source: trunk/src/geometry_calib.m @ 356

Last change on this file since 356 was 356, checked in by sommeria, 9 years ago

civ updated with new functions for opening files, consistently with uvmat
Bugs to be expected (use previous version then)

File size: 60.4 KB
RevLine 
[168]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)
[2]4%
[168]5%OUTPUT:
6% hgeometry_calib=current handles of the GUI geometry_calib.fig
[2]7%
[168]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%
[109]12%A%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
[2]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
[114]52% Last Modified by GUIDE v2.5 05-Oct-2010 13:47:00
[2]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',   []);
[128]62if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback','once'))
[2]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')
[60]79%------------------------------------------------------------------------
[116]80function geometry_calib_OpeningFcn(hObject, eventdata, handles,inputfile,pos)
[60]81%------------------------------------------------------------------------
[2]82% Choose default command line output for geometry_calib
[156]83
[2]84handles.output = hObject;
85
86% Update handles structure
87guidata(hObject, handles);
[71]88set(hObject,'DeleteFcn',{@closefcn})%
[252]89set(hObject,'WindowButtonDownFcn',{'mouse_alt_gui',handles}) % allows mouse action with right button (zoom for uicontrol display)
[71]90
[2]91%set the position of the interface
[156]92if exist('pos','var')&& length(pos)>=4
93%     %pos_gui=get(hObject,'Position');
94%     pos_gui(1)=pos(1);
95%     pos_gui(2)=pos(2);
96    set(hObject,'Position',pos);
[2]97end
[109]98
99%set menu of calibration options
[121]100set(handles.calib_type,'String',{'rescale';'linear';'3D_linear';'3D_quadr';'3D_extrinsic'})
[341]101% inputxml='';
[116]102if exist('inputfile','var')&& ~isempty(inputfile)
[114]103    struct.XmlInputFile=inputfile;
[341]104%     [Pathsub,RootFile,field_count,str2,str_a,str_b,ext]=name2display(inputfile);
105    [RootPath,~,RootFile,~,~,~,~,FileExt]=fileparts_uvmat(inputfile);
106    if ~strcmp(FileExt,'.xml')
107        inputfile=[fullfile(RootPath,RootFile) '.xml'];%xml file corresponding to the input file
[116]108    end
[156]109    set(handles.ListCoord,'String',{'......'})
110    if exist(inputfile,'file')
111        Heading=loadfile(handles,inputfile);% load the point coordiantes existing in the xml file
112        if isfield(Heading,'Campaign')&& ischar(Heading.Campaign)
113            struct.Campaign=Heading.Campaign;
114        end
115    end   
116    set(hObject,'UserData',struct)
[2]117end
[156]118
[2]119set(handles.ListCoord,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function
120
[71]121
[17]122%------------------------------------------------------------------------
[2]123% --- Outputs from this function are returned to the command line.
124function varargout = geometry_calib_OutputFcn(hObject, eventdata, handles)
[17]125%------------------------------------------------------------------------
[2]126% Get default command line output from handles structure
127varargout{1} = handles.output;
128varargout{2}=handles;
[67]129%
[60]130%------------------------------------------------------------------------
[2]131% executed when closing: set the parent interface button to value 0
[67]132function closefcn(gcbo,eventdata)
[60]133%------------------------------------------------------------------------
[2]134huvmat=findobj(allchild(0),'Name','uvmat');
[67]135if ~isempty(huvmat)
136    handles=guidata(huvmat);
137    hobject=findobj(handles.axes3,'tag','calib_points');
138    if ~isempty(hobject)
139        delete(hobject)
140    end
141    hobject=findobj(handles.axes3,'tag','calib_marker');
142    if ~isempty(hobject)
143        delete(hobject)
144    end   
[2]145end
146
[60]147%------------------------------------------------------------------------
[2]148% --- Executes on button press in calibrate_lin.
149function APPLY_Callback(hObject, eventdata, handles)
[60]150%------------------------------------------------------------------------
[109]151%read the current calibration points
[2]152Coord_cell=get(handles.ListCoord,'String');
153Object=read_geometry_calib(Coord_cell);
[109]154Coord=Object.Coord;
155% apply the calibration, whose type is selected in  handles.calib_type
156if ~isempty(Coord)
157    calib_cell=get(handles.calib_type,'String');
158    val=get(handles.calib_type,'Value');
159    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
160else
161    msgbox_uvmat('ERROR','No calibration points, abort')
162    return
163end
[114]164Z_plane=[];
[109]165if ~isempty(Coord)
[114]166    %check error
[109]167    X=Coord(:,1);
168    Y=Coord(:,2);
169    Z=Coord(:,3);
170    x_ima=Coord(:,4);
171    y_ima=Coord(:,5);
[114]172    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
[109]173    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
174    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
175    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
176    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
[341]177    [~,ind_dim]=max(GeometryCalib.ErrorMax);
[109]178    index=index(ind_dim);
[114]179    %set the Z position of the reference plane used for calibration
[109]180    if isequal(max(Z),min(Z))%Z constant
[114]181        Z_plane=Z(1);
[109]182        GeometryCalib.NbSlice=1;
[114]183        GeometryCalib.SliceCoord=[0 0 Z_plane];
[109]184    end
185end
[114]186%set the coordinate unit
[2]187unitlist=get(handles.CoordUnit,'String');
188unit=unitlist{get(handles.CoordUnit,'value')};
189GeometryCalib.CoordUnit=unit;
[114]190%record the points
[109]191GeometryCalib.SourceCalib.PointCoord=Coord;
[114]192display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
[109]193
[114]194% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
[109]195set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
196set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
197set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
[114]198set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
199set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
200set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
[109]201
[114]202% store the calibration data, by default in the xml file of the currently displayed image
[191]203huvmat=findobj(allchild(0),'Name','uvmat');
204UvData=get(huvmat,'UserData');
205NbSlice_j=1;%default
206ZStart=Z_plane;
207ZEnd=Z_plane;
[196]208volume_scan='n';
[191]209if isfield(UvData,'XmlData')
210    UvData.XmlData
211    if isfield(UvData.XmlData,'TranslationMotor')
212        NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice;
[196]213        ZStart=UvData.XmlData.TranslationMotor.ZStart/10;
214        ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10;
215        volume_scan='y';
[191]216    end
217end
218hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
[2]219RootPath='';
[341]220% RootFile='';
[121]221if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
[341]222%     testhandle=1;
[2]223    RootPath=get(hhuvmat.RootPath,'String');
224    RootFile=get(hhuvmat.RootFile,'String');
225    filebase=fullfile(RootPath,RootFile);
[114]226    outputfile=[filebase '.xml'];%xml file associated with the currently displayed image
[2]227else
228    question={'save the calibration data and point coordinates in'};
[121]229    def={fullfile(RootPath,'ObjectCalib.xml')};
[2]230    options.Resize='on';
231    answer=inputdlg(question,'save average in a new file',1,def,options);
232    outputfile=answer{1};
233end
[84]234answer=msgbox_uvmat('INPUT_Y-N',{[outputfile ' updated with calibration data'];...
[2]235    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
[84]236    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
[128]237
238%% record the calibration parameters and display the current image of uvmat in the new phys coordinates
[121]239if strcmp(answer,'Yes')
240    if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
[213]241       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'};
242       input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}];
243        answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on');
[191]244        %answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
245        GeometryCalib.NbSlice=str2double(answer{5});
246        GeometryCalib.VolumeScan=answer{6};
247        if isempty(answer)
[121]248            Z_plane=0; %default
249        else
[191]250            Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice);
251        end     
[196]252        GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
[213]253        GeometryCalib.SliceAngle(:,3)=0;
254        GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise)
255        GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise)
[196]256        GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})];
[207]257        GeometryCalib.RefractionIndex=str2double(answer{4});     
[121]258    end
[114]259    errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file
260    if ~strcmp(errormsg,'')
261        msgbox_uvmat('ERROR',errormsg);
262    end
[128]263   
[84]264    %display image with new calibration in the currently opened uvmat interface
265    hhh=findobj(hhuvmat.axes3,'Tag','calib_marker');% delete calib points and markers
266    if ~isempty(hhh)
[109]267        delete(hhh);     
[84]268    end
269    hhh=findobj(hhuvmat.axes3,'Tag','calib_points');
270    if ~isempty(hhh)
271        delete(hhh);
272    end
[332]273    set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off'
274    set(hhuvmat.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
[116]275    UserData=get(handles.geometry_calib,'UserData');
276    UserData.XmlInputFile=outputfile;%save the current xml file name
277    set(handles.geometry_calib,'UserData',UserData)
[114]278    uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
279    MenuPlot_Callback(hObject, eventdata, handles)
280    set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
281    ListCoord_Callback(hObject, eventdata, handles)
[84]282    figure(handles.geometry_calib)
[2]283end
[69]284
285%------------------------------------------------------------------
[2]286% --- Executes on button press in calibrate_lin.
