source: trunk/src/geometry_calib.m @ 745

Last change on this file since 745 was 745, checked in by sommeria, 11 years ago

set_slice installed

File size: 58.6 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 11-Apr-2014 23:10:57
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
63   [pp,ff]=fileparts(which(varargin{1})); % name of the input file
64   if strcmp(ff,mfilename)% if we are activating a sub-function of geometry_calib
65   % ~isempty(regexp(varargin{1},'_Callback','once'))
66    gui_State.gui_Callback = str2func(varargin{1});
67   end
68end
69
70if nargout
71    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
72else
73    gui_mainfcn(gui_State, varargin{:});
74end
75% End initialization code - DO NOT edit
76
77
78% --- Executes just before geometry_calib is made visible.
79%INPUT:
80%handles: handles of the geometry_calib interface elements
81% PlotHandles: set of handles of the elements contolling the plotting
82% parameters on the uvmat interface (obtained by 'get_plot_handle.m')
83%------------------------------------------------------------------------
84function geometry_calib_OpeningFcn(hObject, eventdata, handles,inputfile)
85%------------------------------------------------------------------------
86% Choose default command line output for geometry_calib
87
88handles.output = hObject;
89
90% Update handles structure
91guidata(hObject, handles);
92set(hObject,'DeleteFcn',{@closefcn})%
93%set(hObject,'WindowButtonDownFcn',{'mouse_alt_gui',handles}) % allows mouse action with right button (zoom for uicontrol display)
94
95%% position
96set(0,'Unit','pixels')
97ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
98Left=ScreenSize(3)- 460; %right edge close to the right, with margin=40 (GUI width=420 px)
99if ScreenSize(4)>920
100    Height=840;%default height of the GUI
101    Bottom=ScreenSize(4)-Height-40; %put fig at top right
102else
103    Height=ScreenSize(4)-80;
104    Bottom=40; % GUI lies o the screen bottom (with margin =40)
105end
106set(handles.calib_type,'Position',[1 Height-40 194 30])%  rank 1
107set(handles.APPLY,'Position',[197 Height-40 110 30])%  rank 1
108set(handles.REPLICATE,'Position',[309 Height-40 110 30])%  rank 1
109set(handles.Intrinsic,'Position',[1 Height-40-2-92 418 92])%  rank 2
110set(handles.Extrinsic,'Position',[1 Height-40-4-92-75 418 75])%  rank 3
111set(handles.PointLists,'Position',[1 Height-40-6-92-75-117 418 117]) %  rank 4
112set(handles.CheckEnableMouse,'Position',[3 Height-40-8-92-75-117-30 180 30])%  rank 5
113set(handles.PLOT,'Position',[3 Height-394 120 30])%  rank 6
114set(handles.Copy,'Position',[151 Height-394 120 30])%  rank 6
115set(handles.CLEAR_PTS,'Position',[297 Height-394 120 30])%  rank 6
116set(handles.ClearLine,'Position',[297 Height-364 120 30])%  rank 6
117set(handles.CoordLine,'Position',[177 Height-364 120 30])%  rank 6
118set(handles.phys_title,'Position',[38 Height-426 125 20])%  rank 7
119set(handles.CoordUnit,'Position',[151 Height-426 120 30])%  rank 7
120set(handles.px_title,'Position',[272 Height-426 125 20])%  rank 7
121set(handles.ListCoord,'Position',[1 20 418 Height-446])% rank 8
122set(handles.geometry_calib,'Position',[Left Bottom 420 Height])
123
124%set menu of calibration options
125set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'})
126if exist('inputfile','var')&& ~isempty(inputfile)
127%     struct.XmlInputFile=inputfile;
128    [RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(inputfile);
129    struct.XmlInputFile=find_imadoc(RootPath,SubDir,RootFile,FileExt);
130%     if ~strcmp(FileExt,'.xml')
131%         inputfile=fullfile(RootPath,[SubDir '.xml']);%xml file corresponding to the input file
132%         if ~exist(inputfile,'file')% case of civ files , removes the extension for subdir
133%             inputfile=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
134%             if ~exist(inputfile,'file')
135%                 inputfile=[fullfile(RootPath,SubDir,RootFile) '.xml'];%old convention
136%                 if ~exist(inputfile,'file')
137%                     inputfile='';
138%                 end
139%             end
140%         end
141%     end
142    set(handles.ListCoord,'Data',[])
143    if exist(struct.XmlInputFile,'file')
144        Heading=loadfile(handles,struct.XmlInputFile);% load data from the xml file and fill the GUI
145        if isfield(Heading,'Campaign')&& ischar(Heading.Campaign)
146            struct.Campaign=Heading.Campaign;
147        end
148    end   
149    set(hObject,'UserData',struct)
150end
151
152%------------------------------------------------------------------------
153% --- Outputs from this function are returned to the command line.
154function varargout = geometry_calib_OutputFcn(~, eventdata, handles)
155%------------------------------------------------------------------------
156% Get default command line output from handles structure
157varargout{1} = handles.output;
158varargout{2}=handles;
159%
160%------------------------------------------------------------------------
161% executed when closing: set the parent interface button to value 0
162function closefcn(gcbo,eventdata)
163%------------------------------------------------------------------------
164huvmat=findobj(allchild(0),'Name','uvmat');
165if ~isempty(huvmat)
166    handles=guidata(huvmat);
167    set(handles.MenuCalib,'Checked','off')
168    hobject=findobj(handles.PlotAxes,'tag','calib_points');
169    if ~isempty(hobject)
170        delete(hobject)
171    end
172    hobject=findobj(handles.PlotAxes,'tag','calib_marker');
173    if ~isempty(hobject)
174        delete(hobject)
175    end   
176end
177
178%------------------------------------------------------------------------
179% --- Executes on button press APPLY (used to launch the calibration).
