diff -u -r1.6 -r1.7
--- AlignmentUtils.java	4 Sep 2012 03:01:12 -0000	1.6
+++ AlignmentUtils.java	28 Sep 2012 22:08:39 -0000	1.7
@@ -16,10 +16,15 @@

 public class AlignmentUtils {
     
 

+    public AlignmentUtils() {
+        _debug = false;
+    }

     public AlignmentUtils(boolean debug) {
         _debug = debug;
     }

-

+    public void setDebug(boolean debug) {
+        _debug = debug;
+    }

     public BasicMatrix calculateLocalHelixDerivatives(HelicalTrackFit trk, HelicalTrackStrip strip, double smax, int _nlc) {
         
         // Calculate the derivative w.r.t. to the track parameters (in order/index):

@@ -46,47 +51,156 @@

         BasicMatrix dfdq = new BasicMatrix(3,5); //3-dim,ntrackparams
         
         

-        dfdq.setElement(0, 0, dx_dd0(xint,xr,d0,phi0,R));
-        dfdq.setElement(0, 1, dx_dz0());
-        dfdq.setElement(0, 2, dx_dslope());
-        dfdq.setElement(0, 3, dx_dphi0(xint,xr,yr,d0,phi0,R));
-        dfdq.setElement(0, 4, dx_dR(xint,xr,yr,d0,phi0,R,phi));
-        
-        
-        dfdq.setElement(1, 0, dy_dd0(xint,xr,d0,phi0,R));
-        dfdq.setElement(1, 1, dy_dz0());
-        dfdq.setElement(1, 2, dy_dslope());
-        dfdq.setElement(1, 3, dy_dphi0(xint,xr,d0,phi0,R));
-        dfdq.setElement(1, 4, dy_dR(xint,xr,d0,phi0,R));
-        
-        
-        dfdq.setElement(2, 0, dz_dd0(xint,xr,yr,d0,phi0,slope,R,phi));
-        dfdq.setElement(2, 1, dz_dz0());
-        dfdq.setElement(2, 2, dz_dslope(xint,xr,yr,d0,phi0,slope,R,phi));
-        dfdq.setElement(2, 3, dz_ddphi(xint,xr,yr,d0,phi0,slope,R,phi));
-        dfdq.setElement(2, 4, dz_dR(xint,xr,yr,d0,phi0,slope,R,phi));

+        dfdq.setElement(0, 0, this.dx_dd0(xint, d0, phi0, R, phi));
+        dfdq.setElement(0, 1, this.dx_dz0(R, phi));
+        dfdq.setElement(0, 2, this.dx_dslope(R, phi));
+        dfdq.setElement(0, 3, this.dx_dphi0(xint, d0, phi0, R, phi));
+        dfdq.setElement(0, 4, this.dx_dR(xint, xr, yr, d0, phi0, R, phi));
+        
+        
+        dfdq.setElement(1, 0, this.dy_dd0(xint, d0, phi0, R, phi));
+        dfdq.setElement(1, 1, this.dy_dz0(R, phi));
+        dfdq.setElement(1, 2, this.dy_dslope(R, phi));
+        dfdq.setElement(1, 3, this.dy_dphi0(xint, d0, phi0, R, phi));
+        dfdq.setElement(1, 4, this.dy_dR(xint, d0, phi0, R, phi));
+        
+        
+        dfdq.setElement(2, 0, this.dz_dd0(xint, d0, phi0, slope, R));
+        dfdq.setElement(2, 1, this.dz_dz0());
+        dfdq.setElement(2, 2, this.dz_dslope(phi0, R, phi));
+        dfdq.setElement(2, 3, this.dz_ddphi0(s, d0, phi0, slope, R));
+        dfdq.setElement(2, 4, this.dz_dR(xint, d0, phi0, slope, R, phi));

         
         
         return dfdq;
         