[128]287
[2]288function REPLICATE_Callback(hObject, eventdata, handles)
[60]289%------------------------------------------------------------------------
[2]290
[128]291%% Apply calibration
292calib_cell=get(handles.calib_type,'String'); %#ok<NASGU>
293val=get(handles.calib_type,'Value'); %#ok<NASGU>
294
[114]295%read the current calibration points
296Coord_cell=get(handles.ListCoord,'String');
297Object=read_geometry_calib(Coord_cell);
298Coord=Object.Coord;
[2]299
[114]300% apply the calibration, whose type is selected in  handles.calib_type
301if ~isempty(Coord)
302    calib_cell=get(handles.calib_type,'String');
303    val=get(handles.calib_type,'Value');
304    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
305else
306    msgbox_uvmat('ERROR','No calibration points, abort')
307    return
308end
309
310if ~isempty(Coord)
311    %check error
312    X=Coord(:,1);
313    Y=Coord(:,2);
314    Z=Coord(:,3);
315    x_ima=Coord(:,4);
316    y_ima=Coord(:,5);
317    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
318    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
[341]319    [GeometryCalib.ErrorMax(1)]=max(abs(Xpoints-x_ima));
[114]320    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
[341]321    [GeometryCalib.ErrorMax(2)]=max(abs(Ypoints-y_ima));
322%     [EM,ind_dim]=max(GeometryCalib.ErrorMax);
[114]323    %set the Z position of the reference plane used for calibration
324    Z_plane=[];
325    if isequal(max(Z),min(Z))
326        Z_plane=Z(1);
327    end
328    answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
[128]329    Z_plane=str2double(answer_1);
[114]330    GeometryCalib.NbSlice=1;
331    GeometryCalib.SliceCoord=[0 0 Z_plane];
332    %set the coordinate unit
333    unitlist=get(handles.CoordUnit,'String');
334    unit=unitlist{get(handles.CoordUnit,'value')};
335    GeometryCalib.CoordUnit=unit;
336    %record the points
337    GeometryCalib.SourceCalib.PointCoord=Coord;
338end
[128]339
340%% display calibration paprameters
[114]341display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
342
343% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
344set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
345set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
346set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
347set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
348set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
349set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
350
[128]351%% open the GUI dataview
[2]352h_dataview=findobj(allchild(0),'name','dataview');
[12]353if ~isempty(h_dataview)
354    delete(h_dataview)
[2]355end
[61]356CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
[341]357% InputFile='';
[114]358if isfield(CalibData,'XmlInputFile')
[128]359    InputDir=fileparts(CalibData.XmlInputFile);
360    [InputDir,DirName]=fileparts(InputDir);
[2]361end
[12]362SubCampaignTest='n'; %default
[128]363testup=0;
364if isfield(CalibData,'SubCampaign')
365    SubCampaignTest='y';
366    dir_ref=CalibData.SubCampaign;
367    testup=1;
368elseif isfield(CalibData,'Campaign')
369    dir_ref=CalibData.Campaign;
370    testup=1;
[2]371end
[128]372while testup
373    [InputDir,DirName]=fileparts(InputDir);
374    if strcmp(DirName,dir_ref)
375        break
[2]376    end
377end
[128]378InputDir=fullfile(InputDir,DirName);
379answer=msgbox_uvmat('INPUT_TXT','Campaign ?',InputDir);
380if strcmp(answer,'Cancel')
381    return
[2]382end
383
[128]384dataview(answer,SubCampaignTest,GeometryCalib);
385
[60]386%------------------------------------------------------------------------
[2]387% determine the parameters for a calibration by an affine function (rescaling and offset, no rotation)
[109]388function GeometryCalib=calib_rescale(Coord,handles)
[60]389%------------------------------------------------------------------------
[2]390X=Coord(:,1);
[109]391Y=Coord(:,2);% Z not used
[2]392x_ima=Coord(:,4);
393y_ima=Coord(:,5);
[341]394[px]=polyfit(X,x_ima,1);
395[py]=polyfit(Y,y_ima,1);
396% T_x=px(2);
397% T_y=py(2);
[2]398GeometryCalib.CalibrationType='rescale';
[121]399GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
[2]400GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
[114]401GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
402GeometryCalib.omc=[0 0 0];
[2]403
[60]404%------------------------------------------------------------------------
[2]405% determine the parameters for a calibration by a linear transform matrix (rescale and rotation)
[242]406
407
[227]408function GeometryCalib=calib_linear(Coord,handles)
[60]409%------------------------------------------------------------------------
[2]410X=Coord(:,1);
[109]411Y=Coord(:,2);% Z not used
[2]412x_ima=Coord(:,4);
413y_ima=Coord(:,5);
414XY_mat=[ones(size(X)) X Y];
415a_X1=XY_mat\x_ima; %transformation matrix for X
416a_Y1=XY_mat\y_ima;%transformation matrix for X
[121]417R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
[242]418epsilon=sign(det(R));
[116]419norm=abs(det(R));
[2]420GeometryCalib.CalibrationType='linear';
[238]421if (a_X1(2)/a_Y1(3))>0
[242]422    GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm);
[238]423else
[242]424    GeometryCalib.fx_fy(1)=-sqrt(-(a_X1(2)/a_Y1(3))*norm);
[238]425end
[121]426GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
[2]427GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
[227]428GeometryCalib.Tx_Ty_Tz=[a_X1(1)/GeometryCalib.fx_fy(1) a_Y1(1)/GeometryCalib.fx_fy(2) 1];
[242]429R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
[121]430R(2,:)=R(2,:)/GeometryCalib.fx_fy(2);
431R=[R;[0 0]];
[242]432GeometryCalib.R=[R [0;0;-epsilon]];
433GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
[109]434%------------------------------------------------------------------------
435% determine the tsai parameters for a view normal to the grid plane
[114]436% NOT USED
[109]437function GeometryCalib=calib_normal(Coord,handles)
438%------------------------------------------------------------------------
439Calib.f1=str2num(get(handles.fx,'String'));
440Calib.f2=str2num(get(handles.fy,'String'));
[114]441Calib.k=str2num(get(handles.kc,'String'));
[109]442Calib.Cx=str2num(get(handles.Cx,'String'));
443Calib.Cy=str2num(get(handles.Cy,'String'));
444%default
445if isempty(Calib.f1)
446    Calib.f1=25/0.012;
447end
448if isempty(Calib.f2)
449    Calib.f2=25/0.012;
450end
451if isempty(Calib.k)
452    Calib.k=0;
453end
454if isempty(Calib.Cx)||isempty(Calib.Cy)
455    huvmat=findobj(allchild(0),'Tag','uvmat');
456    hhuvmat=guidata(huvmat);
[332]457    Calib.Cx=str2num(get(hhuvmat.num_Npx,'String'))/2;
458    Calib.Cx=str2num(get(hhuvmat.num_Npy,'String'))/2;
[109]459end   
460%tsai parameters
461Calib.dpx=0.012;%arbitrary
462Calib.dpy=0.012;
463Calib.sx=Calib.f1*Calib.dpx/(Calib.f2*Calib.dpy);
464Calib.f=Calib.f2*Calib.dpy;
465Calib.kappa1=Calib.k/(Calib.f*Calib.f);
[2]466
[109]467%initial guess
468X=Coord(:,1);
469Y=Coord(:,2);
470Zmean=mean(Coord(:,3));
471x_ima=Coord(:,4)-Calib.Cx;
472y_ima=Coord(:,5)-Calib.Cy;
473XY_mat=[ones(size(X)) X Y];
474a_X1=XY_mat\x_ima; %transformation matrix for X
475a_Y1=XY_mat\y_ima;%transformation matrix for Y
476R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,-1];% rotation+ z axis reversal (upward)
477norm=sqrt(det(-R));
478calib_param(1)=0;% quadratic distortion
479calib_param(2)=a_X1(1);
480calib_param(3)=a_Y1(1);
481calib_param(4)=Calib.f/(norm*Calib.dpx)-R(3,3)*Zmean;
[121]482calib_param(5)=angle(a_X1(2)+1i*a_X1(3));
[109]483display(['initial guess=' num2str(calib_param)])
484
485%optimise the parameters: minimisation of error
[121]486calib_param = fminsearch(@(calib_param) error_calib(calib_param,Calib,Coord),calib_param);
