source: trunk/src/geometry_calib.m @ 213

Last change on this file since 213 was 213, checked in by sommeria, 10 years ago

bug corrected for 3D geometry calib: tilt angles

File size: 63.7 KB
Line 
1%'geometry_calib': associated to the GUI geometry_calib to perform geometric calibration from a set of reference points
2%------------------------------------------------------------------------
3% function hgeometry_calib = geometry_calib(inputfile,pos)
4%
5%OUTPUT:
6% hgeometry_calib=current handles of the GUI geometry_calib.fig
7%
8%INPUT:
9% inputfile: (optional) name of an xml file containing coordinates of reference points
10% pos: (optional) 4 element vector setting the 'Position' of the GUI
11%
12%A%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
14%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15%     This file is part of the toolbox UVMAT.
16%
17%     UVMAT is free software; you can redistribute it and/or modify
18%     it under the terms of the GNU General Public License as published by
19%     the Free Software Foundation; either version 2 of the License, or
20%     (at your option) any later version.
21%
22%     UVMAT is distributed in the hope that it will be useful,
23%     but WITHOUT ANY WARRANTY; without even the implied warranty of
24%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
25%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
26%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27
28function varargout = geometry_calib(varargin)
29% GEOMETRY_CALIB M-file for geometry_calib.fig
30%      GEOMETRY_CALIB, by itself, creates a MenuCoord GEOMETRY_CALIB or raises the existing
31%      singleton*.
32%
33%      H = GEOMETRY_CALIB returns the handle to a MenuCoord GEOMETRY_CALIB or the handle to
34%      the existing singleton*.
35%
36%      GEOMETRY_CALIB('CALLBACK',hObject,eventData,handles,...) calls the local
37%      function named CALLBACK in GEOMETRY_CALIB.M with the given input arguments.
38%
39%      GEOMETRY_CALIB('Property','Value',...) creates a MenuCoord GEOMETRY_CALIB or raises the
40%      existing singleton*.  Starting from the left, property value pairs are
41%      applied to the GUI before geometry_calib_OpeningFunction gets called.  An
42%      unrecognized property name or invalid value makes property application
43%      stop.  All inputs are passed to geometry_calib_OpeningFcn via varargin.
44%
45%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
46%      instance to run (singleton)".
47%
48% See also: GUIDE, GUIDATA, GUIHANDLES
49
50% Edit the above text to modify the response to help geometry_calib
51
52% Last Modified by GUIDE v2.5 05-Oct-2010 13:47:00
53
54% Begin initialization code - DO NOT edit
55gui_Singleton = 1;
56gui_State = struct('gui_Name',       mfilename, ...
57                   'gui_Singleton',  gui_Singleton, ...
58                   'gui_OpeningFcn', @geometry_calib_OpeningFcn, ...
59                   'gui_OutputFcn',  @geometry_calib_OutputFcn, ...
60                   'gui_LayoutFcn',  [] , ...
61                   'gui_Callback',   []);
62if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback','once'))
63    gui_State.gui_Callback = str2func(varargin{1});
64end
65
66if nargout
67    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
68else
69    gui_mainfcn(gui_State, varargin{:});
70end
71% End initialization code - DO NOT edit
72
73
74% --- Executes just before geometry_calib is made visible.
75%INPUT:
76%handles: handles of the geometry_calib interface elements
77% PlotHandles: set of handles of the elements contolling the plotting
78% parameters on the uvmat interface (obtained by 'get_plot_handle.m')
79%------------------------------------------------------------------------
80function geometry_calib_OpeningFcn(hObject, eventdata, handles,inputfile,pos)
81%------------------------------------------------------------------------
82% Choose default command line output for geometry_calib
83
84handles.output = hObject;
85
86% Update handles structure
87guidata(hObject, handles);
88set(hObject,'DeleteFcn',{@closefcn})%
89
90%set the position of the interface
91if exist('pos','var')&& length(pos)>=4
92%     %pos_gui=get(hObject,'Position');
93%     pos_gui(1)=pos(1);
94%     pos_gui(2)=pos(2);
95    set(hObject,'Position',pos);
96end
97
98%set menu of calibration options
99set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'})
100inputxml='';
101if exist('inputfile','var')&& ~isempty(inputfile)
102    struct.XmlInputFile=inputfile;
103    [Pathsub,RootFile,field_count,str2,str_a,str_b,ext]=name2display(inputfile);
104    if ~strcmp(ext,'.xml')
105        inputfile=[fullfile(Pathsub,RootFile) '.xml'];%xml file corresponding to the input file
106    end
107    set(handles.ListCoord,'String',{'......'})
108    if exist(inputfile,'file')
109        Heading=loadfile(handles,inputfile);% load the point coordiantes existing in the xml file
110        if isfield(Heading,'Campaign')&& ischar(Heading.Campaign)
111            struct.Campaign=Heading.Campaign;
112        end
113    end   
114    set(hObject,'UserData',struct)
115end
116
117set(handles.ListCoord,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function
118
119
120%------------------------------------------------------------------------
121% --- Outputs from this function are returned to the command line.
122function varargout = geometry_calib_OutputFcn(hObject, eventdata, handles)
123%------------------------------------------------------------------------
124% Get default command line output from handles structure
125varargout{1} = handles.output;
126varargout{2}=handles;
127%
128%------------------------------------------------------------------------
129% executed when closing: set the parent interface button to value 0
130function closefcn(gcbo,eventdata)
131%------------------------------------------------------------------------
132huvmat=findobj(allchild(0),'Name','uvmat');
133if ~isempty(huvmat)
134    handles=guidata(huvmat);
135%     set(handles.MenuMask,'enable','on')
136%     set(handles.MenuGrid,'enable','on')
137%     set(handles.MenuObject,'enable','on')
138%     set(handles.MenuEdit,'enable','on')
139%     set(handles.edit,'enable','on')
140    hobject=findobj(handles.axes3,'tag','calib_points');
141    if ~isempty(hobject)
142        delete(hobject)
143    end
144    hobject=findobj(handles.axes3,'tag','calib_marker');
145    if ~isempty(hobject)
146        delete(hobject)
147    end   
148end
149
150%------------------------------------------------------------------------
151% --- Executes on button press in calibrate_lin.
152function APPLY_Callback(hObject, eventdata, handles)
153%------------------------------------------------------------------------
154%read the current calibration points
155Coord_cell=get(handles.ListCoord,'String');
156Object=read_geometry_calib(Coord_cell);
157Coord=Object.Coord;
158% apply the calibration, whose type is selected in  handles.calib_type
159if ~isempty(Coord)
160    calib_cell=get(handles.calib_type,'String');
161    val=get(handles.calib_type,'Value');
162    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
163else
164    msgbox_uvmat('ERROR','No calibration points, abort')
165    return
166end
167Z_plane=[];
168if ~isempty(Coord)
169    %check error
170    X=Coord(:,1);
171    Y=Coord(:,2);
172    Z=Coord(:,3);
173    x_ima=Coord(:,4);
174    y_ima=Coord(:,5);
175    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
176    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
177    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
178    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
179    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
180    [EM,ind_dim]=max(GeometryCalib.ErrorMax);
181    index=index(ind_dim);
182    %set the Z position of the reference plane used for calibration
183    if isequal(max(Z),min(Z))%Z constant
184        Z_plane=Z(1);
185        GeometryCalib.NbSlice=1;
186        GeometryCalib.SliceCoord=[0 0 Z_plane];
187    end
188end
189%set the coordinate unit
190unitlist=get(handles.CoordUnit,'String');
191unit=unitlist{get(handles.CoordUnit,'value')};
192GeometryCalib.CoordUnit=unit;
193%record the points
194GeometryCalib.SourceCalib.PointCoord=Coord;
195display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
196
197% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
198set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
199set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
200set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
201set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
202set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
203set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
204
205% store the calibration data, by default in the xml file of the currently displayed image
206huvmat=findobj(allchild(0),'Name','uvmat');
207UvData=get(huvmat,'UserData');
208NbSlice_j=1;%default
209ZStart=Z_plane;
210ZEnd=Z_plane;
211volume_scan='n';
212if isfield(UvData,'XmlData')
213    UvData.XmlData
214    if isfield(UvData.XmlData,'TranslationMotor')
215        NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice;
216        ZStart=UvData.XmlData.TranslationMotor.ZStart/10;
217        ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10;
218        volume_scan='y';
219    end
220end
221hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
222RootPath='';
223RootFile='';
224if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
225    testhandle=1;
226    RootPath=get(hhuvmat.RootPath,'String');
227    RootFile=get(hhuvmat.RootFile,'String');
228    filebase=fullfile(RootPath,RootFile);
229    outputfile=[filebase '.xml'];%xml file associated with the currently displayed image
230else
231    question={'save the calibration data and point coordinates in'};
232    def={fullfile(RootPath,'ObjectCalib.xml')};
233    options.Resize='on';
234    answer=inputdlg(question,'save average in a new file',1,def,options);
235    outputfile=answer{1};
236end
237answer=msgbox_uvmat('INPUT_Y-N',{[outputfile ' updated with calibration data'];...
