source: trunk/src/geometry_calib.m @ 630

Last change on this file since 630 was 630, checked in by sommeria, 8 years ago

generalisation of update_imadoc, improverment of the GUI get_field

File size: 55.4 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 29-Jul-2012 08:46:09
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})%
89set(hObject,'WindowButtonDownFcn',{'mouse_alt_gui',handles}) % allows mouse action with right button (zoom for uicontrol display)
90
91%% position
92set(0,'Unit','points')
93ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
94Width=350;% fig width in points (1/72 inch)
95Height=min(0.9*ScreenSize(4),700);
96Left=ScreenSize(3)- Width-40; %right edge close to the right, with margin=40
97Bottom=ScreenSize(4)-Height-40; %put fig at top right
98set(handles.geometry_calib,'Unit','points')
99set(handles.geometry_calib,'Position',[Left Bottom Width Height])
100
101% %set the position of the interface
102% if exist('pos','var')&& length(pos)>=4
103%     set(hObject,'Position',pos);
104% end
105
106%set menu of calibration options
107set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'})
108if exist('inputfile','var')&& ~isempty(inputfile)
109    struct.XmlInputFile=inputfile;
110    [RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(inputfile);
111    if ~strcmp(FileExt,'.xml')
112        inputfile=fullfile(RootPath,[SubDir '.xml']);%xml file corresponding to the input file
113        if ~exist(inputfile,'file')% case of civ files , removes the extension for subdir
114            inputfile=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
115            if ~exist(inputfile,'file')
116                inputfile=[fullfile(RootPath,SubDir,RootFile) '.xml'];%old convention
117                if ~exist(inputfile,'file')
118                    inputfile='';
119                end
120            end
121        end
122    end
123    set(handles.ListCoord,'String',{'......'})
124    if exist(inputfile,'file')
125        Heading=loadfile(handles,inputfile);% load data from the xml file
126        if isfield(Heading,'Campaign')&& ischar(Heading.Campaign)
127            struct.Campaign=Heading.Campaign;
128        end
129    end   
130    set(hObject,'UserData',struct)
131end
132
133set(handles.ListCoord,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function
134
135
136%------------------------------------------------------------------------
137% --- Outputs from this function are returned to the command line.
138function varargout = geometry_calib_OutputFcn(hObject, eventdata, handles)
139%------------------------------------------------------------------------
140% Get default command line output from handles structure
141varargout{1} = handles.output;
142varargout{2}=handles;
143%
144%------------------------------------------------------------------------
145% executed when closing: set the parent interface button to value 0
146function closefcn(gcbo,eventdata)
147%------------------------------------------------------------------------
148huvmat=findobj(allchild(0),'Name','uvmat');
149if ~isempty(huvmat)
150    handles=guidata(huvmat);
151    hobject=findobj(handles.PlotAxes,'tag','calib_points');
152    if ~isempty(hobject)
153        delete(hobject)
154    end
155    hobject=findobj(handles.PlotAxes,'tag','calib_marker');
156    if ~isempty(hobject)
157        delete(hobject)
158    end   
159end
160
161%------------------------------------------------------------------------
162% --- Executes on button press APPLY (used to launch the calibration).
163function APPLY_Callback(hObject, eventdata, handles)
164%------------------------------------------------------------------------
165%% look for the GUI uvmat and check for an image as input
166huvmat=findobj(allchild(0),'Name','uvmat');
167hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
168
169RootPath='';
170if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
171    RootPath=get(hhuvmat.RootPath,'String');
172    SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
173    outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
174else
175    question={'save the calibration data and point coordinates in'};
176    def={fullfile(RootPath,'ObjectCalib.xml')};
177    options.Resize='on';
178    answer=inputdlg(question,'',1,def,options);
179    outputfile=answer{1};
180end
181[GeometryCalib,index]=calibrate(handles,hhuvmat);% apply calibration
182
183%% copy the xml file from the old location if appropriate, then update with the calibration parameters
184if ~exist(outputfile,'file') && ~isempty(SubDirBase)
185    oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
186    if exist(oldxml,'file')
187        [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
188    end
189end
190errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file
191if ~strcmp(errormsg,'')
192    msgbox_uvmat('ERROR',errormsg);
193end
194
195%% display image with new calibration in the currently opened uvmat interface
196hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');% delete calib points and markers
197if ~isempty(hhh)
198    delete(hhh);
199end
200hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_points');
201if ~isempty(hhh)
202    delete(hhh);
203end
204set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off'
205set(hhuvmat.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
206UserData=get(handles.geometry_calib,'UserData');
207UserData.XmlInputFile=outputfile;%save the current xml file name
208set(handles.geometry_calib,'UserData',UserData)
209uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
210MenuPlot_Callback(hObject, eventdata, handles)
211set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
212ListCoord_Callback(hObject, eventdata, handles)
213figure(handles.geometry_calib)
214
215%------------------------------------------------------------------------
216% --- Executes on button press in REPLICATE
217function REPLICATE_Callback(hObject, eventdata, handles)
218%------------------------------------------------------------------------
219
220%% look for the GUI uvmat and check for an image as input
221huvmat=findobj(allchild(0),'Name','uvmat');
222hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
223GeometryCalib=calibrate(handles,hhuvmat);% apply calibration
224
225%% open the GUI browse_data
226CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
227if isfield(CalibData,'XmlInputFile')
228    InputDir=fileparts(fileparts(CalibData.XmlInputFile));
229end
230answer=msgbox_uvmat('INPUT_TXT','Campaign to calibrate?',InputDir);
231if strcmp(answer,'Cancel')
232    return
233end
234OutPut=browse_data(answer);
235nbcalib=0;
236for ilist=1:numel(OutPut.Experiment)
237    SubDirBase=regexprep(OutPut.Device{1},'\..+$','');
238    XmlName=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']);
239    % copy the xml file from the old location if appropriate, then update with the calibration parameters
240    if ~exist(XmlName,'file') && ~isempty(SubDirBase)
241        oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']);
242        if exist(oldxml,'file')
243            [success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention
244        end
245    end
246    errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file
247    if ~strcmp(errormsg,'')
248        msgbox_uvmat('ERROR',errormsg);
249    else
250        display([XmlName ' updated with calibration parameters'])
251        nbcalib=nbcalib+1;
252    end
253end
254msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']);
255
256%------------------------------------------------------------------------
257% --- activate calibration and store parameters in ouputfile .
