source: trunk/src/geometry_calib.m @ 591

Last change on this file since 591 was 591, checked in by sommeria, 8 years ago

various updates, in particular modification of series to do calculations in the cluster

File size: 54.9 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%set the position of the interface
92if exist('pos','var')&& length(pos)>=4
93    set(hObject,'Position',pos);
94end
95
96%set menu of calibration options
97set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'})
98if exist('inputfile','var')&& ~isempty(inputfile)
99    struct.XmlInputFile=inputfile;
100    [RootPath,SubDir,RootFile,tild,tild,tild,tild,FileExt]=fileparts_uvmat(inputfile);
101    if ~strcmp(FileExt,'.xml')
102        inputfile=fullfile(RootPath,[SubDir '.xml']);%xml file corresponding to the input file
103        if ~exist(inputfile,'file')% case of civ files , removes the extension for subdir
104            inputfile=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
105            if ~exist(inputfile,'file')
106                inputfile=[fullfile(RootPath,SubDir,RootFile) '.xml'];%old convention
107                if ~exist(inputfile,'file')
108                    inputfile='';
109                end
110            end
111        end
112    end
113    set(handles.ListCoord,'String',{'......'})
114    if exist(inputfile,'file')
115        Heading=loadfile(handles,inputfile);% load data from the xml file
116        if isfield(Heading,'Campaign')&& ischar(Heading.Campaign)
117            struct.Campaign=Heading.Campaign;
118        end
119    end   
120    set(hObject,'UserData',struct)
121end
122
123set(handles.ListCoord,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function
124
125
126%------------------------------------------------------------------------
127% --- Outputs from this function are returned to the command line.
128function varargout = geometry_calib_OutputFcn(hObject, eventdata, handles)
129%------------------------------------------------------------------------
130% Get default command line output from handles structure
131varargout{1} = handles.output;
132varargout{2}=handles;
133%
134%------------------------------------------------------------------------
135% executed when closing: set the parent interface button to value 0
136function closefcn(gcbo,eventdata)
137%------------------------------------------------------------------------
138huvmat=findobj(allchild(0),'Name','uvmat');
139if ~isempty(huvmat)
140    handles=guidata(huvmat);
141    hobject=findobj(handles.PlotAxes,'tag','calib_points');
142    if ~isempty(hobject)
143        delete(hobject)
144    end
145    hobject=findobj(handles.PlotAxes,'tag','calib_marker');
146    if ~isempty(hobject)
147        delete(hobject)
148    end   
149end
150
151%------------------------------------------------------------------------
152% --- Executes on button press APPLY (used to launch the calibration).
153function APPLY_Callback(hObject, eventdata, handles)
154%------------------------------------------------------------------------
155%% look for the GUI uvmat and check for an image as input
156huvmat=findobj(allchild(0),'Name','uvmat');
157hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
158
159RootPath='';
160if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
161    RootPath=get(hhuvmat.RootPath,'String');
162    SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$','');
163    outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image
164else
165    question={'save the calibration data and point coordinates in'};
166    def={fullfile(RootPath,'ObjectCalib.xml')};
167    options.Resize='on';
168    answer=inputdlg(question,'',1,def,options);
169    outputfile=answer{1};
170end
171[GeometryCalib,index]=calibrate(handles,hhuvmat);% apply calibration
172
173%% copy the xml file from the old location if appropriate, then update with the calibration parameters
174if ~exist(outputfile,'file') && ~isempty(SubDirBase)
175    oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml'];
176    if exist(oldxml,'file')
177        [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention
178    end
179end
180errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file
181if ~strcmp(errormsg,'')
182    msgbox_uvmat('ERROR',errormsg);
183end
184
185%% display image with new calibration in the currently opened uvmat interface
186hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_marker');% delete calib points and markers
187if ~isempty(hhh)
188    delete(hhh);
189end
190hhh=findobj(hhuvmat.PlotAxes,'Tag','calib_points');
191if ~isempty(hhh)
192    delete(hhh);
193end
194set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off'
195set(hhuvmat.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
196UserData=get(handles.geometry_calib,'UserData');
197UserData.XmlInputFile=outputfile;%save the current xml file name
198set(handles.geometry_calib,'UserData',UserData)
199uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
200MenuPlot_Callback(hObject, eventdata, handles)
201set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
202ListCoord_Callback(hObject, eventdata, handles)
203figure(handles.geometry_calib)
204
205%------------------------------------------------------------------------
206% --- Executes on button press in REPLICATE
207function REPLICATE_Callback(hObject, eventdata, handles)
208%------------------------------------------------------------------------
209
210%% look for the GUI uvmat and check for an image as input
211huvmat=findobj(allchild(0),'Name','uvmat');
212hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
213GeometryCalib=calibrate(handles,hhuvmat);% apply calibration
214
215%% open the GUI browse_data
216CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
217if isfield(CalibData,'XmlInputFile')
218    InputDir=fileparts(fileparts(CalibData.XmlInputFile));
219end
220answer=msgbox_uvmat('INPUT_TXT','Campaign to calibrate?',InputDir);
221if strcmp(answer,'Cancel')
222    return
223end
224OutPut=browse_data(answer);
225nbcalib=0;
226for ilist=1:numel(OutPut.Experiment)
227    SubDirBase=regexprep(OutPut.Device{1},'\..+$','');
228    XmlName=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']);
229    % copy the xml file from the old location if appropriate, then update with the calibration parameters
230    if ~exist(XmlName,'file') && ~isempty(SubDirBase)
231        oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']);
232        if exist(oldxml,'file')
233            [success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention
234        end
235    end
236    errormsg=update_imadoc(GeometryCalib,XmlName);% introduce the calibration data in the xml file
237    if ~strcmp(errormsg,'')
238        msgbox_uvmat('ERROR',errormsg);
239    else
240        display([XmlName ' updated with calibration parameters'])
241        nbcalib=nbcalib+1;
242    end
243end
244msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']);
245
246%------------------------------------------------------------------------
247% --- activate calibration and store parameters in ouputfile .