     }

+
+    
+    
+    
+    
+    
+    //-----------------------------------
+    // Local derivatives of f in the x-direction
+    
+    
+    public double dx_dd0(double x, double d0, double phi0, double R, double phi) {
+        return -Math.sin(phi0) - R * Math.cos(phi)*dphi_dd0(x,d0,phi0,R);
+    }
+    public double dx_dz0(double R, double phi) {
+        return -R*Math.cos(phi)*dphi_dz0();
+    }
+    public double dx_dslope(double R, double phi) {
+        return R*Math.cos(phi)*dphi_dslope();
+    }
+    public double dx_dphi0(double x, double d0, double phi0, double R, double phi) {
+        return (R-d0)*Math.cos(phi0) - R*Math.cos(phi)*dphi_dphi0(x,d0,phi0,R);
+    }
+    public double dx_dR(double x, double xr, double yr, double d0, double phi0, double R, double phi) {
+        return Math.sin(phi0) - R*Math.cos(phi)*dphi_dR(x,d0,phi0,R);
+    }
+    
+    //-----------------------------------
+    
+    //-----------------------------------
+    // Local derivatives of f in the y-direction
+    
+    public double dy_dd0(double x, double d0, double phi0, double R, double phi) {
+        return Math.cos(phi0) - R*Math.sin(phi)*dphi_dd0(x, d0, phi0, R);
+    }
+    public double dy_dz0(double R, double phi) {
+        return -R*Math.sin(phi)*this.dphi_dz0();
+    }
+    public double dy_dslope(double R, double phi) {
+        return -R*Math.sin(phi)*this.dphi_dslope();
+    }
+    
+    public double dy_dphi0(double x, double d0, double phi0, double R, double phi) {
+        return (R-d0)*Math.sin(phi0) - R*Math.sin(phi)*this.dphi_dphi0(x, d0, phi0, R);
+    }
+    public double dy_dR(double x, double d0, double phi0, double R, double phi) {
+        return -Math.cos(phi0) - R*Math.sin(phi)*this.dphi_dR(x, d0, phi0, R);
+    }
+    
+    
+     //-----------------------------------
+    // Local derivatives of f in the z-direction
+
+    
+    public double dz_dd0(double x, double d0, double phi0, double slope, double R) {                
+        return -R*slope*this.dphi_dd0(x, d0, phi0, R);
+    }
+        
+    public double dz_dz0() {
+        return 1.0;
+    }
+
+    public double dz_dslope(double phi0, double R, double phi) {        
+        return -R*(phi-phi0);
+    }
+
+    public double dz_ddphi0(double x, double d0, double phi0, double slope, double R) {                
+        return -R*slope*(this.dphi_dphi0(x, d0, phi0, R)-1);
+    }
+    
+    public double dz_dR(double x, double d0, double phi0, double slope, double R, double phi) {
+        return -slope*(phi-phi0+R*this.dphi_dR(x, d0, phi0, R));
+    }
+
+    
+    //-----------------------------------
+    // Derivatives of phi w.r.t. track parameters
+
+    public double dphi_dd0(double x,double d0, double phi0, double R) {
+        double num = Math.sin(phi0);
+        double den = R*Math.sqrt(Math.pow(x+(d0-R)*Math.sin(phi0), 2)/Math.pow(R,2));
+        return num/den;
+    }
+    
+    public double dphi_dz0() {
+        return 0;
+    }
+    public double dphi_dslope() {
+        return 0;
+    }
+    public double dphi_dphi0(double x,double d0, double phi0, double R) {
+        double num = (d0-R)*Math.sin(phi0);
+        double den = R*Math.sqrt(1-Math.pow(x+(d0-R)*Math.sin(phi0),2)/Math.pow(R, 2));
+        return num/den;
+    }
+    
+    public double dphi_dR(double x,double d0, double phi0, double R) {
+        double num = -x-d0*Math.sin(phi0);
+        double den = Math.pow(R, 2)*Math.sqrt(1-Math.pow(x+(d0-R)*Math.sin(phi0),2)/Math.pow(R, 2));
+        return num/den;
+    }
+    
+    
+    
+    
+    
+    

