source: trunk/src/geometry_calib.m @ 444

Last change on this file since 444 was 444, checked in by sommeria, 9 years ago

masks and calibration updated to fit with the new conventions on file organisation.
bug corrected in mouse_up (object creation)
bug corrected in civ in mode TESTciv

File size: 60.8 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%------------------------------------------------------------------------
[379]151%% look for the GUI uvmat and check for an image as input
152huvmat=findobj(allchild(0),'Name','uvmat');
153hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
154FileExt=get(hhuvmat.FileExt,'String');
155check_input=0;
156if ~isempty(FileExt)
157    if ~isempty(imformats(FileExt(2:end))) ||strcmpi(FileExt,'.avi')
158        check_input=1;
159    end
160end
161if ~check_input
162    msgbox_uvmat('ERROR','open an image with uvmat to perform calibration')
163    return
164end
165
166%% read the current calibration points
[2]167Coord_cell=get(handles.ListCoord,'String');
168Object=read_geometry_calib(Coord_cell);
[109]169Coord=Object.Coord;
170% apply the calibration, whose type is selected in  handles.calib_type
171if ~isempty(Coord)
172    calib_cell=get(handles.calib_type,'String');
173    val=get(handles.calib_type,'Value');
174    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
175else
176    msgbox_uvmat('ERROR','No calibration points, abort')
177    return
178end
[114]179Z_plane=[];
[109]180if ~isempty(Coord)
[114]181    %check error
[109]182    X=Coord(:,1);
183    Y=Coord(:,2);
184    Z=Coord(:,3);
185    x_ima=Coord(:,4);
186    y_ima=Coord(:,5);
[114]187    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
[109]188    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
189    [GeometryCalib.ErrorMax(1),index(1)]=max(abs(Xpoints-x_ima));
190    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
191    [GeometryCalib.ErrorMax(2),index(2)]=max(abs(Ypoints-y_ima));
[341]192    [~,ind_dim]=max(GeometryCalib.ErrorMax);
[109]193    index=index(ind_dim);
[114]194    %set the Z position of the reference plane used for calibration
[109]195    if isequal(max(Z),min(Z))%Z constant
[114]196        Z_plane=Z(1);
[109]197        GeometryCalib.NbSlice=1;
[114]198        GeometryCalib.SliceCoord=[0 0 Z_plane];
[109]199    end
200end
[114]201%set the coordinate unit
[2]202unitlist=get(handles.CoordUnit,'String');
203unit=unitlist{get(handles.CoordUnit,'value')};
204GeometryCalib.CoordUnit=unit;
[114]205%record the points
[109]206GeometryCalib.SourceCalib.PointCoord=Coord;
[114]207display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
[109]208
[114]209% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
[109]210set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
211set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
212set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
[114]213set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
214set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
215set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
[109]216
[379]217%% store the calibration data, by default in the xml file of the currently displayed image
[191]218UvData=get(huvmat,'UserData');
219NbSlice_j=1;%default
220ZStart=Z_plane;
221ZEnd=Z_plane;
[196]222volume_scan='n';
[191]223if isfield(UvData,'XmlData')
224    if isfield(UvData.XmlData,'TranslationMotor')
225        NbSlice_j=UvData.XmlData.TranslationMotor.Nbslice;
[196]226        ZStart=UvData.XmlData.TranslationMotor.ZStart/10;
227        ZEnd=UvData.XmlData.TranslationMotor.ZEnd/10;
228        volume_scan='y';
[191]229    end
230end
[2]231RootPath='';
[341]232% RootFile='';
[121]233if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
[341]234%     testhandle=1;
[2]235    RootPath=get(hhuvmat.RootPath,'String');
[444]236    SubDir=get(hhuvmat.SubDir,'String');
237%     RootFile=get(hhuvmat.RootFile,'String');
238%     filebase=fullfile(RootPath,RootFile);
239    outputfile=[fullfile(RootPath,SubDir) '.xml'];%xml file associated with the currently displayed image
[2]240else
241    question={'save the calibration data and point coordinates in'};
[121]242    def={fullfile(RootPath,'ObjectCalib.xml')};
[2]243    options.Resize='on';
244    answer=inputdlg(question,'save average in a new file',1,def,options);
245    outputfile=answer{1};
246end
[84]247answer=msgbox_uvmat('INPUT_Y-N',{[outputfile ' updated with calibration data'];...
[2]248    ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];...
[84]249    ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']});
[128]250
251%% record the calibration parameters and display the current image of uvmat in the new phys coordinates
[121]252if strcmp(answer,'Yes')
253    if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration
[213]254       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'};
255       input_val=[{num2str(ZEnd)} {num2str(ZStart)} {num2str(ZStart)} {'1.333'} num2str(NbSlice_j) {volume_scan} {'0'} {'0'}];
256        answer=inputdlg(input_key,'slice position(s)',ones(1,8), input_val,'on');
[191]257        %answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
258        GeometryCalib.NbSlice=str2double(answer{5});
259        GeometryCalib.VolumeScan=answer{6};
260        if isempty(answer)
[121]261            Z_plane=0; %default
262        else
[191]263            Z_plane=linspace(str2double(answer{1}),str2double(answer{2}),GeometryCalib.NbSlice);
264        end     
[196]265        GeometryCalib.SliceCoord=Z_plane'*[0 0 1];
[213]266        GeometryCalib.SliceAngle(:,3)=0;
267        GeometryCalib.SliceAngle(:,2)=str2double(answer{7})*ones(GeometryCalib.NbSlice,1);%rotation around y axis (to generalise)
268        GeometryCalib.SliceAngle(:,1)=str2double(answer{8})*ones(GeometryCalib.NbSlice,1);%rotation around x axis (to generalise)
[196]269        GeometryCalib.InterfaceCoord=[0 0 str2double(answer{3})];
[207]270        GeometryCalib.RefractionIndex=str2double(answer{4});     
[121]271    end
[114]272    errormsg=update_imadoc(GeometryCalib,outputfile);% introduce the calibration data in the xml file
273    if ~strcmp(errormsg,'')
274        msgbox_uvmat('ERROR',errormsg);
275    end
[128]276   
[84]277    %display image with new calibration in the currently opened uvmat interface
278    hhh=findobj(hhuvmat.axes3,'Tag','calib_marker');% delete calib points and markers
279    if ~isempty(hhh)
[109]280        delete(hhh);     
[84]281    end
282    hhh=findobj(hhuvmat.axes3,'Tag','calib_points');
283    if ~isempty(hhh)
284        delete(hhh);
285    end
[332]286    set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off'
287    set(hhuvmat.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
[116]288    UserData=get(handles.geometry_calib,'UserData');
289    UserData.XmlInputFile=outputfile;%save the current xml file name
290    set(handles.geometry_calib,'UserData',UserData)
[114]291    uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading  in uvmat, show the image in phys coordinates
292    MenuPlot_Callback(hObject, eventdata, handles)
293    set(handles.ListCoord,'Value',index)% indicate in the list the point with max deviation (possible mistake)
294    ListCoord_Callback(hObject, eventdata, handles)
[84]295    figure(handles.geometry_calib)
[2]296end
[69]297
298%------------------------------------------------------------------
[2]299% --- Executes on button press in calibrate_lin.
