source: trunk/src/geometry_calib.m @ 149

Last change on this file since 149 was 149, checked in by sommeria, 10 years ago

correction of bugs in geometry_calib , point editing and display

File size: 62.4 KB
Line 
1%%
2%'geometry_calib': performs geometric calibration from a set of reference points
3%
4% function varargout = geometry_calib(varargin)
5%
6%A%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
8%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9%     This file is part of the toolbox UVMAT.
10%
11%     UVMAT is free software; you can redistribute it and/or modify
12%     it under the terms of the GNU General Public License as published by
13%     the Free Software Foundation; either version 2 of the License, or
14%     (at your option) any later version.
15%
16%     UVMAT is distributed in the hope that it will be useful,
17%     but WITHOUT ANY WARRANTY; without even the implied warranty of
18%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
19%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
20%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21
22function varargout = geometry_calib(varargin)
23% GEOMETRY_CALIB M-file for geometry_calib.fig
24%      GEOMETRY_CALIB, by itself, creates a MenuCoord GEOMETRY_CALIB or raises the existing
25%      singleton*.
26%
27%      H = GEOMETRY_CALIB returns the handle to a MenuCoord GEOMETRY_CALIB or the handle to
28%      the existing singleton*.
29%
30%      GEOMETRY_CALIB('CALLBACK',hObject,eventData,handles,...) calls the local
31%      function named CALLBACK in GEOMETRY_CALIB.M with the given input arguments.
32%
33%      GEOMETRY_CALIB('Property','Value',...) creates a MenuCoord GEOMETRY_CALIB or raises the
34%      existing singleton*.  Starting from the left, property value pairs are
35%      applied to the GUI before geometry_calib_OpeningFunction gets called.  An
36%      unrecognized property name or invalid value makes property application
37%      stop.  All inputs are passed to geometry_calib_OpeningFcn via varargin.
38%
39%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
40%      instance to run (singleton)".
41%
42% See also: GUIDE, GUIDATA, GUIHANDLES
43
44% Edit the above text to modify the response to help geometry_calib
45
46% Last Modified by GUIDE v2.5 05-Oct-2010 13:47:00
47
48% Begin initialization code - DO NOT edit
49gui_Singleton = 1;
50gui_State = struct('gui_Name',       mfilename, ...
51                   'gui_Singleton',  gui_Singleton, ...
52                   'gui_OpeningFcn', @geometry_calib_OpeningFcn, ...
53                   'gui_OutputFcn',  @geometry_calib_OutputFcn, ...
54                   'gui_LayoutFcn',  [] , ...
55                   'gui_Callback',   []);
56if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback','once'))
57    gui_State.gui_Callback = str2func(varargin{1});
58end
59
60if nargout
61    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
62else
63    gui_mainfcn(gui_State, varargin{:});
64end
65% End initialization code - DO NOT edit
66
67
68% --- Executes just before geometry_calib is made visible.
69%INPUT:
70%handles: handles of the geometry_calib interface elements
71% PlotHandles: set of handles of the elements contolling the plotting
72% parameters on the uvmat interface (obtained by 'get_plot_handle.m')
73%------------------------------------------------------------------------
74function geometry_calib_OpeningFcn(hObject, eventdata, handles,inputfile,pos)
75%------------------------------------------------------------------------
76% Choose default command line output for geometry_calib
77handles.output = hObject;
78
79% Update handles structure
80guidata(hObject, handles);
81set(hObject,'DeleteFcn',{@closefcn})%
82
83%set the position of the interface
84if exist('pos','var')&& length(pos)>2
85    pos_gui=get(hObject,'Position');
86    pos_gui(1)=pos(1);
87    pos_gui(2)=pos(2);
88    set(hObject,'Position',pos_gui);
89end
90
91%set menu of calibration options
92%set(handles.calib_type,'String',{'rescale';'linear';'perspective';'normal';'tsai';'bouguet';'extrinsic'})
93set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'})
94inputxml='';
95if exist('inputfile','var')&& ~isempty(inputfile)
96    struct.XmlInputFile=inputfile;
97    [Pathsub,RootFile,field_count,str2,str_a,str_b,ext]=name2display(inputfile);
98    if ~strcmp(ext,'.xml')
99        inputfile=[fullfile(Pathsub,RootFile) '.xml'];%xml file corresponding to the input file
100    end
101end
102set(handles.ListCoord,'String',{'......'})
103if exist(inputfile,'file')
104    Heading=loadfile(handles,inputfile);% load the point coordiantes existing in the xml file
105end
106if isfield(Heading,'Campaign')&& ischar(Heading.Campaign)
107    struct.Campaign=Heading.Campaign;
108end
109set(hObject,'UserData',struct)
110set(handles.ListCoord,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function
111
112
113%------------------------------------------------------------------------
114% --- Outputs from this function are returned to the command line.
115function varargout = geometry_calib_OutputFcn(hObject, eventdata, handles)
116%------------------------------------------------------------------------
117% Get default command line output from handles structure
118varargout{1} = handles.output;
119varargout{2}=handles;
120%
121%------------------------------------------------------------------------
122% executed when closing: set the parent interface button to value 0
123function closefcn(gcbo,eventdata)
124%------------------------------------------------------------------------
125huvmat=findobj(allchild(0),'Name','uvmat');
126if ~isempty(huvmat)
127    handles=guidata(huvmat);
128    set(handles.MenuMask,'enable','on')
129    set(handles.MenuGrid,'enable','on')
130    set(handles.MenuObject,'enable','on')
131    set(handles.MenuEdit,'enable','on')
132    set(handles.edit,'enable','on')
133    hobject=findobj(handles.axes3,'tag','calib_points');
134    if ~isempty(hobject)
135        delete(hobject)
136    end
137    hobject=findobj(handles.axes3,'tag','calib_marker');
138    if ~isempty(hobject)
139        delete(hobject)
140    end   
141end
142
143%------------------------------------------------------------------------
144% --- Executes on button press in calibrate_lin.
145function APPLY_Callback(hObject, eventdata, handles)
146%------------------------------------------------------------------------
147%read the current calibration points
148Coord_cell=get(handles.ListCoord,'String');
149Object=read_geometry_calib(Coord_cell);
150Coord=Object.Coord;
151% apply the calibration, whose type is selected in  handles.calib_type
152if ~isempty(Coord)
153    calib_cell=get(handles.calib_type,'String');
154    val=get(handles.calib_type,'Value');
155    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
156else
157    msgbox_uvmat('ERROR','No calibration points, abort')
158    return
159end
160Z_plane=[];
161if ~isempty(Coord)
162    %check error
163    X=Coord(:,1);
164    Y=Coord(:,2);
165    Z=Coord(:,3);
166    x_ima=Coord(:,4);
167    y_ima=Coord(:,5);
168    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
169    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
170    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
171    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
172    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
173    [EM,ind_dim]=max(GeometryCalib.ErrorMax);
174    index=index(ind_dim);
175    %set the Z position of the reference plane used for calibration
176    if isequal(max(Z),min(Z))%Z constant
177        Z_plane=Z(1);
178        GeometryCalib.NbSlice=1;
179        GeometryCalib.SliceCoord=[0 0 Z_plane];
180    end
181end
182%set the coordinate unit
183unitlist=get(handles.CoordUnit,'String');
184unit=unitlist{get(handles.CoordUnit,'value')};
185GeometryCalib.CoordUnit=unit;
186%record the points
187GeometryCalib.SourceCalib.PointCoord=Coord;
188display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
189
190% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
191set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
192set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
193set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
194set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
195set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
196set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
197
198% store the calibration data, by default in the xml file of the currently displayed image
199hhuvmat=guidata(findobj(allchild(0),'Name','uvmat'));%handles of elements in the GUI uvmat
200RootPath='';
201RootFile='';
202if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
203    testhandle=1;
204    RootPath=get(hhuvmat.RootPath,'String');
205    RootFile=get(hhuvmat.RootFile,'String');
206    filebase=fullfile(RootPath,RootFile);
207    outputfile=[filebase '.xml'];%xml file associated with the currently displayed image
208else
209    question={'save the calibration data and point coordinates in'};
210    def={fullfile(RootPath,'ObjectCalib.xml')};
211    options.Resize='on';
212    answer=inputdlg(question,'save average in a new file',1,def,options);
213    outputfile=answer{1};
214end
215answer=msgbox_uvmat('INPUT_Y-N',{[outputfile ' updated with calibration data'];...