258function [GeometryCalib,index]=calibrate(handles,hhuvmat)
259%------------------------------------------------------------------------
260%% read the current calibration points
261Coord_cell=get(handles.ListCoord,'String');
262Object=read_geometry_calib(Coord_cell);
263Coord=Object.Coord;
264% apply the calibration, whose type is selected in  handles.calib_type
265if ~isempty(Coord)
266    calib_cell=get(handles.calib_type,'String');
267    val=get(handles.calib_type,'Value');
268    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
269else
270    msgbox_uvmat('ERROR','No calibration points, abort')
271    return
272end
273Z_plane=[];
274if ~isempty(Coord)
275    %check error
276    X=Coord(:,1);
277    Y=Coord(:,2);
278    Z=Coord(:,3);
279    x_ima=Coord(:,4);
280    y_ima=Coord(:,5);
281    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
282    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
283    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
284    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
285    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
286    [tild,ind_dim]=max(GeometryCalib.ErrorMax);
287    index=index(ind_dim);
288    %set the Z position of the reference plane used for calibration
289    if isequal(max(Z),min(Z))%Z constant
290        Z_plane=Z(1);
291        GeometryCalib.NbSlice=1;
292        GeometryCalib.SliceCoord=[0 0 Z_plane];
293    end
294end
295%set the coordinate unit
296unitlist=get(handles.CoordUnit,'String');
297unit=unitlist{get(handles.CoordUnit,'value')};
298GeometryCalib.CoordUnit=unit;
299%record the points
300GeometryCalib.SourceCalib.PointCoord=Coord;
301display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
302
303% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
304set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
305set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
306set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
307set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
308set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
309set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
310
311%% store the calibration data, by default in the xml file of the currently displayed image
312UvData=get(hhuvmat.uvmat,'UserData');
313NbSlice_j=1;%default
314ZStart=Z_plane;
315ZEnd=Z_plane;
316volume_scan='n';
317if isfield(UvData,'XmlData')
318    if isfield(UvData.XmlData,'TranslationMotor')
319        NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice;
320        ZStart=UvData.XmlData.TranslationMotor.ZStart/10;
321        ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10;
322        volume_scan='y';
323    end
324end
325
326answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
327    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
328    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
329
330%% get plane position(s)
331if ~strcmp(answer,'Yes')
332    return
333end
334if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
335    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'};
336    input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}];
337    answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on');
338    GeometryCalib.NbSlice=str2double(answer{5});
339    GeometryCalib.VolumeScan=answer{6};
340    if isempty(answer)
341        Z_plane=0; %default
342    else
343        Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice);
344    end
345    GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
346    GeometryCalib.SliceAngle(:,3)=0;
347    GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise)
348    GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise)
349    GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})];
350    GeometryCalib.RefractionIndex=str2double(answer{4});
351end
352
353
354
355%------------------------------------------------------------------------
356% determine the parameters for a calibration by an affine function (rescaling and offset, no rotation)
357function GeometryCalib=calib_rescale(Coord,handles)
358%------------------------------------------------------------------------
359X=Coord(:,1);
360Y=Coord(:,2);% Z not used
361x_ima=Coord(:,4);
362y_ima=Coord(:,5);
363[px]=polyfit(X,x_ima,1);
364[py]=polyfit(Y,y_ima,1);
365% T_x=px(2);
366% T_y=py(2);
367GeometryCalib.CalibrationType='rescale';
368GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
369GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
370GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
371GeometryCalib.omc=[0 0 0];
372
373%------------------------------------------------------------------------
374% determine the parameters for a calibration by a linear transform matrix (rescale and rotation)
375
376
377function GeometryCalib=calib_linear(Coord,handles)
378%------------------------------------------------------------------------
379X=Coord(:,1);
380Y=Coord(:,2);% Z not used
381x_ima=Coord(:,4);
382y_ima=Coord(:,5);
383XY_mat=[ones(size(X)) X Y];
384a_X1=XY_mat\x_ima; %transformation matrix for X
385a_Y1=XY_mat\y_ima;%transformation matrix for X
386R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
387epsilon=sign(det(R));
388norm=abs(det(R));
389GeometryCalib.CalibrationType='linear';
390if (a_X1(2)/a_Y1(3))>0
391    GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm);
392else
393    GeometryCalib.fx_fy(1)=-sqrt(-(a_X1(2)/a_Y1(3))*norm);
394end
395GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
396GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
397GeometryCalib.Tx_Ty_Tz=[a_X1(1)/GeometryCalib.fx_fy(1) a_Y1(1)/GeometryCalib.fx_fy(2) 1];
398R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
399R(2,:)=R(2,:)/GeometryCalib.fx_fy(2);
400R=[R;[0 0]];
401GeometryCalib.R=[R [0;0;-epsilon]];
402GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
403
404%------------------------------------------------------------------------
405% determine the tsai parameters for a view normal to the grid plane
406% NOT USED
407function GeometryCalib=calib_normal(Coord,handles)
408%------------------------------------------------------------------------
409Calib.f1=str2num(get(handles.fx,'String'));
410Calib.f2=str2num(get(handles.fy,'String'));
411Calib.k=str2num(get(handles.kc,'String'));
412Calib.Cx=str2num(get(handles.Cx,'String'));
413Calib.Cy=str2num(get(handles.Cy,'String'));
414%default
415if isempty(Calib.f1)
416    Calib.f1=25/0.012;
417end
418if isempty(Calib.f2)
419    Calib.f2=25/0.012;
420end
421if isempty(Calib.k)
422    Calib.k=0;
423end
424if isempty(Calib.Cx)||isempty(Calib.Cy)
425    huvmat=findobj(allchild(0),'Tag','uvmat');
426    hhuvmat=guidata(huvmat);
427    Calib.Cx=str2num(get(hhuvmat.num_Npx,'String'))/2;
428    Calib.Cx=str2num(get(hhuvmat.num_Npy,'String'))/2;
429end   
430%tsai parameters
431Calib.dpx=0.012;%arbitrary
432Calib.dpy=0.012;
433Calib.sx=Calib.f1*Calib.dpx/(Calib.f2*Calib.dpy);
434Calib.f=Calib.f2*Calib.dpy;
435Calib.kappa1=Calib.k/(Calib.f*Calib.f);
436
437%initial guess
438X=Coord(:,1);
439Y=Coord(:,2);
440Zmean=mean(Coord(:,3));
441x_ima=Coord(:,4)-Calib.Cx;
442y_ima=Coord(:,5)-Calib.Cy;
443XY_mat=[ones(size(X)) X Y];
444a_X1=XY_mat\x_ima; %transformation matrix for X
445a_Y1=XY_mat\y_ima;%transformation matrix for Y
446R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,-1];% rotation+ z axis reversal (upward)
447norm=sqrt(det(-R));
448calib_param(1)=0;% quadratic distortion
449calib_param(2)=a_X1(1);
450calib_param(3)=a_Y1(1);
451calib_param(4)=Calib.f/(norm*Calib.dpx)-R(3,3)*Zmean;
452calib_param(5)=angle(a_X1(2)+1i*a_X1(3));
453display(['initial guess=' num2str(calib_param)])
454
455%optimise the parameters: minimisation of error