238    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
239    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
240
241%% record the calibration parameters and display the current image of uvmat in the new phys coordinates
242if strcmp(answer,'Yes')
243    if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
244       input_key={'Z (first position)','Z (last position)','Z (water surface)', 'refractive index','NbSlice','volume scan (y/n)','tilt angle y axis','tilt angle x axis'};
245       input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}];
246        answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on');
247        %answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
248        GeometryCalib.NbSlice=str2double(answer{5});
249        GeometryCalib.VolumeScan=answer{6};
250        if isempty(answer)
251            Z_plane=0; %default
252        else
253            Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice);
254        end     
255        GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
256        GeometryCalib.SliceAngle(:,3)=0;
257        GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise)
258        GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise)
259        GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})];
260        GeometryCalib.RefractionIndex=str2double(answer{4});     
261    end
262    errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file
263    if ~strcmp(errormsg,'')
264        msgbox_uvmat('ERROR',errormsg);
265    end
266   
267    %display image with new calibration in the currently opened uvmat interface
268    hhh=findobj(hhuvmat.axes3,'Tag','calib_marker');% delete calib points and markers
269    if ~isempty(hhh)
270        delete(hhh);     
271    end
272    hhh=findobj(hhuvmat.axes3,'Tag','calib_points');
273    if ~isempty(hhh)
274        delete(hhh);
275    end
276    set(hhuvmat.FixLimits,'Value',0)% put FixedLimits option to 'off'
277    set(hhuvmat.FixLimits,'BackgroundColor',[0.7 0.7 0.7])
278    UserData=get(handles.geometry_calib,'UserData');
279    UserData.XmlInputFile=outputfile;%save the current xml file name
280    set(handles.geometry_calib,'UserData',UserData)
281    uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
282    MenuPlot_Callback(hObject, eventdata, handles)
283    set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
284    ListCoord_Callback(hObject, eventdata, handles)
285    figure(handles.geometry_calib)
286end
287
288%------------------------------------------------------------------
289% --- Executes on button press in calibrate_lin.
290
291function REPLICATE_Callback(hObject, eventdata, handles)
292%------------------------------------------------------------------------
293
294%% Apply calibration
295calib_cell=get(handles.calib_type,'String'); %#ok<NASGU>
296val=get(handles.calib_type,'Value'); %#ok<NASGU>
297
298%read the current calibration points
299Coord_cell=get(handles.ListCoord,'String');
300Object=read_geometry_calib(Coord_cell);
301Coord=Object.Coord;
302
303% apply the calibration, whose type is selected in  handles.calib_type
304if ~isempty(Coord)
305    calib_cell=get(handles.calib_type,'String');
306    val=get(handles.calib_type,'Value');
307    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
308else
309    msgbox_uvmat('ERROR','No calibration points, abort')
310    return
311end
312
313if ~isempty(Coord)
314    %check error
315    X=Coord(:,1);
316    Y=Coord(:,2);
317    Z=Coord(:,3);
318    x_ima=Coord(:,4);
319    y_ima=Coord(:,5);
320    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
321    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
322    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
323    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
324    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
325    [EM,ind_dim]=max(GeometryCalib.ErrorMax);
326%     index=index(ind_dim);
327    %set the Z position of the reference plane used for calibration
328    Z_plane=[];
329    if isequal(max(Z),min(Z))
330        Z_plane=Z(1);
331    end
332    answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
333    Z_plane=str2double(answer_1);
334    GeometryCalib.NbSlice=1;
335    GeometryCalib.SliceCoord=[0 0 Z_plane];
336    %set the coordinate unit
337    unitlist=get(handles.CoordUnit,'String');
338    unit=unitlist{get(handles.CoordUnit,'value')};
339    GeometryCalib.CoordUnit=unit;
340    %record the points
341    GeometryCalib.SourceCalib.PointCoord=Coord;
342end
343
344%% display calibration paprameters
345display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
346
347% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
348set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
349set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
350set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
351set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
352set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
353set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
354
355%% open the GUI dataview
356h_dataview=findobj(allchild(0),'name','dataview');
357if ~isempty(h_dataview)
358    delete(h_dataview)
359end
360CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
361InputFile='';
362if isfield(CalibData,'XmlInputFile')
363    InputDir=fileparts(CalibData.XmlInputFile);
364    [InputDir,DirName]=fileparts(InputDir);
365end
366SubCampaignTest='n'; %default
367testup=0;
368if isfield(CalibData,'SubCampaign')
369    SubCampaignTest='y';
370    dir_ref=CalibData.SubCampaign;
371    testup=1;
372elseif isfield(CalibData,'Campaign')
373    dir_ref=CalibData.Campaign;
374    testup=1;
375end
376while testup
377    [InputDir,DirName]=fileparts(InputDir);
378    if strcmp(DirName,dir_ref)
379        break
380    end
381end
382InputDir=fullfile(InputDir,DirName);
383answer=msgbox_uvmat('INPUT_TXT','Campaign ?',InputDir);
384if strcmp(answer,'Cancel')
385    return
386end
387
388dataview(answer,SubCampaignTest,GeometryCalib);
389       
390%     if isfield(Heading,'Device') && isequal([filename ext],Heading.Device)
391%         [XmlInput,filename,ext]=fileparts(XmlInput);
392%         Device=Heading.Device;
393%     end
394%     if isfield(Heading,'Experiment') && isequal([filename ext],Heading.Experiment)
395%         [PP,filename,ext]=fileparts(XmlInput);
396%     end
397%     testinput=0;
398%     if isfield(Heading,'SubCampaign') && isequal([filename ext],Heading.SubCampaign)
399%         SubCampaignTest='y';
400%         testinput=1;
401%     elseif isfield(Heading,'Campaign') && isequal([filename ext],Heading.Campaign)
402%         testinput=1;
403% %     end
404% end
405% if ~testinput
406%     filename='PROJETS';%default
407%     if isfield(CalibData,'XmlInputFile')
408%          [pp,filename]=fileparts(CalibData.XmlInputFile);
409%     end
410%     while ~isequal(filename,'PROJETS') && numel(filename)>1
411%         filename_1=filename;
412%         pp_1=pp;
413%         [pp,filename]=fileparts(pp);
414%     end
415%     XmlInput=fullfile(pp_1,filename_1);
416%     testinput=1;
417% end
418% if testinput
419%     outcome=dataview(XmlInput,SubCampaignTest,GeometryCalib);
420% end
421
422%------------------------------------------------------------------------
423% determine the parameters for a calibration by an affine function (rescaling and offset, no rotation)
424function GeometryCalib=calib_rescale(Coord,handles)
425%------------------------------------------------------------------------
426X=Coord(:,1);
427Y=Coord(:,2);% Z not used
428x_ima=Coord(:,4);
429y_ima=Coord(:,5);
430[px,sx]=polyfit(X,x_ima,1);
431[py,sy]=polyfit(Y,y_ima,1);
432T_x=px(2);
433T_y=py(2);
434GeometryCalib.CalibrationType='rescale';
435GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
436GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
437GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
438%GeometryCalib.R=[1,0,0;0,1,0;0,0,0];
439GeometryCalib.omc=[0 0 0];
440
441%------------------------------------------------------------------------
442% determine the parameters for a calibration by a linear transform matrix (rescale and rotation)
443function GeometryCalib=calib_linear(Coord,handles) %TO UPDATE
444%------------------------------------------------------------------------
445X=Coord(:,1);
446Y=Coord(:,2);% Z not used
447x_ima=Coord(:,4);
448y_ima=Coord(:,5);
449XY_mat=[ones(size(X)) X Y];
450a_X1=XY_mat\x_ima; %transformation matrix for X
451% x1=XY_mat*a_X1;%reconstruction
452% err_X1=max(abs(x1-x_ima));%error
453a_Y1=XY_mat\y_ima;%transformation matrix for X
454% y1=XY_mat*a_Y1;
455% err_Y1=max(abs(y1-y_ima));%error
456% R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,1];
457R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
458norm=abs(det(R));
459GeometryCalib.CalibrationType='linear';
460GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm);
461GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
462GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
463GeometryCalib.Tx_Ty_Tz=[a_X1(1) a_Y1(1) 1];
464R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
465R(2,:)=R(2,:)/GeometryCalib.fx_fy(2);
466R=[R;[0 0]];
467GeometryCalib.R=[R [0;0;1]];
468GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
469%------------------------------------------------------------------------