248function [GeometryCalib,index]=calibrate(handles,hhuvmat)
249%------------------------------------------------------------------------
250%% read the current calibration points
251Coord_cell=get(handles.ListCoord,'String');
252Object=read_geometry_calib(Coord_cell);
253Coord=Object.Coord;
254% apply the calibration, whose type is selected in  handles.calib_type
255if ~isempty(Coord)
256    calib_cell=get(handles.calib_type,'String');
257    val=get(handles.calib_type,'Value');
258    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
259else
260    msgbox_uvmat('ERROR','No calibration points, abort')
261    return
262end
263Z_plane=[];
264if ~isempty(Coord)
265    %check error
266    X=Coord(:,1);
267    Y=Coord(:,2);
268    Z=Coord(:,3);
269    x_ima=Coord(:,4);
270    y_ima=Coord(:,5);
271    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
272    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
273    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
274    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
275    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
276    [tild,ind_dim]=max(GeometryCalib.ErrorMax);
277    index=index(ind_dim);
278    %set the Z position of the reference plane used for calibration
279    if isequal(max(Z),min(Z))%Z constant
280        Z_plane=Z(1);
281        GeometryCalib.NbSlice=1;
282        GeometryCalib.SliceCoord=[0 0 Z_plane];
283    end
284end
285%set the coordinate unit
286unitlist=get(handles.CoordUnit,'String');
287unit=unitlist{get(handles.CoordUnit,'value')};
288GeometryCalib.CoordUnit=unit;
289%record the points
290GeometryCalib.SourceCalib.PointCoord=Coord;
291display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
292
293% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
294set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
295set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
296set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
297set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
298set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
299set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
300
301%% store the calibration data, by default in the xml file of the currently displayed image
302UvData=get(hhuvmat.uvmat,'UserData');
303NbSlice_j=1;%default
304ZStart=Z_plane;
305ZEnd=Z_plane;
306volume_scan='n';
307if isfield(UvData,'XmlData')
308    if isfield(UvData.XmlData,'TranslationMotor')
309        NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice;
310        ZStart=UvData.XmlData.TranslationMotor.ZStart/10;
311        ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10;
312        volume_scan='y';
313    end
314end
315
316answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';...
317    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
318    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
319
320%% get plane position(s)
321if ~strcmp(answer,'Yes')
322    return
323end
324if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
325    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'};
326    input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}];
327    answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on');
328    GeometryCalib.NbSlice=str2double(answer{5});
329    GeometryCalib.VolumeScan=answer{6};
330    if isempty(answer)
331        Z_plane=0; %default
332    else
333        Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice);
334    end
335    GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
336    GeometryCalib.SliceAngle(:,3)=0;
337    GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise)
338    GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise)
339    GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})];
340    GeometryCalib.RefractionIndex=str2double(answer{4});
341end
342
343
344
345%------------------------------------------------------------------------
346% determine the parameters for a calibration by an affine function (rescaling and offset, no rotation)
347function GeometryCalib=calib_rescale(Coord,handles)
348%------------------------------------------------------------------------
349X=Coord(:,1);
350Y=Coord(:,2);% Z not used
351x_ima=Coord(:,4);
352y_ima=Coord(:,5);
353[px]=polyfit(X,x_ima,1);
354[py]=polyfit(Y,y_ima,1);
355% T_x=px(2);
356% T_y=py(2);
357GeometryCalib.CalibrationType='rescale';
358GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
359GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
360GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
361GeometryCalib.omc=[0 0 0];
362
363%------------------------------------------------------------------------
364% determine the parameters for a calibration by a linear transform matrix (rescale and rotation)
365
366
367function GeometryCalib=calib_linear(Coord,handles)
368%------------------------------------------------------------------------
369X=Coord(:,1);
370Y=Coord(:,2);% Z not used
371x_ima=Coord(:,4);
372y_ima=Coord(:,5);
373XY_mat=[ones(size(X)) X Y];
374a_X1=XY_mat\x_ima; %transformation matrix for X
375a_Y1=XY_mat\y_ima;%transformation matrix for X
376R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
377epsilon=sign(det(R));
378norm=abs(det(R));
379GeometryCalib.CalibrationType='linear';
380if (a_X1(2)/a_Y1(3))>0
381    GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm);
382else
383    GeometryCalib.fx_fy(1)=-sqrt(-(a_X1(2)/a_Y1(3))*norm);
384end
385GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
386GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
387GeometryCalib.Tx_Ty_Tz=[a_X1(1)/GeometryCalib.fx_fy(1) a_Y1(1)/GeometryCalib.fx_fy(2) 1];
388R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
389R(2,:)=R(2,:)/GeometryCalib.fx_fy(2);
390R=[R;[0 0]];
391GeometryCalib.R=[R [0;0;-epsilon]];
392GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
393
394%------------------------------------------------------------------------
395% determine the tsai parameters for a view normal to the grid plane
396% NOT USED
397function GeometryCalib=calib_normal(Coord,handles)
398%------------------------------------------------------------------------
399Calib.f1=str2num(get(handles.fx,'String'));
400Calib.f2=str2num(get(handles.fy,'String'));
401Calib.k=str2num(get(handles.kc,'String'));
402Calib.Cx=str2num(get(handles.Cx,'String'));
403Calib.Cy=str2num(get(handles.Cy,'String'));
404%default
405if isempty(Calib.f1)
406    Calib.f1=25/0.012;
407end
408if isempty(Calib.f2)
409    Calib.f2=25/0.012;
410end
411if isempty(Calib.k)
412    Calib.k=0;
413end
414if isempty(Calib.Cx)||isempty(Calib.Cy)
415    huvmat=findobj(allchild(0),'Tag','uvmat');
416    hhuvmat=guidata(huvmat);
417    Calib.Cx=str2num(get(hhuvmat.num_Npx,'String'))/2;
418    Calib.Cx=str2num(get(hhuvmat.num_Npy,'String'))/2;
419end   
420%tsai parameters
421Calib.dpx=0.012;%arbitrary
422Calib.dpy=0.012;
423Calib.sx=Calib.f1*Calib.dpx/(Calib.f2*Calib.dpy);
424Calib.f=Calib.f2*Calib.dpy;
425Calib.kappa1=Calib.k/(Calib.f*Calib.f);
426
427%initial guess
428X=Coord(:,1);
429Y=Coord(:,2);
430Zmean=mean(Coord(:,3));
431x_ima=Coord(:,4)-Calib.Cx;
432y_ima=Coord(:,5)-Calib.Cy;
433XY_mat=[ones(size(X)) X Y];
434a_X1=XY_mat\x_ima; %transformation matrix for X
435a_Y1=XY_mat\y_ima;%transformation matrix for Y
436R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,-1];% rotation+ z axis reversal (upward)
437norm=sqrt(det(-R));
438calib_param(1)=0;% quadratic distortion
439calib_param(2)=a_X1(1);
440calib_param(3)=a_Y1(1);
441calib_param(4)=Calib.f/(norm*Calib.dpx)-R(3,3)*Zmean;
442calib_param(5)=angle(a_X1(2)+1i*a_X1(3));
443display(['initial guess=' num2str(calib_param)])
444
445%optimise the parameters: minimisation of error