216    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
217    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
218
219%% record the calibration parameters and display the current image of uvmat in the new phys coordinates
220if strcmp(answer,'Yes')
221    if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
222        answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
223        if strcmp(answer_1,'Cancel')
224            Z_plane=0; %default
225        else
226            Z_plane=str2double(answer_1);
227        end
228        GeometryCalib.NbSlice=1;
229        GeometryCalib.SliceCoord=[0 0 Z_plane];
230    end
231    errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file
232    if ~strcmp(errormsg,'')
233        msgbox_uvmat('ERROR',errormsg);
234    end
235   
236    %display image with new calibration in the currently opened uvmat interface
237    hhh=findobj(hhuvmat.axes3,'Tag','calib_marker');% delete calib points and markers
238    if ~isempty(hhh)
239        delete(hhh);     
240    end
241    hhh=findobj(hhuvmat.axes3,'Tag','calib_points');
242    if ~isempty(hhh)
243        delete(hhh);
244    end
245    set(hhuvmat.FixedLimits,'Value',0)% put FixedLimits option to 'off'
246    set(hhuvmat.FixedLimits,'BackgroundColor',[0.7 0.7 0.7])
247    UserData=get(handles.geometry_calib,'UserData');
248    UserData.XmlInputFile=outputfile;%save the current xml file name
249    set(handles.geometry_calib,'UserData',UserData)
250    uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
251    MenuPlot_Callback(hObject, eventdata, handles)
252    set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
253    ListCoord_Callback(hObject, eventdata, handles)
254    figure(handles.geometry_calib)
255end
256
257%------------------------------------------------------------------
258% --- Executes on button press in calibrate_lin.
259
260function REPLICATE_Callback(hObject, eventdata, handles)
261%------------------------------------------------------------------------
262
263%% Apply calibration
264calib_cell=get(handles.calib_type,'String'); %#ok<NASGU>
265val=get(handles.calib_type,'Value'); %#ok<NASGU>
266
267%read the current calibration points
268Coord_cell=get(handles.ListCoord,'String');
269Object=read_geometry_calib(Coord_cell);
270Coord=Object.Coord;
271
272% apply the calibration, whose type is selected in  handles.calib_type
273if ~isempty(Coord)
274    calib_cell=get(handles.calib_type,'String');
275    val=get(handles.calib_type,'Value');
276    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
277else
278    msgbox_uvmat('ERROR','No calibration points, abort')
279    return
280end
281
282if ~isempty(Coord)
283    %check error
284    X=Coord(:,1);
285    Y=Coord(:,2);
286    Z=Coord(:,3);
287    x_ima=Coord(:,4);
288    y_ima=Coord(:,5);
289    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
290    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
291    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
292    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
293    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
294    [EM,ind_dim]=max(GeometryCalib.ErrorMax);
295%     index=index(ind_dim);
296    %set the Z position of the reference plane used for calibration
297    Z_plane=[];
298    if isequal(max(Z),min(Z))
299        Z_plane=Z(1);
300    end
301    answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
302    Z_plane=str2double(answer_1);
303    GeometryCalib.NbSlice=1;
304    GeometryCalib.SliceCoord=[0 0 Z_plane];
305    %set the coordinate unit
306    unitlist=get(handles.CoordUnit,'String');
307    unit=unitlist{get(handles.CoordUnit,'value')};
308    GeometryCalib.CoordUnit=unit;
309    %record the points
310    GeometryCalib.SourceCalib.PointCoord=Coord;
311end
312
313%% display calibration paprameters
314display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
315
316% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
317set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
318set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
319set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
320set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
321set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
322set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
323
324%% open the GUI dataview
325h_dataview=findobj(allchild(0),'name','dataview');
326if ~isempty(h_dataview)
327    delete(h_dataview)
328end
329CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
330InputFile='';
331if isfield(CalibData,'XmlInputFile')
332    InputDir=fileparts(CalibData.XmlInputFile);
333    [InputDir,DirName]=fileparts(InputDir);
334end
335SubCampaignTest='n'; %default
336testup=0;
337if isfield(CalibData,'SubCampaign')
338    SubCampaignTest='y';
339    dir_ref=CalibData.SubCampaign;
340    testup=1;
341elseif isfield(CalibData,'Campaign')
342    dir_ref=CalibData.Campaign;
343    testup=1;
344end
345while testup
346    [InputDir,DirName]=fileparts(InputDir);
347    if strcmp(DirName,dir_ref)
348        break
349    end
350end
351InputDir=fullfile(InputDir,DirName);
352answer=msgbox_uvmat('INPUT_TXT','Campaign ?',InputDir);
353if strcmp(answer,'Cancel')
354    return
355end
356
357dataview(answer,SubCampaignTest,GeometryCalib);
358       
359%     if isfield(Heading,'Device') && isequal([filename ext],Heading.Device)
360%         [XmlInput,filename,ext]=fileparts(XmlInput);
361%         Device=Heading.Device;
362%     end
363%     if isfield(Heading,'Experiment') && isequal([filename ext],Heading.Experiment)
364%         [PP,filename,ext]=fileparts(XmlInput);
365%     end
366%     testinput=0;
367%     if isfield(Heading,'SubCampaign') && isequal([filename ext],Heading.SubCampaign)
368%         SubCampaignTest='y';
369%         testinput=1;
370%     elseif isfield(Heading,'Campaign') && isequal([filename ext],Heading.Campaign)
371%         testinput=1;
372% %     end
373% end
374% if ~testinput
375%     filename='PROJETS';%default
376%     if isfield(CalibData,'XmlInputFile')
377%          [pp,filename]=fileparts(CalibData.XmlInputFile);
378%     end
379%     while ~isequal(filename,'PROJETS') && numel(filename)>1
380%         filename_1=filename;
381%         pp_1=pp;
382%         [pp,filename]=fileparts(pp);
383%     end
384%     XmlInput=fullfile(pp_1,filename_1);
385%     testinput=1;
386% end
387% if testinput
388%     outcome=dataview(XmlInput,SubCampaignTest,GeometryCalib);
389% end
390
391%------------------------------------------------------------------------
392% determine the parameters for a calibration by an affine function (rescaling and offset, no rotation)
393function GeometryCalib=calib_rescale(Coord,handles)
394%------------------------------------------------------------------------
395X=Coord(:,1);
396Y=Coord(:,2);% Z not used
397x_ima=Coord(:,4);
398y_ima=Coord(:,5);
399[px,sx]=polyfit(X,x_ima,1);
400[py,sy]=polyfit(Y,y_ima,1);
401T_x=px(2);
402T_y=py(2);
403GeometryCalib.CalibrationType='rescale';
404GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
405GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
406GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
407%GeometryCalib.R=[1,0,0;0,1,0;0,0,0];
408GeometryCalib.omc=[0 0 0];
409
410%------------------------------------------------------------------------
411% determine the parameters for a calibration by a linear transform matrix (rescale and rotation)
412function GeometryCalib=calib_linear(Coord,handles) %TO UPDATE
413%------------------------------------------------------------------------
414X=Coord(:,1);
415Y=Coord(:,2);% Z not used
416x_ima=Coord(:,4);
417y_ima=Coord(:,5);
418XY_mat=[ones(size(X)) X Y];
419a_X1=XY_mat\x_ima; %transformation matrix for X
420% x1=XY_mat*a_X1;%reconstruction
421% err_X1=max(abs(x1-x_ima));%error
422a_Y1=XY_mat\y_ima;%transformation matrix for X
423% y1=XY_mat*a_Y1;
424% err_Y1=max(abs(y1-y_ima));%error
425% R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,1];
426R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
427norm=abs(det(R));
428GeometryCalib.CalibrationType='linear';
429GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm);
430GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
431GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
432GeometryCalib.Tx_Ty_Tz=[a_X1(1) a_Y1(1) 1];
433R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
434R(2,:)=R(2,:)/GeometryCalib.fx_fy(2);
435R=[R;[0 0]];
436GeometryCalib.R=[R [0;0;1]];
437GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
438%------------------------------------------------------------------------
439% determine the tsai parameters for a view normal to the grid plane
440% NOT USED
441function GeometryCalib=calib_normal(Coord,handles)
442%------------------------------------------------------------------------
443Calib.f1=str2num(get(handles.fx,'String'));
444Calib.f2=str2num(get(handles.fy,'String'));
445Calib.k=str2num(get(handles.kc,'String'));
446Calib.Cx=str2num(get(handles.Cx,'String'));