[128]300
[2]301function REPLICATE_Callback(hObject, eventdata, handles)
[60]302%------------------------------------------------------------------------
[2]303
[128]304%% Apply calibration
305calib_cell=get(handles.calib_type,'String'); %#ok<NASGU>
306val=get(handles.calib_type,'Value'); %#ok<NASGU>
307
[114]308%read the current calibration points
309Coord_cell=get(handles.ListCoord,'String');
310Object=read_geometry_calib(Coord_cell);
311Coord=Object.Coord;
[2]312
[114]313% apply the calibration, whose type is selected in  handles.calib_type
314if ~isempty(Coord)
315    calib_cell=get(handles.calib_type,'String');
316    val=get(handles.calib_type,'Value');
317    GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles);
318else
319    msgbox_uvmat('ERROR','No calibration points, abort')
320    return
321end
322
323if ~isempty(Coord)
324    %check error
325    X=Coord(:,1);
326    Y=Coord(:,2);
327    Z=Coord(:,3);
328    x_ima=Coord(:,4);
329    y_ima=Coord(:,5);
330    [Xpoints,Ypoints]=px_XYZ(GeometryCalib,X,Y,Z);
331    GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
[341]332    [GeometryCalib.ErrorMax(1)]=max(abs(Xpoints-x_ima));
[114]333    GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
[341]334    [GeometryCalib.ErrorMax(2)]=max(abs(Ypoints-y_ima));
335%     [EM,ind_dim]=max(GeometryCalib.ErrorMax);
[114]336    %set the Z position of the reference plane used for calibration
337    Z_plane=[];
338    if isequal(max(Z),min(Z))
339        Z_plane=Z(1);
340    end
341    answer_1=msgbox_uvmat('INPUT_TXT',' Z= ',num2str(Z_plane));
[128]342    Z_plane=str2double(answer_1);
[114]343    GeometryCalib.NbSlice=1;
344    GeometryCalib.SliceCoord=[0 0 Z_plane];
345    %set the coordinate unit
346    unitlist=get(handles.CoordUnit,'String');
347    unit=unitlist{get(handles.CoordUnit,'value')};
348    GeometryCalib.CoordUnit=unit;
349    %record the points
350    GeometryCalib.SourceCalib.PointCoord=Coord;
351end
[128]352
353%% display calibration paprameters
[114]354display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters
355
356% Display extrinsinc parameters (rotation and translation of camera with  respect to the phys coordiantes)
357set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
358set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
359set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
360set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
361set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
362set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
363
[128]364%% open the GUI dataview
[2]365h_dataview=findobj(allchild(0),'name','dataview');
[12]366if ~isempty(h_dataview)
367    delete(h_dataview)
[2]368end
[61]369CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata
[341]370% InputFile='';
[114]371if isfield(CalibData,'XmlInputFile')
[128]372    InputDir=fileparts(CalibData.XmlInputFile);
373    [InputDir,DirName]=fileparts(InputDir);
[2]374end
[12]375SubCampaignTest='n'; %default
[128]376testup=0;
377if isfield(CalibData,'SubCampaign')
378    SubCampaignTest='y';
379    dir_ref=CalibData.SubCampaign;
380    testup=1;
381elseif isfield(CalibData,'Campaign')
382    dir_ref=CalibData.Campaign;
383    testup=1;
[2]384end
[128]385while testup
386    [InputDir,DirName]=fileparts(InputDir);
387    if strcmp(DirName,dir_ref)
388        break
[2]389    end
390end
[128]391InputDir=fullfile(InputDir,DirName);
392answer=msgbox_uvmat('INPUT_TXT','Campaign ?',InputDir);
393if strcmp(answer,'Cancel')
394    return
[2]395end
396
[128]397dataview(answer,SubCampaignTest,GeometryCalib);
398
[60]399%------------------------------------------------------------------------
[2]400% determine the parameters for a calibration by an affine function (rescaling and offset, no rotation)
[109]401function GeometryCalib=calib_rescale(Coord,handles)
[60]402%------------------------------------------------------------------------
[2]403X=Coord(:,1);
[109]404Y=Coord(:,2);% Z not used
[2]405x_ima=Coord(:,4);
406y_ima=Coord(:,5);
[341]407[px]=polyfit(X,x_ima,1);
408[py]=polyfit(Y,y_ima,1);
409% T_x=px(2);
410% T_y=py(2);
[2]411GeometryCalib.CalibrationType='rescale';
[121]412GeometryCalib.fx_fy=[px(1) py(1)];%.fx_fy corresponds to pxcm along x and y
[2]413GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
[114]414GeometryCalib.Tx_Ty_Tz=[px(2)/px(1) py(2)/py(1) 1];
415GeometryCalib.omc=[0 0 0];
[2]416
[60]417%------------------------------------------------------------------------
[2]418% determine the parameters for a calibration by a linear transform matrix (rescale and rotation)
[242]419
420
[227]421function GeometryCalib=calib_linear(Coord,handles)
[60]422%------------------------------------------------------------------------
[2]423X=Coord(:,1);
[109]424Y=Coord(:,2);% Z not used
[2]425x_ima=Coord(:,4);
426y_ima=Coord(:,5);
427XY_mat=[ones(size(X)) X Y];
428a_X1=XY_mat\x_ima; %transformation matrix for X
429a_Y1=XY_mat\y_ima;%transformation matrix for X
[121]430R=[a_X1(2),a_X1(3);a_Y1(2),a_Y1(3)];
[242]431epsilon=sign(det(R));
[116]432norm=abs(det(R));
[2]433GeometryCalib.CalibrationType='linear';
[238]434if (a_X1(2)/a_Y1(3))>0
[242]435    GeometryCalib.fx_fy(1)=sqrt((a_X1(2)/a_Y1(3))*norm);
[238]436else
[242]437    GeometryCalib.fx_fy(1)=-sqrt(-(a_X1(2)/a_Y1(3))*norm);
[238]438end
[121]439GeometryCalib.fx_fy(2)=(a_Y1(3)/a_X1(2))*GeometryCalib.fx_fy(1);
[2]440GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
[227]441GeometryCalib.Tx_Ty_Tz=[a_X1(1)/GeometryCalib.fx_fy(1) a_Y1(1)/GeometryCalib.fx_fy(2) 1];
[242]442R(1,:)=R(1,:)/GeometryCalib.fx_fy(1);
[121]443R(2,:)=R(2,:)/GeometryCalib.fx_fy(2);
444R=[R;[0 0]];
[242]445GeometryCalib.R=[R [0;0;-epsilon]];
446GeometryCalib.omc=(180/pi)*[acos(GeometryCalib.R(1,1)) 0 0];
[109]447%------------------------------------------------------------------------
448% determine the tsai parameters for a view normal to the grid plane
[114]449% NOT USED
[109]450function GeometryCalib=calib_normal(Coord,handles)
451%------------------------------------------------------------------------
452Calib.f1=str2num(get(handles.fx,'String'));
453Calib.f2=str2num(get(handles.fy,'String'));
[114]454Calib.k=str2num(get(handles.kc,'String'));
[109]455Calib.Cx=str2num(get(handles.Cx,'String'));
456Calib.Cy=str2num(get(handles.Cy,'String'));
457%default
458if isempty(Calib.f1)
459    Calib.f1=25/0.012;
460end
461if isempty(Calib.f2)
462    Calib.f2=25/0.012;
463end
464if isempty(Calib.k)
465    Calib.k=0;
466end
467if isempty(Calib.Cx)||isempty(Calib.Cy)
468    huvmat=findobj(allchild(0),'Tag','uvmat');
469    hhuvmat=guidata(huvmat);
[332]470    Calib.Cx=str2num(get(hhuvmat.num_Npx,'String'))/2;
471    Calib.Cx=str2num(get(hhuvmat.num_Npy,'String'))/2;
[109]472end   
473%tsai parameters
474Calib.dpx=0.012;%arbitrary
475Calib.dpy=0.012;
476Calib.sx=Calib.f1*Calib.dpx/(Calib.f2*Calib.dpy);
477Calib.f=Calib.f2*Calib.dpy;
478Calib.kappa1=Calib.k/(Calib.f*Calib.f);
[2]479
[109]480%initial guess
481X=Coord(:,1);
482Y=Coord(:,2);
483Zmean=mean(Coord(:,3));
484x_ima=Coord(:,4)-Calib.Cx;
485y_ima=Coord(:,5)-Calib.Cy;
486XY_mat=[ones(size(X)) X Y];
487a_X1=XY_mat\x_ima; %transformation matrix for X
488a_Y1=XY_mat\y_ima;%transformation matrix for Y
489R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,-1];% rotation+ z axis reversal (upward)
490norm=sqrt(det(-R));
491calib_param(1)=0;% quadratic distortion
492calib_param(2)=a_X1(1);
493calib_param(3)=a_Y1(1);
494calib_param(4)=Calib.f/(norm*Calib.dpx)-R(3,3)*Zmean;
[121]495calib_param(5)=angle(a_X1(2)+1i*a_X1(3));
[109]496display(['initial guess=' num2str(calib_param)])
497
498%optimise the parameters: minimisation of error
[121]499calib_param = fminsearch(@(calib_param) error_calib(calib_param,Calib,Coord),calib_param);
[109]500
501GeometryCalib.CalibrationType='tsai_normal';
502GeometryCalib.focal=Calib.f;
503GeometryCalib.dpx_dpy=[Calib.dpx Calib.dpy];
504GeometryCalib.Cx_Cy=[Calib.Cx Calib.Cy];
