source: trunk/src/uvmat.m @ 441

Last change on this file since 441 was 441, checked in by sommeria, 9 years ago

many bugs corrected for the new file organisation

File size: 208.1 KB
RevLine 
[387]1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%%
8%
9%INPUT:
10% input: input file name (if character chain), or input image matrix to
11% visualize, or Matlab structure representing  netcdf fields (with fields
12% ListVarName....)
13%
14%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15%  Copyright Joel Sommeria,  2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%     This open is part of the toolbox UVMAT.
18%
19%     UVMAT is free software; you can redistribute it and/or modify
20%     it under the terms of the GNU General Public License as published by
21%     the Free Software Foundation; either version 2 of the License, or
22%     (at your option) any later version.
23%
24%     UVMAT is distributed in the hope that it will be useful,
25%     but WITHOUT ANY WARRANTY; without even the implied warranty of
26%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
28%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29%
30% Information stored on the interface:
31%    'Strings' of all edit boxes and menus: get(handles.Tag,'String')
32%    'Values' of all menus and toggle buttons: get(handles.Tag,'Value')
33%     Matlab structure called UvData stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface).
34%          It contains the following fields:
35%     - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn)
36%          .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures
37%     - Information read in the documentation open of a series (activated by RootPath_Callback) :
38%          .XmlData, with fields:
39%               .Time: matrix of times of the images with index i and j
40%               .GeometryCalib: [1x1 struct]
41%     - Information defined from the interface:
42%           .NewSeries: =1 when the first view of a new field series is displayed, else 0
43%           .filename:(char string)
44%           .FieldName: (char string) main field selected('image', 'velocity'...)
45%           .CName: (char string)name of the scalar used for vector colors
46%          .MovieObject{1}: movie object representing an input movie
47%          .MovieObject{2}: idem for a second input series (_1)
48%          .filename_1 : last second input file name (to deal with a constant second input without reading again the file)
49%          .ZMin, .ZMax: range of the z coordinate
50%..... to complement
51%     - Information on  projection objects
52%           .Object: {[1x1 struct]}
53%           .CurrentObjectIndex: index of the projection object .Object currently selected for editing
54%     -Information on the current field (Field{i})
55%            .Txt : text information to display (e.g. error message)
56%            .NbDim: number of dimensions (=0 by default)
57%            .NbCoord: number of vector components
58%            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
59%            .dt: time interval for the corresponding image pair
60%            .Mesh: estimated typical distance between vectors
61%            .ZMax:
62%            .ZMin:
63%            .X, .Y, .Z: set of vector coordinates
64%            .U,.V,.W: corresponding set of vector components
65%            .F: corresponding set of warning flags
66%            .FF: corresponding set of false flags, =0 for good vectors
67%            .C: corresponding values of the scalar used for vector color
68%             (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length,
69%                     equal to the number of vectors stored in the input open)
70%            .CName: name of the scalar .C
71%            .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below)
72%            .A image or scalar
73%            .AX: vector of dimension 2 representing the first and last values
74%              of the X coordinates for the image or scalar known on a regular grid,
75%              or vector of dimension .A for a scaler defined on irregular grid.
76%            .AY: same as .AX along the Y direction
77%            .AName: name of the scalar, ='image' for an image
78
79% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
80%
[406]81%
82% 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1
83% (second field), or by the stored file names under  Browse, or as an input of uvmat.
84% 2) These functions call 'display_file_name.m' which detects the file series, and fills the file index boxes
85% 3) Then 'update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file)
86% 4) Then fields are opened and visualised by the main sub-function 'refresh_field.m'
[387]87% The function first reads the name of the input file from the edit boxes  of the GUI
[406]88% A second input file can be introduced for file comparison
[387]89% It then reads the input file(s) with the appropriate function, read for
90% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf
91% files.
92%               Main input open   second input open(_1)        second image (pair animation)
93%            |                 |                             
94%            |                 |                                               
95%                     Field{1}         Field{2}               
96%                                                                         |
97% coord transform (phys.m) or other user defined  fct acting on Field{i}  |
98%                                                                   Field{i}
99%                                                                    |
100% calc_field.m: calculate scalar or other derived fields (vort, div..).
101%
102% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar):
103%              Field{i=1->3}.X --> UvData.X                          |
104%                                                                    |
105%                                                                 UvData
106%                                                                    |
107% plot histograms of the whole  field
108% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object
109%                                                                    |                                                                          |
110%                                                                ObjectData
111%                                                                    |
112% plot_field.m: plot the projected fields and store them as          |
113% UvData.axes3                                        |
114%                                                                    |
115%                                                                AxeData
116%
117%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
118% scalars are displayed either as an image or countour plot, either as a color of
119% velocity vectors. The scalar values in the first case is represented by
120% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
121% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
122% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
123% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
124% coordinates of the four image corners. The scalar name is represented by
125% the strings .AName and/or .CName.
126% If the scalar exists in an input open (image or scalar stored under its
127% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
128% Else only its name AName is recorded in Field{i}, and its field is then calculated
129%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
130     
131% Properties attached to plotting figures (standard Matlab properties):
132%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
133%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
134%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
135%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
136%    'KeyPressFcn': function called by pressing a key on the key board
137%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
138%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
139
140% Properties attached to plotting axes:
141%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
142%     AxeData:=get(gca,'UserData');
143%     AxeData.Drawing  = create: create a new object
144%                       = deform: modify an existing object by moving its defining create
145%                      = off: no current drawing action
146%                     = translate: translate an existing object
147%                    = calibration: move a calibration point
148%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
149%            .CurrentOrigin: Origin of a curently drawn edit_object
150%            .CurrentLine: currently drawn menuline (A REVOIR)
151%            .CurrentObject: handle of the currently drawn edit_object
152%            .CurrentRectZoom: current rectangle used for CheckZoom
153
154% Properties attached to projection objects (create, menuline, menuplane...):
155%    'Tag'='proj_object': for all projection objects
156%    ObjectData.Type=...: style of projection object:
157%              .ProjMode
158%              .Coord: defines the position of the object
159%              .XMin,YMin....
160%              .XMax,YMax....
161%              .DX,DY,DZ
162%              .Phi, .Theta, .Psi : Euler angles
163%              .X,.Y,.U,.V.... : field data projected on the object
164%              .IndexObj: index in the list of UvData.Object
165           %during plotting
166%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
167%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
168% To each projection object #iobj, corresponds an axis
169% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
170% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
171
172%------------------------------------------------------------------------
173%------------------------------------------------------------------------
[406]174%  I - MAIN FUNCTION uvmat
[387]175%------------------------------------------------------------------------
176%------------------------------------------------------------------------
177function varargout = uvmat(varargin)
178
179% Begin initialization code - DO NOT EDIT
180gui_Singleton = 1;
181gui_State = struct('gui_Name',          mfilename, ...
182                   'gui_Singleton',     gui_Singleton, ...
183                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
184                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
185                   'gui_LayoutFcn',     [], ...
186                   'gui_Callback',      []);
187if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
188    gui_State.gui_Callback = str2func(varargin{1});
189end
190
191if nargout
192    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
193else
194    gui_mainfcn(gui_State, varargin{:});
195end
196% End initialization code - DO NOT EDIT
197
198%------------------------------------------------------------------------
199% --- Executes just before the GUI uvmat is made visible.
200function uvmat_OpeningFcn(hObject, eventdata, handles, input )
201%------------------------------------------------------------------------
202
203%% Choose default command menuline output for uvmat (standard GUI)
204handles.output = hObject;
205
206%% Update handles structure (standard GUI)
207guidata(hObject, handles);
208
209%% check the path and date of modification of all functions in uvmat
210path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
211[errormsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m
212date_str=['last modification: ' date_str];
213
214
215%% set the position of colorbar and ancillary GUIs:
216set(hObject,'Units','Normalized')
217movegui(hObject,'center')
218UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
219UvData.OpenParam.SetObjectOrigin=[-0.05 -0.03]; %position for set_object
220UvData.OpenParam.SetObjectSize=[0.3 0.7];
221UvData.OpenParam.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE)
222UvData.OpenParam.CalSize=[0.28 1];
223UvData.axes3=[];%initiate the record of plotted field
224UvData.axes2=[];
225UvData.axes1=[];
226AxeData.LimEditBox=1; %initialise AxeData
227set(handles.axes3,'UserData',AxeData)
228
229%% set functions for the mouse and keyboard
[423]230% set(handles.histo_u,'NextPlot','replacechildren');
[424]231% set(handles.histo_v,'NextPlot','replacechildren');
[387]232set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
233set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
234set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
235set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
236set(hObject,'DeleteFcn',{@closefcn})%
237
238%% refresh projection plane
[432]239% UvData.Object{1}.ProjMode='projection';%main plotting plane
240% UvData.Object{1}.DisplayHandle.uvmat=handles.axes3;
241% UvData.Object{1}.DisplayHandle.view_field=[];
[424]242set(handles.ListObject,'Value',1)% default: empty projection objectproj_field
[429]243set(handles.ListObject,'String',{'plane'})
[410]244set(handles.ListObject_1,'Value',1)% default: empty projection objectproj_field
[429]245set(handles.ListObject_1,'String',{'plane'})
[387]246set(handles.Fields,'Value',1)
247set(handles.Fields,'string',{''})
248
249%% TRANSFORM menu: builtin fcts
250menu_str={'';'phys';'px';'phys_polar'};
251UvData.OpenParam.NbBuiltin=numel(menu_str); %number of functions
252path_uvmat=fileparts(which('uvmat'));
253addpath (path_uvmat) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
254addpath(fullfile(path_uvmat,'transform_field'))%add the path to transform functions,
255fct_handle{1,1}=[];
256testexist=zeros(size(menu_str'));%default
257testexist(1)=1;
258for ilist=2:length(menu_str)
259    if exist(menu_str{ilist},'file')
260        fct_handle{ilist,1}=str2func(menu_str{ilist});
261        testexist(ilist)=1;
262    else
263        testexist(ilist)=0;
264    end
265end
266rmpath(fullfile(path_uvmat,'transform_field'))
267
268%% load the list of previously browsed files in menus Open and Open_1
269 dir_perso=prefdir; % path to the directory .matlab for personal data
270 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
271 if exist(profil_perso,'file')
272      h=load (profil_perso);
273      if isfield(h,'MenuFile')
274          for ifile=1:min(length(h.MenuFile),5)
275              eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
276               eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
277          end
278      end
279      if isfield(h,'transform_fct') && iscell(h.transform_fct)
280         for ilist=1:length(h.transform_fct);
281             if exist(h.transform_fct{ilist},'file')
282                [path,file]=fileparts(h.transform_fct{ilist});
283                addpath(path)
284                h_func=str2func(file);
285                rmpath(path)
286                testexist=[testexist 1];
287             else
288                file='';
289                h_func=[];
290                testexist=[testexist 0];
291             end
292             fct_handle=[fct_handle; {h_func}]; %concatene the list of paths
293             menu_str=[menu_str; {file}];
294         end
295      end
296 end
297menu_str=menu_str(testexist==1);%=menu_str(testexist~=0)
298fct_handle=fct_handle(testexist==1);
299menu_str=[menu_str;{'more...'}];
300set(handles.transform_fct,'String',menu_str)
301set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
302
303%% case of an input argument for uvmat
304testinputfield=0;
305inputfile=[];
306Field=[];
307if exist('input','var')
308%     if ~isempty(errormsg)
309%         msgbox_uvmat('WARNING',errormsg)
310%     end
311    if ishandle(handles.UVMAT_title)
312        delete(handles.UVMAT_title)
313    end   
314    if isstruct(input)
315        if isfield(input,'InputFile')
316            inputfile=input.InputFile;
317        end
318        if isfield(input,'TimeIndex')
319            set(handles.i1,num2str(input.TimeIndex))
320        end
321        if isfield(input,'FieldsString')
322            UvData.FieldsString=input.FieldsString;
323        end
324    elseif ischar(input)% file name introduced as input
325           inputfile=input;
326    elseif isnumeric(input)%simple matrix introduced as input
327        sizinput=size(input);
328        if sizinput(1)<=1 || sizinput(2)<=1
329            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
330            return
331        end
332        UvData.Field.ListVarName={'A','coord_y','coord_x'};
333        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
334        UvData.Field.A=input;
335        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
336        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
337        testinputfield=1;
338    end
339else
340   if ishandle(handles.UVMAT_title)
341       set(handles.UVMAT_title,'String',...
342           [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
343           {'GNU General Public License'};...
344           {path_to_uvmat};...
345           {date_str};...
346           {['SVN revision : ' num2str(svn_info.cur_rev)]};...
347           errormsg]);
348   end
349end
350set(handles.uvmat,'UserData',UvData)
351if ~isempty(inputfile)
352    %%%%% display the input field %%%%%%%
[406]353    display_file_name(handles,inputfile)
[387]354    %%%%%%%
355    testinputfield=1;
356end
357
358%% plot input field if exists
359if testinputfield
360    %delete drawn objects
361    hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects
362    for iobj=1:length(hother)
363        delete_object(hother(iobj))
364    end 
365    if isempty(inputfile)
366        errormsg=refresh_field(handles,[],[],[],[],[],[],{Field});
367        set(handles.MenuTools,'Enable','on')
368        set(handles.OBJECT_txt,'Visible','on')
369        set(handles.edit_object,'Visible','on')
[410]370%         set(handles.ListObject_1,'Visible','on')
[387]371        set(handles.frame_object,'Visible','on')
372        if ~isempty(errormsg)
373            msgbox_uvmat('ERROR',errormsg)
374        end
375    end
376end
377
378set_vec_col_bar(handles) %update the display of color code for vectors
379
380%------------------------------------------------------------------------
381% --- Outputs from this function are returned to the command menuline.
382function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
383varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
384
385%------------------------------------------------------------------------
[402]386% --- executed when closing uvmat: delete or desactivate the associated figures if exist
387function closefcn(gcbo,eventdata)
[387]388%------------------------------------------------------------------------
[402]389hh=findobj(allchild(0),'tag','view_field');
390if ~isempty(hh)
391    delete(hh)
392end
393hh=findobj(allchild(0),'tag','geometry_calib');
394if ~isempty(hh)
395    delete(hh)
396end
397hh=findobj(allchild(0),'tag','set_object');
398if ~isempty(hh)
399    hhh=findobj(hh,'tag','PLOT');
400    set(hhh,'enable','off')
401end
402
403%------------------------------------------------------------------------
404%------------------------------------------------------------------------
[387]405%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
406% automatically sets the global properties when the rootfile name is introduced
407% then activate the view-field action if selected
408% it is activated either by clicking on the RootPath window or by the
409% browser
410%------------------------------------------------------------------------
411%------------------------------------------------------------------------
412% --- Executes on the menu Open/Browse...
413% search the files, recognize their type according to their name and fill the rootfile input windows
414function MenuBrowse_Callback(hObject, eventdata, handles)
415[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
416oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
417if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
418         dir_perso=prefdir;
419         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
420         if exist(profil_perso,'file')
421              h=load (profil_perso);
422             if isfield(h,'MenuFile_1')
423                  oldfile=h.MenuFile_1;
424             end
425         end
426end
[421]427% [FileName, PathName] = uigetfile( ...
428%        {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol;*.nc;*.cmx;*.fig;*.log;*.dat;*.bat;', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.vol,*.nc,*.cmx,*.fig,*.log,*.dat,*.bat)';
429%        '*.xml',  '.xml files '; ...
430%         '*.xls',  '.xls files '; ...
431%         '*.civ',  '.civ files '; ...
432%         '*.jpg',' jpeg image files'; ...
433%         '*.png','.png image files'; ...
434%         '*.tif','.tif image files'; ...
435%         '*.avi;*.AVI','.avi movie files'; ...
436%         '*.vol','.volume images (png)'; ...
437%         '*.nc','.netcdf files'; ...
438%         '*.cdf','.netcdf files'; ...
439%         '*.cmx','.cmx text files ';...
440%         '*.fig','.fig files (matlab fig)';...
441%         '*.log','.log text files ';...
442%         '*.dat','.dat text files ';...
443%         '*.bat','.bat system command text files';...
444%         '*.*',  'All Files (*.*)'}, ...
445%         'Pick a file',oldfile);
446
447[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',oldfile);
[387]448fileinput=[PathName FileName];%complete file name
449sizf=size(fileinput);
450if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
451
452% display the selected field and related information
[406]453display_file_name( handles,fileinput)
[387]454
455% -----------------------------------------------------------------------
456% --- Open again the file whose name has been recorded in MenuFile_1
457function MenuFile_1_Callback(hObject, eventdata, handles)
458%------------------------------------------------------------------------
459fileinput=get(handles.MenuFile_1,'Label');
[406]460display_file_name( handles,fileinput)
[387]461
462% -----------------------------------------------------------------------
463% --- Open again the file whose name has been recorded in MenuFile_2
464function MenuFile_2_Callback(hObject, eventdata, handles)
465%------------------------------------------------------------------------
466fileinput=get(handles.MenuFile_2,'Label');
[406]467display_file_name(handles,fileinput)
[387]468
469% -----------------------------------------------------------------------
470% --- Open again the file whose name has been recorded in MenuFile_3
471function MenuFile_3_Callback(hObject, eventdata, handles)
472%------------------------------------------------------------------------
473fileinput=get(handles.MenuFile_3,'Label');
[406]474display_file_name(handles,fileinput)
[387]475
476% -----------------------------------------------------------------------
477% --- Open again the file whose name has been recorded in MenuFile_4
478function MenuFile_4_Callback(hObject, eventdata, handles)
479%------------------------------------------------------------------------
480fileinput=get(handles.MenuFile_4,'Label');
[406]481display_file_name(handles,fileinput)
[387]482
483% -----------------------------------------------------------------------
484% --- Open again the file whose name has been recorded in MenuFile_5
485function MenuFile_5_Callback(hObject, eventdata, handles)
486%------------------------------------------------------------------------
487fileinput=get(handles.MenuFile_5,'Label');
[406]488display_file_name(handles,fileinput)
[387]489
[402]490%------------------------------------------------------------------------
491% --- Executes on the menu Open/Browse_1 for the second input field,
492%     search the files, recognize their type according to their name and fill the rootfile input windows
493function MenuBrowse_1_Callback(hObject, eventdata, handles)
494%------------------------------------------------------------------------
495RootPath=get(handles.RootPath,'String');
[421]496% [FileName, PathName, filterindex] = uigetfile( ...
497%        {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)';
498%        '*.xml',  '.xml files '; ...
499%         '*.xls',  '.xls files '; ...
500%         '*.civ',  '.civ files '; ...
501%         '*.jpg','.jpg image files'; ...
502%         '*.png','.png image files'; ...
503%         '*.avi;*.AVI','.avi movie files'; ...
504%         '*.nc','.netcdf files'; ...
505%         '*.cdf','.netcdf files'; ...
506%         '*.cmx','.cmx text files';...
507%         '*.cmx2','.cmx2 text files';...
508%         '*.fig','.fig files (matlab fig)';...
509%         '*.log','.log text files ';...
510%         '*.dat','.dat text files ';...
511%         '*.*',  'All Files (*.*)'}, ...