447Calib.Cy=str2num(get(handles.Cy,'String'));
448%default
449if isempty(Calib.f1)
450    Calib.f1=25/0.012;
451end
452if isempty(Calib.f2)
453    Calib.f2=25/0.012;
454end
455if isempty(Calib.k)
456    Calib.k=0;
457end
458if isempty(Calib.Cx)||isempty(Calib.Cy)
459    huvmat=findobj(allchild(0),'Tag','uvmat');
460    hhuvmat=guidata(huvmat);
461    Calib.Cx=str2num(get(hhuvmat.npx,'String'))/2;
462    Calib.Cx=str2num(get(hhuvmat.npy,'String'))/2;
463end   
464%tsai parameters
465Calib.dpx=0.012;%arbitrary
466Calib.dpy=0.012;
467Calib.sx=Calib.f1*Calib.dpx/(Calib.f2*Calib.dpy);
468Calib.f=Calib.f2*Calib.dpy;
469Calib.kappa1=Calib.k/(Calib.f*Calib.f);
470
471%initial guess
472X=Coord(:,1);
473Y=Coord(:,2);
474Zmean=mean(Coord(:,3));
475x_ima=Coord(:,4)-Calib.Cx;
476y_ima=Coord(:,5)-Calib.Cy;
477XY_mat=[ones(size(X)) X Y];
478a_X1=XY_mat\x_ima; %transformation matrix for X
479a_Y1=XY_mat\y_ima;%transformation matrix for Y
480R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,-1];% rotation+ z axis reversal (upward)
481norm=sqrt(det(-R));
482calib_param(1)=0;% quadratic distortion
483calib_param(2)=a_X1(1);
484calib_param(3)=a_Y1(1);
485calib_param(4)=Calib.f/(norm*Calib.dpx)-R(3,3)*Zmean;
486calib_param(5)=angle(a_X1(2)+1i*a_X1(3));
487display(['initial guess=' num2str(calib_param)])
488
489%optimise the parameters: minimisation of error
490calib_param = fminsearch(@(calib_param) error_calib(calib_param,Calib,Coord),calib_param);
491
492GeometryCalib.CalibrationType='tsai_normal';
493GeometryCalib.focal=Calib.f;
494GeometryCalib.dpx_dpy=[Calib.dpx Calib.dpy];
495GeometryCalib.Cx_Cy=[Calib.Cx Calib.Cy];
496GeometryCalib.sx=Calib.sx;
497GeometryCalib.kappa1=calib_param(1);
498GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
499GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)];
500alpha=calib_param(5);
501GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
502
503%------------------------------------------------------------------------
504function GeometryCalib=calib_3D_linear(Coord,handles)
505%------------------------------------------------------------------
506path_uvmat=which('uvmat');% check the path detected for source file uvmat
507path_UVMAT=fileparts(path_uvmat); %path to UVMAT
508huvmat=findobj(allchild(0),'Tag','uvmat');
509hhuvmat=guidata(huvmat);
510coord_files=get(handles.coord_files,'String');
511if ischar(coord_files)
512    coord_files={coord_files};
513end
514if isempty(coord_files{1}) || isequal(coord_files,{''})
515    coord_files={};
516end
517%retrieve the calibration points stored in the files listed in the popup list coord_files
518x_1=Coord(:,4:5)';%px coordinates of the ref points
519nx=str2num(get(hhuvmat.npx,'String'));
520ny=str2num(get(hhuvmat.npy,'String'));
521x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
522X_1=Coord(:,1:3)';%phys coordinates of the ref points
523n_ima=numel(coord_files)+1;
524if ~isempty(coord_files)
525    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
526    for ifile=1:numel(coord_files)
527    t=xmltree(coord_files{ifile});
528    s=convert(t);%convert to matlab structure
529        if isfield(s,'GeometryCalib')
530            if isfield(s.GeometryCalib,'SourceCalib')
531                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
532                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
533                Coord_file=zeros(length(PointCoord),5);%default
534                for i=1:length(PointCoord)
535                    line=str2num(PointCoord{i});
536                    Coord_file(i,4:5)=line(4:5);%px x
537                    Coord_file(i,1:3)=line(1:3);%phys x
538                end
539                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
540                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
541                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
542                end
543            end
544        end
545    end
546end
547n_ima=numel(coord_files)+1;
548est_dist=[0;0;0;0;0];
549est_aspect_ratio=0;
550est_fc=[1;1];
551%fc=[25;25]/0.012;
552center_optim=0;
553run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
554GeometryCalib.CalibrationType='3D_linear';
555GeometryCalib.fx_fy=fc';
556%GeometryCalib.focal=fc(2);
557%GeometryCalib.dpx_dpy=[1 1];
558GeometryCalib.Cx_Cy=cc';
559%GeometryCalib.sx=fc(1)/fc(2);
560GeometryCalib.kc=kc(1);
561%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
562GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
563GeometryCalib.Tx_Ty_Tz=Tc_1';
564GeometryCalib.R=Rc_1;
565GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
566GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
567GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
568GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
569GeometryCalib.ErrorRMS=[];
570GeometryCalib.ErrorMax=[];
571
572%------------------------------------------------------------------------
573function GeometryCalib=calib_3D_quadr(Coord,handles)
574%------------------------------------------------------------------
575
576path_uvmat=which('uvmat');% check the path detected for source file uvmat
577path_UVMAT=fileparts(path_uvmat); %path to UVMAT
578huvmat=findobj(allchild(0),'Tag','uvmat');
579hhuvmat=guidata(huvmat);
580% check_cond=0;
581coord_files=get(handles.coord_files,'String');
582if ischar(coord_files)
583    coord_files={coord_files};
584end
585if isempty(coord_files{1}) || isequal(coord_files,{''})
586    coord_files={};
587end
588
589%retrieve the calibration points stored in the files listed in the popup list coord_files
590x_1=Coord(:,4:5)';%px coordinates of the ref points
591nx=str2num(get(hhuvmat.npx,'String'));
592ny=str2num(get(hhuvmat.npy,'String'));
593x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
594X_1=Coord(:,1:3)';%phys coordinates of the ref points
595n_ima=numel(coord_files)+1;
596if ~isempty(coord_files)
597    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
598    for ifile=1:numel(coord_files)
599    t=xmltree(coord_files{ifile});
600    s=convert(t);%convert to matlab structure
601        if isfield(s,'GeometryCalib')
602            if isfield(s.GeometryCalib,'SourceCalib')
603                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
604                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
605                Coord_file=zeros(length(PointCoord),5);%default
606                for i=1:length(PointCoord)
607                    line=str2num(PointCoord{i});
608                    Coord_file(i,4:5)=line(4:5);%px x
609                    Coord_file(i,1:3)=line(1:3);%phys x
610                end
611                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
612                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
613                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
614                end
615            end
616        end
617    end
618end
619n_ima=numel(coord_files)+1;
620est_dist=[1;0;0;0;0];
621est_aspect_ratio=1;
622%est_fc=[0;0];
623%fc=[25;25]/0.012;
624center_optim=0;
625run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
626
627GeometryCalib.CalibrationType='3D_quadr';
628GeometryCalib.fx_fy=fc';
629%GeometryCalib.focal=fc(2);
630%GeometryCalib.dpx_dpy=[1 1];
631GeometryCalib.Cx_Cy=cc';
632%GeometryCalib.sx=fc(1)/fc(2);
633GeometryCalib.kc=kc(1);
634%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
635GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
636GeometryCalib.Tx_Ty_Tz=Tc_1';
637GeometryCalib.R=Rc_1;
638GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
639GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
640GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
641GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
642GeometryCalib.ErrorRMS=[];
643GeometryCalib.ErrorMax=[];
644
645
646%------------------------------------------------------------------------
647function GeometryCalib=calib_3D_extrinsic(Coord,handles)
648%------------------------------------------------------------------
649path_uvmat=which('geometry_calib');% check the path detected for source file uvmat
650path_UVMAT=fileparts(path_uvmat); %path to UVMAT
651x_1=double(Coord(:,4:5)');%image coordiantes
652X_1=double(Coord(:,1:3)');% phys coordinates
653huvmat=findobj(allchild(0),'Tag','uvmat');
654hhuvmat=guidata(huvmat);
655ny=str2double(get(hhuvmat.npy,'String'));
656x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
657n_ima=1;
658GeometryCalib.CalibrationType='3D_extrinsic';
659GeometryCalib.fx_fy(1)=str2num(get(handles.fx,'String'));
660GeometryCalib.fx_fy(2)=str2num(get(handles.fy,'String'));
661GeometryCalib.Cx_Cy(1)=str2num(get(handles.Cx,'String'));
662GeometryCalib.Cx_Cy(2)=str2num(get(handles.Cy,'String'));
663GeometryCalib.kc=str2num(get(handles.kc,'String'));
664fct_path=fullfile(path_UVMAT,'toolbox_calib');
665addpath(fct_path)
666GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate)
667% [omc1,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
668%     [Calib.f Calib.f*Calib.sx]',...
669%     [Calib.Cx Calib.Cy]',...