505GeometryCalib.sx=Calib.sx;
506GeometryCalib.kappa1=calib_param(1);
507GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
508GeometryCalib.Tx_Ty_Tz=[calib_param(2) calib_param(3) calib_param(4)];
509alpha=calib_param(5);
510GeometryCalib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
511
[60]512%------------------------------------------------------------------------
[109]513function GeometryCalib=calib_3D_linear(Coord,handles)
[69]514%------------------------------------------------------------------
515path_uvmat=which('uvmat');% check the path detected for source file uvmat
516path_UVMAT=fileparts(path_uvmat); %path to UVMAT
[78]517huvmat=findobj(allchild(0),'Tag','uvmat');
518hhuvmat=guidata(huvmat);
[121]519coord_files=get(handles.coord_files,'String');
520if ischar(coord_files)
521    coord_files={coord_files};
522end
523if isempty(coord_files{1}) || isequal(coord_files,{''})
524    coord_files={};
525end
526%retrieve the calibration points stored in the files listed in the popup list coord_files
527x_1=Coord(:,4:5)';%px coordinates of the ref points
[332]528nx=str2num(get(hhuvmat.num_Npx,'String'));
529ny=str2num(get(hhuvmat.num_Npy,'String'));
[121]530x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
531X_1=Coord(:,1:3)';%phys coordinates of the ref points
532n_ima=numel(coord_files)+1;
533if ~isempty(coord_files)
534    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
535    for ifile=1:numel(coord_files)
536    t=xmltree(coord_files{ifile});
537    s=convert(t);%convert to matlab structure
538        if isfield(s,'GeometryCalib')
539            if isfield(s.GeometryCalib,'SourceCalib')
540                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
541                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
542                Coord_file=zeros(length(PointCoord),5);%default
543                for i=1:length(PointCoord)
544                    line=str2num(PointCoord{i});
545                    Coord_file(i,4:5)=line(4:5);%px x
546                    Coord_file(i,1:3)=line(1:3);%phys x
547                end
548                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
549                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
550                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
551                end
552            end
553        end
554    end
555end
556n_ima=numel(coord_files)+1;
[109]557est_dist=[0;0;0;0;0];
558est_aspect_ratio=0;
559est_fc=[1;1];
560%fc=[25;25]/0.012;
561center_optim=0;
562run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
563GeometryCalib.CalibrationType='3D_linear';
[121]564GeometryCalib.fx_fy=fc';
565%GeometryCalib.focal=fc(2);
566%GeometryCalib.dpx_dpy=[1 1];
[109]567GeometryCalib.Cx_Cy=cc';
[121]568%GeometryCalib.sx=fc(1)/fc(2);
569GeometryCalib.kc=kc(1);
570%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
[109]571GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
572GeometryCalib.Tx_Ty_Tz=Tc_1';
573GeometryCalib.R=Rc_1;
[121]574GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
575GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
576GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
577GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
578GeometryCalib.ErrorRMS=[];
579GeometryCalib.ErrorMax=[];
[109]580
581%------------------------------------------------------------------------
582function GeometryCalib=calib_3D_quadr(Coord,handles)
583%------------------------------------------------------------------
584
585path_uvmat=which('uvmat');% check the path detected for source file uvmat
586path_UVMAT=fileparts(path_uvmat); %path to UVMAT
587huvmat=findobj(allchild(0),'Tag','uvmat');
588hhuvmat=guidata(huvmat);
589% check_cond=0;
590coord_files=get(handles.coord_files,'String');
591if ischar(coord_files)
592    coord_files={coord_files};
593end
594if isempty(coord_files{1}) || isequal(coord_files,{''})
595    coord_files={};
596end
597
598%retrieve the calibration points stored in the files listed in the popup list coord_files
[114]599x_1=Coord(:,4:5)';%px coordinates of the ref points
[332]600nx=str2num(get(hhuvmat.num_Npx,'String'));
601ny=str2num(get(hhuvmat.num_Npy,'String'));
[114]602x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
603X_1=Coord(:,1:3)';%phys coordinates of the ref points
[109]604n_ima=numel(coord_files)+1;
605if ~isempty(coord_files)
606    msgbox_uvmat('CONFIRMATION',['The xy coordinates of the calibration points in ' num2str(n_ima) ' planes will be used'])
607    for ifile=1:numel(coord_files)
608    t=xmltree(coord_files{ifile});
609    s=convert(t);%convert to matlab structure
610        if isfield(s,'GeometryCalib')
611            if isfield(s.GeometryCalib,'SourceCalib')
612                if isfield(s.GeometryCalib.SourceCalib,'PointCoord')
613                PointCoord=s.GeometryCalib.SourceCalib.PointCoord;
[121]614                Coord_file=zeros(length(PointCoord),5);%default
[109]615                for i=1:length(PointCoord)
616                    line=str2num(PointCoord{i});
617                    Coord_file(i,4:5)=line(4:5);%px x
618                    Coord_file(i,1:3)=line(1:3);%phys x
619                end
620                eval(['x_' num2str(ifile+1) '=Coord_file(:,4:5)'';']);
[114]621                eval(['x_' num2str(ifile+1) '(2,:)=ny-x_' num2str(ifile+1) '(2,:);' ]);
[109]622                eval(['X_' num2str(ifile+1) '=Coord_file(:,1:3)'';']);
623                end
624            end
625        end
626    end
627end
628n_ima=numel(coord_files)+1;
[108]629est_dist=[1;0;0;0;0];
[109]630est_aspect_ratio=1;
631%est_fc=[0;0];
632%fc=[25;25]/0.012;
633center_optim=0;
[83]634run(fullfile(path_UVMAT,'toolbox_calib','go_calib_optim'));
[69]635
[109]636GeometryCalib.CalibrationType='3D_quadr';
[114]637GeometryCalib.fx_fy=fc';
638%GeometryCalib.focal=fc(2);
639%GeometryCalib.dpx_dpy=[1 1];
[69]640GeometryCalib.Cx_Cy=cc';
[114]641%GeometryCalib.sx=fc(1)/fc(2);
642GeometryCalib.kc=kc(1);
643%GeometryCalib.kappa1=-kc(1)/fc(2)^2;
[69]644GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
645GeometryCalib.Tx_Ty_Tz=Tc_1';
646GeometryCalib.R=Rc_1;
[114]647GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
648GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
649GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
650GeometryCalib.omc=(180/pi)*omc_1;%angles in degrees
[109]651GeometryCalib.ErrorRMS=[];
652GeometryCalib.ErrorMax=[];
[69]653
[109]654
[60]655%------------------------------------------------------------------------
[109]656function GeometryCalib=calib_3D_extrinsic(Coord,handles)
657%------------------------------------------------------------------
658path_uvmat=which('geometry_calib');% check the path detected for source file uvmat
659path_UVMAT=fileparts(path_uvmat); %path to UVMAT
[116]660x_1=double(Coord(:,4:5)');%image coordiantes
661X_1=double(Coord(:,1:3)');% phys coordinates
[114]662huvmat=findobj(allchild(0),'Tag','uvmat');
663hhuvmat=guidata(huvmat);
[332]664ny=str2double(get(hhuvmat.num_Npy,'String'));
[114]665x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates
[109]666n_ima=1;
[114]667GeometryCalib.CalibrationType='3D_extrinsic';
668GeometryCalib.fx_fy(1)=str2num(get(handles.fx,'String'));
669GeometryCalib.fx_fy(2)=str2num(get(handles.fy,'String'));
670GeometryCalib.Cx_Cy(1)=str2num(get(handles.Cx,'String'));
671GeometryCalib.Cx_Cy(2)=str2num(get(handles.Cy,'String'));
672GeometryCalib.kc=str2num(get(handles.kc,'String'));
[109]673fct_path=fullfile(path_UVMAT,'toolbox_calib');
674addpath(fct_path)
[116]675GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%reverse Cx_Cy(2) for calibration (inversion of px ordinate)
[109]676% [omc1,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
677%     [Calib.f Calib.f*Calib.sx]',...
678%     [Calib.Cx Calib.Cy]',...
679%     [-Calib.kappa1*Calib.f^2 0 0 0 0]);
[114]680[omc,Tc1,Rc1,H,x,ex,JJ] = compute_extrinsic(x_1,X_1,...