470% determine the tsai parameters for a view normal to the grid plane
471% NOT USED
472function GeometryCalib=calib_normal(Coord,handles)
473%------------------------------------------------------------------------
474Calib.f1=str2num(get(handles.fx,'String'));
475Calib.f2=str2num(get(handles.fy,'String'));
476Calib.k=str2num(get(handles.kc,'String'));
477Calib.Cx=str2num(get(handles.Cx,'String'));
478Calib.Cy=str2num(get(handles.Cy,'String'));
479%default
480if isempty(Calib.f1)
481    Calib.f1=25/0.012;
482end
483if isempty(Calib.f2)
484    Calib.f2=25/0.012;
485end
486if isempty(Calib.k)
487    Calib.k=0;
488end
489if isempty(Calib.Cx)||isempty(Calib.Cy)
490    huvmat=findobj(allchild(0),'Tag','uvmat');
491    hhuvmat=guidata(huvmat);
492    Calib.Cx=str2num(get(hhuvmat.npx,'String'))/2;
493    Calib.Cx=str2num(get(hhuvmat.npy,'String'))/2;
494end   
495%tsai parameters
496Calib.dpx=0.012;%arbitrary
497Calib.dpy=0.012;
498Calib.sx=Calib.f1*Calib.dpx/(Calib.f2*Calib.dpy);
499Calib.f=Calib.f2*Calib.dpy;
500Calib.kappa1=Calib.k/(Calib.f*Calib.f);
501
502%initial guess
503X=Coord(:,1);
504Y=Coord(:,2);
505Zmean=mean(Coord(:,3));
506x_ima=Coord(:,4)-Calib.Cx;
507y_ima=Coord(:,5)-Calib.Cy;
508XY_mat=[ones(size(X)) X Y];
509a_X1=XY_mat\x_ima; %transformation matrix for X
510a_Y1=XY_mat\y_ima;%transformation matrix for Y
511R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,-1];% rotation+ z axis reversal (upward)
512norm=sqrt(det(-R));
513calib_param(1)=0;% quadratic distortion
514calib_param(2)=a_X1(1);
515calib_param(3)=a_Y1(1);
516calib_param(4)=Calib.f/(norm*Calib.dpx)-R(3,3)*Zmean;
517calib_param(5)=angle(a_X1(2)+1i*a_X1(3));
518display(['initial guess=' num2str(calib_param)])
519
520%optimise the parameters: minimisation of error
521calib_param = fminsearch(@(calib_param) error_calib(calib_param,Calib,Coord),calib_param);
522
523GeometryCalib.CalibrationType='tsai_normal';
524GeometryCalib.focal=Calib.f;
525GeometryCalib.dpx_dpy=[Calib.dpx Calib.dpy];
526GeometryCalib.Cx_Cy=[Calib.Cx Calib.Cy];
527GeometryCalib.sx=Calib.sx;
528GeometryCalib.kappa1=calib_param(1);
529GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
530GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)];
531alpha=calib_param(5);
532GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
533
534%------------------------------------------------------------------------
535function GeometryCalib=calib_3D_linear(Coord,handles)
536%------------------------------------------------------------------
537path_uvmat=which('uvmat');% check the path detected for source file uvmat
538path_UVMAT=fileparts(path_uvmat); %path to UVMAT
539huvmat=findobj(allchild(0),'Tag','uvmat');
540hhuvmat=guidata(huvmat);
541coord_files=get(handles.coord_files,'String');
542if ischar(coord_files)
543    coord_files={coord_files};
544end
545if isempty(coord_files{1}) || isequal(coord_files,{''})
546    coord_files={};
547end
548%retrieve the calibration points stored in the files listed in the popup list coord_files
549x_1=Coord(:,4:5)';%px coordinates of the ref points
550nx=str2num(get(hhuvmat.npx,'String'));
551ny=str2num(get(hhuvmat.npy,'String'));
552x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
553X_1=Coord(:,1:3)';%phys coordinates of the ref points
554n_ima=numel(coord_files)+1;
555if ~isempty(coord_files)
556    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
557    for ifile=1:numel(coord_files)
558    t=xmltree(coord_files{ifile});
559    s=convert(t);%convert to matlab structure
560        if isfield(s,'GeometryCalib')
561            if isfield(s.GeometryCalib,'SourceCalib')
562                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
563                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
564                Coord_file=zeros(length(PointCoord),5);%default
565                for i=1:length(PointCoord)
566                    line=str2num(PointCoord{i});
567                    Coord_file(i,4:5)=line(4:5);%px x
568                    Coord_file(i,1:3)=line(1:3);%phys x
569                end
570                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
571                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
572                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
573                end
574            end
575        end
576    end
577end
578n_ima=numel(coord_files)+1;
579est_dist=[0;0;0;0;0];
580est_aspect_ratio=0;
581est_fc=[1;1];
582%fc=[25;25]/0.012;
583center_optim=0;
584run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
585GeometryCalib.CalibrationType='3D_linear';
586GeometryCalib.fx_fy=fc';
587%GeometryCalib.focal=fc(2);
588%GeometryCalib.dpx_dpy=[1 1];
589GeometryCalib.Cx_Cy=cc';
590%GeometryCalib.sx=fc(1)/fc(2);
591GeometryCalib.kc=kc(1);
592%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
593GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
594GeometryCalib.Tx_Ty_Tz=Tc_1';
595GeometryCalib.R=Rc_1;
596GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
597GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
598GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
599GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
600GeometryCalib.ErrorRMS=[];
601GeometryCalib.ErrorMax=[];
602
603%------------------------------------------------------------------------
604function GeometryCalib=calib_3D_quadr(Coord,handles)
605%------------------------------------------------------------------
606
607path_uvmat=which('uvmat');% check the path detected for source file uvmat
608path_UVMAT=fileparts(path_uvmat); %path to UVMAT
609huvmat=findobj(allchild(0),'Tag','uvmat');
610hhuvmat=guidata(huvmat);
611% check_cond=0;
612coord_files=get(handles.coord_files,'String');
613if ischar(coord_files)
614    coord_files={coord_files};
615end
616if isempty(coord_files{1}) || isequal(coord_files,{''})
617    coord_files={};
618end
619
620%retrieve the calibration points stored in the files listed in the popup list coord_files
621x_1=Coord(:,4:5)';%px coordinates of the ref points
622nx=str2num(get(hhuvmat.npx,'String'));
623ny=str2num(get(hhuvmat.npy,'String'));
624x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
625X_1=Coord(:,1:3)';%phys coordinates of the ref points
626n_ima=numel(coord_files)+1;
627if ~isempty(coord_files)
628    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
629    for ifile=1:numel(coord_files)
630    t=xmltree(coord_files{ifile});
631    s=convert(t);%convert to matlab structure
632        if isfield(s,'GeometryCalib')
633            if isfield(s.GeometryCalib,'SourceCalib')
634                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
635                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
636                Coord_file=zeros(length(PointCoord),5);%default
637                for i=1:length(PointCoord)
638                    line=str2num(PointCoord{i});
639                    Coord_file(i,4:5)=line(4:5);%px x
640                    Coord_file(i,1:3)=line(1:3);%phys x
641                end
642                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
643                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
644                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
645                end
646            end
647        end
648    end
649end
650n_ima=numel(coord_files)+1;
651est_dist=[1;0;0;0;0];
652est_aspect_ratio=1;
653%est_fc=[0;0];
654%fc=[25;25]/0.012;
655center_optim=0;
656run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
657
658GeometryCalib.CalibrationType='3D_quadr';
659GeometryCalib.fx_fy=fc';
660%GeometryCalib.focal=fc(2);
661%GeometryCalib.dpx_dpy=[1 1];
662GeometryCalib.Cx_Cy=cc';
663%GeometryCalib.sx=fc(1)/fc(2);
664GeometryCalib.kc=kc(1);
665%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
666GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
667GeometryCalib.Tx_Ty_Tz=Tc_1';
668GeometryCalib.R=Rc_1;
669GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
670GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
671GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
672GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
673GeometryCalib.ErrorRMS=[];
674GeometryCalib.ErrorMax=[];
675
676
677%------------------------------------------------------------------------
678function GeometryCalib=calib_3D_extrinsic(Coord,handles)
679%------------------------------------------------------------------
680path_uvmat=which('geometry_calib');% check the path detected for source file uvmat
681path_UVMAT=fileparts(path_uvmat); %path to UVMAT
682x_1=double(Coord(:,4:5)');%image coordiantes
683X_1=double(Coord(:,1:3)');% phys coordinates
684huvmat=findobj(allchild(0),'Tag','uvmat');
685hhuvmat=guidata(huvmat);
686ny=str2double(get(hhuvmat.npy,'String'));
687x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
688n_ima=1;
689GeometryCalib.CalibrationType='3D_extrinsic';
690GeometryCalib.fx_fy(1)=str2num(get(handles.fx,'String'));
691GeometryCalib.fx_fy(2)=str2num(get(handles.fy,'String'));
692GeometryCalib.Cx_Cy(1)=str2num(get(handles.Cx,'String'));
693GeometryCalib.Cx_Cy(2)=str2num(get(handles.Cy,'String'));
694GeometryCalib.kc=str2num(get(handles.kc,'String'));
695fct_path=fullfile(path_UVMAT,'toolbox_calib');
696addpath(fct_path)
697GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate)
698% [omc1,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
699%     [Calib.f Calib.f*Calib.sx]',...