180function APPLY_Callback(hObject, eventdata, handles)
181%------------------------------------------------------------------------
182%% look for the GUI uvmat and check for an image as input
183set(handles.APPLY,'BackgroundColor',[1 1 0])
184huvmat=findobj(allchild(0),'Name','uvmat');
185hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
186
187RootPath='';
188if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
189    RootPath=get(hhuvmat.RootPath,'String');
190    SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
191    outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
192else
193    question={'save the calibration data and point coordinates in'};
194    def={fullfile(RootPath,'ObjectCalib.xml')};
195    options.Resize='on';
196    answer=inputdlg(question,'',1,def,options);
197    outputfile=answer{1};
198end
199[GeometryCalib,index]=calibrate(handles,hhuvmat);% apply calibration
200
201if isempty(GeometryCalib) % if calibration cancelled
202    set(handles.APPLY,'BackgroundColor',[1 0 1])
203else   % if calibration confirmed
204   
205    %% copy the xml file from the old location if appropriate, then update with the calibration parameters
206    if ~exist(outputfile,'file') && ~isempty(SubDirBase)
207        oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
208        if exist(oldxml,'file')
209            [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
210        end
211    end
212    errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file
213    if ~strcmp(errormsg,'')
214        msgbox_uvmat('ERROR',errormsg);
215    end
216   
217    %% display image with new calibration in the currently opened uvmat interface
218    FieldList=get(hhuvmat.FieldName,'String');
219    val=get(hhuvmat.FieldName,'Value');
220    if strcmp(FieldList{val},'image')
221        set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image
222        UserData=get(handles.geometry_calib,'UserData');
223        UserData.XmlInputFile=outputfile;%save the current xml file name
224        set(handles.geometry_calib,'UserData',UserData)
225        uvmat('InputFileREFRESH_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
226        PLOT_Callback(hObject, eventdata, handles)
227        set(handles.CoordLine,'string',num2str(index))
228        Coord=get(handles.ListCoord,'Data');
229        update_calib_marker(Coord(index,:)); %indicate the point with max deviations from phys coord to calibration
230        figure(handles.geometry_calib)% put the GUI geometry_calib in front
231        set(handles.APPLY,'BackgroundColor',[1 0 0]) % set APPLY button to red color
232    else
233        msgbox_uvmat('WARNING','open the image to see the effect of the new calibration')
234    end
235end
236
237%------------------------------------------------------------------------
238% --- Executes on button press in REPLICATE
239function REPLICATE_Callback(hObject, eventdata, handles)
240%------------------------------------------------------------------------
241
242%% look for the GUI uvmat and check for an image as input
243huvmat=findobj(allchild(0),'Name','uvmat');
244hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
245GeometryCalib=calibrate(handles,hhuvmat);% apply calibration
246
247%% open the GUI browse_data
248CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
249if isfield(CalibData,'XmlInputFile')
250    InputDir=fileparts(fileparts(CalibData.XmlInputFile));
251end
252answer=msgbox_uvmat('INPUT_TXT','Campaign to calibrate?',InputDir);
253if strcmp(answer,'Cancel')
254    return
255end
256OutPut=browse_data(answer);
257nbcalib=0;
258for ilist=1:numel(OutPut.Experiment)
259    SubDirBase=regexprep(OutPut.DataSeries{1},'\..+$','');
260    XmlName=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']);
261    % copy the xml file from the old location if appropriate, then update with the calibration parameters
262    if ~exist(XmlName,'file') && ~isempty(SubDirBase)
263        oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']);
264        if exist(oldxml,'file')
265            [success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention
266        end
267    end
268    errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file
269    if ~strcmp(errormsg,'')
270        msgbox_uvmat('ERROR',errormsg);
271    else
272        display([XmlName ' updated with calibration parameters'])
273        nbcalib=nbcalib+1;
274    end
275end
276msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']);
277
278%------------------------------------------------------------------------
279% --- activate calibration and store parameters in ouputfile .
280function [GeometryCalib,index]=calibrate(handles,hhuvmat)
281%------------------------------------------------------------------------
282set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points)
283%% read the current calibration points
284index=[];
285Coord=get(handles.ListCoord,'Data');
286Coord(:,6)=[];
287% apply the calibration, whose type is selected in  handles.calib_type
288GeometryCalib=[];
289if ~isempty(Coord)
290    calib_cell=get(handles.calib_type,'String');
291    val=get(handles.calib_type,'Value');
292    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
293else
294    msgbox_uvmat('ERROR','No calibration points, abort')
295end
296if isempty(GeometryCalib)
297    return
298end
299Z_plane=[];
300if ~isempty(Coord)
301    %check error
302    X=Coord(:,1);
303    Y=Coord(:,2);
304    Z=Coord(:,3);
305    x_ima=Coord(:,4);
306    y_ima=Coord(:,5);
307    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
308    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
309    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
310    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
311    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
312    [tild,ind_dim]=max(GeometryCalib.ErrorMax);
313    index=index(ind_dim);
314    %set the Z position of the reference plane used for calibration
315    if isequal(max(Z),min(Z))%Z constant
316        Z_plane=Z(1);
317        GeometryCalib.NbSlice=1;
318        GeometryCalib.SliceCoord=[0 0 Z_plane];
319    end
320end
321%set the coordinate unit
322unitlist=get(handles.CoordUnit,'String');
323unit=unitlist{get(handles.CoordUnit,'value')};
324GeometryCalib.CoordUnit=unit;
325%record the points
326GeometryCalib.SourceCalib.PointCoord=Coord;
327display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
328
329% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
330set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
331set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
332set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
333set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
334set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
335set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
336
337%% store the calibration data, by default in the xml file of the currently displayed image
338UvData=get(hhuvmat.uvmat,'UserData');
339% NbSlice_j=1;%default
340% ZStart=Z_plane;
341% ZEnd=Z_plane;
342% volume_scan='n';
343% if isfield(UvData,'XmlData')
344%     if isfield(UvData.XmlData,'TranslationMotor')
345%         NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice;
346%         ZStart=UvData.XmlData.TranslationMotor.ZStart/10;
347%         ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10;
348%         volume_scan='y';
349%     end
350% end
351
352answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
353    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
354    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
355
356%% get plane position(s)
357if ~strcmp(answer,'Yes')
358    GeometryCalib=[];
359    index=1;
360    return
361end
362if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
363    msgbox_uvmat('CONFIRMATION',{['The current image series is assumed by default in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be modified by MenuSetSlice in the upper bar menu of uvmat'})
364%     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'};
365%     input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}];
366%     answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on');
367%     GeometryCalib.NbSlice=str2double(answer{5});
368%     GeometryCalib.VolumeScan=answer{6};
369%     if isempty(answer)
370%         Z_plane=0; %default
371%     else
372%         Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice);
373%     end
374     GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
375%     GeometryCalib.SliceAngle(:,3)=0;
376%     GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise)
377%     GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise)