446calib_param = fminsearch(@(calib_param) error_calib(calib_param,Calib,Coord),calib_param);
447
448GeometryCalib.CalibrationType='tsai_normal';
449GeometryCalib.focal=Calib.f;
450GeometryCalib.dpx_dpy=[Calib.dpx Calib.dpy];
451GeometryCalib.Cx_Cy=[Calib.Cx Calib.Cy];
452GeometryCalib.sx=Calib.sx;
453GeometryCalib.kappa1=calib_param(1);
454GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
455GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)];
456alpha=calib_param(5);
457GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
458
459%------------------------------------------------------------------------
460function GeometryCalib=calib_3D_linear(Coord,handles)
461%------------------------------------------------------------------
462path_uvmat=which('uvmat');% check the path detected for source file uvmat
463path_UVMAT=fileparts(path_uvmat); %path to UVMAT
464huvmat=findobj(allchild(0),'Tag','uvmat');
465hhuvmat=guidata(huvmat);
466coord_files=get(handles.coord_files,'String');
467if ischar(coord_files)
468    coord_files={coord_files};
469end
470if isempty(coord_files{1}) || isequal(coord_files,{''})
471    coord_files={};
472end
473%retrieve the calibration points stored in the files listed in the popup list coord_files
474x_1=Coord(:,4:5)';%px coordinates of the ref points
475nx=str2num(get(hhuvmat.num_Npx,'String'));
476ny=str2num(get(hhuvmat.num_Npy,'String'));
477x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
478X_1=Coord(:,1:3)';%phys coordinates of the ref points
479n_ima=numel(coord_files)+1;
480if ~isempty(coord_files)
481    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
482    for ifile=1:numel(coord_files)
483    t=xmltree(coord_files{ifile});
484    s=convert(t);%convert to matlab structure
485        if isfield(s,'GeometryCalib')
486            if isfield(s.GeometryCalib,'SourceCalib')
487                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
488                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
489                Coord_file=zeros(length(PointCoord),5);%default
490                for i=1:length(PointCoord)
491                    line=str2num(PointCoord{i});
492                    Coord_file(i,4:5)=line(4:5);%px x
493                    Coord_file(i,1:3)=line(1:3);%phys x
494                end
495                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
496                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
497                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
498                end
499            end
500        end
501    end
502end
503n_ima=numel(coord_files)+1;
504est_dist=[0;0;0;0;0];
505est_aspect_ratio=0;
506est_fc=[1;1];
507%fc=[25;25]/0.012;
508center_optim=0;
509run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
510GeometryCalib.CalibrationType='3D_linear';
511GeometryCalib.fx_fy=fc';
512%GeometryCalib.focal=fc(2);
513%GeometryCalib.dpx_dpy=[1 1];
514GeometryCalib.Cx_Cy=cc';
515%GeometryCalib.sx=fc(1)/fc(2);
516GeometryCalib.kc=kc(1);
517%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
518GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
519GeometryCalib.Tx_Ty_Tz=Tc_1';
520GeometryCalib.R=Rc_1;
521GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
522GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
523GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
524GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
525GeometryCalib.ErrorRMS=[];
526GeometryCalib.ErrorMax=[];
527
528%------------------------------------------------------------------------
529function GeometryCalib=calib_3D_quadr(Coord,handles)
530%------------------------------------------------------------------
531
532path_uvmat=which('uvmat');% check the path detected for source file uvmat
533path_UVMAT=fileparts(path_uvmat); %path to UVMAT
534huvmat=findobj(allchild(0),'Tag','uvmat');
535hhuvmat=guidata(huvmat);
536% check_cond=0;
537coord_files=get(handles.coord_files,'String');
538if ischar(coord_files)
539    coord_files={coord_files};
540end
541if isempty(coord_files{1}) || isequal(coord_files,{''})
542    coord_files={};
543end
544
545%retrieve the calibration points stored in the files listed in the popup list coord_files
546x_1=Coord(:,4:5)';%px coordinates of the ref points
547nx=str2num(get(hhuvmat.num_Npx,'String'));
548ny=str2num(get(hhuvmat.num_Npy,'String'));
549x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
550X_1=Coord(:,1:3)';%phys coordinates of the ref points
551n_ima=numel(coord_files)+1;
552if ~isempty(coord_files)
553    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
554    for ifile=1:numel(coord_files)
555    t=xmltree(coord_files{ifile});
556    s=convert(t);%convert to matlab structure
557        if isfield(s,'GeometryCalib')
558            if isfield(s.GeometryCalib,'SourceCalib')
559                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
560                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
561                Coord_file=zeros(length(PointCoord),5);%default
562                for i=1:length(PointCoord)
563                    line=str2num(PointCoord{i});
564                    Coord_file(i,4:5)=line(4:5);%px x
565                    Coord_file(i,1:3)=line(1:3);%phys x
566                end
567                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
568                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
569                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
570                end
571            end
572        end
573    end
574end
575n_ima=numel(coord_files)+1;
576est_dist=[1;0;0;0;0];
577est_aspect_ratio=1;
578%est_fc=[0;0];
579%fc=[25;25]/0.012;
580center_optim=0;
581run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
582
583GeometryCalib.CalibrationType='3D_quadr';
584GeometryCalib.fx_fy=fc';
585%GeometryCalib.focal=fc(2);
586%GeometryCalib.dpx_dpy=[1 1];
587GeometryCalib.Cx_Cy=cc';
588%GeometryCalib.sx=fc(1)/fc(2);
589GeometryCalib.kc=kc(1);
590%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
591GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
592GeometryCalib.Tx_Ty_Tz=Tc_1';
593GeometryCalib.R=Rc_1;
594GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
595GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
596GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
597GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
598GeometryCalib.ErrorRMS=[];
599GeometryCalib.ErrorMax=[];
600
601
602%------------------------------------------------------------------------
603function GeometryCalib=calib_3D_extrinsic(Coord,handles)
604%------------------------------------------------------------------
605path_uvmat=which('geometry_calib');% check the path detected for source file uvmat
606path_UVMAT=fileparts(path_uvmat); %path to UVMAT
607x_1=double(Coord(:,4:5)');%image coordiantes
608X_1=double(Coord(:,1:3)');% phys coordinates
609huvmat=findobj(allchild(0),'Tag','uvmat');
610hhuvmat=guidata(huvmat);
611ny=str2double(get(hhuvmat.num_Npy,'String'));
612x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
613n_ima=1;
614GeometryCalib.CalibrationType='3D_extrinsic';
615GeometryCalib.fx_fy(1)=str2num(get(handles.fx,'String'));
616GeometryCalib.fx_fy(2)=str2num(get(handles.fy,'String'));
617GeometryCalib.Cx_Cy(1)=str2num(get(handles.Cx,'String'));
618GeometryCalib.Cx_Cy(2)=str2num(get(handles.Cy,'String'));
619GeometryCalib.kc=str2num(get(handles.kc,'String'));
620fct_path=fullfile(path_UVMAT,'toolbox_calib');
621addpath(fct_path)
622GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate)
623% [omc1,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
624%     [Calib.f Calib.f*Calib.sx]',...