-    public double dphi_dx(double xint,double xr, double yr, double d0, double phi0, double R, double phi) {
-        double arg1 = Math.sin(phi0) - (xint-x0(xr,d0,phi0))/R;
-        double arg2 = Math.cos(phi0) + (y(xint,xr,yr,d0,phi0,R,phi)-y0(yr,d0,phi0))/R;
-        return (-1/R)*arg2/(arg2*arg2+arg1*arg1);

+    public double dphi_dx(double xint, double d0, double phi0, double R, double phi) {
+        double num = -Math.pow(R, 2)*sign(R);
+        double den1 = Math.sqrt( Math.pow(R, 2) - Math.pow(xint+(d0-R)*Math.sin(phi0), 2)   );
+        double den2 = -Math.pow(xint+(d0-R)*Math.sin(phi0),2);
+        double den3 = sign(R)*sign(R)*(-Math.pow(R, 2)+Math.pow(xint, 2)+2*(d0-R)*xint*Math.sin(phi0)+Math.pow(d0-R,2)*Math.pow(Math.sin(phi0),2) );
+        return num/(den1*(den2+den3));

     }
 

-    public double dphi_dy(double xint,double xr, double yr, double d0, double phi0, double R, double phi) {
-        if(_debug) System.out.println("dphi_dy:");
-        double arg1 = Math.sin(phi0) - (xint-x0(xr,d0,phi0))/R;
-        double arg2 = Math.cos(phi0) + (y(xint,xr,yr,d0,phi0,R,phi)-y0(yr,d0,phi0))/R;
-        if(_debug) System.out.println("dphi_dy: arg1=" + arg1 + " arg2="+arg2 + " R =" + R );
-        if(_debug) System.out.println("dphi_dy ===> " + (-1/R)*arg1/(arg2*arg2+arg1*arg1));
-        return (-1/R)*arg1/(arg2*arg2+arg1*arg1);

+    public double dphi_dy(double y, double d0, double phi0, double R, double phi) {
+        double c0 = Math.cos(phi0);
+        double num = Math.pow(R,2)*sign(R)*sign(R);
+        double den1 = Math.sqrt(Math.pow(R, 2)-Math.pow(y+(d0-R)*c0, 2));
+        double den2 = -Math.pow(y+(d0-R)*c0,2);
+        double den3 =  (-Math.pow(R,2) + Math.pow(y, 2) + 2*(d0-R)*y*c0 + Math.pow(d0-R, 2)*Math.pow(c0, 2))*sign(R)*sign(R);        
+        return num/(den1*(den2+den3));

     }

+

     public double dphi_dz(double slope, double R) {
         return -1/(R*slope);
     }

@@ -103,36 +217,32 @@

         return 1;
     }
     

-    public double dy_dx(double xint, double xr, double yr ,double d0, double phi0, double R, double phi) { 
-        return -1*sign(R)*R*phi*this.dphi_dx(xint, xr, yr, d0, phi0, R, phi);
-        //return -1*sign(R)*R*this.phi(xint, xr, yr, d0, phi0, R)*this.dphi_dx(xint, xr, yr, d0, phi0, R);

+    public double dy_dx(double xint, double d0, double phi0, double R, double phi) { 
+        return -R*Math.sin(phi)*this.dphi_dx(xint, d0, phi0, R, phi);

     }
     

-    

     public double dz_dx(double xint, double xr,double yr,double d0, double phi0, double slope, double R, double phi) {   

-        return -slope*R*this.dphi_dx(xint, xr, yr, d0, phi0, R, phi);

+        return -R*slope*this.dphi_dx(xint, d0, phi0, R, phi);

     }
     

-    public double dx_dy(double xint, double xr, double yr ,double d0, double phi0, double R, double phi) {
-        if(_debug) System.out.println("dx_dy: xint=" + xint + " phi0="+phi0+" R="+R );
-        if(_debug) System.out.println("dx_dy: cos(phi)="+Math.cos(phi) + " dphi_dy="+this.dphi_dy(xint, xr, yr, d0, phi0, R, phi));
-        if(_debug) System.out.println("dx_dy: ====> R*cos*dphi_dy = "+ sign(R)*R*Math.cos(phi)*this.dphi_dy(xint, xr, yr, d0, phi0, R, phi));
-        return sign(R)*R*Math.cos(phi)*this.dphi_dy(xint, xr, yr, d0, phi0, R, phi);