378%     GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})];
379%     GeometryCalib.RefractionIndex=str2double(answer{4});
380end
381
382%------------------------------------------------------------------------
383% --- determine the parameters for a calibration by an affine function (rescaling and offset, no rotation)
384function GeometryCalib=calib_rescale(Coord,handles)
385%------------------------------------------------------------------------
386X=Coord(:,1);
387Y=Coord(:,2);% Z not used
388x_ima=Coord(:,4);
389y_ima=Coord(:,5);
390[px]=polyfit(X,x_ima,1);
391[py]=polyfit(Y,y_ima,1);
392% T_x=px(2);
393% T_y=py(2);
394GeometryCalib.CalibrationType='rescale';
395GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
396GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
397GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
398GeometryCalib.omc=[0 0 0];
399
400%------------------------------------------------------------------------
401% --- determine the parameters for a calibration by a linear transform matrix (rescale and rotation)
402function GeometryCalib=calib_linear(Coord,handles)
403%------------------------------------------------------------------------
404X=Coord(:,1);
405Y=Coord(:,2);% Z not used
406x_ima=Coord(:,4);
407y_ima=Coord(:,5);
408XY_mat=[ones(size(X)) X Y];
409a_X1=XY_mat\x_ima; %transformation matrix for X
410a_Y1=XY_mat\y_ima;%transformation matrix for X
411R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
412epsilon=sign(det(R));
413norm=abs(det(R));
414GeometryCalib.CalibrationType='linear';
415if (a_X1(2)/a_Y1(3))>0
416    GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm);
417else
418    GeometryCalib.fx_fy(1)=-sqrt(-(a_X1(2)/a_Y1(3))*norm);
419end
420GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
421GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
422GeometryCalib.Tx_Ty_Tz=[a_X1(1)/GeometryCalib.fx_fy(1) a_Y1(1)/GeometryCalib.fx_fy(2) 1];
423R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
424R(2,:)=R(2,:)/GeometryCalib.fx_fy(2);
425R=[R;[0 0]];
426GeometryCalib.R=[R [0;0;-epsilon]];
427GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
428
429%------------------------------------------------------------------------
430% --- determine the tsai parameters for a view normal to the grid plane
431% NOT USED
432function GeometryCalib=calib_normal(Coord,handles)
433%------------------------------------------------------------------------
434Calib.f1=str2num(get(handles.fx,'String'));
435Calib.f2=str2num(get(handles.fy,'String'));
436Calib.k=str2num(get(handles.kc,'String'));
437Calib.Cx=str2num(get(handles.Cx,'String'));
438Calib.Cy=str2num(get(handles.Cy,'String'));
439%default
440if isempty(Calib.f1)
441    Calib.f1=25/0.012;
442end
443if isempty(Calib.f2)
444    Calib.f2=25/0.012;
445end
446if isempty(Calib.k)
447    Calib.k=0;
448end
449if isempty(Calib.Cx)||isempty(Calib.Cy)
450    huvmat=findobj(allchild(0),'Tag','uvmat');
451    hhuvmat=guidata(huvmat);
452    Calib.Cx=str2num(get(hhuvmat.num_Npx,'String'))/2;
453    Calib.Cx=str2num(get(hhuvmat.num_Npy,'String'))/2;
454end   
455%tsai parameters
456Calib.dpx=0.012;%arbitrary
457Calib.dpy=0.012;
458Calib.sx=Calib.f1*Calib.dpx/(Calib.f2*Calib.dpy);
459Calib.f=Calib.f2*Calib.dpy;
460Calib.kappa1=Calib.k/(Calib.f*Calib.f);
461
462%initial guess
463X=Coord(:,1);
464Y=Coord(:,2);
465Zmean=mean(Coord(:,3));
466x_ima=Coord(:,4)-Calib.Cx;
467y_ima=Coord(:,5)-Calib.Cy;
468XY_mat=[ones(size(X)) X Y];
469a_X1=XY_mat\x_ima; %transformation matrix for X
470a_Y1=XY_mat\y_ima;%transformation matrix for Y
471R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,-1];% rotation+ z axis reversal (upward)
472norm=sqrt(det(-R));
473calib_param(1)=0;% quadratic distortion
474calib_param(2)=a_X1(1);
475calib_param(3)=a_Y1(1);
476calib_param(4)=Calib.f/(norm*Calib.dpx)-R(3,3)*Zmean;
477calib_param(5)=angle(a_X1(2)+1i*a_X1(3));
478display(['initial guess=' num2str(calib_param)])
479
480%optimise the parameters: minimisation of error
481calib_param = fminsearch(@(calib_param) error_calib(calib_param,Calib,Coord),calib_param);
482
483GeometryCalib.CalibrationType='tsai_normal';
484GeometryCalib.focal=Calib.f;
485GeometryCalib.dpx_dpy=[Calib.dpx Calib.dpy];
486GeometryCalib.Cx_Cy=[Calib.Cx Calib.Cy];
487GeometryCalib.sx=Calib.sx;
488GeometryCalib.kappa1=calib_param(1);
489GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
490GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)];
491alpha=calib_param(5);
492GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
493
494%------------------------------------------------------------------------
495function GeometryCalib=calib_3D_linear(Coord,handles)
496%------------------------------------------------------------------------
497path_uvmat=which('uvmat');% check the path detected for source file uvmat
498path_UVMAT=fileparts(path_uvmat); %path to UVMAT
499huvmat=findobj(allchild(0),'Tag','uvmat');
500hhuvmat=guidata(huvmat);
501coord_files=get(handles.ListCoordFiles,'String');
502if ischar(coord_files)
503    coord_files={coord_files};
504end
505if isempty(coord_files{1}) || isequal(coord_files,{''})
506    coord_files={};
507end
508%retrieve the calibration points stored in the files listed in the popup list ListCoordFiles
509x_1=Coord(:,4:5)';%px coordinates of the ref points
510nx=str2num(get(hhuvmat.num_Npx,'String'));
511ny=str2num(get(hhuvmat.num_Npy,'String'));
512x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
513X_1=Coord(:,1:3)';%phys coordinates of the ref points
514n_ima=numel(coord_files)+1;
515if ~isempty(coord_files)
516    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
517    for ifile=1:numel(coord_files)
518    t=xmltree(coord_files{ifile});
519    s=convert(t);%convert to matlab structure
520        if isfield(s,'GeometryCalib')
521            if isfield(s.GeometryCalib,'SourceCalib')
522                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
523                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
524                Coord_file=zeros(length(PointCoord),5);%default
525                for i=1:length(PointCoord)
526                    line=str2num(PointCoord{i});
527                    Coord_file(i,4:5)=line(4:5);%px x
528                    Coord_file(i,1:3)=line(1:3);%phys x
529                end
530                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
531                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
532                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
533                end
534            end
535        end
536    end
537end
538n_ima=numel(coord_files)+1;
539est_dist=[0;0;0;0;0];
540est_aspect_ratio=0;
541est_fc=[1;1];
542center_optim=0;
543run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));% apply fct 'toolbox_calib/go_calib_optim'
544if exist('Rc_1','var')
545    GeometryCalib.CalibrationType='3D_linear';
546    GeometryCalib.fx_fy=fc';
547    GeometryCalib.Cx_Cy=cc';
548    GeometryCalib.kc=kc(1);
549    GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
550    GeometryCalib.Tx_Ty_Tz=Tc_1';
551    GeometryCalib.R=Rc_1;
552    GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
553    GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
554    GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
555    GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
556    GeometryCalib.ErrorRMS=[];
557    GeometryCalib.ErrorMax=[];
558else
559    msgbox_uvmat('ERROR',['calibration function ' fullfile('toolbox_calib','go_calib_optim') ' did not converge: use multiple views or option 3D_extrinsic'])
560    GeometryCalib=[];
561end
562
563%------------------------------------------------------------------------
564function GeometryCalib=calib_3D_quadr(Coord,handles)
565%------------------------------------------------------------------
566
567path_uvmat=which('uvmat');% check the path detected for source file uvmat
568path_UVMAT=fileparts(path_uvmat); %path to UVMAT
569huvmat=findobj(allchild(0),'Tag','uvmat');
570hhuvmat=guidata(huvmat);
571% check_cond=0;
572coord_files=get(handles.ListCoordFiles,'String');
573if ischar(coord_files)
574    coord_files={coord_files};
575end
576if isempty(coord_files{1}) || isequal(coord_files,{''})
577    coord_files={};
578end
579
580%retrieve the calibration points stored in the files listed in the popup list ListCoordFiles
581x_1=Coord(:,4:5)';%px coordinates of the ref points
582nx=str2num(get(hhuvmat.num_Npx,'String'));
583ny=str2num(get(hhuvmat.num_Npy,'String'));
584x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
585X_1=Coord(:,1:3)';%phys coordinates of the ref points
586n_ima=numel(coord_files)+1;
587if ~isempty(coord_files)