456calib_param = fminsearch(@(calib_param) error_calib(calib_param,Calib,Coord),calib_param);
457
458GeometryCalib.CalibrationType='tsai_normal';
459GeometryCalib.focal=Calib.f;
460GeometryCalib.dpx_dpy=[Calib.dpx Calib.dpy];
461GeometryCalib.Cx_Cy=[Calib.Cx Calib.Cy];
462GeometryCalib.sx=Calib.sx;
463GeometryCalib.kappa1=calib_param(1);
464GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
465GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)];
466alpha=calib_param(5);
467GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
468
469%------------------------------------------------------------------------
470function GeometryCalib=calib_3D_linear(Coord,handles)
471%------------------------------------------------------------------
472path_uvmat=which('uvmat');% check the path detected for source file uvmat
473path_UVMAT=fileparts(path_uvmat); %path to UVMAT
474huvmat=findobj(allchild(0),'Tag','uvmat');
475hhuvmat=guidata(huvmat);
476coord_files=get(handles.coord_files,'String');
477if ischar(coord_files)
478    coord_files={coord_files};
479end
480if isempty(coord_files{1}) || isequal(coord_files,{''})
481    coord_files={};
482end
483%retrieve the calibration points stored in the files listed in the popup list coord_files
484x_1=Coord(:,4:5)';%px coordinates of the ref points
485nx=str2num(get(hhuvmat.num_Npx,'String'));
486ny=str2num(get(hhuvmat.num_Npy,'String'));
487x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
488X_1=Coord(:,1:3)';%phys coordinates of the ref points
489n_ima=numel(coord_files)+1;
490if ~isempty(coord_files)
491    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
492    for ifile=1:numel(coord_files)
493    t=xmltree(coord_files{ifile});
494    s=convert(t);%convert to matlab structure
495        if isfield(s,'GeometryCalib')
496            if isfield(s.GeometryCalib,'SourceCalib')
497                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
498                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
499                Coord_file=zeros(length(PointCoord),5);%default
500                for i=1:length(PointCoord)
501                    line=str2num(PointCoord{i});
502                    Coord_file(i,4:5)=line(4:5);%px x
503                    Coord_file(i,1:3)=line(1:3);%phys x
504                end
505                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
506                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
507                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
508                end
509            end
510        end
511    end
512end
513n_ima=numel(coord_files)+1;
514est_dist=[0;0;0;0;0];
515est_aspect_ratio=0;
516est_fc=[1;1];
517%fc=[25;25]/0.012;
518center_optim=0;
519run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
520GeometryCalib.CalibrationType='3D_linear';
521GeometryCalib.fx_fy=fc';
522%GeometryCalib.focal=fc(2);
523%GeometryCalib.dpx_dpy=[1 1];
524GeometryCalib.Cx_Cy=cc';
525%GeometryCalib.sx=fc(1)/fc(2);
526GeometryCalib.kc=kc(1);
527%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
528GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
529GeometryCalib.Tx_Ty_Tz=Tc_1';
530GeometryCalib.R=Rc_1;
531GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
532GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
533GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
534GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
535GeometryCalib.ErrorRMS=[];
536GeometryCalib.ErrorMax=[];
537
538%------------------------------------------------------------------------
539function GeometryCalib=calib_3D_quadr(Coord,handles)
540%------------------------------------------------------------------
541
542path_uvmat=which('uvmat');% check the path detected for source file uvmat
543path_UVMAT=fileparts(path_uvmat); %path to UVMAT
544huvmat=findobj(allchild(0),'Tag','uvmat');
545hhuvmat=guidata(huvmat);
546% check_cond=0;
547coord_files=get(handles.coord_files,'String');
548if ischar(coord_files)
549    coord_files={coord_files};
550end
551if isempty(coord_files{1}) || isequal(coord_files,{''})
552    coord_files={};
553end
554
555%retrieve the calibration points stored in the files listed in the popup list coord_files
556x_1=Coord(:,4:5)';%px coordinates of the ref points
557nx=str2num(get(hhuvmat.num_Npx,'String'));
558ny=str2num(get(hhuvmat.num_Npy,'String'));
559x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
560X_1=Coord(:,1:3)';%phys coordinates of the ref points
561n_ima=numel(coord_files)+1;
562if ~isempty(coord_files)
563    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
564    for ifile=1:numel(coord_files)
565    t=xmltree(coord_files{ifile});
566    s=convert(t);%convert to matlab structure
567        if isfield(s,'GeometryCalib')
568            if isfield(s.GeometryCalib,'SourceCalib')
569                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
570                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
571                Coord_file=zeros(length(PointCoord),5);%default
572                for i=1:length(PointCoord)
573                    line=str2num(PointCoord{i});
574                    Coord_file(i,4:5)=line(4:5);%px x
575                    Coord_file(i,1:3)=line(1:3);%phys x
576                end
577                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
578                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
579                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
580                end
581            end
582        end
583    end
584end
585n_ima=numel(coord_files)+1;
586est_dist=[1;0;0;0;0];
587est_aspect_ratio=1;
588%est_fc=[0;0];
589%fc=[25;25]/0.012;
590center_optim=0;
591run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
592
593GeometryCalib.CalibrationType='3D_quadr';
594GeometryCalib.fx_fy=fc';
595%GeometryCalib.focal=fc(2);
596%GeometryCalib.dpx_dpy=[1 1];
597GeometryCalib.Cx_Cy=cc';
598%GeometryCalib.sx=fc(1)/fc(2);
599GeometryCalib.kc=kc(1);
600%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
601GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
602GeometryCalib.Tx_Ty_Tz=Tc_1';
603GeometryCalib.R=Rc_1;
604GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
605GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
606GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
607GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
608GeometryCalib.ErrorRMS=[];
609GeometryCalib.ErrorMax=[];
610
611
612%------------------------------------------------------------------------
613function GeometryCalib=calib_3D_extrinsic(Coord,handles)
614%------------------------------------------------------------------
615path_uvmat=which('geometry_calib');% check the path detected for source file uvmat
616path_UVMAT=fileparts(path_uvmat); %path to UVMAT
617x_1=double(Coord(:,4:5)');%image coordiantes
618X_1=double(Coord(:,1:3)');% phys coordinates
619huvmat=findobj(allchild(0),'Tag','uvmat');
620hhuvmat=guidata(huvmat);
621ny=str2double(get(hhuvmat.num_Npy,'String'));
622x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
623n_ima=1;
624GeometryCalib.CalibrationType='3D_extrinsic';
625GeometryCalib.fx_fy(1)=str2num(get(handles.fx,'String'));
626GeometryCalib.fx_fy(2)=str2num(get(handles.fy,'String'));
627GeometryCalib.Cx_Cy(1)=str2num(get(handles.Cx,'String'));
628GeometryCalib.Cx_Cy(2)=str2num(get(handles.Cy,'String'));
629GeometryCalib.kc=str2num(get(handles.kc,'String'));
630fct_path=fullfile(path_UVMAT,'toolbox_calib');
631addpath(fct_path)
632GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate)
633% [omc1,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
634%     [Calib.f Calib.f*Calib.sx]',...