700%     [Calib.Cx Calib.Cy]',...
701%     [-Calib.kappa1*Calib.f^2 0 0 0 0]);
702[omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
703    (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]);
704rmpath(fct_path);
705GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
706GeometryCalib.Tx_Ty_Tz=Tc1';
707%inversion of z axis
708GeometryCalib.R=Rc1;
709GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
710GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
711GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
712GeometryCalib.omc=(180/pi)*omc';
713%GeometryCalib.R(3,1:3)=-GeometryCalib.R(3,1:3);%inversion for z upward
714
715
716
717%------------------------------------------------------------------------
718%function GeometryCalib=calib_tsai_heikkila(Coord)
719% TEST: NOT IMPLEMENTED
720%------------------------------------------------------------------
721% path_uvmat=which('uvmat');% check the path detected for source file uvmat
722% path_UVMAT=fileparts(path_uvmat); %path to UVMAT
723% path_calib=fullfile(path_UVMAT,'toolbox_calib_heikkila');
724% addpath(path_calib)
725% npoints=size(Coord,1);
726% Coord(:,1:3)=10*Coord(:,1:3);
727% Coord=[Coord zeros(npoints,2) -ones(npoints,1)];
728% [par,pos,iter,res,er,C]=cacal('dalsa',Coord);
729% GeometryCalib.CalibrationType='tsai';
730% GeometryCalib.focal=par(2);
731
732
733%--------------------------------------------------------------------------
734function GeometryCalib=calib_tsai(Coord,handles)% OBSOLETE: old version using gauthier's bianry ccal_fo
735% NOT USED
736%------------------------------------------------------------------------
737%TSAI
738path_uvmat=which('uvmat');% check the path detected for source file uvmat
739path_UVMAT=fileparts(path_uvmat); %path to UVMAT
740xmlfile=fullfile(path_UVMAT,'PARAM.xml');%name of the file containing names of binary executables
741if exist(xmlfile,'file')
742    t=xmltree(xmlfile);% read the (xml) file containing names of binary executables
743    sparam=convert(t);% convert to matlab structure
744end
745if ~isfield(sparam,'GeometryCalibBin')
746    msgbox_uvmat('ERROR',['calibration program <GeometryCalibBin> undefined in parameter file ' xmlfile])
747    return
748end
749Tsai_exe=sparam.GeometryCalibBin;
750if ~exist(Tsai_exe,'file')%the binary is defined in /bin, default setting
751     Tsai_exe=fullfile(path_UVMAT,Tsai_exe);
752end
753if ~exist(Tsai_exe,'file')
754    msgbox_uvmat('ERROR',['calibration program ' sparam.GeometryCalibBin ' defined in PARAM.xml does not exist'])
755    return
756end
757
758textcoord=num2str(Coord,4);
759dlmwrite('t.txt',textcoord,''); 
760% ['!' Tsai_exe ' -fx 0 -fy t.txt']
761eval(['!' Tsai_exe ' -f t.txt > tsaicalib.log']);
762if ~exist('calib.dat','file')
763    msgbox_uvmat('ERROR','no output from calibration program Tsai_exe: possibly too few points')
764end
765calibdat=dlmread('calib.dat');
766delete('calib.dat')
767%delete('t.txt')
768GeometryCalib.CalibrationType='tsai';
769GeometryCalib.focal=calibdat(10);
770GeometryCalib.dpx_dpy=[calibdat(5) calibdat(6)];
771GeometryCalib.Cx_Cy=[calibdat(7) calibdat(8)];
772GeometryCalib.sx=calibdat(9);
773GeometryCalib.kappa1=calibdat(11);
774GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
775GeometryCalib.Tx_Ty_Tz=[calibdat(12) calibdat(13) calibdat(14)];
776Rx_Ry_Rz=calibdat(15:17);
777sa = sin(Rx_Ry_Rz(1)) ;
778ca=cos(Rx_Ry_Rz(1));
779sb=sin(Rx_Ry_Rz(2));
780cb =cos(Rx_Ry_Rz(2));
781sg =sin(Rx_Ry_Rz(3));
782cg =cos(Rx_Ry_Rz(3));
783r1 = cb * cg;
784r2 = cg * sa * sb - ca * sg;
785r3 = sa * sg + ca * cg * sb;
786r4 = cb * sg;
787r5 = sa * sb * sg + ca * cg;
788r6 = ca * sb * sg - cg * sa;
789r7 = -sb;
790r8 = cb * sa;
791r9 = ca * cb;
792%EN DEDUIRE MATRICE R ??
793GeometryCalib.R=[r1,r2,r3;r4,r5,r6;r7,r8,r9];
794
795%------------------------------------------------------------------------
796% --- determine the rms of calibration error
797function ErrorRms=error_calib(calib_param,Calib,Coord)
798%calib_param: vector of free calibration parameters (to optimise)
799%Calib: structure of the given calibration parameters
800%Coord: list of phys coordinates (columns 1-3, and pixel coordinates (columns 4-5)
801Calib.f=25;
802Calib.dpx=0.012;
803Calib.dpy=0.012;
804Calib.sx=1;
805Calib.Cx=512;
806Calib.Cy=512;
807Calib.kappa1=calib_param(1);
808Calib.Tx=calib_param(2);
809Calib.Ty=calib_param(3);
810Calib.Tz=calib_param(4);
811alpha=calib_param(5);
812Calib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
813
814X=Coord(:,1);
815Y=Coord(:,2);
816Z=Coord(:,3);
817x_ima=Coord(:,4);
818y_ima=Coord(:,5);
819[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z);
820ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
821ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
822ErrorRms=mean(ErrorRms);
823
824%------------------------------------------------------------------------
825function XImage_Callback(hObject, eventdata, handles)
826%------------------------------------------------------------------------
827update_list(hObject, eventdata,handles)
828
829%------------------------------------------------------------------------
830function YImage_Callback(hObject, eventdata, handles)
831%------------------------------------------------------------------------
832update_list(hObject, eventdata,handles)
833
834%------------------------------------------------------------------------
835% --- Executes on button press in STORE.
836function STORE_Callback(hObject, eventdata, handles)
837Coord_cell=get(handles.ListCoord,'String');
838Object=read_geometry_calib(Coord_cell);
839unitlist=get(handles.CoordUnit,'String');
840unit=unitlist{get(handles.CoordUnit,'value')};
841GeometryCalib.CoordUnit=unit;
842GeometryCalib.SourceCalib.PointCoord=Object.Coord;
843huvmat=findobj(allchild(0),'Name','uvmat');
844hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
845% RootPath='';
846% RootFile='';
847if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
848    testhandle=1;
849    RootPath=get(hhuvmat.RootPath,'String');
850    RootFile=get(hhuvmat.RootFile,'String');
851    filebase=fullfile(RootPath,RootFile);
852    while exist([filebase '.xml'],'file')
853        filebase=[filebase '~'];
854    end
855    outputfile=[filebase '.xml'];
856    errormsg=update_imadoc(GeometryCalib,outputfile);
857    if ~strcmp(errormsg,'')
858        msgbox_uvmat('ERROR',errormsg);
859    end
860    listfile=get(handles.coord_files,'string');
861    if isequal(listfile,{''})
862        listfile={outputfile};
863    else
864        listfile=[listfile;{outputfile}];%update the list of coord files
865    end
866    set(handles.coord_files,'string',listfile);
867end
868set(handles.ListCoord,'Value',1)% refresh the display of coordinates
869set(handles.ListCoord,'String',{'......'})
870
871% --------------------------------------------------------------------
872% --- Executes on button press in CLEAR_PTS: clear the list of calibration points
873function CLEAR_PTS_Callback(hObject, eventdata, handles)
874% --------------------------------------------------------------------
875set(handles.ListCoord,'Value',1)% refresh the display of coordinates
876set(handles.ListCoord,'String',{'......'})
877MenuPlot_Callback(hObject, eventdata, handles)
878
879%------------------------------------------------------------------------
880% --- Executes on button press in CLEAR.