[109]487
488GeometryCalib.CalibrationType='tsai_normal';
489GeometryCalib.focal=Calib.f;
490GeometryCalib.dpx_dpy=[Calib.dpx Calib.dpy];
491GeometryCalib.Cx_Cy=[Calib.Cx Calib.Cy];
492GeometryCalib.sx=Calib.sx;
493GeometryCalib.kappa1=calib_param(1);
494GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
495GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)];
496alpha=calib_param(5);
497GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
498
[60]499%------------------------------------------------------------------------
[109]500function GeometryCalib=calib_3D_linear(Coord,handles)
[69]501%------------------------------------------------------------------
502path_uvmat=which('uvmat');% check the path detected for source file uvmat
503path_UVMAT=fileparts(path_uvmat); %path to UVMAT
[78]504huvmat=findobj(allchild(0),'Tag','uvmat');
505hhuvmat=guidata(huvmat);
[121]506coord_files=get(handles.coord_files,'String');
507if ischar(coord_files)
508    coord_files={coord_files};
509end
510if isempty(coord_files{1}) || isequal(coord_files,{''})
511    coord_files={};
512end
513%retrieve the calibration points stored in the files listed in the popup list coord_files
514x_1=Coord(:,4:5)';%px coordinates of the ref points
[332]515nx=str2num(get(hhuvmat.num_Npx,'String'));
516ny=str2num(get(hhuvmat.num_Npy,'String'));
[121]517x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
518X_1=Coord(:,1:3)';%phys coordinates of the ref points
519n_ima=numel(coord_files)+1;
520if ~isempty(coord_files)
521    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
522    for ifile=1:numel(coord_files)
523    t=xmltree(coord_files{ifile});
524    s=convert(t);%convert to matlab structure
525        if isfield(s,'GeometryCalib')
526            if isfield(s.GeometryCalib,'SourceCalib')
527                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
528                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
529                Coord_file=zeros(length(PointCoord),5);%default
530                for i=1:length(PointCoord)
531                    line=str2num(PointCoord{i});
532                    Coord_file(i,4:5)=line(4:5);%px x
533                    Coord_file(i,1:3)=line(1:3);%phys x
534                end
535                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
536                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
537                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
538                end
539            end
540        end
541    end
542end
543n_ima=numel(coord_files)+1;
[109]544est_dist=[0;0;0;0;0];
545est_aspect_ratio=0;
546est_fc=[1;1];
547%fc=[25;25]/0.012;
548center_optim=0;
549run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
550GeometryCalib.CalibrationType='3D_linear';
[121]551GeometryCalib.fx_fy=fc';
552%GeometryCalib.focal=fc(2);
553%GeometryCalib.dpx_dpy=[1 1];
[109]554GeometryCalib.Cx_Cy=cc';
[121]555%GeometryCalib.sx=fc(1)/fc(2);
556GeometryCalib.kc=kc(1);
557%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
[109]558GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
559GeometryCalib.Tx_Ty_Tz=Tc_1';
560GeometryCalib.R=Rc_1;
[121]561GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
562GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
563GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
564GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
565GeometryCalib.ErrorRMS=[];
566GeometryCalib.ErrorMax=[];
[109]567
568%------------------------------------------------------------------------
569function GeometryCalib=calib_3D_quadr(Coord,handles)
570%------------------------------------------------------------------
571
572path_uvmat=which('uvmat');% check the path detected for source file uvmat
573path_UVMAT=fileparts(path_uvmat); %path to UVMAT
574huvmat=findobj(allchild(0),'Tag','uvmat');
575hhuvmat=guidata(huvmat);
576% check_cond=0;
577coord_files=get(handles.coord_files,'String');
578if ischar(coord_files)
579    coord_files={coord_files};
580end
581if isempty(coord_files{1}) || isequal(coord_files,{''})
582    coord_files={};
583end
584
585%retrieve the calibration points stored in the files listed in the popup list coord_files
[114]586x_1=Coord(:,4:5)';%px coordinates of the ref points
[332]587nx=str2num(get(hhuvmat.num_Npx,'String'));
588ny=str2num(get(hhuvmat.num_Npy,'String'));
[114]589x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
590X_1=Coord(:,1:3)';%phys coordinates of the ref points
[109]591n_ima=numel(coord_files)+1;
592if ~isempty(coord_files)
593    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
594    for ifile=1:numel(coord_files)
595    t=xmltree(coord_files{ifile});
596    s=convert(t);%convert to matlab structure
597        if isfield(s,'GeometryCalib')
598            if isfield(s.GeometryCalib,'SourceCalib')
599                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
600                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
[121]601                Coord_file=zeros(length(PointCoord),5);%default
[109]602                for i=1:length(PointCoord)
603                    line=str2num(PointCoord{i});
604                    Coord_file(i,4:5)=line(4:5);%px x
605                    Coord_file(i,1:3)=line(1:3);%phys x
606                end
607                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
[114]608                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
[109]609                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
610                end
611            end
612        end
613    end
614end
615n_ima=numel(coord_files)+1;
[108]616est_dist=[1;0;0;0;0];
[109]617est_aspect_ratio=1;
618%est_fc=[0;0];
619%fc=[25;25]/0.012;
620center_optim=0;
[83]621run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
[69]622
[109]623GeometryCalib.CalibrationType='3D_quadr';
[114]624GeometryCalib.fx_fy=fc';
625%GeometryCalib.focal=fc(2);
626%GeometryCalib.dpx_dpy=[1 1];
[69]627GeometryCalib.Cx_Cy=cc';
[114]628%GeometryCalib.sx=fc(1)/fc(2);
629GeometryCalib.kc=kc(1);
630%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
[69]631GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
632GeometryCalib.Tx_Ty_Tz=Tc_1';
633GeometryCalib.R=Rc_1;
[114]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_1;%angles in degrees
[109]638GeometryCalib.ErrorRMS=[];
639GeometryCalib.ErrorMax=[];
[69]640
[109]641
[60]642%------------------------------------------------------------------------
[109]643function GeometryCalib=calib_3D_extrinsic(Coord,handles)
644%------------------------------------------------------------------
645path_uvmat=which('geometry_calib');% check the path detected for source file uvmat
646path_UVMAT=fileparts(path_uvmat); %path to UVMAT
[116]647x_1=double(Coord(:,4:5)');%image coordiantes
648X_1=double(Coord(:,1:3)');% phys coordinates
[114]649huvmat=findobj(allchild(0),'Tag','uvmat');
650hhuvmat=guidata(huvmat);
[332]651ny=str2double(get(hhuvmat.num_Npy,'String'));
[114]652x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
[109]653n_ima=1;
[114]654GeometryCalib.CalibrationType='3D_extrinsic';
655GeometryCalib.fx_fy(1)=str2num(get(handles.fx,'String'));
656GeometryCalib.fx_fy(2)=str2num(get(handles.fy,'String'));
657GeometryCalib.Cx_Cy(1)=str2num(get(handles.Cx,'String'));
658GeometryCalib.Cx_Cy(2)=str2num(get(handles.Cy,'String'));
659GeometryCalib.kc=str2num(get(handles.kc,'String'));
[109]660fct_path=fullfile(path_UVMAT,'toolbox_calib');
661addpath(fct_path)
[116]662GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate)
[109]663% [omc1,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
664%     [Calib.f Calib.f*Calib.sx]',...