[116]681    (GeometryCalib.fx_fy)',GeometryCalib.Cx_Cy',[GeometryCalib.kc 0 0 0 0]);
[109]682rmpath(fct_path);
683GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function
684GeometryCalib.Tx_Ty_Tz=Tc1';
685%inversion of z axis
686GeometryCalib.R=Rc1;
[114]687GeometryCalib.R(2,1:3)=-GeometryCalib.R(2,1:3);%inversion of the y image coordinate
688GeometryCalib.Tx_Ty_Tz(2)=-GeometryCalib.Tx_Ty_Tz(2);%inversion of the y image coordinate
[116]689GeometryCalib.Cx_Cy(2)=ny-GeometryCalib.Cx_Cy(2);%inversion of the y image coordinate
[114]690GeometryCalib.omc=(180/pi)*omc';
[109]691%GeometryCalib.R(3,1:3)=-GeometryCalib.R(3,1:3);%inversion for z upward
692
693
[116]694
[109]695%------------------------------------------------------------------------
696%function GeometryCalib=calib_tsai_heikkila(Coord)
697% TEST: NOT IMPLEMENTED
698%------------------------------------------------------------------
699% path_uvmat=which('uvmat');% check the path detected for source file uvmat
700% path_UVMAT=fileparts(path_uvmat); %path to UVMAT
701% path_calib=fullfile(path_UVMAT,'toolbox_calib_heikkila');
702% addpath(path_calib)
703% npoints=size(Coord,1);
704% Coord(:,1:3)=10*Coord(:,1:3);
705% Coord=[Coord zeros(npoints,2) -ones(npoints,1)];
706% [par,pos,iter,res,er,C]=cacal('dalsa',Coord);
707% GeometryCalib.CalibrationType='tsai';
708% GeometryCalib.focal=par(2);
709
710
711%------------------------------------------------------------------------
712% --- determine the rms of calibration error
713function ErrorRms=error_calib(calib_param,Calib,Coord)
714%calib_param: vector of free calibration parameters (to optimise)
715%Calib: structure of the given calibration parameters
716%Coord: list of phys coordinates (columns 1-3, and pixel coordinates (columns 4-5)
717Calib.f=25;
718Calib.dpx=0.012;
719Calib.dpy=0.012;
720Calib.sx=1;
721Calib.Cx=512;
722Calib.Cy=512;
723Calib.kappa1=calib_param(1);
724Calib.Tx=calib_param(2);
725Calib.Ty=calib_param(3);
726Calib.Tz=calib_param(4);
727alpha=calib_param(5);
728Calib.R=[cos(alpha) sin(alpha) 0;-sin(alpha) cos(alpha) 0;0 0 -1];
[2]729
[109]730X=Coord(:,1);
731Y=Coord(:,2);
732Z=Coord(:,3);
733x_ima=Coord(:,4);
734y_ima=Coord(:,5);
735[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z);
736ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima)));
737ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima)));
738ErrorRms=mean(ErrorRms);
739
[60]740%------------------------------------------------------------------------
[2]741function XImage_Callback(hObject, eventdata, handles)
[60]742%------------------------------------------------------------------------
[2]743update_list(hObject, eventdata,handles)
744
[60]745%------------------------------------------------------------------------
[2]746function YImage_Callback(hObject, eventdata, handles)
[60]747%------------------------------------------------------------------------
[2]748update_list(hObject, eventdata,handles)
749
[109]750%------------------------------------------------------------------------
751% --- Executes on button press in STORE.
752function STORE_Callback(hObject, eventdata, handles)
753Coord_cell=get(handles.ListCoord,'String');
754Object=read_geometry_calib(Coord_cell);
755unitlist=get(handles.CoordUnit,'String');
756unit=unitlist{get(handles.CoordUnit,'value')};
757GeometryCalib.CoordUnit=unit;
758GeometryCalib.SourceCalib.PointCoord=Object.Coord;
759huvmat=findobj(allchild(0),'Name','uvmat');
760hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
[128]761% RootPath='';
762% RootFile='';
[121]763if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile)
[341]764%     testhandle=1;
[109]765    RootPath=get(hhuvmat.RootPath,'String');
766    RootFile=get(hhuvmat.RootFile,'String');
767    filebase=fullfile(RootPath,RootFile);
768    while exist([filebase '.xml'],'file')
769        filebase=[filebase '~'];
770    end
771    outputfile=[filebase '.xml'];
[114]772    errormsg=update_imadoc(GeometryCalib,outputfile);
773    if ~strcmp(errormsg,'')
774        msgbox_uvmat('ERROR',errormsg);
775    end
[109]776    listfile=get(handles.coord_files,'string');
777    if isequal(listfile,{''})
778        listfile={outputfile};
779    else
[128]780        listfile=[listfile;{outputfile}];%update the list of coord files
[109]781    end
782    set(handles.coord_files,'string',listfile);
783end
784set(handles.ListCoord,'Value',1)% refresh the display of coordinates
785set(handles.ListCoord,'String',{'......'})
786
[114]787% --------------------------------------------------------------------
788% --- Executes on button press in CLEAR_PTS: clear the list of calibration points
789function CLEAR_PTS_Callback(hObject, eventdata, handles)
790% --------------------------------------------------------------------
791set(handles.ListCoord,'Value',1)% refresh the display of coordinates
792set(handles.ListCoord,'String',{'......'})
793MenuPlot_Callback(hObject, eventdata, handles)
794
[109]795%------------------------------------------------------------------------
796% --- Executes on button press in CLEAR.
797function CLEAR_Callback(hObject, eventdata, handles)
798%------------------------------------------------------------------------
799set(handles.coord_files,'Value',1)
800set(handles.coord_files,'String',{''})
801
802%------------------------------------------------------------------------
[2]803function XObject_Callback(hObject, eventdata, handles)
[109]804%------------------------------------------------------------------------
[2]805update_list(hObject, eventdata,handles)
806
[109]807%------------------------------------------------------------------------
[2]808function YObject_Callback(hObject, eventdata, handles)
[109]809%------------------------------------------------------------------------
[2]810update_list(hObject, eventdata,handles)
811
[109]812%------------------------------------------------------------------------
[2]813function ZObject_Callback(hObject, eventdata, handles)
[109]814%------------------------------------------------------------------------
[2]815update_list(hObject, eventdata,handles)
816
[60]817%------------------------------------------------------------------------
[2]818function update_list(hObject, eventdata, handles)
[60]819%------------------------------------------------------------------------
[149]820newval(4)=str2double(get(handles.XImage,'String'));
821newval(5)=str2double(get(handles.YImage,'String'));
822newval(1)=str2double(get(handles.XObject,'String'));
823newval(2)=str2double(get(handles.YObject,'String'));
824newval(3)=str2double(get(handles.ZObject,'String'));
825if isnan(newval(3))
826    newval(3)=0;%put z to 0 by default
[2]827end
828Coord=get(handles.ListCoord,'String');
[149]829Coord(end)=[]; %remove last string '.....'
[2]830val=get(handles.ListCoord,'Value');
[149]831data=read_geometry_calib(Coord);
832data.Coord(val,:)=newval;
833for i=1:size(data.Coord,1)
834    for j=1:5
835          Coord_cell{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
836    end
837end
838
839Tabchar=cell2tab(Coord_cell,' | ');
840Tabchar=[Tabchar ;{'......'}];
841set(handles.ListCoord,'String',Tabchar)
842
[60]843%update the plot
844ListCoord_Callback(hObject, eventdata, handles)
[67]845MenuPlot_Callback(hObject, eventdata, handles)
[71]846
[60]847%------------------------------------------------------------------------
[2]848% --- Executes on selection change in ListCoord.
849function ListCoord_Callback(hObject, eventdata, handles)
[60]850%------------------------------------------------------------------------
[71]851huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
852hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
853hhh=findobj(hplot,'Tag','calib_marker');
[2]854Coord_cell=get(handles.ListCoord,'String');
855val=get(handles.ListCoord,'Value');
[78]856if numel(val)>1
857    return %no action if several lines have been selected
858end
[71]859coord_str=Coord_cell{val};
[128]860k=findstr(' | ',coord_str);
[71]861if isempty(k)%last line '.....' selected
862    if ~isempty(hhh)
863        delete(hhh)%delete the circle marker
[2]864    end
[71]865    return
866end
867%fill the edit boxex
[149]868set(handles.XObject,'String',coord_str(1:k(1)-1))
869set(handles.YObject,'String',coord_str(k(1)+3:k(2)-1))
870set(handles.ZObject,'String',coord_str(k(2)+3:k(3)-1))
871set(handles.XImage,'String',coord_str(k(3)+3:k(4)-1))
872set(handles.YImage,'String',coord_str(k(4)+3:end))
[71]873h_menu_coord=findobj(huvmat,'Tag','transform_fct');
874menu=get(h_menu_coord,'String');
875choice=get(h_menu_coord,'Value');
876if iscell(menu)
877    option=menu{choice};
878else
879    option='px'; %default
880end
881if isequal(option,'phys')
[149]882    XCoord=str2double(coord_str(1:k(1)-1));
883    YCoord=str2double(coord_str(k(1)+3:k(2)-1));
[71]884elseif isequal(option,'px')|| isequal(option,'')
[149]885    XCoord=str2double(coord_str(k(3)+3:k(4)-1));
886    YCoord=str2double(coord_str(k(4)+3:end));
[71]887else
888    msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be px or phys ')
889end
890if isempty(XCoord)||isempty(YCoord)
891     if ~isempty(hhh)
892        delete(hhh)%delete the circle marker
[2]893    end
[71]894    return
[2]895end
[71]896xlim=get(hplot,'XLim');
897ylim=get(hplot,'YLim');
898ind_range=max(abs(xlim(2)-xlim(1)),abs(ylim(end)-ylim(1)))/20;%defines the size of the circle marker
899if isempty(hhh)
[149]900    set(0,'CurrentFig',huvmat)
901    set(huvmat,'CurrentAxes',hplot)
[71]902    rectangle('Curvature',[1 1],...