588    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
589    for ifile=1:numel(coord_files)
590    t=xmltree(coord_files{ifile});
591    s=convert(t);%convert to matlab structure
592        if isfield(s,'GeometryCalib')
593            if isfield(s.GeometryCalib,'SourceCalib')
594                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
595                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
596                Coord_file=zeros(length(PointCoord),5);%default
597                for i=1:length(PointCoord)
598                    line=str2num(PointCoord{i});
599                    Coord_file(i,4:5)=line(4:5);%px x
600                    Coord_file(i,1:3)=line(1:3);%phys x
601                end
602                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
603                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
604                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
605                end
606            end
607        end
608    end
609end
610n_ima=numel(coord_files)+1;
611est_dist=[1;0;0;0;0];
612est_aspect_ratio=1;
613center_optim=0;
614run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));% apply fct 'toolbox_calib/go_calib_optim'
615
616if exist('Rc_1','var')
617    GeometryCalib.CalibrationType='3D_quadr';
618    GeometryCalib.fx_fy=fc';
619    GeometryCalib.Cx_Cy=cc';
620    GeometryCalib.kc=kc(1);
621    GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
622    GeometryCalib.Tx_Ty_Tz=Tc_1';
623    GeometryCalib.R=Rc_1;
624    GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
625    GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
626    GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
627    GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
628    GeometryCalib.ErrorRMS=[];
629    GeometryCalib.ErrorMax=[];
630else
631    msgbox_uvmat('ERROR',['calibration function ' fullfile('toolbox_calib','go_calib_optim') ' did not converge: use multiple views or option 3D_extrinsic'])
632    GeometryCalib=[];
633end
634
635%------------------------------------------------------------------------
636function GeometryCalib=calib_3D_extrinsic(Coord,handles)
637%------------------------------------------------------------------
638path_uvmat=which('geometry_calib');% check the path detected for source file uvmat
639path_UVMAT=fileparts(path_uvmat); %path to UVMAT
640x_1=double(Coord(:,4:5)');%image coordinates
641X_1=double(Coord(:,1:3)');% phys coordinates
642huvmat=findobj(allchild(0),'Tag','uvmat');
643hhuvmat=guidata(huvmat);
644ny=str2double(get(hhuvmat.num_Npy,'String'));
645x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
646n_ima=1;
647GeometryCalib.CalibrationType='3D_extrinsic';
648fx=str2num(get(handles.fx,'String'));
649fy=str2num(get(handles.fy,'String'));
650Cx=str2num(get(handles.Cx,'String'));
651Cy=str2num(get(handles.Cy,'String'));
652errormsg='';
653if isempty(fx)
654    errormsg='focal length fx needs to be introduced';
655elseif isempty(fy)
656    errormsg='focal length fy needs to be introduced';
657elseif isempty(Cx)
658    errormsg='shift Cx to image centre needs to be introduced';
659elseif isempty(Cy)
660    errormsg='shift Cy to image centre needs to be introduced';
661end
662if ~isempty(errormsg)
663    GeometryCalib=[];
664    msgbox_uvmat('ERROR',errormsg)
665    return
666end
667GeometryCalib.fx_fy(1)=str2num(get(handles.fx,'String'));
668GeometryCalib.fx_fy(2)=str2num(get(handles.fy,'String'));
669GeometryCalib.Cx_Cy(1)=str2num(get(handles.Cx,'String'));
670GeometryCalib.Cx_Cy(2)=str2num(get(handles.Cy,'String'));
671GeometryCalib.kc=str2num(get(handles.kc,'String'));
672fct_path=fullfile(path_UVMAT,'toolbox_calib');
673addpath(fct_path)
674GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate)
675[omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
676   (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]);
677rmpath(fct_path);
678GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
679GeometryCalib.Tx_Ty_Tz=Tc1';
680%inversion of z axis
681GeometryCalib.R=Rc1;
682GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
683GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
684GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
685GeometryCalib.omc=(180/pi)*omc';
686
687%------------------------------------------------------------------------
688%function GeometryCalib=calib_tsai_heikkila(Coord)
689% TEST: NOT IMPLEMENTED
690%------------------------------------------------------------------
691% path_uvmat=which('uvmat');% check the path detected for source file uvmat
692% path_UVMAT=fileparts(path_uvmat); %path to UVMAT
693% path_calib=fullfile(path_UVMAT,'toolbox_calib_heikkila');
694% addpath(path_calib)
695% npoints=size(Coord,1);
696% Coord(:,1:3)=10*Coord(:,1:3);
697% Coord=[Coord zeros(npoints,2) -ones(npoints,1)];
698% [par,pos,iter,res,er,C]=cacal('dalsa',Coord);
699% GeometryCalib.CalibrationType='tsai';
700% GeometryCalib.focal=par(2);
701
702
703%------------------------------------------------------------------------
704% --- determine the rms of calibration error
705function ErrorRms=error_calib(calib_param,Calib,Coord)
706%------------------------------------------------------------------------
707%calib_param: vector of free calibration parameters (to optimise)
708%Calib: structure of the given calibration parameters
709%Coord: list of phys coordinates (columns 1-3, and pixel coordinates (columns 4-5)
710Calib.f=25;
711Calib.dpx=0.012;
712Calib.dpy=0.012;
713Calib.sx=1;
714Calib.Cx=512;
715Calib.Cy=512;
716Calib.kappa1=calib_param(1);
717Calib.Tx=calib_param(2);
718Calib.Ty=calib_param(3);
719Calib.Tz=calib_param(4);
720alpha=calib_param(5);
721Calib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
722
723X=Coord(:,1);
724Y=Coord(:,2);
725Z=Coord(:,3);
726x_ima=Coord(:,4);
727y_ima=Coord(:,5);
728[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z);
729ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
730ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
731ErrorRms=mean(ErrorRms);
732
733
734%------------------------------------------------------------------------
735% --- Executes on button press in STORE.
736function STORE_Callback(hObject, eventdata, handles)
737%------------------------------------------------------------------------
738Coord=get(handles.ListCoord,'Data');
739%Object=read_geometry_calib(Coord_cell);
740unitlist=get(handles.CoordUnit,'String');
741unit=unitlist{get(handles.CoordUnit,'value')};
742GeometryCalib.CoordUnit=unit;
743GeometryCalib.SourceCalib.PointCoord=Coord(:,1:5);
744huvmat=findobj(allchild(0),'Name','uvmat');
745hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
746% RootPath='';
747% RootFile='';
748if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
749%     testhandle=1;
750    RootPath=get(hhuvmat.RootPath,'String');
751    RootFile=get(hhuvmat.RootFile,'String');
752    filebase=[fullfile(RootPath,RootFile) '~'];
753    while exist([filebase '.xml'],'file')
754        filebase=[filebase '~'];
755    end
756    outputfile=[filebase '.xml'];
757    errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');
758    if ~strcmp(errormsg,'')
759        msgbox_uvmat('ERROR',errormsg);
760    end
761    listfile=get(handles.ListCoordFiles,'string');
762    if isequal(listfile,{''})
763        listfile={outputfile};
764    else
765        listfile=[listfile;{outputfile}];%update the list of coord files
766    end
767    set(handles.ListCoordFiles,'string',listfile);
768end
769CLEAR_PTS_Callback(hObject, eventdata, handles)% clear the current list and point plots
770
771% --------------------------------------------------------------------
772% --- Executes on button press in CLEAR_PTS: clear the list of calibration points
773function CLEAR_PTS_Callback(hObject, eventdata, handles)
774% --------------------------------------------------------------------
775set(handles.ListCoord,'Data',[])
776PLOT_Callback(hObject, eventdata, handles)
777update_calib_marker([]);%remove circle marker
778set(handles.APPLY,'backgroundColor',[1 0 0])% set APPLY button to red color: no calibration wanted without points
779set(handles.CheckEnableMouse,'value',1); %activate mouse to pick new points
780
781%------------------------------------------------------------------------
782% --- Executes on button press in CLEAR LIST
783function CLEAR_Callback(hObject, eventdata, handles)
784%------------------------------------------------------------------------
785set(handles.ListCoordFiles,'Value',1)
786set(handles.ListCoordFiles,'String',{''})
787
788%------------------------------------------------------------------------
789% --- Executes on selection change in CheckEnableMouse.