881function CLEAR_Callback(hObject, eventdata, handles)
882%------------------------------------------------------------------------
883set(handles.coord_files,'Value',1)
884set(handles.coord_files,'String',{''})
885
886%------------------------------------------------------------------------
887function XObject_Callback(hObject, eventdata, handles)
888%------------------------------------------------------------------------
889update_list(hObject, eventdata,handles)
890
891%------------------------------------------------------------------------
892function YObject_Callback(hObject, eventdata, handles)
893%------------------------------------------------------------------------
894update_list(hObject, eventdata,handles)
895
896%------------------------------------------------------------------------
897function ZObject_Callback(hObject, eventdata, handles)
898%------------------------------------------------------------------------
899update_list(hObject, eventdata,handles)
900
901%------------------------------------------------------------------------
902function update_list(hObject, eventdata, handles)
903%------------------------------------------------------------------------
904newval(4)=str2double(get(handles.XImage,'String'));
905newval(5)=str2double(get(handles.YImage,'String'));
906newval(1)=str2double(get(handles.XObject,'String'));
907newval(2)=str2double(get(handles.YObject,'String'));
908newval(3)=str2double(get(handles.ZObject,'String'));
909if isnan(newval(3))
910    newval(3)=0;%put z to 0 by default
911end
912Coord=get(handles.ListCoord,'String');
913Coord(end)=[]; %remove last string '.....'
914val=get(handles.ListCoord,'Value');
915data=read_geometry_calib(Coord);
916data.Coord(val,:)=newval;
917for i=1:size(data.Coord,1)
918    for j=1:5
919          Coord_cell{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
920    end
921end
922
923Tabchar=cell2tab(Coord_cell,' | ');
924Tabchar=[Tabchar ;{'......'}];
925set(handles.ListCoord,'String',Tabchar)
926
927%update the plot
928ListCoord_Callback(hObject, eventdata, handles)
929MenuPlot_Callback(hObject, eventdata, handles)
930
931%------------------------------------------------------------------------
932% --- Executes on selection change in ListCoord.
933function ListCoord_Callback(hObject, eventdata, handles)
934%------------------------------------------------------------------------
935huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
936hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
937hhh=findobj(hplot,'Tag','calib_marker');
938Coord_cell=get(handles.ListCoord,'String');
939val=get(handles.ListCoord,'Value');
940if numel(val)>1
941    return %no action if several lines have been selected
942end
943coord_str=Coord_cell{val};
944k=findstr(' | ',coord_str);
945if isempty(k)%last line '.....' selected
946    if ~isempty(hhh)
947        delete(hhh)%delete the circle marker
948    end
949    return
950end
951%fill the edit boxex
952set(handles.XObject,'String',coord_str(1:k(1)-1))
953set(handles.YObject,'String',coord_str(k(1)+3:k(2)-1))
954set(handles.ZObject,'String',coord_str(k(2)+3:k(3)-1))
955set(handles.XImage,'String',coord_str(k(3)+3:k(4)-1))
956set(handles.YImage,'String',coord_str(k(4)+3:end))
957h_menu_coord=findobj(huvmat,'Tag','transform_fct');
958menu=get(h_menu_coord,'String');
959choice=get(h_menu_coord,'Value');
960if iscell(menu)
961    option=menu{choice};
962else
963    option='px'; %default
964end
965if isequal(option,'phys')
966    XCoord=str2double(coord_str(1:k(1)-1));
967    YCoord=str2double(coord_str(k(1)+3:k(2)-1));
968elseif isequal(option,'px')|| isequal(option,'')
969    XCoord=str2double(coord_str(k(3)+3:k(4)-1));
970    YCoord=str2double(coord_str(k(4)+3:end));
971else
972    msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be px or phys ')
973end
974if isempty(XCoord)||isempty(YCoord)
975     if ~isempty(hhh)
976        delete(hhh)%delete the circle marker
977    end
978    return
979end
980xlim=get(hplot,'XLim');
981ylim=get(hplot,'YLim');
982ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/20;%defines the size of the circle marker
983if isempty(hhh)
984    set(0,'CurrentFig',huvmat)
985    set(huvmat,'CurrentAxes',hplot)
986    rectangle('Curvature',[1 1],...
987              'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range],'EdgeColor','m',...
988              'LineStyle','-','Tag','calib_marker');
989else
990    set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
991end
992
993%------------------------------------------------------------------------
994% --- Executes on selection change in edit_append.
995function edit_append_Callback(hObject, eventdata, handles)
996%------------------------------------------------------------------------
997choice=get(handles.edit_append,'Value');
998if choice
999    set(handles.edit_append,'BackgroundColor',[1 1 0])
1000    huvmat=findobj(allchild(0),'tag','uvmat');
1001    if ishandle(huvmat)
1002        hhuvmat=guidata(huvmat);
1003        set(hhuvmat.edit_object,'Value',0)
1004        set(hhuvmat.edit_object,'BackgroundColor',[0.7 0.7 0.7])
1005    end
1006else
1007    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
1008end
1009   
1010function NEW_Callback(hObject, eventdata, handles)
1011%A METTRE SOUS UN BOUTON
1012huvmat=findobj(allchild(0),'Name','uvmat');
1013hchild=get(huvmat,'children');
1014hcoord=findobj(hchild,'Tag','menu_coord');
1015coordtype=get(hcoord,'Value');
1016haxes=findobj(hchild,'Tag','axes3');
1017AxeData=get(haxes,'UserData');
1018if ~isequal(hcoord,2)
1019    set(hcoord,'Value',2)
1020    huvmat=uvmat(AxeData);
1021    'relancer uvmat';
1022end
1023if ~isfield(AxeData,'ZoomAxes')
1024    msgbox_uvmat('ERROR','first draw a window around a grid marker')
1025    return
1026end
1027XLim=get(AxeData.ZoomAxes,'XLim');
1028YLim=get(AxeData.ZoomAxes,'YLim');
1029np=size(AxeData.A);
1030ind_sub_x=round(XLim);
1031ind_sub_y=np(1)-round(YLim);
1032Mfiltre=AxeData.A([ind_sub_y(2):ind_sub_y(1)] ,ind_sub_x,:);
1033Mfiltre_norm=double(Mfiltre);
1034Mfiltre_norm=Mfiltre_norm/sum(sum(Mfiltre_norm));
1035Mfiltre_norm=100*(Mfiltre_norm-mean(mean(Mfiltre_norm)));
1036Atype=class(AxeData.A);
1037Data.NbDim=2;
1038Data.A=filter2(Mfiltre_norm,double(AxeData.A));
1039Data.A=feval(Atype,Data.A);
1040Data.AName='image';
1041Data.AX=AxeData.AX;
1042Data.AY=AxeData.AY;
1043Data.CoordType='px';
1044plot_field(Data)
1045
1046%------------------------------------------------------------------------
1047function MenuPlot_Callback(hObject, eventdata, handles)
1048%------------------------------------------------------------------------
1049huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
1050%UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface
1051hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat
1052%hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
1053h_menu_coord=findobj(huvmat,'Tag','transform_fct');
1054menu=get(h_menu_coord,'String');
1055choice=get(h_menu_coord,'Value');
1056if iscell(menu)
1057    option=menu{choice};
1058else
1059    option='px'; %default
1060end
1061Coord_cell=get(handles.ListCoord,'String');
1062ObjectData=read_geometry_calib(Coord_cell);
1063%ObjectData=read_geometry_calib(handles);%read the interface input parameters defining the object
1064if ~isempty(ObjectData.Coord)
1065    if isequal(option,'phys')
1066        ObjectData.Coord=ObjectData.Coord(:,[1:3]);
1067    elseif isequal(option,'px')||isequal(option,'')
1068        ObjectData.Coord=ObjectData.Coord(:,[4:5]);
1069    else
1070        msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be '''', px or phys ')
1071    end
1072end
1073axes(hhuvmat.axes3)
1074hh=findobj('Tag','calib_points');
1075if  ~isempty(ObjectData.Coord) && isempty(hh)
1076    hh=line(ObjectData.Coord(:,1),ObjectData.Coord(:,2),'Color','m','Tag','calib_points','LineStyle','.','Marker','+');
1077elseif isempty(ObjectData.Coord)%empty list of points, suppress the plot
1078    delete(hh)
1079else
1080    set(hh,'XData',ObjectData.Coord(:,1))
1081    set(hh,'YData',ObjectData.Coord(:,2))
1082end
1083pause(.1)
1084figure(handles.geometry_calib)
1085
1086% --------------------------------------------------------------------
1087function MenuHelp_Callback(hObject, eventdata, handles)
1088path_to_uvmat=which('uvmat');% check the path of uvmat
1089pathelp=fileparts(path_to_uvmat);
1090helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
1091if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
1092else
1093   addpath (fullfile(pathelp,'uvmat_doc'))
1094   web([helpfile '#geometry_calib'])
1095end
1096
1097%------------------------------------------------------------------------
1098function MenuCreateGrid_Callback(hObject, eventdata, handles)
1099%------------------------------------------------------------------------
1100%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1101CalibData=get(handles.geometry_calib,'UserData');
1102Tinput=[];%default
1103if isfield(CalibData,'grid')
1104    Tinput=CalibData.grid;
1105end
1106[T,CalibData.grid]=create_grid(Tinput);%display the GUI create_grid
1107set(handles.geometry_calib,'UserData',CalibData)
1108
1109%grid in phys space
1110Coord=get(handles.ListCoord,'String');
1111val=get(handles.ListCoord,'Value');
1112data=read_geometry_calib(Coord);
1113%nbpoints=size(data.Coord,1); %nbre of calibration points
1114data.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
1115% for i=1:nbpoints
1116%    for j=1:5
1117%           Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
1118%    end
1119% end
1120%update the phys coordinates starting from the selected point (down in the
1121Coord(end,:)=[]; %remove last string '.....'