903              'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range],'EdgeColor','m',...
904              'LineStyle','-','Tag','calib_marker');
905else
906    set(hhh,'Position',[XCoord-ind_range/2 YCoord-ind_range/2 ind_range ind_range])
907end
[2]908
[60]909%------------------------------------------------------------------------
[2]910% --- Executes on selection change in edit_append.
911function edit_append_Callback(hObject, eventdata, handles)
[60]912%------------------------------------------------------------------------
[2]913choice=get(handles.edit_append,'Value');
[78]914if choice
915    set(handles.edit_append,'BackgroundColor',[1 1 0])
[177]916    huvmat=findobj(allchild(0),'tag','uvmat');
917    if ishandle(huvmat)
918        hhuvmat=guidata(huvmat);
919        set(hhuvmat.edit_object,'Value',0)
920        set(hhuvmat.edit_object,'BackgroundColor',[0.7 0.7 0.7])
921    end
[78]922else
923    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
[2]924end
925   
926function NEW_Callback(hObject, eventdata, handles)
927%A METTRE SOUS UN BOUTON
928huvmat=findobj(allchild(0),'Name','uvmat');
929hchild=get(huvmat,'children');
930hcoord=findobj(hchild,'Tag','menu_coord');
931coordtype=get(hcoord,'Value');
932haxes=findobj(hchild,'Tag','axes3');
933AxeData=get(haxes,'UserData');
934if ~isequal(hcoord,2)
935    set(hcoord,'Value',2)
936    huvmat=uvmat(AxeData);
937    'relancer uvmat';
938end
939if ~isfield(AxeData,'ZoomAxes')
[42]940    msgbox_uvmat('ERROR','first draw a window around a grid marker')
[2]941    return
942end
943XLim=get(AxeData.ZoomAxes,'XLim');
944YLim=get(AxeData.ZoomAxes,'YLim');
945np=size(AxeData.A);
946ind_sub_x=round(XLim);
947ind_sub_y=np(1)-round(YLim);
[227]948Mfiltre=AxeData.A(ind_sub_y(2):ind_sub_y(1) ,ind_sub_x,:);
[2]949Mfiltre_norm=double(Mfiltre);
950Mfiltre_norm=Mfiltre_norm/sum(sum(Mfiltre_norm));
951Mfiltre_norm=100*(Mfiltre_norm-mean(mean(Mfiltre_norm)));
952Atype=class(AxeData.A);
953Data.NbDim=2;
954Data.A=filter2(Mfiltre_norm,double(AxeData.A));
955Data.A=feval(Atype,Data.A);
956Data.AName='image';
957Data.AX=AxeData.AX;
958Data.AY=AxeData.AY;
959Data.CoordType='px';
960plot_field(Data)
961
[60]962%------------------------------------------------------------------------
[2]963function MenuPlot_Callback(hObject, eventdata, handles)
[60]964%------------------------------------------------------------------------
[2]965huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle
[128]966%UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface
[2]967hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat
[128]968%hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat
[60]969h_menu_coord=findobj(huvmat,'Tag','transform_fct');
[2]970menu=get(h_menu_coord,'String');
971choice=get(h_menu_coord,'Value');
972if iscell(menu)
973    option=menu{choice};
974else
975    option='px'; %default
976end
977Coord_cell=get(handles.ListCoord,'String');
978ObjectData=read_geometry_calib(Coord_cell);
979%ObjectData=read_geometry_calib(handles);%read the interface input parameters defining the object
[71]980if ~isempty(ObjectData.Coord)
981    if isequal(option,'phys')
[227]982        ObjectData.Coord=ObjectData.Coord(:,1:3);
[71]983    elseif isequal(option,'px')||isequal(option,'')
[227]984        ObjectData.Coord=ObjectData.Coord(:,4:5);
[71]985    else
986        msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be '''', px or phys ')
987    end
[2]988end
[231]989%axes(hhuvmat.axes3)
990set(0,'CurrentFigure',huvmat)
991set(huvmat,'CurrentAxes',hhuvmat.axes3)
[2]992hh=findobj('Tag','calib_points');
[71]993if  ~isempty(ObjectData.Coord) && isempty(hh)
[2]994    hh=line(ObjectData.Coord(:,1),ObjectData.Coord(:,2),'Color','m','Tag','calib_points','LineStyle','.','Marker','+');
[71]995elseif isempty(ObjectData.Coord)%empty list of points, suppress the plot
996    delete(hh)
[2]997else
998    set(hh,'XData',ObjectData.Coord(:,1))
999    set(hh,'YData',ObjectData.Coord(:,2))
1000end
[61]1001pause(.1)
1002figure(handles.geometry_calib)
[2]1003
1004% --------------------------------------------------------------------
1005function MenuHelp_Callback(hObject, eventdata, handles)
[116]1006path_to_uvmat=which('uvmat');% check the path of uvmat
[2]1007pathelp=fileparts(path_to_uvmat);
[116]1008helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
[36]1009if 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]1010else
[36]1011   addpath (fullfile(pathelp,'uvmat_doc'))
[2]1012   web([helpfile '#geometry_calib'])
1013end
1014
[17]1015%------------------------------------------------------------------------
[2]1016function MenuCreateGrid_Callback(hObject, eventdata, handles)
[17]1017%------------------------------------------------------------------------
[36]1018%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
[61]1019CalibData=get(handles.geometry_calib,'UserData');
[12]1020Tinput=[];%default
1021if isfield(CalibData,'grid')
1022    Tinput=CalibData.grid;
1023end
[71]1024[T,CalibData.grid]=create_grid(Tinput);%display the GUI create_grid
[61]1025set(handles.geometry_calib,'UserData',CalibData)
[2]1026
[12]1027%grid in phys space
[71]1028Coord=get(handles.ListCoord,'String');
1029val=get(handles.ListCoord,'Value');
1030data=read_geometry_calib(Coord);
1031%nbpoints=size(data.Coord,1); %nbre of calibration points
1032data.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
1033% for i=1:nbpoints
1034%    for j=1:5
1035%           Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
1036%    end
1037% end
1038%update the phys coordinates starting from the selected point (down in the
1039Coord(end,:)=[]; %remove last string '.....'