635%     [Calib.Cx Calib.Cy]',...
636%     [-Calib.kappa1*Calib.f^2 0 0 0 0]);
637[omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
638    (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]);
639rmpath(fct_path);
640GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
641GeometryCalib.Tx_Ty_Tz=Tc1';
642%inversion of z axis
643GeometryCalib.R=Rc1;
644GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
645GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
646GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
647GeometryCalib.omc=(180/pi)*omc';
648%GeometryCalib.R(3,1:3)=-GeometryCalib.R(3,1:3);%inversion for z upward
649
650
651
652%------------------------------------------------------------------------
653%function GeometryCalib=calib_tsai_heikkila(Coord)
654% TEST: NOT IMPLEMENTED
655%------------------------------------------------------------------
656% path_uvmat=which('uvmat');% check the path detected for source file uvmat
657% path_UVMAT=fileparts(path_uvmat); %path to UVMAT
658% path_calib=fullfile(path_UVMAT,'toolbox_calib_heikkila');
659% addpath(path_calib)
660% npoints=size(Coord,1);
661% Coord(:,1:3)=10*Coord(:,1:3);
662% Coord=[Coord zeros(npoints,2) -ones(npoints,1)];
663% [par,pos,iter,res,er,C]=cacal('dalsa',Coord);
664% GeometryCalib.CalibrationType='tsai';
665% GeometryCalib.focal=par(2);
666
667
668%------------------------------------------------------------------------
669% --- determine the rms of calibration error
670function ErrorRms=error_calib(calib_param,Calib,Coord)
671%calib_param: vector of free calibration parameters (to optimise)
672%Calib: structure of the given calibration parameters
673%Coord: list of phys coordinates (columns 1-3, and pixel coordinates (columns 4-5)
674Calib.f=25;
675Calib.dpx=0.012;
676Calib.dpy=0.012;
677Calib.sx=1;
678Calib.Cx=512;
679Calib.Cy=512;
680Calib.kappa1=calib_param(1);
681Calib.Tx=calib_param(2);
682Calib.Ty=calib_param(3);
683Calib.Tz=calib_param(4);
684alpha=calib_param(5);
685Calib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
686
687X=Coord(:,1);
688Y=Coord(:,2);
689Z=Coord(:,3);
690x_ima=Coord(:,4);
691y_ima=Coord(:,5);
692[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z);
693ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
694ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
695ErrorRms=mean(ErrorRms);
696
697%------------------------------------------------------------------------
698function XImage_Callback(hObject, eventdata, handles)
699%------------------------------------------------------------------------
700update_list(hObject, eventdata,handles)
701
702%------------------------------------------------------------------------
703function YImage_Callback(hObject, eventdata, handles)
704%------------------------------------------------------------------------
705update_list(hObject, eventdata,handles)
706
707%------------------------------------------------------------------------
708% --- Executes on button press in STORE.
709function STORE_Callback(hObject, eventdata, handles)
710Coord_cell=get(handles.ListCoord,'String');
711Object=read_geometry_calib(Coord_cell);
712unitlist=get(handles.CoordUnit,'String');
713unit=unitlist{get(handles.CoordUnit,'value')};
714GeometryCalib.CoordUnit=unit;
715GeometryCalib.SourceCalib.PointCoord=Object.Coord;
716huvmat=findobj(allchild(0),'Name','uvmat');
717hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
718% RootPath='';
719% RootFile='';
720if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
721%     testhandle=1;
722    RootPath=get(hhuvmat.RootPath,'String');
723    RootFile=get(hhuvmat.RootFile,'String');
724    filebase=fullfile(RootPath,RootFile);
725    while exist([filebase '.xml'],'file')
726        filebase=[filebase '~'];
727    end
728    outputfile=[filebase '.xml'];
729    errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');
730    if ~strcmp(errormsg,'')
731        msgbox_uvmat('ERROR',errormsg);
732    end
733    listfile=get(handles.coord_files,'string');
734    if isequal(listfile,{''})
735        listfile={outputfile};
736    else
737        listfile=[listfile;{outputfile}];%update the list of coord files
738    end
739    set(handles.coord_files,'string',listfile);
740end
741set(handles.ListCoord,'Value',1)% refresh the display of coordinates
742set(handles.ListCoord,'String',{'......'})
743
744% --------------------------------------------------------------------
745% --- Executes on button press in CLEAR_PTS: clear the list of calibration points
746function CLEAR_PTS_Callback(hObject, eventdata, handles)
747% --------------------------------------------------------------------
748set(handles.ListCoord,'Value',1)% refresh the display of coordinates
749set(handles.ListCoord,'String',{'......'})
750MenuPlot_Callback(hObject, eventdata, handles)
751
752%------------------------------------------------------------------------
753% --- Executes on button press in CLEAR.
754function CLEAR_Callback(hObject, eventdata, handles)
755%------------------------------------------------------------------------
756set(handles.coord_files,'Value',1)
757set(handles.coord_files,'String',{''})
758
759%------------------------------------------------------------------------
760function XObject_Callback(hObject, eventdata, handles)
761%------------------------------------------------------------------------
762update_list(hObject, eventdata,handles)
763
764%------------------------------------------------------------------------
765function YObject_Callback(hObject, eventdata, handles)
766%------------------------------------------------------------------------
767update_list(hObject, eventdata,handles)
768
769%------------------------------------------------------------------------
770function ZObject_Callback(hObject, eventdata, handles)
771%------------------------------------------------------------------------
772update_list(hObject, eventdata,handles)
773
774%------------------------------------------------------------------------
775function update_list(hObject, eventdata, handles)
776%------------------------------------------------------------------------
777newval(4)=str2double(get(handles.XImage,'String'));
778newval(5)=str2double(get(handles.YImage,'String'));
779newval(1)=str2double(get(handles.XObject,'String'));
780newval(2)=str2double(get(handles.YObject,'String'));
781newval(3)=str2double(get(handles.ZObject,'String'));
782if isnan(newval(3))
783    newval(3)=0;%put z to 0 by default
784end
785Coord=get(handles.ListCoord,'String');
786Coord(end)=[]; %remove last string '.....'