512%         'Pick a second file for comparison',RootPath);
513[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath);
[402]514fileinput_1=[PathName FileName];%complete file name
515sizf=size(fileinput_1);
516if (~ischar(fileinput_1)||~isequal(sizf(1),1)),return;end
517
518% refresh the current displayed field
519set(handles.SubField,'Value',1)
[406]520display_file_name(handles,fileinput_1,2)
[402]521
522%update list of recent files in the menubar
523MenuFile_1=fileinput_1;
524MenuFile_2=get(handles.MenuFile_1,'Label');
525MenuFile_3=get(handles.MenuFile_2,'Label');
526MenuFile_4=get(handles.MenuFile_3,'Label');
527MenuFile_5=get(handles.MenuFile_4,'Label');
528set(handles.MenuFile_1,'Label',MenuFile_1)
529set(handles.MenuFile_2,'Label',MenuFile_2)
530set(handles.MenuFile_3,'Label',MenuFile_3)
531set(handles.MenuFile_4,'Label',MenuFile_4)
532set(handles.MenuFile_5,'Label',MenuFile_5)
533set(handles.MenuFile_1_1,'Label',MenuFile_1)
534set(handles.MenuFile_2_1,'Label',MenuFile_2)
535set(handles.MenuFile_3_1,'Label',MenuFile_3)
536set(handles.MenuFile_4_1,'Label',MenuFile_4)
537set(handles.MenuFile_5_1,'Label',MenuFile_5)
538dir_perso=prefdir;
539profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
540if exist(profil_perso,'file')
541    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
542else
543    txt=ver('MATLAB');
544    Release=txt.Release;
545    relnumb=str2double(Release(3:4));
546    if relnumb >= 14
547        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
548    else
549        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
550    end
551end
552
553% -----------------------------------------------------------------------
554% --- Open again as second field the file whose name has been recorded in MenuFile_1
555function MenuFile_1_1_Callback(hObject, eventdata, handles)
556% -----------------------------------------------------------------------
557fileinput_1=get(handles.MenuFile_1_1,'Label');
558set(handles.SubField,'Value',1)
[406]559display_file_name(handles,fileinput_1,2)
[402]560
561% -----------------------------------------------------------------------
562% --- Open again as second field the file whose name has been recorded in MenuFile_2
563function MenuFile_2_1_Callback(hObject, eventdata, handles)
564% -----------------------------------------------------------------------
565fileinput_1=get(handles.MenuFile_2_1,'Label');
566set(handles.SubField,'Value',1)
[406]567display_file_name(handles,fileinput_1,2)
[402]568
569% -----------------------------------------------------------------------
570% --- Open again as second field the file whose name has been recorded in MenuFile_3
571function MenuFile_3_1_Callback(hObject, eventdata, handles)
572% -----------------------------------------------------------------------
573fileinput_1=get(handles.MenuFile_3_1,'Label');
574set(handles.SubField,'Value',1)
[406]575display_file_name(handles,fileinput_1,2)
[402]576
577% -----------------------------------------------------------------------
578% --- Open again as second field the file whose name has been recorded in MenuFile_4
579function MenuFile_4_1_Callback(hObject, eventdata, handles)
580% -----------------------------------------------------------------------
581fileinput_1=get(handles.MenuFile_4_1,'Label');
582set(handles.SubField,'Value',1)
[406]583display_file_name(handles,fileinput_1,2)
[402]584
585% -----------------------------------------------------------------------
586% --- Open again as second field the file whose name has been recorded in MenuFile_5
587function MenuFile_5_1_Callback(hObject, eventdata, handles)
588% -----------------------------------------------------------------------
589fileinput_1=get(handles.MenuFile_5_1,'Label');
590set(handles.SubField,'Value',1)
[406]591display_file_name(handles,fileinput_1,2)
[402]592
593%------------------------------------------------------------------------
594% --- Called by action in RootPath edit box
595function RootPath_Callback(hObject,eventdata,handles)
596%------------------------------------------------------------------------
597% read the current input file name:
598[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
599% detect the file type, get the movie object if relevant, and look for the corresponding file series:
600[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
601% initiate the input file series and refresh the current field view:
[406]602update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);
[402]603
604%-----------------------------------------------------------------------
605% --- Called by action in RootPath_1 edit box
606function RootPath_1_Callback(hObject,eventdata,handles)
607% -----------------------------------------------------------------------
608% update_rootinfo_1(hObject,eventdata,handles)
609[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
610% detect the file type, get the movie object if relevant, and look for the corresponding file series:
611[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
612% initiate the input file series and refresh the current field view:
613update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
614
615%------------------------------------------------------------------------
616% --- Called by action in RootFile edit box
617function SubDir_Callback(hObject, eventdata, handles)
618%------------------------------------------------------------------------
619%refresh the menu of input fields
620Fields_Callback(hObject, eventdata, handles);
621% refresh the current field view
622run0_Callback(hObject, eventdata, handles);
623
624%------------------------------------------------------------------------
625% --- Called by action in RootFile edit box
626function RootFile_Callback(hObject, eventdata, handles)
627%------------------------------------------------------------------------
628RootPath_Callback(hObject,eventdata,handles)
629
630%-----------------------------------------------------------------------
631% --- Called by action in RootFile_1 edit box
632function RootFile_1_Callback(hObject, eventdata, handles)
633% -----------------------------------------------------------------------
634RootPath_1_Callback(hObject,eventdata,handles)
635
636%------------------------------------------------------------------------
637% --- Called by action in FileIndex edit box
638function FileIndex_Callback(hObject, eventdata, handles)
639%------------------------------------------------------------------------
640[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
641set(handles.i1,'String',num2str(i1));
642set(handles.i2,'String',num2str(i2));
643set(handles.j1,'String',num2str(j1));
644set(handles.j2,'String',num2str(j2));
645
646% refresh the current field view
647run0_Callback(hObject, eventdata, handles)
648
649%------------------------------------------------------------------------
650% --- Called by action in FileIndex_1 edit box
651function FileIndex_1_Callback(hObject, eventdata, handles)
652%------------------------------------------------------------------------
653run0_Callback(hObject, eventdata, handles)
654
655%------------------------------------------------------------------------
656% --- Called by action in NomType edit box
657function NomType_Callback(hObject, eventdata, handles)
658%------------------------------------------------------------------------
659i1=str2num(get(handles.i1,'String'));
660i2=str2num(get(handles.i2,'String'));
661j1=str2num(get(handles.j1,'String'));
662j2=str2num(get(handles.j2,'String'));
663FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
664set(handles.FileIndex,'String',FileIndex)
665% refresh the current settings and refresh the field view
666RootPath_Callback(hObject,eventdata,handles)
667
668%------------------------------------------------------------------------
669% --- Called by action in NomType edit box
670function NomType_1_Callback(hObject, eventdata, handles)
671%------------------------------------------------------------------------
672i1=str2num(get(handles.i1,'String'));
673i2=str2num(get(handles.i2,'String'));
674j1=str2num(get(handles.j1,'String'));
675j2=str2num(get(handles.j2,'String'));
676FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
677set(handles.FileIndex_1,'String',FileIndex)
678% refresh the current settings and refresh the field view
679RootPath_1_Callback(hObject,eventdata,handles)
680
[387]681%------------------------------------------------------------------------
682% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
[406]683function display_file_name(handles,fileinput,index)
[387]684%------------------------------------------------------------------------
685%% look for the input file existence
686if ~exist(fileinput,'file')
687    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
688    return
689end
690
691%% set the mouse pointer to 'watch'
692set(handles.uvmat,'Pointer','watch')
693set(handles.RootPath,'BackgroundColor',[1 1 0])
694drawnow
695
[406]696%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
[387]697if ~exist('index','var')
698    index=1;
699end
700if index==1
701    handles_RootPath=handles.RootPath;
702    handles_SubDir=handles.SubDir;
703    handles_RootFile=handles.RootFile;
704    handles_FileIndex=handles.FileIndex;
705    handles_NomType=handles.NomType;
706    handles_FileExt=handles.FileExt;
707elseif index==2
708    handles_RootPath=handles.RootPath_1;
709    handles_SubDir=handles.SubDir_1;
710    handles_RootFile=handles.RootFile_1;
711    handles_FileIndex=handles.FileIndex_1;
712    handles_NomType=handles.NomType_1;
713    handles_FileExt=handles.FileExt_1;
714    set(handles.RootPath_1,'Visible','on')
715    set(handles.RootFile_1,'Visible','on')
716    set(handles.SubDir_1,'Visible','on');
717    set(handles.FileIndex_1,'Visible','on');
718    set(handles.FileExt_1,'Visible','on');
719    set(handles.NomType_1,'Visible','on');
720end
721
722%% detect root name, nomenclature and indices in the input file name:
[398]723[FilePath,FileName,FileExt]=fileparts(fileinput);
[387]724% detect the file type, get the movie object if relevant, and look for the corresponding file series:
[398]725% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
726[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
[387]727
728%% open the file or fill the GUI uvmat according to the detected file type
729switch FileType
730    case ''
731        msgbox_uvmat('ERROR','invalid input file type')
732    case 'txt'
733        edit(fileinput)
734    case 'figure'                           %display matlab figure
735        hfig=open(fileinput);
736        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
737        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
738        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
739    case {'xml','xls'}                % edit xml or Excel files
740        editxml(fileinput);
741    otherwise
742        set(handles_RootPath,'String',RootPath);
743        rootname=fullfile(RootPath,SubDir,RootFile);
744        set(handles_SubDir,'String',['/' SubDir]);
745        set(handles_RootFile,'String',['/' RootFile]); %display the separator
746        indices=fileinput(length(rootname)+1:end);
747        indices(end-length(FileExt)+1:end)=[]; %remove extension
748        set(handles_FileIndex,'String',indices);
749        set(handles_NomType,'String',NomType);
750        set(handles_FileExt,'String',FileExt);
751        if index==1
752            % fill file index counters if the first file series is opened
753            set(handles.i1,'String',num2str(i1));
754            set(handles.i2,'String',num2str(i2));
755            set(handles.j1,'String',num2stra(j1,NomType));
756            set(handles.j2,'String',num2stra(j2,NomType));
757        else %read the current field index if the second file series is opened
758            i1=str2num(get(handles.i1,'String'));
759            i2=str2num(get(handles.i2,'String'));
760            j1=stra2num(get(handles.j1,'String'));
761            j2=stra2num(get(handles.j2,'String'));
762        end
763       
764        % synchronise indices of the second  input file if it exists
765        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
766            Input=read_GUI(handles.InputFile);
767            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
768                Input.RootPath_1=Input.RootPath;
769            end
770            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
771                Input.SubDir_1=Input.SubDir;
772            end
773            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
774                Input.RootFile_1=Input.RootFile;
775            end
[405]776            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
777                Input.FileExt_1=Input.FileExt;
778            end
779            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
780                Input.NomType_1=Input.NomType;
781            end
[387]782            %updtate the indices of the second field series to correspond to the newly opened one
783            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1,i2,j1,j2);
784            if exist(FileName_1,'file')
785                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
786                set(handles.FileIndex_1,'String',FileIndex_1)
787            else
[408]788                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
789%                 set(handles.SubField,'Value',0)
790%                 SubField_Callback([], [], handles)
[387]791            end
792        end
793       
794        %enable other menus
795        set(handles.MenuOpen_1,'Enable','on')
796        set(handles.MenuFile_1_1,'Enable','on')
797        set(handles.MenuFile_2_1,'Enable','on')
798        set(handles.MenuFile_3_1,'Enable','on')
799        set(handles.MenuFile_4_1,'Enable','on')
800        set(handles.MenuFile_5_1,'Enable','on')
801        set(handles.MenuExport,'Enable','on')
802        set(handles.MenuExportFigure,'Enable','on')
803        set(handles.MenuExportMovie,'Enable','on')
804        set(handles.MenuTools,'Enable','on')
[424]805%         set(handles.OBJECT_txt,'Visible','on')
806%         set(handles.edit_object,'Visible','on')
807%          set(handles.ListObject_1,'Visible','on')
808%          set(handles.ViewObject,'Visible','on')
809%         set(handles.frame_object,'Visible','on')
[387]810       
811        % initiate input file series and refresh the current field view:     
812        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
813
814end
815
816%% set back the mouse pointer to arrow
817set(handles.uvmat,'Pointer','arrow')
818
819
820%------------------------------------------------------------------------
821% --- Update information about a new field series (indices to scan, timing,
822%     calibration from an xml file, then refresh current plots
[397]823function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
[387]824%------------------------------------------------------------------------
825%% define the relevant handles depending on the index (1=first file series, 2= second file series)
826if ~exist('index','var')
827    index=1;
828end
829if index==1
830    handles_RootPath=handles.RootPath;
831    handles_Fields=handles.Fields;
832elseif index==2
833    handles_RootPath=handles.RootPath_1;
834    handles_Fields=handles.Fields_1;
835end
836
837set(handles_RootPath,'BackgroundColor',[1 1 0])
838drawnow
839set(handles.Fields,'UserData',[])% reinialize data from uvmat opening
840UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
841UvData.NewSeries=1; %flag for run0: begin a new series
842UvData.TestInputFile=1;
843UvData.FileType{index}=FileType;
844UvData.i1_series{index}=i1_series;
845UvData.i2_series{index}=i2_series;
846UvData.j1_series{index}=j1_series;
847UvData.j2_series{index}=j2_series;
848% set(handles.CheckFixPair,'Value',1) % activate by default the comp_input '-'input window
849set(handles.FixVelType,'Value',0); %desactivate fixed veltype
850if index==1
851    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
852else
853    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
854end
855FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
856FileBase=fullfile(RootPath,RootFile);
857if ~exist(FileName,'file')
858   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
859    return
860end
861nbfield=[];%default
862nbfield_j=[];%default
863
864%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
865XmlData.Time=[];%default
866XmlData.GeometryCalib=[];%default
867TimeUnit=[];%default
868testima=0; %test for image input
869imainfo=[];
870ColorType='falsecolor'; %default
[397]871hhh=[];
872UvData.MovieObject{index}=VideoObject;
873if ~isempty(VideoObject)
874    imainfo=get(VideoObject);
[387]875    testima=1;
876    nbfield_j=1;
877    TimeUnit='s';
[397]878    XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
879    % %         nbfield=imainfo.NumberOfFrames;
880    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
881    ColorType='truecolor';
[387]882elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
883    testima=1;
884    if ~isequal(SubDir,'')
[397]885        RootFile=get(handles.RootFile,'String');
[387]886        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
887    else
888        imainfo=imfinfo([FileBase FileIndices FileExt]);
889    end
890    ColorType=imainfo.ColorType;%='truecolor' for color images
891    if length(imainfo) >1 %case of image with multiple frames
892        nbfield=length(imainfo);
893        nbfield_j=1;
[397]894    end
[387]895end
896if isfield(imainfo,'Width') && isfield(imainfo,'Height')
897    if length(imainfo)>1
898        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
899        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
900    else
901        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
902        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
903    end
904else
905    set(handles.num_Npx,'String','');%fills nbre of pixels x box
906    set(handles.num_Npy,'String','');%fills nbre of pixels x box
907end
908set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
909
910%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
[441]911SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
912filexml=fullfile(RootPath,[SubDirBase '.xml']);% new convention: xml above the image dir
913if ~exist(filexml,'file')
914    filexml=fullfile(RootPath,SubDir,[RootFile '.xml']);%old convention: xml within the image directroy
915end
[387]916warntext='';%default warning message
917NbSlice=1;%default
918set(handles.RootPath,'BackgroundColor',[1 1 1])
919if exist(filexml,'file')
920    set(handles.view_xml,'Visible','on')
921    set(handles.view_xml,'BackgroundColor',[1 1 0])
922    set(handles.view_xml,'String','view .xml')
923    drawnow
924    [XmlData,warntext]=imadoc2struct(filexml);
925    if ~isempty(warntext)
926        msgbox_uvmat('WARNING',warntext)
927    end
928    if isfield(XmlData,'TimeUnit')
929        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
930            TimeUnit=XmlData.TimeUnit;
931        end
932    end
933    set(handles.view_xml,'BackgroundColor',[1 1 1])
934    drawnow
935    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
936        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
937            set (handles.nb_slice,'String','volume')
938        end
939        hgeometry_calib=findobj('tag','geometry_calib');
940        if ~isempty(hgeometry_calib)
941            GUserData=get(hgeometry_calib,'UserData');
942            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
943                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
944                if strcmp(answer,'Yes')
945                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
946                end
947            end
948        end
949    end 
950else
[441]951    fileciv=fullfile(RootPath,SubDir,[RootFile '.civ']);
952    if exist(fileciv,'file')% if .civ file found (very old convention)
953        [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext(fileciv);
954        GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
955        GeometryCalib.Tx=0;
956        GeometryCalib.Ty=0;
957        GeometryCalib.Tz=1;
958        GeometryCalib.dpx=1;
959        GeometryCalib.dpy=1;
960        GeometryCalib.sx=1;
961        GeometryCalib.Cx=0;
962        GeometryCalib.Cy=0;
963        GeometryCalib.f=1;
964        GeometryCalib.kappa1=0;
965        GeometryCalib.CoordUnit='cm';
966        XmlData.GeometryCalib=GeometryCalib;
967        if error==2, warntext=['no file ' fileciv];
968        elseif error==1, warntext='inconsistent number of fields in the .civ file';
969        end
970        set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
971        set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
972        set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
973        set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
974        set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
975        set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
976        set(handles.view_xml,'Visible','on')
977        set(handles.view_xml,'String','view .civ')
978    else
979        set(handles.view_xml,'Visible','off')
980    end
[387]981end
982
983%% store last index in handles.lat_i and .last_j
984nbfield=max(max(i2_series));
985if isempty(nbfield)
986    nbfield=max(max(i1_series));
987end
988nbfield_j=max(max(j2_series));
989if isempty(nbfield_j)
990    nbfield_j=max(max(j1_series));
991end
992if ~isempty(XmlData.Time)
993    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
[441]994    if isequal(size(XmlData.Time,1),1)
995%     if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
[387]996        NomType=get(handles.NomType,'String');
[441]997%         if isempty(nbfield_j)
998%         if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
[387]999            XmlData.Time=(XmlData.Time)';
1000    end
1001end
1002last_i_cell=get(handles.last_i,'String');
1003if isempty(nbfield)
1004    last_i_cell{1}='';
1005else
1006    last_i_cell{1}=num2str(nbfield);
1007end
1008set(handles.last_i,'String',last_i_cell)
1009last_j_cell=get(handles.last_j,'String');
1010if isempty(nbfield_j)
1011     last_j_cell{1}='';
1012else
1013     last_j_cell{1}=num2str(nbfield_j);
1014end
1015set(handles.last_j,'String',last_j_cell);
1016
1017%% store geometric calibration in UvData
1018if isfield(XmlData,'GeometryCalib')
1019    GeometryCalib=XmlData.GeometryCalib;
1020    if isempty(GeometryCalib)
1021        set(handles.pxcm,'String','')
1022        set(handles.pycm,'String','')
1023        set(handles.transform_fct,'Value',1); %  no transform by default
1024    else
1025        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
1026            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
1027            set(handles.pxcm,'String','var')
1028            set(handles.pycm,'String','var')
1029        elseif isfield(GeometryCalib,'fx_fy')
1030            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
1031            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
1032            set(handles.pxcm,'String',num2str(pixcmx))
1033            set(handles.pycm,'String',num2str(pixcmy))
1034        end
1035        if ~get(handles.CheckFixLimits,'Value')
1036            set(handles.transform_fct,'Value',2); % phys transform by default if fixedLimits is off
1037        end
1038        if isfield(GeometryCalib,'SliceCoord')
1039           
1040           siz=size(GeometryCalib.SliceCoord);
1041           if siz(1)>1
1042               NbSlice=siz(1);
1043               set(handles.slices,'Visible','on')
1044               set(handles.slices,'Value',1)
1045           end
1046           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
1047               set(handles.nb_slice,'String','volume')
1048           else
1049               set(handles.nb_slice,'String',num2str(NbSlice))
1050           end
1051           slices_Callback([],[], handles)
1052        end           
1053    end
1054end
1055
1056%% update the data attached to the uvmat interface
1057if ~isempty(TimeUnit)
1058    set(handles.time_txt,'String',['time (' TimeUnit ')'])
1059end
1060UvData.TimeUnit=TimeUnit;
1061UvData.XmlData{index}=XmlData;
1062UvData.NewSeries=1;
1063% UvData.MovieObject=MovieObject;
1064
1065%display warning message
1066if ~isequal(warntext,'')
1067    msgbox_uvmat('WARNING',warntext);
1068end
1069
1070%% set default options in menu 'Fields'
1071if ~testima
1072    testcivx=0;
1073    if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
1074        set(handles_Fields,'Value',1)
1075        set(handles_Fields,'String',{'get_field...'})
1076        UvData=rmfield(UvData,'FieldsString');
1077    else
1078        Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
1079        if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
1080            FieldList=calc_field;
1081            set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
1082            set(handles_Fields,'Value',2) % set menu to 'velocity'
1083            col_vec=FieldList;
1084            col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
1085            testcivx=1;
1086        end
1087        if ~testcivx
1088            set(handles_Fields,'Value',1) % set menu to 'get_field...
1089            set(handles_Fields,'String',{'get_field...'})
1090            col_vec={'get_field...'};
1091        end
[405]1092        set(handles.ColorScalar,'String',col_vec)
[387]1093    end
1094end
1095set(handles.uvmat,'UserData',UvData)
1096
1097%% set index navigation options and refresh plots
1098scan_option='i';%default
1099state_j='off'; %default
1100if index==2
1101    if get(handles.scan_j,'Value')
1102        scan_option='j'; %keep the scan option for the second fiel series
1103    end
1104    if strcmp(get(handles.j1,'Visible'),'on')
1105        state_j='on';
1106    end
1107end
1108if ~isempty(j1_series)
1109        state_j='on';
1110        if isequal(nbfield,1) &&index==1
1111            scan_option='j'; %scan j index by default if nbfield=1               
1112        end
1113end
1114if isequal(scan_option,'i')
1115     set(handles.scan_i,'Value',1)
1116     scan_i_Callback([],[], handles);
1117else
1118     set(handles.scan_j,'Value',1)
1119     scan_j_Callback([],[], handles);
1120end
1121set(handles.scan_j,'Visible',state_j)
1122set(handles.j1,'Visible',state_j)
1123set(handles.j2,'Visible',state_j)
1124set(handles.last_j,'Visible',state_j);
1125set(handles.frame_j,'Visible',state_j);
1126set(handles.j_text,'Visible',state_j);
1127if ~isempty(i2_series)||~isempty(j2_series)
1128    set(handles.CheckFixPair,'Visible','on')
1129elseif index==1
1130    set(handles.CheckFixPair,'Visible','off')
1131end
1132
1133%% view the field 
1134run0_Callback([],[], handles); %view field
1135mask_test=get(handles.CheckMask,'value');
1136if mask_test
1137    MaskData=get(handles.CheckMask,'UserData');
1138    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1139          delete(MaskData.maskhandle)    %delete old mask
1140    end
1141    CheckMask_Callback([],[],handles)
1142end
1143
[406]1144%% update list of recent files in the menubar and save it for future opening
[387]1145MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
1146    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
1147str_find=strcmp(FileName,MenuFile);
1148if isempty(find(str_find,1))
1149    MenuFile=[{FileName};MenuFile];%insert the current file if not already in the list
1150end
1151for ifile=1:min(length(MenuFile),5)
1152    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
1153    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
1154end
1155dir_perso=prefdir;
1156profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1157if exist(profil_perso,'file')
1158    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1159else
1160    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
1161end
1162
1163
1164%------------------------------------------------------------------------
1165% --- switch file index scanning options scan_i and scan_j in an exclusive way
1166function scan_i_Callback(hObject, eventdata, handles)
1167%------------------------------------------------------------------------
1168if get(handles.scan_i,'Value')==1
1169    set(handles.scan_i,'BackgroundColor',[1 1 0])
1170    set(handles.scan_j,'Value',0)
1171else
1172    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1173    set(handles.scan_j,'Value',1)
1174end
1175scan_j_Callback(hObject, eventdata, handles)
1176
1177%------------------------------------------------------------------------
1178% --- switch file index scanning options scan_i and scan_j in an exclusive way
1179function scan_j_Callback(hObject, eventdata, handles)
1180%------------------------------------------------------------------------
1181if get(handles.scan_j,'Value')==1
1182    set(handles.scan_j,'BackgroundColor',[1 1 0])
1183    set(handles.scan_i,'Value',0)
1184    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1185%     NomType=get(handles.NomType,'String');
1186%     switch NomType
1187%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1188%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1189%     otherwise
1190%         set(handles.CheckFixPair,'Visible','off')
1191%     end
1192else
1193    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1194    set(handles.scan_i,'Value',1)
1195    set(handles.scan_i,'BackgroundColor',[1 1 0])
1196    set(handles.CheckFixPair,'Visible','off')
1197end
1198
1199%------------------------------------------------------------------------
1200function i1_Callback(hObject, eventdata, handles)
1201%------------------------------------------------------------------------
1202set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])
1203NomType=get(handles.NomType,'String');
1204i1=stra2num(get(handles.i1,'String'));
1205i2=stra2num(get(handles.i2,'String'));
1206j1=stra2num(get(handles.j1,'String'));
1207j2=stra2num(get(handles.j2,'String'));
1208indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1209%indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,'');
1210set(handles.FileIndex,'String',indices)
1211set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])
1212if get(handles.SubField,'Value')==1
1213    NomType_1=get(handles.NomType_1,'String');
1214    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1215     %indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,'');
1216     set(handles.FileIndex_1,'String',indices)
1217     set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])
1218end
1219
1220%------------------------------------------------------------------------
1221function i2_Callback(hObject, eventdata, handles)
1222%------------------------------------------------------------------------
1223set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])
1224i1_Callback(hObject, eventdata, handles)
1225
1226%------------------------------------------------------------------------
1227function j1_Callback(hObject, eventdata, handles)
1228%------------------------------------------------------------------------
1229set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])
1230i1_Callback(hObject, eventdata, handles)
1231
1232%------------------------------------------------------------------------
1233function j2_Callback(hObject, eventdata, handles)
1234%------------------------------------------------------------------------
1235set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])
1236i1_Callback(hObject, eventdata, handles)
1237
1238%------------------------------------------------------------------------
1239function slices_Callback(hObject, eventdata, handles)
1240%------------------------------------------------------------------------
1241if get(handles.slices,'Value')==1
1242    set(handles.slices,'BackgroundColor',[1 1 0])
1243    set(handles.nb_slice,'Visible','on')
1244    set(handles.z_text,'Visible','on')
1245    set(handles.z_index,'Visible','on')
1246    nb_slice_Callback(hObject, eventdata, handles)
1247else
1248    set(handles.nb_slice,'Visible','off')
1249    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1250    set(handles.z_text,'Visible','off')
1251    set(handles.z_index,'Visible','off')
1252    set(handles.masklevel,'Value',1)
1253    set(handles.masklevel,'String',{'1'})
1254end
1255
1256%------------------------------------------------------------------------
1257function nb_slice_Callback(hObject, eventdata, handles)
1258%------------------------------------------------------------------------
1259nb_slice_str=get(handles.nb_slice,'String');
1260if isequal(nb_slice_str,'volume')
1261    num=stra2num(get(handles.j1,'String'));
1262    last_j=get(handles.last_j,'String');
1263    nbslice=str2double(last_j{1});
1264else
1265    num=str2double(get(handles.i1,'String'));
1266    nbslice=str2double(get(handles.nb_slice,'String'));
1267end
1268z=mod(num-1,nbslice)+1;
1269set(handles.z_index,'String',num2str(z))
1270for ilist=1:nbslice
1271    list_index{ilist,1}=num2str(ilist);
1272end   
1273set(handles.masklevel,'String',list_index)
1274set(handles.masklevel,'Value',z)
1275
1276%------------------------------------------------------------------------
1277% --- Executes on button press in view_xml.