665%     [Calib.Cx Calib.Cy]',...
666%     [-Calib.kappa1*Calib.f^2 0 0 0 0]);
[114]667[omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
[116]668    (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]);
[109]669rmpath(fct_path);
670GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
671GeometryCalib.Tx_Ty_Tz=Tc1';
672%inversion of z axis
673GeometryCalib.R=Rc1;
[114]674GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
675GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
[116]676GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
[114]677GeometryCalib.omc=(180/pi)*omc';
[109]678%GeometryCalib.R(3,1:3)=-GeometryCalib.R(3,1:3);%inversion for z upward
679
680
[116]681
[109]682%------------------------------------------------------------------------
683%function GeometryCalib=calib_tsai_heikkila(Coord)
684% TEST: NOT IMPLEMENTED
685%------------------------------------------------------------------
686% path_uvmat=which('uvmat');% check the path detected for source file uvmat
687% path_UVMAT=fileparts(path_uvmat); %path to UVMAT
688% path_calib=fullfile(path_UVMAT,'toolbox_calib_heikkila');
689% addpath(path_calib)
690% npoints=size(Coord,1);
691% Coord(:,1:3)=10*Coord(:,1:3);
692% Coord=[Coord zeros(npoints,2) -ones(npoints,1)];
693% [par,pos,iter,res,er,C]=cacal('dalsa',Coord);
694% GeometryCalib.CalibrationType='tsai';
695% GeometryCalib.focal=par(2);
696
697
698%------------------------------------------------------------------------
699% --- determine the rms of calibration error
700function ErrorRms=error_calib(calib_param,Calib,Coord)
701%calib_param: vector of free calibration parameters (to optimise)
702%Calib: structure of the given calibration parameters
703%Coord: list of phys coordinates (columns 1-3, and pixel coordinates (columns 4-5)
704Calib.f=25;
705Calib.dpx=0.012;
706Calib.dpy=0.012;
707Calib.sx=1;
708Calib.Cx=512;
709Calib.Cy=512;
710Calib.kappa1=calib_param(1);
711Calib.Tx=calib_param(2);
712Calib.Ty=calib_param(3);
713Calib.Tz=calib_param(4);
714alpha=calib_param(5);
715Calib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
[2]716
[109]717X=Coord(:,1);
718Y=Coord(:,2);
719Z=Coord(:,3);
720x_ima=Coord(:,4);
721y_ima=Coord(:,5);
722[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z);
723ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
724ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
725ErrorRms=mean(ErrorRms);
726
[60]727%------------------------------------------------------------------------
[2]728function XImage_Callback(hObject, eventdata, handles)
[60]729%------------------------------------------------------------------------
[2]730update_list(hObject, eventdata,handles)
731
[60]732%------------------------------------------------------------------------
[2]733function YImage_Callback(hObject, eventdata, handles)
[60]734%------------------------------------------------------------------------
[2]735update_list(hObject, eventdata,handles)
736
[109]737%------------------------------------------------------------------------
738% --- Executes on button press in STORE.
739function STORE_Callback(hObject, eventdata, handles)
740Coord_cell=get(handles.ListCoord,'String');
741Object=read_geometry_calib(Coord_cell);
742unitlist=get(handles.CoordUnit,'String');
743unit=unitlist{get(handles.CoordUnit,'value')};
744GeometryCalib.CoordUnit=unit;
745GeometryCalib.SourceCalib.PointCoord=Object.Coord;
746huvmat=findobj(allchild(0),'Name','uvmat');
747hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
[128]748% RootPath='';
749% RootFile='';
[121]750if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
[341]751%     testhandle=1;
[109]752    RootPath=get(hhuvmat.RootPath,'String');
753    RootFile=get(hhuvmat.RootFile,'String');
754    filebase=fullfile(RootPath,RootFile);
755    while exist([filebase '.xml'],'file')
756        filebase=[filebase '~'];
757    end
758    outputfile=[filebase '.xml'];
[114]759    errormsg=update_imadoc(GeometryCalib,outputfile);
760    if ~strcmp(errormsg,'')
761        msgbox_uvmat('ERROR',errormsg);
762    end
[109]763    listfile=get(handles.coord_files,'string');
764    if isequal(listfile,{''})
765        listfile={outputfile};
766    else
[128]767        listfile=[listfile;{outputfile}];%update the list of coord files
[109]768    end
769    set(handles.coord_files,'string',listfile);
770end
771set(handles.ListCoord,'Value',1)% refresh the display of coordinates
772set(handles.ListCoord,'String',{'......'})
773
[114]774% --------------------------------------------------------------------
775% --- Executes on button press in CLEAR_PTS: clear the list of calibration points
776function CLEAR_PTS_Callback(hObject, eventdata, handles)
777% --------------------------------------------------------------------
778set(handles.ListCoord,'Value',1)% refresh the display of coordinates
779set(handles.ListCoord,'String',{'......'})
780MenuPlot_Callback(hObject, eventdata, handles)
781
[109]782%------------------------------------------------------------------------
783% --- Executes on button press in CLEAR.
784function CLEAR_Callback(hObject, eventdata, handles)
785%------------------------------------------------------------------------
786set(handles.coord_files,'Value',1)
787set(handles.coord_files,'String',{''})
788
789%------------------------------------------------------------------------
[2]790function XObject_Callback(hObject, eventdata, handles)
[109]791%------------------------------------------------------------------------
[2]792update_list(hObject, eventdata,handles)
793
[109]794%------------------------------------------------------------------------
[2]795function YObject_Callback(hObject, eventdata, handles)
[109]796%------------------------------------------------------------------------
[2]797update_list(hObject, eventdata,handles)
798
[109]799%------------------------------------------------------------------------
[2]800function ZObject_Callback(hObject, eventdata, handles)
[109]801%------------------------------------------------------------------------
[2]802update_list(hObject, eventdata,handles)
803
[60]804%------------------------------------------------------------------------
[2]805function update_list(hObject, eventdata, handles)
[60]806%------------------------------------------------------------------------
[149]807newval(4)=str2double(get(handles.XImage,'String'));
808newval(5)=str2double(get(handles.YImage,'String'));
809newval(1)=str2double(get(handles.XObject,'String'));
810newval(2)=str2double(get(handles.YObject,'String'));
811newval(3)=str2double(get(handles.ZObject,'String'));
812if isnan(newval(3))
813    newval(3)=0;%put z to 0 by default
[2]814end
815Coord=get(handles.ListCoord,'String');
[149]816Coord(end)=[]; %remove last string '.....'
[2]817val=get(handles.ListCoord,'Value');
[149]818data=read_geometry_calib(Coord);
819data.Coord(val,:)=newval;
820for i=1:size(data.Coord,1)
821    for j=1:5
822          Coord_cell{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
823    end
824end
825
826Tabchar=cell2tab(Coord_cell,' | ');
827Tabchar=[Tabchar ;{'......'}];
828set(handles.ListCoord,'String',Tabchar)
829
[60]830%update the plot
831ListCoord_Callback(hObject, eventdata, handles)
[67]832MenuPlot_Callback(hObject, eventdata, handles)
[71]833
[60]834%------------------------------------------------------------------------
[2]835% --- Executes on selection change in ListCoord.