1122for i=1:size(data.Coord,1)
1123    for j=1:5
1124          Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
1125    end
1126end
1127
1128%size(data.Coord,1)
1129Tabchar=cell2tab(Coord,' | ');
1130Tabchar=[Tabchar ;{'......'}];
1131set(handles.ListCoord,'String',Tabchar)
1132
1133% -----------------------------------------------------------------------
1134% --- automatic grid dectection from local maxima of the images
1135function MenuDetectGrid_Callback(hObject, eventdata, handles)
1136%------------------------------------------------------------------------
1137%% initiate the grid
1138CalibData=get(handles.geometry_calib,'UserData');%get information stored on the GUI geometry_calib
1139grid_input=[];%default
1140if isfield(CalibData,'grid')
1141    grid_input=CalibData.grid;%retrieve the previously used grid
1142end
1143[T,CalibData.grid,white_test]=create_grid(grid_input,'detect_grid');%display the GUI create_grid, read the set of phys coordinates T
1144set(handles.geometry_calib,'UserData',CalibData)%store the phys grid parameters for later use
1145
1146%% read the four last point coordinates in pixels
1147Coord_cell=get(handles.ListCoord,'String');%read list of coordinates on geometry_calib
1148data=read_geometry_calib(Coord_cell);
1149nbpoints=size(data.Coord,1); %nbre of calibration points
1150if nbpoints~=4
1151    msgbox_uvmat('ERROR','four points must have be selected by the mouse, beginning by the new x axis, to delimitate the phys grid area')
1152    return
1153end
1154corners_X=(data.Coord(end:-1:end-3,4)); %pixel absissa of the four corners
1155corners_Y=(data.Coord(end:-1:end-3,5));
1156
1157%reorder the last two points (the two first in the list) if needed
1158angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1)));
1159if abs(angles(4)-angles(2))>abs(angles(3)-angles(2))
1160      X_end=corners_X(4);
1161      Y_end=corners_Y(4);
1162      corners_X(4)=corners_X(3);
1163      corners_Y(4)=corners_Y(3);
1164      corners_X(3)=X_end;
1165      corners_Y(3)=Y_end;
1166end
1167
1168%% read the current image, displayed in the GUI uvmat
1169huvmat=findobj(allchild(0),'Name','uvmat');
1170UvData=get(huvmat,'UserData');
1171A=UvData.Field.A;
1172npxy=size(A);
1173X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates (cm)
1174Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates (cm)
1175
1176%calculate transform matrices for plane projection
1177% reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
1178B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
1179      zeros(4,3)        X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ];
1180B = reshape (B', 8 , 8 )';
1181D = [ corners_X , corners_Y ];
1182D = reshape (D', 8 , 1 );
1183l = (B' * B)\B' * D;
1184Amat = reshape([l(1:6)' 0 0 1 ],3,3)';
1185C = [l(7:8)' 1];
1186
1187% transform grid image into 'phys' coordinates
1188GeometryCalib.fx_fy=[1 1];
1189GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
1190GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
1191GeometryCalib.CoordUnit='cm';
1192path_uvmat=which('uvmat');% check the path detected for source file uvmat
1193path_UVMAT=fileparts(path_uvmat); %path to UVMAT
1194addpath(fullfile(path_UVMAT,'transform_field'))
1195Data.ListVarName={'AY','AX','A'};
1196Data.VarDimName={'AY','AX',{'AY','AX'}};
1197if ndims(A)==3
1198    A=mean(A,3);
1199end
1200Data.A=A-min(min(A));
1201Data.AY=[npxy(1)-0.5 0.5];
1202Data.AX=[0.5 npxy(2)];
1203Data.CoordUnit='pixel';
1204Calib.GeometryCalib=GeometryCalib;
1205DataOut=phys(Data,Calib);
1206rmpath(fullfile(path_UVMAT,'transform_field'))
1207Amod=DataOut.A;
1208Rangx=DataOut.AX;
1209Rangy=DataOut.AY;
1210if white_test
1211    Amod=double(Amod);%case of white grid markers: will look for image maxima
1212else
1213    Amod=-double(Amod);%case of black grid markers: will look for image minima
1214end
1215% figure(12) %display corrected image
1216% Amax=max(max(Amod));
1217% image(Rangx,Rangy,uint8(255*Amod/Amax))
1218
1219%% detection of local image extrema in each direction
1220Dx=(Rangx(2)-Rangx(1))/(npxy(2)-1); %x mesh in real space
1221Dy=(Rangy(2)-Rangy(1))/(npxy(1)-1); %y mesh in real space
1222ind_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
1223ind_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
1224nbpoints=size(T,1);
1225for ipoint=1:nbpoints
1226    i0=1+round((T(ipoint,1)-Rangx(1))/Dx);%round(Xpx(ipoint));
1227    j0=1+round((T(ipoint,2)-Rangy(1))/Dy);%round(Xpx(ipoint));
1228    j0min=max(j0-ind_range_y,1);
1229    j0max=min(j0+ind_range_y,size(Amod,1));
1230    i0min=max(i0-ind_range_x,1);
1231    i0max=min(i0+ind_range_x,size(Amod,2));
1232    Asub=Amod(j0min:j0max,i0min:i0max);
1233    x_profile=sum(Asub,1);
1234    y_profile=sum(Asub,2);
1235    [Amax,ind_x_max]=max(x_profile);
1236    [Amax,ind_y_max]=max(y_profile);
1237    %sub-pixel improvement using moments
1238    x_shift=0;
1239    y_shift=0;
1240    if ind_x_max+2<=numel(x_profile) && ind_x_max-2>=1
1241        Atop=x_profile(ind_x_max-2:ind_x_max+2);
1242        x_shift=sum(Atop.*[-2 -1 0 1 2])/sum(Atop);
1243    end
1244    if ind_y_max+2<=numel(y_profile) && ind_y_max-2>=1
1245        Atop=y_profile(ind_y_max-2:ind_y_max+2);
1246        y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop);
1247    end
1248    Delta(ipoint,1)=(x_shift+ind_x_max+i0min-i0-1)*Dx;%shift from the initial guess
1249    Delta(ipoint,2)=(y_shift+ind_y_max+j0min-j0-1)*Dy;
1250end
1251Tmod=T(:,(1:2))+Delta;
1252[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));
1253for ipoint=1:nbpoints
1254     Coord{ipoint,1}=num2str(T(ipoint,1),4);%display coordiantes with 4 digits
1255     Coord{ipoint,2}=num2str(T(ipoint,2),4);%display coordiantes with 4 digits
1256     Coord{ipoint,3}=num2str(T(ipoint,3),4);%display coordiantes with 4 digits;
1257     Coord{ipoint,4}=num2str(Xpx(ipoint),4);%display coordiantes with 4 digits
1258     Coord{ipoint,5}=num2str(Ypx(ipoint),4);%display coordiantes with 4 digits
1259end
1260Tabchar=cell2tab(Coord(end:-1:1,:),' | ');
1261Tabchar=[Tabchar ;{'......'}];
1262set(handles.ListCoord,'Value',1)
1263set(handles.ListCoord,'String',Tabchar)
1264MenuPlot_Callback(hObject, eventdata, handles)
1265
1266%-----------------------------------------------------------------------
1267function MenuTranslatePoints_Callback(hObject, eventdata, handles)
1268%-----------------------------------------------------------------------
1269%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1270CalibData=get(handles.geometry_calib,'UserData');
1271Tinput=[];%default
1272if isfield(CalibData,'translate')
1273    Tinput=CalibData.translate;
1274end
1275T=translate_points(Tinput);%display translate_points GUI and get shift parameters
1276CalibData.translate=T;
1277set(handles.geometry_calib,'UserData',CalibData)
1278%translation
1279Coord_cell=get(handles.ListCoord,'String');
1280data=read_geometry_calib(Coord_cell);
1281data.Coord(:,1)=T(1)+data.Coord(:,1);
1282data.Coord(:,2)=T(2)+data.Coord(:,2);
1283data.Coord(:,3)=T(3)+data.Coord(:,3);
1284data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1285for i=1:size(data.Coord,1)
1286    for j=1:5
1287          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1288   end
1289end
1290Tabchar=cell2tab(Coord,' | ');
1291Tabchar=[Tabchar; {'.....'}];
1292%set(handles.ListCoord,'Value',1)
1293set(handles.ListCoord,'String',Tabchar)
1294
