Index: /trunk/src/transform_field/phys.m
===================================================================
--- /trunk/src/transform_field/phys.m	(revision 240)
+++ /trunk/src/transform_field/phys.m	(revision 241)
@@ -269,128 +269,2 @@
 end
 
-%------------------------------------------------------------------------
-%'phys_XYZ':transforms image (px) to real world (phys) coordinates using geometric calibration parameters
-% function [Xphys,Yphys]=phys_XYZ(Calib,X,Y,Z)
-%
-%OUTPUT:
-%
-%INPUT:
-%Z: index of plane
-function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Zindex)
-%------------------------------------------------------------------------
-testangle=0;
-test_refraction=0;
-if exist('Zindex','var')&& isequal(Zindex,round(Zindex))&& Zindex>0 && isfield(Calib,'SliceCoord')&&length(Calib.SliceCoord)>=Zindex
-    if isfield(Calib, 'SliceAngle') && ~isequal(Calib.SliceAngle,[0 0 0])
-        testangle=1;
-        om=norm(Calib.SliceAngle(Zindex,:));%norm of rotation angle in radians
-        OmAxis=Calib.SliceAngle(Zindex,:)/om; %unit vector marking the rotation axis
-        cos_om=cos(pi*om/180);
-        sin_om=sin(pi*om/180);
-        coeff=OmAxis(3)*(1-cos_om);
-        norm_plane(1)=OmAxis(1)*coeff+OmAxis(2)*sin_om;
-        norm_plane(2)=OmAxis(2)*coeff-OmAxis(1)*sin_om;
-        norm_plane(3)=OmAxis(3)*coeff+cos_om;
-        Z0=norm_plane*Calib.SliceCoord(Zindex,:)'/norm_plane(3);
-    else
-        Z0=Calib.SliceCoord(Zindex,3);%horizontal plane z=cte
-    end
-    Z0virt=Z0;
-    if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') 
-        H=Calib.InterfaceCoord(3);
-        if H>Z0
-            Z0virt=H-(H-Z0)/Calib.RefractionIndex; %corrected z (virtual object)
-            test_refraction=1;
-        end
-    end   
-else
-    Z0=0;
-    Z0virt=0;
-end
-if ~exist('X','var')||~exist('Y','var')
-    Xphys=[];
-    Yphys=[];%default
-    return
-end
-%coordinate transform
-if ~isfield(Calib,'fx_fy')
-     Calib.fx_fy=[1 1];
-end
-if ~isfield(Calib,'Tx_Ty_Tz')
-     Calib.Tx_Ty_Tz=[0 0 1];
-end
-if ~isfield(Calib,'Cx_Cy')
-     Calib.Cx_Cy=[0 0];
-end
-if ~isfield(Calib,'kc')
-     Calib.kc=0;
-end
-if isfield(Calib,'R')
-    R=(Calib.R)';
-    if testangle
-        a=-norm_plane(1)/norm_plane(3);
-        b=-norm_plane(2)/norm_plane(3);
-        if test_refraction
-            a=a/Calib.RefractionIndex;
-            b=b/Calib.RefractionIndex;
-        end
-        R(1)=R(1)+a*R(3);
-        R(2)=R(2)+b*R(3);
-        R(4)=R(4)+a*R(6);
-        R(5)=R(5)+b*R(6);
-        R(7)=R(7)+a*R(9);
-        R(8)=R(8)+b*R(9);
-    end
-    Tx=Calib.Tx_Ty_Tz(1);
-    Ty=Calib.Tx_Ty_Tz(2);
-    Tz=Calib.Tx_Ty_Tz(3);
-    f=Calib.fx_fy(1);%dpy=1; sx=1
-    dpx=Calib.fx_fy(2)/Calib.fx_fy(1);
-    Dx=R(5)*R(7)-R(4)*R(8);
-    Dy=R(1)*R(8)-R(2)*R(7);
-    D0=f*(R(2)*R(4)-R(1)*R(5));
-    Z11=R(6)*R(8)-R(5)*R(9);
-    Z12=R(2)*R(9)-R(3)*R(8);  
-    Z21=R(4)*R(9)-R(6)*R(7);
-    Z22=R(3)*R(7)-R(1)*R(9);
-    Zx0=R(3)*R(5)-R(2)*R(6);
-    Zy0=R(1)*R(6)-R(3)*R(4);
-    A11=R(8)*Ty-R(5)*Tz+Z11*Z0virt;
-    A12=R(2)*Tz-R(8)*Tx+Z12*Z0virt;
-    A21=-R(7)*Ty+R(4)*Tz+Z21*Z0virt;
-    A22=-R(1)*Tz+R(7)*Tx+Z22*Z0virt;
-    X0=f*(R(5)*Tx-R(2)*Ty+Zx0*Z0virt);
-    Y0=f*(-R(4)*Tx+R(1)*Ty+Zy0*Z0virt);
-        %px to camera:
-    Xd=dpx*(X-Calib.Cx_Cy(1)); % sensor coordinates
-    Yd=(Y-Calib.Cx_Cy(2));
-    dist_fact=1+Calib.kc*(Xd.*Xd+Yd.*Yd)/(f*f); %distortion factor
-    Xu=Xd./dist_fact;%undistorted sensor coordinates
-    Yu=Yd./dist_fact;
-    denom=Dx*Xu+Dy*Yu+D0;
-    Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates
-    Yphys=(A21.*Xu+A22.*Yu+Y0)./denom;
-    if testangle
-        Zphys=Z0+a*Xphys+b*Yphys;
-    else
-        Zphys=Z0;
-    end
-else
-    Xphys=-Calib.Tx_Ty_Tz(1)+X/Calib.fx_fy(1);
-    Yphys=-Calib.Tx_Ty_Tz(2)+Y/Calib.fx_fy(2);
-end
-
-%'px_XYZ': transform phys coordinates to image coordinates (px)
-%
-% OUPUT:
-% X,Y: array of coordinates in the image cooresponding to the input physical positions 
-%                    (origin at lower leftcorner, unit=pixel)
-
-% INPUT:
-% Calib: structure containing the calibration parameters (read from the ImaDoc .xml file)
-% Xphys, Yphys: array of x,y physical coordinates
-% [Z0]: corresponding array of z physical coordinates (0 by default)
-
-
-
-