836function ListCoord_Callback(hObject, eventdata, handles)
[60]837%------------------------------------------------------------------------
[71]838huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
839hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
840hhh=findobj(hplot,'Tag','calib_marker');
[2]841Coord_cell=get(handles.ListCoord,'String');
842val=get(handles.ListCoord,'Value');
[78]843if numel(val)>1
844    return %no action if several lines have been selected
845end
[71]846coord_str=Coord_cell{val};
[128]847k=findstr(' | ',coord_str);
[71]848if isempty(k)%last line '.....' selected
849    if ~isempty(hhh)
850        delete(hhh)%delete the circle marker
[2]851    end
[71]852    return
853end
854%fill the edit boxex
[149]855set(handles.XObject,'String',coord_str(1:k(1)-1))
856set(handles.YObject,'String',coord_str(k(1)+3:k(2)-1))
857set(handles.ZObject,'String',coord_str(k(2)+3:k(3)-1))
858set(handles.XImage,'String',coord_str(k(3)+3:k(4)-1))
859set(handles.YImage,'String',coord_str(k(4)+3:end))
[71]860h_menu_coord=findobj(huvmat,'Tag','transform_fct');
861menu=get(h_menu_coord,'String');
862choice=get(h_menu_coord,'Value');
863if iscell(menu)
864    option=menu{choice};
865else
866    option='px'; %default
867end
868if isequal(option,'phys')
[149]869    XCoord=str2double(coord_str(1:k(1)-1));
870    YCoord=str2double(coord_str(k(1)+3:k(2)-1));
[71]871elseif isequal(option,'px')|| isequal(option,'')
[149]872    XCoord=str2double(coord_str(k(3)+3:k(4)-1));
873    YCoord=str2double(coord_str(k(4)+3:end));
[71]874else
875    msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be px or phys ')
876end
877if isempty(XCoord)||isempty(YCoord)
878     if ~isempty(hhh)
879        delete(hhh)%delete the circle marker
[2]880    end
[71]881    return
[2]882end
[71]883xlim=get(hplot,'XLim');
884ylim=get(hplot,'YLim');
885ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/20;%defines the size of the circle marker
886if isempty(hhh)
[149]887    set(0,'CurrentFig',huvmat)
888    set(huvmat,'CurrentAxes',hplot)
[71]889    rectangle('Curvature',[1 1],...
890              'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range],'EdgeColor','m',...
891              'LineStyle','-','Tag','calib_marker');
892else
893    set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
894end
[2]895
[60]896%------------------------------------------------------------------------
[2]897% --- Executes on selection change in edit_append.
898function edit_append_Callback(hObject, eventdata, handles)
[60]899%------------------------------------------------------------------------
[2]900choice=get(handles.edit_append,'Value');
[78]901if choice
902    set(handles.edit_append,'BackgroundColor',[1 1 0])
[177]903    huvmat=findobj(allchild(0),'tag','uvmat');
904    if ishandle(huvmat)
905        hhuvmat=guidata(huvmat);
906        set(hhuvmat.edit_object,'Value',0)
907        set(hhuvmat.edit_object,'BackgroundColor',[0.7 0.7 0.7])
908    end
[78]909else
910    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
[2]911end
912   
913function NEW_Callback(hObject, eventdata, handles)
914%A METTRE SOUS UN BOUTON
915huvmat=findobj(allchild(0),'Name','uvmat');
916hchild=get(huvmat,'children');
917hcoord=findobj(hchild,'Tag','menu_coord');
918coordtype=get(hcoord,'Value');
919haxes=findobj(hchild,'Tag','axes3');
920AxeData=get(haxes,'UserData');
921if ~isequal(hcoord,2)
922    set(hcoord,'Value',2)
923    huvmat=uvmat(AxeData);
924    'relancer uvmat';
925end
926if ~isfield(AxeData,'ZoomAxes')
[42]927    msgbox_uvmat('ERROR','first draw a window around a grid marker')
[2]928    return
929end
930XLim=get(AxeData.ZoomAxes,'XLim');
931YLim=get(AxeData.ZoomAxes,'YLim');
932np=size(AxeData.A);
933ind_sub_x=round(XLim);
934ind_sub_y=np(1)-round(YLim);
[227]935Mfiltre=AxeData.A(ind_sub_y(2):ind_sub_y(1) ,ind_sub_x,:);
[2]936Mfiltre_norm=double(Mfiltre);
937Mfiltre_norm=Mfiltre_norm/sum(sum(Mfiltre_norm));
938Mfiltre_norm=100*(Mfiltre_norm-mean(mean(Mfiltre_norm)));
939Atype=class(AxeData.A);
940Data.NbDim=2;
941Data.A=filter2(Mfiltre_norm,double(AxeData.A));
942Data.A=feval(Atype,Data.A);
943Data.AName='image';
944Data.AX=AxeData.AX;
945Data.AY=AxeData.AY;
946Data.CoordType='px';
947plot_field(Data)
948
[60]949%------------------------------------------------------------------------
[2]950function MenuPlot_Callback(hObject, eventdata, handles)
[60]951%------------------------------------------------------------------------
[2]952huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
[128]953%UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface
[2]954hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat
[128]955%hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
[60]956h_menu_coord=findobj(huvmat,'Tag','transform_fct');
[2]957menu=get(h_menu_coord,'String');
958choice=get(h_menu_coord,'Value');
959if iscell(menu)
960    option=menu{choice};
961else
962    option='px'; %default
963end
964Coord_cell=get(handles.ListCoord,'String');
965ObjectData=read_geometry_calib(Coord_cell);
966%ObjectData=read_geometry_calib(handles);%read the interface input parameters defining the object
[71]967if ~isempty(ObjectData.Coord)
968    if isequal(option,'phys')
[227]969        ObjectData.Coord=ObjectData.Coord(:,1:3);
[71]970    elseif isequal(option,'px')||isequal(option,'')
[227]971        ObjectData.Coord=ObjectData.Coord(:,4:5);
[71]972    else
973        msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be '''', px or phys ')
974    end
[2]975end
[231]976%axes(hhuvmat.axes3)
977set(0,'CurrentFigure',huvmat)
978set(huvmat,'CurrentAxes',hhuvmat.axes3)
[2]979hh=findobj('Tag','calib_points');
[71]980if  ~isempty(ObjectData.Coord) && isempty(hh)
[2]981    hh=line(ObjectData.Coord(:,1),ObjectData.Coord(:,2),'Color','m','Tag','calib_points','LineStyle','.','Marker','+');
[71]982elseif isempty(ObjectData.Coord)%empty list of points, suppress the plot
983    delete(hh)
[2]984else
985    set(hh,'XData',ObjectData.Coord(:,1))
986    set(hh,'YData',ObjectData.Coord(:,2))
987end
[61]988pause(.1)
989figure(handles.geometry_calib)
[2]990
991% --------------------------------------------------------------------
992function MenuHelp_Callback(hObject, eventdata, handles)
[116]993path_to_uvmat=which('uvmat');% check the path of uvmat
[2]994pathelp=fileparts(path_to_uvmat);
[116]995helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
[36]996if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
[2]997else
[36]998   addpath (fullfile(pathelp,'uvmat_doc'))
[2]999   web([helpfile '#geometry_calib'])
1000end
1001
[17]1002%------------------------------------------------------------------------
[2]1003function MenuCreateGrid_Callback(hObject, eventdata, handles)
[17]1004%------------------------------------------------------------------------
[36]1005%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
[61]1006CalibData=get(handles.geometry_calib,'UserData');
[12]1007Tinput=[];%default
1008if isfield(CalibData,'grid')
1009    Tinput=CalibData.grid;
1010end
[71]1011[T,CalibData.grid]=create_grid(Tinput);%display the GUI create_grid
[61]1012set(handles.geometry_calib,'UserData',CalibData)
[2]1013
[12]1014%grid in phys space
[71]1015Coord=get(handles.ListCoord,'String');
1016val=get(handles.ListCoord,'Value');
1017data=read_geometry_calib(Coord);
1018%nbpoints=size(data.Coord,1); %nbre of calibration points
1019data.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
1020% for i=1:nbpoints
1021%    for j=1:5
1022%           Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
1023%    end
1024% end
1025%update the phys coordinates starting from the selected point (down in the
1026Coord(end,:)=[]; %remove last string '.....'