1295
1296% --------------------------------------------------------------------
1297function MenuRotatePoints_Callback(hObject, eventdata, handles)
1298%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1299CalibData=get(handles.geometry_calib,'UserData');
1300Tinput=[];%default
1301if isfield(CalibData,'rotate')
1302    Tinput=CalibData.rotate;
1303end
1304T=rotate_points(Tinput);%display translate_points GUI and get shift parameters
1305CalibData.rotate=T;
1306set(handles.geometry_calib,'UserData',CalibData)
1307%-----------------------------------------------------
1308%rotation
1309Phi=T(1);
1310O_x=0;%default
1311O_y=0;%default
1312if numel(T)>=2
1313    O_x=T(2);%default
1314end
1315if numel(T)>=3
1316    O_y=T(3);%default
1317end
1318Coord_cell=get(handles.ListCoord,'String');
1319data=read_geometry_calib(Coord_cell);
1320r1=cos(pi*Phi/180);
1321r2=-sin(pi*Phi/180);
1322r3=sin(pi*Phi/180);
1323r4=cos(pi*Phi/180);
1324x=data.Coord(:,1)-O_x;
1325y=data.Coord(:,2)-O_y;
1326data.Coord(:,1)=r1*x+r2*y;
1327data.Coord(:,2)=r3*x+r4*y;
1328% data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1329for i=1:size(data.Coord,1)
1330    for j=1:5
1331          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1332   end
1333end
1334Tabchar=cell2tab(Coord,' | ');
1335Tabchar=[Tabchar;{'......'}];
1336set(handles.ListCoord,'Value',1)
1337set(handles.ListCoord,'String',Tabchar)
1338
1339
1340% %------------------------------------------------------------------------
1341% % --- Executes on button press in rotation.
1342% function rotation_Callback(hObject, eventdata, handles)
1343% %------------------------------------------------------------------------
1344% angle_rot=(pi/180)*str2num(get(handles.Phi,'String'));
1345% Coord_cell=get(handles.ListCoord,'String');
1346% data=read_geometry_calib(Coord_cell);
1347% data.Coord(:,1)=cos(angle_rot)*data.Coord(:,1)+sin(angle_rot)*data.Coord(:,2);
1348% data.Coord(:,1)=-sin(angle_rot)*data.Coord(:,1)+cos(angle_rot)*data.Coord(:,2);
1349% set(handles.XObject,'String',num2str(data.Coord(:,1),4));
1350% set(handles.YObject,'String',num2str(data.Coord(:,2),4));
1351
1352
1353%------------------------------------------------------------------------
1354% image transform from px to phys
1355%INPUT:
1356%Zindex: index of plane
1357% function [A_out,Rangx,Rangy]=phys_Ima(A,Calib,ZIndex)
1358% %------------------------------------------------------------------------
1359% xcorner=[];
1360% ycorner=[];
1361% npx=[];
1362% npy=[];
1363% siz=size(A)
1364% npx=[npx siz(2)];
1365% npy=[npy siz(1)]
1366% xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners
1367% yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
1368% [xcorner,ycorner]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates
1369% Rangx(1)=min(xcorner);
1370% Rangx(2)=max(xcorner);
1371% Rangy(2)=min(ycorner);
1372% Rangy(1)=max(ycorner);
1373% test_multi=(max(npx)~=min(npx)) | (max(npy)~=min(npy));
1374% npx=max(npx);
1375% npy=max(npy);
1376% x=linspace(Rangx(1),Rangx(2),npx);
1377% y=linspace(Rangy(1),Rangy(2),npy);
1378% [X,Y]=meshgrid(x,y);%grid in physical coordiantes
1379% vec_B=[];
1380%
1381% zphys=0; %default
1382% if isfield(Calib,'SliceCoord') %.Z= index of plane
1383%    SliceCoord=Calib.SliceCoord(ZIndex,:);
1384%    zphys=SliceCoord(3); %to generalize for non-parallel planes
1385% end
1386% [XIMA,YIMA]=px_XYZ(Calib,X,Y,zphys);%corresponding image indices for each point in the real space grid
1387% XIMA=reshape(round(XIMA),1,npx*npy);%indices reorganized in 'line'
1388% YIMA=reshape(round(YIMA),1,npx*npy);
1389% flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image
1390% testuint8=isa(A,'uint8');
1391% testuint16=isa(A,'uint16');
1392% if numel(siz)==2 %(B/W images)
1393%     vec_A=reshape(A,1,npx*npy);%put the original image in line
1394%     ind_in=find(flagin);
1395%     ind_out=find(~flagin);
1396%     ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
1397%     ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
1398%     vec_B(ind_in)=vec_A(ICOMB);
1399%     vec_B(ind_out)=zeros(size(ind_out));
1400%     A_out=reshape(vec_B,npy,npx);%new image in real coordinates
1401% elseif numel(siz)==3     
1402%     for icolor=1:siz(3)
1403%         vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line
1404%         ind_in=find(flagin);
1405%         ind_out=find(~flagin);
1406%         ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
1407%         ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
1408%         vec_B(ind_in)=vec_A(ICOMB);
1409%         vec_B(ind_out)=zeros(size(ind_out));
1410%         A_out(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates
1411%     end
1412% end
1413% if testuint8
1414%     A_out=uint8(A_out);
1415% end
1416% if testuint16
1417%     A_out=uint16(A_out);
1418% end
1419
1420%------------------------------------------------------------------------
1421% pointwise transform from px to phys
1422%INPUT:
1423%Z: index of plane
1424% function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Z)
1425% %------------------------------------------------------------------------
1426% if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'SliceCoord')&length(Calib.SliceCoord)>=Z
1427%     Zindex=Z;
1428%     Zphys=Calib.SliceCoord(Zindex,3);%GENERALISER AUX CAS AVEC ANGLE
1429% else
1430%     Zphys=0;
1431% end
1432% if ~exist('X','var')||~exist('Y','var')
1433%     Xphys=[];
1434%     Yphys=[];%default
1435%     return
1436% end
1437% Xphys=X;%default
1438% Yphys=Y;
1439% %image transform
1440% if isfield(Calib,'R')
1441%     R=(Calib.R)';
1442%     Dx=R(5)*R(7)-R(4)*R(8);
1443%     Dy=R(1)*R(8)-R(2)*R(7);
1444%     D0=Calib.f*(R(2)*R(4)-R(1)*R(5));
1445%     Z11=R(6)*R(8)-R(5)*R(9);
1446%     Z12=R(2)*R(9)-R(3)*R(8); 
1447%     Z21=R(4)*R(9)-R(6)*R(7);
1448%     Z22=R(3)*R(7)-R(1)*R(9);
1449%     Zx0=R(3)*R(5)-R(2)*R(6);
1450%     Zy0=R(1)*R(6)-R(3)*R(4);
1451%     A11=R(8)*Calib.Ty-R(5)*Calib.Tz+Z11*Zphys;
1452%     A12=R(2)*Calib.Tz-R(8)*Calib.Tx+Z12*Zphys;
1453%     A21=-R(7)*Calib.Ty+R(4)*Calib.Tz+Z21*Zphys;
1454%     A22=-R(1)*Calib.Tz+R(7)*Calib.Tx+Z11*Zphys;
1455%     X0=Calib.f*(R(5)*Calib.Tx-R(2)*Calib.Ty+Zx0*Zphys);
1456%     Y0=Calib.f*(-R(4)*Calib.Tx+R(1)*Calib.Ty+Zy0*Zphys);
1457%         %px to camera:
1458%     Xd=(Calib.dpx/Calib.sx)*(X-Calib.Cx); % sensor coordinates
1459%     Yd=Calib.dpy*(Y-Calib.Cy);
1460%     dist_fact=1+Calib.kappa1*(Xd.*Xd+Yd.*Yd); %distortion factor
1461%     Xu=dist_fact.*Xd;%undistorted sensor coordinates
1462%     Yu=dist_fact.*Yd;
1463%     denom=Dx*Xu+Dy*Yu+D0;
1464%     % denom2=denom.*denom;
1465%     Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates
1466%     Yphys=(A21.*Xu+A22.*Yu+Y0)./denom;
1467% end
1468
1469
1470% --------------------------------------------------------------------
1471function MenuImportPoints_Callback(hObject, eventdata, handles)
1472fileinput=browse_xml(hObject, eventdata, handles);
1473if isempty(fileinput)
1474    return
1475end
1476[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1477GeometryCalib=s.GeometryCalib;
1478%GeometryCalib=load_calib(hObject, eventdata, handles)
1479calib=reshape(GeometryCalib.PointCoord,[],1);
1480for ilist=1:numel(calib)
1481    CoordCell{ilist}=num2str(calib(ilist));
1482end
1483CoordCell=reshape(CoordCell,[],5);
1484Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
