                            Tabcell{iline,2}=val;
2019                        else
2020                            Tabcell{iline,2}=num2str(val);
2021                        end
2022                    end
2023                end
2024                if ~isempty(Tabcell)
2025                    Tabchar=cell2tab(Tabcell,'=');
2026                    Tabchar=[{''};Tabchar];
2027                end
2028            end
2029            set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field
2030        else
2031            [Field{2},VelType_out_1]=read_civxdata(filename_1,[],VelType_1);
2032            CivStage_1=Field{2}.CivStage;
2033        end
2034        if testima
2035            VelType_out=VelType_out_1;
2036        end
2037    end
2038end
2039
2040%update the display buttons for the first velocity type (first menuline)
2041veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2042if testima
2043    reset_vel_type(veltype_handles)
2044elseif isempty(VelType)
2045    set_veltype_display(veltype_handles,CivStage)%update the display of available velocity types for the first field
2046    if isempty(VelType_out)
2047        reset_vel_type(veltype_handles)
2048    else
2049        handle1=eval(['handles.' VelType_out]);
2050        reset_vel_type(veltype_handles,handle1)
2051    end
2052end
2053
2054%update the display buttons for the second velocity type (second menuline)
2055veltype_handles_1=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
2056if testima_1
2057    reset_vel_type(veltype_handles_1)
2058elseif isempty(VelType_1)
2059    set_veltype_display(veltype_handles_1,CivStage_1)%update the display of available velocity types for the first field
2060    if isempty(VelType_out_1)
2061        reset_vel_type(veltype_handles_1)
2062    else
2063        handle1=eval(['handles.' VelType_out_1 '_1']);
2064        reset_vel_type(veltype_handles_1,handle1)
2065    end
2066end
2067
2068%introduce w as background image by default for a new series (only for nbdim=2)
2069if ~isfield(UvData,'NewSeries')
2070    UvData.NewSeries=1;
2071end
2072%put W as background image by default if NbDim=2:
2073if ~isfield(UvData,'NbDim')|isempty(UvData.NbDim)|~isequal(UvData.NbDim,3)
2074    if UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W);
2075        set(handles.SubField,'Value',1);
2076        menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w'
2077        set(handles.RootPath_1,'String','"')
2078        set(handles.RootFile_1,'String','"')
2079        set(handles.SubDir_1,'String','"');
2080        [indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,'');
2081        set(handles.FileIndex_1,'String',indices)
2082        set(handles.FileExt_1,'String','"');
2083        set(handles.Fields_1,'Visible','on');
2084        set(handles.Fields_1,'Visible','on');
2085        set(handles.RootPath_1,'Visible','on')
2086        set(handles.RootFile_1,'Visible','on')
2087        set(handles.SubDir_1,'Visible','on');
2088        set(handles.FileIndex_1,'Visible','on');
2089        set(handles.FileExt_1,'Visible','on');
2090        set(handles.Fields_1,'Visible','on');
2091        Field{1}.AName='w';
2092        testscal=1;
2093    end
2094end           
2095
2096%multislice case
2097if TestInputFile &&(~isfield(UvData,'NbDim') || isequal(UvData.NbDim,2))&&...%2D case
2098      isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')&& isfield(UvData.XmlData.GeometryCalib,'SliceCoord')
2099%     nbfield2=str2num(get(handles.last_j,'String'));
2100       siz=size(UvData.XmlData.GeometryCalib.SliceCoord);
2101       if siz(1)>1
2102           NbSlice=siz(1);
2103           set(handles.slices,'Visible','on')
2104           set(handles.slices,'Value',1)
2105       else
2106           NbSlice=1;
2107       end
2108       set(handles.nb_slice,'String',num2str(NbSlice))
2109       slices_Callback(hObject, eventdata, handles)
2110%        Coord=UvData.XmlData.GeometryCalib.SliceCoord;
2111%        ZIndex=num_i1-NbSlice*(floor((num_i1-1)/NbSlice));
2112%        Field{1}.Z=ZIndex;
2113end
2114
2115%store the current open names, fields and vel types in uvmat interface
2116UvData.filename=filename;
2117UvData.filename_1=filename_1;
2118UvData.VelType=VelType;
2119UvData.VelType_1=VelType_1;
2120UvData.FieldName=FieldName;
2121UvData.FieldName_1=FieldName_1;
2122if ~isempty(scal_color)
2123    UvData.CName=scal_color;
2124end
2125
2126%coordinate transform or user fct
2127XmlData=[];%default
2128if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2129    XmlData=UvData.XmlData;
2130end
2131XmlData_1=[];%default
2132if isfield(UvData,'XmlData_1')
2133   XmlData_1=UvData.XmlData_1;
2134end
2135menu_transform=get(handles.menu_coord,'String');
2136choice_value=get(handles.menu_coord,'Value');
2137transform=menu_transform{choice_value};%name of the transform fct  given by the menu 'menu_coord'
2138
2139% z index
2140if TestInputFile
2141    Field{1}.ZIndex=mod(num_i1-1,nbslice)+1;
2142end
2143%px to phys or other transform on field
2144if  ~isequal(transform,'')
2145    if length(Field)>=2
2146        Field{2}.ZIndex=mod(num_i1-1,nbslice)+1;
2147        [Field{1},Field{2}]=feval(transform,Field{1},XmlData,Field{2},XmlData_1);
2148        if isempty(Field{2})
2149            Field(2)=[];
2150        end
2151    else
2152        Field{1}=feval(transform,Field{1},XmlData);
2153    end
2154end
2155
2156%calculate scalar
2157if ~testima && ~isequal(FieldName,'get_field...')%
2158    Field{1}=calc_field(InputField,Field{1});
2159end
2160if length(Field)==2 && ~testima_1 && ~isequal(FieldName,'get_field...')
2161    Field{2}=calc_field(InputField_1,Field{2});
2162end
2163
2164% combine the two input fields (e.g. substract velocity fields)
2165if numel(Field)==2
2166    if ~(isequal(get(handles.movie_pair,'Value'),1) & isequal(FieldName,'image') & isequal(FieldName_1,'image')) %combine fields if not viewing image pairs
2167        UvData.Field=sub_field(Field{1},Field{2}); %TO UPDATE FOR MORE GENERAL INPUT
2168    end
2169else
2170   UvData.Field=Field{1};
2171end
2172UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2173% test 3D , default projection menuplane and typical mesh (needed to menuopen set_object)
2174test_x=0;
2175test_z=0;% test for unstructured z coordinate
2176UvData.ZMax=0;
2177UvData.ZMin=0;%default
2178UvData.Mesh=1; %default
2179[UvData.Field,errormsg]=check_field_structure(UvData.Field);
2180if ~isempty(errormsg)
2181    msgbox_uvmat('ERROR',['error in uvmat/run0_Callback/check_field_structure: ' errormsg])
2182    return
2183end
2184[CellVarIndex,NbDim,VarType]=find_field_indices(UvData.Field);
2185[NbDim,imax]=max(NbDim);
2186if isempty(imax)
2187   DimVarIndex=0;   
2188    coord_x=[];
2189else
2190    VarIndex=CellVarIndex{imax};
2191    coord_x=VarType{imax}.coord_x;
2192end
2193if isfield(UvData,'NbDim') & ~isempty(UvData.NbDim)
2194    NbDim=UvData.NbDim;
2195else 
2196    UvData.NbDim=NbDim;
2197end
2198if ~isempty(CellVarIndex) & ~isempty(VarType{imax}.coord_x)  & ~isempty(VarType{imax}.coord_y)    %unstructured coordinate z
2199    XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
2200    YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2201    test_x=1;
2202elseif isfield(UvData.Field,'X')&isfield(UvData.Field,'Y')
2203    XName='X';
2204    YName='Y';
2205    test_x=1;
2206end
2207if test_x
2208    eval(['UvData.XMax=max(UvData.Field.' XName ');'])
2209    eval(['UvData.XMin=min(UvData.Field.' XName ');'])
2210    eval(['UvData.YMax=max(UvData.Field.' YName ');'])
2211    eval(['UvData.YMin=min(UvData.Field.' YName ');'])
2212    eval(['nbvec=length(UvData.Field.' XName ');'])
2213    if NbDim==3%
2214        if ~isempty(CellVarIndex) & ~isempty(VarType{imax}.coord_z)%unstructured coordinate z
2215            ZName=UvData.ListVarName{VarType{imax}.coord_z};
2216            eval(['UvData.ZMax=max(UvData.Field.' ZName ');'])
2217            eval(['UvData.ZMin=min(UvData.Field.' ZName ');'])
2218            test_z=1;   
2219        elseif isfield(UvData,'Z')% usual civ data
2220            UvData.ZMax=max(UvData.Z);
2221            UvData.ZMin=min(UvData.Z);
2222            test_z=1;
2223        end
2224    end
2225    if isequal(UvData.ZMin,UvData.ZMax)%no z dependency
2226        NbDim=2;
2227        test_z=0;
2228    end   
2229    if test_z
2230         UvData.Mesh=((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)*(UvData.ZMax-UvData.ZMin))/nbvec;% volume per vector
2231         UvData.Mesh=(UvData.Mesh)^(1/3);
2232    else
2233        UvData.Mesh=sqrt((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)/nbvec);%2D
2234    end
2235end
2236%case of structured coordinates
2237if isfield(UvData.Field,'AX') & isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')
2238    UvData.XMax=max(UvData.Field.AX);
2239    UvData.XMin=min(UvData.Field.AX);
2240    UvData.YMax=max(UvData.Field.AY);
2241    UvData.YMin=min(UvData.Field.AY);
2242    np_A=size(UvData.Field.A);
2243    UvData.Mesh=sqrt((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)/((np_A(1)-1) * (np_A(2)-1))) ;
2244end
2245if  isempty(coord_x)&~isempty(CellVarIndex)
2246    VarIndex=CellVarIndex{imax}; % list of variable indices
2247    DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable
2248    if NbDim==3
2249        nbpoints=UvData.Field.DimValue(DimIndex(1));
2250        %Zvar=DimVarIndex(DimIndex(1));
2251         %Zvar=DimVarIndex(1);
2252         Zvar=VarType{imax}.coord_3;
2253        if Zvar~=0 % z is a dimension variable
2254            ZName=UvData.Field.ListVarName{Zvar};
2255            eval(['UvData.ZMax=max(UvData.Field.' ZName ');'])
2256            eval(['UvData.ZMin=min(UvData.Field.' ZName ');'])
2257        else
2258            testcoord_z=0;
2259            if length(UvData.Field.VarAttribute)>=VarIndex(1)
2260                if isfield(UvData.Field.VarAttribute{VarIndex(1)},'Coord_1')%regular grid
2261                    Coord_z=UvData.Field.VarAttribute{VarIndex(1)}.Coord_1;
2262                    UvData.ZMax=max(Coord_z);
2263                    UvData.ZMin=min(Coord_z);
2264                    testcoord_z=1;
2265                end
2266            end
2267            if ~testcoord_z
2268                  UvData.ZMin=1;
2269                  UvData.ZMax=UvData.Field.DimValue(DimIndex(1));
2270            end
2271        end
2272        UvData.Mesh=(UvData.ZMax-UvData.ZMin)/(nbpoints-1);
2273    elseif NbDim==2
2274        nbpoints_y=UvData.Field.DimValue(DimIndex(1));       
2275        Yvar=VarType{imax}.coord_y;
2276        if Yvar~=0  % x is a dimension variable
2277            YName=UvData.Field.ListVarName{Yvar};
2278            eval(['UvData.YMax=max(UvData.Field.' YName ');'])
2279            eval(['UvData.YMin=min(UvData.Field.' YName ');'])
2280        else
2281            testcoord_y=0;
2282            if ~testcoord_y
2283                  UvData.YMin=1;
2284                  UvData.YMax=UvData.Field.DimValue(DimIndex(1));
2285            end
2286        end
2287        DY=(UvData.YMax-UvData.YMin)/(nbpoints_y-1);
2288        nbpoints_x=UvData.Field.DimValue(DimIndex(2));
2289        Xvar=VarType{imax}.coord_x;
2290        if Xvar~=0  % x is a dimension variable
2291            XName=UvData.Field.ListVarName{Xvar};
2292            eval(['UvData.XMax=max(UvData.Field.' XName ');'])
2293            eval(['UvData.XMin=min(UvData.Field.' XName ');'])
2294        else
2295            testcoord_x=0;
2296            if ~testcoord_x
2297                  UvData.XMin=1;
2298                  UvData.XMax=UvData.Field.DimValue(DimIndex(2));
2299            end
2300        end
2301        DX=(UvData.XMax-UvData.XMin)/(nbpoints_x-1);
2302        UvData.Mesh= sqrt(DX*DY);
2303    end
2304end
2305
2306%create a default projection menuplane
2307UvData.Object{1}.Style='plane';%main plotting plane
2308UvData.Object{1}.ProjMode='projection';%main plotting plane
2309if ~isfield(UvData.Object{1},'plotaxes')
2310    UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis
2311    set(handles.list_object,'String',{'1-PLANE';'...'});
2312    set(handles.list_object,'Value',1);
2313end
2314
2315%3D case (menuvolume)
2316if NbDim==3
2317    UvData.Object{1}.NbDim=UvData.NbDim;%test for 3D objects
2318    UvData.Object{1}.RangeZ=UvData.Mesh;%main plotting plane
2319    UvData.Object{1}.Coord(1,3)=(UvData.ZMin+UvData.ZMax)/2;%section at a middle plane chosen
2320    UvData.Object{1}.Phi=0;
2321    UvData.Object{1}.Theta=0;
2322    UvData.Object{1}.Psi=0;
2323    UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR 
2324    PlotHandles=get_plot_handles(handles);
2325    ZBounds(1)=UvData.ZMin; %minimum for the Z slider
2326    ZBounds(2)=UvData.ZMax;%maximum for the Z slider
2327    set_object(UvData.Object{1},PlotHandles,ZBounds);
2328    set(handles.list_object,'Value',1);
2329%multilevel case (single menuplane in a 3D space)
2330elseif isfield(UvData,'Z')
2331    if isfield(UvData,'CoordType')& isequal(UvData.CoordType,'phys') & isfield(UvData,'XmlData')
2332        XmlData=UvData.XmlData;
2333        if isfield(XmlData,'PlanePos')
2334             UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2335        end
2336        if isfield(XmlData,'PlaneAngle')
2337            siz=size(XmlData.PlaneAngle);
2338            indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)             
2339            UvData.Object{1}.Phi=XmlData.PlaneAngle(indangle,1);
2340            UvData.Object{1}.Theta=XmlData.PlaneAngle(indangle,2);
2341            UvData.Object{1}.Psi=XmlData.PlaneAngle(indangle,3);
2342        end
2343    elseif isfield(UvData,'ZIndex')
2344        UvData.Object{1}.ZObject=UvData.ZIndex;
2345    end
2346end
2347
2348%Plot the projections on all existing  projection objects
2349keeplim=get(handles.FixedLimits,'Value');
2350%reset the min and max of scalar if only the mask is displayed
2351if isfield(UvData,'Mask')&~isfield(UvData,'A')
2352    set(handles.MinA,'String','0')
2353    set(handles.MaxA,'String','255')
2354end
2355
2356Object=UvData.Object;
2357for iobj=1:length(Object)
2358    if ~isempty(Object{iobj})%& isfield(Object{iobj},'plotaxes')& ishandle(Object{iobj}.plotaxes)
2359        %Projeter les champs sur l'objet:*
2360        ObjectData=proj_field(UvData.Field,Object{iobj},iobj);
2361   
2362        %use of mask
2363        if isfield(ObjectData,'NbDim')&isequal(ObjectData.NbDim,2)
2364            if isfield(ObjectData,'Mask') & isfield(ObjectData,'A')
2365                 flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2366                 AX=ObjectData.AX;
2367                 AY=ObjectData.AY;
2368                 MaskX=ObjectData.MaskX;