625%     [Calib.Cx Calib.Cy]',...
626%     [-Calib.kappa1*Calib.f^2 0 0 0 0]);
627[omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
628    (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]);
629rmpath(fct_path);
630GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
631GeometryCalib.Tx_Ty_Tz=Tc1';
632%inversion of z axis
633GeometryCalib.R=Rc1;
634GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
635GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
636GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
637GeometryCalib.omc=(180/pi)*omc';
638%GeometryCalib.R(3,1:3)=-GeometryCalib.R(3,1:3);%inversion for z upward
639
640
641
642%------------------------------------------------------------------------
643%function GeometryCalib=calib_tsai_heikkila(Coord)
644% TEST: NOT IMPLEMENTED
645%------------------------------------------------------------------
646% path_uvmat=which('uvmat');% check the path detected for source file uvmat
647% path_UVMAT=fileparts(path_uvmat); %path to UVMAT
648% path_calib=fullfile(path_UVMAT,'toolbox_calib_heikkila');
649% addpath(path_calib)
650% npoints=size(Coord,1);
651% Coord(:,1:3)=10*Coord(:,1:3);
652% Coord=[Coord zeros(npoints,2) -ones(npoints,1)];
653% [par,pos,iter,res,er,C]=cacal('dalsa',Coord);
654% GeometryCalib.CalibrationType='tsai';
655% GeometryCalib.focal=par(2);
656
657
658%------------------------------------------------------------------------
659% --- determine the rms of calibration error
660function ErrorRms=error_calib(calib_param,Calib,Coord)
661%calib_param: vector of free calibration parameters (to optimise)
662%Calib: structure of the given calibration parameters
663%Coord: list of phys coordinates (columns 1-3, and pixel coordinates (columns 4-5)
664Calib.f=25;
665Calib.dpx=0.012;
666Calib.dpy=0.012;
667Calib.sx=1;
668Calib.Cx=512;
669Calib.Cy=512;
670Calib.kappa1=calib_param(1);
671Calib.Tx=calib_param(2);
672Calib.Ty=calib_param(3);
673Calib.Tz=calib_param(4);
674alpha=calib_param(5);
675Calib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
676
677X=Coord(:,1);
678Y=Coord(:,2);
679Z=Coord(:,3);
680x_ima=Coord(:,4);
681y_ima=Coord(:,5);
682[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z);
683ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
684ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
685ErrorRms=mean(ErrorRms);
686
687%------------------------------------------------------------------------
688function XImage_Callback(hObject, eventdata, handles)
689%------------------------------------------------------------------------
690update_list(hObject, eventdata,handles)
691
692%------------------------------------------------------------------------
693function YImage_Callback(hObject, eventdata, handles)
694%------------------------------------------------------------------------
695update_list(hObject, eventdata,handles)
696
697%------------------------------------------------------------------------
698% --- Executes on button press in STORE.
699function STORE_Callback(hObject, eventdata, handles)
700Coord_cell=get(handles.ListCoord,'String');
701Object=read_geometry_calib(Coord_cell);
702unitlist=get(handles.CoordUnit,'String');
703unit=unitlist{get(handles.CoordUnit,'value')};
704GeometryCalib.CoordUnit=unit;
705GeometryCalib.SourceCalib.PointCoord=Object.Coord;
706huvmat=findobj(allchild(0),'Name','uvmat');
707hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
708% RootPath='';
709% RootFile='';
710if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
711%     testhandle=1;
712    RootPath=get(hhuvmat.RootPath,'String');
713    RootFile=get(hhuvmat.RootFile,'String');
714    filebase=fullfile(RootPath,RootFile);
715    while exist([filebase '.xml'],'file')
716        filebase=[filebase '~'];
717    end
718    outputfile=[filebase '.xml'];
719    errormsg=update_imadoc(GeometryCalib,outputfile);
720    if ~strcmp(errormsg,'')
721        msgbox_uvmat('ERROR',errormsg);
722    end
723    listfile=get(handles.coord_files,'string');
724    if isequal(listfile,{''})
725        listfile={outputfile};
726    else
727        listfile=[listfile;{outputfile}];%update the list of coord files
728    end
729    set(handles.coord_files,'string',listfile);
730end
731set(handles.ListCoord,'Value',1)% refresh the display of coordinates
732set(handles.ListCoord,'String',{'......'})
733
734% --------------------------------------------------------------------
735% --- Executes on button press in CLEAR_PTS: clear the list of calibration points
736function CLEAR_PTS_Callback(hObject, eventdata, handles)
737% --------------------------------------------------------------------
738set(handles.ListCoord,'Value',1)% refresh the display of coordinates
739set(handles.ListCoord,'String',{'......'})
740MenuPlot_Callback(hObject, eventdata, handles)
741
742%------------------------------------------------------------------------
743% --- Executes on button press in CLEAR.
744function CLEAR_Callback(hObject, eventdata, handles)
745%------------------------------------------------------------------------
746set(handles.coord_files,'Value',1)
747set(handles.coord_files,'String',{''})
748
749%------------------------------------------------------------------------
750function XObject_Callback(hObject, eventdata, handles)
751%------------------------------------------------------------------------
752update_list(hObject, eventdata,handles)
753
754%------------------------------------------------------------------------
755function YObject_Callback(hObject, eventdata, handles)
756%------------------------------------------------------------------------
757update_list(hObject, eventdata,handles)
758
759%------------------------------------------------------------------------
760function ZObject_Callback(hObject, eventdata, handles)
761%------------------------------------------------------------------------
762update_list(hObject, eventdata,handles)
763
764%------------------------------------------------------------------------
765function update_list(hObject, eventdata, handles)
766%------------------------------------------------------------------------
767newval(4)=str2double(get(handles.XImage,'String'));
768newval(5)=str2double(get(handles.YImage,'String'));
769newval(1)=str2double(get(handles.XObject,'String'));
770newval(2)=str2double(get(handles.YObject,'String'));
771newval(3)=str2double(get(handles.ZObject,'String'));
772if isnan(newval(3))
773    newval(3)=0;%put z to 0 by default
774end
775Coord=get(handles.ListCoord,'String');
776Coord(end)=[]; %remove last string '.....'