790function CheckEnableMouse_Callback(hObject, eventdata, handles)
791%------------------------------------------------------------------------
792choice=get(handles.CheckEnableMouse,'Value');
793if choice
794    huvmat=findobj(allchild(0),'tag','uvmat');
795    if ishandle(huvmat)
796        hhuvmat=guidata(huvmat);
797        set(hhuvmat.MenuRuler,'checked','off')%desactivate ruler
798        if get(hhuvmat.CheckEditObject,'Value')
799            set(hhuvmat.CheckEditObject,'Value',0)
800            uvmat('CheckEditObject_Callback',hhuvmat.CheckEditObject,[],hhuvmat)
801        end
802        set(hhuvmat.MenuRuler,'checked','off')%desactivate ruler
803    end
804end
805
806
807% --------------------------------------------------------------------
808function MenuHelp_Callback(hObject, eventdata, handles)
809path_to_uvmat=which('uvmat');% check the path of uvmat
810pathelp=fileparts(path_to_uvmat);
811helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
812if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
813else
814   addpath (fullfile(pathelp,'uvmat_doc'))
815   web([helpfile '#geometry_calib'])
816end
817
818% --------------------------------------------------------------------
819function MenuSetScale_Callback(hObject, eventdata, handles)
820
821 answer=msgbox_uvmat('INPUT_TXT','scale pixel/cm?','');
822 %create test points
823 huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
824UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface
825npy=size(UvData.Field.A,1);
826npx=size(UvData.Field.A,2);
827Xima=[0.25*npx 0.75*npx 0.75*npx 0.25*npx]';
828Yima=[0.25*npy 0.25*npy 0.75*npy 0.75*npy]';
829x=Xima/str2num(answer);
830y=Yima/str2num(answer);
831Coord=[x y zeros(4,1) Xima Yima zeros(4,1)];
832set(handles.ListCoord,'Data',Coord)
833set(handles.APPLY,'BackgroundColor',[1 0 1])
834set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points
835
836%------------------------------------------------------------------------
837function MenuCreateGrid_Callback(hObject, eventdata, handles)
838%------------------------------------------------------------------------
839CalibData=get(handles.geometry_calib,'UserData');
840Tinput=[];%default
841if isfield(CalibData,'grid')
842    Tinput=CalibData.grid;
843end
844[T,CalibData.grid]=create_grid(Tinput);%display the GUI create_grid
845set(handles.geometry_calib,'UserData',CalibData)
846
847%grid in phys space
848Coord=get(handles.ListCoord,'Data');
849Coord(1:size(T,1),1:3)=T;%update the existing list of phys coordinates from the GUI create_grid
850set(handles.ListCoord,'Data',Coord)
851set(handles.APPLY,'BackgroundColor',[1 0 1])
852set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points
853
854% -----------------------------------------------------------------------
855% --- automatic grid dectection from local maxima of the images
856function MenuDetectGrid_Callback(hObject, eventdata, handles)
857%------------------------------------------------------------------------
858%% read the four last point coordinates in pixels
859Coord=get(handles.ListCoord,'Data');%read list of coordinates on geometry_calib
860nbpoints=size(Coord,1); %nbre of calibration points
861if nbpoints~=4
862    msgbox_uvmat('ERROR','four points must have be selected by the mouse to delimitate the phys grid area; the Ox axis will be defined by the two first points')
863    return
864end
865% corners_X=(Coord(end:-1:end-3,4)); %pixel absissa of the four corners
866% corners_Y=(Coord(end:-1:end-3,5));
867corners_X=(Coord(:,4)); %pixel absissa of the four corners
868corners_Y=(Coord(:,5));
869
870%%%%%%
871%   corners_X=1000*[1.5415  1.7557 1.7539 1.5415]';
872%   corners_Y=1000*[1.1515 1.1509 1.3645  1.3639]';
873
874%reorder the last two points (the two first in the list) if needed
875angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1)));
876if abs(angles(4)-angles(2))>abs(angles(3)-angles(2))
877      X_end=corners_X(4);
878      Y_end=corners_Y(4);
879      corners_X(4)=corners_X(3);
880      corners_Y(4)=corners_Y(3);
881      corners_X(3)=X_end;
882      corners_Y(3)=Y_end;
883end
884
885%% initiate the grid in phys coordinates
886CalibData=get(handles.geometry_calib,'UserData');%get information stored on the GUI geometry_calib
887grid_input=[];%default
888if isfield(CalibData,'grid')
889    grid_input=CalibData.grid;%retrieve the previously used grid
890end
891[T,CalibData.grid,CalibData.grid.CheckWhite]=create_grid(grid_input,'detect_grid');%display the GUI create_grid, read the set of phys coordinates T
892set(handles.geometry_calib,'UserData',CalibData)%store the phys grid parameters for later use
893X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates (cm)
894Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates (cm)
895
896%% read the current image, displayed in the GUI uvmat
897huvmat=findobj(allchild(0),'Name','uvmat');
898UvData=get(huvmat,'UserData');
899A=UvData.Field.A;%currently displayed image
900npxy=size(A);
901
902%% calculate transform matrices for plane projection: rectangle assumed to be viewed in perspective
903% reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
904B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
905      zeros(4,3)        X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ];
906B = reshape (B', 8 , 8 )';
907D = [ corners_X , corners_Y ];
908D = reshape (D', 8 , 1 );
909l = (B' * B)\B' * D;
910Amat = reshape([l(1:6)' 0 0 1 ],3,3)';
911C = [l(7:8)' 1];
912
913%% transform grid image into 'phys' coordinates
914GeometryCalib.CalibrationType='3D_linear';
915GeometryCalib.fx_fy=[1 1];
916GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
917GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
918GeometryCalib.CoordUnit='cm';
919path_uvmat=which('uvmat');% check the path detected for source file uvmat
920path_UVMAT=fileparts(path_uvmat); %path to UVMAT
921addpath(fullfile(path_UVMAT,'transform_field'))
922Data.ListVarName={'AY','AX','A'};
923Data.VarDimName={'AY','AX',{'AY','AX'}};
924if ndims(A)==3
925    A=mean(A,3);
926end
927Data.A=A-min(min(A));
928Data.AY=[npxy(1)-0.5 0.5];
929Data.AX=[0.5 npxy(2)];
930Data.CoordUnit='pixel';
931Calib.GeometryCalib=GeometryCalib;
932DataOut=phys(Data,Calib);
933rmpath(fullfile(path_UVMAT,'transform_field'))
934Amod=DataOut.A;% current image expressed in 'phys' coord
935Rangx=DataOut.AX;% x coordinates of first and last pixel centres in phys
936Rangy=DataOut.AY;% y coordinates of first and last pixel centres in phys
937if CalibData.grid.CheckWhite
938    Amod=double(Amod);%case of white grid markers: will look for image maxima
939else
940    Amod=-double(Amod);%case of black grid markers: will look for image minima
941end
942
943%% detection of local image extrema in each direction
944Dx=(Rangx(2)-Rangx(1))/(npxy(2)-1); %x mesh in real space
945Dy=(Rangy(2)-Rangy(1))/(npxy(1)-1); %y mesh in real space
946ind_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
947ind_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
948nbpoints=size(T,1);
949TIndex=ones(size(T));% image indices corresponding to point coordinates
950%look for image maxima around each expected grid point
951for ipoint=1:nbpoints
952    i0=1+round((T(ipoint,1)-Rangx(1))/Dx);% x index of the expected point in the phys image Amod