2369                 MaskY=ObjectData.MaskY;
2370                 if ~isequal(MaskX,AX)|~isequal(MaskY,AY)
2371                     nxy=size(flag_mask);
2372                     sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2373                     sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2374                     x_mask=[ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end)]; % pixel x coordinates for image display
2375                     y_mask=[ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end)];% pixel x coordinates for image display
2376                     %project on the positions of the scalar
2377                     npxy=size(ObjectData.A);
2378                     dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2379                     dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2380                     xi=[ObjectData.AX(1):dxy(2):ObjectData.AX(end)];
2381                     yi=[ObjectData.AY(1):dxy(1):ObjectData.AY(end)];     
2382                     [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2383                    flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2384                 end
2385                 AClass=class(ObjectData.A);
2386                 ObjectData.A=flag_mask.*double(ObjectData.A);
2387                 ObjectData.A=feval(AClass,ObjectData.A);
2388                 ind_off=[];
2389                 if isfield(ObjectData,'ListVarName')
2390                      for ilist=1:length(ObjectData.ListVarName)
2391                           if isequal(ObjectData.ListVarName{ilist},'Mask')|isequal(ObjectData.ListVarName{ilist},'MaskX')|isequal(ObjectData.ListVarName{ilist},'MaskY')
2392                               ind_off=[ind_off ilist];
2393                           end
2394                      end
2395                      ObjectData.ListVarName(ind_off)=[];
2396                      ObjectData.VarDimIndex(ind_off)=[];
2397                      ind_off=[];       
2398                      for ilist=1:length(ObjectData.ListDimName)       
2399                           if isequal(ObjectData.ListDimName{ilist},'MaskX')|isequal(ObjectData.ListDimName{ilist},'MaskY')
2400                               ind_off=[ind_off ilist];
2401                           end
2402                      end
2403                      ObjectData.ListDimName(ind_off)=[];
2404                      ObjectData.DimValue(ind_off)=[];
2405                 end
2406            end 
2407        end
2408        if ~isempty(ObjectData)
2409            haxes=[];%default
2410            if isfield(Object{iobj},'plotaxes')
2411                haxes=Object{iobj}.plotaxes;%axes used for representing the projection on the object
2412            end
2413            PosColorbar=[];%default: no colorbar
2414            if ishandle(haxes) & isequal(get(haxes,'Tag'),'axes3')& isfield(UvData,'PosColorbar')
2415                PosColorbar=UvData.PosColorbar;%prescribe the colorbar position on the uvmat interface
2416            else
2417                PosColorbar='*';%default position
2418            end
2419            PlotParam=read_plot_param(handles);%read plotting parameters on the uvmat interface
2420            [PlotType,ScalOut,UvData.Object{iobj}.plotaxes]=plot_field(ObjectData,haxes,PlotParam,keeplim,PosColorbar);
2421            if isequal(PlotType,'none')
2422                hget_field=findobj(allchild(0),'name','get_field');
2423                if isempty(hget_field)
2424                    get_field([],ObjectData)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2425                else
2426                    msgbox_uvmat('ERROR','The field defined by get_field cannot be plotted')
2427                end
2428            end 
2429            UvData.Object{iobj}.PlotParam=ScalOut; %record the plotting parameters
2430        end
2431       
2432    end
2433end
2434
2435%display the updated plotting parameters for the base menuplane
2436write_plot_param(handles,UvData.Object{1}.PlotParam);% update the display of the plotting parameters
2437set(huvmat,'UserData',UvData)
2438
2439%update the mask
2440if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
2441   update_mask(handles,num_i1,num_i2);
2442end
2443
2444%prepare the menus of histograms (for the whole menuvolume in 3D case)
2445menu_histo=(UvData.Field.ListVarName)';
2446ind_bad=[];
2447nb_histo=1;
2448for ivar=1:numel(menu_histo)
2449    if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2450        Role=UvData.Field.VarAttribute{ivar}.Role;
2451        switch Role
2452            case {'coord_x','coord_y','coord_z','dimvar'}
2453                ind_bad=[ind_bad ivar];
2454            case {'vector_y'}
2455                nb_histo=nb_histo+1;
2456        end
2457    end
2458    DimCell=UvData.Field.VarDimName{ivar};
2459    DimName='';
2460    if ischar(DimCell)
2461        DimName=DimCell;
2462    elseif iscell(DimCell)&& numel(DimCell)==1
2463        DimName=DimCell{1};
2464    end
2465    if strcmp(DimName,menu_histo{ivar})
2466        ind_bad=[ind_bad ivar];
2467    end
2468end
2469menu_histo(ind_bad)=[];
2470test_v=0;
2471if ~isempty(menu_histo)
2472    set(handles.histo1_menu,'Value',1)
2473    set(handles.histo1_menu,'String',menu_histo)
2474    histo1_menu_Callback(hObject, eventdata, handles)
2475    if nb_histo > 1
2476        test_v=1;
2477        set(handles.histo2_menu,'Visible','on')
2478        set(handles.histo_v,'Visible','on')
2479        set(handles.histo2_menu,'String',menu_histo)
2480        set(handles.histo2_menu,'Value',2)
2481        histo2_menu_Callback(hObject, eventdata, handles)
2482    end
2483end
2484if ~test_v
2485    set(handles.histo2_menu,'Visible','off')
2486    set(handles.histo_v,'Visible','off')
2487    cla(handles.histo_v)
2488    set(handles.histo2_menu,'Value',1)
2489end
2490
2491%display time
2492testimedoc=0;
2493if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'Time')
2494    if isempty(num_i2)
2495        num_i2=num_i1;
2496    end
2497    if isempty(num_j1)
2498        num_j1=1;
2499    end
2500    if isempty(num_j2)
2501        num_j2=num_j1;
2502    end
2503    siz=size(UvData.XmlData.Time);
2504    if siz(1)>=max(num_i1,num_i2) & siz(2)>=max(num_j1,num_j2)
2505        abstime=(UvData.XmlData.Time(num_i1,num_j1)+UvData.XmlData.Time(num_i2,num_j2))/2;%overset the time read from files
2506        dt=(UvData.XmlData.Time(num_i2,num_j2)-UvData.XmlData.Time(num_i1,num_j1));
2507        testimedoc=1;
2508    end
2509end
2510if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time')
2511    [P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2512    num_i2=str2num(str2);
2513    if isempty(num_i2)
2514        num_i2=num_i1;
2515    end
2516    num_j1=str2num(str_a);
2517    if isempty(num_j1)
2518        num_j1=1;
2519    end
2520    num_j2=str2num(str_b);
2521    if isempty(num_j2)
2522        num_j2=num_j1;
2523    end
2524    num_i1=str2num(str1);
2525    siz=size(UvData.XmlData_1.Time);
2526    if siz(1)>=max(num_i1,num_i2) & siz(2)>=max(num_j1,num_j2)
2527        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
2528    end
2529end
2530set(handles.abs_time,'String',num2str(abstime,4))
2531set(handles.abs_time_1,'String',num2str(abstime_1,4))
2532if testimedoc && isfield(UvData,'dt')
2533    dt=UvData.dt;
2534end
2535if isequal(dt,0)
2536    set(handles.Dt_txt,'String','')
2537else
2538    if ~(isfield(UvData,'TimeUnit') && ~isempty(UvData.TimeUnit))
2539        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2540    else
2541        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' UvData.TimeUnit] )
2542    end
2543end
2544set(handles.run0,'BackgroundColor',[1 0 0])
2545
2546
2547
2548%-------------------------------------------------------------------
2549% --- translate coordinate to matrix index
2550%-------------------------------------------------------------------
2551function [indx,indy]=pos2ind(x0,rangx0,nxy)
2552indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2553indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2554
2555%-------------------------------------------------------------------
2556% --- Executes on button press in 'FixedLimits'.
2557%-------------------------------------------------------------------
2558function FixedLimits_Callback(hObject, eventdata, handles)
2559test=get(handles.FixedLimits,'Value');
2560if test
2561    set(handles.FixedLimits,'BackgroundColor',[1 1 0])
2562else
2563    set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7])
2564end
2565
2566%-------------------------------------------------------------------
2567% --- Executes on button press in auto_xy.
2568function auto_xy_Callback(hObject, eventdata, handles)
2569test=get(handles.auto_xy,'Value');
2570if test
2571    set(handles.auto_xy,'BackgroundColor',[1 1 0])
2572    cla(handles.axes3)
2573    update_plot(handles)
2574else
2575    set(handles.auto_xy,'BackgroundColor',[0.7 0.7 0.7])
2576    update_plot(handles)
2577%     axis(handles.axes3,'image')
2578end
2579
2580
2581%-------------------------------------------------------------------
2582
2583%-------------------------------------------------------------------
2584% --- Executes on button press in 'zoom'.
2585%-------------------------------------------------------------------
2586function zoom_Callback(hObject, eventdata, handles)
2587huvmat=get(handles.zoom,'parent');%general input
2588UvData=get(huvmat,'UserData');
2589if (get(handles.zoom,'Value') == 1);
2590    set(handles.zoom,'BackgroundColor',[1 1 0])
2591    set(handles.FixedLimits,'Value',1)% propose by default fixed limits for the plotting axes
2592    set(handles.FixedLimits,'BackgroundColor',[1 1 0])
2593    %UvData.ZoomOn=1;   %test for mouse action   
2594else
2595    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
2596    %UvData.ZoomOn=0;  %test for mouse action
2597end
2598set(huvmat,'UserData',UvData);
2599
2600%-------------------------------------------------------------------
2601%----Executes on button press in 'record': records the current flags of manual correction.
2602%-------------------------------------------------------------------
2603function record_Callback(hObject, eventdata, handles)
2604% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2605filename=read_file_boxes(handles);
2606AxeData=get(gca,'UserData');
2607[erread,message]=fileattrib(filename);
2608if ~isempty(message) & ~isequal(message.UserWrite,1)
2609     msgbox_uvmat('ERROR',['no writting access to ' filename])
2610     return
2611end
2612nc=netcdf(filename,'write'); %open netcdf file
2613result=redef(nc);
2614if isempty(result), warndlg_uvmat('##Bad redef operation.','ERROR'),end
2615test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2616if ~test_civ2
2617    test_civ1=isequal(get(handles.civ1,'BackgroundColor'),[1 1 0]);
2618end
2619if test_civ2 % for civ2 
2620   
2621    theDim=nc('nb_vectors2') ;% get the number of velocity vectors
2622    nb_vectors2=size(theDim);
2623    var_FixFlag=ncvar('vec2_FixFlag',nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2624    var_FixFlag(1:nb_vectors2)=AxeData.FF;%
2625elseif test_civ1 % for civ1
2626   
2627    theDim=nc('nb_vectors') ;% get the number of velocity vectors
2628    nb_vectors=size(theDim);
2629     var_FixFlag=ncvar('vec_FixFlag',nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2630    var_FixFlag(1:nb_vectors)=AxeData.FF;%
2631else
2632    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2633end
2634fin=close(nc);
2635
2636
2637
2638%-------------------------------------------------------------------
2639%determines the fields to read from the interface
2640%------------------------------------------------------------------
2641function [VelType,civ]=setfield(handles)
2642
2643VelType=[]; %default
2644if (get(handles.civ1,'Value') == 1);
2645        VelType='civ1';
2646% interp1   
2647elseif (get(handles.interp1,'Value') == 1);
2648    VelType='interp1';
2649% filter1   
2650elseif (get(handles.filter1,'Value') == 1);
2651    VelType='filter1'; 
2652% CIV2
2653elseif (get(handles.civ2,'Value') == 1);
2654    VelType='civ2';
2655% interp2   
2656elseif (get(handles.interp2,'Value') == 1);
2657    VelType='interp2';
2658% filter2   
2659elseif (get(handles.filter2,'Value') == 1); 
2660    VelType='filter2';
2661end
2662
2663if isequal(get(handles.filter2,'Visible'),'on');
2664    civ=6;
2665% interp1   
2666elseif isequal(get(handles.interp2,'Visible'),'on');
2667    civ=5;
2668% filter1   
2669elseif isequal(get(handles.civ2,'Visible'),'on');
2670    civ=4; 
2671% CIV2
2672elseif isequal(get(handles.filter1,'Visible'),'on');
2673   civ=3;
2674% interp2   
2675elseif isequal(get(handles.interp1,'Visible'),'on');
2676    civ=2;
2677% filter2   
2678elseif isequal(get(handles.civ1,'Visible'),'on'); 
2679    civ=1;
2680else
2681    civ=0;
2682end
2683
2684%-------------------------------------------------------------------
2685%determines the veltype of the second field to read from the iinterface
2686%------------------------------------------------------------------
2687function VelType=setfield_1(handles)
2688
2689VelType=[]; %default
2690if (get(handles.civ1_1,'Value') == 1);
2691    VelType='civ1';
2692% interp1   
2693elseif (get(handles.interp1_1,'Value') == 1);
2694    VelType='interp1';
2695% filter1   
2696elseif (get(handles.filter1_1,'Value') == 1);
2697    VelType='filter1'; 
2698% CIV2
2699elseif (get(handles.civ2_1,'Value') == 1);
2700    VelType='civ2';
2701% interp2   
2702elseif (get(handles.interp2_1,'Value') == 1);
2703    VelType='interp2';
2704% filter2   
2705elseif (get(handles.filter2_1,'Value') == 1); 
2706    VelType='filter2';
2707end
2708
2709
2710%---------------------------------------------------
2711% --- Executes on button press in SubField
2712function SubField_Callback(hObject, eventdata, handles)
2713huvmat=get(handles.run0,'parent');
2714UvData=get(huvmat,'UserData');
2715if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2716    set(handles.RootPath_1,'String','')
2717    set(handles.RootFile_1,'String','')
2718    set(handles.SubDir_1,'String','');
2719    set(handles.FileIndex_1,'String','');
2720    set(handles.FileExt_1,'String','');
2721    set(handles.RootPath_1,'Visible','off')
2722    set(handles.RootFile_1,'Visible','off')
2723    set(handles.SubDir_1,'Visible','off');
2724    set(handles.FileIndex_1,'Visible','off');
2725    set(handles.FileExt_1,'Visible','off');
2726    set(handles.Fields_1,'Value',1);%set to blank state
2727    set_veltype_display([handles.civ1_1 handles.interp1_1 handles.filter1_1 ...