777val=get(handles.ListCoord,'Value');
778data=read_geometry_calib(Coord);
779data.Coord(val,:)=newval;
780for i=1:size(data.Coord,1)
781    for j=1:5
782          Coord_cell{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
783    end
784end
785
786Tabchar=cell2tab(Coord_cell,' | ');
787Tabchar=[Tabchar ;{'......'}];
788set(handles.ListCoord,'String',Tabchar)
789
790%update the plot
791ListCoord_Callback(hObject, eventdata, handles)
792MenuPlot_Callback(hObject, eventdata, handles)
793
794%------------------------------------------------------------------------
795% --- Executes on selection change in ListCoord.
796function ListCoord_Callback(hObject, eventdata, handles)
797%------------------------------------------------------------------------
798huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
799hplot=findobj(huvmat,'Tag','PlotAxes');%main plotting axis of uvmat
800hhh=findobj(hplot,'Tag','calib_marker');
801Coord_cell=get(handles.ListCoord,'String');
802val=get(handles.ListCoord,'Value');
803if numel(val)>1
804    return %no action if several lines have been selected
805end
806coord_str=Coord_cell{val};
807k=findstr(' | ',coord_str);
808if isempty(k)%last line '.....' selected
809    if ~isempty(hhh)
810        delete(hhh)%delete the circle marker
811    end
812    return
813end
814%fill the edit boxe
815set(handles.XObject,'String',coord_str(1:k(1)-1))
816set(handles.YObject,'String',coord_str(k(1)+3:k(2)-1))
817set(handles.ZObject,'String',coord_str(k(2)+3:k(3)-1))
818set(handles.XImage,'String',coord_str(k(3)+3:k(4)-1))
819set(handles.YImage,'String',coord_str(k(4)+3:end))
820h_menu_coord=findobj(huvmat,'Tag','TransformName');
821menu=get(h_menu_coord,'String');
822choice=get(h_menu_coord,'Value');
823if iscell(menu)
824    option=menu{choice};
825else
826    option='px'; %default
827end
828if isequal(option,'phys')
829    XCoord=str2double(coord_str(1:k(1)-1));
830    YCoord=str2double(coord_str(k(1)+3:k(2)-1));
831elseif isequal(option,'px')|| isequal(option,'')
832    XCoord=str2double(coord_str(k(3)+3:k(4)-1));
833    YCoord=str2double(coord_str(k(4)+3:end));
834else
835    msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be px or phys ')
836end
837if isempty(XCoord)||isempty(YCoord)
838     if ~isempty(hhh)
839        delete(hhh)%delete the circle marker
840    end
841    return
842end
843xlim=get(hplot,'XLim');
844ylim=get(hplot,'YLim');
845ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/20;%defines the size of the circle marker
846if isempty(hhh)
847    set(0,'CurrentFig',huvmat)
848    set(huvmat,'CurrentAxes',hplot)
849    rectangle('Curvature',[1 1],...
850              'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range],'EdgeColor','m',...
851              'LineStyle','-','Tag','calib_marker');
852else
853    set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
854end
855
856%------------------------------------------------------------------------
857% --- Executes on selection change in edit_append.
858function edit_append_Callback(hObject, eventdata, handles)
859%------------------------------------------------------------------------
860choice=get(handles.edit_append,'Value');
861if choice
862    set(handles.edit_append,'BackgroundColor',[1 1 0])
863    huvmat=findobj(allchild(0),'tag','uvmat');
864    if ishandle(huvmat)
865        hhuvmat=guidata(huvmat);
866        set(hhuvmat.edit_object,'Value',0)
867        set(hhuvmat.edit_object,'BackgroundColor',[0.7 0.7 0.7])
868    end
869else
870    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
871end
872   
873function NEW_Callback(hObject, eventdata, handles)
874%A METTRE SOUS UN BOUTON
875huvmat=findobj(allchild(0),'Name','uvmat');
876hchild=get(huvmat,'children');
877hcoord=findobj(hchild,'Tag','menu_coord');
878coordtype=get(hcoord,'Value');
879haxes=findobj(hchild,'Tag','axes3');
880AxeData=get(haxes,'UserData');
881if ~isequal(hcoord,2)
882    set(hcoord,'Value',2)
883    huvmat=uvmat(AxeData);
884    'relancer uvmat';
885end
886if ~isfield(AxeData,'ZoomAxes')
887    msgbox_uvmat('ERROR','first draw a window around a grid marker')
888    return
889end
890XLim=get(AxeData.ZoomAxes,'XLim');
891YLim=get(AxeData.ZoomAxes,'YLim');
892np=size(AxeData.A);
893ind_sub_x=round(XLim);
894ind_sub_y=np(1)-round(YLim);
895Mfiltre=AxeData.A(ind_sub_y(2):ind_sub_y(1) ,ind_sub_x,:);
896Mfiltre_norm=double(Mfiltre);
897Mfiltre_norm=Mfiltre_norm/sum(sum(Mfiltre_norm));
898Mfiltre_norm=100*(Mfiltre_norm-mean(mean(Mfiltre_norm)));
899Atype=class(AxeData.A);
900Data.NbDim=2;
901Data.A=filter2(Mfiltre_norm,double(AxeData.A));
902Data.A=feval(Atype,Data.A);
903Data.AName='image';
904Data.AX=AxeData.AX;
905Data.AY=AxeData.AY;
906Data.CoordType='px';
907plot_field(Data)
908
909%------------------------------------------------------------------------
910function MenuPlot_Callback(hObject, eventdata, handles)
911%------------------------------------------------------------------------
912huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
913%UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface
914hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat
915%hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
916h_menu_coord=findobj(huvmat,'Tag','TransformName');
917menu=get(h_menu_coord,'String');
918choice=get(h_menu_coord,'Value');
919if iscell(menu)
920    option=menu{choice};
921else
922    option='px'; %default
923end
924Coord_cell=get(handles.ListCoord,'String');
925ObjectData=read_geometry_calib(Coord_cell);
926%ObjectData=read_geometry_calib(handles);%read the interface input parameters defining the object
927if ~isempty(ObjectData.Coord)
928    if isequal(option,'phys')
929        ObjectData.Coord=ObjectData.Coord(:,1:3);
930    elseif isequal(option,'px')||isequal(option,'')
931        ObjectData.Coord=ObjectData.Coord(:,4:5);
932    else
933        msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be '''', px or phys ')
934    end
935end
936
937set(0,'CurrentFigure',huvmat)
938set(huvmat,'CurrentAxes',hhuvmat.PlotAxes)
939hh=findobj('Tag','calib_points');
940if  ~isempty(ObjectData.Coord) && isempty(hh)
941    hh=line(ObjectData.Coord(:,1),ObjectData.Coord(:,2),'Color','m','Tag','calib_points','LineStyle','.','Marker','+');
942elseif isempty(ObjectData.Coord)%empty list of points, suppress the plot
943    delete(hh)
944else
945    set(hh,'XData',ObjectData.Coord(:,1))
946    set(hh,'YData',ObjectData.Coord(:,2))
947end
948pause(.1)
949figure(handles.geometry_calib)
950
951% --------------------------------------------------------------------
952function MenuHelp_Callback(hObject, eventdata, handles)
953path_to_uvmat=which('uvmat');% check the path of uvmat
954pathelp=fileparts(path_to_uvmat);
955helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
956if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
957else
958   addpath (fullfile(pathelp,'uvmat_doc'))
959   web([helpfile '#geometry_calib'])
960end
961
962%------------------------------------------------------------------------
963function MenuCreateGrid_Callback(hObject, eventdata, handles)
964%------------------------------------------------------------------------
965%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
966CalibData=get(handles.geometry_calib,'UserData');
967Tinput=[];%default
968if isfield(CalibData,'grid')
969    Tinput=CalibData.grid;
970end
971[T,CalibData.grid]=create_grid(Tinput);%display the GUI create_grid
972set(handles.geometry_calib,'UserData',CalibData)
973
974%grid in phys space
975Coord=get(handles.ListCoord,'String');
976val=get(handles.ListCoord,'Value');
977data=read_geometry_calib(Coord);
978%nbpoints=size(data.Coord,1); %nbre of calibration points
979data.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
980% for i=1:nbpoints
981%    for j=1:5
982%           Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
983%    end
984% end
985%update the phys coordinates starting from the selected point (down in the
986Coord(end,:)=[]; %remove last string '.....'