787val=get(handles.ListCoord,'Value');
788data=read_geometry_calib(Coord);
789data.Coord(val,:)=newval;
790for i=1:size(data.Coord,1)
791    for j=1:5
792          Coord_cell{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
793    end
794end
795
796Tabchar=cell2tab(Coord_cell,' | ');
797Tabchar=[Tabchar ;{'......'}];
798set(handles.ListCoord,'String',Tabchar)
799
800%update the plot
801ListCoord_Callback(hObject, eventdata, handles)
802MenuPlot_Callback(hObject, eventdata, handles)
803
804%------------------------------------------------------------------------
805% --- Executes on selection change in ListCoord.
806function ListCoord_Callback(hObject, eventdata, handles)
807%------------------------------------------------------------------------
808huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
809hplot=findobj(huvmat,'Tag','PlotAxes');%main plotting axis of uvmat
810hhh=findobj(hplot,'Tag','calib_marker');
811Coord_cell=get(handles.ListCoord,'String');
812val=get(handles.ListCoord,'Value');
813if numel(val)>1
814    return %no action if several lines have been selected
815end
816coord_str=Coord_cell{val};
817k=findstr(' | ',coord_str);
818if isempty(k)%last line '.....' selected
819    if ~isempty(hhh)
820        delete(hhh)%delete the circle marker
821    end
822    return
823end
824%fill the edit boxe
825set(handles.XObject,'String',coord_str(1:k(1)-1))
826set(handles.YObject,'String',coord_str(k(1)+3:k(2)-1))
827set(handles.ZObject,'String',coord_str(k(2)+3:k(3)-1))
828set(handles.XImage,'String',coord_str(k(3)+3:k(4)-1))
829set(handles.YImage,'String',coord_str(k(4)+3:end))
830h_menu_coord=findobj(huvmat,'Tag','TransformName');
831menu=get(h_menu_coord,'String');
832choice=get(h_menu_coord,'Value');
833if iscell(menu)
834    option=menu{choice};
835else
836    option='px'; %default
837end
838if isequal(option,'phys')
839    XCoord=str2double(coord_str(1:k(1)-1));
840    YCoord=str2double(coord_str(k(1)+3:k(2)-1));
841elseif isequal(option,'px')|| isequal(option,'')
842    XCoord=str2double(coord_str(k(3)+3:k(4)-1));
843    YCoord=str2double(coord_str(k(4)+3:end));
844else
845    msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be px or phys ')
846end
847if isempty(XCoord)||isempty(YCoord)
848     if ~isempty(hhh)
849        delete(hhh)%delete the circle marker
850    end
851    return
852end
853xlim=get(hplot,'XLim');
854ylim=get(hplot,'YLim');
855ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/20;%defines the size of the circle marker
856if isempty(hhh)
857    set(0,'CurrentFig',huvmat)
858    set(huvmat,'CurrentAxes',hplot)
859    rectangle('Curvature',[1 1],...
860              'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range],'EdgeColor','m',...
861              'LineStyle','-','Tag','calib_marker');
862else
863    set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
864end
865
866%------------------------------------------------------------------------
867% --- Executes on selection change in edit_append.
868function edit_append_Callback(hObject, eventdata, handles)
869%------------------------------------------------------------------------
870choice=get(handles.edit_append,'Value');
871if choice
872    set(handles.edit_append,'BackgroundColor',[1 1 0])
873    huvmat=findobj(allchild(0),'tag','uvmat');
874    if ishandle(huvmat)
875        hhuvmat=guidata(huvmat);
876        set(hhuvmat.edit_object,'Value',0)
877        set(hhuvmat.edit_object,'BackgroundColor',[0.7 0.7 0.7])
878    end
879else
880    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
881end
882   
883function NEW_Callback(hObject, eventdata, handles)
884%A METTRE SOUS UN BOUTON
885huvmat=findobj(allchild(0),'Name','uvmat');
886hchild=get(huvmat,'children');
887hcoord=findobj(hchild,'Tag','menu_coord');
888coordtype=get(hcoord,'Value');
889haxes=findobj(hchild,'Tag','axes3');
890AxeData=get(haxes,'UserData');
891if ~isequal(hcoord,2)
892    set(hcoord,'Value',2)
893    huvmat=uvmat(AxeData);
894    'relancer uvmat';
895end
896if ~isfield(AxeData,'ZoomAxes')
897    msgbox_uvmat('ERROR','first draw a window around a grid marker')
898    return
899end
900XLim=get(AxeData.ZoomAxes,'XLim');
901YLim=get(AxeData.ZoomAxes,'YLim');
902np=size(AxeData.A);
903ind_sub_x=round(XLim);
904ind_sub_y=np(1)-round(YLim);
905Mfiltre=AxeData.A(ind_sub_y(2):ind_sub_y(1) ,ind_sub_x,:);
906Mfiltre_norm=double(Mfiltre);
907Mfiltre_norm=Mfiltre_norm/sum(sum(Mfiltre_norm));
908Mfiltre_norm=100*(Mfiltre_norm-mean(mean(Mfiltre_norm)));
909Atype=class(AxeData.A);
910Data.NbDim=2;
911Data.A=filter2(Mfiltre_norm,double(AxeData.A));
912Data.A=feval(Atype,Data.A);
913Data.AName='image';
914Data.AX=AxeData.AX;
915Data.AY=AxeData.AY;
916Data.CoordType='px';
917plot_field(Data)
918
919%------------------------------------------------------------------------
920function MenuPlot_Callback(hObject, eventdata, handles)
921%------------------------------------------------------------------------
922huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
923%UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface
924hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat
925%hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
926h_menu_coord=findobj(huvmat,'Tag','TransformName');
927menu=get(h_menu_coord,'String');
928choice=get(h_menu_coord,'Value');
929if iscell(menu)
930    option=menu{choice};
931else
932    option='px'; %default
933end
934Coord_cell=get(handles.ListCoord,'String');
935ObjectData=read_geometry_calib(Coord_cell);
936%ObjectData=read_geometry_calib(handles);%read the interface input parameters defining the object
937if ~isempty(ObjectData.Coord)
938    if isequal(option,'phys')
939        ObjectData.Coord=ObjectData.Coord(:,1:3);
940    elseif isequal(option,'px')||isequal(option,'')
941        ObjectData.Coord=ObjectData.Coord(:,4:5);
942    else
943        msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be '''', px or phys ')
944    end
945end
946
947set(0,'CurrentFigure',huvmat)
948set(huvmat,'CurrentAxes',hhuvmat.PlotAxes)
949hh=findobj('Tag','calib_points');
950if  ~isempty(ObjectData.Coord) && isempty(hh)
951    hh=line(ObjectData.Coord(:,1),ObjectData.Coord(:,2),'Color','m','Tag','calib_points','LineStyle','.','Marker','+');
952elseif isempty(ObjectData.Coord)%empty list of points, suppress the plot
953    delete(hh)
954else
955    set(hh,'XData',ObjectData.Coord(:,1))
956    set(hh,'YData',ObjectData.Coord(:,2))
957end
958pause(.1)
959figure(handles.geometry_calib)
960
961% --------------------------------------------------------------------
962function MenuHelp_Callback(hObject, eventdata, handles)
963path_to_uvmat=which('uvmat');% check the path of uvmat
964pathelp=fileparts(path_to_uvmat);
965helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
966if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
967else
968   addpath (fullfile(pathelp,'uvmat_doc'))
969   web([helpfile '#geometry_calib'])
970end
971
972%------------------------------------------------------------------------
973function MenuCreateGrid_Callback(hObject, eventdata, handles)
974%------------------------------------------------------------------------
975%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
976CalibData=get(handles.geometry_calib,'UserData');
977Tinput=[];%default
978if isfield(CalibData,'grid')
979    Tinput=CalibData.grid;
980end
981[T,CalibData.grid]=create_grid(Tinput);%display the GUI create_grid
982set(handles.geometry_calib,'UserData',CalibData)
983
984%grid in phys space
985Coord=get(handles.ListCoord,'String');
986val=get(handles.ListCoord,'Value');
987data=read_geometry_calib(Coord);
988%nbpoints=size(data.Coord,1); %nbre of calibration points
989data.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
990% for i=1:nbpoints
991%    for j=1:5
992%           Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
993%    end
994% end
995%update the phys coordinates starting from the selected point (down in the
996Coord(end,:)=[]; %remove last string '.....'