2728            handles.civ2_1 handles.interp2_1 handles.filter2_1],0)
2729    if isfield(UvData,'XmlData_1')
2730        UvData=rmfield(UvData,'XmlData_1');
2731    end
2732    set(huvmat,'UserData',UvData);
2733    run0_Callback(hObject, eventdata, handles); %run
2734else
2735    MenuBrowse_1_Callback(hObject, eventdata, handles)
2736end
2737
2738% %----------------------------------------------
2739% %read the data displayed for the input rootfile windows (new)
2740% %-------------------------------------------------
2741function [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles)
2742RootPath=get(handles.RootPath,'String');
2743FileName=RootPath; %default
2744SubDir=get(handles.SubDir,'String');
2745if ~isempty(SubDir) && ~isequal(SubDir,'')
2746    if (isequal(SubDir(1),'/')|| isequal(SubDir(1),'\'))
2747        SubDir(1)=[]; %suppress possible / or \ separator
2748    end
2749    FileName=fullfile(RootPath,SubDir);
2750end
2751RootFile=get(handles.RootFile,'String');
2752if ~isempty(RootFile) && ~isequal(RootFile,'')
2753    if (isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
2754        RootFile(1)=[]; %suppress possible / or \ separator
2755    end
2756    FileName=fullfile(FileName,RootFile);
2757end
2758FileBase=fullfile(RootPath,RootFile);
2759FileIndices=get(handles.FileIndex,'String');
2760FileExt=get(handles.FileExt,'String');
2761FileName=[FileName FileIndices FileExt];
2762
2763%----------------------------------------------
2764%read the data displayed for the second input rootfile windows
2765%-------------------------------------------------
2766function [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles)
2767RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
2768if isequal(RootPath_1,'"'),RootPath_1=get(handles.RootPath,'String'); end;
2769FileName_1=RootPath_1; %default
2770SubDir_1=get(handles.SubDir_1,'String');
2771if isequal(SubDir_1,'"')
2772    SubDir_1=get(handles.SubDir,'String');
2773end
2774if ~isempty(SubDir_1) && ~isequal(SubDir_1,'')
2775    if (isequal(SubDir_1(1),'/')|| isequal(SubDir_1(1),'\'))
2776        SubDir_1(1)=[]; %suppress possible / or \ separator
2777    end
2778    FileName_1=fullfile(RootPath_1,SubDir_1);
2779end
2780RootFile_1=get(handles.RootFile_1,'String');
2781if isequal(RootFile_1,'"'),RootFile_1=get(handles.RootFile,'String'); end;
2782if ~isempty(RootFile_1) && ~isequal(RootFile_1,'')
2783    if ~(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
2784        RootFile_1(1)=[];%suppress possible / or \ separator
2785    end
2786    FileName_1=fullfile(FileName_1,RootFile_1);
2787end
2788FileBase_1=fullfile(RootPath_1,RootFile_1);
2789FileIndices_1=get(handles.FileIndex_1,'String');
2790FileExt_1=get(handles.FileExt_1,'String');
2791if isequal(FileExt_1,'"'),FileExt_1=get(handles.FileExt,'String'); end;
2792FileName_1=[FileName_1 FileIndices_1 FileExt_1];
2793
2794%---------------------------------------------------
2795% --- Executes on menu selection Fields
2796function Fields_Callback(hObject, eventdata, handles)
2797%-------------------------------------------------
2798huvmat=get(handles.Fields,'parent');
2799list_fields=get(handles.Fields,'String');% list menu fields
2800index_fields=get(handles.Fields,'Value');% selected string index
2801field= list_fields{index_fields(1)}; % selected string
2802if isequal(field,'get_field...')
2803     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2804     set_veltype_display(veltype_handles,0) % unvisible civ buttons
2805     filename=read_file_boxes(handles);
2806     hget_field=findobj(allchild(0),'name','get_field');
2807     if ~isempty(hget_field)
2808         delete(hget_field)
2809     end
2810     get_field(filename)
2811    return %no action
2812end
2813list_fields=get(handles.Fields_1,'String');% list menu fields
2814index_fields=get(handles.Fields_1,'Value');% selected string index
2815field_1= list_fields{index_fields(1)}; % selected string
2816UvData=get(huvmat,'UserData');
2817
2818%read the rootfile input display
2819FileExt=get(handles.FileExt,'String');
2820[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt]);
2821NomTypeNew=NomType;%default
2822if isequal(field,'image')
2823    % transform netc type to the corresponding image type
2824    if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')|| isequal(NomType,'#_ab')|| isequal(NomType,'_i1-i2')
2825        UvData.SubDir=get(handles.SubDir,'String'); %preserve the subdir in memory
2826        if ~isempty(UvData.SubDir) && (isequal(UvData.SubDir(1),'/')|isequal(UvData.SubDir(1),'/'))
2827            UvData.SubDir(1)=[];
2828        end
2829        set(handles.SubDir,'String','')
2830        set(handles.FileExt,'String','.png');
2831        if isequal(NomType,'_i1-i2_j')|isequal(NomType,'_i_j1-j2')
2832            NomTypeNew='_i_j';
2833        elseif isequal(NomType,'#_ab')
2834            NomTypeNew='#a';
2835        elseif isequal(NomType,'_i1-i2')
2836            NomTypeNew='_i';
2837        end 
2838    end
2839    veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2840    set_veltype_display(veltype_handles,0) % unvisible civ buttons
2841else
2842    ext=get(handles.FileExt,'String');
2843    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
2844         MenuBrowse_Callback(hObject, eventdata, handles)
2845    end
2846    if isequal(field,'vort') || isequal(field,'div') || isequal(field,'strain')
2847        set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
2848        set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
2849        set(handles.interp1,'BackgroundColor',[0.702 0.702 0.702])
2850        set(handles.interp2,'BackgroundColor',[0.702 0.702 0.702])
2851    elseif isequal(field,'more...');
2852        set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
2853        set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702])
2854        str=calc_field;%get the list of available scalars by the function calc_scal
2855        [ind_answer,v] = listdlg('PromptString','Select a file:',...
2856                'SelectionMode','single',...
2857                'ListString',str);
2858       % edit the choice in the field and action menu
2859        scalar=cell2mat(str(ind_answer));
2860        menu=update_menu(handles.Fields,scalar);
2861        menu=[{''};menu];
2862        set(handles.Fields_1,'String',menu);% store the selected scalar type
2863    end
2864end
2865indices=name_generator('',str2num(str1),str2num(str_a),'',NomTypeNew,1,str2num(str2),str2num(str_b),'');
2866set(handles.FileIndex,'String',indices)
2867set(handles.FileIndex,'UserData',NomTypeNew)
2868%common to Fields_1_Callback
2869if isequal(field,'image')|isequal(field_1,'image')
2870    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
2871    set(handles.npy_title,'Visible','on')
2872    set(handles.npx,'Visible','on')
2873    set(handles.npy,'Visible','on')
2874    set(handles.fix_pair,'Value',0)
2875else
2876    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
2877    set(handles.npy_title,'Visible','off')
2878    set(handles.npx,'Visible','off')
2879    set(handles.npy,'Visible','off')
2880    set(handles.fix_pair,'Value',1)
2881end
2882if isequal(field,'velocity')|isequal(field_1,'velocity');
2883    state_vect='on';
2884else
2885    state_vect='off';
2886end
2887if ~isequal(field,'velocity')|(~isequal(field_1,'velocity'));
2888    state_scal='on';
2889else
2890    state_scal='off';
2891end
2892setfield(handles);% update the field structure ('civ1'....)
2893
2894if ~isfield(UvData,'NewSeries')|isequal(UvData.NewSeries,0)
2895    run0_Callback(hObject, eventdata, handles)
2896end
2897
2898%---------------------------------------------------
2899% --- Executes on menu selection Fields
2900function Fields_1_Callback(hObject, eventdata, handles)
2901%-------------------------------------------------
2902huvmat=get(handles.Fields_1,'parent');
2903list_fields=get(handles.Fields,'String');% list menu fields
2904index_fields=get(handles.Fields,'Value');% selected string index
2905field= list_fields{index_fields(1)}; % selected string
2906list_fields=get(handles.Fields_1,'String');% list menu fields
2907index_fields=get(handles.Fields_1,'Value');% selected string index
2908field_1= list_fields{index_fields(1)}; % selected string for the second field
2909if isequal(field_1,'') %remove second field if 'blank' field is selected
2910    set(handles.SubField,'Value',0)
2911    SubField_Callback(hObject, eventdata, handles)
2912    return
2913end
2914UvData=get(huvmat,'UserData');
2915
2916%read the rootfile input display
2917FileExt_prev=get(handles.FileExt_1,'String');
2918if isempty(FileExt_prev)|isequal(FileExt_prev,'')
2919    FileExt_1=get(handles.FileExt,'String');
2920else
2921    FileExt_1=FileExt_prev;
2922end
2923NomType_1=get(handles.FileIndex_1,'UserData');
2924if isempty(NomType_1)|isequal(NomType_1,'')
2925    NomType_1=get(handles.FileIndex,'UserData');
2926end
2927NomTypeNew=NomType_1;%default
2928
2929set(handles.SubField,'Value',1)%introduce second field
2930if isfield(UvData,'XmlData')
2931    UvData.XmlData_1=UvData.XmlData;
2932end
2933set(handles.FileIndex_1,'Visible','on')
2934set(handles.FileExt_1,'Visible','on')
2935RootPath_1=get(handles.RootPath_1,'String');
2936RootFile_1=get(handles.RootFile_1,'String');
2937if isempty(RootPath_1)|isequal(RootPath_1,'')
2938    set(handles.RootPath_1,'String','"')
2939end
2940if isempty(RootFile_1) | isequal(RootFile_1,'')
2941    set(handles.RootFile_1,'String','"')
2942end
2943if ~isempty(RootFile_1)&(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
2944    RootFile_1(1)=[];
2945end
2946
2947if isequal(field_1,'get_field...')
2948     veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2];
2949     set_veltype_display(veltype_handles,0) % unvisible civ buttons
2950     filename=read_file_boxes_1(handles);
2951     hget_field=findobj(allchild(0),'name','get_field_1');
2952     if ~isempty(hget_field)
2953         delete(hget_field)
2954     end
2955     hget_field=get_field(filename);
2956     set(hget_field,'name','get_field_1')
2957    return %no action
2958end
2959if isequal(field_1,'image')
2960    % transform netc type to the corresponding image type
2961    set(handles.FileExt_1,'String','.png');
2962    if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')| isequal(NomType_1,'#_ab')| isequal(NomType_1,'_i1-i2')
2963        UvData.SubDir_1=get(handles.SubDir_1,'String'); %preserve the subdir in memory
2964        set(handles.SubDir_1,'String','')
2965%         set(handles.FileExt_1,'String','.png');       
2966        if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')
2967            NomTypeNew='_i_j';
2968        elseif isequal(NomType_1,'#_ab')
2969            NomTypeNew='#a';
2970        elseif isequal(NomType_1,'_i1-i2')
2971            NomTypeNew='_i';
2972        end 
2973    end
2974    veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
2975    set_veltype_display(veltype_handles,0) % unvisible civ buttons
2976else
2977    set(handles.SubDir_1,'Visible','on')
2978    if ~isequal(FileExt_prev,'.nc') %find the new NomType if the previous display was not already a netcdf file
2979        veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1];
2980        set_veltype_display(veltype_handles,6); % make all civ buttons visible
2981        RootPath_1=get(handles.RootPath_1,'String');
2982        RootFile_1=get(handles.RootFile_1,'String');
2983        if isempty(RootPath_1)|isequal(RootPath_1,'')
2984            set(handles.RootPath_1,'String','"')
2985        end
2986        if isempty(RootFile_1) | isequal(RootFile_1,'')
2987            set(handles.RootFile_1,'String','"')
2988        end
2989        if ~isempty(RootFile_1)&(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\'))
2990            RootFile_1(1)=[];
2991        end
2992        filebase_1=fullfile(RootPath_1,RootFile_1);
2993        SubDir_1=get(handles.SubDir,'String');
2994        if isempty(SubDir_1)|isequal(SubDir_1,'')
2995            if isfield(UvData,'SubDir_1')
2996                SubDir_1=UvData.SubDir_1;%retrieve previous subdir
2997            else
2998                SubDir_1='?';
2999            end
3000        end
3001        if isequal(NomType_1,'#_ab')|isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')|isequal(NomType_1,'_i1-i2')
3002            NomTypeNew=NomType_1;
3003        elseif isequal(NomType_1,'#a')
3004             [filename,idetect,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1, str2num(str1),str2num(str_a),'.nc','#_ab',0,[],[],SubDir_1);
3005             NomTypeNew='#_ab';
3006        elseif isequal(NomType_1,'_i_j')
3007             [filename,idetect,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),str2num(str_a),'.nc','_i1-i2_j',0,str2num(str1),[],SubDir_1);
3008            if idetect==1
3009                NomTypeNew='_i1-i2_j';
3010            else
3011                NomTypeNew='_i_j1-j2';
3012            end
3013        else %for instance avi files or any ima_num series
3014            [filename,idetect,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),str2num(str_a),'.nc','_i1-i2',0,str2num(str1),[],SubDir_1);
3015            NomTypeNew='_i1-i2';
3016        end           
3017        [Path,Name]=fileparts(filebase_1);
3018        set(handles.FileExt_1,'String','.nc');
3019        if ~isempty(SubDir_1) & ~isequal(SubDir_1,'''')& ~isequal(SubDir_1,'"')
3020            SubDir_1=['/' SubDir_1];
3021        end
3022        set(handles.SubDir_1,'String',SubDir_1);
3023    end
3024    if isequal(field,'vort') | isequal(field,'div') | isequal(field,'strain')
3025        set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3026        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3027        set(handles.interp1_1,'BackgroundColor',[0.702 0.702 0.702])
3028        set(handles.interp2_1,'BackgroundColor',[0.702 0.702 0.702])
3029    elseif isequal(field_1,'more...'); %add new item to the menu
3030        set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey
3031        set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702])
3032        str=calc_field;%get the list of available scalars by the function calc_scal
3033        [ind_answer,v] = listdlg('PromptString','Select a file:',...