670%     [-Calib.kappa1*Calib.f^2 0 0 0 0]);
671[omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
672    (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]);
673rmpath(fct_path);
674GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
675GeometryCalib.Tx_Ty_Tz=Tc1';
676%inversion of z axis
677GeometryCalib.R=Rc1;
678GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
679GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
680GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
681GeometryCalib.omc=(180/pi)*omc';
682%GeometryCalib.R(3,1:3)=-GeometryCalib.R(3,1:3);%inversion for z upward
683
684
685
686%------------------------------------------------------------------------
687%function GeometryCalib=calib_tsai_heikkila(Coord)
688% TEST: NOT IMPLEMENTED
689%------------------------------------------------------------------
690% path_uvmat=which('uvmat');% check the path detected for source file uvmat
691% path_UVMAT=fileparts(path_uvmat); %path to UVMAT
692% path_calib=fullfile(path_UVMAT,'toolbox_calib_heikkila');
693% addpath(path_calib)
694% npoints=size(Coord,1);
695% Coord(:,1:3)=10*Coord(:,1:3);
696% Coord=[Coord zeros(npoints,2) -ones(npoints,1)];
697% [par,pos,iter,res,er,C]=cacal('dalsa',Coord);
698% GeometryCalib.CalibrationType='tsai';
699% GeometryCalib.focal=par(2);
700
701
702%--------------------------------------------------------------------------
703function GeometryCalib=calib_tsai(Coord,handles)% OBSOLETE: old version using gauthier's bianry ccal_fo
704% NOT USED
705%------------------------------------------------------------------------
706%TSAI
707path_uvmat=which('uvmat');% check the path detected for source file uvmat
708path_UVMAT=fileparts(path_uvmat); %path to UVMAT
709xmlfile=fullfile(path_UVMAT,'PARAM.xml');%name of the file containing names of binary executables
710if exist(xmlfile,'file')
711    t=xmltree(xmlfile);% read the (xml) file containing names of binary executables
712    sparam=convert(t);% convert to matlab structure
713end
714if ~isfield(sparam,'GeometryCalibBin')
715    msgbox_uvmat('ERROR',['calibration program <GeometryCalibBin> undefined in parameter file ' xmlfile])
716    return
717end
718Tsai_exe=sparam.GeometryCalibBin;
719if ~exist(Tsai_exe,'file')%the binary is defined in /bin, default setting
720     Tsai_exe=fullfile(path_UVMAT,Tsai_exe);
721end
722if ~exist(Tsai_exe,'file')
723    msgbox_uvmat('ERROR',['calibration program ' sparam.GeometryCalibBin ' defined in PARAM.xml does not exist'])
724    return
725end
726
727textcoord=num2str(Coord,4);
728dlmwrite('t.txt',textcoord,''); 
729% ['!' Tsai_exe ' -fx 0 -fy t.txt']
730eval(['!' Tsai_exe ' -f t.txt > tsaicalib.log']);
731if ~exist('calib.dat','file')
732    msgbox_uvmat('ERROR','no output from calibration program Tsai_exe: possibly too few points')
733end
734calibdat=dlmread('calib.dat');
735delete('calib.dat')
736%delete('t.txt')
737GeometryCalib.CalibrationType='tsai';
738GeometryCalib.focal=calibdat(10);
739GeometryCalib.dpx_dpy=[calibdat(5) calibdat(6)];
740GeometryCalib.Cx_Cy=[calibdat(7) calibdat(8)];
741GeometryCalib.sx=calibdat(9);
742GeometryCalib.kappa1=calibdat(11);
743GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
744GeometryCalib.Tx_Ty_Tz=[calibdat(12) calibdat(13) calibdat(14)];
745Rx_Ry_Rz=calibdat(15:17);
746sa = sin(Rx_Ry_Rz(1)) ;
747ca=cos(Rx_Ry_Rz(1));
748sb=sin(Rx_Ry_Rz(2));
749cb =cos(Rx_Ry_Rz(2));
750sg =sin(Rx_Ry_Rz(3));
751cg =cos(Rx_Ry_Rz(3));
752r1 = cb * cg;
753r2 = cg * sa * sb - ca * sg;
754r3 = sa * sg + ca * cg * sb;
755r4 = cb * sg;
756r5 = sa * sb * sg + ca * cg;
757r6 = ca * sb * sg - cg * sa;
758r7 = -sb;
759r8 = cb * sa;
760r9 = ca * cb;
761%EN DEDUIRE MATRICE R ??
762GeometryCalib.R=[r1,r2,r3;r4,r5,r6;r7,r8,r9];
763
764%------------------------------------------------------------------------
765% --- determine the rms of calibration error
766function ErrorRms=error_calib(calib_param,Calib,Coord)
767%calib_param: vector of free calibration parameters (to optimise)
768%Calib: structure of the given calibration parameters
769%Coord: list of phys coordinates (columns 1-3, and pixel coordinates (columns 4-5)
770Calib.f=25;
771Calib.dpx=0.012;
772Calib.dpy=0.012;
773Calib.sx=1;
774Calib.Cx=512;
775Calib.Cy=512;
776Calib.kappa1=calib_param(1);
777Calib.Tx=calib_param(2);
778Calib.Ty=calib_param(3);
779Calib.Tz=calib_param(4);
780alpha=calib_param(5);
781Calib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
782
783X=Coord(:,1);
784Y=Coord(:,2);
785Z=Coord(:,3);
786x_ima=Coord(:,4);
787y_ima=Coord(:,5);
788[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z);
789ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
790ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
791ErrorRms=mean(ErrorRms);
792
793%------------------------------------------------------------------------
794function XImage_Callback(hObject, eventdata, handles)
795%------------------------------------------------------------------------
796update_list(hObject, eventdata,handles)
797
798%------------------------------------------------------------------------
799function YImage_Callback(hObject, eventdata, handles)
800%------------------------------------------------------------------------
801update_list(hObject, eventdata,handles)
802
803%------------------------------------------------------------------------
804% --- Executes on button press in STORE.
805function STORE_Callback(hObject, eventdata, handles)
806Coord_cell=get(handles.ListCoord,'String');
807Object=read_geometry_calib(Coord_cell);
808unitlist=get(handles.CoordUnit,'String');
809unit=unitlist{get(handles.CoordUnit,'value')};
810GeometryCalib.CoordUnit=unit;
811GeometryCalib.SourceCalib.PointCoord=Object.Coord;
812huvmat=findobj(allchild(0),'Name','uvmat');
813hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
814% RootPath='';
815% RootFile='';
816if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
817    testhandle=1;
818    RootPath=get(hhuvmat.RootPath,'String');
819    RootFile=get(hhuvmat.RootFile,'String');
820    filebase=fullfile(RootPath,RootFile);
821    while exist([filebase '.xml'],'file')
822        filebase=[filebase '~'];
823    end
824    outputfile=[filebase '.xml'];
825    errormsg=update_imadoc(GeometryCalib,outputfile);
826    if ~strcmp(errormsg,'')
827        msgbox_uvmat('ERROR',errormsg);
828    end
829    listfile=get(handles.coord_files,'string');
830    if isequal(listfile,{''})
831        listfile={outputfile};
832    else
833        listfile=[listfile;{outputfile}];%update the list of coord files
834    end
835    set(handles.coord_files,'string',listfile);
836end
837set(handles.ListCoord,'Value',1)% refresh the display of coordinates
838set(handles.ListCoord,'String',{'......'})
839
840% --------------------------------------------------------------------
841% --- Executes on button press in CLEAR_PTS: clear the list of calibration points
842function CLEAR_PTS_Callback(hObject, eventdata, handles)
843% --------------------------------------------------------------------
844set(handles.ListCoord,'Value',1)% refresh the display of coordinates
845set(handles.ListCoord,'String',{'......'})
846MenuPlot_Callback(hObject, eventdata, handles)
847
848%------------------------------------------------------------------------
849% --- Executes on button press in CLEAR.
850function CLEAR_Callback(hObject, eventdata, handles)
851%------------------------------------------------------------------------
852set(handles.coord_files,'Value',1)
853set(handles.coord_files,'String',{''})
854
855%------------------------------------------------------------------------
856function XObject_Callback(hObject, eventdata, handles)
857%------------------------------------------------------------------------
858update_list(hObject, eventdata,handles)
859
860%------------------------------------------------------------------------
861function YObject_Callback(hObject, eventdata, handles)
862%------------------------------------------------------------------------
863update_list(hObject, eventdata,handles)
864
865%------------------------------------------------------------------------
866function ZObject_Callback(hObject, eventdata, handles)
867%------------------------------------------------------------------------
868update_list(hObject, eventdata,handles)
869
870%------------------------------------------------------------------------
871function update_list(hObject, eventdata, handles)
872%------------------------------------------------------------------------
873newval(4)=str2double(get(handles.XImage,'String'));
874newval(5)=str2double(get(handles.YImage,'String'));
875newval(1)=str2double(get(handles.XObject,'String'));
876newval(2)=str2double(get(handles.YObject,'String'));
877newval(3)=str2double(get(handles.ZObject,'String'));
878if isnan(newval(3))
879    newval(3)=0;%put z to 0 by default
880end
881Coord=get(handles.ListCoord,'String');
882Coord(end)=[]; %remove last string '.....'