987for i=1:size(data.Coord,1)
988    for j=1:5
989          Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
990    end
991end
992
993%size(data.Coord,1)
994Tabchar=cell2tab(Coord,' | ');
995Tabchar=[Tabchar ;{'......'}];
996set(handles.ListCoord,'String',Tabchar)
997
998% -----------------------------------------------------------------------
999% --- automatic grid dectection from local maxima of the images
1000function MenuDetectGrid_Callback(hObject, eventdata, handles)
1001%------------------------------------------------------------------------
1002%% read the four last point coordinates in pixels
1003Coord_cell=get(handles.ListCoord,'String');%read list of coordinates on geometry_calib
1004data=read_geometry_calib(Coord_cell);
1005nbpoints=size(data.Coord,1); %nbre of calibration points
1006if nbpoints~=4
1007    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')
1008    return
1009end
1010corners_X=(data.Coord(end:-1:end-3,4)); %pixel absissa of the four corners
1011corners_Y=(data.Coord(end:-1:end-3,5));
1012
1013%reorder the last two points (the two first in the list) if needed
1014angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1)));
1015if abs(angles(4)-angles(2))>abs(angles(3)-angles(2))
1016      X_end=corners_X(4);
1017      Y_end=corners_Y(4);
1018      corners_X(4)=corners_X(3);
1019      corners_Y(4)=corners_Y(3);
1020      corners_X(3)=X_end;
1021      corners_Y(3)=Y_end;
1022end
1023
1024%% initiate the grid
1025CalibData=get(handles.geometry_calib,'UserData');%get information stored on the GUI geometry_calib
1026grid_input=[];%default
1027if isfield(CalibData,'grid')
1028    grid_input=CalibData.grid;%retrieve the previously used grid
1029end
1030[T,CalibData.grid,white_test]=create_grid(grid_input,'detect_grid');%display the GUI create_grid, read the set of phys coordinates T
1031set(handles.geometry_calib,'UserData',CalibData)%store the phys grid parameters for later use
1032
1033
1034
1035%% read the current image, displayed in the GUI uvmat
1036huvmat=findobj(allchild(0),'Name','uvmat');
1037UvData=get(huvmat,'UserData');
1038A=UvData.Field.A;
1039npxy=size(A);
1040X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates (cm)
1041Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates (cm)
1042
1043%calculate transform matrices for plane projection
1044% reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
1045B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
1046      zeros(4,3)        X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ];
1047B = reshape (B', 8 , 8 )';
1048D = [ corners_X , corners_Y ];
1049D = reshape (D', 8 , 1 );
1050l = (B' * B)\B' * D;
1051Amat = reshape([l(1:6)' 0 0 1 ],3,3)';
1052C = [l(7:8)' 1];
1053
1054% transform grid image into 'phys' coordinates
1055GeometryCalib.CalibrationType='linear';
1056GeometryCalib.fx_fy=[1 1];
1057GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
1058GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
1059GeometryCalib.CoordUnit='cm';
1060path_uvmat=which('uvmat');% check the path detected for source file uvmat
1061path_UVMAT=fileparts(path_uvmat); %path to UVMAT
1062addpath(fullfile(path_UVMAT,'transform_field'))
1063Data.ListVarName={'AY','AX','A'};
1064Data.VarDimName={'AY','AX',{'AY','AX'}};
1065if ndims(A)==3
1066    A=mean(A,3);
1067end
1068Data.A=A-min(min(A));
1069Data.AY=[npxy(1)-0.5 0.5];
1070Data.AX=[0.5 npxy(2)];
1071Data.CoordUnit='pixel';
1072Calib.GeometryCalib=GeometryCalib;
1073DataOut=phys(Data,Calib);
1074rmpath(fullfile(path_UVMAT,'transform_field'))
1075Amod=DataOut.A;
1076Rangx=DataOut.AX;
1077Rangy=DataOut.AY;
1078if white_test
1079    Amod=double(Amod);%case of white grid markers: will look for image maxima
1080else
1081    Amod=-double(Amod);%case of black grid markers: will look for image minima
1082end
1083% figure(12) %display corrected image
1084% Amax=max(max(Amod));
1085% image(Rangx,Rangy,uint8(255*Amod/Amax))
1086
1087%% detection of local image extrema in each direction
1088Dx=(Rangx(2)-Rangx(1))/(npxy(2)-1); %x mesh in real space
1089Dy=(Rangy(2)-Rangy(1))/(npxy(1)-1); %y mesh in real space
1090ind_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
1091ind_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
1092nbpoints=size(T,1);
1093for ipoint=1:nbpoints
1094    i0=1+round((T(ipoint,1)-Rangx(1))/Dx);%round(Xpx(ipoint));
1095    j0=1+round((T(ipoint,2)-Rangy(1))/Dy);%round(Xpx(ipoint));
1096    j0min=max(j0-ind_range_y,1);
1097    j0max=min(j0+ind_range_y,size(Amod,1));
1098    i0min=max(i0-ind_range_x,1);
1099    i0max=min(i0+ind_range_x,size(Amod,2));
1100    Asub=Amod(j0min:j0max,i0min:i0max);
1101    x_profile=sum(Asub,1);
1102    y_profile=sum(Asub,2);
1103    [Amax,ind_x_max]=max(x_profile);
1104    [Amax,ind_y_max]=max(y_profile);
1105    %sub-pixel improvement using moments
1106    x_shift=0;
1107    y_shift=0;
1108    if ind_x_max+2<=numel(x_profile) && ind_x_max-2>=1
1109        Atop=x_profile(ind_x_max-2:ind_x_max+2);
1110        x_shift=sum(Atop.*[-2 -1 0 1 2])/sum(Atop);
1111    end
1112    if ind_y_max+2<=numel(y_profile) && ind_y_max-2>=1
1113        Atop=y_profile(ind_y_max-2:ind_y_max+2);
1114        y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop);
1115    end
1116    Delta(ipoint,1)=(x_shift+ind_x_max+i0min-i0-1)*Dx;%shift from the initial guess
1117    Delta(ipoint,2)=(y_shift+ind_y_max+j0min-j0-1)*Dy;
1118end
1119Tmod=T(:,(1:2))+Delta;
1120[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));
1121for ipoint=1:nbpoints
1122     Coord{ipoint,1}=num2str(T(ipoint,1),4);%display coordiantes with 4 digits