3034                'SelectionMode','single',...
3035                'ListString',str);
3036       % edit the choice in the field and action menu
3037        scalar=cell2mat(str(ind_answer));
3038        menu=update_menu(handles.Fields_1,scalar);
3039        set(handles.Fields_1,'String',menu);% store the selected scalar type
3040    end
3041end
3042str1=get(handles.i1,'String');
3043str2=get(handles.i2,'String');
3044str_a=get(handles.j1,'String');
3045str_b=get(handles.j2,'String');
3046indices=name_generator('',str2num(str1),stra2num(str_a),'',NomTypeNew,1,str2num(str2),stra2num(str_b),'');
3047set(handles.FileIndex_1,'String',indices)
3048set(handles.FileIndex_1,'UserData',NomTypeNew)
3049
3050%common to Fields_Callback
3051if isequal(field,'image')|isequal(field_1,'image')
3052    set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons
3053    set(handles.npy_title,'Visible','on')
3054    set(handles.npx,'Visible','on')
3055    set(handles.npy,'Visible','on')
3056    set(handles.fix_pair,'Value',0)
3057else
3058    set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons
3059    set(handles.npy_title,'Visible','off')
3060    set(handles.npx,'Visible','off')
3061    set(handles.npy,'Visible','off')
3062    set(handles.fix_pair,'Value',1)
3063end
3064if isequal(field,'velocity')|isequal(field_1,'velocity');
3065    state_vect='on';
3066else
3067    state_vect='off';
3068end
3069if ~isequal(field,'velocity')|(~isequal(field_1,'velocity')&~isequal(field_1,''));
3070    state_scal='on';
3071else
3072    state_scal='off';
3073end
3074set(huvmat,'UserData',UvData)
3075setfield(handles);% update the field structure ('civ1'....)
3076if ~isfield(UvData,'NewSeries')|isequal(UvData.NewSeries,0)
3077    run0_Callback(hObject, eventdata, handles)
3078end
3079
3080
3081%-----------------------------------
3082%set the visibility of relevant velocity type menus:
3083%-----------------------------------
3084%Civ=0; all states 'off'
3085%Civ=6; all states 'on'
3086function set_veltype_display(handles,Civ)
3087if isequal(Civ,0)
3088    imax=0;
3089%    set(handles(1),'Visible','on')  % unvisible civ buttons
3090% else
3091%    set(handles(1),'String','civ1')
3092% end
3093elseif isequal(Civ,1)
3094   imax=1;
3095elseif isequal(Civ,2) | isequal(Civ,3)
3096    imax=3;
3097elseif isequal(Civ,4) | isequal(Civ,5)
3098    imax=4;
3099elseif isequal(Civ,6)
3100    imax=6;
3101end
3102for ibutton=1:imax;
3103    set(handles(ibutton),'Visible','on')  % unvisible civ buttons
3104end
3105% for ibutton=max(imax+1,2):6;
3106for ibutton=imax+1:6;
3107    set(handles(ibutton),'Visible','off')  % unvisible civ buttons
3108    set(handles(ibutton),'Value',0)%unactivate unvisible buttons
3109end
3110
3111%-------------------------------------------------------------------
3112% --- Executes on button press in civ1.
3113function civ1_Callback(hObject, eventdata, handles)
3114%-------------------------------------------------------------------
3115if get(handles.civ1,'Value')==1
3116    reset_vel_type([handles.interp1 handles.civ2 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ1)
3117else
3118    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3119end
3120run0_Callback(hObject, eventdata, handles)
3121
3122%-------------------------------------------------------------------
3123% --- Executes on button press in interp1.
3124function interp1_Callback(hObject, eventdata, handles)
3125%-------------------------------------------------------------------
3126if get(handles.interp1,'Value')==1
3127    reset_vel_type([handles.civ1 handles.civ2 handles.filter1 handles.interp2 handles.filter2],handles.interp1)
3128else
3129     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3130end
3131run0_Callback(hObject, eventdata, handles)
3132
3133%-------------------------------------------------------------------
3134% --- Executes on button press in filter1.
3135function filter1_Callback(hObject, eventdata, handles)
3136%-------------------------------------------------------------------
3137if get(handles.filter1,'Value')==1
3138    reset_vel_type([handles.civ1 handles.civ2 handles.interp1 handles.interp2 handles.filter2],handles.filter1)
3139else
3140     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3141end
3142run0_Callback(hObject, eventdata, handles)
3143
3144%-------------------------------------------------------------------
3145% --- Executes on button press in civ2.
3146function civ2_Callback(hObject, eventdata, handles)
3147%-------------------------------------------------------------------
3148if get(handles.civ2,'Value')==1
3149    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ2)
3150else
3151     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3152end
3153run0_Callback(hObject, eventdata, handles)
3154
3155%-----------------------------------------
3156% --- Executes on button press in interp2.
3157%-------------------------------------------
3158function interp2_Callback(hObject, eventdata, handles)
3159if get(handles.interp2,'Value')==1
3160    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.filter2],handles.interp2)
3161else
3162     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3163end
3164run0_Callback(hObject, eventdata, handles)
3165%---------------------------------------------
3166% --- Executes on button press in filter2.
3167%-------------------------------------------
3168function filter2_Callback(hObject, eventdata, handles)
3169if get(handles.filter2,'Value')==1
3170    reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2],handles.filter2)
3171else
3172     reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2])
3173end
3174run0_Callback(hObject, eventdata, handles)
3175
3176%---------------------------------------------
3177function civ1_1_Callback(hObject, eventdata, handles)
3178%---------------------------------------------
3179if get(handles.civ1_1,'Value')==1
3180    reset_vel_type([handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.civ1_1)
3181else
3182     reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3183end
3184run0_Callback(hObject, eventdata, handles)
3185
3186%--------------------------------------------
3187function interp1_1_Callback(hObject, eventdata, handles)
3188%--------------------------------------------
3189if get(handles.interp1_1,'Value')==1
3190    reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.interp1_1)
3191else
3192    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3193end
3194run0_Callback(hObject, eventdata, handles)
3195
3196%--------------------------------------------
3197function filter1_1_Callback(hObject, eventdata, handles)
3198%--------------------------------------------
3199if get(handles.filter1_1,'Value')==1
3200    reset_vel_type([handles.interp1_1 handles.civ2_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.filter1_1)
3201else
3202    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3203end
3204run0_Callback(hObject, eventdata, handles)
3205
3206%--------------------------------------------
3207function civ2_1_Callback(hObject, eventdata, handles)
3208%--------------------------------------------
3209if get(handles.civ2_1,'Value')==1
3210    reset_vel_type([handles.civ1_1 handles.interp1_1  handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.civ2_1)
3211else
3212    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3213end
3214run0_Callback(hObject, eventdata, handles)
3215
3216%--------------------------------------------
3217function interp2_1_Callback(hObject, eventdata, handles)
3218%--------------------------------------------
3219if get(handles.interp2_1,'Value')==1
3220    reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.filter2_1],handles.interp2_1)
3221else
3222    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3223end
3224run0_Callback(hObject, eventdata, handles)
3225
3226%--------------------------------------------
3227function filter2_1_Callback(hObject, eventdata, handles)
3228%--------------------------------------------
3229if get(handles.filter2_1,'Value')==1
3230    reset_vel_type([handles.civ1_1 handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1],handles.filter2_1)
3231else
3232    reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1])
3233end
3234run0_Callback(hObject, eventdata, handles)
3235
3236%-----------------------------------------------
3237% --- reset civ buttons
3238function reset_vel_type(handles_civ0,handle1)
3239for ibutton=1:length(handles_civ0)
3240    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3241    set(handles_civ0(ibutton),'Value',0)
3242end
3243if exist('handle1','var')%handles of selected button
3244        set(handle1,'BackgroundColor',[1 1 0]) 
3245end
3246
3247%------------------------------------------------
3248function create_Callback(hObject,eventdata,handles)
3249%------------------------------------------------
3250if ishandle(handles.UVMAT_title)
3251    delete(handles.UVMAT_title)
3252end
3253huvmat=get(handles.create,'parent');
3254UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface (handles huvmat)
3255if isequal(get(handles.create,'Value'),1)
3256    set(handles.zoom,'Value',0)
3257    zoom_Callback(hObject, eventdata, handles)
3258     set(handles.create,'BackgroundColor',[1 1 0]) %visualise in yellow
3259    set(handles.edit_vect,'Value',0) 
3260    edit_vect_Callback(hObject, eventdata, handles)
3261    set(handles.edit,'Value',0)
3262    set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3263    list_object=get(handles.list_object,'String');
3264    if ~isempty(list_object)
3265        set(handles.list_object,'Value',length(list_object))
3266    end
3267    MouseAction='create_object';
3268    hset_object=findobj(allchild(0),'Name','set_object');
3269    uistack(hset_object,'top')
3270else
3271    set(handles.create,'BackgroundColor',[0 1 0])
3272    set(handles.edit,'Value',1)
3273    set(handles.edit,'BackgroundColor',[1 1 0])
3274    MouseAction='none';
3275end
3276
3277UvData.MouseAction=MouseAction;
3278set(huvmat,'UserData',UvData);
3279
3280%------------------------------------------------
3281function POINTS_Callback(hObject,eventdata,handles)
3282%------------------------------------------------
3283if ishandle(handles.UVMAT_title)
3284    delete(handles.UVMAT_title)
3285end
3286huvmat=get(handles.create,'parent');
3287UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface (handles huvmat)
3288if isequal(get(handles.create,'Value'),1)
3289    set(handles.zoom,'Value',0)
3290    zoom_Callback(hObject, eventdata, handles)
3291    set(handles.edit_vect,'Value',0) 
3292    edit_vect_Callback(hObject, eventdata, handles)
3293    set(handles.edit,'Value',0)
3294    set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3295    %set(handles.grid,'Value',0)
3296    %set(handles.grid,'BackgroundColor',[0 1 0])
3297    % initiate set_object GUI
3298     data.TITLE='POINTS';
3299    if isfield(UvData,'CoordType')
3300        data.CoordType=UvData.CoordType;
3301    end
3302    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3303        data.RangeY=UvData.Mesh;
3304    elseif isfield(UvData,'AX')&isfield(UvData,'AY')& isfield(UvData,'A')%only image
3305        np=size(UvData.Field.A);
3306        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3307        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3308        data.RangeY=max(meshx,meshy);
3309        data.DX=max(meshx,meshy);
3310    end
3311    data.Coord=[0 0 0]; %default
3312    data.ParentButton=handles.create;
3313    PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters
3314    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface
3315    if isfield(UvData,'SetObjectOrigin')
3316    pos_uvmat=get(huvmat,'Position');
3317    pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3318    pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
3319    set(hset_object,'Position',pos_set_object)
3320    end
3321    %set(hset_object,'Position',[pos_uvmat(1) pos_uvmat(2)-0.05*pos_uvmat(4) 0.2*pos_uvmat(3)  0.5*pos_uvmat(4)]);
3322    list_object=get(handles.list_object,'String');
3323    if ~isempty(list_object)
3324        set(handles.list_object,'Value',length(list_object))
3325    end
3326    MouseAction='create_object';
3327    %UvData.ZoomOn=0;
3328else
3329    set(handles.create,'BackgroundColor',[0 1 0])
3330    set(handles.edit,'Value',1)
3331    set(handles.edit,'BackgroundColor',[1 1 0])
3332    MouseAction='none';
3333end
3334
3335UvData.MouseAction=MouseAction;
3336set(huvmat,'UserData',UvData);
3337
3338%-----------------------------------------------------------
3339function LINE_Callback(hObject, eventdata, handles)
3340%-------------------------------------------------
3341if ishandle(handles.UVMAT_title)
3342    delete(handles.UVMAT_title)
3343end
3344huvmat=get(handles.create,'parent');
3345UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3346% if (get(handles.LINE,'Value')==1)
3347    %suppress the other options if MENULINE is chosen
3348    set(handles.zoom,'Value',0)
3349    zoom_Callback(hObject, eventdata, handles)
3350%     set(handles.create,'Value',0)
3351%     set(handles.create,'BackgroundColor',[0 1 0])
3352%     set(handles.LINE,'Value',1)
3353%     set(handles.LINE,'BackgroundColor',[1 1 0])
3354%     set(handles.PATCH,'Value',0)
3355%     set(handles.PATCH,'BackgroundColor',[0 1 0])
3356%     set(handles.PLANE,'Value',0)
3357%     set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow
3358%     set(handles.VOLUME,'Value',0)
3359%     set(handles.VOLUME,'BackgroundColor',[0 1 0])
3360    %et(handles.makemask,'Value',0)
3361    %makemask_Callback(hObject, eventdata, handles)
3362    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3363    set(handles.edit_vect,'Value',0)
3364    edit_vect_Callback(hObject, eventdata, handles)
3365    set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3366    set(handles.edit,'Value',0)
3367    set(handles.list_object,'Value',1);
3368    edit_vect_Callback(hObject, eventdata, handles)
3369    set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3370    set(handles.cal,'Value',0)
3371    set(handles.cal,'BackgroundColor',[0 1 0])
3372   % set(handles.grid,'Value',0)
3373   % set(handles.grid,'BackgroundColor',[0 1 0])
3374%  initiate the set_object GUI
3375    data.TITLE='LINE';
3376    if isfield(UvData,'CoordType')
3377        data.CoordType=UvData.CoordType;
3378    end
3379    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3380        data.RangeX=UvData.Mesh;
3381        data.RangeY=UvData.Mesh;
3382%         data.YMax=UvData.Mesh;
3383%         data.XMax=UvData.Mesh;
3384        data.DX=UvData.Mesh;
3385        data.DY=UvData.Mesh;
3386    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3387        np=size(UvData.Field.A);
3388        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3389        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3390        data.RangeY=max(meshx,meshy);
3391        data.RangeX=max(meshx,meshy);
3392%         data.YMax=max(meshx,meshy);
3393%         data.XMax=max(meshx,meshy);
3394        data.DX=max(meshx,meshy);
3395    end
3396    if isfield(data,'DX')
3397        data.Coord=[[0 0 0];[data.DX 0 0]]; %default
3398    else
3399        data.Coord=[[0 0 0];[1 0 0]]; %default
3400    end
3401    data.ParentButton=handles.create;
3402    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3403    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3404                                                      % associate the set_edit interface handle to the plotting axes
3405    pos_uvmat=get(huvmat,'Position');
3406    if isfield(UvData,'SetObjectOrigin')
3407        pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3408        pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); 
3409        set(hset_object,'Position',pos_set_object)
3410    end
3411    list_object=get(handles.list_object,'String');
3412    if ~isempty(list_object)
3413        set(handles.list_object,'Value',length(list_object))
3414    end
3415     MouseAction='create_object';
3416% else
3417%     set(handles.LINE,'BackgroundColor',[0 1 0])
3418%      MouseAction='none';
3419% end
3420
3421UvData.MouseAction=MouseAction;
3422set(huvmat,'UserData',UvData)
3423
3424%-----------------------------------------------------------
3425function PATCH_Callback(hObject, eventdata, handles)
3426%-----------------------------------------------------------
3427if ishandle(handles.UVMAT_title)
3428    delete(handles.UVMAT_title)
3429end
3430huvmat=get(handles.create,'parent');
3431UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3432% if isequal(get(handles.PATCH,'Value'),1)
3433    set(handles.zoom,'Value',0)
3434    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3435%     set(handles.create,'Value',0)%suppress the other options if LINE is chosen
3436%     set(handles.create,'BackgroundColor',[0 1 0])
3437%     set(handles.LINE,'Value',0)
3438%     set(handles.LINE,'BackgroundColor',[0 1 0])
3439%     set(handles.PATCH,'Value',1)
3440%     set(handles.PATCH,'BackgroundColor',[1 1 0])
3441%     set(handles.PLANE,'Value',0)
3442%     set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow
3443%     set(handles.VOLUME,'Value',0)
3444%     set(handles.VOLUME,'BackgroundColor',[0 1 0])
3445    %set(handles.makemask,'Value',0)
3446    %makemask_Callback(hObject, eventdata, handles)
3447    set(handles.edit_vect,'Value',0)