953    j0=1+round((T(ipoint,2)-Rangy(1))/Dy);% y index of the expected point in the phys image Amod
954    j0min=max(j0-ind_range_y,1);% min y index selected for the subimage (cut at the edge to avoid index <1)
955    j0max=min(j0+ind_range_y,size(Amod,1));% max y index selected for the subimage (cut at the edge to avoid index > size)
956    i0min=max(i0-ind_range_x,1);% min x index selected for the subimage (cut at the edge to avoid index <1)
957    i0max=min(i0+ind_range_x,size(Amod,2));% max x index selected for the subimage (cut at the edge to avoid index > size)
958    Asub=Amod(j0min:j0max,i0min:i0max); %subimage used to find brigthness extremum
959    x_profile=sum(Asub,1);%profile of subimage summed over y
960    y_profile=sum(Asub,2);%profile of subimage summed over x
961
962    [tild,ind_x_max]=max(x_profile);% index of max for the x profile
963    [tild,ind_y_max]=max(y_profile);% index of max for the y profile
964    %sub-pixel improvement using moments
965    x_shift=0;
966    y_shift=0;
967    if ind_x_max+2<=numel(x_profile) && ind_x_max-2>=1
968        Atop=x_profile(ind_x_max-2:ind_x_max+2);% extract x profile around the max
969        x_shift=sum(Atop.*[-2 -1 0 1 2])/sum(Atop);
970    end
971    if ind_y_max+2<=numel(y_profile) && ind_y_max-2>=1
972        Atop=y_profile(ind_y_max-2:ind_y_max+2);% extract y profile around the max
973        y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop);
974    end
975        %%%%
976%     if ipoint==9
977%                 figure(11)
978%   imagesc(Asub)
979%     figure(12)
980%     plot(x_profile,'r')
981%     hold on
982%     plot(y_profile,'b')
983%     grid on
984%     end
985    %%%%
986    TIndex(ipoint,1)=(i0min+ind_x_max-1+x_shift);% x position of the maximum (in index of Amod)
987    TIndex(ipoint,2)=(j0min+ind_y_max-1+y_shift);% y position of the maximum (in index of Amod)
988end
989Tmod(:,1)=(TIndex(:,1)-1)*Dx+Rangx(1);
990Tmod(:,2)=(TIndex(:,2)-1)*Dy+Rangy(1);
991%Tmod=T(:,(1:2))+Delta;% 'phys' coordinates of the detected points
992[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));% image coordinates of the detected points
993Coord=[T Xpx Ypx zeros(size(T,1),1)];
994set(handles.ListCoord,'Data',Coord)
995PLOT_Callback(hObject, eventdata, handles)
996set(handles.APPLY,'BackgroundColor',[1 0 1])
997set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid spurious points
998
999
1000%-----------------------------------------------------------------------
1001function MenuTranslatePoints_Callback(hObject, eventdata, handles)
1002%-----------------------------------------------------------------------
1003%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1004CalibData=get(handles.geometry_calib,'UserData');
1005Tinput=[];%default
1006if isfield(CalibData,'translate')
1007    Tinput=CalibData.translate;
1008end
1009T=translate_points(Tinput);%display translate_points GUI and get shift parameters
1010CalibData.translate=T;
1011set(handles.geometry_calib,'UserData',CalibData)
1012%translation
1013Coord=get(handles.ListCoord,'Data');
1014Coord(:,1)=T(1)+Coord(:,1);
1015Coord(:,2)=T(2)+Coord(:,2);
1016Coord(:,3)=T(3)+Coord(:,3);
1017set(handles.ListCoord,'Data',Coord);
1018set(handles.APPLY,'BackgroundColor',[1 0 1])
1019
1020% --------------------------------------------------------------------
1021function MenuRotatePoints_Callback(hObject, eventdata, handles)
1022%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1023CalibData=get(handles.geometry_calib,'UserData');
1024Tinput=[];%default
1025if isfield(CalibData,'rotate')
1026    Tinput=CalibData.rotate;
1027end
1028T=rotate_points(Tinput);%display rotate_points GUI to introduce rotation parameters
1029CalibData.rotate=T;
1030set(handles.geometry_calib,'UserData',CalibData)
1031%-----------------------------------------------------
1032%rotation
1033Phi=T(1);
1034O_x=0;%default
1035O_y=0;%default
1036if numel(T)>=2
1037    O_x=T(2);%default
1038end
1039if numel(T)>=3
1040    O_y=T(3);%default
1041end
1042Coord=get(handles.ListCoord,'Data');
1043r1=cos(pi*Phi/180);
1044r2=-sin(pi*Phi/180);
1045r3=sin(pi*Phi/180);
1046r4=cos(pi*Phi/180);
1047x=Coord(:,1)-O_x;
1048y=Coord(:,2)-O_y;
1049Coord(:,1)=r1*x+r2*y;
1050Coord(:,2)=r3*x+r4*y;
1051set(handles.ListCoord,'Data',Coord)
1052set(handles.APPLY,'BackgroundColor',[1 0 1])
1053
1054% --------------------------------------------------------------------
1055function MenuImportPoints_Callback(hObject, eventdata, handles)
1056fileinput=browse_xml(hObject, eventdata, handles);
1057if isempty(fileinput)
1058    return
1059end
1060[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1061if ~isfield(s,'GeometryCalib')
1062    msgbox_uvmat('ERROR','invalid input file: no geometry_calib data')
1063    return
1064end
1065GeometryCalib=s.GeometryCalib;
1066if ~(isfield(GeometryCalib,'SourceCalib')&&isfield(GeometryCalib.SourceCalib,'PointCoord'))
1067        msgbox_uvmat('ERROR','invalid input file: no calibration points')
1068    return
1069end
1070Coord=GeometryCalib.SourceCalib.PointCoord;
1071Coord=[Coord zeros(size(Coord,1),1)];
1072set(handles.ListCoord,'Data',Coord)
1073PLOT_Callback(handles.geometry_calib, [], handles)
1074set(handles.APPLY,'BackgroundColor',[1 0 1])
1075set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid modifications by default
1076
1077% -----------------------------------------------------------------------
1078function MenuImportIntrinsic_Callback(hObject, eventdata, handles)
1079%------------------------------------------------------------------------
1080fileinput=browse_xml(hObject, eventdata, handles);
1081if isempty(fileinput)
1082    return
1083end
1084[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1085GeometryCalib=s.GeometryCalib;
1086display_intrinsic(GeometryCalib,handles)
1087
1088% -----------------------------------------------------------------------
1089function MenuImportAll_Callback(hObject, eventdata, handles)
1090%------------------------------------------------------------------------
1091fileinput=browse_xml(hObject, eventdata, handles);
1092if ~isempty(fileinput)
1093    loadfile(handles,fileinput)
1094end
1095set(handles.CheckEnableMouse,'value',0); %desactivate mouse to avoid modifications by default
1096
1097% -----------------------------------------------------------------------
1098% --- Executes on menubar option Import/Grid file: introduce previous grid files
1099function MenuGridFile_Callback(hObject, eventdata, handles)
1100% -----------------------------------------------------------------------
1101inputfile=browse_xml(hObject, eventdata, handles);
1102listfile=get(handles.ListCoordFiles,'String');
1103if isequal(listfile,{''})
1104    listfile={inputfile};
1105else
1106    listfile=[listfile;{inputfile}];%update the list of coord files
1107end
1108set(handles.ListCoordFiles,'String',listfile);
1109
1110
1111%------------------------------------------------------------------------
1112function fileinput=browse_xml(hObject, eventdata, handles)
1113%------------------------------------------------------------------------
1114fileinput=[];%default
1115oldfile=''; %default
1116UserData=get(handles.geometry_calib,'UserData');
1117if isfield(UserData,'XmlInputFile')
1118    oldfile=UserData.XmlInputFile;
1119end
1120[FileName, PathName, filterindex] = uigetfile( ...