1278function view_xml_Callback(hObject, eventdata, handles)
1279%------------------------------------------------------------------------
1280%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1281 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1282FileBase=fullfile(RootPath,RootFile);
1283option=get(handles.view_xml,'String');
1284if isequal(option,'view .xml')
1285    FileXml=[FileBase '.xml'];
1286    heditxml=editxml(FileXml);
1287end
1288
1289%------------------------------------------------------------------------
1290% --- Executes on button press in CheckMask.
1291function CheckMask_Callback(hObject, eventdata, handles)
1292%------------------------------------------------------------------------
1293%case of view mask selection
1294if isequal(get(handles.CheckMask,'Value'),1)
1295   % [FF,RootPath,FileBase]=read_file_boxes(handles);
1296     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1297     FileBase=fullfile(RootPath,RootFile);
1298    num_i1=stra2num(get(handles.i1,'String'));
1299    num_j1=stra2num(get(handles.j1,'String'));
1300    currentdir=pwd; 
1301    cd(RootPath);
1302    maskfiles=dir('*_*mask_*.png');%look for a mask file
1303    cd(currentdir);%come back to the working directory
1304    mdetect=0;
1305    if ~isempty(maskfiles)
1306        for ilist=1:length(maskfiles)
1307            maskname=maskfiles(ilist).name;% take the first mask file in the list
1308            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1309%             [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname);
1310             [tild,Name]=fileparts(maskname);
1311            Namedouble=double(Name);
1312            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1313            ind_mask=findstr('mask',Name);
1314            i=ind_mask-1;
1315            while val(i)==0 && i>0
1316                i=i-1;
1317            end
1318            nbmask_str=str2num(Name(i+1:ind_mask-1));
1319            if ~isempty(nbmask_str)
1320                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1321            end
1322        end
1323        if isequal(min(nbslice),max(nbslice))
1324            nbslice=nbslice(1);
1325        else
1326            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1327            return
1328        end
1329        if ~isempty(nbslice) && Name(i)=='_'
1330            Mask.Base=[FileBase Name(i:ind_mask+3)];
1331            Mask.NbSlice=nbslice;
1332            num_i1=mod(num_i1-1,nbslice)+1;
1333            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1334            [RootPath,RootFile]=fileparts(Mask.Base);
1335            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1336            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1337            mdetect=exist(maskname,'file');
1338            if mdetect
1339                set(handles.nb_slice,'String',Name(i+1:ind_mask-1));
1340                set(handles.nb_slice,'BackgroundColor',[1 1 0])
1341                set(handles.CheckMask,'UserData',Mask);
1342                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1343                if nbslice > 1
1344                    set(handles.slices,'value',1)
1345                    slices_Callback(hObject, eventdata, handles)
1346                end
1347            end
1348        end
1349    end
1350    errormsg=[];%default
1351    if mdetect==0
1352        [FileName, PathName, filterindex] = uigetfile( ...
1353            {'*.png', ' (*.png)';
1354            '*.png',  '.png files '; ...
1355            '*.*', 'All Files (*.*)'}, ...
1356            'Pick a mask file *.png',FileBase);
1357        maskname=fullfile(PathName,FileName);
1358        if ~exist(maskname,'file')
1359            errormsg='no file browsed';
1360        end
1361        [RootDir,tild,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1362%         [RootDir,RootFile,x1,x2,xa,xb,xext,Mask.NomType]=name2display(maskname);
1363        Mask.Base=fullfile(RootDir,RootFile);
1364        Mask.NbSlice=1;
1365        set(handles.CheckMask,'UserData',Mask);
1366        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1367    end
1368    if isempty(errormsg)
1369        errormsg=update_mask(handles,num_i1,num_j1);
1370    end
1371    if ~isempty(errormsg)
1372            set(handles.CheckMask,'Value',0)
1373            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1374     end
1375else % desactivate mask display
1376    MaskData=get(handles.CheckMask,'UserData');
1377    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1378          delete(MaskData.maskhandle)   
1379    end
1380    set(handles.CheckMask,'UserData',[])   
1381    UvData=get(handles.uvmat,'UserData');
1382    if isfield(UvData,'MaskName')
1383        UvData=rmfield(UvData,'MaskName');
1384        set(handles.uvmat,'UserData',UvData)
1385    end
1386    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1387end
1388
1389%------------------------------------------------------------------------
1390function errormsg=update_mask(handles,num_i1,num_j1)
1391%------------------------------------------------------------------------
1392errormsg=[];%default
1393MaskData=get(handles.CheckMask,'UserData');
1394if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1395    uistack(MaskData.maskhandle,'top');
1396end
1397num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1398[RootPath,RootFile]=fileparts(MaskData.Base);
1399MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1400%MaskName=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType);
1401% huvmat=get(handles.CheckMask,'parent');
1402UvData=get(handles.uvmat,'UserData');
1403%update mask image if the mask is new
1404if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1405    UvData.MaskName=MaskName; %update the recorded name on UvData
1406    set(handles.uvmat,'UserData',UvData);
1407    if ~exist(MaskName,'file')
1408        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1409            delete(MaskData.maskhandle)   
1410        end
1411    else
1412        %read mask image
1413        Mask.AName='image';
1414        Mask.A=imread(MaskName);
1415        npxy=size(Mask.A);
1416        test_error=0;
1417        if length(npxy)>2
1418            errormsg=[MaskName ' is not a grey scale image'];
1419            return
1420        elseif ~isa(Mask.A,'uint8')
1421            errormsg=[MaskName ' is not a 8 bit grey level image'];
1422            return
1423        end
1424        Mask.AX=[0.5 npxy(2)-0.5];
1425        Mask.AY=[npxy(1)-0.5 0.5 ];
1426        Mask.CoordUnit='pixel';
1427        if isequal(get(handles.slices,'Value'),1)
1428           NbSlice=str2num(get(handles.nb_slice,'String'));
1429           num_i1=str2num(get(handles.i1,'String'));
1430           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1431        end
1432        %px to phys or other transform on field
1433         menu_transform=get(handles.transform_fct,'String');
1434        choice_value=get(handles.transform_fct,'Value');
1435        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1436        transform_list=get(handles.transform_fct,'UserData');
1437        transform=transform_list{choice_value};
1438        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1439            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1440                Calib=UvData.XmlData{1}.GeometryCalib;
1441                Mask=transform(Mask,UvData.XmlData{1});
1442            end
1443        end
1444        flagmask=Mask.A < 200;
1445       
1446        %make brown color image
1447        imflag(:,:,1)=0.9*flagmask;
1448        imflag(:,:,2)=0.7*flagmask;
1449        imflag(:,:,3)=zeros(size(flagmask));
1450       
1451        %update mask image
1452        hmask=[]; %default
1453        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1454            hmask=MaskData.maskhandle;
1455        end
1456        if ~isempty(hmask)
1457            set(hmask,'CData',imflag)   
1458            set(hmask,'AlphaData',flagmask*0.6)
1459            set(hmask,'XData',Mask.AX);
1460            set(hmask,'YData',Mask.AY);
1461%             uistack(hmask,'top')
1462        else
1463            axes(handles.axes3)
1464            hold on   
1465            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1466%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1467            set(handles.CheckMask,'UserData',MaskData)
1468        end
1469    end
1470end
1471
1472%------------------------------------------------------------------------
1473%------------------------------------------------------------------------
1474% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1475%------------------------------------------------------------------------
1476
1477%------------------------------------------------------------------------
1478% --- Executes on button press in runplus: make one step forward and call
1479% --- run0. The step forward is along the fields series 1 or 2 depending on
1480% --- the scan_i and scan_j check box (exclusive each other)
1481function runplus_Callback(hObject, eventdata, handles)
1482%------------------------------------------------------------------------
1483set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1484drawnow
1485%TODO: introduce the option: increment ='*' to move to the next available view
1486increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1487% if isnan(increment)
1488%     set(handles.increment_scan,'String','1')%default value
1489%     increment=1;
1490% end
1491errormsg=runpm(hObject,eventdata,handles,increment);
1492if ~isempty(errormsg)
1493    msgbox_uvmat('ERROR',errormsg);
1494end
1495set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1496
1497%------------------------------------------------------------------------
1498% --- Executes on button press in runmin: make one step backward and call
1499% --- run0. The step backward is along the fields series 1 or 2 depending on
1500% --- the scan_i and scan_j check box (exclusive each other)
1501function runmin_Callback(hObject, eventdata, handles)
1502%------------------------------------------------------------------------
1503set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1504drawnow
1505increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1506% if isnan(increment)
1507%     set(handles.increment_scan,'String','1')%default value
1508%     increment=1;
1509% end
1510errormsg=runpm(hObject,eventdata,handles,increment);
1511if ~isempty(errormsg)
1512    msgbox_uvmat('ERROR',errormsg);
1513end
1514set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1515
1516%------------------------------------------------------------------------
1517% -- Executes on button press in Movie: make a series of +> steps
1518function Movie_Callback(hObject, eventdata, handles)
1519%------------------------------------------------------------------------
1520set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1521drawnow
1522increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
1523% if isnan(increment)
1524%     set(handles.increment_scan,'String','1')%default value
1525%     increment=1;
1526% end
1527set(handles.STOP,'Visible','on')
1528set(handles.speed,'Visible','on')
1529set(handles.speed_txt,'Visible','on')
1530set(handles.Movie,'BusyAction','queue')
1531UvData=get(handles.uvmat,'UserData');
1532
[435]1533while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
[387]1534        errormsg=runpm(hObject,eventdata,handles,increment);
1535        if ~isempty(errormsg)
1536            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1537            return
1538        end
1539        pause(1.02-get(handles.speed,'Value'))% wait for next image
1540end
1541if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1542    UvData.aviobj=close(UvData.aviobj);
1543   set(handles.uvmat,'UserData',UvData);
1544end
1545set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1546
1547%------------------------------------------------------------------------
1548% -- Executes on button press in Movie: make a series of <- steps
1549function MovieBackward_Callback(hObject, eventdata, handles)
1550%------------------------------------------------------------------------
1551set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1552drawnow
1553increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d
1554set(handles.STOP,'Visible','on')
1555set(handles.speed,'Visible','on')
1556set(handles.speed_txt,'Visible','on')
1557set(handles.MovieBackward,'BusyAction','queue')
1558UvData=get(handles.uvmat,'UserData');
1559
[435]1560while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
[387]1561        errormsg=runpm(hObject,eventdata,handles,increment);
1562        if ~isempty(errormsg)
1563            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1564            return
1565        end
1566        pause(1.02-get(handles.speed,'Value'))% wait for next image
1567end
1568if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1569    UvData.aviobj=close(UvData.aviobj);
1570   set(handles.uvmat,'UserData',UvData);
1571end
1572set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1573
1574%------------------------------------------------------------------------
1575function STOP_Callback(hObject, eventdata, handles)
1576%------------------------------------------------------------------------
1577set(handles.movie_pair,'BusyAction','Cancel')
1578set(handles.movie_pair,'value',0)
1579set(handles.Movie,'BusyAction','Cancel')
1580set(handles.MovieBackward,'BusyAction','Cancel')
1581set(handles.MenuExportMovie,'BusyAction','Cancel')
1582set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1583set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1584set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1585
1586%------------------------------------------------------------------------
1587% --- function activated by runplus and run minus
1588function errormsg=runpm(hObject,eventdata,handles,increment)
1589%------------------------------------------------------------------------
1590errormsg='';%default
1591%% check for movie pair status
1592movie_status=get(handles.movie_pair,'Value');
1593if isequal(movie_status,1)
1594    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1595end
1596
1597%% read the current input file name(s) and field indices
1598InputFile=read_GUI(handles.InputFile);
1599InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1600InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1601FileExt=InputFile.FileExt;
1602NomType=get(handles.NomType,'String');
1603i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1604i2=[];%default
1605if strcmp(get(handles.i2,'Visible'),'on')
1606    i2=str2num(get(handles.i2,'String'));
1607end
1608j1=[];
1609if strcmp(get(handles.j1,'Visible'),'on')
1610    j1=stra2num(get(handles.j1,'String'));
1611end
1612j2=j1;
1613if strcmp(get(handles.j2,'Visible'),'on')
1614    j2=stra2num(get(handles.j2,'String'));
1615end
1616sub_value= get(handles.SubField,'Value');
1617if sub_value % a second input file has been entered
[428]1618     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1619    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);
1620%     InputFile.NomType_1=get(handles.NomType_1,'String');
[387]1621else
1622    filename_1=[];
1623end   
1624
1625%% increment (or decrement) the field indices and update the input filename(s)
1626CheckSearch=0;
1627if isempty(increment)
1628    CheckSearch=1;% search for the next available file
1629    set(handles.CheckFixPair,'Value',0)
1630end
1631CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
[427]1632
1633% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
[387]1634if CheckFixPair
1635    if get(handles.scan_i,'Value')==1% case of scanning along index i
1636        i1=i1+increment;
1637        i2=i2+increment;
1638        if sub_value
1639            i1_1=i1_1+increment;
1640            i2_1=i2_1+increment;
1641        end
1642    else % case of scanning along index j (burst numbers)
1643        j1=j1+increment;
1644        j2=j2+increment;
1645        if sub_value
1646            j1_1=j1_1+increment;
1647            j2_1=j2_1+increment;
1648        end
1649    end
[427]1650   
1651% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected):
1652% the list of existing indices recorded in UvData is used
[387]1653else
1654    UvData=get(handles.uvmat,'UserData');
1655    ref_i=i1;
1656    if ~isempty(i2)
[427]1657        ref_i=floor((i1+i2)/2);% current reference index i
[387]1658    end
1659    ref_j=1;
1660    if ~isempty(j1)
1661        ref_j=j1;
1662        if ~isempty(j2)
[427]1663            ref_j=floor((j1+j2)/2);% current reference index j
[387]1664        end
1665    end
1666    if ~isempty(increment)
1667        if get(handles.scan_i,'Value')==1% case of scanning along index i
[427]1668            ref_i=ref_i+increment;% increment the current reference index i
[387]1669        else % case of scanning along index j (burst numbers)
[427]1670            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
[387]1671        end
[388]1672    else % free increment
[387]1673        if isequal(get(handles.runplus,'BackgroundColor'),[1 1 0])% if runplus is activated
1674            step=1;
1675        else
1676            step=-1;
1677        end
1678        if get(handles.scan_i,'Value')==1% case of scanning along index i
1679            ref_i=ref_i+step;
1680            while ref_i>=0  && size(UvData.i1_series{1},1)>=ref_i+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
1681                ref_i=ref_i+step;
1682            end
1683        else % case of scanning along index j (burst numbers)
1684            ref_j=ref_j+step;
1685            while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0
1686                ref_j=ref_j+step;
1687            end
1688        end
1689    end
1690    if ref_i<0
1691        errormsg='minimum i index reached';
1692    elseif ref_j<0
1693        errormsg='minimum j index reached';
1694    elseif ref_i+1>size(UvData.i1_series{1},1)
1695        errormsg='maximum i index reached';
1696    elseif ref_j+1>size(UvData.i1_series{1},2)
1697        errormsg='maximum j index reached';
1698    end
1699    if ~isempty(errormsg)
1700        return
1701    end
[427]1702    i1_subseries=UvData.i1_series{1}(ref_i+1,ref_j+1,:);
[387]1703    i1_subseries=i1_subseries(i1_subseries>0);
1704    if isempty(i1_subseries)
1705        errormsg='no next file';
1706        return
[427]1707    else
1708        i1=i1_subseries(end);
[387]1709    end
1710    if ~isempty(UvData.i2_series{1})
[427]1711        i2_subseries=UvData.i2_series{1}(ref_i+1,ref_j+1,:);
[387]1712        i2_subseries=i2_subseries(i2_subseries>0);
1713        i2=i2_subseries(end);
1714    end
1715    if ~isempty(UvData.j1_series{1})
[427]1716        j1_subseries=UvData.j1_series{1}(ref_i+1,ref_j+1,:);
[387]1717        j1_subseries=j1_subseries(j1_subseries>0);
1718        j1=j1_subseries(end);
1719    end
1720    if ~isempty(UvData.j2_series{1})
[427]1721        j2_subseries=UvData.j2_series{1}(ref_i+1,ref_j+1,:);
[387]1722        j2_subseries=j2_subseries(j2_subseries>0);
1723        j2=j2_subseries(end);
[427]1724    end 
1725    % case of a second file series
1726    if numel(UvData.i1_series)>=2
1727        i1_subseries=UvData.i1_series{2}(ref_i+1,ref_j+1,:);
1728        i1_subseries=i1_subseries(i1_subseries>0);
1729        i1_1=i1_subseries(end);
1730        if ~isempty(UvData.i2_series{2})
1731            i2_subseries=UvData.i2_series{2}(ref_i+1,ref_j+1,:);
1732            i2_subseries=i2_subseries(i2_subseries>0);
1733            i2_1=i2_subseries(end);
1734        end
1735        if ~isempty(UvData.j1_series{2})
1736            j1_subseries=UvData.j1_series{2}(ref_i+1,ref_j+1,:);
1737            j1_subseries=j1_subseries(j1_subseries>0);
1738            j1_1=j1_subseries(end);
1739        end
1740        if ~isempty(UvData.j2_series{2})
1741            j2_subseries=UvData.j2_series{2}(ref_i+1,ref_j+1,:);
1742            j2_subseries=j2_subseries(j2_subseries>0);
1743            j2_1=j2_subseries(end);
1744        end
[387]1745    end
1746end
1747filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1748if sub_value
[428]1749    filename_1=fullfile_uvmat(InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileExt_1,InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
[387]1750end
1751
1752%% refresh plots
1753errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2);
1754
1755%% update the index counters if the index move is successfull
1756if isempty(errormsg)
1757    set(handles.i1,'String',num2stra(i1,NomType,1));
1758    if isequal(i2,i1)
1759        set(handles.i2,'String','');
1760    else
1761        set(handles.i2,'String',num2stra(i2,NomType,1));
1762    end
1763    set(handles.j1,'String',num2stra(j1,NomType,2));
1764    if isequal(j2,j1)
1765        set(handles.j2,'String','');
1766    else
1767        set(handles.j2,'String',num2stra(j2,NomType,2));
1768    end
1769    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1770    set(handles.FileIndex,'String',indices);
1771    if ~isempty(filename_1)
[428]1772        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
[387]1773        set(handles.FileIndex_1,'String',indices_1);
1774    end
1775    if isequal(movie_status,1)
1776        set(handles.movie_pair,'Value',1)
1777        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1778    end
1779end
1780
1781%------------------------------------------------------------------------
1782% --- Executes on button press in movie_pair: create an alternating movie with two view
1783function movie_pair_Callback(hObject, eventdata, handles)
1784%------------------------------------------------------------------------
1785%% stop movie action if the movie_pair button is off
1786if ~get(handles.movie_pair,'value')
1787    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1788    set(handles.i2,'String','')
1789    set(handles.j2,'String','')
1790    return
1791else
1792    set(handles.movie_pair,'BusyAction','queue')
1793end
1794
1795%% initialisation
1796set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1797drawnow
1798list_fields=get(handles.Fields,'String');% list menu fields
1799index_fields=get(handles.Fields,'Value');% selected string index
1800FieldName=list_fields{index_fields}; % selected field
1801UvData=get(handles.uvmat,'UserData');
1802if isequal(FieldName,'image')
1803    test_1=0;
1804    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1805    NomType=get(handles.NomType,'String');
1806else
1807    list_fields=get(handles.Fields_1,'String');% list menu fields
1808    index_fields=get(handles.Fields_1,'Value');% selected string index
1809    FieldName=list_fields{index_fields}; % selected field
1810    if isequal(FieldName,'image')
1811        test_1=1;
1812        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1813    else
1814        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1815        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1816        set(handles.movie_pair,'Value',0)
1817        return
1818    end
1819end
1820num_i1=str2num(get(handles.i1,'String'));
1821num_j1=stra2num(get(handles.j1,'String'));
1822num_i2=str2num(get(handles.i2,'String'));
1823num_j2=stra2num(get(handles.j2,'String'));
1824if isempty(num_j2)
1825    if isempty(num_i2)   
1826        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1827        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1828         set(handles.movie_pair,'Value',0)
1829        return
1830    else
1831        num_j2=num_j1;%repeat the index i1 by default
1832    end
1833end
1834if isempty(num_i2)
1835    num_i2=num_i1;%repeat the index i1 by default
1836end
1837% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType);
[439]1838imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
[387]1839if ~exist(imaname_1,'file')
1840      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1841      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1842       set(handles.movie_pair,'Value',0)
1843      return
1844end
1845
1846%% read the second image
1847Field.AName='image';
1848if test_1
1849    Field_a=UvData.Field_1;
1850else
1851    Field_a=UvData.Field;
1852end
1853Field_b.AX=Field_a.AX;
1854Field_b.AY=Field_a.AY;
1855% z index
1856nbslice=str2double(get(handles.nb_slice,'String'));
1857if ~isempty(nbslice)
1858    Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1859end
1860Field_b.CoordUnit='pixel';
1861
1862%% determine the input file type
1863if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1864    FileType='movie';
1865elseif isequal(lower(Ext),'.avi')
1866    FileType='avi';
1867elseif isequal(lower(Ext),'.vol')
1868    FileType='vol';
1869else
1870   form=imformats(Ext(2:end));
1871   if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1872       if isequal(NomType,'*');
1873           FileType='multimage';
1874       else
1875           FileType='image';
1876       end
1877   end
1878end
1879switch FileType
1880        case 'movie'
1881            if test_1
1882                Field_b.A=read(UvData.MovieObject{2},num_i2);
1883            else
1884                Field_b.A=read(UvData.MovieObject{1},num_i2);
1885            end
1886        case 'avi'
1887            mov=aviread(imaname_1,num_i2);
1888            Field_b.A=frame2im(mov(1));
1889        case 'vol'
1890            Field_b.A=imread(imaname_1);
1891        case 'multimage'
1892            Field_b.A=imread(imaname_1,num_i2);
1893        case 'image'
1894            Field_b.A=imread(imaname_1);
1895end
1896if get(handles.slices,'Value')
1897    Field.ZIndex=str2double(get(handles.z_index,'String'));
1898end
1899
1900%px to phys or other transform on field
1901menu_transform=get(handles.transform_fct,'String');
1902choice_value=get(handles.transform_fct,'Value');
1903transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1904transform_list=get(handles.transform_fct,'UserData');
1905transform=transform_list{choice_value};
1906if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1907    if test_1 && isfield(UvData,'XmlData') && numel(UvData.XmlData)==2 && isfield(UvData.XmlData{2},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1908        Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform
1909        Field_b=transform(Field_b,UvData.XmlData{2});
1910    elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib
1911        Field_b=transform(Field_b,UvData.XmlData{1});
1912    end
1913end
1914
1915 % make movie until movie speed is set to 0 or STOP is activated
1916hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER)
1917set(handles.STOP,'Visible','on')
1918set(handles.speed,'Visible','on')
1919set(handles.speed_txt,'Visible','on')
1920while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1921    % read and plot the series of images in non erase mode
1922    set(hima,'CData',Field_b.A);
1923    pause(1.02-get(handles.speed,'Value'));% wait for next image
1924    set(hima,'CData',Field_a.A);
1925    pause(1.02-get(handles.speed,'Value'));% wait for next image
1926end
1927set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1928 set(handles.movie_pair,'Value',0)
1929
1930%------------------------------------------------------------------------
1931% --- Executes on button press in run0.