3448    edit_vect_Callback(hObject, eventdata, handles)
3449    set(handles.edit,'Value',0)
3450    set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3451    set(handles.edit_vect,'Value',0) 
3452    edit_vect_Callback(hObject, eventdata, handles)
3453    set(handles.cal,'Value',0)
3454    set(handles.cal,'BackgroundColor',[0 1 0])
3455    %set(handles.grid,'Value',0)
3456    %set(handles.grid,'BackgroundColor',[0 1 0])
3457    %initiate set_object GUI
3458    data.TITLE='PATCH';
3459    if isfield(UvData,'CoordType')
3460        data.CoordType=UvData.CoordType;
3461    end
3462    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3463        data.YMax=UvData.Mesh;
3464    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3465        np=size(UvData.Field.A);
3466        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1);
3467        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1);
3468        data.YMax=max(meshx,meshy);
3469        data.DX=max(meshx,meshy);
3470    end
3471    data.Coord=[0 0 0]; %default
3472    data.ParentButton=handles.create;
3473    PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters
3474    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface
3475    pos_uvmat=get(huvmat,'Position');
3476    if isfield(UvData,'SetObjectOrigin')
3477        pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3478        pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
3479        set(hset_object,'Position',pos_set_object)
3480    end
3481    list_object=get(handles.list_object,'String');
3482    if ~isempty(list_object)
3483        set(handles.list_object,'Value',length(list_object))
3484    end
3485    UvData.MouseAction='create_object';
3486    set(huvmat,'UserData',UvData);
3487%-------------------------------------------------------
3488function PLANE_Callback(hObject, eventdata, handles)
3489%-------------------------------------------------------
3490if ishandle(handles.UVMAT_title)
3491    delete(handles.UVMAT_title)
3492end
3493huvmat=get(handles.create,'parent');
3494UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3495set(handles.zoom,'Value',0)
3496set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3497set(handles.edit_vect,'Value',0)
3498edit_vect_Callback(hObject, eventdata, handles)
3499set(handles.edit,'Value',0)
3500set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3501set(handles.cal,'Value',0)
3502set(handles.cal,'BackgroundColor',[0 1 0])
3503%set(handles.grid,'Value',0)
3504%set(handles.grid,'BackgroundColor',[0 1 0])
3505%initiate set_object GUI
3506data.TITLE='PLANE';
3507if isfield(UvData,'CoordType')
3508    data.CoordType=UvData.CoordType;
3509end
3510%Si 3D data.nbdim=3;
3511%Si 2D
3512if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3513    data.ZMax=UvData.Mesh;
3514    data.DX=UvData.Mesh;
3515    data.DY=UvData.Mesh;
3516elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3517    np=size(UvData.Field.A);
3518    meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1);
3519    meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1);
3520    data.DX=max(meshx,meshy);
3521end
3522if isfield(UvData,'DX')
3523    data.DX=UvData.DX;
3524end
3525if isfield(UvData,'DY')
3526    data.DY=UvData.DY;
3527elseif isfield(UvData,'Mesh')
3528    data.DY=UvData.Mesh;
3529end
3530if isfield(UvData.Field,'X')& isfield(UvData.Field,'Y')
3531    data.Coord=[0 0 0];
3532    data.Style='plane';
3533    data.Phi=0;
3534    data.IndexObj=1; %act on the first reference plane by default
3535    haxes= handles.axes3;%GENERALISER
3536    plot_object(data,[],haxes,'m'); %plot the axes of the default plane 
3537end
3538data.ParentButton=handles.create;
3539PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters
3540ZBounds=0; % default
3541if isfield(UvData,'ZMin') && isfield(UvData,'ZMax')
3542    ZBounds(1)=UvData.ZMin; %minimum for the Z slider
3543    ZBounds(2)=UvData.ZMax;%maximum for the Z slider
3544end
3545[hset_object,UvData.sethandles]=set_object(data,PlotHandles,ZBounds);% call the set_object interface with action on haxes,
3546if isfield(UvData,'SetObjectOrigin')
3547pos_uvmat=get(huvmat,'Position');
3548pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3549pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); 
3550set(hset_object,'Position',pos_set_object)
3551end
3552list_object=get(handles.list_object,'String');
3553nbobject=length(list_object);
3554set(handles.list_object,'Value',nbobject)
3555UvData.MouseAction='create_object';
3556set(huvmat,'UserData',UvData)
3557
3558%-------------------------------------------------------
3559% --- Executes on button press in MENUVOLUME.
3560%-------------------------------------------------------
3561function VOLUME_Callback(hObject, eventdata, handles)
3562%errordlg('command VOL not implemented yet')
3563if ishandle(handles.UVMAT_title)
3564    delete(handles.UVMAT_title)
3565end
3566huvmat=get(handles.create,'parent');
3567UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3568if isequal(get(handles.VOLUME,'Value'),1)
3569    set(handles.zoom,'Value',0)
3570    set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3571    set(handles.edit_vect,'Value',0)
3572    edit_vect_Callback(hObject, eventdata, handles)
3573    set(handles.edit,'Value',0)
3574    set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3575    set(handles.cal,'Value',0)
3576    set(handles.cal,'BackgroundColor',[0 1 0])
3577    set(handles.edit_vect,'Value',0)
3578    edit_vect_Callback(hObject, eventdata, handles)
3579    %initiate set_object GUI
3580    data.TITLE='VOLUME';
3581    if isfield(UvData,'CoordType')
3582        data.CoordType=UvData.CoordType;
3583    end
3584    if isfield(UvData,'Mesh')&~isempty(UvData.Mesh)
3585        data.RangeY=UvData.Mesh;
3586        data.RangeX=UvData.Mesh;
3587        data.DX=UvData.Mesh;
3588        data.DY=UvData.Mesh;
3589    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3590        np=size(UvData.Field.A);
3591        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3592        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3593        data.RangeY=max(meshx,meshy);
3594        data.RangeX=max(meshx,meshy);
3595        data.DX=max(meshx,meshy);
3596    end
3597    data.ParentButton=handles.VOLUME;
3598    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3599    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3600                                                      % associate the set_edit interface handle to the plotting axes
3601    if isfield(UvData,'SetObjectOrigin')                                               
3602    pos_uvmat=get(huvmat,'Position');
3603    pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
3604    pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); 
3605    set(hset_object,'Position',pos_set_object)
3606    end
3607    UvData.MouseAction='create_object';
3608else
3609    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3610    UvData.MouseAction='none';
3611end
3612set(huvmat,'UserData',UvData)
3613
3614%-------------------------------------------------------
3615function edit_vect_Callback(hObject, eventdata, handles)
3616%-------------------------------------------------------
3617huvmat=get(handles.edit_vect,'parent');
3618UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3619if isequal(get(handles.edit_vect,'Value'),1)
3620    set(handles.record,'Visible','on')
3621    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3622    set(handles.edit,'Value',0)
3623    set(handles.create,'Value',0)
3624    set(handles.create,'BackgroundColor',[0 1 0])
3625    set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3626    set(gcf,'Pointer','arrow')
3627    UvData.MouseAction='edit_vect';
3628else
3629    set(handles.record,'Visible','off')
3630    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3631    UvData.MouseAction='none';
3632end
3633set(huvmat,'UserData',UvData)
3634
3635%----------------------------------------------
3636function save_mask_Callback(hObject, eventdata, handles)
3637%-----------------------------------------------------------------------
3638huvmat=get(handles.save_mask,'parent');
3639UvData=get(huvmat,'UserData');
3640
3641hpatch=findobj(huvmat,'Type','patch');
3642flag=1;
3643npx=size(UvData.Field.A,2);
3644npy=size(UvData.Field.A,1);
3645xi=[0.5:npx-0.5];
3646yi=[0.5:npy-0.5];
3647[Xi,Yi]=meshgrid(xi,yi);
3648if isfield(UvData,'Object')
3649    for iobj=1:length(UvData.Object)
3650        ObjectData=UvData.Object{iobj};
3651        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3652            flagobj=1;
3653            testphys=0; %coordinates in pixels by default
3654            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3655                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib')
3656                    Calib=UvData.XmlData.GeometryCalib;
3657                    testphys=1;
3658                end
3659            end
3660            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3661                if isequal(ObjectData.Style,'polygon')
3662                    X=ObjectData.Coord(:,1);
3663                    Y=ObjectData.Coord(:,2);
3664                    if testphys
3665                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3666                    end
3667                    flagobj=~inpolygon(Xi,Yi,X,Y);%=0 inside the polygon, 1 outside                 
3668                elseif isequal(ObjectData.Style,'ellipse')
3669                    if testphys
3670                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3671                    end
3672                    RangeX=max(ObjectData.RangeX);
3673                    RangeY=max(ObjectData.RangeY);
3674                    X2Max=RangeX*RangeX;
3675                    Y2Max=RangeY*RangeY;
3676                    distX=(Xi-ObjectData.Coord(1,1));
3677                    distY=(Yi-ObjectData.Coord(1,2));
3678                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3679                elseif isequal(ObjectData.Style,'rectangle')
3680                    if testphys
3681                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3682                    end
3683                    distX=abs(Xi-ObjectData.Coord(1,1));
3684                    distY=abs(Yi-ObjectData.Coord(1,2));
3685                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3686                end
3687                if isequal(ObjectData.ProjMode,'mask_outside')
3688                    flagobj=~flagobj;
3689                end
3690                flag=flag & flagobj;
3691            end
3692        end
3693    end
3694end
3695% flag=~flag;
3696%mask name
3697RootPath=get(handles.RootPath,'String');
3698RootFile=get(handles.RootFile,'String');
3699if ~isempty(RootFile)&(isequal(RootFile(1),'/')| isequal(RootFile(1),'\'))
3700        RootFile(1)=[];
3701end
3702filebase=fullfile(RootPath,RootFile);
3703list=get(handles.masklevel,'String');
3704masknumber=num2str(length(list));
3705maskindex=get(handles.masklevel,'Value');
3706mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3707imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3708imflag=flipdim(imflag,1);
3709% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3710warndlg_uvmat([mask_name ' saved'],'CONFIRMATION')
3711imwrite(imflag,mask_name,'BitDepth',8);
3712
3713%display the mask
3714%update_mask(handles,num_i1,num_j1)
3715figure;
3716vec=linspace(0,1,256);%define a linear greyscale colormap
3717map=[vec' vec' vec'];
3718colormap(map)
3719
3720image(imflag);
3721
3722%-------------------------------------------------------------------
3723%-------------------------------------------------------------------
3724%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3725
3726%------------------------------------------------------------------
3727
3728
3729
3730%------------------------------------------------------------------
3731% --- Executes on selection change in col_vec: choice of the color code.
3732%
3733function col_vec_Callback(hObject, eventdata, handles)
3734%------------------------------------------------------------------
3735% edit the choice for color code
3736list_code=get(handles.col_vec,'String');% list menu fields
3737index_code=get(handles.col_vec,'Value');% selected string index
3738col_code= list_code{index_code(1)}; % selected field
3739if isequal(col_code,'black') | isequal(col_code,'white')
3740   set(handles.slider1,'Visible','off')
3741   set(handles.slider2,'Visible','off')
3742   set(handles.colcode1,'Visible','off')
3743   set(handles.colcode2,'Visible','off')
3744   set(handles.AutoVecColor,'Visible','off')
3745   set_vec_col_bar(handles)
3746else
3747   set(handles.slider1,'Visible','on')
3748   set(handles.slider2,'Visible','on')
3749   set(handles.colcode1,'Visible','on')
3750   set(handles.colcode2,'Visible','on')
3751   set(handles.AutoVecColor,'Visible','on') 
3752   if isequal(col_code,'ima_cor')
3753       set(handles.AutoVecColor,'Value',0)%fixed scale by default
3754       set(handles.vec_col_bar,'Value',0)% 3 colors r,g,b by default
3755       set(handles.slider1,'Min',0);
3756       set(handles.slider1,'Max',1);
3757       set(handles.slider2,'Min',0);
3758       set(handles.slider2,'Max',1);
3759 %      set(handles.min_title_vec,'String','0')
3760       set(handles.max_vec,'String','1')
3761       set(handles.colcode1,'String','0.333')
3762       colcode1_Callback(hObject, eventdata, handles)
3763       set(handles.colcode2,'String','0.666')
3764       colcode2_Callback(hObject, eventdata, handles)
3765   else
3766       set(handles.AutoVecColor,'Value',1)%auto scale between min,max by default
3767       set(handles.vec_col_bar,'Value',1)% colormap 'jet' by default
3768       minval=get(handles.slider1,'Min');
3769       maxval=get(handles.slider1,'Max');
3770       set(handles.slider1,'Value',minval)
3771       set(handles.slider2,'Value',maxval)
3772       set_vec_col_bar(handles)
3773   end
3774%    slider_update(handles)
3775end
3776%replot the current graph
3777run0_Callback(hObject, eventdata, handles)
3778
3779
3780%----------------------------------------------------------------
3781% -- Executes on slider movement to set the color code
3782%
3783function slider1_Callback(hObject, eventdata, handles)
3784%------------------------------------------------------------------
3785slider1=get(handles.slider1,'Value');
3786min_val=str2num(get(handles.min_vec,'String'));
3787max_val=str2num(get(handles.max_vec,'String'));
3788col=min_val+(max_val-min_val)*slider1;
3789set(handles.colcode1,'String',num2str(col))
3790if(get(handles.slider2,'Value') < col)%move also the second slider at the same value if needed
3791    set(handles.slider2,'Value',col)
3792    set(handles.colcode2,'String',num2str(col))
3793end
3794colcode1_Callback(hObject, eventdata, handles)
3795
3796%----------------------------------------------------------------
3797% Executes on slider movement to set the color code
3798%----------------------------------------------------------------
3799function slider2_Callback(hObject, eventdata, handles)
3800slider2=get(handles.slider2,'Value');
3801min_val=str2num(get(handles.min_vec,'String'));
3802max_val=str2num(get(handles.max_vec,'String'));
3803col=min_val+(max_val-min_val)*slider2;
3804set(handles.colcode2,'String',num2str(col))
3805if(get(handles.slider1,'Value') > col)%move also the first slider at the same value if needed
3806    set(handles.slider1,'Value',col)
3807    set(handles.colcode1,'String',num2str(col))
3808end
3809colcode2_Callback(hObject, eventdata, handles)
3810
3811%----------------------------------------------------------------
3812%execute on return carriage on the edit box corresponding to slider 1
3813%----------------------------------------------------------------
3814function colcode1_Callback(hObject, eventdata, handles)
3815% col=str2num(get(handles.colcode1,'String'));
3816% set(handles.slider1,'Value',col)
3817set_vec_col_bar(handles)
3818update_plot(handles)
3819
3820%----------------------------------------------------------------
3821%execute on return carriage on the edit box corresponding to slider 2
3822%----------------------------------------------------------------
3823function colcode2_Callback(hObject, eventdata, handles)
3824% col=str2num(get(handles.colcode2,'String'));
3825% set(handles.slider2,'Value',col)
3826% slider2_Callback(hObject, eventdata, handles)
3827set_vec_col_bar(handles)
3828update_plot(handles)
3829%------------------------------------------------------------
3830%update the slider values after displaying vectors
3831%--------------------------------------------------------
3832% function slider_update(handles,auto,minC,colcode1,colcode2,maxC)
3833% set(handles.slider1,'Min',minC)
3834% set(handles.slider1,'Max',maxC)
3835% set(handles.slider2,'Min',minC)
3836% set(handles.slider2,'Max',maxC)
3837% set(handles.min_title_vec,'String',num2str(minC))
3838% set(handles.max_vec,'String',num2str(maxC))
3839% if auto
3840%         set(handles.colcode1,'String',num2str(colcode1,3))%update display
3841%         set(handles.colcode2,'String',num2str(colcode2,3))
3842% end
3843% set(handles.slider1,'Value',colcode1)%update slider with constant display
3844% set(handles.slider2,'Value',colcode2)
3845% set_vec_col_bar(handles)
3846
3847
3848%-------------------------------------------------------
3849% --- Executes on button press in AutoVecColor.