883val=get(handles.ListCoord,'Value');
884data=read_geometry_calib(Coord);
885data.Coord(val,:)=newval;
886for i=1:size(data.Coord,1)
887    for j=1:5
888          Coord_cell{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
889    end
890end
891
892Tabchar=cell2tab(Coord_cell,' | ');
893Tabchar=[Tabchar ;{'......'}];
894set(handles.ListCoord,'String',Tabchar)
895
896%update the plot
897ListCoord_Callback(hObject, eventdata, handles)
898MenuPlot_Callback(hObject, eventdata, handles)
899
900%------------------------------------------------------------------------
901% --- Executes on selection change in ListCoord.
902function ListCoord_Callback(hObject, eventdata, handles)
903%------------------------------------------------------------------------
904huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
905hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
906hhh=findobj(hplot,'Tag','calib_marker');
907Coord_cell=get(handles.ListCoord,'String');
908val=get(handles.ListCoord,'Value');
909if numel(val)>1
910    return %no action if several lines have been selected
911end
912coord_str=Coord_cell{val};
913k=findstr(' | ',coord_str);
914if isempty(k)%last line '.....' selected
915    if ~isempty(hhh)
916        delete(hhh)%delete the circle marker
917    end
918    return
919end
920%fill the edit boxex
921set(handles.XObject,'String',coord_str(1:k(1)-1))
922set(handles.YObject,'String',coord_str(k(1)+3:k(2)-1))
923set(handles.ZObject,'String',coord_str(k(2)+3:k(3)-1))
924set(handles.XImage,'String',coord_str(k(3)+3:k(4)-1))
925set(handles.YImage,'String',coord_str(k(4)+3:end))
926h_menu_coord=findobj(huvmat,'Tag','transform_fct');
927menu=get(h_menu_coord,'String');
928choice=get(h_menu_coord,'Value');
929if iscell(menu)
930    option=menu{choice};
931else
932    option='px'; %default
933end
934if isequal(option,'phys')
935    XCoord=str2double(coord_str(1:k(1)-1));
936    YCoord=str2double(coord_str(k(1)+3:k(2)-1));
937elseif isequal(option,'px')|| isequal(option,'')
938    XCoord=str2double(coord_str(k(3)+3:k(4)-1));
939    YCoord=str2double(coord_str(k(4)+3:end));
940else
941    msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be px or phys ')
942end
943if isempty(XCoord)||isempty(YCoord)
944     if ~isempty(hhh)
945        delete(hhh)%delete the circle marker
946    end
947    return
948end
949xlim=get(hplot,'XLim');
950ylim=get(hplot,'YLim');
951ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/20;%defines the size of the circle marker
952if isempty(hhh)
953    set(0,'CurrentFig',huvmat)
954    set(huvmat,'CurrentAxes',hplot)
955    rectangle('Curvature',[1 1],...
956              'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range],'EdgeColor','m',...
957              'LineStyle','-','Tag','calib_marker');
958else
959    set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
960end
961
962%------------------------------------------------------------------------
963% --- Executes on selection change in edit_append.
964function edit_append_Callback(hObject, eventdata, handles)
965%------------------------------------------------------------------------
966choice=get(handles.edit_append,'Value');
967if choice
968    set(handles.edit_append,'BackgroundColor',[1 1 0])
969else
970    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
971end
972   
973function NEW_Callback(hObject, eventdata, handles)
974%A METTRE SOUS UN BOUTON
975huvmat=findobj(allchild(0),'Name','uvmat');
976hchild=get(huvmat,'children');
977hcoord=findobj(hchild,'Tag','menu_coord');
978coordtype=get(hcoord,'Value');
979haxes=findobj(hchild,'Tag','axes3');
980AxeData=get(haxes,'UserData');
981if ~isequal(hcoord,2)
982    set(hcoord,'Value',2)
983    huvmat=uvmat(AxeData);
984    'relancer uvmat';
985end
986if ~isfield(AxeData,'ZoomAxes')
987    msgbox_uvmat('ERROR','first draw a window around a grid marker')
988    return
989end
990XLim=get(AxeData.ZoomAxes,'XLim');
991YLim=get(AxeData.ZoomAxes,'YLim');
992np=size(AxeData.A);
993ind_sub_x=round(XLim);
994ind_sub_y=np(1)-round(YLim);
995Mfiltre=AxeData.A([ind_sub_y(2):ind_sub_y(1)] ,ind_sub_x,:);
996Mfiltre_norm=double(Mfiltre);
997Mfiltre_norm=Mfiltre_norm/sum(sum(Mfiltre_norm));
998Mfiltre_norm=100*(Mfiltre_norm-mean(mean(Mfiltre_norm)));
999Atype=class(AxeData.A);
1000Data.NbDim=2;
1001Data.A=filter2(Mfiltre_norm,double(AxeData.A));
1002Data.A=feval(Atype,Data.A);
1003Data.AName='image';
1004Data.AX=AxeData.AX;
1005Data.AY=AxeData.AY;
1006Data.CoordType='px';
1007plot_field(Data)
1008
1009%------------------------------------------------------------------------
1010function MenuPlot_Callback(hObject, eventdata, handles)
1011%------------------------------------------------------------------------
1012huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
1013%UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface
1014hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat
1015%hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
1016h_menu_coord=findobj(huvmat,'Tag','transform_fct');
1017menu=get(h_menu_coord,'String');
1018choice=get(h_menu_coord,'Value');
1019if iscell(menu)
1020    option=menu{choice};
1021else
1022    option='px'; %default
1023end
1024Coord_cell=get(handles.ListCoord,'String');
1025ObjectData=read_geometry_calib(Coord_cell);
1026%ObjectData=read_geometry_calib(handles);%read the interface input parameters defining the object
1027if ~isempty(ObjectData.Coord)
1028    if isequal(option,'phys')
1029        ObjectData.Coord=ObjectData.Coord(:,[1:3]);
1030    elseif isequal(option,'px')||isequal(option,'')
1031        ObjectData.Coord=ObjectData.Coord(:,[4:5]);
1032    else
1033        msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be '''', px or phys ')
1034    end
1035end
1036axes(hhuvmat.axes3)
1037hh=findobj('Tag','calib_points');
1038if  ~isempty(ObjectData.Coord) && isempty(hh)
1039    hh=line(ObjectData.Coord(:,1),ObjectData.Coord(:,2),'Color','m','Tag','calib_points','LineStyle','.','Marker','+');
1040elseif isempty(ObjectData.Coord)%empty list of points, suppress the plot
1041    delete(hh)
1042else
1043    set(hh,'XData',ObjectData.Coord(:,1))
1044    set(hh,'YData',ObjectData.Coord(:,2))
1045end
1046pause(.1)
1047figure(handles.geometry_calib)
1048
1049% --------------------------------------------------------------------
1050function MenuHelp_Callback(hObject, eventdata, handles)
1051path_to_uvmat=which('uvmat');% check the path of uvmat
1052pathelp=fileparts(path_to_uvmat);
1053helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
1054if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
1055else
1056   addpath (fullfile(pathelp,'uvmat_doc'))
1057   web([helpfile '#geometry_calib'])
1058end
1059
1060%------------------------------------------------------------------------
1061function MenuCreateGrid_Callback(hObject, eventdata, handles)
1062%------------------------------------------------------------------------
1063%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1064CalibData=get(handles.geometry_calib,'UserData');
1065Tinput=[];%default
1066if isfield(CalibData,'grid')
1067    Tinput=CalibData.grid;
1068end
1069[T,CalibData.grid]=create_grid(Tinput);%display the GUI create_grid
1070set(handles.geometry_calib,'UserData',CalibData)
1071
1072%grid in phys space
1073Coord=get(handles.ListCoord,'String');
1074val=get(handles.ListCoord,'Value');
1075data=read_geometry_calib(Coord);
1076%nbpoints=size(data.Coord,1); %nbre of calibration points
1077data.Coord(val:val+size(T,1)-1,1:3)=T(end:-1:1,:);%update the existing list of phys coordinates from the GUI create_grid
1078% for i=1:nbpoints
1079%    for j=1:5
1080%           Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
1081%    end
1082% end
1083%update the phys coordinates starting from the selected point (down in the
1084Coord(end,:)=[]; %remove last string '.....'