1932function run0_Callback(hObject, eventdata, handles)
1933%------------------------------------------------------------------------
1934set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1935drawnow
1936[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1937filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
1938filename_1=[];%default
1939if get(handles.SubField,'Value')
1940    [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
1941    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
1942end
1943num_i1=stra2num(get(handles.i1,'String'));
1944num_i2=stra2num(get(handles.i2,'String'));
1945num_j1=stra2num(get(handles.j1,'String'));
1946num_j2=stra2num(get(handles.j2,'String'));
1947
1948errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
1949
1950if ~isempty(errormsg)
1951      msgbox_uvmat('ERROR',errormsg);
1952else
1953    set(handles.i1,'BackgroundColor',[1 1 1])
1954    set(handles.i2,'BackgroundColor',[1 1 1])
1955    set(handles.j1,'BackgroundColor',[1 1 1])
1956    set(handles.j2,'BackgroundColor',[1 1 1])
1957    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1958    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1959end   
1960set(handles.run0,'BackgroundColor',[1 0 0])
1961
1962
1963%------------------------------------------------------------------------
1964% --- read the input files and refresh all the plots, including projection.
1965% OUTPUT:
1966%  errormsg: error message char string  =[] by default
1967% INPUT:
1968% filename: first input file (=[] in the absence of input file)
1969% filename_1: second input file (=[] in the asbsenc of secodn input file)
1970% num_i1,num_i2,num_j1,num_j2; frame indices
1971% Field: structure describing an optional input field (then replace the input file)
[397]1972
[387]1973function errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,Field)
1974%------------------------------------------------------------------------
1975
1976%% initialisation
1977abstime=[];
1978abstime_1=[];
1979dt=[];
1980if ~exist('Field','var')
1981    Field={};
1982end
1983UvData=get(handles.uvmat,'UserData');
1984if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1985    delete(handles.UVMAT_title)
1986end
1987
1988%% determine the main input file information for action
1989FileType=[];%default
1990if ~exist(filename,'file')
1991    errormsg=['input file ' filename ' does not exist'];
1992    return
1993end
1994NomType=get(handles.NomType,'String');
1995% NomType=get(handles.FileIndex,'UserData');
1996%update the z position index
1997nbslice_str=get(handles.nb_slice,'String');
1998if isequal(nbslice_str,'volume')%NOT USED
1999    z_index=num_j1;
2000    set(handles.z_index,'String',num2str(z_index))
2001else
2002    nbslice=str2num(nbslice_str);
2003    z_index=mod(num_i1-1,nbslice)+1;
2004    set(handles.z_index,'String',num2str(z_index))
2005end
2006% refresh menu for save_mask if relevant
2007masknumber=get(handles.masklevel,'String');
2008if length(masknumber)>=z_index
2009    set(handles.masklevel,'Value',z_index)
2010end
2011
2012%% read the first input field if a filename has been introduced
[421]2013ParamIn.ColorVar='';%default variable name for vector color
[387]2014if ~isempty(filename)
2015    ObjectName=filename;
[404]2016    FieldName='';%default
2017    VelType='';%default
2018%     FileType=UvData.FileType{1};
2019    switch UvData.FileType{1}
[387]2020        case {'civx','civdata','netcdf'};
2021            list_fields=get(handles.Fields,'String');% list menu fields
[404]2022  %          index_fields=get(handles.Fields,'Value');% selected string index
2023            FieldName= list_fields{get(handles.Fields,'Value')}; % selected field
[387]2024            if ~strcmp(FieldName,'get_field...')
[389]2025                if get(handles.FixVelType,'Value')
2026                    VelTypeList=get(handles.VelType,'String');
2027                    VelType=VelTypeList{get(handles.VelType,'Value')};
[387]2028                end
2029            end
2030            if strcmp(FieldName,'velocity')
[405]2031                list_code=get(handles.ColorCode,'String');% list menu fields
2032                index_code=get(handles.ColorCode,'Value');% selected string index
[387]2033                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
[405]2034                    list_code=get(handles.ColorScalar,'String');% list menu fields
2035                    index_code=get(handles.ColorScalar,'Value');% selected string index
[387]2036                    ParamIn.ColorVar= list_code{index_code}; % selected field
2037                end
2038            end
[435]2039        case {'video','mmreader'}
[387]2040            ObjectName=UvData.MovieObject{1};         
2041        case 'vol' %TODO: update
2042            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2043                ParamIn.Npy=UvData.XmlData.Npy;
2044                ParamIn.Npx=UvData.XmlData.Npx;
2045            else           
2046                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2047                return
2048            end
2049    end
2050    ParamIn.FieldName=FieldName;
2051    ParamIn.VelType=VelType;
2052    ParamIn.GUIName='get_field';
[404]2053    [Field{1},ParamOut,errormsg] = read_field(ObjectName,UvData.FileType{1},ParamIn,num_i1);
[387]2054    if ~isempty(errormsg)
2055        errormsg=['error in reading ' filename ': ' errormsg];
2056        return
2057    end 
2058    if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2059        set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2060        set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2061    end
[415]2062    if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
[387]2063        set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2064    end
2065    if isfield(ParamOut,'TimeValue')
[415]2066        Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
[387]2067    end
2068end
2069
[405]2070%% choose and read a second field filename_1 if defined
[387]2071VelType_1=[];%default
2072FieldName_1=[];
2073ParamOut_1=[];
2074if ~isempty(filename_1)
2075    if ~exist(filename_1,'file')
2076        errormsg=['second file ' filename_1 ' does not exist'];
2077        return
2078    end
2079    Name=filename_1;
[404]2080    switch UvData.FileType{2}
[387]2081        case {'civx','civdata','netcdf'};
2082            list_fields=get(handles.Fields_1,'String');% list menu fields
[389]2083            FieldName_1= list_fields{get(handles.Fields_1,'Value')}; % selected field
[387]2084            if ~strcmp(FieldName,'get_field...')
[389]2085                if get(handles.FixVelType,'Value')
2086                    VelTypeList=get(handles.VelType_1,'String');
2087                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
[387]2088                end
2089            end
[405]2090            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2091                list_code=get(handles.ColorCode,'String');% list menu fields
2092                index_code=get(handles.ColorCode,'Value');% selected string index
[387]2093                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
[405]2094                    list_code=get(handles.ColorScalar,'String');% list menu fields
2095                    index_code=get(handles.ColorScalar,'Value');% selected string index
2096                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
[387]2097                end
2098            end
[435]2099        case {'video','mmreader'}
[387]2100            Name=UvData.MovieObject{2};
2101        case 'vol' %TODO: update
2102            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
[405]2103                ParamIn_1.Npy=UvData.XmlData.Npy;
2104                ParamIn_1.Npx=UvData.XmlData.Npx;
[387]2105            else
2106                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2107                return
2108            end
2109    end
[428]2110    if isequal(get(handles.NomType_1,'Visible'),'on')
[387]2111    NomType_1=get(handles.NomType_1,'String');
[428]2112    else
2113        NomType_1=get(handles.NomType,'String');
2114    end
[387]2115    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2116    if ~isequal(NomType_1,'*')%in case of a series of files (not avi movie)
[389]2117        if isfield(UvData,'filename_1')%&& isfield(UvData,'VelType_1') && isfield(UvData,'FieldName_1')
2118            test_keepdata_1= strcmp(filename_1,UvData.filename_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
[387]2119        end
2120    end
2121    if test_keepdata_1
[389]2122        Field{2}=UvData.Field_1;% keep the stored field
[427]2123        ParamOut_1=UvData.ParamOut_1;
[387]2124    else
[405]2125        ParamIn_1.FieldName=FieldName_1;
2126        ParamIn_1.VelType=VelType_1;
2127        ParamIn_1.GUIName='get_field_1';
2128        [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,num_i1);
[387]2129        if ~isempty(errormsg)
2130            errormsg=['error in reading ' FieldName_1 ' in ' filename_1 ': ' errormsg];
2131            return
2132        end
[405]2133%         UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
[387]2134    end
2135end
2136
2137%% update uvmat interface
2138if isfield(ParamOut,'Npx')
2139    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2140    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2141elseif isfield(ParamOut_1,'Npx')
2142    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2143    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2144end
2145
2146%% update the display menu for the first velocity type (first menuline)
2147test_veltype=0;
2148% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
[404]2149if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
[387]2150    test_veltype=1;
2151    set(handles.VelType,'Visible','on')
2152    set(handles.VelType_1,'Visible','on')
2153    set(handles.FixVelType,'Visible','on')
[404]2154    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
[387]2155    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2156    index_val=find(index_menu,1);
2157    if isempty(index_val)
2158        index_val=1;
2159    end
2160    set(handles.VelType,'Value',index_val)
2161    if ~get(handles.SubField,'value')
2162        set(handles.VelType,'String',menu)
2163        set(handles.VelType_1,'Value',1)
2164        set(handles.VelType_1,'String',[{''};menu])
2165    end
2166else
2167    set(handles.VelType,'Visible','off')
2168end
[405]2169% display the Fields menu from the input file and pick the selected one:
[387]2170field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2171set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2172set(handles.Fields,'Value',find(field_index,1))
2173
2174%% update the display menu for the second velocity type (second menuline)
2175test_veltype_1=0;
2176if isempty(filename_1)
2177    set(handles.Fields_1,'Value',1); %update the field menu
2178    set(handles.Fields_1,'String',[{''};ParamOut.FieldList]); %update the field menu
[405]2179elseif ~test_keepdata_1
[404]2180    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
[387]2181        set(handles.VelType_1,'Visible','off')
[405]2182    else
[387]2183        test_veltype_1=1;
2184        set(handles.VelType_1,'Visible','on')
[405]2185%         if ~get(handles.FixVelType,'Value')
[387]2186            menu=set_veltype_display(ParamOut_1.CivStage);
2187            index_menu=strcmp(ParamOut_1.VelType,menu);
2188            set(handles.VelType_1,'Value',1+find(index_menu,1))
2189            set(handles.VelType_1,'String',[{''};menu])
[405]2190%         end
[387]2191    end
[405]2192    % update the second field menu: the same quantity
2193    set(handles.Fields_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2194    % display the Fields menu from the input file and pick the selected one:
2195    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2196    set(handles.Fields_1,'Value',find(field_index,1)+1) 
2197%     % synchronise  with the first menu if the first selection is not 'velocity'
2198%     if ~strcmp(ParamOut.FieldName,'velocity')
2199%         field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2200%         set(handles.Fields_1,'Value',field_index); %update the field menu
2201%         ParamOut_1.FieldName=ParamOut.FieldName;
2202%         set(handles.Fields_1,'String',ParamOut_1.FieldList)
2203%     end
[387]2204end
2205if test_veltype||test_veltype_1
2206     set(handles.FixVelType,'Visible','on')
2207else
2208     set(handles.FixVelType,'Visible','off')
2209end
[405]2210
2211% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2212% set(handles.Fields,'String',ParamOut.FieldList); %update the field menu
2213% set(handles.Fields,'Value',find(field_index,1))
[387]2214   
2215%% introduce w as background image by default for a new series (only for nbdim=2)
2216if ~isfield(UvData,'NewSeries')
2217    UvData.NewSeries=1;
2218end
2219%put W as background image by default if NbDim=2:
2220if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2221        set(handles.SubField,'Value',1);
2222        set(handles.RootPath_1,'String','"')
2223        set(handles.RootFile_1,'String','"')
2224        set(handles.SubDir_1,'String','"');
2225         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2226        set(handles.FileIndex_1,'String',indices)
2227        set(handles.FileExt_1,'String','"');
2228        set(handles.Fields_1,'Visible','on');
2229        set(handles.Fields_1,'Visible','on');
2230        set(handles.RootPath_1,'Visible','on')
2231        set(handles.RootFile_1,'Visible','on')
2232        set(handles.SubDir_1,'Visible','on');
2233        set(handles.FileIndex_1,'Visible','on');
2234        set(handles.FileExt_1,'Visible','on');
2235        set(handles.Fields_1,'Visible','on');
2236        Field{1}.AName='w';
2237end           
2238
[415]2239%% display time
2240testimedoc=0;
2241TimeUnit='';
2242if isfield(Field{1},'Time')
2243    abstime=Field{1}.Time;%time read from the netcdf input file
2244end
2245if numel(Field)==2 && isfield(Field{2},'Time')
2246    abstime_1=Field{2}.Time;%time read from the netcdf input file
2247end
2248if isfield(Field{1},'Dt')
2249    dt=Field{1}.Dt;%dt read from the netcdf input file
2250    if isfield(Field{1},'TimeUnit')
2251       TimeUnit=Field{1}.TimeUnit;
2252    end
2253elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2254    dt=Field{2}.Dt;%dt read from the netcdf input file
2255    if isfield(Field{2},'TimeUnit')
2256       TimeUnit=Field{2}.TimeUnit;
2257    end
2258end
2259% time from xml file overset previous result
2260if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2261    if isempty(num_i2)||isnan(num_i2)
2262        num_i2=num_i1;
2263    end
2264    if isempty(num_j1)||isnan(num_j1)
2265        num_j1=1;
2266    end
2267    if isempty(num_j2)||isnan(num_j2)
2268        num_j2=num_j1;
2269    end
2270    siz=size(UvData.XmlData{1}.Time);
2271    if siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2272        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2273        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2274        Field{1}.Dt=dt;
2275        if isfield(UvData.XmlData{1},'TimeUnit')
2276            TimeUnit=UvData.XmlData{1}.TimeUnit;
2277        end
2278    end
2279    if numel(UvData.XmlData)==2
2280        [tild,tild,tild,num_i1,num_i2,num_j1,num_j2]=fileparts_uvmat(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]);
2281        if isempty(num_i2)
2282            num_i2=num_i1;
2283        end
2284        if isempty(num_j1)
2285            num_j1=1;
2286        end
2287        if isempty(num_j2)
2288            num_j2=num_j1;
2289        end
2290        siz=size(UvData.XmlData{2}.Time);
2291        if ~isempty(num_i1) && siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2292            abstime_1=(UvData.XmlData{2}.Time(num_i1,num_j1)+UvData.XmlData{2}.Time(num_i2,num_j2))/2;%overset the time read from files
2293            Field{2}.Dt=(UvData.XmlData{2}.Time(num_i2,num_j2)-UvData.XmlData{2}.Time(num_i1,num_j1));
2294        end
2295    end
2296end
2297if ~isequal(numel(abstime),1)
2298    abstime=[];
2299end
2300if ~isequal(numel(abstime_1),1)
2301      abstime_1=[];
2302end 
2303set(handles.abs_time,'String',num2str(abstime,4))
2304set(handles.abs_time_1,'String',num2str(abstime_1,4))
2305% if testimedoc && isfield(UvData,'dt')
2306%     dt=UvData.dt;
2307% end
2308if isempty(dt)||isequal(dt,0)
2309    set(handles.Dt_txt,'String','')
2310else
2311    if  isempty(TimeUnit)
2312        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2313    else
2314        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2315    end
2316end
2317
2318
[387]2319%% store the current open names, fields and vel types in uvmat interface
2320UvData.filename_1=filename_1;
2321
2322%% apply coordinate transform or other user fct
2323XmlData=[];%default
2324XmlData_1=[];%default
2325if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2326    XmlData=UvData.XmlData{1};
2327    if numel(UvData.XmlData)==2
2328        XmlData_1=UvData.XmlData{2};
2329    end
2330end
2331choice_value=get(handles.transform_fct,'Value');
2332transform_list=get(handles.transform_fct,'UserData');
2333transform=transform_list{choice_value};%selected function handles
2334% z index
2335if ~isempty(filename)
2336    Field{1}.ZIndex=z_index;
2337end
[389]2338if ~isempty(transform)
[387]2339    if length(Field)>=2
2340        Field{2}.ZIndex=z_index;
2341        [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1);
2342        if isempty(Field{2})
2343            Field(2)=[];
2344        end
2345    else
2346        Field{1}=transform(Field{1},XmlData);
2347    end
[389]2348    %% update tps in phys coordinates if needed
[404]2349    if (strcmp(VelType,'filter1')||strcmp(VelType,'filter2'))&& strcmp(UvData.FileType{1},'civdata')&&isfield(Field{1},'U')&& isfield(Field{1},'V')
[389]2350        Field{1}.X=Field{1}.X(Field{1}.FF==0);
2351        Field{1}.Y=Field{1}.Y(Field{1}.FF==0);
2352        Field{1}.U=Field{1}.U(Field{1}.FF==0);
2353        Field{1}.V=Field{1}.V(Field{1}.FF==0);
2354        [Field{1}.SubRange,Field{1}.NbSites,Field{1}.Coord_tps,Field{1}.U_tps,Field{1}.V_tps]=filter_tps([Field{1}.X Field{1}.Y],Field{1}.U,Field{1}.V,[],Field{1}.Patch1_SubDomain,0);
2355    end
[404]2356    if numel(Field)==2 && ~test_keepdata_1 && isequal(UvData.FileType{2}(1:3),'civ') && ~isequal(ParamOut_1.FieldName,'get_field...')%&&~isempty(FieldName_1)
[389]2357        %update tps in phys coordinates if needed
[404]2358        if (strcmp(VelType_1,'filter1')||strcmp(VelType_1,'filter2'))&& strcmp(UvData.FileType{2},'civdata')&&isfield(Field{2},'U')&& isfield(Field{2},'V')
[389]2359            Field{2}.X=Field{2}.X(Field{2}.FF==0);
2360            Field{2}.Y=Field{1}.Y(Field{2}.FF==0);
2361            Field{2}.U=Field{1}.U(Field{2}.FF==0);
2362            Field{2}.V=Field{1}.V(Field{2}.FF==0);
2363            [Field{2}.SubRange,Field{2}.NbSites,Field{2}.Coord_tps,Field{2}.U_tps,Field{2}.V_tps]=filter_tps([Field{2}.X Field{2}.Y],Field{2}.U,Field{2}.V,[],1500,0);
2364        end
2365    end
[387]2366end
2367
2368%% calculate scalar
[421]2369if ~strcmp(ParamOut.FieldName,'get_field...')&& (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))%&&~strcmp(ParamOut.FieldName,'velocity')&& ~strcmp(ParamOut.FieldName,'get_field...');% ~isequal(ParamOut.CivStage,0)%&&~isempty(FieldName)%
[405]2370    Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1});
2371end
[421]2372if numel(Field)==2 && ~strcmp(ParamOut_1.FieldName,'get_field...')&& ~test_keepdata_1 && (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))  &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
[405]2373     Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2374end
[387]2375
2376%% combine the two input fields (e.g. substract velocity fields)
[405]2377%Field{1}.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}];
[387]2378if numel(Field)==2
[405]2379%    Field{2}.FieldList=[{ParamOut_1.FieldName} {ParamOut_1.ColorVar}];
[402]2380   [UvData.Field,errormsg]=sub_field(Field{1},Field{2}); 
[405]2381   UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
[427]2382   UvData.ParamOut_1=ParamOut_1;
[387]2383else
2384   UvData.Field=Field{1};
2385end
[402]2386if ~isempty(errormsg)
2387    errormsg=['error in uvmat/refresh_field/sub_field:' errormsg];
2388    return
2389end
[404]2390%UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation
[387]2391
[434]2392%% analyse input field
[387]2393test_x=0;
2394test_z=0;% test for unstructured z coordinate
[434]2395[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
[387]2396if ~isempty(errormsg)
[434]2397    errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
[387]2398    return
2399end
[434]2400[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);% analyse  the input field structure
[387]2401if ~isempty(errormsg)
[434]2402    errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];% display error
[387]2403    return
2404end
[421]2405[NbDim,imax]=max(NbDim);% spatial dimension of the input field
[387]2406if isfield(UvData.Field,'NbDim')
2407    NbDim=UvData.Field.NbDim;% deal with plane fields containing z coordinates
2408end
[434]2409
2410%% get bounds and mesh (needed for mouse action and to open set_object)
[435]2411if NbDim>1
2412    XName=''; %default
2413    YName='';
2414    %unstructured coordinates
2415    if ~isempty(VarType{imax}.coord_x)&&~isempty(VarType{imax}.coord_y)
2416        XName=UvData.Field.ListVarName{VarType{imax}.coord_x};
[434]2417        YName=UvData.Field.ListVarName{VarType{imax}.coord_y};
2418        %nbvec=length(UvData.Field.(XName));%nbre of measurement points (e.g. vectors)
2419        test_x=1;%test for unstructured coordinates
2420        if ~isempty(VarType{imax}.coord_z)
2421            ZName=UvData.Field.ListVarName{VarType{imax}.coord_z};
2422        else
2423            NbDim=2;
2424        end
[435]2425        %structured coordinate
2426    elseif numel(VarType)>=imax && numel(VarType{imax}.coord)>=NbDim && VarType{imax}.coord(NbDim)>0
2427        XName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim)};
2428        if NbDim> 1 && VarType{imax}.coord(NbDim-1)>0
2429            YName=UvData.Field.ListVarName{VarType{imax}.coord(NbDim-1)}; %structured coordinates
2430        end
2431        % VarIndex=CellVarIndex{imax}; % list of variable indices
2432        DimIndex=VarDimIndex{CellVarIndex{imax}(1)}; %list of dim indices for the variable
2433        nbpoints_x=DimValue(DimIndex(NbDim));
2434        XMax=nbpoints_x;%default
2435        XMin=1;%default
[387]2436    end
[435]2437   
2438    if NbDim==3
2439        if ~test_x
2440            ZName=UvData.Field.ListVarName{VarType{imax}.coord(1)};%structured coordinates in 3D
2441        end
2442        ZMax=max(UvData.Field.(ZName));
2443        ZMin=min(UvData.Field.(ZName));
2444        UvData.Field.ZMax=ZMax;
2445        UvData.Field.ZMin=ZMin;
2446        test_z=1;
2447        if isequal(ZMin,ZMax)%no z dependency