3850%-------------------------------------------------------
3851function vec_col_bar_Callback(hObject, eventdata, handles)
3852set_vec_col_bar(handles)
3853
3854% %--------------------------------------------
3855% %update the display of color code for vectors
3856% %--------------------------------------------
3857% function set_vec_col_bar(handles)
3858% %get the image of the color display button 'vec_col_bar' in pixels
3859% uni=get(handles.vec_col_bar,'Unit');
3860% set(handles.vec_col_bar,'Unit','pixel')
3861% pos_vert=get(handles.vec_col_bar,'Position');
3862% set(handles.vec_col_bar,'Unit','Normalized')
3863% width=ceil(pos_vert(3));
3864% height=ceil(pos_vert(4));
3865% %get slider indications
3866% colcode.min=get(handles.slider1,'Min');
3867% colcode.max=get(handles.slider1,'Max');
3868% colcode.colcode1=get(handles.slider1,'Value');
3869% colcode.colcode2=get(handles.slider2,'Value');
3870% colcode.option=get(handles.vec_col_bar,'Value');
3871% colcode.auto=1;
3872% list_code=get(handles.col_vec,'String');% list menu fields
3873% index_code=get(handles.col_vec,'Value');% selected string index
3874% colcode.CName= list_code{index_code(1)}; % selected field used for vector color
3875% vec_C=colcode.min+(colcode.max-colcode.min)*[0.5:width-0.5]/width;%sample of vec_C values from min to max
3876% [colorlist,col_vec]=set_col_vec(colcode,vec_C);
3877% oneheight=ones(1,height);
3878% A1=colorlist(col_vec,1)*oneheight;
3879% A2=colorlist(col_vec,2)*oneheight;
3880% A3=colorlist(col_vec,3)*oneheight;
3881% A(:,:,1)=A1';
3882% A(:,:,2)=A2';
3883% A(:,:,3)=A3';
3884% set(handles.vec_col_bar,'Cdata',A)
3885
3886%--------------------------------------------------------
3887% --- Executes on button press in cal.
3888function cal_Callback(hObject, eventdata, handles)
3889
3890huvmat=get(handles.cal,'parent');%handles of the uvmat interface
3891UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
3892%reinitialize the edit interface associated with uvmat
3893value=get(handles.cal,'Value');
3894if value
3895        set(handles.cal,'BackgroundColor',[1 1 0])
3896        %suppress the other options if MENULINE is chosen
3897        set(handles.zoom,'Value',0)
3898        set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
3899        set(handles.create,'Value',0)
3900        set(handles.create,'BackgroundColor',[0 1 0])
3901        set(handles.create,'enable','off')     
3902        set(handles.edit_vect,'Value',0)
3903        set(handles.edit_vect,'enable','off')
3904        edit_vect_Callback(hObject, eventdata, handles)
3905        set(handles.edit,'Value',0)
3906        set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
3907        set(handles.edit,'enable','off')
3908        set(handles.list_object,'Value',1)     
3909        % initiate display of GUI geometry_calib
3910        data=[]; %default
3911                if isfield(UvData,'CoordType')
3912            data.CoordType=UvData.CoordType;
3913        end
3914        %data.ParentButton=handles.cal; % transmit the handles of the calling button to the GUI geometry_calib
3915                pos=get(huvmat,'Position');
3916                pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
3917                pos(2)=pos(2)-0.02;
3918        [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles);
3919%         [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
3920%         [inputfile,idetect]=name_generator(filebase,num_i1,num_j1,Ext,NomType,1,num_i2,num_j2,SubDir);
3921                [UvData.hset_object,UvData.sethandles]=geometry_calib(handles,pos,FileName);% call the set_object interface     
3922        pos_uvmat=get(huvmat,'Position');
3923        %pos_cal(1:2)=UvData.CalOrigin + pos_uvmat(1:2);
3924        if isfield(UvData,'CalOrigin')
3925            pos_cal(1)=pos_uvmat(1)+UvData.CalOrigin(1)*pos_uvmat(3);
3926            pos_cal(2)=pos_uvmat(2)+UvData.CalOrigin(2)*pos_uvmat(4);
3927            pos_cal(3:4)=UvData.CalSize .* pos_uvmat(3:4);
3928            set(UvData.hset_object,'Position',pos_cal)
3929        end
3930        UvData.MouseAction='calib';
3931else
3932     UvData.MouseAction='none';     
3933     hgeometry_calib=findobj(allchild(0),'Name','geometry_calib');
3934%      if ~isempty(hgeometry_calib)
3935%          answer=questdlg('close the GUI geometry-calib?');
3936%          if isequal(answer,'Yes')
3937%              delete(hgeometry_calib)
3938%              set(handles.cal,'BackgroundColor',[0 1 0])
3939%          else
3940%              set(handles.cal,'Value',1)% keep the calibration function active
3941%          end
3942%      end
3943     set(handles.edit_vect,'enable','on')
3944     set(handles.edit,'enable','on')
3945     set(handles.create,'enable','on')
3946%      set(handles.LINE,'enable','on')
3947%      set(handles.PATCH,'enable','on')
3948%      set(handles.PLANE,'enable','on')
3949%      set(handles.VOLUME,'enable','on')
3950     %set(handles.makemask,'enable','on')
3951     hh=findobj(handles.axes3,'Tag','calib_points');
3952     if ~isempty(hh)
3953         delete(hh)
3954     end
3955     hhh=findobj(handles.axes3,'Tag','calib_marker');
3956     if ~isempty(hhh)
3957         delete(hhh)
3958     end   
3959end
3960set(huvmat,'UserData',UvData);
3961
3962%-------------------------------------------------------------
3963% --- Executes on selection change in menu_coord.
3964function menu_coord_Callback(hObject, eventdata, handles)
3965%-------------------------------------------------------------
3966huvmat=get(handles.menu_coord,'parent');
3967menu=get(handles.menu_coord,'String');
3968ind_coord=get(handles.menu_coord,'Value');
3969coord_option=menu{ind_coord};
3970list_path=get(handles.menu_coord,'UserData');
3971   
3972if isequal(coord_option,'more...');
3973    coord_fct='';
3974    dir_perso=prefdir;
3975    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3976    if exist(profil_perso,'file')
3977          h=load (profil_perso);
3978         if isfield(h,'coord_fct')
3979                coord_fct=h.coord_fct;
3980         end
3981    end
3982    prompt = {'Enter the name of the transform function'};
3983    dlg_title = 'user defined transform';
3984    num_lines= 1;
3985    [FileName, PathName, filterindex] = uigetfile( ...
3986       {'*.m', ' (*.m)';
3987        '*.m',  '.m files '; ...
3988        '*.*', 'All Files (*.*)'}, ...
3989        'Pick a file', coord_fct);
3990    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3991        PathName(end)=[];
3992    end
3993    coord_fct=fullfile(PathName,FileName);
3994    if ~exist(coord_fct,'file')
3995           msgbox_uvmat('ERROR',['image procesing fct ' coord_fct ' not found'])
3996    else
3997       transform=FileName(1:end-2);%
3998       menu=update_menu(handles.menu_coord,transform);%add the selected fct to the menu
3999       ind_coord=get(handles.menu_coord,'Value');
4000       list_path{ind_coord}=PathName;
4001       set(handles.menu_coord,'UserData',list_path)
4002       if exist(profil_perso,'file')
4003            save (profil_perso,'coord_fct','-append'); %store the root name for future opening of uvmat
4004        end
4005    end   
4006end
4007
4008%check the current path to the selected function
4009PathName=list_path{ind_coord};
4010CurrentPath=fileparts(which(coord_option));
4011if ~isequal(PathName,CurrentPath)&&~isequal(CurrentPath,fullfile(PathName,'private'))
4012    addpath(PathName)
4013    errormsg=check_functions;
4014    msgbox_uvmat('WARNING',[['path ' PathName ' added to the current Matlab pathes'];errormsg])
4015end
4016set(handles.path_transform,'String',fullfile(PathName,' ')); %show the path to the senlected function
4017set(handles.FixedLimits,'Value',0)
4018set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7])
4019
4020UvData=get(huvmat,'UserData');
4021
4022%delete drawn objects
4023hother=findobj('Tag','proj_object');%find all the proj objects
4024for iobj=1:length(hother)
4025    delete_object(hother(iobj))
4026end
4027hother=findobj('Tag','DeformPoint');%find all the proj objects
4028for iobj=1:length(hother)
4029    delete_object(hother(iobj))
4030end
4031hh=findobj('Tag','calib_points');
4032if ~isempty(hh)
4033    delete(hh)
4034end
4035hhh=findobj('Tag','calib_marker');
4036if ~isempty(hhh)
4037    delete(hhh)
4038end
4039if isfield(UvData,'Object')
4040    nbobject=length(UvData.Object);
4041    UvData.Object([2:nbobject])=[];
4042end
4043
4044%delete mask if it is displayed
4045if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on
4046   UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
4047end
4048set(huvmat,'UserData',UvData)
4049run0_Callback(hObject, eventdata, handles)
4050
4051%--------------------------------------------
4052function histo1_menu_Callback(hObject, eventdata, handles)
4053%--------------------------------------------
4054%plot first histo
4055huvmat=get(handles.histo1_menu,'parent');
4056histo_menu=get(handles.histo1_menu,'String');
4057histo_value=get(handles.histo1_menu,'Value');
4058FieldName=histo_menu{histo_value};
4059UvData=get(huvmat,'UserData');
4060update_histo(handles.histo_u,huvmat,FieldName)
4061
4062%----------------------------------------------
4063function histo2_menu_Callback(hObject, eventdata, handles)
4064%----------------------------------------------
4065%plot second histo
4066huvmat=get(handles.histo2_menu,'parent');
4067histo_menu=get(handles.histo2_menu,'String');
4068histo_value=get(handles.histo2_menu,'Value');
4069FieldName=histo_menu{histo_value};
4070UvData=get(huvmat,'UserData');
4071update_histo(handles.histo_v,huvmat,FieldName)
4072
4073
4074%--------------------------------------------
4075%read the field .Fieldname stored in UvData and plot its histogram
4076function update_histo(haxes,huvmat,FieldName)
4077UvData=get(huvmat,'UserData');
4078
4079if ~isfield(UvData.Field,FieldName)
4080    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
4081    return
4082end
4083Field=UvData.Field;
4084FieldHisto=eval(['Field.' FieldName]);
4085if isfield(Field,'FF') & ~isempty(Field.FF) & isequal(size(Field.FF),size(FieldHisto))
4086    indsel=find(Field.FF==0);%find values marked as false
4087    if ~isempty(indsel)
4088        FieldHisto=FieldHisto(indsel);
4089    end
4090end
4091if isempty(Field)
4092    msgbox_uvmat('ERROR',['empty field ' FieldName])
4093else
4094    nxy=size(FieldHisto);
4095    Amin=double(min(min(min(FieldHisto))));%min of image
4096    Amax=double(max(max(max(FieldHisto))));%max of image
4097    if isequal(Amin,Amax)
4098       Histo.Txt=['uniform field =' num2str(Amin)];
4099    else
4100    Histo.ListVarName={FieldName,'histo'};
4101    if numel(nxy)==2
4102        Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
4103    else %color images
4104        Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram
4105    end
4106    %unit
4107    units=[]; %default
4108    for ivar=1:numel(Field.ListVarName)   
4109        if strcmp(Field.ListVarName{ivar},FieldName)
4110            if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
4111                units=Field.VarAttribute{ivar}.units;
4112                break
4113            end
4114        end
4115    end
4116    if ~isempty(units)
4117        Histo.VarAttribute{1}.units=units;
4118    end
4119    eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
4120    for col=1:size(FieldHisto,3)
4121        B=FieldHisto(:,:,col);
4122        C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
4123       eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']);  %calculate histogram
4124    end
4125    set(haxes,'XLimMode','auto')%reset auto mode (after zoom effect)
4126    set(haxes,'YLimMode','auto')
4127    plot_field(Histo,haxes);
4128    end
4129end
4130
4131
4132
4133%------------------------------------------------
4134%CALLBACKS FOR PLOTTING PARAMETERS
4135%-------------------------------------------------
4136
4137%-----------------------------------------------------------------
4138function MinA_Callback(hObject, eventdata, handles)
4139%------------------------------------------
4140set(handles.AutoScal,'Value',1) %suppress auto mode
4141set(handles.AutoScal,'BackgroundColor',[1 1 0])
4142update_plot(handles)
4143
4144%-----------------------------------------------------------------
4145function MaxA_Callback(hObject, eventdata, handles)
4146%--------------------------------------------
4147set(handles.AutoScal,'Value',1) %suppress auto mode
4148set(handles.AutoScal,'BackgroundColor',[1 1 0])
4149update_plot(handles)
4150
4151%-----------------------------------------------
4152function AutoScal_Callback(hObject, eventdata, handles)
4153%--------------------------------------------
4154test=get(handles.AutoScal,'Value');
4155if test
4156    set(handles.AutoScal,'BackgroundColor',[1 1 0])
4157else
4158    set(handles.AutoScal,'BackgroundColor',[0.7 0.7 0.7])
4159    update_plot(handles);
4160%     set(handles.MinA,'String',num2str(ScalOut.MinA,3))
4161%     set(handles.MaxA,'String',num2str(ScalOut.MaxA,3))
4162end
4163
4164%-------------------------------------------------------------------
4165function BW_Callback(hObject, eventdata, handles)
4166%-------------------------------------------------------------------
4167update_plot(handles)
4168
4169%-------------------------------------------------------------------
4170function Contours_Callback(hObject, eventdata, handles)
4171%-------------------------------------------------------------------
4172val=get(handles.Contours,'Value');
4173if val==2
4174    set(handles.interval_txt,'Visible','on')
4175    set(handles.IncrA,'Visible','on')
4176else
4177    set(handles.interval_txt,'Visible','off')
4178    set(handles.IncrA,'Visible','off')
4179end
4180update_plot(handles)
4181
4182%-------------------------------------------------------------------
4183function IncrA_Callback(hObject, eventdata, handles)
4184%-------------------------------------------------------------------
4185update_plot(handles)
4186
4187%-------------------------------------------------------------------
4188function HideWarning_Callback(hObject, eventdata, handles)
4189%-------------------------------------------------------------------
4190update_plot(handles)
4191
4192%-------------------------------------------------------------------
4193function HideFalse_Callback(hObject, eventdata, handles)
4194%-------------------------------------------------------------------
4195update_plot(handles)
4196
4197%-------------------------------------------------------------------
4198function VecScale_Callback(hObject, eventdata, handles)
4199%-------------------------------------------------------------------
4200set(handles.AutoVec,'Value',1);
4201set(handles.AutoVec,'BackgroundColor',[1 1 0])
4202update_plot(handles)
4203
4204%-------------------------------------------------------------------
4205function AutoVec_Callback(hObject, eventdata, handles)
4206%-------------------------------------------------------------------
4207test=get(handles.AutoVec,'Value');
4208if test
4209    set(handles.AutoVec,'BackgroundColor',[1 1 0])
4210else
4211    update_plot(handles);
4212    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4213    set(handles.AutoVec,'BackgroundColor',[0.7 0.7 0.7])
4214end
4215
4216%-------------------------------------------------------
4217% --- Executes on selection change in decimate4 (nb_vec/4).