1485Tabchar=[Tabchar;{'......'}];
1486set(handles.ListCoord,'Value',1)
1487set(handles.ListCoord,'String',Tabchar)
1488MenuPlot_Callback(handles.geometry_calib, [], handles)
1489
1490% -----------------------------------------------------------------------
1491function MenuImportIntrinsic_Callback(hObject, eventdata, handles)
1492%------------------------------------------------------------------------
1493fileinput=browse_xml(hObject, eventdata, handles);
1494if isempty(fileinput)
1495    return
1496end
1497[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1498GeometryCalib=s.GeometryCalib;
1499display_intrinsic(GeometryCalib,handles)
1500
1501% -----------------------------------------------------------------------
1502function MenuImportAll_Callback(hObject, eventdata, handles)
1503%------------------------------------------------------------------------
1504fileinput=browse_xml(hObject, eventdata, handles);
1505if ~isempty(fileinput)
1506    loadfile(handles,fileinput)
1507end
1508
1509% -----------------------------------------------------------------------
1510% --- Executes on menubar option Import/Grid file: introduce previous grid files
1511function MenuGridFile_Callback(hObject, eventdata, handles)
1512% -----------------------------------------------------------------------
1513inputfile=browse_xml(hObject, eventdata, handles);
1514listfile=get(handles.coord_files,'string');
1515if isequal(listfile,{''})
1516    listfile={inputfile};
1517else
1518    listfile=[listfile;{inputfile}];%update the list of coord files
1519end
1520set(handles.coord_files,'string',listfile);
1521
1522%------------------------------------------------------------------------
1523% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
1524function key_press_fcn(hObject,eventdata,handles)
1525%------------------------------------------------------------------------
1526xx=double(get(handles.geometry_calib,'CurrentCharacter')); %get the keyboard character
1527if ismember(xx,[8 127])%backspace or delete
1528    Coord_cell=get(handles.ListCoord,'String');
1529    val=get(handles.ListCoord,'Value');
1530     if max(val)<numel(Coord_cell) % the last element '...' has not been selected
1531        Coord_cell(val)=[];%remove the selected line
1532        set(handles.ListCoord,'Value',min(val))
1533        set(handles.ListCoord,'String',Coord_cell)         
1534        ListCoord_Callback(hObject, eventdata, handles)
1535        MenuPlot_Callback(hObject,eventdata,handles)
1536     end
1537end
1538
1539%------------------------------------------------------------------------
1540function fileinput=browse_xml(hObject, eventdata, handles)
1541%------------------------------------------------------------------------
1542fileinput=[];%default
1543oldfile=''; %default
1544UserData=get(handles.geometry_calib,'UserData');
1545if isfield(UserData,'XmlInputFile')
1546    oldfile=UserData.XmlInputFile;
1547end
1548[FileName, PathName, filterindex] = uigetfile( ...
1549       {'*.xml;*.mat', ' (*.xml,*.mat)';
1550       '*.xml',  '.xml files '; ...
1551        '*.mat',  '.mat matlab files '}, ...
1552        'Pick a file',oldfile);
1553fileinput=[PathName FileName];%complete file name
1554testblank=findstr(fileinput,' ');%look for blanks
1555if ~isempty(testblank)
1556    msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed')
1557    return
1558end
1559sizf=size(fileinput);
1560if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1561UserData.XmlInputFile=fileinput;
1562set(handles.geometry_calib,'UserData',UserData)%record current file foer further use of browser
1563
1564% -----------------------------------------------------------------------
1565function Heading=loadfile(handles,fileinput)
1566%------------------------------------------------------------------------
1567Heading=[];%default
1568[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1569if ~isempty(errormsg)
1570    msgbox_uvmat('ERROR',['Error for reading ' fileinput ': '  errormsg])
1571    return
1572end
1573if ~isempty(s.Heading)
1574    Heading=s.Heading;
1575end
1576   
1577GeometryCalib=s.GeometryCalib;
1578fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
1579%     Tabchar={};
1580CoordCell={};
1581%     kc=0;%default
1582%     f1=1000;
1583%     f2=1000;
1584%     hhuvmat=guidata(findobj(allchild(0),'Name','uvmat'));
1585%     Cx=str2num(get(hhuvmat.npx,'String'))/2;
1586%     Cy=str2num(get(hhuvmat.npy,'String'))/2;
1587Tabchar={};%default
1588val_cal=1;%default
1589if ~isempty(GeometryCalib)
1590    % choose the calibration option
1591    if isfield(GeometryCalib,'CalibrationType')
1592       calib_list=get(handles.calib_type,'String');
1593       for ilist=1:numel(calib_list)
1594           if strcmp(calib_list{ilist},GeometryCalib.CalibrationType)
1595               val_cal=ilist;
1596               break
1597           end
1598       end
1599    end
1600    display_intrinsic(GeometryCalib,handles)%intrinsic param
1601    %extrinsic param
1602    if isfield(GeometryCalib,'Tx_Ty_Tz')
1603        Tx_Ty_Tz=GeometryCalib.Tx_Ty_Tz;
1604        set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
1605        set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
1606        set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
1607    end
1608    if isfield(GeometryCalib,'omc')
1609        set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
1610        set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
1611        set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
1612    end
1613    calib=reshape(GeometryCalib.PointCoord,[],1);
1614    for ilist=1:numel(calib)
1615        CoordCell{ilist}=num2str(calib(ilist));
1616    end
1617    CoordCell=reshape(CoordCell,[],5);
1618    Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
1619    MenuPlot_Callback(handles.geometry_calib, [], handles)
1620end
1621set(handles.calib_type,'Value',val_cal)
1622Tabchar=[Tabchar;{'......'}];
1623set(handles.ListCoord,'Value',1)
1624set(handles.ListCoord,'String',Tabchar)
1625
1626if isempty(CoordCell)% allow mouse action by default in the absence of input points
1627    set(handles.edit_append,'Value',1)
1628    set(handles.edit_append,'BackgroundColor',[1 1 0])
1629else % does not allow mouse action by default in the presence of input points
1630    set(handles.edit_append,'Value',0)
1631    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
1632end
1633
1634%------------------------------------------------------------------------
1635%---display calibration intrinsic parameters
1636function display_intrinsic(GeometryCalib,handles)
1637%------------------------------------------------------------------------
1638fx=[];
1639fy=[];
1640if isfield(GeometryCalib,'fx_fy')
1641    fx=GeometryCalib.fx_fy(1);
1642    fy=GeometryCalib.fx_fy(2);
1643end
1644Cx_Cy=[0 0];%default
1645if isfield(GeometryCalib,'Cx_Cy')
1646    Cx_Cy=GeometryCalib.Cx_Cy;
1647end
1648kc=0;
1649if isfield(GeometryCalib,'kc')
1650    kc=GeometryCalib.kc; %* GeometryCalib.focal*GeometryCalib.focal;
1651end
1652set(handles.fx,'String',num2str(fx,5))
1653set(handles.fy,'String',num2str(fy,5))
1654set(handles.Cx,'String',num2str(Cx_Cy(1),'%1.1f'))
1655set(handles.Cy,'String',num2str(Cx_Cy(2),'%1.1f'))
1656set(handles.kc,'String',num2str(kc,'%1.4f'))
1657
1658
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