2448            NbDim=2;
2449            test_z=0;
2450        end
[387]2451    end
[435]2452    if ~isempty (XName)
2453        XMax=max(max(UvData.Field.(XName)));
2454        XMin=min(min(UvData.Field.(XName)));
2455        UvData.Field.NbDim=NbDim;
2456        UvData.Field.XMax=XMax;
2457        UvData.Field.XMin=XMin;
2458        if NbDim >1&& ~isempty(YName)
2459            YMax=max(max(UvData.Field.(YName)));
2460            YMin=min(min(UvData.Field.(YName)));
2461            UvData.Field.YMax=YMax;
2462            UvData.Field.YMin=YMin;
2463        end
2464        nbvec=length(UvData.Field.(XName));
2465        if test_x %unstructured coordinates
2466            if test_z
2467                UvData.Field.Mesh=((XMax-XMin)*(YMax-YMin)*(ZMax-ZMin))/nbvec;% volume per vector
2468                UvData.Field.Mesh=(UvData.Field.Mesh)^(1/3);
2469            else
2470                UvData.Field.Mesh=sqrt((XMax-XMin)*(YMax-YMin)/nbvec);%2D
2471            end
2472        end
2473    end
2474    % case of structured coordinates
[387]2475    if ~test_x
[435]2476        DX=(XMax-XMin)/(nbpoints_x-1);
2477        if NbDim >1
2478            nbpoints_y=DimValue(DimIndex(NbDim-1));
2479            if isempty(YName)% if the y coordinate is not expressed, it is taken as the matrix index
2480                DY=1;
2481                UvData.Field.YMax=nbpoints_y;
2482                UvData.Field.YMin=1;
2483            else
2484                DY=(YMax-YMin)/(nbpoints_y-1);
2485            end
[387]2486        end
[435]2487        if NbDim==3
2488            nbpoints_z=DimValue(DimIndex(1));
2489            DZ=(ZMax-ZMin)/(nbpoints_z-1);
2490            UvData.Field.Mesh=(DX*DY*DZ)^(1/3);
2491            UvData.Field.ZMax=ZMax;
2492            UvData.Field.ZMin=ZMin;
[421]2493        else
[435]2494            UvData.Field.Mesh=DX;%sqrt(DX*DY);
[387]2495        end
2496    end
[435]2497    % adjust the mesh to a value 1, 2 , 5 *10^n
2498    ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude
2499    if UvData.Field.Mesh/ord>=5
2500        UvData.Field.Mesh=5*ord;
2501    elseif UvData.Field.Mesh/ord>=2
2502        UvData.Field.Mesh=2*ord;
[404]2503    else
[435]2504        UvData.Field.Mesh=ord;
[404]2505    end
[435]2506    UvData.Object{1}.Type='plane';%main plotting plane
2507    UvData.Object{1}.ProjMode='projection';%main plotting plane
2508    UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2509    UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2510   
2511    %% 3D case (menuvolume)
2512    if NbDim==3% && UvData.NewSeries
2513        test_set_object=1;
2514        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2515        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2516        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2517        if ~isempty(hset_object) %if set_object is detected
2518            delete(hset_object);% delete the GUI set_object if it does not fit
[387]2519        end
[435]2520        if test_set_object% reinitiate the GUI set_object
2521            delete_object(1);% delete the current projection object in the list UvData.Object, delete its graphic representations and update the list displayed in handles.ListObject and 2
2522            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2523            UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2524            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2525            UvData.Object{1}.Angle=[0 0 0];
2526            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2527            UvData.Object{1}.Name='1-PLANE';
2528            UvData.Object{1}.enable_plot=1;
2529            set_object(UvData.Object{1},handles,ZBounds);
2530            set(handles.ListObject,'Value',1);
2531            set(handles.ListObject,'String',{'1-PLANE'});
2532            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2533            edit_object_Callback([],[], handles)
[387]2534        end
[435]2535        %multilevel case (single menuplane in a 3D space)
2536    elseif isfield(UvData,'Z')
2537        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2538            XmlData=UvData.XmlData{1};
2539            if isfield(XmlData,'PlanePos')
2540                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2541            end
2542            if isfield(XmlData,'PlaneAngle')
2543                siz=size(XmlData.PlaneAngle);
2544                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2545                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2546            end
2547        elseif isfield(UvData,'ZIndex')
2548            UvData.Object{1}.ZObject=UvData.ZIndex;
2549        end
[387]2550    end
2551end
[435]2552
[387]2553testnewseries=UvData.NewSeries;
2554UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2555set(handles.uvmat,'UserData',UvData)
2556
2557%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
[405]2558% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2559%     set(handles.num_MinA,'String','0')
2560%     set(handles.num_MaxA,'String','255')
2561% end
[387]2562
[434]2563%% usual 1D (x,y) plots
2564if NbDim<=1
2565    set(handles.Objects,'Visible','off')
2566    set(handles.ListObject_1_title,'Visible','off')
2567    set(handles.ListObject_1,'Visible','off')
2568    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.axes3,read_GUI(handles.uvmat));
2569    write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2570%     if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2571%         ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2572%     end
2573   
2574%% 2D or 3D fields are generally projected
[387]2575else
[434]2576    set(handles.Objects,'Visible','on')
2577    set(handles.ListObject_1_title,'Visible','on')
2578    set(handles.ListObject_1,'Visible','on')
2579   
2580    %% Plot the projections on the selected  projection objects
2581    % main projection object (uvmat display)
2582    list_object=get(handles.ListObject_1,'String');
2583    if isequal(list_object,{''})%refresh list of objects if the menu is empty
2584        UvData.Object={[]};
2585        set(handles.ListObject_1,'Value',1)
[387]2586    end
[434]2587    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2588    if IndexObj(1)> numel(UvData.Object)
2589        IndexObj(1)=1;%select the first object if the selected one does not exist
2590        set(handles.ListObject_1,'Value',1)
[387]2591    end
[434]2592    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2593    if isequal(IndexObj(2),IndexObj(1))
2594        IndexObj(2)=[];
2595    end
2596    plot_handles{1}=handles;
2597    if isfield(UvData,'plotaxes')%case of movies
2598        haxes(1)=UvData.plotaxes;
2599    else
2600        haxes(1)=handles.axes3;
2601    end
2602    PlotParam{1}=read_GUI(handles.uvmat);
2603    %default settings if vectors not visible
2604    if ~isfield(PlotParam{1},'Vectors')
2605        PlotParam{1}.Vectors.MaxVec=1;
2606        PlotParam{1}.Vectors.MinVec=0;
2607        PlotParam{1}.Vectors.CheckFixVecColor=1;
2608        PlotParam{1}.Vectors.ColCode1=0.33;
2609        PlotParam{1}.Vectors.ColCode2=0.66;
2610        PlotParam{1}.Vectors.ColorScalar={'ima_cor'};
2611        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2612    end
2613    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2614   
2615    %% second projection object (view_field display)
2616    if length( IndexObj)>=2
2617        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2618        if ~isempty(view_field_handle)
2619            plot_handles{2}=guidata(view_field_handle);
2620            haxes(2)=plot_handles{2}.axes3;
2621            PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2622            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
[421]2623        end
[387]2624    end
[434]2625   
2626    %% loop on the projection objects: one or two
2627   
2628    for imap=1:numel(IndexObj)
2629        iobj=IndexObj(imap);
2630        %      if imap==2 || check_proj==0  % field not yet projected) && ~isfield(UvData.Object{iobj},'Type')% case with no projection (only for the first empty object)
2631        % %          [ObjectData,errormsg]=calc_field(UvData.Field.FieldList,UvData.Field);
2632        % %      else
2633        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2634        %      end
2635        if ~isempty(errormsg)
2636            return
[387]2637        end
[434]2638        if testnewseries
2639            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2640            if isfield(ObjectData,'CoordUnit')
2641                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2642                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
[387]2643            end
[434]2644        end
2645        %use of mask (TODO: check)
2646        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2647            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2648            AX=ObjectData.AX;%x coordiantes for the scalar field
2649            AY=ObjectData.AY;%y coordinates for the scalar field
2650            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2651            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2652            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2653                nxy=size(flag_mask);
2654                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2655                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2656                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2657                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2658                %project on the positions of the scalar
2659                npxy=size(ObjectData.A);
2660                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2661                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2662                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2663                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2664                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2665                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2666            end
2667            AClass=class(ObjectData.A);
2668            ObjectData.A=flag_mask.*double(ObjectData.A);
2669            ObjectData.A=feval(AClass,ObjectData.A);
[387]2670            ind_off=[];
[434]2671            if isfield(ObjectData,'ListVarName')
2672                for ilist=1:length(ObjectData.ListVarName)
2673                    if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2674                        ind_off=[ind_off ilist];
2675                    end
[387]2676                end
[434]2677                ObjectData.ListVarName(ind_off)=[];
2678                VarDimIndex(ind_off)=[];
2679                ind_off=[];
2680                for ilist=1:length(ListDimName)
2681                    if isequal(ListDimName{ilist},'MaskX') || isequal(ListDimName{ilist},'MaskY')
2682                        ind_off=[ind_off ilist];
2683                    end
2684                end
2685                ListDimName(ind_off)=[];
2686                DimValue(ind_off)=[];
[387]2687            end
2688        end
[434]2689        if ~isempty(ObjectData)
2690            PlotType='none'; %default
2691            if imap==2 && isempty(view_field_handle)
2692                view_field(ObjectData)
2693            else
2694                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2695                write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2696                if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2697                    ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2698                end
[387]2699            end
[434]2700            if isequal(PlotType,'none')
2701                hget_field=findobj(allchild(0),'name','get_field');
2702                if isempty(hget_field)
2703                    get_field(filename)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field)
2704                end
2705                errormsg='The field defined by get_field cannot be plotted';
2706                return
[387]2707            end
2708        end
2709    end
[434]2710   
2711    %% update the mask
2712    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2713        update_mask(handles,num_i1,num_i2);
2714    end
2715   
2716    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2717    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2718    ind_skip=[];
2719    % nb_histo=1;
2720    Ustring='';
2721    Vstring='';
2722    % suppress coordinates from the histogram menu
2723    for ivar=1:numel(menu_histo)%l loop on field variables:
2724        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2725            Role=UvData.Field.VarAttribute{ivar}.Role;
2726            switch Role
2727                case {'coord_x','coord_y','coord_z','dimvar'}
2728                    ind_skip=[ind_skip ivar];
2729                case {'vector_x'}
2730                    Ustring=UvData.Field.ListVarName{ivar};
2731                    ind_skip=[ind_skip ivar];
2732                case {'vector_y'}
2733                    Vstring=UvData.Field.ListVarName{ivar};
2734                    ind_skip=[ind_skip ivar];
2735            end
[387]2736        end
[434]2737        DimCell=UvData.Field.VarDimName{ivar};
2738        DimName='';
2739        if ischar(DimCell)
2740            DimName=DimCell;
2741        elseif iscell(DimCell)&& numel(DimCell)==1
2742            DimName=DimCell{1};
2743        end
2744        if strcmp(DimName,menu_histo{ivar})
2745            ind_skip=[ind_skip ivar];
2746        end
[387]2747    end
[434]2748    menu_histo(ind_skip)=[];% remove skipped items
2749    if ~isempty(Ustring)
2750        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
[387]2751    end
[434]2752   
2753    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2754    % display menus and plot histograms
2755    test_v=0;
2756    if ~isempty(menu_histo)
2757        set(handles.histo1_menu,'Value',1)
2758        set(handles.histo1_menu,'String',menu_histo)
2759        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
[387]2760    end
2761end
2762
[424]2763%------------------------------------------------------------------------
2764function histo1_menu_Callback(hObject, eventdata, handles)
2765%--------------------------------------------
2766%plot first histo
2767%huvmat=get(handles.histo1_menu,'parent');
2768histo_menu=get(handles.histo1_menu,'String');
2769histo_value=get(handles.histo1_menu,'Value');
2770FieldName=histo_menu{histo_value};
2771% update_histo(handles.histo_u,handles.uvmat,FieldName)
2772%
2773% %------------------------------------------------------------------------
2774% function histo2_menu_Callback(hObject, eventdata, handles)
2775% %------------------------------------------------------------------------
2776% %plot second histo
2777% %huvmat=get(handles.histo2_menu,'parent');
2778% histo_menu=get(handles.histo2_menu,'String');
2779% histo_value=get(handles.histo2_menu,'Value');
2780% FieldName=histo_menu{histo_value};
2781% update_histo(handles.histo_v,handles.uvmat,FieldName)
2782%
2783% %------------------------------------------------------------------------
2784% %read the field .Fieldname stored in UvData and plot its histogram
2785% function update_histo(haxes,huvmat,FieldName)
2786%------------------------------------------------------------------------
2787UvData=get(handles.uvmat,'UserData');
2788Field=UvData.Field;
2789r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2790FieldName_2='';
2791if ~isempty(r)
2792    FieldName=r.var1;
2793    FieldName_2=r.var2;
2794end
2795if ~isfield(UvData.Field,FieldName)
2796    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2797    return
2798end
2799FieldHisto=Field.(FieldName);
2800if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2801    indsel=find(Field.FF==0);%find values marked as false
2802    if ~isempty(indsel)
2803        FieldHisto=FieldHisto(indsel);
2804        if ~isempty(FieldName_2)
2805            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2806        end
[387]2807    end
2808end
[424]2809if isempty(Field)
2810    msgbox_uvmat('ERROR',['empty field ' FieldName])
2811else
2812    nxy=size(FieldHisto);
2813    Amin=double(min(min(min(FieldHisto))));%min of field value
2814    Amax=double(max(max(max(FieldHisto))));%max of field value
2815    if isequal(Amin,Amax)
2816        cla(handles.histo_u)
2817    else
2818        Histo.ListVarName={FieldName,'histo'};
2819        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2820            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2821        else
2822            if numel(nxy)==2
2823                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2824            else
2825                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2826            end
2827        end
2828        %unit
2829        units=[]; %default
2830        for ivar=1:numel(Field.ListVarName)
2831            if strcmp(Field.ListVarName{ivar},FieldName)
2832                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2833                    units=Field.VarAttribute{ivar}.units;
2834                    break
2835                end
2836            end
2837        end
2838        if ~isempty(units)
2839            Histo.VarAttribute{1}.units=units;
2840        end
2841        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2842        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2843            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2844            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2845        else
2846            for col=1:size(FieldHisto,3)
2847                B=FieldHisto(:,:,col);
2848                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2849                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2850            end
2851        end
2852        plot_field(Histo,handles.histo_u);
[426]2853        hlegend=legend;
2854        if isempty(FieldName_2)
2855        set(hlegend,'String',FieldName)
2856        else
2857            set(hlegend,'String',{FieldName;FieldName_2})
2858        end
2859%         hh=get(handles.histo_u,'children');
2860%         get(hh(1))
2861%         get(hh(2))
[424]2862    end
[387]2863end
2864
2865%-------------------------------------------------------------------
2866% --- translate coordinate to matrix index
2867%-------------------------------------------------------------------
2868function [indx,indy]=pos2ind(x0,rangx0,nxy)
2869indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2870indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2871
[428]2872
[387]2873%-------------------------------------------------------------------
[428]2874% --- Executes on button press in 'CheckZoom'.
2875%-------------------------------------------------------------------
2876function CheckZoom_Callback(hObject, eventdata, handles)
2877
2878if (get(handles.CheckZoom,'Value') == 1);
2879    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2880    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2881    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2882else
2883    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2884end
2885
2886%-------------------------------------------------------------------
[387]2887% --- Executes on button press in 'CheckFixLimits'.
2888%-------------------------------------------------------------------
2889function CheckFixLimits_Callback(hObject, eventdata, handles)
2890test=get(handles.CheckFixLimits,'Value');
2891if test
2892    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2893else
2894    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2895    update_plot(handles);
2896end
2897
2898%-------------------------------------------------------------------
[428]2899% --- Executes on button press in CheckFixAspectRatio.
2900function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2901%-------------------------------------------------------------------
2902if get(handles.CheckFixAspectRatio,'Value')
2903    set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
[387]2904    update_plot(handles);
2905else
[428]2906    set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
[387]2907    update_plot(handles);
2908end
2909
2910%-------------------------------------------------------------------
[428]2911function num_AspectRatio_Callback(hObject, eventdata, handles)
[387]2912%-------------------------------------------------------------------
[428]2913set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2914set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2915update_plot(handles);
[387]2916%-------------------------------------------------------------------
2917
[428]2918%-------------------------------------------------------------------
[387]2919
[428]2920
2921
[387]2922%-------------------------------------------------------------------
2923%----Executes on button press in 'record': records the current flags of manual correction.
2924%-------------------------------------------------------------------
2925function record_Callback(hObject, eventdata, handles)
2926% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2927[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2928filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2929%filename=read_file_boxes(handles);
2930[erread,message]=fileattrib(filename);
2931if ~isempty(message) && ~isequal(message.UserWrite,1)
2932     msgbox_uvmat('ERROR',['no writting access to ' filename])
2933     return
2934end
2935test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2936test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2937if ~test_civ2 && ~test_civ1
2938    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2939end
2940if test_civ2
2941    nbname='nb_vectors2';
2942   flagname='vec2_FixFlag';
2943   attrname='fix2';
2944end
2945if test_civ1
2946    nbname='nb_vectors';
2947   flagname='vec_FixFlag';
2948   attrname='fix';
2949end
2950%write fix flags in the netcdf file
2951UvData=get(handles.uvmat,'UserData');
2952hhh=which('netcdf.open');% look for built-in matlab netcdf library
2953if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2954    nc=netcdf.open(filename,'NC_WRITE');
2955    netcdf.reDef(nc);
2956    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2957    dimid = netcdf.inqDimID(nc,nbname);
2958    try
2959        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2960    catch
2961        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2962    end
2963    netcdf.endDef(nc);
2964    netcdf.putVar(nc,varid,UvData.axes3.FF);
2965    netcdf.close(nc); 
2966else %old netcdf library
2967    netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2968end
2969
2970%-------------------------------------------------------------------
2971%----Correct the netcdf file, using toolbox (old versions of Matlab).