997for i=1:size(data.Coord,1)
998    for j=1:5
999          Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
1000    end
1001end
1002
1003%size(data.Coord,1)
1004Tabchar=cell2tab(Coord,' | ');
1005Tabchar=[Tabchar ;{'......'}];
1006set(handles.ListCoord,'String',Tabchar)
1007
1008% -----------------------------------------------------------------------
1009% --- automatic grid dectection from local maxima of the images
1010function MenuDetectGrid_Callback(hObject, eventdata, handles)
1011%------------------------------------------------------------------------
1012%% read the four last point coordinates in pixels
1013Coord_cell=get(handles.ListCoord,'String');%read list of coordinates on geometry_calib
1014data=read_geometry_calib(Coord_cell);
1015nbpoints=size(data.Coord,1); %nbre of calibration points
1016if nbpoints~=4
1017    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')
1018    return
1019end
1020corners_X=(data.Coord(end:-1:end-3,4)); %pixel absissa of the four corners
1021corners_Y=(data.Coord(end:-1:end-3,5));
1022
1023%reorder the last two points (the two first in the list) if needed
1024angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1)));
1025if abs(angles(4)-angles(2))>abs(angles(3)-angles(2))
1026      X_end=corners_X(4);
1027      Y_end=corners_Y(4);
1028      corners_X(4)=corners_X(3);
1029      corners_Y(4)=corners_Y(3);
1030      corners_X(3)=X_end;
1031      corners_Y(3)=Y_end;
1032end
1033
1034%% initiate the grid
1035CalibData=get(handles.geometry_calib,'UserData');%get information stored on the GUI geometry_calib
1036grid_input=[];%default
1037if isfield(CalibData,'grid')
1038    grid_input=CalibData.grid;%retrieve the previously used grid
1039end
1040[T,CalibData.grid,white_test]=create_grid(grid_input,'detect_grid');%display the GUI create_grid, read the set of phys coordinates T
1041set(handles.geometry_calib,'UserData',CalibData)%store the phys grid parameters for later use
1042
1043
1044
1045%% read the current image, displayed in the GUI uvmat
1046huvmat=findobj(allchild(0),'Name','uvmat');
1047UvData=get(huvmat,'UserData');
1048A=UvData.Field.A;
1049npxy=size(A);
1050X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates (cm)
1051Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates (cm)
1052
1053%calculate transform matrices for plane projection
1054% reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
1055B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
1056      zeros(4,3)        X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ];
1057B = reshape (B', 8 , 8 )';
1058D = [ corners_X , corners_Y ];
1059D = reshape (D', 8 , 1 );
1060l = (B' * B)\B' * D;
1061Amat = reshape([l(1:6)' 0 0 1 ],3,3)';
1062C = [l(7:8)' 1];
1063
1064% transform grid image into 'phys' coordinates
1065GeometryCalib.CalibrationType='linear';
1066GeometryCalib.fx_fy=[1 1];
1067GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
1068GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
1069GeometryCalib.CoordUnit='cm';
1070path_uvmat=which('uvmat');% check the path detected for source file uvmat
1071path_UVMAT=fileparts(path_uvmat); %path to UVMAT
1072addpath(fullfile(path_UVMAT,'transform_field'))
1073Data.ListVarName={'AY','AX','A'};
1074Data.VarDimName={'AY','AX',{'AY','AX'}};
1075if ndims(A)==3
1076    A=mean(A,3);
1077end
1078Data.A=A-min(min(A));
1079Data.AY=[npxy(1)-0.5 0.5];
1080Data.AX=[0.5 npxy(2)];
1081Data.CoordUnit='pixel';
1082Calib.GeometryCalib=GeometryCalib;
1083DataOut=phys(Data,Calib);
1084rmpath(fullfile(path_UVMAT,'transform_field'))
1085Amod=DataOut.A;
1086Rangx=DataOut.AX;
1087Rangy=DataOut.AY;
1088if white_test
1089    Amod=double(Amod);%case of white grid markers: will look for image maxima
1090else
1091    Amod=-double(Amod);%case of black grid markers: will look for image minima
1092end
1093% figure(12) %display corrected image
1094% Amax=max(max(Amod));
1095% image(Rangx,Rangy,uint8(255*Amod/Amax))
1096
1097%% detection of local image extrema in each direction
1098Dx=(Rangx(2)-Rangx(1))/(npxy(2)-1); %x mesh in real space
1099Dy=(Rangy(2)-Rangy(1))/(npxy(1)-1); %y mesh in real space
1100ind_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
1101ind_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
1102nbpoints=size(T,1);
1103for ipoint=1:nbpoints
1104    i0=1+round((T(ipoint,1)-Rangx(1))/Dx);%round(Xpx(ipoint));
1105    j0=1+round((T(ipoint,2)-Rangy(1))/Dy);%round(Xpx(ipoint));
1106    j0min=max(j0-ind_range_y,1);
1107    j0max=min(j0+ind_range_y,size(Amod,1));
1108    i0min=max(i0-ind_range_x,1);
1109    i0max=min(i0+ind_range_x,size(Amod,2));
1110    Asub=Amod(j0min:j0max,i0min:i0max);
1111    x_profile=sum(Asub,1);
1112    y_profile=sum(Asub,2);
1113    [Amax,ind_x_max]=max(x_profile);
1114    [Amax,ind_y_max]=max(y_profile);
1115    %sub-pixel improvement using moments
1116    x_shift=0;
1117    y_shift=0;
1118    if ind_x_max+2<=numel(x_profile) && ind_x_max-2>=1
1119        Atop=x_profile(ind_x_max-2:ind_x_max+2);
1120        x_shift=sum(Atop.*[-2 -1 0 1 2])/sum(Atop);
1121    end
1122    if ind_y_max+2<=numel(y_profile) && ind_y_max-2>=1
1123        Atop=y_profile(ind_y_max-2:ind_y_max+2);
1124        y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop);
1125    end
1126    Delta(ipoint,1)=(x_shift+ind_x_max+i0min-i0-1)*Dx;%shift from the initial guess
1127    Delta(ipoint,2)=(y_shift+ind_y_max+j0min-j0-1)*Dy;
1128end
1129Tmod=T(:,(1:2))+Delta;
1130[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));
1131for ipoint=1:nbpoints
1132     Coord{ipoint,1}=num2str(T(ipoint,1),4);%display coordiantes with 4 digits