1121       {'*.xml;*.mat', ' (*.xml,*.mat)';
1122       '*.xml',  '.xml files '; ...
1123        '*.mat',  '.mat matlab files '}, ...
1124        'Pick a file',oldfile);
1125fileinput=[PathName FileName];%complete file name
1126testblank=findstr(fileinput,' ');%look for blanks
1127if ~isempty(testblank)
1128    msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed')
1129    return
1130end
1131sizf=size(fileinput);
1132if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1133UserData.XmlInputFile=fileinput;
1134set(handles.geometry_calib,'UserData',UserData)%record current file foer further use of browser
1135
1136% -----------------------------------------------------------------------
1137function Heading=loadfile(handles,fileinput)
1138%------------------------------------------------------------------------
1139Heading=[];%default
1140[s,errormsg]=imadoc2struct(fileinput,'Heading','GeometryCalib');
1141if ~isempty(errormsg)
1142    msgbox_uvmat('ERROR',errormsg)
1143    return
1144end
1145if ~isempty(s.Heading)
1146    Heading=s.Heading;
1147end
1148
1149GeometryCalib=s.GeometryCalib;
1150fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
1151CoordCell={};
1152Tabchar={};%default
1153val_cal=1;%default
1154if ~isempty(GeometryCalib)
1155    % choose the calibration option
1156    if isfield(GeometryCalib,'CalibrationType')
1157        calib_list=get(handles.calib_type,'String');
1158        for ilist=1:numel(calib_list)
1159            if strcmp(calib_list{ilist},GeometryCalib.CalibrationType)
1160                val_cal=ilist;
1161                break
1162            end
1163        end
1164    end
1165    display_intrinsic(GeometryCalib,handles)%intrinsic param
1166    %extrinsic param
1167    if isfield(GeometryCalib,'Tx_Ty_Tz')
1168        Tx_Ty_Tz=GeometryCalib.Tx_Ty_Tz;
1169        set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
1170        set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
1171        set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
1172    end
1173    if isfield(GeometryCalib,'omc')
1174        set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
1175        set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
1176        set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
1177    end
1178    if isfield(GeometryCalib,'SourceCalib')&& isfield(GeometryCalib.SourceCalib,'PointCoord')
1179        calib=GeometryCalib.SourceCalib.PointCoord;
1180        Coord=[calib zeros(size(calib,1),1)];
1181        set(handles.ListCoord,'Data',Coord)
1182    end
1183    PLOT_Callback(handles.geometry_calib, [], handles)
1184    set(handles.APPLY,'BackgroundColor',[1 0 1])
1185end
1186set(handles.calib_type,'Value',val_cal)
1187
1188if isempty(CoordCell)% allow mouse action by default in the absence of input points
1189    set(handles.CheckEnableMouse,'Value',1)
1190    set(handles.CheckEnableMouse,'BackgroundColor',[1 1 0])
1191else % does not allow mouse action by default in the presence of input points
1192    set(handles.CheckEnableMouse,'Value',0)
1193    set(handles.CheckEnableMouse,'BackgroundColor',[0.7 0.7 0.7])
1194end
1195
1196%------------------------------------------------------------------------
1197%---display calibration intrinsic parameters
1198function display_intrinsic(GeometryCalib,handles)
1199%------------------------------------------------------------------------
1200fx=[];
1201fy=[];
1202if isfield(GeometryCalib,'fx_fy')
1203    fx=GeometryCalib.fx_fy(1);
1204    fy=GeometryCalib.fx_fy(2);
1205end
1206Cx_Cy=[0 0];%default
1207if isfield(GeometryCalib,'Cx_Cy')
1208    Cx_Cy=GeometryCalib.Cx_Cy;
1209end
1210kc=0;
1211if isfield(GeometryCalib,'kc')
1212    kc=GeometryCalib.kc; %* GeometryCalib.focal*GeometryCalib.focal;
1213end
1214set(handles.fx,'String',num2str(fx,5))
1215set(handles.fy,'String',num2str(fy,5))
1216set(handles.Cx,'String',num2str(Cx_Cy(1),'%1.1f'))
1217set(handles.Cy,'String',num2str(Cx_Cy(2),'%1.1f'))
1218set(handles.kc,'String',num2str(kc,'%1.4f'))
1219
1220
1221% --- Executes when user attempts to close geometry_calib.
1222function geometry_calib_CloseRequestFcn(hObject, eventdata, handles)
1223
1224delete(hObject); % closes the figure
1225
1226%------------------------------------------------------------------------
1227% --- Executes on button press in PLOT.
1228%------------------------------------------------------------------------
1229function PLOT_Callback(hObject, eventdata, handles)
1230huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
1231hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat
1232h_menu_coord=findobj(huvmat,'Tag','TransformName');
1233menu=get(h_menu_coord,'String');
1234choice=get(h_menu_coord,'Value');
1235option='';
1236if iscell(menu)
1237    option=menu{choice};
1238end
1239Coord=get(handles.ListCoord,'Data');
1240if ~isempty(Coord)
1241    if isequal(option,'phys')
1242        Coord_plot=Coord(:,1:3);
1243    elseif isempty(option);%optionoption,'px')||isequal(option,'')
1244        Coord_plot=Coord(:,4:5);
1245    else
1246        msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank or phys ')
1247    end
1248end
1249
1250set(0,'CurrentFigure',huvmat)
1251set(huvmat,'CurrentAxes',hhuvmat.PlotAxes)
1252hh=findobj('Tag','calib_points');
1253if  ~isempty(Coord) && isempty(hh)
1254    hh=line(Coord_plot(:,1),Coord_plot(:,2),'Color','m','Tag','calib_points','LineStyle','.','Marker','+','MarkerSize',10);
1255elseif isempty(Coord)%empty list of points, suppress the plot
1256    delete(hh)
1257else
1258    set(hh,'XData',Coord_plot(:,1))
1259    set(hh,'YData',Coord_plot(:,2))
1260end
1261pause(.1)
1262figure(handles.geometry_calib)
1263
1264%------------------------------------------------------------------------
1265% --- Executes on button press in Copy: display Coord on the Matlab work space
1266%------------------------------------------------------------------------
1267function Copy_Callback(hObject, eventdata, handles)
1268global Coord
1269evalin('base','global Coord')%make CurData global in the workspace
1270Coord=get(handles.ListCoord,'Data');
1271display('coordinates of calibration points (phys,px,marker) :')
1272evalin('base','Coord') %display CurData in the workspace
1273commandwindow; %brings the Matlab command window to the front
1274
1275%------------------------------------------------------------------------
1276% --- Executes when selected cell(s) is changed in ListCoord.