1040for i=1:size(data.Coord,1)
1041    for j=1:5
[17]1042          Coord{i,j}=num2str(data.Coord(i,j),4);%display coordiantes with 4 digits
1043    end
1044end
1045
1046%size(data.Coord,1)
[128]1047Tabchar=cell2tab(Coord,' | ');
[71]1048Tabchar=[Tabchar ;{'......'}];
[12]1049set(handles.ListCoord,'String',Tabchar)
[2]1050
[71]1051% -----------------------------------------------------------------------
1052% --- automatic grid dectection from local maxima of the images
[60]1053function MenuDetectGrid_Callback(hObject, eventdata, handles)
[71]1054%------------------------------------------------------------------------
[159]1055%% read the four last point coordinates in pixels
[108]1056Coord_cell=get(handles.ListCoord,'String');%read list of coordinates on geometry_calib
[60]1057data=read_geometry_calib(Coord_cell);
1058nbpoints=size(data.Coord,1); %nbre of calibration points
[62]1059if nbpoints~=4
[227]1060    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]1061    return
[60]1062end
[71]1063corners_X=(data.Coord(end:-1:end-3,4)); %pixel absissa of the four corners
1064corners_Y=(data.Coord(end:-1:end-3,5));
[60]1065
[71]1066%reorder the last two points (the two first in the list) if needed
[121]1067angles=angle((corners_X-corners_X(1))+1i*(corners_Y-corners_Y(1)));
[62]1068if abs(angles(4)-angles(2))>abs(angles(3)-angles(2))
1069      X_end=corners_X(4);
1070      Y_end=corners_Y(4);
1071      corners_X(4)=corners_X(3);
1072      corners_Y(4)=corners_Y(3);
1073      corners_X(3)=X_end;
1074      corners_Y(3)=Y_end;
1075end
1076
[227]1077%% initiate the grid
1078CalibData=get(handles.geometry_calib,'UserData');%get information stored on the GUI geometry_calib
1079grid_input=[];%default
1080if isfield(CalibData,'grid')
1081    grid_input=CalibData.grid;%retrieve the previously used grid
1082end
1083[T,CalibData.grid,white_test]=create_grid(grid_input,'detect_grid');%display the GUI create_grid, read the set of phys coordinates T
1084set(handles.geometry_calib,'UserData',CalibData)%store the phys grid parameters for later use
1085
1086
1087
[159]1088%% read the current image, displayed in the GUI uvmat
[60]1089huvmat=findobj(allchild(0),'Name','uvmat');
1090UvData=get(huvmat,'UserData');
1091A=UvData.Field.A;
1092npxy=size(A);
[159]1093X=[CalibData.grid.x_0 CalibData.grid.x_1 CalibData.grid.x_0 CalibData.grid.x_1]';%corner absissa in the phys coordinates (cm)
1094Y=[CalibData.grid.y_0 CalibData.grid.y_0 CalibData.grid.y_1 CalibData.grid.y_1]';%corner ordinates in the phys coordinates (cm)
[109]1095
[159]1096%calculate transform matrices for plane projection
[108]1097% reference: http://alumni.media.mit.edu/~cwren/interpolator/ by Christopher R. Wren
1098B = [ X Y ones(size(X)) zeros(4,3)        -X.*corners_X -Y.*corners_X ...
1099      zeros(4,3)        X Y ones(size(X)) -X.*corners_Y -Y.*corners_Y ];
1100B = reshape (B', 8 , 8 )';
1101D = [ corners_X , corners_Y ];
1102D = reshape (D', 8 , 1 );
[121]1103l = (B' * B)\B' * D;
[108]1104Amat = reshape([l(1:6)' 0 0 1 ],3,3)';
1105C = [l(7:8)' 1];
1106
[159]1107% transform grid image into 'phys' coordinates
[114]1108GeometryCalib.fx_fy=[1 1];
1109GeometryCalib.Tx_Ty_Tz=[Amat(1,3) Amat(2,3) 1];
[108]1110GeometryCalib.R=[Amat(1,1),Amat(1,2),0;Amat(2,1),Amat(2,2),0;C(1),C(2),0];
[159]1111GeometryCalib.CoordUnit='cm';
[114]1112path_uvmat=which('uvmat');% check the path detected for source file uvmat
1113path_UVMAT=fileparts(path_uvmat); %path to UVMAT
1114addpath(fullfile(path_UVMAT,'transform_field'))
1115Data.ListVarName={'AY','AX','A'};
1116Data.VarDimName={'AY','AX',{'AY','AX'}};
1117if ndims(A)==3
1118    A=mean(A,3);
1119end
1120Data.A=A-min(min(A));
1121Data.AY=[npxy(1)-0.5 0.5];
1122Data.AX=[0.5 npxy(2)];
[158]1123Data.CoordUnit='pixel';
[114]1124Calib.GeometryCalib=GeometryCalib;
[121]1125DataOut=phys(Data,Calib);
[114]1126rmpath(fullfile(path_UVMAT,'transform_field'))
1127Amod=DataOut.A;
1128Rangx=DataOut.AX;
1129Rangy=DataOut.AY;
[156]1130if white_test
[159]1131    Amod=double(Amod);%case of white grid markers: will look for image maxima
[156]1132else
[159]1133    Amod=-double(Amod);%case of black grid markers: will look for image minima
[156]1134end
[114]1135% figure(12) %display corrected image
[109]1136% Amax=max(max(Amod));
1137% image(Rangx,Rangy,uint8(255*Amod/Amax))
[114]1138
[159]1139%% detection of local image extrema in each direction
[88]1140Dx=(Rangx(2)-Rangx(1))/(npxy(2)-1); %x mesh in real space
1141Dy=(Rangy(2)-Rangy(1))/(npxy(1)-1); %y mesh in real space
[121]1142ind_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
1143ind_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]1144nbpoints=size(T,1);
1145for ipoint=1:nbpoints
1146    i0=1+round((T(ipoint,1)-Rangx(1))/Dx);%round(Xpx(ipoint));
1147    j0=1+round((T(ipoint,2)-Rangy(1))/Dy);%round(Xpx(ipoint));
[109]1148    j0min=max(j0-ind_range_y,1);
1149    j0max=min(j0+ind_range_y,size(Amod,1));
1150    i0min=max(i0-ind_range_x,1);
1151    i0max=min(i0+ind_range_x,size(Amod,2));
1152    Asub=Amod(j0min:j0max,i0min:i0max);
[60]1153    x_profile=sum(Asub,1);
1154    y_profile=sum(Asub,2);
1155    [Amax,ind_x_max]=max(x_profile);
1156    [Amax,ind_y_max]=max(y_profile);
[61]1157    %sub-pixel improvement using moments
1158    x_shift=0;
1159    y_shift=0;
[109]1160    if ind_x_max+2<=numel(x_profile) && ind_x_max-2>=1
[61]1161        Atop=x_profile(ind_x_max-2:ind_x_max+2);
1162        x_shift=sum(Atop.*[-2 -1 0 1 2])/sum(Atop);
1163    end
[114]1164    if ind_y_max+2<=numel(y_profile) && ind_y_max-2>=1
[61]1165        Atop=y_profile(ind_y_max-2:ind_y_max+2);
1166        y_shift=sum(Atop.*[-2 -1 0 1 2]')/sum(Atop);
1167    end
[109]1168    Delta(ipoint,1)=(x_shift+ind_x_max+i0min-i0-1)*Dx;%shift from the initial guess
1169    Delta(ipoint,2)=(y_shift+ind_y_max+j0min-j0-1)*Dy;
[60]1170end
1171Tmod=T(:,(1:2))+Delta;
1172[Xpx,Ypx]=px_XYZ(GeometryCalib,Tmod(:,1),Tmod(:,2));
[63]1173for ipoint=1:nbpoints
1174     Coord{ipoint,1}=num2str(T(ipoint,1),4);%display coordiantes with 4 digits
1175     Coord{ipoint,2}=num2str(T(ipoint,2),4);%display coordiantes with 4 digits
[109]1176     Coord{ipoint,3}=num2str(T(ipoint,3),4);%display coordiantes with 4 digits;
1177     Coord{ipoint,4}=num2str(Xpx(ipoint),4);%display coordiantes with 4 digits
1178     Coord{ipoint,5}=num2str(Ypx(ipoint),4);%display coordiantes with 4 digits
[60]1179end
[128]1180Tabchar=cell2tab(Coord(end:-1:1,:),' | ');
[71]1181Tabchar=[Tabchar ;{'......'}];
[60]1182set(handles.ListCoord,'Value',1)
1183set(handles.ListCoord,'String',Tabchar)
[67]1184MenuPlot_Callback(hObject, eventdata, handles)
[60]1185
[71]1186%-----------------------------------------------------------------------
1187function MenuTranslatePoints_Callback(hObject, eventdata, handles)
1188%-----------------------------------------------------------------------
1189%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1190CalibData=get(handles.geometry_calib,'UserData');
1191Tinput=[];%default
1192if isfield(CalibData,'translate')
1193    Tinput=CalibData.translate;
1194end
1195T=translate_points(Tinput);%display translate_points GUI and get shift parameters
1196CalibData.translate=T;
1197set(handles.geometry_calib,'UserData',CalibData)
1198%translation
1199Coord_cell=get(handles.ListCoord,'String');
1200data=read_geometry_calib(Coord_cell);
1201data.Coord(:,1)=T(1)+data.Coord(:,1);
1202data.Coord(:,2)=T(2)+data.Coord(:,2);
1203data.Coord(:,3)=T(3)+data.Coord(:,3);
1204data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1205for i=1:size(data.Coord,1)
1206    for j=1:5
1207          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1208   end
1209end
[128]1210Tabchar=cell2tab(Coord,' | ');
[88]1211Tabchar=[Tabchar; {'.....'}];
[71]1212%set(handles.ListCoord,'Value',1)
1213set(handles.ListCoord,'String',Tabchar)
1214
1215
1216% --------------------------------------------------------------------
1217function MenuRotatePoints_Callback(hObject, eventdata, handles)
1218%hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib
1219CalibData=get(handles.geometry_calib,'UserData');
1220Tinput=[];%default
1221if isfield(CalibData,'rotate')
1222    Tinput=CalibData.rotate;
1223end
[356]1224T=rotate_points(Tinput);%display rotate_points GUI to introduce rotation parameters
[71]1225CalibData.rotate=T;
1226set(handles.geometry_calib,'UserData',CalibData)
1227%-----------------------------------------------------
1228%rotation
1229Phi=T(1);
1230O_x=0;%default
1231O_y=0;%default
1232if numel(T)>=2
1233    O_x=T(2);%default
1234end
1235if numel(T)>=3
1236    O_y=T(3);%default
1237end
1238Coord_cell=get(handles.ListCoord,'String');
1239data=read_geometry_calib(Coord_cell);
1240r1=cos(pi*Phi/180);
1241r2=-sin(pi*Phi/180);
1242r3=sin(pi*Phi/180);
1243r4=cos(pi*Phi/180);
1244x=data.Coord(:,1)-O_x;
1245y=data.Coord(:,2)-O_y;
1246data.Coord(:,1)=r1*x+r2*y;
1247data.Coord(:,2)=r3*x+r4*y;
1248% data.Coord(:,[4 5])=data.Coord(:,[4 5]);
1249for i=1:size(data.Coord,1)
1250    for j=1:5
1251          Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z
1252   end
1253end
[148]1254Tabchar=cell2tab(Coord,' | ');
[71]1255Tabchar=[Tabchar;{'......'}];
1256set(handles.ListCoord,'Value',1)
1257set(handles.ListCoord,'String',Tabchar)
1258
[109]1259
1260% %------------------------------------------------------------------------
1261% % --- Executes on button press in rotation.