4218%-------------------------------------------------------
4219function decimate4_Callback(hObject, eventdata, handles)
4220update_plot(handles)
4221
4222
4223%-------------------------------------------------------
4224% --- Executes on selection change in color_code menu
4225%-------------------------------------------------------
4226function color_code_Callback(hObject, eventdata, handles)
4227set_vec_col_bar(handles)
4228update_plot(handles);
4229
4230%-------------------------------------------------------
4231% --- Executes on button press in AutoVecColor.
4232%-------------------------------------------------------
4233function AutoVecColor_Callback(hObject, eventdata, handles)
4234test=get(handles.AutoVecColor,'Value');
4235if test
4236    set(handles.AutoVecColor,'BackgroundColor',[1 1 0])
4237else
4238    update_plot(handles);
4239    %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3))
4240    set(handles.AutoVecColor,'BackgroundColor',[0.7 0.7 0.7])
4241end
4242%set_vec_col_bar(handles)
4243
4244%-------------------------------------------------------
4245% --- Executes on selection change in max_vec.
4246%-------------------------------------------------------
4247function min_vec_Callback(hObject, eventdata, handles)
4248max_vec_Callback(hObject, eventdata, handles)
4249
4250% --- Executes on selection change in max_vec.
4251function max_vec_Callback(hObject, eventdata, handles)
4252set(handles.AutoVecColor,'Value',1)
4253AutoVecColor_Callback(hObject, eventdata, handles)
4254min_val=str2num(get(handles.min_vec,'String'));
4255max_val=str2num(get(handles.max_vec,'String'));
4256slider1=get(handles.slider1,'Value');
4257slider2=get(handles.slider2,'Value');
4258colcode1=min_val+(max_val-min_val)*slider1;
4259colcode2=min_val+(max_val-min_val)*slider2;
4260set(handles.colcode1,'String',num2str(colcode1))
4261set(handles.colcode2,'String',num2str(colcode2))
4262update_plot(handles);
4263
4264%-------------------------------------------------------------------
4265%update the display of color code for vectors
4266function set_vec_col_bar(handles)
4267%-------------------------------------------------------------------
4268%get the image of the color display button 'vec_col_bar' in pixels
4269set(handles.vec_col_bar,'Unit','pixel');
4270pos_vert=get(handles.vec_col_bar,'Position');
4271set(handles.vec_col_bar,'Unit','Normalized');
4272width=ceil(pos_vert(3));
4273height=ceil(pos_vert(4));
4274
4275%get slider indications
4276list=get(handles.color_code,'String');
4277ichoice=get(handles.color_code,'Value');
4278colcode.ColorCode=list{ichoice};
4279colcode.MinC=str2num(get(handles.min_vec,'String'));
4280colcode.MaxC=str2num(get(handles.max_vec,'String'));
4281test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
4282if test3color
4283%     set(handles.colcode1,'Visible','on')
4284%     set(handles.colcode2,'Visible','on')
4285%     set(handles.slider1,'Visible','on')
4286%     set(handles.slider2,'Visible','on')
4287    colcode.colcode1=str2num(get(handles.colcode1,'String'));
4288    colcode.colcode2=str2num(get(handles.colcode2,'String'));
4289else
4290%     set(handles.colcode1,'Visible','off')
4291%     set(handles.colcode2,'Visible','off')
4292%     set(handles.slider1,'Visible','off')
4293%     set(handles.slider2,'Visible','off')
4294%     colcode.colcode1=colcode.min;
4295%     colcode.colcode2=colcode.max;
4296end
4297% colcode.option=get(handles.vec_col_bar,'Value');
4298colcode.FixedCbounds=0;
4299% list_code=get(handles.col_vec,'String');% list menu fields
4300% index_code=get(handles.col_vec,'Value');% selected string index
4301% colcode.CName= list_code{index_code(1)}; % selected field used for vector color
4302colcode.FixedCbounds=1;
4303vec_C=colcode.MinC+(colcode.MaxC-colcode.MinC)*[0.5:width-0.5]/width;%sample of vec_C values from min to max
4304[colorlist,col_vec]=set_col_vec(colcode,vec_C);
4305oneheight=ones(1,height);
4306A1=colorlist(col_vec,1)*oneheight;
4307A2=colorlist(col_vec,2)*oneheight;
4308A3=colorlist(col_vec,3)*oneheight;
4309A(:,:,1)=A1';
4310A(:,:,2)=A2';
4311A(:,:,3)=A3';
4312set(handles.vec_col_bar,'Cdata',A)
4313
4314
4315%-------------------------------------------------------------------
4316function [PlotType,ScalOut]=update_plot(handles)
4317%-------------------------------------------------------------------
4318haxes= handles.axes3;
4319AxeData=get(haxes,'UserData');
4320PlotParam=read_plot_param(handles);
4321[PlotType,PlotParamOut]= plot_field(AxeData,haxes,PlotParam,1);
4322write_plot_param(handles,PlotParamOut); %update the auto plot parameters
4323
4324%-------------------------------------------------------------------
4325% --- Executes on button press in grid.
4326function grid_Callback(hObject, eventdata, handles)
4327%-------------------------------------------------------------------
4328huvmat=get(handles.create,'parent');
4329UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
4330
4331%suppress the other options if grid is chosen
4332set(handles.create,'Value',0)
4333set(handles.create,'BackgroundColor',[0 1 0])
4334set(handles.edit_vect,'Value',0)
4335edit_vect_Callback(hObject, eventdata, handles)
4336set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
4337set(handles.edit_vect,'Value',0) 
4338edit_vect_Callback(hObject, eventdata, handles)
4339set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
4340set(handles.list_object,'Value',1)     
4341set(handles.cal,'Value',0)
4342set(handles.cal,'BackgroundColor',[0 1 0])   
4343
4344%prepare display of the set_grid GUI
4345data.fixedtitle=1;
4346FileName=read_file_boxes(handles);
4347[hset_object,UvData.sethandles]=set_grid(FileName);% call the set_object interface
4348set(huvmat,'UserData',UvData);
4349
4350
4351%-------------------------------------------------------------------
4352% --- Executes on selection change in edit.
4353function edit_Callback(hObject, eventdata, handles)
4354%-------------------------------------------------------------------
4355huvmat=get(handles.list_object,'parent');
4356UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
4357test=get(handles.edit,'Value');
4358if test
4359    UvData.MouseAction='edit_object';
4360    set(handles.edit,'BackgroundColor',[1,1,0]) 
4361    %suppress the other options
4362    set(handles.zoom,'Value',0)
4363    zoom_Callback(hObject, eventdata, handles)
4364    set(handles.create,'Value',0)
4365    set(handles.create,'BackgroundColor',[0 1 0])
4366%     set(handles.LINE,'Value',0)
4367%     set(handles.LINE,'BackgroundColor',[0 1 0])
4368%     set(handles.PATCH,'Value',0)
4369%     set(handles.PATCH,'BackgroundColor',[0 1 0])
4370%     set(handles.PLANE,'Value',0)
4371%     set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow
4372%     set(handles.VOLUME,'Value',0)
4373%     set(handles.VOLUME,'BackgroundColor',[0 1 0])
4374    set(handles.edit_vect,'Value',0)
4375    edit_vect_Callback(hObject, eventdata, handles) 
4376    set(handles.cal,'Value',0)
4377    set(handles.cal,'BackgroundColor',[0 1 0])   
4378    %set(handles.grid,'Value',0)
4379    %set(handles.grid,'BackgroundColor',[0 1 0])
4380    list_object_Callback(hObject, eventdata, handles)
4381else
4382    UvData.MouseAction='none';
4383    set(handles.edit,'BackgroundColor',[0.7,0.7,0.7])   
4384end
4385set(huvmat,'UserData',UvData);
4386
4387%--------------------------------------------------------
4388% --- Executes on selection change in list_object.
4389%--------------------------------------------------------
4390function list_object_Callback(hObject, eventdata, handles)
4391huvmat=get(handles.list_object,'parent');
4392UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
4393list_str=get(handles.list_object,'String');
4394IndexObj=get(handles.list_object,'Value');
4395
4396if ~(length(UvData.Object)>=IndexObj);
4397    return
4398end
4399ObjectData=UvData.Object{IndexObj};
4400ObjectData.desable_open=1; % desable the OPEN option in the set_object GUI (editing mode)
4401if isequal(get(handles.edit,'Value'),0)
4402    ObjectData.desable_plot=1; % desable the PLOT option in the set_object GUI (editing mode
4403end
4404PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
4405ZBounds=0; % default
4406    if isfield(UvData,'ZMin') && isfield(UvData,'ZMax')
4407        ZBounds(1)=UvData.ZMin; %minimum for the Z slider
4408        ZBounds(2)=UvData.ZMax;%maximum for the Z slider
4409    end
4410AxeData.hset_object=set_object(ObjectData,PlotHandles,ZBounds);% call the set_object interface,
4411pos_uvmat=get(huvmat,'Position');
4412if isfield(UvData,'SetObjectOrigin')
4413pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
4414pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
4415set(AxeData.hset_object,'Position',pos_set_object)
4416end
4417hother=findobj('Tag','proj_object');%find all the proj objects
4418for iobj=1:length(hother)
4419    if isequal(get(hother(iobj),'Type'),'rectangle')|isequal(get(hother(iobj),'Type'),'patch')
4420        set(hother(iobj),'EdgeColor','b')
4421        if isequal(get(hother(iobj),'FaceColor'),'m')
4422            set(hother(iobj),'FaceColor','b')
4423        end
4424    elseif isequal(get(hother(iobj),'Type'),'image')
4425           Acolor=get(hother(iobj),'CData');
4426           Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4427           set(hother(iobj),'CData',Acolor);
4428    else
4429         set(hother(iobj),'Color','b')
4430    end
4431    set(hother(iobj),'Selected','off')
4432end
4433hother=findobj('Tag','DeformPoint');
4434set(hother,'Color','b');
4435set(hother,'Selected','off')   
4436if isfield(ObjectData,'HandlesDisplay')
4437    for iview=1:length(ObjectData.HandlesDisplay)
4438        if ishandle(ObjectData.HandlesDisplay(iview))
4439            uistack(ObjectData.HandlesDisplay(iview),'top')
4440            linetype=get(ObjectData.HandlesDisplay(iview),'Type');
4441            if isequal(linetype,'line')
4442                set(ObjectData.HandlesDisplay(iview),'Color','m'); %set the selected object to magenta color
4443            elseif isequal(linetype,'rectangle')
4444                set(ObjectData.HandlesDisplay(iview),'EdgeColor','m'); %set the selected object to magenta color
4445            elseif isequal(linetype,'patch')
4446                set(ObjectData.HandlesDisplay(iview),'FaceColor','m'); %set the selected object to magenta color
4447            end
4448            SubObjectData=get(ObjectData.HandlesDisplay(iview),'UserData');
4449            if isfield(SubObjectData,'SubObject')& ishandle(SubObjectData.SubObject)
4450                uistack(SubObjectData.SubObject,'top')
4451                for iobj=1:length(SubObjectData.SubObject)
4452                    hsub=SubObjectData.SubObject(iobj);
4453                    if isequal(get(hsub,'Type'),'rectangle')
4454                        set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4455                    elseif isequal(get(hsub,'Type'),'image')
4456                       Acolor=get(hsub,'CData');
4457                       Acolor(:,:,1)=Acolor(:,:,3);
4458                       set(hsub,'CData',Acolor);
4459                    else
4460                        set(hsub,'Color','m')
4461                    end
4462                end
4463            end
4464            if isfield(SubObjectData,'DeformPoint')& ishandle(SubObjectData.DeformPoint)
4465                set(SubObjectData.DeformPoint,'Color','m')
4466            end
4467        end
4468    end
4469end
4470
4471%------------------------------------------------------
4472% --- Executes on button press in Menu/Export/field in workspace.