1123     Coord{ipoint,2}=num2str(T(ipoint,2),4);%display coordiantes with 4 digits
1124     Coord{ipoint,3}=num2str(T(ipoint,3),4);%display coordiantes with 4 digits;
1125     Coord{ipoint,4}=num2str(Xpx(ipoint),4);%display coordiantes with 4 digits
1126     Coord{ipoint,5}=num2str(Ypx(ipoint),4);%display coordiantes with 4 digits
1127end
1128Tabchar=cell2tab(Coord(end:-1:1,:),' | ');
1129Tabchar=[Tabchar ;{'......'}];
1130set(handles.ListCoord,'Value',1)
1131set(handles.ListCoord,'String',Tabchar)
1132MenuPlot_Callback(hObject, eventdata, handles)
1133
1134%-----------------------------------------------------------------------
1135function MenuTranslatePoints_Callback(hObject, eventdata, handles)
1136%-----------------------------------------------------------------------
1137%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1138CalibData=get(handles.geometry_calib,'UserData');
1139Tinput=[];%default
1140if isfield(CalibData,'translate')
1141    Tinput=CalibData.translate;
1142end
1143T=translate_points(Tinput);%display translate_points GUI and get shift parameters
1144CalibData.translate=T;
1145set(handles.geometry_calib,'UserData',CalibData)
1146%translation
1147Coord_cell=get(handles.ListCoord,'String');
1148data=read_geometry_calib(Coord_cell);
1149data.Coord(:,1)=T(1)+data.Coord(:,1);
1150data.Coord(:,2)=T(2)+data.Coord(:,2);
1151data.Coord(:,3)=T(3)+data.Coord(:,3);
1152data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1153for i=1:size(data.Coord,1)
1154    for j=1:5
1155          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1156   end
1157end
1158Tabchar=cell2tab(Coord,' | ');
1159Tabchar=[Tabchar; {'.....'}];
1160%set(handles.ListCoord,'Value',1)
1161set(handles.ListCoord,'String',Tabchar)
1162
1163
1164% --------------------------------------------------------------------
1165function MenuRotatePoints_Callback(hObject, eventdata, handles)
1166%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1167CalibData=get(handles.geometry_calib,'UserData');
1168Tinput=[];%default
1169if isfield(CalibData,'rotate')
1170    Tinput=CalibData.rotate;
1171end
1172T=rotate_points(Tinput);%display rotate_points GUI to introduce rotation parameters
1173CalibData.rotate=T;
1174set(handles.geometry_calib,'UserData',CalibData)
1175%-----------------------------------------------------
1176%rotation
1177Phi=T(1);
1178O_x=0;%default
1179O_y=0;%default
1180if numel(T)>=2
1181    O_x=T(2);%default
1182end
1183if numel(T)>=3
1184    O_y=T(3);%default
1185end
1186Coord_cell=get(handles.ListCoord,'String');
1187data=read_geometry_calib(Coord_cell);
1188r1=cos(pi*Phi/180);
1189r2=-sin(pi*Phi/180);
1190r3=sin(pi*Phi/180);
1191r4=cos(pi*Phi/180);
1192x=data.Coord(:,1)-O_x;
1193y=data.Coord(:,2)-O_y;
1194data.Coord(:,1)=r1*x+r2*y;
1195data.Coord(:,2)=r3*x+r4*y;
1196% data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1197for i=1:size(data.Coord,1)
1198    for j=1:5
1199          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1200   end
1201end
1202Tabchar=cell2tab(Coord,' | ');
1203Tabchar=[Tabchar;{'......'}];
1204set(handles.ListCoord,'Value',1)
1205set(handles.ListCoord,'String',Tabchar)
1206
1207% --------------------------------------------------------------------
1208function MenuImportPoints_Callback(hObject, eventdata, handles)
1209fileinput=browse_xml(hObject, eventdata, handles);
1210if isempty(fileinput)
1211    return
1212end
1213[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1214GeometryCalib=s.GeometryCalib;
1215%GeometryCalib=load_calib(hObject, eventdata, handles)
1216calib=reshape(GeometryCalib.PointCoord,[],1);
1217for ilist=1:numel(calib)
1218    CoordCell{ilist}=num2str(calib(ilist));
1219end
1220CoordCell=reshape(CoordCell,[],5);
1221Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
1222Tabchar=[Tabchar;{'......'}];
1223set(handles.ListCoord,'Value',1)
1224set(handles.ListCoord,'String',Tabchar)
1225MenuPlot_Callback(handles.geometry_calib, [], handles)
1226
1227% -----------------------------------------------------------------------
1228function MenuImportIntrinsic_Callback(hObject, eventdata, handles)
1229%------------------------------------------------------------------------
1230fileinput=browse_xml(hObject, eventdata, handles);
1231if isempty(fileinput)
1232    return
1233end
1234[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1235GeometryCalib=s.GeometryCalib;
1236display_intrinsic(GeometryCalib,handles)
1237
1238% -----------------------------------------------------------------------
1239function MenuImportAll_Callback(hObject, eventdata, handles)
1240%------------------------------------------------------------------------
1241fileinput=browse_xml(hObject, eventdata, handles);
1242if ~isempty(fileinput)
1243    loadfile(handles,fileinput)
1244end
1245
1246% -----------------------------------------------------------------------
1247% --- Executes on menubar option Import/Grid file: introduce previous grid files
1248function MenuGridFile_Callback(hObject, eventdata, handles)
1249% -----------------------------------------------------------------------
1250inputfile=browse_xml(hObject, eventdata, handles);
1251listfile=get(handles.coord_files,'string');
1252if isequal(listfile,{''})
1253    listfile={inputfile};
1254else
1255    listfile=[listfile;{inputfile}];%update the list of coord files
1256end
1257set(handles.coord_files,'string',listfile);
1258
1259%------------------------------------------------------------------------
1260% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
1261function key_press_fcn(hObject,eventdata,handles)
1262%------------------------------------------------------------------------