1133     Coord{ipoint,2}=num2str(T(ipoint,2),4);%display coordiantes with 4 digits
1134     Coord{ipoint,3}=num2str(T(ipoint,3),4);%display coordiantes with 4 digits;
1135     Coord{ipoint,4}=num2str(Xpx(ipoint),4);%display coordiantes with 4 digits
1136     Coord{ipoint,5}=num2str(Ypx(ipoint),4);%display coordiantes with 4 digits
1137end
1138Tabchar=cell2tab(Coord(end:-1:1,:),' | ');
1139Tabchar=[Tabchar ;{'......'}];
1140set(handles.ListCoord,'Value',1)
1141set(handles.ListCoord,'String',Tabchar)
1142MenuPlot_Callback(hObject, eventdata, handles)
1143
1144%-----------------------------------------------------------------------
1145function MenuTranslatePoints_Callback(hObject, eventdata, handles)
1146%-----------------------------------------------------------------------
1147%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1148CalibData=get(handles.geometry_calib,'UserData');
1149Tinput=[];%default
1150if isfield(CalibData,'translate')
1151    Tinput=CalibData.translate;
1152end
1153T=translate_points(Tinput);%display translate_points GUI and get shift parameters
1154CalibData.translate=T;
1155set(handles.geometry_calib,'UserData',CalibData)
1156%translation
1157Coord_cell=get(handles.ListCoord,'String');
1158data=read_geometry_calib(Coord_cell);
1159data.Coord(:,1)=T(1)+data.Coord(:,1);
1160data.Coord(:,2)=T(2)+data.Coord(:,2);
1161data.Coord(:,3)=T(3)+data.Coord(:,3);
1162data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1163for i=1:size(data.Coord,1)
1164    for j=1:5
1165          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1166   end
1167end
1168Tabchar=cell2tab(Coord,' | ');
1169Tabchar=[Tabchar; {'.....'}];
1170%set(handles.ListCoord,'Value',1)
1171set(handles.ListCoord,'String',Tabchar)
1172
1173
1174% --------------------------------------------------------------------
1175function MenuRotatePoints_Callback(hObject, eventdata, handles)
1176%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1177CalibData=get(handles.geometry_calib,'UserData');
1178Tinput=[];%default
1179if isfield(CalibData,'rotate')
1180    Tinput=CalibData.rotate;
1181end
1182T=rotate_points(Tinput);%display rotate_points GUI to introduce rotation parameters
1183CalibData.rotate=T;
1184set(handles.geometry_calib,'UserData',CalibData)
1185%-----------------------------------------------------
1186%rotation
1187Phi=T(1);
1188O_x=0;%default
1189O_y=0;%default
1190if numel(T)>=2
1191    O_x=T(2);%default
1192end
1193if numel(T)>=3
1194    O_y=T(3);%default
1195end
1196Coord_cell=get(handles.ListCoord,'String');
1197data=read_geometry_calib(Coord_cell);
1198r1=cos(pi*Phi/180);
1199r2=-sin(pi*Phi/180);
1200r3=sin(pi*Phi/180);
1201r4=cos(pi*Phi/180);
1202x=data.Coord(:,1)-O_x;
1203y=data.Coord(:,2)-O_y;
1204data.Coord(:,1)=r1*x+r2*y;
1205data.Coord(:,2)=r3*x+r4*y;
1206% data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1207for i=1:size(data.Coord,1)
1208    for j=1:5
1209          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1210   end
1211end
1212Tabchar=cell2tab(Coord,' | ');
1213Tabchar=[Tabchar;{'......'}];
1214set(handles.ListCoord,'Value',1)
1215set(handles.ListCoord,'String',Tabchar)
1216
1217% --------------------------------------------------------------------
1218function MenuImportPoints_Callback(hObject, eventdata, handles)
1219fileinput=browse_xml(hObject, eventdata, handles);
1220if isempty(fileinput)
1221    return
1222end
1223[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1224GeometryCalib=s.GeometryCalib;
1225%GeometryCalib=load_calib(hObject, eventdata, handles)
1226calib=reshape(GeometryCalib.PointCoord,[],1);
1227for ilist=1:numel(calib)
1228    CoordCell{ilist}=num2str(calib(ilist));
1229end
1230CoordCell=reshape(CoordCell,[],5);
1231Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
1232Tabchar=[Tabchar;{'......'}];
1233set(handles.ListCoord,'Value',1)
1234set(handles.ListCoord,'String',Tabchar)
1235MenuPlot_Callback(handles.geometry_calib, [], handles)
1236
1237% -----------------------------------------------------------------------
1238function MenuImportIntrinsic_Callback(hObject, eventdata, handles)
1239%------------------------------------------------------------------------
1240fileinput=browse_xml(hObject, eventdata, handles);
1241if isempty(fileinput)
1242    return
1243end
1244[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1245GeometryCalib=s.GeometryCalib;
1246display_intrinsic(GeometryCalib,handles)
1247
1248% -----------------------------------------------------------------------
1249function MenuImportAll_Callback(hObject, eventdata, handles)
1250%------------------------------------------------------------------------
1251fileinput=browse_xml(hObject, eventdata, handles);
1252if ~isempty(fileinput)
1253    loadfile(handles,fileinput)
1254end
1255
1256% -----------------------------------------------------------------------
1257% --- Executes on menubar option Import/Grid file: introduce previous grid files
1258function MenuGridFile_Callback(hObject, eventdata, handles)
1259% -----------------------------------------------------------------------
1260inputfile=browse_xml(hObject, eventdata, handles);
1261listfile=get(handles.coord_files,'string');
1262if isequal(listfile,{''})
1263    listfile={inputfile};
1264else
1265    listfile=[listfile;{inputfile}];%update the list of coord files
1266end
1267set(handles.coord_files,'string',listfile);
1268
1269%------------------------------------------------------------------------
1270% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
1271function key_press_fcn(hObject,eventdata,handles)
1272%------------------------------------------------------------------------