1262% function rotation_Callback(hObject, eventdata, handles)
1263% %------------------------------------------------------------------------
1264% angle_rot=(pi/180)*str2num(get(handles.Phi,'String'));
1265% Coord_cell=get(handles.ListCoord,'String');
1266% data=read_geometry_calib(Coord_cell);
1267% data.Coord(:,1)=cos(angle_rot)*data.Coord(:,1)+sin(angle_rot)*data.Coord(:,2);
1268% data.Coord(:,1)=-sin(angle_rot)*data.Coord(:,1)+cos(angle_rot)*data.Coord(:,2);
1269% set(handles.XObject,'String',num2str(data.Coord(:,1),4));
1270% set(handles.YObject,'String',num2str(data.Coord(:,2),4));
1271
1272
[108]1273%------------------------------------------------------------------------
1274% image transform from px to phys
1275%INPUT:
1276%Zindex: index of plane
[114]1277% function [A_out,Rangx,Rangy]=phys_Ima(A,Calib,ZIndex)
1278% %------------------------------------------------------------------------
1279% xcorner=[];
1280% ycorner=[];
1281% npx=[];
1282% npy=[];
1283% siz=size(A)
1284% npx=[npx siz(2)];
1285% npy=[npy siz(1)]
1286% xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners
1287% yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
1288% [xcorner,ycorner]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates
1289% Rangx(1)=min(xcorner);
1290% Rangx(2)=max(xcorner);
1291% Rangy(2)=min(ycorner);
1292% Rangy(1)=max(ycorner);
1293% test_multi=(max(npx)~=min(npx)) | (max(npy)~=min(npy));
1294% npx=max(npx);
1295% npy=max(npy);
1296% x=linspace(Rangx(1),Rangx(2),npx);
1297% y=linspace(Rangy(1),Rangy(2),npy);
1298% [X,Y]=meshgrid(x,y);%grid in physical coordiantes
1299% vec_B=[];
1300%
1301% zphys=0; %default
1302% if isfield(Calib,'SliceCoord') %.Z= index of plane
1303%    SliceCoord=Calib.SliceCoord(ZIndex,:);
1304%    zphys=SliceCoord(3); %to generalize for non-parallel planes
1305% end
1306% [XIMA,YIMA]=px_XYZ(Calib,X,Y,zphys);%corresponding image indices for each point in the real space grid
1307% XIMA=reshape(round(XIMA),1,npx*npy);%indices reorganized in 'line'
1308% YIMA=reshape(round(YIMA),1,npx*npy);
1309% flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image
1310% testuint8=isa(A,'uint8');
1311% testuint16=isa(A,'uint16');
1312% if numel(siz)==2 %(B/W images)
1313%     vec_A=reshape(A,1,npx*npy);%put the original image in line
1314%     ind_in=find(flagin);
1315%     ind_out=find(~flagin);
1316%     ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
1317%     ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
1318%     vec_B(ind_in)=vec_A(ICOMB);
1319%     vec_B(ind_out)=zeros(size(ind_out));
1320%     A_out=reshape(vec_B,npy,npx);%new image in real coordinates
1321% elseif numel(siz)==3     
1322%     for icolor=1:siz(3)
1323%         vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line
1324%         ind_in=find(flagin);
1325%         ind_out=find(~flagin);
1326%         ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
1327%         ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
1328%         vec_B(ind_in)=vec_A(ICOMB);
1329%         vec_B(ind_out)=zeros(size(ind_out));
1330%         A_out(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates
1331%     end
1332% end
1333% if testuint8
1334%     A_out=uint8(A_out);
1335% end
1336% if testuint16
1337%     A_out=uint16(A_out);
1338% end
[60]1339
[108]1340%------------------------------------------------------------------------
1341% pointwise transform from px to phys
[60]1342%INPUT:
1343%Z: index of plane
[114]1344% function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Z)
1345% %------------------------------------------------------------------------
1346% if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'SliceCoord')&length(Calib.SliceCoord)>=Z
1347%     Zindex=Z;
1348%     Zphys=Calib.SliceCoord(Zindex,3);%GENERALISER AUX CAS AVEC ANGLE
1349% else
1350%     Zphys=0;
1351% end
1352% if ~exist('X','var')||~exist('Y','var')
1353%     Xphys=[];
1354%     Yphys=[];%default
1355%     return
1356% end
1357% Xphys=X;%default
1358% Yphys=Y;
1359% %image transform
1360% if isfield(Calib,'R')
1361%     R=(Calib.R)';
1362%     Dx=R(5)*R(7)-R(4)*R(8);
1363%     Dy=R(1)*R(8)-R(2)*R(7);
1364%     D0=Calib.f*(R(2)*R(4)-R(1)*R(5));
1365%     Z11=R(6)*R(8)-R(5)*R(9);
1366%     Z12=R(2)*R(9)-R(3)*R(8); 
1367%     Z21=R(4)*R(9)-R(6)*R(7);
1368%     Z22=R(3)*R(7)-R(1)*R(9);
1369%     Zx0=R(3)*R(5)-R(2)*R(6);
1370%     Zy0=R(1)*R(6)-R(3)*R(4);
1371%     A11=R(8)*Calib.Ty-R(5)*Calib.Tz+Z11*Zphys;
1372%     A12=R(2)*Calib.Tz-R(8)*Calib.Tx+Z12*Zphys;
1373%     A21=-R(7)*Calib.Ty+R(4)*Calib.Tz+Z21*Zphys;
1374%     A22=-R(1)*Calib.Tz+R(7)*Calib.Tx+Z11*Zphys;
1375%     X0=Calib.f*(R(5)*Calib.Tx-R(2)*Calib.Ty+Zx0*Zphys);
1376%     Y0=Calib.f*(-R(4)*Calib.Tx+R(1)*Calib.Ty+Zy0*Zphys);
1377%         %px to camera:
1378%     Xd=(Calib.dpx/Calib.sx)*(X-Calib.Cx); % sensor coordinates
1379%     Yd=Calib.dpy*(Y-Calib.Cy);
1380%     dist_fact=1+Calib.kappa1*(Xd.*Xd+Yd.*Yd); %distortion factor
1381%     Xu=dist_fact.*Xd;%undistorted sensor coordinates
1382%     Yu=dist_fact.*Yd;
1383%     denom=Dx*Xu+Dy*Yu+D0;
1384%     % denom2=denom.*denom;
1385%     Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates
1386%     Yphys=(A21.*Xu+A22.*Yu+Y0)./denom;
1387% end
[109]1388
1389
1390% --------------------------------------------------------------------
1391function MenuImportPoints_Callback(hObject, eventdata, handles)
[121]1392fileinput=browse_xml(hObject, eventdata, handles);
[109]1393if isempty(fileinput)
1394    return
1395end
1396[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1397GeometryCalib=s.GeometryCalib;
[114]1398%GeometryCalib=load_calib(hObject, eventdata, handles)
[116]1399calib=reshape(GeometryCalib.PointCoord,[],1);
[109]1400for ilist=1:numel(calib)
1401    CoordCell{ilist}=num2str(calib(ilist));
1402end
1403CoordCell=reshape(CoordCell,[],5);
[128]1404Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
[109]1405Tabchar=[Tabchar;{'......'}];
1406set(handles.ListCoord,'Value',1)
1407set(handles.ListCoord,'String',Tabchar)
1408MenuPlot_Callback(handles.geometry_calib, [], handles)
1409
1410% -----------------------------------------------------------------------
1411function MenuImportIntrinsic_Callback(hObject, eventdata, handles)
1412%------------------------------------------------------------------------
1413fileinput=browse_xml(hObject, eventdata, handles);
1414if isempty(fileinput)
1415    return
1416end
1417[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
1418GeometryCalib=s.GeometryCalib;
[114]1419display_intrinsic(GeometryCalib,handles)
[109]1420
1421% -----------------------------------------------------------------------
1422function MenuImportAll_Callback(hObject, eventdata, handles)