1277%------------------------------------------------------------------------
1278function ListCoord_CellSelectionCallback(hObject, eventdata, handles)
1279if ~isempty(eventdata.Indices)
1280    iline=eventdata.Indices(1);% selected line number
1281    set(handles.CoordLine,'String',num2str(iline))
1282     Data=get(handles.ListCoord,'Data');
1283     update_calib_marker(Data(iline,:))
1284end
1285
1286%------------------------------------------------------------------------
1287% --- Executes when entered data in editable cell(s) in ListCoord.
1288%------------------------------------------------------------------------
1289function ListCoord_CellEditCallback(hObject, eventdata, handles)
1290
1291Input=str2num(eventdata.EditData);%pasted input
1292Coord=get(handles.ListCoord,'Data');
1293iline=eventdata.Indices(1);% selected line number
1294if size(Coord,1)<iline+numel(Input)
1295    Coord=[Coord ; zeros(iline+numel(Input)-size(Coord,1),6)];% append zeros to fit the new column
1296end
1297Coord(iline:iline+numel(Input)-1,eventdata.Indices(2))=Input';
1298set(handles.ListCoord,'Data',Coord)
1299PLOT_Callback(hObject, eventdata, handles)
1300
1301%------------------------------------------------------------------------
1302% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
1303%------------------------------------------------------------------------
1304function ListCoord_KeyPressFcn(hObject, eventdata, handles)
1305iline=str2num(get(handles.CoordLine,'String'));
1306xx=double(get(handles.geometry_calib,'CurrentCharacter'));%get the keyboard character
1307if ismember(xx,[28 29 30 31])% directional arrow
1308    Coord=get(handles.ListCoord,'Data');
1309    switch xx
1310        case 30 % arrow upward
1311            iline=iline-1;
1312        case 31% arrow downward
1313            iline=iline+1;
1314    end
1315    if iline>=1 && iline<=size(Coord,1)
1316        set(handles.CoordLine,'String',num2str(iline))
1317        update_calib_marker(Coord(iline,1:5))% show the point corresponding to the selected line
1318    end
1319else
1320    set(handles.APPLY,'BackgroundColor',[1 0 1])% paint APPLY in magenta to indicate that the table content has be modified
1321end
1322
1323
1324%------------------------------------------------------------------------
1325% --- update the plot of calibration points
1326%------------------------------------------------------------------------
1327% draw a circle around the point defined by the input coordinates Coord as given by line in the table Listcoord
1328function update_calib_marker(Coord)
1329
1330%% read config on uvmat
1331huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
1332hhuvmat=guidata(huvmat);
1333hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');
1334if numel(Coord)<5
1335    if ~isempty(hhh)
1336        delete(hhh)%delete the circle marker in case of no valid input
1337    end
1338    return
1339end
1340menu=get(hhuvmat.TransformName,'String');
1341choice=get(hhuvmat.TransformName,'Value');
1342option='';
1343if iscell(menu)
1344    option=menu{choice};
1345end
1346
1347%% read appropriate coordinates (px or phys) in the table ListCoord
1348if isequal(option,'phys') % use phys coord
1349    XCoord=Coord(1);
1350    YCoord=Coord(2);
1351elseif isempty(option)% use coord in pixels
1352    XCoord=Coord(4);
1353    YCoord=Coord(5);
1354else
1355    msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be blank or phys ')
1356    return
1357end
1358
1359%% adjust the plot limits if needed
1360xlim=get(hhuvmat.PlotAxes,'XLim');
1361ylim=get(hhuvmat.PlotAxes,'YLim');
1362ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/25;%defines the size of the circle marker
1363check_xlim=0;
1364if XCoord>xlim(2)
1365    xlim=xlim+XCoord-xlim(2)+ind_range;% translate plot limit
1366    check_xlim=1;
1367elseif XCoord<xlim(1)
1368    xlim=xlim-XCoord+xlim(1)-ind_range;% translate plot limit
1369    check_xlim=1;
1370end
1371if check_xlim
1372    set(hhuvmat.PlotAxes,'XLim',xlim);
1373    set(hhuvmat.num_MaxX,'String',num2str(xlim(2)));
1374    set(hhuvmat.num_MinX,'String',num2str(xlim(1)));
1375end
1376check_ylim=0;
1377if YCoord>ylim(2)
1378    ylim=ylim+YCoord-ylim(2)+ind_range;% translate plot limit
1379    check_ylim=1;
1380elseif YCoord<ylim(1)
1381    ylim=ylim-YCoord+ylim(1)-ind_range;% translate plot limit
1382    check_ylim=1;
1383end
1384if check_ylim
1385    set(hhuvmat.PlotAxes,'YLim',ylim);
1386    set(hhuvmat.num_MaxY,'String',num2str(ylim(2)));
1387    set(hhuvmat.num_MinY,'String',num2str(ylim(1)));
1388end
1389
1390%% plot a circle around the selected point
1391if isempty(hhh)
1392    set(0,'CurrentFig',huvmat)
1393    set(huvmat,'CurrentAxes',hhuvmat.PlotAxes)
1394    rectangle('Curvature',[1 1],...
1395        'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range],'EdgeColor','m',...
1396        'LineStyle','-','Tag','calib_marker');
1397else
1398    set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
1399end
1400
1401%------------------------------------------------------------------------
1402% --- Executes on button press in ClearLine: remove the selected line in the table Coord
1403%------------------------------------------------------------------------
1404function ClearLine_Callback(hObject, eventdata, handles)
1405
1406Coord=get(handles.ListCoord,'Data');
1407iline=str2num(get(handles.CoordLine,'String'));
1408if isempty(iline)
1409    msgbox_uvmat('WARNING','no line suppressed, select a line in the table')
1410else
1411    answer=msgbox_uvmat('INPUT_Y-N',['suppress line ' num2str(iline) '?']);
1412    if isequal(answer,'Yes')
1413        Coord(iline,:)=[];
1414        set(handles.APPLY,'BackgroundColor',[1 0 1])
1415        set(handles.ListCoord,'Data',Coord);
1416        set(handles.CoordLine,'String','')
1417        PLOT_Callback(hObject,eventdata,handles)
1418        update_calib_marker([]);%remove circle marker
1419    end
1420end
1421
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