2972%-------------------------------------------------------------------
2973function netcdf_toolbox(filename,AxeData,attrname,nbname,flagname)
2974nc=netcdf(filename,'write'); %open netcdf file
2975result=redef(nc);
2976eval(['nc.' attrname '=1;']);
2977theDim=nc(nbname) ;% get the number of velocity vectors
2978nb_vectors=size(theDim);
2979var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2980var_FixFlag(1:nb_vectors)=AxeData.FF;%
2981fin=close(nc);
2982
[428]2983%-------------------------------------------------------------------
[387]2984% --- Executes on button press in SubField
2985function SubField_Callback(hObject, eventdata, handles)
[428]2986%-------------------------------------------------------------------
[387]2987UvData=get(handles.uvmat,'UserData');
2988if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2989    set(handles.RootPath_1,'String','')
2990    set(handles.RootFile_1,'String','')
2991    set(handles.SubDir_1,'String','');
2992    set(handles.FileIndex_1,'String','');
2993    set(handles.FileExt_1,'String','');
2994    set(handles.RootPath_1,'Visible','off')
2995    set(handles.RootFile_1,'Visible','off')
2996    set(handles.SubDir_1,'Visible','off');
2997    set(handles.NomType_1,'Visible','off');
2998    set(handles.abs_time_1,'Visible','off')
2999    set(handles.FileIndex_1,'Visible','off');
3000    set(handles.FileExt_1,'Visible','off');
3001    set(handles.Fields_1,'Value',1);%set to blank state
3002    set(handles.VelType_1,'Value',1);%set to blank state
[428]3003    set(handles.num_Opacity,'String','')% desactivate opacity setting
[387]3004    if ~strcmp(get(handles.VelType,'Visible'),'on')
3005        set(handles.VelType_1,'Visible','off')
3006    end
3007    if isfield(UvData,'XmlData_1')
3008        UvData=rmfield(UvData,'XmlData_1');
3009    end
3010    set(handles.uvmat,'UserData',UvData);
3011    run0_Callback(hObject, eventdata, handles); %run
3012else
3013    MenuBrowse_1_Callback(hObject, eventdata, handles)
3014end
3015
3016%------------------------------------------------------------------------
3017% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
3018
3019function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
3020%------------------------------------------------------------------------
3021InputFile=read_GUI(handles.InputFile);
3022RootPath=InputFile.RootPath;
3023SubDir=regexprep(InputFile.SubDir,'/|\','');
3024RootFile=regexprep(InputFile.RootFile,'/|\','');
3025FileIndices=InputFile.FileIndex;
3026FileExt=InputFile.FileExt;
3027
3028
3029%------------------------------------------------------------------------
3030% ---- read the data displayed for the second input rootfile windows
3031function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
3032%------------------------------------------------------------------------
3033RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
3034if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
3035    RootPath_1=get(handles.RootPath,'String');
3036end;
3037SubDir_1=get(handles.SubDir_1,'String');
3038if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
3039    SubDir_1=get(handles.SubDir,'String');
3040end
3041SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3042RootFile_1=get(handles.RootFile_1,'String');
3043if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
3044    RootFile_1=get(handles.RootFile,'String');
3045end
3046RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3047FileIndex_1=get(handles.FileIndex_1,'String');
3048if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
3049    FileIndex_1=get(handles.FileIndex,'String');
3050end
3051FileExt_1=get(handles.FileExt_1,'String');
3052if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
3053    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
3054end
3055NomType_1=get(handles.NomType_1,'String');
3056if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
3057    NomType_1=get(handles.NomType,'String');%read FileExt by default
3058end
3059%------------------------------------------------------------------------
3060% --- Executes on menu selection Fields
3061function Fields_Callback(hObject, eventdata, handles)
3062%------------------------------------------------------------------------
3063list_fields=get(handles.Fields,'String');% list menu fields
3064index_fields=get(handles.Fields,'Value');% selected string index
3065field= list_fields{index_fields(1)}; % selected string
3066if isequal(field,'get_field...')
3067    set(handles.FixVelType,'visible','off')
3068    set(handles.VelType,'visible','off')
3069    set(handles.VelType_1,'visible','off')
3070    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3071    filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3072    %filename=read_file_boxes(handles);
3073    hget_field=findobj(allchild(0),'name','get_field');
3074    if ~isempty(hget_field)
3075        delete(hget_field)
3076    end
3077    hget_field=get_field(filename);
3078    set(hget_field,'Name','get_field')
3079    hhget_field=guidata(hget_field);
3080    set(hhget_field.list_fig,'Value',1)
3081    set(hhget_field.list_fig,'String',{'uvmat'})
3082    set(handles.transform_fct,'Value',1)% no transform by default
3083    set(handles.path_transform,'String','')
3084    return %no action
3085end
3086list_fields=get(handles.Fields_1,'String');% list menu fields
3087index_fields=get(handles.Fields_1,'Value');% selected string index
3088field_1= list_fields{index_fields(1)}; % selected string
3089UvData=get(handles.uvmat,'UserData');
3090
3091%read the rootfile input display
3092[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3093FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3094[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3095% NomTypeNew=NomType;%default
3096if isequal(field,'image')
3097%     if isequal(NomType,'_1-2_1')||isequal(NomType,'_1_1-2')
3098%         NomTypeNew='_1_1';
3099%     elseif isequal(NomType,'#_ab')
3100%         NomTypeNew='#a';
3101%     elseif isequal(NomType,'_1-2')
3102%         NomTypeNew='_1';
3103%     end
3104    imagename=fullfile_uvmat(RootPath,SubDir,RootFile,'.png',NomType,i1,[],j1,[]);
3105    if ~exist(imagename,'file')
3106        [FileName,PathName] = uigetfile( ...
3107            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3108            '*.jpg',' jpeg image files'; ...
3109            '*.png','.png image files'; ...
3110            '*.tif','.tif image files'; ...
3111            '*.avi;*.AVI','.avi movie files'; ...
3112            '*.vol','.volume images (png)'; ...
3113            '*.*',  'All Files (*.*)'}, ...
3114            'Pick an image',imagename);   
3115        imagename=[PathName FileName];
3116    end
3117     % display the selected field and related information
[406]3118    display_file_name(handles,imagename)%display the image
[387]3119    return
3120else
3121    ext=get(handles.FileExt,'String');
3122    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3123        [FileName,PathName] = uigetfile( ...
3124            {'*.nc', ' (*.nc)';
3125            '*.nc',' netcdf files'; ...
3126            '*.*',  'All Files (*.*)'}, ...
3127            'Pick a netcdf file',FileBase);
3128        filename=[PathName FileName];
3129        % display the selected field and related information
[406]3130        display_file_name( handles,filename)
[387]3131        return
3132    end
3133end
3134indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3135set(handles.FileIndex,'String',indices)
3136% set(handles.NomType,'String',NomType)
3137
3138%common to Fields_1_Callback
3139if isequal(field,'image')||isequal(field_1,'image')
3140    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3141    set(handles.TitleNpy,'Visible','on')
3142    set(handles.num_Npx,'Visible','on')
3143    set(handles.num_Npy,'Visible','on')
3144else
3145    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3146    set(handles.TitleNpy,'Visible','off')
3147    set(handles.num_Npx,'Visible','off')
3148    set(handles.num_Npy,'Visible','off')
3149end
3150if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3151    run0_Callback(hObject, eventdata, handles)
3152end
3153
3154%---------------------------------------------------
3155% --- Executes on menu selection Fields
3156function Fields_1_Callback(hObject, eventdata, handles)
3157%-------------------------------------------------
3158%% read input data
3159check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3160UvData=get(handles.uvmat,'UserData');
3161if check_new && isfield(UvData,'XmlData')
3162    UvData.XmlData{2}=UvData.XmlData{1};
3163end
[389]3164if isfield(UvData,'Field_1')
3165    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3166end
[402]3167UvData.filename_1='';% desactivate the use of a constant second file
[387]3168list_fields=get(handles.Fields,'String');% list menu fields
[405]3169field= list_fields{get(handles.Fields,'Value')}; % selected string
[387]3170list_fields=get(handles.Fields_1,'String');% list menu fields
[405]3171field_1= list_fields{get(handles.Fields_1,'Value')}; % selected string for the second field
3172if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
[387]3173    set(handles.SubField,'Value',0)
3174    SubField_Callback(hObject, eventdata, handles)
[428]3175    return
[405]3176else
3177    set(handles.SubField,'Value',1)%state that a second field is now entered
[387]3178end
3179
3180%% read the rootfile input display
[405]3181[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
[387]3182filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3183[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
[405]3184% set(handles.FileIndex_1,'Visible','on')
3185% set(handles.FileExt_1,'Visible','on')
[387]3186switch field_1
3187    case 'get_field...'
3188        set_veltype_display(0) % no veltype display
3189        hget_field=findobj(allchild(0),'name','get_field_1');
3190        if ~isempty(hget_field)
3191            delete(hget_field)
3192        end
3193        hget_field=get_field(filename_1);
3194        set(hget_field,'name','get_field_1')
3195        hhget_field=guidata(hget_field);
3196        set(hhget_field.list_fig,'Value',1)
3197        set(hhget_field.list_fig,'String',{'uvmat'})
3198        set(handles.transform_fct,'Value',1)% no transform by default
3199        set(handles.path_transform,'String','')
[428]3200        if check_new
3201            UvData.FileType{2}=UvData.FileType{1};
3202            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3203%             set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3204              set(handles.uvmat,'UserData',UvData)
3205        end
[387]3206    case 'image'
[405]3207        % guess the image name corresponding to the current netcdf name (no unique correspondance)
3208        imagename=fullfile_uvmat(RootPath_1,'',RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3209        if ~exist(imagename,'file') % browse for images if it is not found
[387]3210            [FileName,PathName] = uigetfile( ...
3211                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3212                '*.jpg',' jpeg image files'; ...
3213                '*.png','.png image files'; ...
3214                '*.tif','.tif image files'; ...
3215                '*.avi;*.AVI','.avi movie files'; ...
3216                '*.vol','.volume images (png)'; ...
3217                '*.*',  'All Files (*.*)'}, ...
3218                'Pick an image',imagename);
3219            imagename=[PathName FileName];
3220        end
[405]3221        if ~ischar(imagename)% quit if the browser has  been closed
3222            set(handles.SubField,'Value',0)
3223        else %valid browser input:  display the selected image
3224            set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3225            set(handles.TitleNpy,'Visible','on')
3226            set(handles.num_Npx,'Visible','on')
3227            set(handles.num_Npy,'Visible','on')
[406]3228            display_file_name(handles,imagename,2)%display the imag
[405]3229        end
[387]3230    otherwise
3231        if check_new
3232            UvData.FileType{2}=UvData.FileType{1};
3233            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3234            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3235        end
3236        if ~isequal(field,'image')
3237            set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3238            set(handles.TitleNpy,'Visible','off')
3239            set(handles.num_Npx,'Visible','off')
3240            set(handles.num_Npy,'Visible','off')
3241        end
3242        set(handles.uvmat,'UserData',UvData)
3243        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3244            run0_Callback(hObject, eventdata, handles)
3245        end
3246end
3247
3248%------------------------------------------------------------------------
3249% --- set the visibility of relevant velocity type menus:
3250function menu=set_veltype_display(Civ,FileType)
3251%------------------------------------------------------------------------
3252if ~exist('FileType','var')
3253    FileType='civx';
3254end
3255switch FileType
3256    case 'civx'
[389]3257        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3258        if isequal(Civ,0)
3259            imax=0;
3260        elseif isequal(Civ,1) || isequal(Civ,2)
3261            imax=1;
3262        elseif isequal(Civ,3)
3263            imax=3;
3264        elseif isequal(Civ,4) || isequal(Civ,5)
3265            imax=4;
3266        elseif isequal(Civ,6) %patch2
3267            imax=6;
3268        end
[387]3269    case 'civdata'
[389]3270        menu={'civ1';'filter1';'civ2';'filter2'};
3271        if isequal(Civ,0)
3272            imax=0;
3273        elseif isequal(Civ,1) || isequal(Civ,2)
3274            imax=1;
3275        elseif isequal(Civ,3)
3276            imax=2;
3277        elseif isequal(Civ,4) || isequal(Civ,5)
3278            imax=3;
3279        elseif isequal(Civ,6) %patch2
3280            imax=4;
3281        end
[387]3282end
3283menu=menu(1:imax);
3284
3285%------------------------------------------------------------------------
[402]3286% --- Executes on button press in FixVelType.
3287function FixVelType_Callback(hObject, eventdata, handles)
3288%------------------------------------------------------------------------
[405]3289% refresh the current plot if the fixed  veltype is unselected
3290if ~get(handles.FixVelType,'Value')
[402]3291    run0_Callback(hObject, eventdata, handles)
3292end
3293
3294%------------------------------------------------------------------------
[387]3295% --- Executes on button press in VelType.
3296function VelType_Callback(hObject, eventdata, handles)
3297%------------------------------------------------------------------------
3298set(handles.FixVelType,'Value',1)
3299run0_Callback(hObject, eventdata, handles)
3300
3301%------------------------------------------------------------------------
[402]3302% --- Executes on button press in VelType_1.
[387]3303function VelType_1_Callback(hObject, eventdata, handles)
3304%------------------------------------------------------------------------
3305set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
[389]3306UvData=get(handles.uvmat,'UserData');
[405]3307%refresh field with a second filename=first file name
[387]3308set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
3309drawnow   
3310InputFile=read_GUI(handles.InputFile);
3311[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3312filename=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
[405]3313
[389]3314if isempty(InputFile.VelType_1)
[387]3315        filename_1='';% we plot the current field without the second field
3316        set(handles.SubField,'Value',0)
3317        SubField_Callback(hObject, eventdata, handles)
3318elseif get(handles.SubField,'Value')% if subfield is already 'on'
3319      [RootPath_1,SubDir_1,RootFile_1,FileIndices_1,FileExt_1]=read_file_boxes_1(handles);
3320     filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndices_1 FileExt_1];
3321else
[405]3322     filename_1=filename;% we compare two fields in the same file by default
[389]3323     UvData.FileType{2}=UvData.FileType{1};
[387]3324     set(handles.SubField,'Value',1)
3325end
[389]3326if isfield(UvData,'Field_1')
3327    UvData=rmfield(UvData,'Field_1');% removes the stored second field if it exists
3328end
[402]3329UvData.filename_1='';% desactivate the use of a constant second file
[389]3330set(handles.uvmat,'UserData',UvData)
[387]3331num_i1=stra2num(get(handles.i1,'String'));
3332num_i2=stra2num(get(handles.i2,'String'));
3333num_j1=stra2num(get(handles.j1,'String'));
3334num_j2=stra2num(get(handles.j2,'String'));
3335
3336errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2);
3337
3338if ~isempty(errormsg)
3339    msgbox_uvmat('ERROR',errormsg);
3340else
3341    set(handles.i1,'BackgroundColor',[1 1 1])
3342    set(handles.i2,'BackgroundColor',[1 1 1])
3343    set(handles.j1,'BackgroundColor',[1 1 1])
3344    set(handles.j2,'BackgroundColor',[1 1 1])
3345    set(handles.FileIndex,'BackgroundColor',[1 1 1])
3346    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3347end
3348set(handles.run0,'BackgroundColor',[1 0 0])
3349
3350%-----------------------------------------------
3351% --- reset civ buttons
3352function reset_vel_type(handles_civ0,handle1)
3353for ibutton=1:length(handles_civ0)
3354    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3355    set(handles_civ0(ibutton),'Value',0)
3356end
3357if exist('handle1','var')%handles of selected button
3358        set(handle1,'BackgroundColor',[1 1 0]) 
3359end
3360
3361%-------------------------------------------------------
3362% --- Executes on button press in MENUVOLUME.
3363%-------------------------------------------------------
3364function VOLUME_Callback(hObject, eventdata, handles)
3365%errordlg('command VOL not implemented yet')
3366if ishandle(handles.UVMAT_title)
3367    delete(handles.UVMAT_title)
3368end
3369UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3370if isequal(get(handles.VOLUME,'Value'),1)
3371    set(handles.CheckZoom,'Value',0)
3372    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3373    set(handles.edit_vect,'Value',0)
3374    edit_vect_Callback(hObject, eventdata, handles)
3375    set(handles.edit_object,'Value',0)
3376    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3377%     set(handles.cal,'Value',0)
3378%     set(handles.cal,'BackgroundColor',[0 1 0])
3379    set(handles.edit_vect,'Value',0)
3380    edit_vect_Callback(hObject, eventdata, handles)
3381    %initiate set_object GUI
3382    data.Name='VOLUME';
3383    if isfield(UvData,'CoordType')
3384        data.CoordType=UvData.CoordType;
3385    end
[404]3386    if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh)
3387        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3388        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3389        data.DX=UvData.Field.Mesh;
3390        data.DY=UvData.Field.Mesh;
[387]3391    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3392        np=size(UvData.Field.A);
3393        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3394        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3395        data.RangeY=max(meshx,meshy);
3396        data.RangeX=max(meshx,meshy);
3397        data.DX=max(meshx,meshy);
3398    end
3399    data.ParentButton=handles.VOLUME;
3400    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3401    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3402                                                      % associate the set_object interface handle to the plotting axes
3403    if isfield(UvData.OpenParam,'SetObjectOrigin')                                               
3404    pos_uvmat=get(handles.uvmat,'Position');
3405    pos_set_object(1:2)=UvData.OpenParam.SetObjectOrigin + pos_uvmat(1:2);
3406    pos_set_object(3:4)=UvData.OpenParam.SetObjectSize .* pos_uvmat(3:4); 
3407    set(hset_object,'Position',pos_set_object)
3408    end
3409    UvData.MouseAction='create_object';
3410else
3411    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3412    UvData.MouseAction='none';
3413end
3414set(handles.uvmat,'UserData',UvData)
3415
3416%-------------------------------------------------------
3417function edit_vect_Callback(hObject, eventdata, handles)
3418%-------------------------------------------------------
3419%
3420% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3421if isequal(get(handles.edit_vect,'Value'),1)
3422    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3423    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3424    if ~test_civ2 && ~test_civ1
3425        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3426    end
3427    set(handles.record,'Visible','on')
3428    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3429    set(handles.edit_object,'Value',0)
3430    set(handles.CheckZoom,'Value',0)
3431    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3432%     set(handles.create,'Value',0)
3433%     set(handles.create,'BackgroundColor',[0 1 0])
3434    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3435    set(gcf,'Pointer','arrow')
3436%     UvData.MouseAction='edit_vect';
3437else
3438    set(handles.record,'Visible','off')
3439    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3440%     UvData.MouseAction='none';
3441end
3442% set(handles.uvmat,'UserData',UvData)
3443
3444%----------------------------------------------
3445function save_mask_Callback(hObject, eventdata, handles)
3446%-----------------------------------------------------------------------
3447UvData=get(handles.uvmat,'UserData');
3448
3449flag=1;
3450npx=size(UvData.Field.A,2);
3451npy=size(UvData.Field.A,1);
3452xi=0.5:npx-0.5;
3453yi=0.5:npy-0.5;
3454[Xi,Yi]=meshgrid(xi,yi);
3455if isfield(UvData,'Object')
3456    for iobj=1:length(UvData.Object)
3457        ObjectData=UvData.Object{iobj};
3458        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3459            flagobj=1;
3460            testphys=0; %coordinates in pixels by default
3461            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3462                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3463                    Calib=UvData.XmlData{1}.GeometryCalib;
3464                    testphys=1;
3465                end
3466            end
3467            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3468                if isequal(ObjectData.Type,'polygon')
3469                    X=ObjectData.Coord(:,1);
3470                    Y=ObjectData.Coord(:,2);
3471                    if testphys
3472                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3473                    end
3474                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3475                elseif isequal(ObjectData.Type,'ellipse')
3476                    if testphys
3477                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3478                    end
3479                    RangeX=max(ObjectData.RangeX);
3480                    RangeY=max(ObjectData.RangeY);
3481                    X2Max=RangeX*RangeX;
3482                    Y2Max=RangeY*RangeY;
3483                    distX=(Xi-ObjectData.Coord(1,1));
3484                    distY=(Yi-ObjectData.Coord(1,2));
3485                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3486                elseif isequal(ObjectData.Type,'rectangle')
3487                    if testphys
3488                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3489                    end
3490                    distX=abs(Xi-ObjectData.Coord(1,1));
3491                    distY=abs(Yi-ObjectData.Coord(1,2));
3492                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3493                end
3494                if isequal(ObjectData.ProjMode,'mask_outside')
3495                    flagobj=~flagobj;
3496                end
3497                flag=flag & flagobj;
3498            end
3499        end
3500    end
3501end
3502% flag=~flag;
3503%mask name
3504RootPath=get(handles.RootPath,'String');
3505RootFile=get(handles.RootFile,'String');
3506RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3507filebase=fullfile(RootPath,RootFile);
3508list=get(handles.masklevel,'String');
3509masknumber=num2str(length(list));
3510maskindex=get(handles.masklevel,'Value');
3511mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3512%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3513imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3514imflag=flipdim(imflag,1);
3515% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3516msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3517imwrite(imflag,mask_name,'BitDepth',8);
3518
3519%display the mask
3520figure;
3521vec=linspace(0,1,256);%define a linear greyscale colormap
3522map=[vec' vec' vec'];
3523colormap(map)
3524
3525image(imflag);
3526
3527%-------------------------------------------------------------------
3528%-------------------------------------------------------------------
3529%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3530
3531%------------------------------------------------------------------
3532%-------------------------------------------------------------
3533% --- Executes on selection change in transform_fct.
3534function transform_fct_Callback(hObject, eventdata, handles)
3535%-------------------------------------------------------------
3536UvData=get(handles.uvmat,'UserData');
3537menu=get(handles.transform_fct,'String');
3538ind_coord=get(handles.transform_fct,'Value');
3539coord_option=menu{ind_coord};
3540list_transform=get(handles.transform_fct,'UserData');
3541ff=functions(list_transform{end}); 
3542if isequal(coord_option,'more...');
3543    coord_fct='';
3544    prompt = {'Enter the name of the transform function'};
3545    dlg_title = 'user defined transform';
3546    num_lines= 1;
3547    [FileName, PathName] = uigetfile( ...
3548       {'*.m', ' (*.m)';
3549        '*.m',  '.m files '; ...
3550        '*.*', 'All Files (*.*)'}, ...