1423%------------------------------------------------------------------------
[121]1424fileinput=browse_xml(hObject, eventdata, handles);
[109]1425if ~isempty(fileinput)
1426    loadfile(handles,fileinput)
1427end
1428
1429% -----------------------------------------------------------------------
1430% --- Executes on menubar option Import/Grid file: introduce previous grid files
1431function MenuGridFile_Callback(hObject, eventdata, handles)
1432% -----------------------------------------------------------------------
[121]1433inputfile=browse_xml(hObject, eventdata, handles);
[109]1434listfile=get(handles.coord_files,'string');
1435if isequal(listfile,{''})
1436    listfile={inputfile};
1437else
[121]1438    listfile=[listfile;{inputfile}];%update the list of coord files
[109]1439end
1440set(handles.coord_files,'string',listfile);
1441
1442%------------------------------------------------------------------------
[114]1443% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
1444function key_press_fcn(hObject,eventdata,handles)
1445%------------------------------------------------------------------------
1446xx=double(get(handles.geometry_calib,'CurrentCharacter')); %get the keyboard character
1447if ismember(xx,[8 127])%backspace or delete
1448    Coord_cell=get(handles.ListCoord,'String');
1449    val=get(handles.ListCoord,'Value');
1450     if max(val)<numel(Coord_cell) % the last element '...' has not been selected
1451        Coord_cell(val)=[];%remove the selected line
1452        set(handles.ListCoord,'Value',min(val))
1453        set(handles.ListCoord,'String',Coord_cell)         
1454        ListCoord_Callback(hObject, eventdata, handles)
1455        MenuPlot_Callback(hObject,eventdata,handles)
1456     end
1457end
1458
1459%------------------------------------------------------------------------
[109]1460function fileinput=browse_xml(hObject, eventdata, handles)
1461%------------------------------------------------------------------------
1462fileinput=[];%default
1463oldfile=''; %default
[116]1464UserData=get(handles.geometry_calib,'UserData');
[114]1465if isfield(UserData,'XmlInputFile')
1466    oldfile=UserData.XmlInputFile;
[109]1467end
1468[FileName, PathName, filterindex] = uigetfile( ...
1469       {'*.xml;*.mat', ' (*.xml,*.mat)';
1470       '*.xml',  '.xml files '; ...
1471        '*.mat',  '.mat matlab files '}, ...
1472        'Pick a file',oldfile);
1473fileinput=[PathName FileName];%complete file name
1474testblank=findstr(fileinput,' ');%look for blanks
1475if ~isempty(testblank)
1476    msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed')
1477    return
1478end
1479sizf=size(fileinput);
1480if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
[114]1481UserData.XmlInputFile=fileinput;
[109]1482set(handles.geometry_calib,'UserData',UserData)%record current file foer further use of browser
1483
1484% -----------------------------------------------------------------------
[128]1485function Heading=loadfile(handles,fileinput)
[109]1486%------------------------------------------------------------------------
[128]1487Heading=[];%default
[121]1488[s,errormsg]=imadoc2struct(fileinput,'GeometryCalib');
[128]1489if ~isempty(errormsg)
1490    msgbox_uvmat('ERROR',['Error for reading ' fileinput ': '  errormsg])
1491    return
1492end
1493if ~isempty(s.Heading)
1494    Heading=s.Heading;
1495end
1496   
[116]1497GeometryCalib=s.GeometryCalib;
[114]1498fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
1499%     Tabchar={};
1500CoordCell={};
1501%     kc=0;%default
1502%     f1=1000;
1503%     f2=1000;
1504%     hhuvmat=guidata(findobj(allchild(0),'Name','uvmat'));
[332]1505%     Cx=str2num(get(hhuvmat.num_Npx,'String'))/2;
1506%     Cy=str2num(get(hhuvmat.num_Npy,'String'))/2;
[114]1507Tabchar={};%default
1508val_cal=1;%default
1509if ~isempty(GeometryCalib)
1510    % choose the calibration option
1511    if isfield(GeometryCalib,'CalibrationType')
1512       calib_list=get(handles.calib_type,'String');
1513       for ilist=1:numel(calib_list)
1514           if strcmp(calib_list{ilist},GeometryCalib.CalibrationType)
1515               val_cal=ilist;
1516               break
1517           end
1518       end
1519    end
1520    display_intrinsic(GeometryCalib,handles)%intrinsic param
1521    %extrinsic param
1522    if isfield(GeometryCalib,'Tx_Ty_Tz')
1523        Tx_Ty_Tz=GeometryCalib.Tx_Ty_Tz;
1524        set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4))
1525        set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4))
1526        set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4))
1527    end
1528    if isfield(GeometryCalib,'omc')
1529        set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4))
1530        set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4))
1531        set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4))
1532    end
[116]1533    calib=reshape(GeometryCalib.PointCoord,[],1);
[109]1534    for ilist=1:numel(calib)
1535        CoordCell{ilist}=num2str(calib(ilist));
1536    end
1537    CoordCell=reshape(CoordCell,[],5);
[128]1538    Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display
[109]1539    MenuPlot_Callback(handles.geometry_calib, [], handles)
1540end
[114]1541set(handles.calib_type,'Value',val_cal)
[109]1542Tabchar=[Tabchar;{'......'}];
[114]1543set(handles.ListCoord,'Value',1)
1544set(handles.ListCoord,'String',Tabchar)
1545
[109]1546if isempty(CoordCell)% allow mouse action by default in the absence of input points
1547    set(handles.edit_append,'Value',1)
1548    set(handles.edit_append,'BackgroundColor',[1 1 0])
1549else % does not allow mouse action by default in the presence of input points
1550    set(handles.edit_append,'Value',0)
1551    set(handles.edit_append,'BackgroundColor',[0.7 0.7 0.7])
1552end
1553
[114]1554%------------------------------------------------------------------------
1555%---display calibration intrinsic parameters
1556function display_intrinsic(GeometryCalib,handles)
1557%------------------------------------------------------------------------
1558fx=[];
1559fy=[];
1560if isfield(GeometryCalib,'fx_fy')
1561    fx=GeometryCalib.fx_fy(1);
1562    fy=GeometryCalib.fx_fy(2);
1563end
1564Cx_Cy=[0 0];%default
1565if isfield(GeometryCalib,'Cx_Cy')
1566    Cx_Cy=GeometryCalib.Cx_Cy;
1567end
1568kc=0;
1569if isfield(GeometryCalib,'kc')
[121]1570    kc=GeometryCalib.kc; %* GeometryCalib.focal*GeometryCalib.focal;
[114]1571end
1572set(handles.fx,'String',num2str(fx,5))
1573set(handles.fy,'String',num2str(fy,5))
1574set(handles.Cx,'String',num2str(Cx_Cy(1),'%1.1f'))
1575set(handles.Cy,'String',num2str(Cx_Cy(2),'%1.1f'))
1576set(handles.kc,'String',num2str(kc,'%1.4f'))
[109]1577
1578
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