4473%------------------------------------------------------
4474function MenuExportField_Callback(hObject, eventdata, handles)
4475
4476global CurData
4477huvmat=get(handles.RootPath,'parent');
4478CurData=get(huvmat,'UserData');
4479evalin('base','global CurData')%make CurData global in the workspace
4480display(['UserData of uvmat :'])
4481evalin('base','CurData') %display CurData in the workspace
4482commandwindow;
4483
4484%------------------------------------------------------
4485% --- Executes on button press in Menu/Export/extract figure.
4486%------------------------------------------------------
4487function MenuExport_plot_Callback(hObject, eventdata, handles)
4488huvmat=get(handles.MenuExport_plot,'parent');
4489UvData=get(huvmat,'UserData');
4490hfig=figure;
4491newaxes=copyobj(handles.axes3,hfig);
4492map=colormap(handles.axes3);
4493colormap(map);%transmit the current colormap to the zoom fig
4494colorbar
4495
4496
4497% --------------------------------------------------------------------
4498function Insert_Callback(hObject, eventdata, handles)
4499
4500
4501% --------------------------------------------------------------------
4502function MenuRun_Callback(hObject, eventdata, handles)
4503% --------------------------------------------------------------------
4504
4505% --------------------------------------------------------------------
4506function MenuHelp_Callback(hObject, eventdata, handles)
4507% --------------------------------------------------------------------
4508path_to_uvmat=which ('uvmat');% check the path of uvmat
4509pathelp=fileparts(path_to_uvmat);
4510helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html');
4511if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC')
4512else
4513    web(helpfile);
4514end
4515
4516% --------------------------------------------------------------------
4517function MenuOpen_Callback(hObject, eventdata, handles)
4518% --------------------------------------------------------------------
4519% --------------------------------------------------------------------
4520function MenuOpen_1_Callback(hObject, eventdata, handles)
4521% --------------------------------------------------------------------
4522% --------------------------------------------------------------------
4523function MenuExport_Callback(hObject, eventdata, handles)
4524% --------------------------------------------------------------------
4525
4526% --------------------------------------------------------------------
4527function MenuExportMovie_Callback(hObject, eventdata, handles)
4528% --------------------------------------------------------------------
4529set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4530huvmat=get(handles.run0,'parent');
4531UvData=get(huvmat,'UserData');
4532[xx,xx,FileBase]=read_file_boxes(handles);
4533 %read the current input file name
4534prompt = {'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)'};
4535dlg_title = 'select properties of the output avi movie';
4536num_lines= 1;
4537nbfield_cell=get(handles.last_i,'String');
4538def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4539answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4540aviname=answer{1};
4541fps=str2num(answer{2});
4542% check for existing file with output name aviname
4543if exist(aviname,'file')
4544    backup=aviname;
4545    testexist=2;
4546    while testexist==2
4547        backup=[backup '~'];
4548        testexist=exist(backup,'file');     
4549    end
4550    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4551    if isequal(success,1)
4552        delete(aviname)%delete existing file
4553    else
4554        msgbox_uvmat('ERROR',message)
4555        return
4556    end
4557end
4558%create avi open
4559aviobj=avifile(aviname,'Compression','None','fps',fps);
4560
4561%display first view for tests
4562newfig=figure;
4563newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4564set(newaxes,'Tag','movieaxes')
4565nbpix=[512 384]*str2num(answer{3});
4566set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4567set(newaxes,'Position',eval(answer{4}));
4568map=colormap(handles.axes3);
4569colormap(map);%transmit the current colormap to the zoom fig
4570msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4571        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4572UvData.Object{1}.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4573set(huvmat,'UserData',UvData);
4574increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4575set(handles.STOP,'Visible','on')
4576set(handles.speed,'Visible','on')
4577set(handles.speed_txt,'Visible','on')
4578set(handles.RunMovie,'BusyAction','queue')
4579
4580imin=str2num(get(handles.i1,'String'));
4581imax=str2num(answer{5});
4582% if isfield(UvData,'Time')
4583htitle=get(newaxes,'Title');
4584xlim=get(newaxes,'XLim');
4585ylim=get(newaxes,'YLim');
4586set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4587time_str=get(handles.abs_time,'String');
4588set(htitle,'String',['t=' time_str])
4589set(handles.speed,'Value',1)
4590for i=1:imax
4591    if get(handles.speed,'Value')~=0 & isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4592            runpm(hObject,eventdata,handles,increment)
4593            drawnow
4594            time_str=get(handles.abs_time,'String');
4595            if ishandle(htitle)
4596             set(htitle,'String',['t=' time_str])
4597            end
4598            mov=getframe(newfig);
4599            aviobj=addframe(aviobj,mov);
4600    end
4601end
4602aviobj=close(aviobj);
4603UvData.Object{1}.plotaxes=handles.axes3;
4604set(huvmat,'UserData',UvData);
4605msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4606
4607% --------------------------------------------------------------------
4608function MenuPoints_Callback(hObject, eventdata, handles)
4609set(handles.create,'Visible','on')
4610set(handles.create,'Value',1)
4611POINTS_Callback(hObject,eventdata,handles)
4612
4613% --------------------------------------------------------------------
4614function MenuLine_Callback(hObject, eventdata, handles)
4615set(handles.create,'Visible','on')
4616set(handles.create,'Value',1)
4617LINE_Callback(hObject,eventdata,handles)
4618
4619% ------------------------------------------------------------------
4620function MenuPatch_Callback(hObject, eventdata, handles)
4621set(handles.create,'Visible','on')
4622set(handles.create,'Value',1)
4623PATCH_Callback(hObject,eventdata,handles)
4624
4625% ------------------------------------------------------------------
4626function MenuPlane_Callback(hObject, eventdata, handles)
4627set(handles.create,'Visible','on')
4628set(handles.create,'Value',1)
4629PLANE_Callback(hObject,eventdata,handles)
4630
4631% ------------------------------------------------------------------
4632function MenuVolume_Callback(hObject, eventdata, handles)
4633set(handles.create,'Visible','on')
4634set(handles.create,'Value',1)
4635VOLUME_Callback(hObject,eventdata,handles)
4636
4637% ------------------------------------------------------------------
4638function MenuCalib_Callback(hObject, eventdata, handles)
4639set(handles.TOOLS_txt,'Visible','on')
4640set(handles.frame_tools,'Visible','on')
4641set(handles.cal,'Visible','on')
4642set(handles.cal,'Value',1)
4643cal_Callback(hObject,eventdata,handles)
4644
4645% ------------------------------------------------------------------
4646function MenuMask_Callback(hObject, eventdata, handles)
4647set(handles.TOOLS_txt,'Visible','on')
4648set(handles.frame_tools,'Visible','on')
4649set(handles.create,'Visible','on')
4650set(handles.create,'Value',1)
4651set(handles.create,'BackgroundColor',[1 1 0]) %visualise in yellow
4652set(handles.save_mask,'Visible','on')
4653set(handles.masklevel,'Visible','on')
4654if isequal(get(handles.z_index,'Visible'),'on')
4655    nb_slice=str2num(get(handles.nb_slice,'String'));
4656    for ilist=1:nb_slice
4657        list_index{ilist,1}=num2str(ilist);
4658    end   
4659    set(handles.masklevel,'String',list_index)
4660    val=str2num(get(handles.z_index,'String'));
4661    if val<=nb_slice
4662        set(handles.masklevel,'Value',val)
4663    end
4664else
4665    set(handles.masklevel,'String',{'1'})
4666    set(handles.masklevel,'Value',1)
4667end
4668if ishandle(handles.UVMAT_title)
4669    delete(handles.UVMAT_title)
4670end
4671huvmat=get(handles.create,'parent');
4672UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface
4673set(handles.zoom,'Value',0)
4674set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7])
4675set(handles.edit_vect,'Value',0)
4676edit_vect_Callback(hObject, eventdata, handles)
4677set(handles.edit,'Value',0)
4678set(handles.edit,'BackgroundColor',[0.7 0.7 0.7])
4679set(handles.edit_vect,'Value',0) 
4680edit_vect_Callback(hObject, eventdata, handles)
4681set(handles.cal,'Value',0)
4682set(handles.cal,'BackgroundColor',[0 1 0])
4683
4684%initiate the GUI set_object
4685data.TITLE='MASK';
4686if isfield(UvData,'CoordType')
4687    data.CoordType=UvData.CoordType;
4688end
4689if isfield(UvData,'Mesh')&&~isempty(UvData.Mesh)
4690    data.YMax=UvData.Mesh;
4691elseif isfield(UvData.Field,'AX')&&isfield(UvData.Field,'AY')&& isfield(UvData.Field,'A')%only image
4692    np=size(UvData.Field.A);
4693    meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1);
4694    meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1);
4695    data.YMax=max(meshx,meshy);
4696    data.DX=max(meshx,meshy);
4697end
4698data.Coord=[0 0 0]; %default
4699PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters
4700[hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface
4701pos_uvmat=get(huvmat,'Position');
4702if isfield(UvData,'SetObjectOrigin')
4703    pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2);
4704    pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4);
4705    set(hset_object,'Position',pos_set_object)
4706end
4707list_object=get(handles.list_object,'String');
4708if ~isempty(list_object)
4709    set(handles.list_object,'Value',length(list_object))
4710end
4711UvData.MouseAction='create_object';
4712set(huvmat,'UserData',UvData);
4713
4714% ------------------------------------------------------------------
4715%-- open the GUI set_grid.fig to create grid
4716function MenuGrid_Callback(hObject, eventdata, handles)
4717set(handles.TOOLS_txt,'Visible','on')
4718set(handles.frame_tools,'Visible','on')
4719grid_Callback(hObject,eventdata,handles)
4720
4721%----------------------------------------------------------------
4722% open the GUI 'series'
4723%----------------------------------------------------------------
4724function MenuSeries_Callback(hObject, eventdata, handles)
4725
4726[param.FileName]=read_file_boxes(handles);
4727if isequal(get(handles.SubField,'Value'),1)
4728    FileName_1=read_file_boxes_1(handles);%
4729    if ~isequal(FileName_1,param.FileName)
4730        param.FileName_1=FileName_1;
4731    end
4732end
4733param.NomType=get(handles.FileIndex,'UserData');
4734param.NomType_1=get(handles.FileIndex_1,'UserData');
4735param.comp_input=get(handles.fix_pair,'Value');
4736huvmat=get(handles.MenuSeries,'parent');
4737UvData=get(huvmat,'UserData');
4738if isfield(UvData,'Time')
4739    param.Time=UvData.XmlData.Time;
4740end
4741if isequal(get(handles.scan_i,'Value'),1)
4742    param.incr_i=str2num(get(handles.increment_scan,'String'));
4743elseif isequal(get(handles.scan_j,'Value'),1)
4744    param.incr_j=str2num(get(handles.increment_scan,'String'));
4745end
4746param.list_fields=get(handles.Fields,'String');% list menu fields
4747param.list_fields(1)=[]; %suppress  'image' option
4748param.index_fields=get(handles.Fields,'Value');% selected string index
4749if param.index_fields>1
4750    param.index_fields=param.index_fields-1;
4751end
4752param.list_fields_1=get(handles.Fields_1,'String');% list menu fields
4753param.list_fields_1(1)=[]; %suppress  'image' option
4754param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index
4755if param.index_fields_1>1
4756    param.index_fields_1=param.index_fields_1-1;
4757end
4758param.civ1=get(handles.civ1,'Value');
4759param.civ2=get(handles.civ2,'Value');
4760param.interp1=get(handles.interp1,'Value');
4761param.interp2=get(handles.interp2,'Value');
4762param.filter1=get(handles.filter1,'Value');
4763param.filter2=get(handles.filter2,'Value');
4764param.menu_coord_str=get(handles.menu_coord,'String');
4765param.menu_coord_val=get(handles.menu_coord,'Value');
4766
4767series(param); %run the series interface
4768
4769% ------------------------------------------------------------------
4770% -- open the GUI civ.fig for civx (PIV)
4771% ------------------------------------------------------------------
4772function MenuPIV_Callback(hObject, eventdata, handles)
4773 
4774[FileName,RootPath,filebase,FileIndices,ext,SubDir]=read_file_boxes(handles);
4775[P,F,str1,str2,str_a,str_b]=name2display(FileName);
4776num1=stra2num(str1);
4777num2=stra2num(str2);
4778num_a=stra2num(str_a);
4779num_b=stra2num(str_b);
4780NomType=get(handles.FileIndex,'UserData');
4781ind_opening=1; % default (images): will advice civ1 option by default in the civ interface
4782if isequal(ext,'.nc') ||  isequal(ext,'.cdf')% netcdf files
4783    ind_opening=2;% propose 'fix' as the default option
4784% +read the current netcdf rootfile
4785    Data=nc2struct(FileName,[]);
4786    if isfield(Data,'fix') & isequal(Data.fix,1)
4787        ind_opening=3;
4788    end
4789    if isfield(Data,'patch') & isequal(Data.patch,1)
4790        ind_opening=4;
4791    end
4792    if isfield(Data,'civ2') & isequal(Data.civ2,1)
4793        ind_opening=5;
4794    end
4795    if isfield(Data,'fix2') & isequal(Data.fix2,1)
4796        ind_opening=6;
4797    end
4798end     
4799varargin{1}=filebase;
4800varargin{2}=NomType;
4801varargin{3}=num1;
4802varargin{4}=num2;
4803varargin{5}=num_a;
4804varargin{6}=num_b;
4805varargin{7}=SubDir;
4806varargin{8}=ind_opening;% A REVOIR +TRANSMETTRE IMADOC INFO
4807varargin{11}=ext;
4808civ(varargin);% interface de civ(not in the uvmat file)
4809
4810% ------------------------------------------------------------------
4811function MenuTools_Callback(hObject, eventdata, handles)
4812
4813% ------------------------------------------------------------------
4814function MenuEdit_Callback(hObject, eventdata, handles)
4815
4816%--------------------------------------------------------------------------
4817function enable_transform(handles,state)
4818set(handles.menu_coord,'Visible',state)
4819set(handles.TRANSFORM_txt,'Visible',state)   
4820set(handles.menu_coord,'Visible',state) 
4821set(handles.path_transform,'Visible',state)
4822set(handles.pxcmx_txt,'Visible',state)
4823set(handles.pxcmy_txt,'Visible',state)
4824set(handles.pxcm,'Visible',state)
4825set(handles.pycm,'Visible',state)
4826
4827% --------------------------------------------------------------------
4828function MenuEditVectors_Callback(hObject, eventdata, handles)
4829set(handles.edit_vect,'Visible','on')
4830set(handles.edit_vect,'Value',1)
4831edit_vect_Callback(hObject, eventdata, handles)
4832
4833
4834
4835
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