1027for i=1:size(data.Coord,1)
1028    for j=1:5
[17]1029          Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
1030    end
1031end
1032
1033%size(data.Coord,1)
[128]1034Tabchar=cell2tab(Coord,' | ');
[71]1035Tabchar=[Tabchar ;{'......'}];
[12]1036set(handles.ListCoord,'String',Tabchar)
[2]1037
[71]1038% -----------------------------------------------------------------------
1039% --- automatic grid dectection from local maxima of the images
[60]1040function MenuDetectGrid_Callback(hObject, eventdata, handles)
[71]1041%------------------------------------------------------------------------
[159]1042%% read the four last point coordinates in pixels
[108]1043Coord_cell=get(handles.ListCoord,'String');%read list of coordinates on geometry_calib
[60]1044data=read_geometry_calib(Coord_cell);
1045nbpoints=size(data.Coord,1); %nbre of calibration points
[62]1046if nbpoints~=4
[227]1047    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')
[71]1048    return
[60]1049end
[71]1050corners_X=(data.Coord(end:-1:end-3,4)); %pixel absissa of the four corners
1051corners_Y=(data.Coord(end:-1:end-3,5));
[60]1052
[71]1053%reorder the last two points (the two first in the list) if needed
[121]1054angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1)));
[62]1055if abs(angles(4)-angles(2))>abs(angles(3)-angles(2))
1056      X_end=corners_X(4);
1057      Y_end=corners_Y(4);
1058      corners_X(4)=corners_X(3);
1059      corners_Y(4)=corners_Y(3);
1060      corners_X(3)=X_end;
1061      corners_Y(3)=Y_end;
1062end
1063
[227]1064%% initiate the grid
1065CalibData=get(handles.geometry_calib,'UserData');%get information stored on the GUI geometry_calib
1066grid_input=[];%default
1067if isfield(CalibData,'grid')
1068    grid_input=CalibData.grid;%retrieve the previously used grid
1069end
1070[T,CalibData.grid,white_test]=create_grid(grid_input,'detect_grid');%display the GUI create_grid, read the set of phys coordinates T
1071set(handles.geometry_calib,'UserData',CalibData)%store the phys grid parameters for later use
1072
1073
1074
[159]1075%% read the current image, displayed in the GUI uvmat
[60]1076huvmat=findobj(allchild(0),'Name','uvmat');
1077UvData=get(huvmat,'UserData');
1078A=UvData.Field.A;
1079npxy=size(A);
[159]1080X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates (cm)
1081Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates (cm)
[109]1082
[159]1083%calculate transform matrices for plane projection
[108]1084% reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
1085B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
1086      zeros(4,3)        X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ];
1087B = reshape (B', 8 , 8 )';
1088D = [ corners_X , corners_Y ];
1089D = reshape (D', 8 , 1 );
[121]1090l = (B' * B)\B' * D;
[108]1091Amat = reshape([l(1:6)' 0 0 1 ],3,3)';
1092C = [l(7:8)' 1];
1093
[159]1094% transform grid image into 'phys' coordinates
[114]1095GeometryCalib.fx_fy=[1 1];
1096GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
[108]1097GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
[159]1098GeometryCalib.CoordUnit='cm';
[114]1099path_uvmat=which('uvmat');% check the path detected for source file uvmat
1100path_UVMAT=fileparts(path_uvmat); %path to UVMAT
1101addpath(fullfile(path_UVMAT,'transform_field'))
1102Data.ListVarName={'AY','AX','A'};
1103Data.VarDimName={'AY','AX',{'AY','AX'}};
1104if ndims(A)==3
1105    A=mean(A,3);
1106end
1107Data.A=A-min(min(A));
1108Data.AY=[npxy(1)-0.5 0.5];
1109Data.AX=[0.5 npxy(2)];
[158]1110Data.CoordUnit='pixel';
[114]1111Calib.GeometryCalib=GeometryCalib;
[121]1112DataOut=phys(Data,Calib);
[114]1113rmpath(fullfile(path_UVMAT,'transform_field'))
1114Amod=DataOut.A;
1115Rangx=DataOut.AX;
1116Rangy=DataOut.AY;
[156]1117if white_test
[159]1118    Amod=double(Amod);%case of white grid markers: will look for image maxima
[156]1119else
[159]1120    Amod=-double(Amod);%case of black grid markers: will look for image minima
[156]1121end
[114]1122% figure(12) %display corrected image
[109]1123% Amax=max(max(Amod));
1124% image(Rangx,Rangy,uint8(255*Amod/Amax))
[114]1125
[159]1126%% detection of local image extrema in each direction
[88]1127Dx=(Rangx(2)-Rangx(1))/(npxy(2)-1); %x mesh in real space
1128Dy=(Rangy(2)-Rangy(1))/(npxy(1)-1); %y mesh in real space
[121]1129ind_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
1130ind_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
[60]1131nbpoints=size(T,1);
1132for ipoint=1:nbpoints
1133    i0=1+round((T(ipoint,1)-Rangx(1))/Dx);%round(Xpx(ipoint));
1134    j0=1+round((T(ipoint,2)-Rangy(1))/Dy);%round(Xpx(ipoint));
[109]1135    j0min=max(j0-ind_range_y,1);
1136    j0max=min(j0+ind_range_y,size(Amod,1));
1137    i0min=max(i0-ind_range_x,1);
1138    i0max=min(i0+ind_range_x,size(Amod,2));
1139    Asub=Amod(j0min:j0max,i0min:i0max);
[60]1140    x_profile=sum(Asub,1);
1141    y_profile=sum(Asub,2);
1142    [Amax,ind_x_max]=max(x_profile);
1143    [Amax,ind_y_max]=max(y_profile);
[61]1144    %sub-pixel improvement using moments
1145    x_shift=0;
1146    y_shift=0;
[109]1147    if ind_x_max+2<=numel(x_profile) && ind_x_max-2>=1
[61]1148        Atop=x_profile(ind_x_max-2:ind_x_max+2);
1149        x_shift=sum(Atop.*[-2 -1 0 1 2])/sum(Atop);
1150    end
[114]1151    if ind_y_max+2<=numel(y_profile) && ind_y_max-2>=1
[61]1152        Atop=y_profile(ind_y_max-2:ind_y_max+2);
1153        y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop);
1154    end
[109]1155    Delta(ipoint,1)=(x_shift+ind_x_max+i0min-i0-1)*Dx;%shift from the initial guess
1156    Delta(ipoint,2)=(y_shift+ind_y_max+j0min-j0-1)*Dy;
[60]1157end
1158Tmod=T(:,(1:2))+Delta;
1159[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));
[63]1160for ipoint=1:nbpoints
1161     Coord{ipoint,1}=num2str(T(ipoint,1),4);%display coordiantes with 4 digits
1162     Coord{ipoint,2}=num2str(T(ipoint,2),4);%display coordiantes with 4 digits
[109]1163     Coord{ipoint,3}=num2str(T(ipoint,3),4);%display coordiantes with 4 digits;
1164     Coord{ipoint,4}=num2str(Xpx(ipoint),4);%display coordiantes with 4 digits
1165     Coord{ipoint,5}=num2str(Ypx(ipoint),4);%display coordiantes with 4 digits
[60]1166end
[128]1167Tabchar=cell2tab(Coord(end:-1:1,:),' | ');
[71]1168Tabchar=[Tabchar ;{'......'}];
[60]1169set(handles.ListCoord,'Value',1)
1170set(handles.ListCoord,'String',Tabchar)
[67]1171MenuPlot_Callback(hObject, eventdata, handles)
[60]1172
[71]1173%-----------------------------------------------------------------------
1174function MenuTranslatePoints_Callback(hObject, eventdata, handles)
1175%-----------------------------------------------------------------------
1176%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1177CalibData=get(handles.geometry_calib,'UserData');
1178Tinput=[];%default
1179if isfield(CalibData,'translate')
1180    Tinput=CalibData.translate;
1181end
1182T=translate_points(Tinput);%display translate_points GUI and get shift parameters
1183CalibData.translate=T;
1184set(handles.geometry_calib,'UserData',CalibData)
1185%translation
1186Coord_cell=get(handles.ListCoord,'String');
1187data=read_geometry_calib(Coord_cell);
1188data.Coord(:,1)=T(1)+data.Coord(:,1);
1189data.Coord(:,2)=T(2)+data.Coord(:,2);
1190data.Coord(:,3)=T(3)+data.Coord(:,3);
1191data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1192for i=1:size(data.Coord,1)
1193    for j=1:5
1194          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1195   end
1196end
[128]1197Tabchar=cell2tab(Coord,' | ');
[88]1198Tabchar=[Tabchar; {'.....'}];
[71]1199%set(handles.ListCoord,'Value',1)
1200set(handles.ListCoord,'String',Tabchar)
1201
1202
1203% --------------------------------------------------------------------
1204function MenuRotatePoints_Callback(hObject, eventdata, handles)
1205%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1206CalibData=get(handles.geometry_calib,'UserData');
1207Tinput=[];%default
1208if isfield(CalibData,'rotate')
1209    Tinput=CalibData.rotate;
1210end
[356]1211T=rotate_points(Tinput);%display rotate_points GUI to introduce rotation parameters
[71]1212CalibData.rotate=T;
1213set(handles.geometry_calib,'UserData',CalibData)
1214%-----------------------------------------------------
1215%rotation
1216Phi=T(1);
1217O_x=0;%default
1218O_y=0;%default
1219if numel(T)>=2
1220    O_x=T(2);%default
1221end
1222if numel(T)>=3
1223    O_y=T(3);%default
1224end
1225Coord_cell=get(handles.ListCoord,'String');
1226data=read_geometry_calib(Coord_cell);
1227r1=cos(pi*Phi/180);
1228r2=-sin(pi*Phi/180);
1229r3=sin(pi*Phi/180);
1230r4=cos(pi*Phi/180);
1231x=data.Coord(:,1)-O_x;
1232y=data.Coord(:,2)-O_y;
1233data.Coord(:,1)=r1*x+r2*y;
1234data.Coord(:,2)=r3*x+r4*y;
1235% data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1236for i=1:size(data.Coord,1)
1237    for j=1:5
1238          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1239   end
1240end
[148]1241Tabchar=cell2tab(Coord,' | ');
[71]1242Tabchar=[Tabchar;{'......'}];
1243set(handles.ListCoord,'Value',1)
1244set(handles.ListCoord,'String',Tabchar)
1245
[109]1246
1247% %------------------------------------------------------------------------
1248% % --- Executes on button press in rotation.