3551        'Pick a file', ff.file);
3552    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
3553        PathName(end)=[];
3554    end
3555    transform_selected =fullfile(PathName,FileName);
3556    if ~exist(transform_selected,'file')
3557           return
3558    end
3559   [ppp,transform,ext_fct]=fileparts(FileName);% removes extension .m
3560   if ~isequal(ext_fct,'.m')
3561        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3562        return
3563   end
3564   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
3565   ind_coord=get(handles.transform_fct,'Value');
3566   addpath(PathName)
3567   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
3568   set(handles.transform_fct,'UserData',list_transform)
3569   rmpath(PathName)
3570   % save the new menu in the personal file 'uvmat_perso.mat'
3571   dir_perso=prefdir;%personal Matalb directory
3572   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3573   if exist(profil_perso,'file')
3574       nb_builtin=UvData.OpenParam.NbBuiltin;
3575       for ilist=nb_builtin+1:numel(list_transform)
3576           ff=functions(list_transform{ilist});
3577           transform_fct{ilist-nb_builtin}=ff.file;
3578       end
3579        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3580   end   
3581end
3582
[429]3583%% check the current path to the selected function
[387]3584if isa(list_transform{ind_coord},'function_handle')
3585    func=functions(list_transform{ind_coord});
3586    set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
3587else
3588    set(handles.path_transform,'String','')
3589end
3590
3591set(handles.CheckFixLimits,'Value',0)
3592set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3593
[429]3594%% delete drawn objects
[387]3595hother=findobj('Tag','proj_object');%find all the proj objects
3596for iobj=1:length(hother)
3597    delete_object(hother(iobj))
3598end
3599hother=findobj('Tag','DeformPoint');%find all the proj objects
3600for iobj=1:length(hother)
3601    delete_object(hother(iobj))
3602end
3603hh=findobj('Tag','calib_points');
3604if ~isempty(hh)
3605    delete(hh)
3606end
3607hhh=findobj('Tag','calib_marker');
3608if ~isempty(hhh)
3609    delete(hhh)
3610end
3611if isfield(UvData,'Object')
3612     UvData.Object=UvData.Object(1);
3613end
3614set(handles.ListObject,'Value',1)
[429]3615set(handles.ListObject,'String',{'plane'})
3616set(handles.ListObject_1,'Value',1)
3617set(handles.ListObject_1,'String',{'plane'})
[387]3618
3619%delete mask if it is displayed
[411]3620% if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
3621%    UvData=rmfield(UvData,'MaskName'); %will impose mask refresh 
3622% end
[387]3623set(handles.uvmat,'UserData',UvData)
3624run0_Callback(hObject, eventdata, handles)
3625
3626
3627
3628%------------------------------------------------
3629%CALLBACKS FOR PLOTTING PARAMETERS
3630%-------------------------------------------------
[405]3631%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3632% Plot coordinates
3633%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[387]3634%------------------------------------------------------------------------
3635function num_MinX_Callback(hObject, eventdata, handles)
3636%------------------------------------------------------------------------
3637set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3638set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3639update_plot(handles);
3640
3641%------------------------------------------------------------------------
3642function num_MaxX_Callback(hObject, eventdata, handles)
3643%------------------------------------------------------------------------
3644set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3645set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3646update_plot(handles);
3647
3648%------------------------------------------------------------------------
3649function num_MinY_Callback(hObject, eventdata, handles)
3650%------------------------------------------
3651set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3652set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3653update_plot(handles);
3654
3655%------------------------------------------------------------------------
3656function num_MaxY_Callback(hObject, eventdata, handles)
3657%------------------------------------------------------------------------
3658set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3659set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3660update_plot(handles);
3661
[405]3662%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3663% Scalar or image representation
3664%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[387]3665%------------------------------------------------------------------------
3666function num_MinA_Callback(hObject, eventdata, handles)
3667%------------------------------------------
3668set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3669set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3670MinA=str2double(get(handles.num_MinA,'String'));
3671MaxA=str2double(get(handles.num_MaxA,'String'));
3672if MinA>MaxA% switch minA and maxA in case of error
3673    MinA_old=MinA;
3674    MinA=MaxA;
3675    MaxA=MinA_old;
3676    set(handles.num_MinA,'String',num2str(MinA,5));
3677    set(handles.num_MaxA,'String',num2str(MaxA,5));
3678end
3679update_plot(handles);
3680
3681%------------------------------------------------------------------------
3682function num_MaxA_Callback(hObject, eventdata, handles)
3683%------------------------------------------------------------------------
3684set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3685set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3686MinA=str2double(get(handles.num_MinA,'String'));
3687MaxA=str2double(get(handles.num_MaxA,'String'));
3688if MinA>MaxA% switch minA and maxA in case of error
3689        MinA_old=MinA;
3690    MinA=MaxA;
3691    MaxA=MinA_old;
3692    set(handles.num_MinA,'String',num2str(MinA,5));
3693    set(handles.num_MaxA,'String',num2str(MaxA,5));
3694end
3695update_plot(handles);
3696
3697%------------------------------------------------------------------------
3698function CheckFixScalar_Callback(hObject, eventdata, handles)
3699%------------------------------------------------------------------------
3700test=get(handles.CheckFixScalar,'Value');
3701if test
3702    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3703else
3704    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3705    update_plot(handles);
3706end
3707
3708%-------------------------------------------------------------------
3709function CheckBW_Callback(hObject, eventdata, handles)
3710%-------------------------------------------------------------------
3711update_plot(handles);
3712
3713%-------------------------------------------------------------------
[428]3714function num_Opacity_Callback(hObject, eventdata, handles)
3715update_plot(handles);
3716%-------------------------------------------------------------------
3717
3718%-------------------------------------------------------------------
[387]3719function ListContour_Callback(hObject, eventdata, handles)
3720%-------------------------------------------------------------------
3721val=get(handles.ListContour,'Value');
3722if val==2
3723    set(handles.interval_txt,'Visible','on')
3724    set(handles.num_IncrA,'Visible','on')
3725else
3726    set(handles.interval_txt,'Visible','off')
3727    set(handles.num_IncrA,'Visible','off')
3728end
3729update_plot(handles);
3730
3731%-------------------------------------------------------------------
3732function num_IncrA_Callback(hObject, eventdata, handles)
3733%-------------------------------------------------------------------
3734update_plot(handles);
3735
[405]3736
3737%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3738% Vector representation
3739%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[387]3740%-------------------------------------------------------------------
3741function CheckHideWarning_Callback(hObject, eventdata, handles)
3742%-------------------------------------------------------------------
3743update_plot(handles);
3744
3745%-------------------------------------------------------------------
3746function CheckHideFalse_Callback(hObject, eventdata, handles)
3747%-------------------------------------------------------------------
3748update_plot(handles);
3749
3750%-------------------------------------------------------------------
3751function num_VecScale_Callback(hObject, eventdata, handles)
3752%-------------------------------------------------------------------
3753set(handles.CheckFixVectors,'Value',1);
3754set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3755update_plot(handles);
3756
3757%-------------------------------------------------------------------
3758function CheckFixVectors_Callback(hObject, eventdata, handles)
3759%-------------------------------------------------------------------
3760test=get(handles.CheckFixVectors,'Value');
3761if test
3762    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3763else
3764    update_plot(handles);
3765    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3766    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3767end
3768
3769%------------------------------------------------------------------------
3770% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3771function CheckDecimate4_Callback(hObject, eventdata, handles)
3772%------------------------------------------------------------------------
3773update_plot(handles);
3774
3775%------------------------------------------------------------------------
[405]3776% --- Executes on selection change in ColorCode menu
3777function ColorCode_Callback(hObject, eventdata, handles)
[387]3778%------------------------------------------------------------------------
[405]3779% edit the choice for color code
3780update_color_code_boxes(handles);
3781update_plot(handles);
3782
3783%------------------------------------------------------------------------
3784function update_color_code_boxes(handles)
3785%------------------------------------------------------------------------
3786list_code=get(handles.ColorCode,'String');% list menu fields
3787colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3788enable_slider='off';%default
3789enable_bounds='off';%default
3790enable_scalar='off';%default
3791switch colcode
3792    case {'rgb','bgr'}
3793        enable_slider='on';
3794        enable_bounds='on';
3795        enable_scalar='on';
3796    case '64 colors'
3797        enable_bounds='on';
3798        enable_scalar='on';
3799end
3800set(handles.Slider1,'Visible',enable_slider)
3801set(handles.Slider2,'Visible', enable_slider)
3802set(handles.num_ColCode1,'Visible',enable_slider)
3803set(handles.num_ColCode2,'Visible',enable_slider)
3804set(handles.TitleColCode1,'Visible',enable_slider)
3805set(handles.TitleColCode2,'Visible',enable_slider)
3806set(handles.CheckFixVecColor,'Visible',enable_bounds)
3807set(handles.num_MinVec,'Visible',enable_bounds)
3808set(handles.num_MaxVec,'Visible',enable_bounds)
3809set(handles.ColorScalar,'Visible',enable_scalar)
[387]3810set_vec_col_bar(handles)
[405]3811
3812%------------------------------------------------------------------
3813% --- Executes on selection change in ColorScalar: choice of the color code.
3814function ColorScalar_Callback(hObject, eventdata, handles)
3815%------------------------------------------------------------------
3816% edit the choice for color code
3817list_scalar=get(handles.ColorScalar,'String');% list menu fields
3818col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3819if isequal(col_scalar,'ima_cor')
3820    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3821    ColorCode='rgb';
3822    set(handles.num_MinVec,'String','0')
3823    set(handles.num_MaxVec,'String','1')
3824    set(handles.num_ColCode1,'String','0.333')
3825    set(handles.num_ColCode2,'String','0.666')
3826else
3827    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3828    ColorCode='64 colors';
3829end
3830ColorCodeList=get(handles.ColorCode,'String');
3831ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3832set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3833
3834update_color_code_boxes(handles);
3835%replot the current graph
3836run0_Callback(hObject, eventdata, handles)
3837
3838%----------------------------------------------------------------
3839% -- Executes on slider movement to set the color code
3840%
3841function Slider1_Callback(hObject, eventdata, handles)
3842%------------------------------------------------------------------
3843slider1=get(handles.Slider1,'Value');
3844min_val=str2num(get(handles.num_MinVec,'String'));
3845max_val=str2num(get(handles.num_MaxVec,'String'));
3846col=min_val+(max_val-min_val)*slider1;
3847set(handles.num_ColCode1,'String',num2str(col))
3848if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3849    set(handles.Slider2,'Value',col)
3850    set(handles.num_ColCode2,'String',num2str(col))
3851end
3852set_vec_col_bar(handles)
[387]3853update_plot(handles);
3854
[405]3855%----------------------------------------------------------------
3856% Executes on slider movement to set the color code
3857%----------------------------------------------------------------
3858function Slider2_Callback(hObject, eventdata, handles)
3859slider2=get(handles.Slider2,'Value');
3860min_val=str2num(get(handles.num_MinVec,'String'));
3861max_val=str2num(get(handles.num_MaxVec,'String'));
3862col=min_val+(max_val-min_val)*slider2;
3863set(handles.num_ColCode2,'String',num2str(col))
3864if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3865    set(handles.Slider1,'Value',col)
3866    set(handles.num_ColCode1,'String',num2str(col))
3867end
3868set_vec_col_bar(handles)
3869update_plot(handles);
3870
3871%----------------------------------------------------------------
3872% --- Execute on return carriage on the edit box corresponding to slider 1
3873%----------------------------------------------------------------
3874function num_ColCode1_Callback(hObject, eventdata, handles)
3875set_vec_col_bar(handles)
3876update_plot(handles);
3877
3878%----------------------------------------------------------------
3879% --- Execute on return carriage on the edit box corresponding to slider 2
3880%----------------------------------------------------------------
3881function num_ColCode2_Callback(hObject, eventdata, handles)
3882set_vec_col_bar(handles)
3883update_plot(handles);
[387]3884%------------------------------------------------------------------------
[405]3885%-------------------------------------------------------
[387]3886% --- Executes on button press in CheckFixVecColor.
[405]3887%-------------------------------------------------------
3888function VecColBar_Callback(hObject, eventdata, handles)
3889set_vec_col_bar(handles)
3890
3891%------------------------------------------------------------------------
3892% --- Executes on button press in CheckFixVecColor.
[387]3893function CheckFixVecColor_Callback(hObject, eventdata, handles)
3894%------------------------------------------------------------------------
[405]3895if ~get(handles.CheckFixVecColor,'Value')
[387]3896    update_plot(handles);
3897end
3898
3899%------------------------------------------------------------------------
3900% --- Executes on selection change in num_MaxVec.
3901function num_MinVec_Callback(hObject, eventdata, handles)
3902%------------------------------------------------------------------------
3903max_vec_Callback(hObject, eventdata, handles)
3904
3905%------------------------------------------------------------------------
3906% --- Executes on selection change in num_MaxVec.
3907function num_MaxVec_Callback(hObject, eventdata, handles)
3908%------------------------------------------------------------------------
3909set(handles.CheckFixVecColor,'Value',1)
3910CheckFixVecColor_Callback(hObject, eventdata, handles)
3911min_val=str2num(get(handles.num_MinVec,'String'));
3912max_val=str2num(get(handles.num_MaxVec,'String'));
3913slider1=get(handles.Slider1,'Value');
3914slider2=get(handles.Slider2,'Value');
3915colcode1=min_val+(max_val-min_val)*slider1;
3916colcode2=min_val+(max_val-min_val)*slider2;
3917set(handles.num_ColCode1,'String',num2str(colcode1))
3918set(handles.num_ColCode2,'String',num2str(colcode2))
3919update_plot(handles);
3920
3921%------------------------------------------------------------------------
[405]3922% --- update the display of color code for vectors (on vecColBar)
[387]3923function set_vec_col_bar(handles)
3924%------------------------------------------------------------------------
3925%get the image of the color display button 'VecColBar' in pixels
3926set(handles.VecColBar,'Unit','pixel');
3927pos_vert=get(handles.VecColBar,'Position');
3928set(handles.VecColBar,'Unit','Normalized');
3929width=ceil(pos_vert(3));
3930height=ceil(pos_vert(4));
3931
3932%get slider indications
[405]3933list=get(handles.ColorCode,'String');
3934ichoice=get(handles.ColorCode,'Value');
3935colcode.ColorCode=list{ichoice};
[387]3936colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3937colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
[405]3938test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
[387]3939if test3color
3940    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3941    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3942end
3943vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3944[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3945oneheight=ones(1,height);
3946A1=colorlist(col_vec,1)*oneheight;
3947A2=colorlist(col_vec,2)*oneheight;
3948A3=colorlist(col_vec,3)*oneheight;
3949A(:,:,1)=A1';
3950A(:,:,2)=A2';
3951A(:,:,3)=A3';
3952set(handles.VecColBar,'Cdata',A)
3953
3954%-------------------------------------------------------------------
3955function update_plot(handles)
3956%-------------------------------------------------------------------
3957UvData=get(handles.uvmat,'UserData');
3958AxeData=UvData.axes3;% retrieve the current plotted data
3959PlotParam=read_GUI(handles.uvmat);
[399]3960[tild,PlotParamOut]= plot_field(AxeData,handles.axes3,PlotParam);
[387]3961write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3962
[402]3963%------------------------------------------------------------------------
3964%------------------------------------------------------------------------
3965%   SELECTION AND EDITION OF PROJECTION OBJECTS
3966%------------------------------------------------------------------------
3967%------------------------------------------------------------------------
[387]3968
[410]3969% --- Executes on selection change in ListObject_1.
3970function ListObject_1_Callback(hObject, eventdata, handles)
[432]3971list_str=get(handles.ListObject,'String');
[410]3972UvData=get(handles.uvmat,'UserData');
3973ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
3974
3975%% update the projection plot on uvmat
[432]3976ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
3977plot_field(ProjData,handles.axes3,read_GUI(handles.uvmat));% plot the projected field;
3978%replot all the objects within the new projected field
3979for IndexObj=1:numel(list_str)
3980    IndexObj
3981        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat
3982        if isempty(hobject) || ~ishandle(hobject)
3983            hobject=handles.axes3
3984        end
3985        if isequal(IndexObj,get(handles.ListObject,'Value'))
3986            objectcolor='m'; %paint in magenta the currently selected object in ListObject
3987        else
3988            objectcolor='b';
3989        end
3990        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
3991end
3992set(handles.uvmat,'UserData',UvData)
[410]3993
3994%% display the object parameters if the GUI set_object is already opened
[425]3995if ~get(handles.ViewObject,'Value')
[410]3996    ZBounds=0; % default
3997    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3998        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3999        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4000    end
[425]4001    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
[410]4002    set_object(ObjectData,[],ZBounds);
[424]4003    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
[410]4004end
[432]4005
[410]4006%  desactivate the edit object mode
4007set(handles.edit_object,'Value',0)
4008set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4009
[387]4010%------------------------------------------------------------------------
4011% --- Executes on selection change in ListObject.
4012function ListObject_Callback(hObject, eventdata, handles)
4013%------------------------------------------------------------------------
4014list_str=get(handles.ListObject,'String');
4015IndexObj=get(handles.ListObject,'Value');%present object selection
4016
[410]4017%% The object  is displayed in set_object if this GUI is already opened
[402]4018UvData=get(handles.uvmat,'UserData');
[410]4019ObjectData=UvData.Object{IndexObj};
[402]4020hset_object=findobj(allchild(0),'tag','set_object');
4021if ~isempty(hset_object)
4022    ZBounds=0; % default
4023    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4024        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4025        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4026    end
[410]4027    ObjectData.Name=list_str{IndexObj};
[402]4028    set_object(ObjectData,[],ZBounds);
[424]4029    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
[402]4030end
[429]4031
4032%%  desactivate the edit object mode
[402]4033set(handles.edit_object,'Value',0)
4034set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4035
[429]4036%% update the  plot on view_field if view_field is already openened
4037hview_field=findobj(allchild(0),'tag','view_field');
4038if isempty(hview_field)
4039    hhview_field.axes3=[];
4040else
4041    Data=get(hview_field,'UserData');
4042    hhview_field=guidata(hview_field);
4043    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4044    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
4045    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4046    haxes=findobj(hview_field,'tag','axes3');
4047    pos=get(hview_field,'Position'); 
4048    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4049        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4050        pos_table=get(h_TableDisplay,'Position');
4051        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4052        drawnow% needed to change position before the next command
4053        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4054    else
4055        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
[387]4056    end
4057end
4058
[402]4059%% update the color of the graphic object representation: the selected object in magenta, others in blue
[432]4060update_object_color(handles.axes3,hhview_field.axes3,UvData.Object{IndexObj}.DisplayHandle.uvmat)
[387]4061
4062%------------------------------------------------------------------------
[402]4063%--- update the color representation of objects (indicating the selected ones)
4064function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
[387]4065%------------------------------------------------------------------------
[402]4066if isempty(axes_view_field)% case with no view_field plot
4067hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
[387]4068else
[402]4069hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4070findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
[387]4071end
4072for iobj=1:length(hother)
4073    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4074        set(hother(iobj),'EdgeColor','b')
4075        if isequal(get(hother(iobj),'FaceColor'),'m')
4076            set(hother(iobj),'FaceColor','b')
4077        end
4078    elseif isequal(get(hother(iobj),'Type'),'image')
4079        Acolor=get(hother(iobj),'CData');
4080        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4081        set(hother(iobj),'CData',Acolor);
4082    else
4083        set(hother(iobj),'Color','b')
4084    end
4085    set(hother(iobj),'Selected','off')
4086end
[432]4087if ishandle(DisplayHandle)
[402]4088    linetype=get(DisplayHandle,'Type');
4089    if isequal(linetype,'line')
4090        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4091    elseif isequal(linetype,'rectangle')
4092        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4093    elseif isequal(linetype,'patch')
4094        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4095    end
4096    SubObjectData=get(DisplayHandle,'UserData');
4097    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4098        for iobj=1:length(SubObjectData.SubObject)
4099            hsub=SubObjectData.SubObject(iobj);
4100            if isequal(get(hsub,'Type'),'rectangle')
4101                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4102            elseif isequal(get(hsub,'Type'),'image')
4103                Acolor=get(hsub,'CData');
4104                Acolor(:,:,1)=Acolor(:,:,3);
4105                set(hsub,'CData',Acolor);
4106            else
4107                set(hsub,'Color','m')
4108            end
[387]4109        end
4110    end
[402]4111    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4112        set(SubObjectData.DeformPoint,'Color','m')
4113    end
[387]4114end
[402]4115
[427]4116%-------------------------------------------------------------------
4117% --- Executes on selection change in edit_object.
4118function edit_object_Callback(hObject, eventdata, handles)
4119%-------------------------------------------------------------------
4120UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4121hset_object=findobj(allchild(0),'Tag','set_object');
4122if get(handles.edit_object,'Value')
4123    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4124    %suppress the other options
4125    set(handles.CheckZoom,'Value',0)
4126    CheckZoom_Callback(hObject, eventdata, handles)
4127    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4128    if ishandle(hgeometry_calib)
4129        hhgeometry_calib=guidata(hgeometry_calib);
4130        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4131        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4132    end
4133    set(handles.ViewObject,'value',1)
4134    ViewObject_Callback(hObject, eventdata, handles)
4135%     if isempty(hset_object)% open the GUI set_object with data of the currently selected object
4136%         ViewObject_Callback(hObject, eventdata, handles)
4137%         %         hset_object=findobj(allchild(0),'Tag','set_object');
4138%     else
4139%         hhset_object=guidata(hset_object);
4140%         set(hhset_object.PLOT,'enable','on');
4141%         set(get(hset_object,'children'),'enable','on')
4142%     end
4143else % desctivate object edit mode
4144    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4145    if ~isempty(hset_object)% open the
4146        hhset_object=guidata(hset_object);
4147        set(hhset_object.PLOT,'enable','off');
4148        set(get(hset_object,'children'),'enable','inactive')
4149    end
4150end
4151
4152
[402]4153%------------------------------------------------------------------------
[424]4154% --- Executes on button press in ViewObject.