1263xx=double(get(handles.geometry_calib,'CurrentCharacter')); %get the keyboard character
1264if ismember(xx,[8 127])%backspace or delete
1265    Coord_cell=get(handles.ListCoord,'String');
1266    val=get(handles.ListCoord,'Value');
1267     if max(val)<numel(Coord_cell) % the last element '...' has not been selected
1268        Coord_cell(val)=[];%remove the selected line
1269        set(handles.ListCoord,'Value',min(val))
1270        set(handles.ListCoord,'String',Coord_cell)         
1271        ListCoord_Callback(hObject, eventdata, handles)
1272        MenuPlot_Callback(hObject,eventdata,handles)
1273     end
1274end
1275
1276%------------------------------------------------------------------------
1277function fileinput=browse_xml(hObject, eventdata, handles)
1278%------------------------------------------------------------------------
1279fileinput=[];%default
1280oldfile=''; %default
1281UserData=get(handles.geometry_calib,'UserData');
1282if isfield(UserData,'XmlInputFile')
1283    oldfile=UserData.XmlInputFile;
1284end
1285[FileName, PathName, filterindex] = uigetfile( ...
1286       {'*.xml;*.mat', ' (*.xml,*.mat)';
1287       '*.xml',  '.xml files '; ...
1288        '*.mat',  '.mat matlab files '}, ...
1289        'Pick a file',oldfile);
1290fileinput=[PathName FileName];%complete file name
1291testblank=findstr(fileinput,' ');%look for blanks
1292if ~isempty(testblank)
1293    msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed')
1294    return
1295end
1296sizf=size(fileinput);
1297if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1298UserData.XmlInputFile=fileinput;
1299set(handles.geometry_calib,'UserData',UserData)%record current file foer further use of browser
1300
1301% -----------------------------------------------------------------------
1302function Heading=loadfile(handles,fileinput)
1303%------------------------------------------------------------------------
1304Heading=[];%default
1305[s,errormsg]=imadoc2struct(fileinput,'Heading','GeometryCalib');
1306if ~isempty(errormsg)
1307    msgbox_uvmat('ERROR',errormsg)
1308    return
1309end
1310if ~isempty(s.Heading)
1311    Heading=s.Heading;
1312end
1313   
1314GeometryCalib=s.GeometryCalib;
1315fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
1316CoordCell={};
1317Tabchar={};%default
1318val_cal=1;%default
1319if ~isempty(GeometryCalib)
1320    % choose the calibration option
1321    if isfield(GeometryCalib,'CalibrationType')
1322       calib_list=get(handles.calib_type,'String');
1323       for ilist=1:numel(calib_list)
1324           if strcmp(calib_list{ilist},GeometryCalib.CalibrationType)
1325               val_cal=ilist;
1326               break
1327           end
1328       end
1329    end
1330    display_intrinsic(GeometryCalib,handles)%intrinsic param
1331    %extrinsic param
1332    if isfield(GeometryCalib,'Tx_Ty_Tz')
1333        Tx_Ty_Tz=GeometryCalib.Tx_Ty_Tz;
1334        set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
1335        set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
1336        set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
1337    end
1338    if isfield(GeometryCalib,'omc')
1339        set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
1340        set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
1341        set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
1342    end
1343    calib=reshape(GeometryCalib.SourceCalib.PointCoord,[],1);
1344    for ilist=1:numel(calib)
1345        CoordCell{ilist}=num2str(calib(ilist));
1346    end
1347    CoordCell=reshape(CoordCell,[],5);
1348    Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
1349    MenuPlot_Callback(handles.geometry_calib, [], handles)
1350end
1351set(handles.calib_type,'Value',val_cal)
1352Tabchar=[Tabchar;{'......'}];
1353set(handles.ListCoord,'Value',1)
1354set(handles.ListCoord,'String',Tabchar)
1355
1356if isempty(CoordCell)% allow mouse action by default in the absence of input points
1357    set(handles.edit_append,'Value',1)
1358    set(handles.edit_append,'BackgroundColor',[1 1 0])
1359else % does not allow mouse action by default in the presence of input points
1360    set(handles.edit_append,'Value',0)
1361    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
1362end
1363
1364%------------------------------------------------------------------------
1365%---display calibration intrinsic parameters
1366function display_intrinsic(GeometryCalib,handles)
1367%------------------------------------------------------------------------
1368fx=[];
1369fy=[];
1370if isfield(GeometryCalib,'fx_fy')
1371    fx=GeometryCalib.fx_fy(1);
1372    fy=GeometryCalib.fx_fy(2);
1373end
1374Cx_Cy=[0 0];%default
1375if isfield(GeometryCalib,'Cx_Cy')
1376    Cx_Cy=GeometryCalib.Cx_Cy;
1377end
1378kc=0;
1379if isfield(GeometryCalib,'kc')
1380    kc=GeometryCalib.kc; %* GeometryCalib.focal*GeometryCalib.focal;
1381end
1382set(handles.fx,'String',num2str(fx,5))
1383set(handles.fy,'String',num2str(fy,5))
1384set(handles.Cx,'String',num2str(Cx_Cy(1),'%1.1f'))
1385set(handles.Cy,'String',num2str(Cx_Cy(2),'%1.1f'))
1386set(handles.kc,'String',num2str(kc,'%1.4f'))
1387
1388
1389% --- Executes when user attempts to close geometry_calib.
1390function geometry_calib_CloseRequestFcn(hObject, eventdata, handles)
1391% hObject    handle to geometry_calib (see GCBO)
1392% eventdata  reserved - to be defined in a future version of MATLAB
1393% handles    structure with handles and user data (see GUIDATA)
1394
1395% Hint: delete(hObject) closes the figure
1396delete(hObject);
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