1249% function rotation_Callback(hObject, eventdata, handles)
1250% %------------------------------------------------------------------------
1251% angle_rot=(pi/180)*str2num(get(handles.Phi,'String'));
1252% Coord_cell=get(handles.ListCoord,'String');
1253% data=read_geometry_calib(Coord_cell);
1254% data.Coord(:,1)=cos(angle_rot)*data.Coord(:,1)+sin(angle_rot)*data.Coord(:,2);
1255% data.Coord(:,1)=-sin(angle_rot)*data.Coord(:,1)+cos(angle_rot)*data.Coord(:,2);
1256% set(handles.XObject,'String',num2str(data.Coord(:,1),4));
1257% set(handles.YObject,'String',num2str(data.Coord(:,2),4));
1258
1259
[108]1260%------------------------------------------------------------------------
1261% image transform from px to phys
1262%INPUT:
1263%Zindex: index of plane
[114]1264% function [A_out,Rangx,Rangy]=phys_Ima(A,Calib,ZIndex)
1265% %------------------------------------------------------------------------
1266% xcorner=[];
1267% ycorner=[];
1268% npx=[];
1269% npy=[];
1270% siz=size(A)
1271% npx=[npx siz(2)];
1272% npy=[npy siz(1)]
1273% xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners
1274% yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
1275% [xcorner,ycorner]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates
1276% Rangx(1)=min(xcorner);
1277% Rangx(2)=max(xcorner);
1278% Rangy(2)=min(ycorner);
1279% Rangy(1)=max(ycorner);
1280% test_multi=(max(npx)~=min(npx)) | (max(npy)~=min(npy));
1281% npx=max(npx);
1282% npy=max(npy);
1283% x=linspace(Rangx(1),Rangx(2),npx);
1284% y=linspace(Rangy(1),Rangy(2),npy);
1285% [X,Y]=meshgrid(x,y);%grid in physical coordiantes
1286% vec_B=[];
1287%
1288% zphys=0; %default
1289% if isfield(Calib,'SliceCoord') %.Z= index of plane
1290%    SliceCoord=Calib.SliceCoord(ZIndex,:);
1291%    zphys=SliceCoord(3); %to generalize for non-parallel planes
1292% end
1293% [XIMA,YIMA]=px_XYZ(Calib,X,Y,zphys);%corresponding image indices for each point in the real space grid
1294% XIMA=reshape(round(XIMA),1,npx*npy);%indices reorganized in 'line'
1295% YIMA=reshape(round(YIMA),1,npx*npy);
1296% flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image
1297% testuint8=isa(A,'uint8');
1298% testuint16=isa(A,'uint16');
1299% if numel(siz)==2 %(B/W images)
1300%     vec_A=reshape(A,1,npx*npy);%put the original image in line
1301%     ind_in=find(flagin);
1302%     ind_out=find(~flagin);
1303%     ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
1304%     ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
1305%     vec_B(ind_in)=vec_A(ICOMB);
1306%     vec_B(ind_out)=zeros(size(ind_out));
1307%     A_out=reshape(vec_B,npy,npx);%new image in real coordinates
1308% elseif numel(siz)==3     
1309%     for icolor=1:siz(3)
1310%         vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line
1311%         ind_in=find(flagin);
1312%         ind_out=find(~flagin);
1313%         ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
1314%         ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
1315%         vec_B(ind_in)=vec_A(ICOMB);
1316%         vec_B(ind_out)=zeros(size(ind_out));
1317%         A_out(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates
1318%     end
1319% end
1320% if testuint8
1321%     A_out=uint8(A_out);
1322% end
1323% if testuint16
1324%     A_out=uint16(A_out);
1325% end
[60]1326
[108]1327%------------------------------------------------------------------------
1328% pointwise transform from px to phys
[60]1329%INPUT:
1330%Z: index of plane
[114]1331% function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Z)
1332% %------------------------------------------------------------------------
1333% if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'SliceCoord')&length(Calib.SliceCoord)>=Z
1334%     Zindex=Z;
1335%     Zphys=Calib.SliceCoord(Zindex,3);%GENERALISER AUX CAS AVEC ANGLE
1336% else
1337%     Zphys=0;
1338% end
1339% if ~exist('X','var')||~exist('Y','var')
1340%     Xphys=[];
1341%     Yphys=[];%default
1342%     return
1343% end
1344% Xphys=X;%default
1345% Yphys=Y;
1346% %image transform
1347% if isfield(Calib,'R')
1348%     R=(Calib.R)';
1349%     Dx=R(5)*R(7)-R(4)*R(8);
1350%     Dy=R(1)*R(8)-R(2)*R(7);
1351%     D0=Calib.f*(R(2)*R(4)-R(1)*R(5));
1352%     Z11=R(6)*R(8)-R(5)*R(9);
1353%     Z12=R(2)*R(9)-R(3)*R(8); 
1354%     Z21=R(4)*R(9)-R(6)*R(7);
1355%     Z22=R(3)*R(7)-R(1)*R(9);
1356%     Zx0=R(3)*R(5)-R(2)*R(6);
1357%     Zy0=R(1)*R(6)-R(3)*R(4);
1358%     A11=R(8)*Calib.Ty-R(5)*Calib.Tz+Z11*Zphys;
1359%     A12=R(2)*Calib.Tz-R(8)*Calib.Tx+Z12*Zphys;
1360%     A21=-R(7)*Calib.Ty+R(4)*Calib.Tz+Z21*Zphys;
1361%     A22=-R(1)*Calib.Tz+R(7)*Calib.Tx+Z11*Zphys;
1362%     X0=Calib.f*(R(5)*Calib.Tx-R(2)*Calib.Ty+Zx0*Zphys);
1363%     Y0=Calib.f*(-R(4)*Calib.Tx+R(1)*Calib.Ty+Zy0*Zphys);
1364%         %px to camera:
1365%     Xd=(Calib.dpx/Calib.sx)*(X-Calib.Cx); % sensor coordinates
1366%     Yd=Calib.dpy*(Y-Calib.Cy);
1367%     dist_fact=1+Calib.kappa1*(Xd.*Xd+Yd.*Yd); %distortion factor
1368%     Xu=dist_fact.*Xd;%undistorted sensor coordinates
1369%     Yu=dist_fact.*Yd;
1370%     denom=Dx*Xu+Dy*Yu+D0;
1371%     % denom2=denom.*denom;
1372%     Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates
1373%     Yphys=(A21.*Xu+A22.*Yu+Y0)./denom;
1374% end
[109]1375
1376
1377% --------------------------------------------------------------------
1378function MenuImportPoints_Callback(hObject, eventdata, handles)
[121]1379fileinput=browse_xml(hObject, eventdata, handles);
[109]1380if isempty(fileinput)
1381    return
1382end
1383[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1384GeometryCalib=s.GeometryCalib;
[114]1385%GeometryCalib=load_calib(hObject, eventdata, handles)
[116]1386calib=reshape(GeometryCalib.PointCoord,[],1);
[109]1387for ilist=1:numel(calib)
1388    CoordCell{ilist}=num2str(calib(ilist));
1389end
1390CoordCell=reshape(CoordCell,[],5);
[128]1391Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
[109]1392Tabchar=[Tabchar;{'......'}];
1393set(handles.ListCoord,'Value',1)
1394set(handles.ListCoord,'String',Tabchar)
1395MenuPlot_Callback(handles.geometry_calib, [], handles)
1396
1397% -----------------------------------------------------------------------
1398function MenuImportIntrinsic_Callback(hObject, eventdata, handles)
1399%------------------------------------------------------------------------
1400fileinput=browse_xml(hObject, eventdata, handles);
1401if isempty(fileinput)
1402    return
1403end
1404[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1405GeometryCalib=s.GeometryCalib;
[114]1406display_intrinsic(GeometryCalib,handles)
[109]1407
1408% -----------------------------------------------------------------------
1409function MenuImportAll_Callback(hObject, eventdata, handles)