4155function ViewObject_Callback(hObject, eventdata, handles)
[410]4156%------------------------------------------------------------------------
[424]4157check_view=get(handles.ViewObject,'Value');
[410]4158
4159if check_view %activate set_object   
[424]4160    IndexObj=get(handles.ListObject,'Value');
4161    list_object=get(handles.ListObject,'String');
[410]4162    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4163    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4164    if numel(UvData.Object)<IndexObj;% error in UvData
4165        msgbox_uvmat('ERROR','invalid object list')
4166        return
4167    end
4168    ZBounds=0; % default
4169    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4170        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4171        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4172    end
[424]4173%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
[410]4174    data=UvData.Object{IndexObj};
4175    if ~isfield(data,'Type')% default plane
4176        data.Type='plane';
4177    end
4178    if isfield(UvData,'Field')
4179        Field=UvData.Field;
4180        if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4181            data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4182            if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4183                data.RangeY=UvData.Field.Mesh;
4184            else
4185                data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4186            end
4187            data.DX=UvData.Field.Mesh;
4188            data.DY=UvData.Field.Mesh;
4189        end
4190        if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4191            data.Coord=[0 0 0]; %default
4192        end
4193        if isfield(Field,'CoordUnit')
4194            data.CoordUnit=Field.CoordUnit;
4195        end
4196    end
4197    hset_object=set_object(data,[],ZBounds);
4198    hhset_object=guidata(hset_object);
4199    if get(handles.edit_object,'Value')% edit mode
4200        set(hhset_object.PLOT,'Enable','on')
[424]4201        set(get(hset_object,'children'),'enable','on')
[410]4202    else
4203        set(hhset_object.PLOT,'Enable','off')
[427]4204        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4205        set(hhset_object.SAVE,'Enable','on')
[410]4206    end
4207else
4208    hset_object=findobj(allchild(0),'tag','set_object');
4209    if ~isempty(hset_object)
4210        delete(hset_object)% delete existing version of set_object
4211    end
4212end
4213 
[424]4214
[410]4215%------------------------------------------------------------------------
[424]4216% --- Executes on button press in ViewField.
4217function ViewField_Callback(hObject, eventdata, handles)
[402]4218%------------------------------------------------------------------------
[424]4219check_view=get(handles.ViewField,'Value');
[387]4220
[410]4221if check_view
4222    IndexObj=get(handles.ListObject,'Value');
4223    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4224    if numel(UvData.Object)<IndexObj(end);% error in UvData
4225        msgbox_uvmat('ERROR','invalid object list')
4226        return
4227    end
4228    ZBounds=0; % default
4229    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4230        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4231        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4232    end
4233    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4234    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4235        UvData.Object{IndexObj(1)}.Type='plane';
4236    end
4237    list_object=get(handles.ListObject,'String');
4238    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4239   
[429]4240    %% show the projection of the selected object on view_field
4241    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
[402]4242    hview_field=findobj(allchild(0),'tag','view_field');
4243    if isempty(hview_field)
4244        hview_field=view_field;
4245    end
[429]4246    hhview_field=guidata(hview_field);
4247    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.axes3,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4248    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4249    haxes=findobj(hview_field,'tag','axes3');
4250    pos=get(hview_field,'Position');
4251    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4252        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4253        pos_table=get(h_TableDisplay,'Position');
4254        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4255    else
4256        Data=get(hview_field,'UserData');
[432]4257        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
[429]4258    end
[410]4259else
[424]4260    hview_field=findobj(allchild(0),'tag','view_field');
4261    if ~isempty(hview_field)
4262        delete(hview_field)% delete existing version of set_object
[410]4263    end
[402]4264end
4265
[424]4266
[402]4267%------------------------------------------------------------------------
4268% --- Executes on button press in delete_object.
4269function delete_object_Callback(hObject, eventdata, handles)
4270%------------------------------------------------------------------------
4271IndexObj=get(handles.ListObject,'Value');
[410]4272IndexObj_1=get(handles.ListObject_1,'Value');
4273if IndexObj>1 && ~isequal(IndexObj,IndexObj_1)
4274    delete_object(IndexObj)
[402]4275end
4276
4277%------------------------------------------------------------------------
4278%------------------------------------------------------------------------
4279%  II - TOOLS FROM THE UPPER MENU BAR
4280%------------------------------------------------------------------------
4281%------------------------------------------------------------------------
4282
4283%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4284% Export  Menu Callbacks
4285%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4286%------------------------------------------------------------------------
[387]4287% --- Executes on button press in Menu/Export/field in workspace.
4288function MenuExportField_Callback(hObject, eventdata, handles)
[402]4289%------------------------------------------------------------------------
[387]4290global Data_uvmat
4291Data_uvmat=get(handles.uvmat,'UserData');
4292evalin('base','global Data_uvmat')%make CurData global in the workspace
4293display('current field :')
4294evalin('base','Data_uvmat') %display CurData in the workspace
4295commandwindow; %brings the Matlab command window to the front
4296
[402]4297%------------------------------------------------------------------------
[387]4298% --- Executes on button press in Menu/Export/extract figure.
[402]4299function MenuExportFigure_Callback(hObject, eventdata, handles)
4300%------------------------------------------------------------------------
4301% huvmat=get(handles.MenuExport,'parent');
[387]4302hfig=figure;
[402]4303copyobj(handles.axes3,hfig);
[387]4304map=colormap(handles.axes3);
4305colormap(map);%transmit the current colormap to the zoom fig
4306colorbar
4307
[402]4308% %------------------------------------------------------
4309% % --- Executes on button press in Menu/Export/extract figure.
4310% %------------------------------------------------------
4311% function MenuExport_plot_Callback(hObject, eventdata, handles)
4312% huvmat=get(handles.MenuExport_plot,'parent');
4313% UvData=get(huvmat,'UserData');
4314% hfig=figure;
4315% newaxes=copyobj(handles.axes3,hfig);
4316% map=colormap(handles.axes3);
4317% colormap(map);%transmit the current colormap to the zoom fig
4318% colorbar
[387]4319
[402]4320%
4321% % --------------------------------------------------------------------
4322% function Insert_Callback(hObject, eventdata, handles)
4323%
[387]4324
4325%------------------------------------------------------------------------
4326% --------------------------------------------------------------------
4327function MenuExportMovie_Callback(hObject, eventdata, handles)
4328% --------------------------------------------------------------------
4329set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4330huvmat=get(handles.run0,'parent');
4331UvData=get(huvmat,'UserData');
4332%[xx,xx,FileBase]=read_file_boxes(handles);
4333[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4334FileBase=fullfile(RootPath,RootFile);
4335 %read the current input file name
4336prompt = {'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)'};
4337dlg_title = 'select properties of the output avi movie';
4338num_lines= 1;
4339% nbfield_cell=get(handles.last_i,'String');
4340def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4341answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4342aviname=answer{1};
4343fps=str2double(answer{2});
4344% check for existing file with output name aviname
4345if exist(aviname,'file')
4346    backup=aviname;
4347    testexist=2;
4348    while testexist==2
4349        backup=[backup '~'];
4350        testexist=exist(backup,'file');     
4351    end
4352    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4353    if isequal(success,1)
4354        delete(aviname)%delete existing file
4355    else
4356        msgbox_uvmat('ERROR',message)
4357        return
4358    end
4359end
4360%create avi open
4361aviobj=avifile(aviname,'Compression','None','fps',fps);
4362
4363%display first view for tests
4364newfig=figure;
4365newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure
4366set(newaxes,'Tag','movieaxes')
4367nbpix=[512 384]*str2double(answer{3});
4368set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4369set(newaxes,'Position',eval(answer{4}));
4370map=colormap(handles.axes3);
4371colormap(map);%transmit the current colormap to the zoom fig
4372msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4373        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4374UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4375set(huvmat,'UserData',UvData);
4376increment=str2num(get(handles.increment_scan,'String')); %get the field increment d
4377set(handles.STOP,'Visible','on')
4378set(handles.speed,'Visible','on')
4379set(handles.speed_txt,'Visible','on')
4380set(handles.Movie,'BusyAction','queue')
4381
4382%imin=str2double(get(handles.i1,'String'));
4383imax=str2double(answer{5});
4384% if isfield(UvData,'Time')
4385htitle=get(newaxes,'Title');
4386xlim=get(newaxes,'XLim');
4387ylim=get(newaxes,'YLim');
4388set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4389time_str=get(handles.abs_time,'String');
4390set(htitle,'String',['t=' time_str])
4391set(handles.speed,'Value',1)
4392for i=1:imax
4393    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4394            runpm(hObject,eventdata,handles,increment)% run plus
4395            drawnow
4396            time_str=get(handles.abs_time,'String');
4397            if ishandle(htitle)
4398             set(htitle,'String',['t=' time_str])
4399            end
4400            mov=getframe(newfig);
4401            aviobj=addframe(aviobj,mov);
4402    end
4403end
4404aviobj=close(aviobj);
4405UvData=rmfield(UvData,'plotaxes');
4406%UvData.Object{1}.plotaxes=handles.axes3;
4407set(huvmat,'UserData',UvData);
4408msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4409
[402]4410
4411%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4412% Projection Objects Menu Callbacks
4413%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4414
4415% -----------------------------------------------------------------------
4416function Menupoints_Callback(hObject, eventdata, handles)
[387]4417%------------------------------------------------------------------------
[402]4418data.Type='points';
4419data.ProjMode='projection';%default
[410]4420data.ProjModeMenu={};% do not restrict ProjMode menus
[402]4421create_object(data,handles)
4422
4423% -----------------------------------------------------------------------
4424function Menuline_Callback(hObject, eventdata, handles)
4425%------------------------------------------------------------------------
4426data.Type='line';
4427data.ProjMode='projection';%default
[410]4428data.ProjModeMenu={};% do not restrict ProjMode menus
[402]4429create_object(data,handles)
4430
4431%------------------------------------------------------------------------
4432function Menupolyline_Callback(hObject, eventdata, handles)
4433%------------------------------------------------------------------------
4434data.Type='polyline';
4435data.ProjMode='projection';%default
[410]4436data.ProjModeMenu={};% do not restrict ProjMode menus
[402]4437create_object(data,handles)
4438
4439%------------------------------------------------------------------------
4440function Menupolygon_Callback(hObject, eventdata, handles)
4441%------------------------------------------------------------------------
4442data.Type='polygon';
4443data.ProjMode='inside';%default
[410]4444data.ProjModeMenu={};% do not restrict ProjMode menus
[402]4445create_object(data,handles)
4446
4447%------------------------------------------------------------------------
4448function Menurectangle_Callback(hObject, eventdata, handles)
4449%------------------------------------------------------------------------
4450data.Type='rectangle';
4451data.ProjMode='inside';%default
[410]4452data.ProjModeMenu={};% do not restrict ProjMode menus
[402]4453create_object(data,handles)
4454
4455%------------------------------------------------------------------------
4456function Menuellipse_Callback(hObject, eventdata, handles)
4457%------------------------------------------------------------------------
4458data.Type='ellipse';
4459data.ProjMode='inside';%default
[410]4460data.ProjModeMenu={};% do not restrict ProjMode menus
[402]4461create_object(data,handles)
4462
4463%------------------------------------------------------------------------
4464function MenuMaskObject_Callback(hObject, eventdata, handles)
4465%------------------------------------------------------------------------
4466data.Type='polygon';
4467data.TypeMenu={'polygon'};
4468data.ProjMode='mask_inside';%default
4469data.ProjModeMenu={'mask_inside';'mask_outside'};
4470create_object(data,handles)
4471
4472%------------------------------------------------------------------------
4473function Menuplane_Callback(hObject, eventdata, handles)
4474%------------------------------------------------------------------------
4475data.Type='plane';
4476data.ProjMode='projection';%default
[410]4477data.ProjModeMenu={};% do not restrict ProjMode menus
[402]4478create_object(data,handles)
4479
4480%------------------------------------------------------------------------
4481function Menuvolume_Callback(hObject, eventdata, handles)
4482%------------------------------------------------------------------------
4483data.Type='volume';
4484data.ProjMode='interp';%default
[410]4485data.ProjModeMenu={};
[402]4486% set(handles.create,'Visible','on')
4487% set(handles.create,'Value',1)
[410]4488% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
[402]4489create_object(data,handles)
4490
4491%------------------------------------------------------------------------
4492% --- generic function used for the creation of a projection object
4493function create_object(data,handles)
4494%------------------------------------------------------------------------
[410]4495% desactivate geometric calibration if opened
[402]4496hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4497if ishandle(hgeometry_calib)
4498    hhgeometry_calib=guidata(hgeometry_calib);
4499    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4500    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4501end
4502set(handles.edit_object,'Value',0); %suppress the object edit mode
4503set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
[429]4504ListObject=get(handles.ListObject,'String');
4505if ~strcmp(ListObject{end},'')
4506    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4507    set(handles.ListObject,'String',ListObject)
4508end
4509IndexObj=length(ListObject);
4510set(handles.ListObject,'Value',IndexObj)
[410]4511UvData=get(handles.uvmat,'UserData');
[429]4512UvData.Object{IndexObj}=[]; %create a new empty object
[432]4513UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.axes3; % axes for plot_object
4514UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
[410]4515data.Name=data.Type;% default name=type
[402]4516data.Coord=[0 0]; %default
4517if isfield(UvData,'Field')
4518    Field=UvData.Field;
[404]4519    if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4520        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
[410]4521        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
[406]4522            data.RangeY=UvData.Field.Mesh;
4523        else
4524            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4525        end
[404]4526        data.DX=UvData.Field.Mesh;
4527        data.DY=UvData.Field.Mesh;
[402]4528    end
4529    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4530         data.Coord=[0 0 0]; %default
4531    end
4532    if isfield(Field,'CoordUnit')
4533        data.CoordUnit=Field.CoordUnit;
4534    end
4535end
4536if ishandle(handles.UVMAT_title)
4537    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4538end
4539hset_object=set_object(data,handles);% call the set_object interface
4540hhset_object=guidata(hset_object);
[421]4541hchild=get(hset_object,'children');
4542set(hchild,'enable','on')
[402]4543set(handles.uvmat,'UserData',UvData)
[410]4544set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
[402]4545CheckZoom_Callback(handles.uvmat, [], handles)
4546set(handles.delete_object,'Visible','on')
4547
4548%------------------------------------------------------------------------
4549function MenuBrowseObject_Callback(hObject, eventdata, handles)
4550%------------------------------------------------------------------------
4551%get the object file
4552[FileName, PathName, filterindex] = uigetfile( ...
4553       {'*.xml;*.mat', ' (*.xml,*.mat)';
4554       '*.xml',  '.xml files '; ...
4555        '*.mat',  '.mat matlab files '}, ...
4556        'Pick an xml Object file',get(handles.RootPath,'String'));
4557fileinput=[PathName FileName];%complete file name
4558sizf=size(fileinput);
4559if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4560
4561%read the file
4562data=xml2struct(fileinput);
[429]4563
[427]4564[tild,data.Name]=fileparts(FileName);% object name set as file name
[429]4565ListObject=get(handles.ListObject,'String');
4566if ~strcmp(ListObject{end},'')
4567    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4568    set(handles.ListObject,'String',ListObject)
4569end
[432]4570UvData=get(handles.uvmat,'UserData');
4571UvData.Object{IndexObj}=[]; %create a new empty object
4572UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4573UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4574set(handles.uvmat,'UserData',UvData)
[429]4575set(handles.ListObject,'Value',length(ListObject))
[427]4576hset_object=set_object(data);% call the set_object interface
4577set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
[402]4578set(handles.edit_object,'Value',0); %suppress the object edit mode
4579set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4580set(handles.delete_object,'Visible','on')
4581
[432]4582
[402]4583%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4584% MenuEdit Callbacks
4585%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4586%------------------------------------------------------------------------
4587function MenuEditObject_Callback(hObject, eventdata, handles)
4588%------------------------------------------------------------------------
4589set(handles.edit_object,'Value',1)
4590edit_Callback(hObject, eventdata, handles)
4591
4592% %------------------------------------------------------------------------
4593% function enable_transform(handles,state)
4594% %------------------------------------------------------------------------
4595% set(handles.transform_fct,'Visible',state)
4596% set(handles.TRANSFORM_txt,'Visible',state)   
4597% set(handles.transform_fct,'Visible',state) 
4598% set(handles.path_transform,'Visible',state)
4599% set(handles.pxcmx_txt,'Visible',state)
4600% set(handles.pxcmy_txt,'Visible',state)
4601% set(handles.pxcm,'Visible',state)
4602% set(handles.pycm,'Visible',state)
4603
4604%------------------------------------------------------------------------
4605function MenuEditVectors_Callback(hObject, eventdata, handles)
4606%------------------------------------------------------------------------
4607set(handles.edit_vect,'Visible','on')
4608set(handles.edit_vect,'Value',1)
4609edit_vect_Callback(hObject, eventdata, handles)
4610
4611%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4612% MenuTools Callbacks
4613%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4614%------------------------------------------------------------------------
[387]4615function MenuCalib_Callback(hObject, eventdata, handles)
4616%------------------------------------------------------------------------
4617
4618UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4619
4620%suppress competing options
4621set(handles.CheckZoom,'Value',0)
4622set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4623set(handles.ListObject,'Value',1)     
4624% initiate display of GUI geometry_calib
4625data=[]; %default
4626if isfield(UvData,'CoordType')
4627    data.CoordType=UvData.CoordType;
4628end
4629pos=get(handles.uvmat,'Position');
4630pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen)
4631pos(2)=pos(2)-0.02;
4632[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4633FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4634set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4635if isfield(UvData.OpenParam,'CalOrigin')
4636    pos_uvmat=get(handles.uvmat,'Position');
4637    pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.CalOrigin(1)*pos_uvmat(3);
4638    pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.CalOrigin(2)*pos_uvmat(4);
4639    pos_cal(3:4)=UvData.OpenParam.CalSize .* pos_uvmat(3:4);
4640end
4641geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4642set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4643set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4644
4645%------------------------------------------------------------------------
4646function MenuMask_Callback(hObject, eventdata, handles)
4647%------------------------------------------------------------------------
4648UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4649ListObj=UvData.Object;
4650select=zeros(1,numel(ListObj));
4651for iobj=1:numel(ListObj);
4652    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4653        select(iobj)=1;
4654    end
4655end
4656val=find(select);
4657if isempty(val)
4658    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4659    return
4660else
[410]4661%     set(handles.ListObject,'Max',2);%allow multiple selection
[387]4662    set(handles.ListObject,'Value',val);
4663    flag=1;
4664    npx=size(UvData.Field.A,2);
4665    npy=size(UvData.Field.A,1);
4666    xi=0.5:npx-0.5;
4667    yi=0.5:npy-0.5;
4668    [Xi,Yi]=meshgrid(xi,yi);
4669    if isfield(UvData,'Object')
4670        for iobj=1:length(UvData.Object)
4671            ObjectData=UvData.Object{iobj};
4672            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4673                flagobj=1;
4674                testphys=0; %coordinates in pixels by default
4675                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4676                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4677                        Calib=UvData.XmlData{1}.GeometryCalib;
4678                        testphys=1;
4679                    end
4680                end
4681                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4682                    if isequal(ObjectData.Type,'polygon')
4683                        X=ObjectData.Coord(:,1);
4684                        Y=ObjectData.Coord(:,2);
4685                        if testphys
4686                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4687                        end
4688                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4689                    elseif isequal(ObjectData.Type,'ellipse')
4690                        if testphys
4691                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4692                        end
4693                        RangeX=max(ObjectData.RangeX);
4694                        RangeY=max(ObjectData.RangeY);
4695                        X2Max=RangeX*RangeX;
4696                        Y2Max=RangeY*RangeY;
4697                        distX=(Xi-ObjectData.Coord(1,1));
4698                        distY=(Yi-ObjectData.Coord(1,2));
4699                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4700                    elseif isequal(ObjectData.Type,'rectangle')
4701                        if testphys
4702                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4703                        end
4704                        distX=abs(Xi-ObjectData.Coord(1,1));
4705                        distY=abs(Yi-ObjectData.Coord(1,2));
4706                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4707                    end
4708                    if isequal(ObjectData.ProjMode,'mask_outside')
4709                        flagobj=~flagobj;
4710                    end
4711                    flag=flag & flagobj;
4712                end
4713            end
4714        end
4715    end
4716    %mask name
4717    RootPath=get(handles.RootPath,'String');
4718    RootFile=get(handles.RootFile,'String');
4719    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4720        RootFile(1)=[];
4721    end
4722    filebase=fullfile(RootPath,RootFile);
4723    list=get(handles.masklevel,'String');
4724    masknumber=num2str(length(list));
4725    maskindex=get(handles.masklevel,'Value');
4726    mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4727    %mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
4728    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4729    imflag=flipdim(imflag,1);
4730
4731    %display the mask
4732    hfigmask=figure;
4733    set(hfigmask,'Name','mask image')
4734    vec=linspace(0,1,256);%define a linear greyscale colormap
4735    map=[vec' vec' vec'];
4736    colormap(map)
4737    image(imflag);
4738    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4739    if ~strcmp(answer,'Cancel')
4740        mask_dir=fileparts(answer);
4741        if ~exist(mask_dir,'dir')
4742            msgbox_uvmat('ERROR',['directory ' mask_dir ' does not exist'])
4743            return
4744        end
4745        imwrite(imflag,answer,'BitDepth',8);
4746    end
4747    set(handles.ListObject,'Value',1)
4748%     set(handles.ListObject,'Max',1)
4749end
4750
4751%------------------------------------------------------------------------
4752%-- open the GUI set_grid.fig to create grid
4753function MenuGrid_Callback(hObject, eventdata, handles)
4754%------------------------------------------------------------------------
4755%suppress the other options if grid is chosen
4756set(handles.edit_vect,'Value',0)
4757edit_vect_Callback(hObject, eventdata, handles)
4758set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4759set(handles.ListObject,'Value',1)     
4760
4761%prepare display of the set_grid GUI
4762[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
4763FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
4764CoordList=get(handles.transform_fct,'String');
4765val=get(handles.transform_fct,'Value');
4766set_grid(FileName,CoordList{val});% call the set_object interface
4767
[402]4768
[387]4769%------------------------------------------------------------------------
[402]4770function MenuRuler_Callback(hObject, eventdata, handles)
4771%------------------------------------------------------------------------
4772set(handles.CheckZoom,'Value',0)
4773CheckZoom_Callback(handles.uvmat, [], handles)
4774set(handles.MenuRuler,'checked','on')
4775UvData=get(handles.uvmat,'UserData');
4776UvData.MouseAction='ruler';
4777set(handles.uvmat,'UserData',UvData);
4778