1085for i=1:size(data.Coord,1)
1086    for j=1:5
1087          Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
1088    end
1089end
1090
1091%size(data.Coord,1)
1092Tabchar=cell2tab(Coord,' | ');
1093Tabchar=[Tabchar ;{'......'}];
1094set(handles.ListCoord,'String',Tabchar)
1095
1096% -----------------------------------------------------------------------
1097% --- automatic grid dectection from local maxima of the images
1098function MenuDetectGrid_Callback(hObject, eventdata, handles)
1099%------------------------------------------------------------------------
1100CalibData=get(handles.geometry_calib,'UserData');%get information stored on the GUI geometry_calib
1101grid_input=[];%default
1102if isfield(CalibData,'grid')
1103    grid_input=CalibData.grid;%retrieve the previously used grid
1104end
1105[T,CalibData.grid]=create_grid(grid_input,'detect_grid');%display the GUI create_grid, read the set of phys coordinates T
1106
1107set(handles.geometry_calib,'UserData',CalibData)%store the phys grid parameters for later use
1108
1109%read the four last point coordinates in pixels
1110Coord_cell=get(handles.ListCoord,'String');%read list of coordinates on geometry_calib
1111data=read_geometry_calib(Coord_cell);
1112nbpoints=size(data.Coord,1); %nbre of calibration points
1113if nbpoints~=4
1114    msgbox_uvmat('ERROR','four points must be selected by the mouse, beginning by the new x axis, to delimitate the phs grid area')
1115    return
1116end
1117corners_X=(data.Coord(end:-1:end-3,4)); %pixel absissa of the four corners
1118corners_Y=(data.Coord(end:-1:end-3,5));
1119
1120%reorder the last two points (the two first in the list) if needed
1121angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1)));
1122if abs(angles(4)-angles(2))>abs(angles(3)-angles(2))
1123      X_end=corners_X(4);
1124      Y_end=corners_Y(4);
1125      corners_X(4)=corners_X(3);
1126      corners_Y(4)=corners_Y(3);
1127      corners_X(3)=X_end;
1128      corners_Y(3)=Y_end;
1129end
1130
1131%read the current image, displayed in the GUI uvmat
1132huvmat=findobj(allchild(0),'Name','uvmat');
1133UvData=get(huvmat,'UserData');
1134A=UvData.Field.A;
1135npxy=size(A);
1136%linear transform on the current image
1137X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates
1138Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates
1139
1140%calculate transform matrices:
1141% reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
1142B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
1143      zeros(4,3)        X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ];
1144B = reshape (B', 8 , 8 )';
1145D = [ corners_X , corners_Y ];
1146D = reshape (D', 8 , 1 );
1147%l = inv(B' * B) * B' * D;
1148l = (B' * B)\B' * D;
1149Amat = reshape([l(1:6)' 0 0 1 ],3,3)';
1150C = [l(7:8)' 1];
1151
1152%GeometryCalib.CalibrationType='tsai';
1153%GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
1154% GeometryCalib.f=1;
1155% GeometryCalib.dpx=1;
1156% GeometryCalib.dpy=1;
1157% GeometryCalib.sx=1;
1158% GeometryCalib.Cx=0;
1159% GeometryCalib.Cy=0;
1160% GeometryCalib.kappa1=0;
1161% GeometryCalib.Tx=Amat(1,3);
1162% GeometryCalib.Ty=Amat(2,3);
1163% GeometryCalib.Tz=1;
1164% GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
1165%
1166% [Amod,Rangx,Rangy]=phys_Ima(A-min(min(A)),GeometryCalib,0);
1167
1168GeometryCalib.fx_fy=[1 1];
1169GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
1170GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
1171path_uvmat=which('uvmat');% check the path detected for source file uvmat
1172path_UVMAT=fileparts(path_uvmat); %path to UVMAT
1173addpath(fullfile(path_UVMAT,'transform_field'))
1174Data.ListVarName={'AY','AX','A'};
1175Data.VarDimName={'AY','AX',{'AY','AX'}};
1176if ndims(A)==3
1177    A=mean(A,3);
1178end
1179Data.A=A-min(min(A));
1180Data.AY=[npxy(1)-0.5 0.5];
1181Data.AX=[0.5 npxy(2)];
1182Data.CoordType='px';
1183Calib.GeometryCalib=GeometryCalib;
1184DataOut=phys(Data,Calib);
1185rmpath(fullfile(path_UVMAT,'transform_field'))
1186Amod=DataOut.A;
1187Rangx=DataOut.AX;
1188Rangy=DataOut.AY;
1189% GeometryCalib.dpx=1;
1190% GeometryCalib.dpy=1;
1191% GeometryCalib.sx=1;
1192% GeometryCalib.Cx=0;
1193% GeometryCalib.Cy=0;
1194% GeometryCalib.kappa1=0;
1195% GeometryCalib.Tx=Amat(1,3);
1196% GeometryCalib.Ty=Amat(2,3);
1197% GeometryCalib.Tz=1;
1198% GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
1199%
1200% [Amod,Rangx,Rangy]=phys_Ima(A-min(min(A)),GeometryCalib,0);
1201
1202
1203Amod=double(Amod);
1204% figure(12) %display corrected image
1205% Amax=max(max(Amod));
1206% image(Rangx,Rangy,uint8(255*Amod/Amax))
1207
1208Dx=(Rangx(2)-Rangx(1))/(npxy(2)-1); %x mesh in real space
1209Dy=(Rangy(2)-Rangy(1))/(npxy(1)-1); %y mesh in real space
1210ind_range_x=ceil(abs(GeometryCalib.R(1,1)*CalibData.grid.Dx/3));% range of search of image ma around each point obtained by linear interpolation from the marked points
1211ind_range_y=ceil(abs(GeometryCalib.R(2,2)*CalibData.grid.Dy/3));% range of search of image ma around each point obtained by linear interpolation from the marked points
1212nbpoints=size(T,1);
1213for ipoint=1:nbpoints
1214    i0=1+round((T(ipoint,1)-Rangx(1))/Dx);%round(Xpx(ipoint));
1215    j0=1+round((T(ipoint,2)-Rangy(1))/Dy);%round(Xpx(ipoint));
1216    j0min=max(j0-ind_range_y,1);
1217    j0max=min(j0+ind_range_y,size(Amod,1));
1218    i0min=max(i0-ind_range_x,1);
1219    i0max=min(i0+ind_range_x,size(Amod,2));
1220    Asub=Amod(j0min:j0max,i0min:i0max);
1221    x_profile=sum(Asub,1);
1222    y_profile=sum(Asub,2);
1223    [Amax,ind_x_max]=max(x_profile);
1224    [Amax,ind_y_max]=max(y_profile);
1225    %sub-pixel improvement using moments
1226    x_shift=0;
1227    y_shift=0;
1228    %if ind_x_max+2<=2*ind_range_x+1 && ind_x_max-2>=1
1229    if ind_x_max+2<=numel(x_profile) && ind_x_max-2>=1
1230        Atop=x_profile(ind_x_max-2:ind_x_max+2);
1231        x_shift=sum(Atop.*[-2 -1 0 1 2])/sum(Atop);
1232    end
1233    if ind_y_max+2<=numel(y_profile) && ind_y_max-2>=1
1234        Atop=y_profile(ind_y_max-2:ind_y_max+2);
1235        y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop);
1236    end
1237    Delta(ipoint,1)=(x_shift+ind_x_max+i0min-i0-1)*Dx;%shift from the initial guess
1238    Delta(ipoint,2)=(y_shift+ind_y_max+j0min-j0-1)*Dy;
1239end
1240Tmod=T(:,(1:2))+Delta;
1241[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));
1242for ipoint=1:nbpoints
1243     Coord{ipoint,1}=num2str(T(ipoint,1),4);%display coordiantes with 4 digits
1244     Coord{ipoint,2}=num2str(T(ipoint,2),4);%display coordiantes with 4 digits
1245     Coord{ipoint,3}=num2str(T(ipoint,3),4);%display coordiantes with 4 digits;
1246     Coord{ipoint,4}=num2str(Xpx(ipoint),4);%display coordiantes with 4 digits
1247     Coord{ipoint,5}=num2str(Ypx(ipoint),4);%display coordiantes with 4 digits
1248end
1249Tabchar=cell2tab(Coord(end:-1:1,:),' | ');
1250Tabchar=[Tabchar ;{'......'}];
1251set(handles.ListCoord,'Value',1)
1252set(handles.ListCoord,'String',Tabchar)
1253MenuPlot_Callback(hObject, eventdata, handles)
1254
1255%-----------------------------------------------------------------------
1256function MenuTranslatePoints_Callback(hObject, eventdata, handles)
1257%-----------------------------------------------------------------------
1258%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1259CalibData=get(handles.geometry_calib,'UserData');
1260Tinput=[];%default
1261if isfield(CalibData,'translate')
1262    Tinput=CalibData.translate;
1263end
1264T=translate_points(Tinput);%display translate_points GUI and get shift parameters
1265CalibData.translate=T;
1266set(handles.geometry_calib,'UserData',CalibData)