1410%------------------------------------------------------------------------
[121]1411fileinput=browse_xml(hObject, eventdata, handles);
[109]1412if ~isempty(fileinput)
1413    loadfile(handles,fileinput)
1414end
1415
1416% -----------------------------------------------------------------------
1417% --- Executes on menubar option Import/Grid file: introduce previous grid files
1418function MenuGridFile_Callback(hObject, eventdata, handles)
1419% -----------------------------------------------------------------------
[121]1420inputfile=browse_xml(hObject, eventdata, handles);
[109]1421listfile=get(handles.coord_files,'string');
1422if isequal(listfile,{''})
1423    listfile={inputfile};
1424else
[121]1425    listfile=[listfile;{inputfile}];%update the list of coord files
[109]1426end
1427set(handles.coord_files,'string',listfile);
1428
1429%------------------------------------------------------------------------
[114]1430% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
1431function key_press_fcn(hObject,eventdata,handles)
1432%------------------------------------------------------------------------
1433xx=double(get(handles.geometry_calib,'CurrentCharacter')); %get the keyboard character
1434if ismember(xx,[8 127])%backspace or delete
1435    Coord_cell=get(handles.ListCoord,'String');
1436    val=get(handles.ListCoord,'Value');
1437     if max(val)<numel(Coord_cell) % the last element '...' has not been selected
1438        Coord_cell(val)=[];%remove the selected line
1439        set(handles.ListCoord,'Value',min(val))
1440        set(handles.ListCoord,'String',Coord_cell)         
1441        ListCoord_Callback(hObject, eventdata, handles)
1442        MenuPlot_Callback(hObject,eventdata,handles)
1443     end
1444end
1445
1446%------------------------------------------------------------------------
[109]1447function fileinput=browse_xml(hObject, eventdata, handles)
1448%------------------------------------------------------------------------
1449fileinput=[];%default
1450oldfile=''; %default
[116]1451UserData=get(handles.geometry_calib,'UserData');
[114]1452if isfield(UserData,'XmlInputFile')
1453    oldfile=UserData.XmlInputFile;
[109]1454end
1455[FileName, PathName, filterindex] = uigetfile( ...
1456       {'*.xml;*.mat', ' (*.xml,*.mat)';
1457       '*.xml',  '.xml files '; ...
1458        '*.mat',  '.mat matlab files '}, ...
1459        'Pick a file',oldfile);
1460fileinput=[PathName FileName];%complete file name
1461testblank=findstr(fileinput,' ');%look for blanks
1462if ~isempty(testblank)
1463    msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed')
1464    return
1465end
1466sizf=size(fileinput);
1467if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
[114]1468UserData.XmlInputFile=fileinput;
[109]1469set(handles.geometry_calib,'UserData',UserData)%record current file foer further use of browser
1470
1471% -----------------------------------------------------------------------
[128]1472function Heading=loadfile(handles,fileinput)
[109]1473%------------------------------------------------------------------------
[128]1474Heading=[];%default
[121]1475[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
[128]1476if ~isempty(errormsg)
1477    msgbox_uvmat('ERROR',['Error for reading ' fileinput ': '  errormsg])
1478    return
1479end
1480if ~isempty(s.Heading)
1481    Heading=s.Heading;
1482end
1483   
[116]1484GeometryCalib=s.GeometryCalib;
[114]1485fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
1486%     Tabchar={};
1487CoordCell={};
1488%     kc=0;%default
1489%     f1=1000;
1490%     f2=1000;
1491%     hhuvmat=guidata(findobj(allchild(0),'Name','uvmat'));
[332]1492%     Cx=str2num(get(hhuvmat.num_Npx,'String'))/2;
1493%     Cy=str2num(get(hhuvmat.num_Npy,'String'))/2;
[114]1494Tabchar={};%default
1495val_cal=1;%default
1496if ~isempty(GeometryCalib)
1497    % choose the calibration option
1498    if isfield(GeometryCalib,'CalibrationType')
1499       calib_list=get(handles.calib_type,'String');
1500       for ilist=1:numel(calib_list)
1501           if strcmp(calib_list{ilist},GeometryCalib.CalibrationType)
1502               val_cal=ilist;
1503               break
1504           end
1505       end
1506    end
1507    display_intrinsic(GeometryCalib,handles)%intrinsic param
1508    %extrinsic param
1509    if isfield(GeometryCalib,'Tx_Ty_Tz')
1510        Tx_Ty_Tz=GeometryCalib.Tx_Ty_Tz;
1511        set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
1512        set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
1513        set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
1514    end
1515    if isfield(GeometryCalib,'omc')
1516        set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
1517        set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
1518        set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
1519    end
[116]1520    calib=reshape(GeometryCalib.PointCoord,[],1);
[109]1521    for ilist=1:numel(calib)
1522        CoordCell{ilist}=num2str(calib(ilist));
1523    end
1524    CoordCell=reshape(CoordCell,[],5);
[128]1525    Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
[109]1526    MenuPlot_Callback(handles.geometry_calib, [], handles)
1527end
[114]1528set(handles.calib_type,'Value',val_cal)
[109]1529Tabchar=[Tabchar;{'......'}];
[114]1530set(handles.ListCoord,'Value',1)
1531set(handles.ListCoord,'String',Tabchar)
1532
[109]1533if isempty(CoordCell)% allow mouse action by default in the absence of input points
1534    set(handles.edit_append,'Value',1)
1535    set(handles.edit_append,'BackgroundColor',[1 1 0])
1536else % does not allow mouse action by default in the presence of input points
1537    set(handles.edit_append,'Value',0)
1538    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
1539end
1540
[114]1541%------------------------------------------------------------------------
1542%---display calibration intrinsic parameters
1543function display_intrinsic(GeometryCalib,handles)
1544%------------------------------------------------------------------------
1545fx=[];
1546fy=[];
1547if isfield(GeometryCalib,'fx_fy')
1548    fx=GeometryCalib.fx_fy(1);
1549    fy=GeometryCalib.fx_fy(2);
1550end
1551Cx_Cy=[0 0];%default
1552if isfield(GeometryCalib,'Cx_Cy')
1553    Cx_Cy=GeometryCalib.Cx_Cy;
1554end
1555kc=0;
1556if isfield(GeometryCalib,'kc')
[121]1557    kc=GeometryCalib.kc; %* GeometryCalib.focal*GeometryCalib.focal;
[114]1558end
1559set(handles.fx,'String',num2str(fx,5))
1560set(handles.fy,'String',num2str(fy,5))
1561set(handles.Cx,'String',num2str(Cx_Cy(1),'%1.1f'))
1562set(handles.Cy,'String',num2str(Cx_Cy(2),'%1.1f'))
1563set(handles.kc,'String',num2str(kc,'%1.4f'))
[109]1564
1565
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