1273xx=double(get(handles.geometry_calib,'CurrentCharacter')); %get the keyboard character
1274if ismember(xx,[8 127])%backspace or delete
1275    Coord_cell=get(handles.ListCoord,'String');
1276    val=get(handles.ListCoord,'Value');
1277     if max(val)<numel(Coord_cell) % the last element '...' has not been selected
1278        Coord_cell(val)=[];%remove the selected line
1279        set(handles.ListCoord,'Value',min(val))
1280        set(handles.ListCoord,'String',Coord_cell)         
1281        ListCoord_Callback(hObject, eventdata, handles)
1282        MenuPlot_Callback(hObject,eventdata,handles)
1283     end
1284end
1285
1286%------------------------------------------------------------------------
1287function fileinput=browse_xml(hObject, eventdata, handles)
1288%------------------------------------------------------------------------
1289fileinput=[];%default
1290oldfile=''; %default
1291UserData=get(handles.geometry_calib,'UserData');
1292if isfield(UserData,'XmlInputFile')
1293    oldfile=UserData.XmlInputFile;
1294end
1295[FileName, PathName, filterindex] = uigetfile( ...
1296       {'*.xml;*.mat', ' (*.xml,*.mat)';
1297       '*.xml',  '.xml files '; ...
1298        '*.mat',  '.mat matlab files '}, ...
1299        'Pick a file',oldfile);
1300fileinput=[PathName FileName];%complete file name
1301testblank=findstr(fileinput,' ');%look for blanks
1302if ~isempty(testblank)
1303    msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed')
1304    return
1305end
1306sizf=size(fileinput);
1307if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1308UserData.XmlInputFile=fileinput;
1309set(handles.geometry_calib,'UserData',UserData)%record current file foer further use of browser
1310
1311% -----------------------------------------------------------------------
1312function Heading=loadfile(handles,fileinput)
1313%------------------------------------------------------------------------
1314Heading=[];%default
1315[s,errormsg]=imadoc2struct(fileinput,'Heading','GeometryCalib');
1316if ~isempty(errormsg)
1317    msgbox_uvmat('ERROR',errormsg)
1318    return
1319end
1320if ~isempty(s.Heading)
1321    Heading=s.Heading;
1322end
1323   
1324GeometryCalib=s.GeometryCalib;
1325fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
1326CoordCell={};
1327Tabchar={};%default
1328val_cal=1;%default
1329if ~isempty(GeometryCalib)
1330    % choose the calibration option
1331    if isfield(GeometryCalib,'CalibrationType')
1332       calib_list=get(handles.calib_type,'String');
1333       for ilist=1:numel(calib_list)
1334           if strcmp(calib_list{ilist},GeometryCalib.CalibrationType)
1335               val_cal=ilist;
1336               break
1337           end
1338       end
1339    end
1340    display_intrinsic(GeometryCalib,handles)%intrinsic param
1341    %extrinsic param
1342    if isfield(GeometryCalib,'Tx_Ty_Tz')
1343        Tx_Ty_Tz=GeometryCalib.Tx_Ty_Tz;
1344        set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
1345        set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
1346        set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
1347    end
1348    if isfield(GeometryCalib,'omc')
1349        set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
1350        set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
1351        set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
1352    end
1353    calib=reshape(GeometryCalib.SourceCalib.PointCoord,[],1);
1354    for ilist=1:numel(calib)
1355        CoordCell{ilist}=num2str(calib(ilist));
1356    end
1357    CoordCell=reshape(CoordCell,[],5);
1358    Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
1359    MenuPlot_Callback(handles.geometry_calib, [], handles)
1360end
1361set(handles.calib_type,'Value',val_cal)
1362Tabchar=[Tabchar;{'......'}];
1363set(handles.ListCoord,'Value',1)
1364set(handles.ListCoord,'String',Tabchar)
1365
1366if isempty(CoordCell)% allow mouse action by default in the absence of input points
1367    set(handles.edit_append,'Value',1)
1368    set(handles.edit_append,'BackgroundColor',[1 1 0])
1369else % does not allow mouse action by default in the presence of input points
1370    set(handles.edit_append,'Value',0)
1371    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
1372end
1373
1374%------------------------------------------------------------------------
1375%---display calibration intrinsic parameters
1376function display_intrinsic(GeometryCalib,handles)
1377%------------------------------------------------------------------------
1378fx=[];
1379fy=[];
1380if isfield(GeometryCalib,'fx_fy')
1381    fx=GeometryCalib.fx_fy(1);
1382    fy=GeometryCalib.fx_fy(2);
1383end
1384Cx_Cy=[0 0];%default
1385if isfield(GeometryCalib,'Cx_Cy')
1386    Cx_Cy=GeometryCalib.Cx_Cy;
1387end
1388kc=0;
1389if isfield(GeometryCalib,'kc')
1390    kc=GeometryCalib.kc; %* GeometryCalib.focal*GeometryCalib.focal;
1391end
1392set(handles.fx,'String',num2str(fx,5))
1393set(handles.fy,'String',num2str(fy,5))
1394set(handles.Cx,'String',num2str(Cx_Cy(1),'%1.1f'))
1395set(handles.Cy,'String',num2str(Cx_Cy(2),'%1.1f'))
1396set(handles.kc,'String',num2str(kc,'%1.4f'))
1397
1398
1399% --- Executes when user attempts to close geometry_calib.
1400function geometry_calib_CloseRequestFcn(hObject, eventdata, handles)
1401% hObject    handle to geometry_calib (see GCBO)
1402% eventdata  reserved - to be defined in a future version of MATLAB
1403% handles    structure with handles and user data (see GUIDATA)
1404
1405% Hint: delete(hObject) closes the figure
1406delete(hObject);
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