1267%translation
1268Coord_cell=get(handles.ListCoord,'String');
1269data=read_geometry_calib(Coord_cell);
1270data.Coord(:,1)=T(1)+data.Coord(:,1);
1271data.Coord(:,2)=T(2)+data.Coord(:,2);
1272data.Coord(:,3)=T(3)+data.Coord(:,3);
1273data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1274for i=1:size(data.Coord,1)
1275    for j=1:5
1276          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1277   end
1278end
1279Tabchar=cell2tab(Coord,' | ');
1280Tabchar=[Tabchar; {'.....'}];
1281%set(handles.ListCoord,'Value',1)
1282set(handles.ListCoord,'String',Tabchar)
1283
1284
1285% --------------------------------------------------------------------
1286function MenuRotatePoints_Callback(hObject, eventdata, handles)
1287%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1288CalibData=get(handles.geometry_calib,'UserData');
1289Tinput=[];%default
1290if isfield(CalibData,'rotate')
1291    Tinput=CalibData.rotate;
1292end
1293T=rotate_points(Tinput);%display translate_points GUI and get shift parameters
1294CalibData.rotate=T;
1295set(handles.geometry_calib,'UserData',CalibData)
1296%-----------------------------------------------------
1297%rotation
1298Phi=T(1);
1299O_x=0;%default
1300O_y=0;%default
1301if numel(T)>=2
1302    O_x=T(2);%default
1303end
1304if numel(T)>=3
1305    O_y=T(3);%default
1306end
1307Coord_cell=get(handles.ListCoord,'String');
1308data=read_geometry_calib(Coord_cell);
1309r1=cos(pi*Phi/180);
1310r2=-sin(pi*Phi/180);
1311r3=sin(pi*Phi/180);
1312r4=cos(pi*Phi/180);
1313x=data.Coord(:,1)-O_x;
1314y=data.Coord(:,2)-O_y;
1315data.Coord(:,1)=r1*x+r2*y;
1316data.Coord(:,2)=r3*x+r4*y;
1317% data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1318for i=1:size(data.Coord,1)
1319    for j=1:5
1320          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1321   end
1322end
1323Tabchar=cell2tab(Coord,' | ');
1324Tabchar=[Tabchar;{'......'}];
1325set(handles.ListCoord,'Value',1)
1326set(handles.ListCoord,'String',Tabchar)
1327
1328
1329% %------------------------------------------------------------------------
1330% % --- Executes on button press in rotation.
1331% function rotation_Callback(hObject, eventdata, handles)
1332% %------------------------------------------------------------------------
1333% angle_rot=(pi/180)*str2num(get(handles.Phi,'String'));
1334% Coord_cell=get(handles.ListCoord,'String');
1335% data=read_geometry_calib(Coord_cell);
1336% data.Coord(:,1)=cos(angle_rot)*data.Coord(:,1)+sin(angle_rot)*data.Coord(:,2);
1337% data.Coord(:,1)=-sin(angle_rot)*data.Coord(:,1)+cos(angle_rot)*data.Coord(:,2);
1338% set(handles.XObject,'String',num2str(data.Coord(:,1),4));
1339% set(handles.YObject,'String',num2str(data.Coord(:,2),4));
1340
1341
1342%------------------------------------------------------------------------
1343% image transform from px to phys
1344%INPUT:
1345%Zindex: index of plane
1346% function [A_out,Rangx,Rangy]=phys_Ima(A,Calib,ZIndex)
1347% %------------------------------------------------------------------------
1348% xcorner=[];
1349% ycorner=[];
1350% npx=[];
1351% npy=[];
1352% siz=size(A)
1353% npx=[npx siz(2)];
1354% npy=[npy siz(1)]
1355% xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners
1356% yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
1357% [xcorner,ycorner]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates
1358% Rangx(1)=min(xcorner);
1359% Rangx(2)=max(xcorner);
1360% Rangy(2)=min(ycorner);
1361% Rangy(1)=max(ycorner);
1362% test_multi=(max(npx)~=min(npx)) | (max(npy)~=min(npy));
1363% npx=max(npx);
1364% npy=max(npy);
1365% x=linspace(Rangx(1),Rangx(2),npx);
1366% y=linspace(Rangy(1),Rangy(2),npy);
1367% [X,Y]=meshgrid(x,y);%grid in physical coordiantes
1368% vec_B=[];
1369%
1370% zphys=0; %default
1371% if isfield(Calib,'SliceCoord') %.Z= index of plane
1372%    SliceCoord=Calib.SliceCoord(ZIndex,:);
1373%    zphys=SliceCoord(3); %to generalize for non-parallel planes
1374% end
1375% [XIMA,YIMA]=px_XYZ(Calib,X,Y,zphys);%corresponding image indices for each point in the real space grid
1376% XIMA=reshape(round(XIMA),1,npx*npy);%indices reorganized in 'line'
1377% YIMA=reshape(round(YIMA),1,npx*npy);
1378% flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image
1379% testuint8=isa(A,'uint8');
1380% testuint16=isa(A,'uint16');
1381% if numel(siz)==2 %(B/W images)
1382%     vec_A=reshape(A,1,npx*npy);%put the original image in line
1383%     ind_in=find(flagin);
1384%     ind_out=find(~flagin);
1385%     ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
1386%     ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
1387%     vec_B(ind_in)=vec_A(ICOMB);
1388%     vec_B(ind_out)=zeros(size(ind_out));
1389%     A_out=reshape(vec_B,npy,npx);%new image in real coordinates
1390% elseif numel(siz)==3     
1391%     for icolor=1:siz(3)
1392%         vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line
1393%         ind_in=find(flagin);
1394%         ind_out=find(~flagin);
1395%         ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
1396%         ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
1397%         vec_B(ind_in)=vec_A(ICOMB);
1398%         vec_B(ind_out)=zeros(size(ind_out));
1399%         A_out(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates
1400%     end
1401% end
1402% if testuint8
1403%     A_out=uint8(A_out);
1404% end
1405% if testuint16
1406%     A_out=uint16(A_out);
1407% end
1408
1409%------------------------------------------------------------------------
1410% pointwise transform from px to phys
1411%INPUT:
1412%Z: index of plane
1413% function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Z)
1414% %------------------------------------------------------------------------
1415% if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'SliceCoord')&length(Calib.SliceCoord)>=Z
1416%     Zindex=Z;
1417%     Zphys=Calib.SliceCoord(Zindex,3);%GENERALISER AUX CAS AVEC ANGLE
1418% else
1419%     Zphys=0;
1420% end
1421% if ~exist('X','var')||~exist('Y','var')
1422%     Xphys=[];
1423%     Yphys=[];%default
1424%     return
1425% end
1426% Xphys=X;%default
1427% Yphys=Y;
1428% %image transform
1429% if isfield(Calib,'R')
1430%     R=(Calib.R)';
1431%     Dx=R(5)*R(7)-R(4)*R(8);
1432%     Dy=R(1)*R(8)-R(2)*R(7);
1433%     D0=Calib.f*(R(2)*R(4)-R(1)*R(5));
1434%     Z11=R(6)*R(8)-R(5)*R(9);
1435%     Z12=R(2)*R(9)-R(3)*R(8); 
1436%     Z21=R(4)*R(9)-R(6)*R(7);
1437%     Z22=R(3)*R(7)-R(1)*R(9);
1438%     Zx0=R(3)*R(5)-R(2)*R(6);
1439%     Zy0=R(1)*R(6)-R(3)*R(4);
1440%     A11=R(8)*Calib.Ty-R(5)*Calib.Tz+Z11*Zphys;
1441%     A12=R(2)*Calib.Tz-R(8)*Calib.Tx+Z12*Zphys;
1442%     A21=-R(7)*Calib.Ty+R(4)*Calib.Tz+Z21*Zphys;
1443%     A22=-R(1)*Calib.Tz+R(7)*Calib.Tx+Z11*Zphys;
1444%     X0=Calib.f*(R(5)*Calib.Tx-R(2)*Calib.Ty+Zx0*Zphys);
1445%     Y0=Calib.f*(-R(4)*Calib.Tx+R(1)*Calib.Ty+Zy0*Zphys);
1446%         %px to camera:
1447%     Xd=(Calib.dpx/Calib.sx)*(X-Calib.Cx); % sensor coordinates
1448%     Yd=Calib.dpy*(Y-Calib.Cy);
1449%     dist_fact=1+Calib.kappa1*(Xd.*Xd+Yd.*Yd); %distortion factor
1450%     Xu=dist_fact.*Xd;%undistorted sensor coordinates
1451%     Yu=dist_fact.*Yd;
1452%     denom=Dx*Xu+Dy*Yu+D0;
1453%     % denom2=denom.*denom;
1454%     Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates
1455%     Yphys=(A21.*Xu+A22.*Yu+Y0)./denom;
1456% end
1457
1458
1459% --------------------------------------------------------------------
1460function MenuImportPoints_Callback(hObject, eventdata, handles)
1461fileinput=browse_xml(hObject, eventdata, handles);
1462if isempty(fileinput)
1463    return
1464end
1465[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1466GeometryCalib=s.GeometryCalib;
1467%GeometryCalib=load_calib(hObject, eventdata, handles)
1468calib=reshape(GeometryCalib.PointCoord,[],1);
1469for ilist=1:numel(calib)
1470    CoordCell{ilist}=num2str(calib(ilist));
1471end
1472CoordCell=reshape(CoordCell,[],5);
1473Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
1474Tabchar=[Tabchar;{'......'}];
1475set(handles.ListCoord,'Value',1)
1476set(handles.ListCoord,'String',Tabchar)
1477MenuPlot_Callback(handles.geometry_calib, [], handles)
1478
1479% -----------------------------------------------------------------------
1480function MenuImportIntrinsic_Callback(hObject, eventdata, handles)
1481%------------------------------------------------------------------------
1482fileinput=browse_xml(hObject, eventdata, handles);
1483if isempty(fileinput)
1484    return
1485end
1486[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1487GeometryCalib=s.GeometryCalib;
1488display_intrinsic(GeometryCalib,handles)
1489
1490% -----------------------------------------------------------------------
1491function MenuImportAll_Callback(hObject, eventdata, handles)
1492%------------------------------------------------------------------------
1493fileinput=browse_xml(hObject, eventdata, handles);
1494if ~isempty(fileinput)
1495    loadfile(handles,fileinput)
1496end
1497
1498% -----------------------------------------------------------------------
1499% --- Executes on menubar option Import/Grid file: introduce previous grid files
1500function MenuGridFile_Callback(hObject, eventdata, handles)
1501% -----------------------------------------------------------------------
1502inputfile=browse_xml(hObject, eventdata, handles);
1503listfile=get(handles.coord_files,'string');
1504if isequal(listfile,{''})
1505    listfile={inputfile};
1506else
1507    listfile=[listfile;{inputfile}];%update the list of coord files
1508end
1509set(handles.coord_files,'string',listfile);
1510
1511%------------------------------------------------------------------------
1512% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
1513function key_press_fcn(hObject,eventdata,handles)
1514%------------------------------------------------------------------------
1515xx=double(get(handles.geometry_calib,'CurrentCharacter')); %get the keyboard character
1516if ismember(xx,[8 127])%backspace or delete
1517    Coord_cell=get(handles.ListCoord,'String');
1518    val=get(handles.ListCoord,'Value');
1519     if max(val)<numel(Coord_cell) % the last element '...' has not been selected
1520        Coord_cell(val)=[];%remove the selected line
1521        set(handles.ListCoord,'Value',min(val))
1522        set(handles.ListCoord,'String',Coord_cell)         
1523        ListCoord_Callback(hObject, eventdata, handles)
1524        MenuPlot_Callback(hObject,eventdata,handles)
1525     end
1526end
1527
1528%------------------------------------------------------------------------
1529function fileinput=browse_xml(hObject, eventdata, handles)
1530%------------------------------------------------------------------------
1531fileinput=[];%default
1532oldfile=''; %default
1533UserData=get(handles.geometry_calib,'UserData');
1534if isfield(UserData,'XmlInputFile')
1535    oldfile=UserData.XmlInputFile;
1536end
1537[FileName, PathName, filterindex] = uigetfile( ...
1538       {'*.xml;*.mat', ' (*.xml,*.mat)';
1539       '*.xml',  '.xml files '; ...
1540        '*.mat',  '.mat matlab files '}, ...
1541        'Pick a file',oldfile);
1542fileinput=[PathName FileName];%complete file name
1543testblank=findstr(fileinput,' ');%look for blanks
1544if ~isempty(testblank)
1545    msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed')
1546    return
1547end
1548sizf=size(fileinput);
1549if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1550UserData.XmlInputFile=fileinput;
1551set(handles.geometry_calib,'UserData',UserData)%record current file foer further use of browser
1552
1553% -----------------------------------------------------------------------
1554function Heading=loadfile(handles,fileinput)
1555%------------------------------------------------------------------------
1556Heading=[];%default
1557[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1558if ~isempty(errormsg)
1559    msgbox_uvmat('ERROR',['Error for reading ' fileinput ': '  errormsg])
1560    return
1561end
1562if ~isempty(s.Heading)
1563    Heading=s.Heading;
1564end
1565   
1566GeometryCalib=s.GeometryCalib;
1567fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
1568%     Tabchar={};
1569CoordCell={};
1570%     kc=0;%default
1571%     f1=1000;
1572%     f2=1000;
1573%     hhuvmat=guidata(findobj(allchild(0),'Name','uvmat'));
1574%     Cx=str2num(get(hhuvmat.npx,'String'))/2;
1575%     Cy=str2num(get(hhuvmat.npy,'String'))/2;
1576Tabchar={};%default
1577val_cal=1;%default
1578if ~isempty(GeometryCalib)
1579    % choose the calibration option
1580    if isfield(GeometryCalib,'CalibrationType')
1581       calib_list=get(handles.calib_type,'String');
1582       for ilist=1:numel(calib_list)
1583           if strcmp(calib_list{ilist},GeometryCalib.CalibrationType)
1584               val_cal=ilist;
1585               break
1586           end
1587       end
1588    end
1589    display_intrinsic(GeometryCalib,handles)%intrinsic param
1590    %extrinsic param
1591    if isfield(GeometryCalib,'Tx_Ty_Tz')
1592        Tx_Ty_Tz=GeometryCalib.Tx_Ty_Tz;
1593        set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
1594        set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
1595        set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
1596    end
1597    if isfield(GeometryCalib,'omc')
1598        set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
1599        set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
1600        set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
1601    end
1602    calib=reshape(GeometryCalib.PointCoord,[],1);
1603    for ilist=1:numel(calib)
1604        CoordCell{ilist}=num2str(calib(ilist));
1605    end
1606    CoordCell=reshape(CoordCell,[],5);
1607    Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
1608    MenuPlot_Callback(handles.geometry_calib, [], handles)
1609end
1610set(handles.calib_type,'Value',val_cal)
1611Tabchar=[Tabchar;{'......'}];
1612set(handles.ListCoord,'Value',1)
1613set(handles.ListCoord,'String',Tabchar)
1614
1615if isempty(CoordCell)% allow mouse action by default in the absence of input points
1616    set(handles.edit_append,'Value',1)
1617    set(handles.edit_append,'BackgroundColor',[1 1 0])
1618else % does not allow mouse action by default in the presence of input points
1619    set(handles.edit_append,'Value',0)
1620    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
1621end
1622
1623%------------------------------------------------------------------------
1624%---display calibration intrinsic parameters
1625function display_intrinsic(GeometryCalib,handles)
1626%------------------------------------------------------------------------
1627fx=[];
1628fy=[];
1629if isfield(GeometryCalib,'fx_fy')
1630    fx=GeometryCalib.fx_fy(1);
1631    fy=GeometryCalib.fx_fy(2);
1632end
1633Cx_Cy=[0 0];%default
1634if isfield(GeometryCalib,'Cx_Cy')
1635    Cx_Cy=GeometryCalib.Cx_Cy;
1636end
1637kc=0;
1638if isfield(GeometryCalib,'kc')
1639    kc=GeometryCalib.kc; %* GeometryCalib.focal*GeometryCalib.focal;
1640end
1641set(handles.fx,'String',num2str(fx,5))
1642set(handles.fy,'String',num2str(fy,5))
1643set(handles.Cx,'String',num2str(Cx_Cy(1),'%1.1f'))
1644set(handles.Cy,'String',num2str(Cx_Cy(2),'%1.1f'))
1645set(handles.kc,'String',num2str(kc,'%1.4f'))
1646
1647
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