+    public double dx_dy(double y, double d0, double phi0, double R, double phi) {
+        return R*Math.cos(phi)*this.dphi_dy(y, d0, phi0, R, phi);

     }
      
     public double dy_dy() {
         return 1;
     }
     

-    public double dz_dy(double xint, double xr ,double d0, double phi0, double slope, double R, double phi) {
-        return -R*slope*this.dphi_dy(xint, xr, xr, d0, phi0, R, phi);

+    public double dz_dy(double y,double d0, double phi0, double slope, double R, double phi) {
+        return -R*slope*this.dphi_dy(y, d0, phi0, R, phi);

     }

+     

-    public double dx_dz(double xint, double xr, double yr ,double d0, double phi0, double slope, double R, double phi) {

+    public double dx_dz(double slope, double R, double phi) {

         return sign(R)*R*Math.cos(phi)*this.dphi_dz(slope, R);

-    }

+    }   

-    public double dy_dz(double xint, double xr, double yr ,double d0, double phi0, double slope, double R, double phi) {     

+    public double dy_dz(double slope, double R, double phi) {     

         return -sign(R)*R*Math.sin(phi)*this.dphi_dz(slope, R);
     }
     

@@ -187,97 +297,6 @@

-    
-    
-    //d0,z0,slope,phi0,R
-    
-    
-    //-----------------------------------
-    // Derivatives of x 
-    
-    
-    public double dx_dd0(double x, double xr,double d0, double phi0, double R) {
-        return -Math.sin(phi0) + sign(R)*ddeltayc_dd0(x, xr, d0,phi0,R);    
-    }
-    public double dx_dz0() {
-        return 0.0;
-    }
-    public double dx_dslope() {
-        return 0.0;
-    }
-    public double dx_dphi0(double x, double xr, double yr, double d0, double phi0, double R) {
-        return (-d0+R)*Math.cos(phi0) + sign(R)*ddeltayc_dphi0(x,xr,yr,d0,phi0,R); 
-    
-    }
-    public double dx_dR(double x, double xr, double yr, double d0, double phi0, double R, double phi) {
-        return Math.sin(phi0) +  deltayc(x,xr,yr,d0,phi0,R,phi)*dsign_dR(R) + sign(R)*ddeltayc_dR(x,xr,d0,phi0,R);
-    }
-    
-    //-----------------------------------
-    
-    //-----------------------------------
-    // Derivatives of y 
-    public double dy_dd0(double x, double xr,double d0, double phi0, double R) {
-        //double num = sign(R)*Math.sin(phi0)*( x - xr + (d0-R)*Math.sin(phi0)  );
-        //double den =  Math.sqrt( R*R - Math.pow(x-xr+(d0-R)*Math.sin(phi0),2)   );   
-        //simplify using xc
-        double num = sign(R)*Math.sin(phi0)*( x - xc(xr,d0,phi0,R) );
-        double den =  Math.sqrt( R*R - Math.pow(x-xc(xr,d0,phi0,R),2)   );   
-        return Math.cos(phi0) - num/den;
-    }
-    public double dy_dz0() {
-        return 0.0;
-    }
-    public double dy_dslope() {
-        return 0.0;
-    }
-    
-    public double dy_dphi0(double x, double xr,double d0, double phi0, double R) {
-        //simplify using xc
-        double num = Math.cos(phi0)*sign(R)*( x - xc(xr,d0,phi0,R) );
-        double den = Math.sqrt( R*R - Math.pow( x - xc(xr,d0,phi0,R) ,2)  );
-        return (-d0+R)*( Math.sin(phi0) + num/den  );
-    }
-    public double dy_dR(double x, double xr,double d0, double phi0, double R) {
-        //Simplify with xc
-        double num = sign(R) * ( d0 + R + (-d0+R)*Math.cos(2*phi0) + 2*(x-xr)*Math.sin(phi0) ); 
-        double den = 2*Math.sqrt( R*R - Math.pow( x - xc(xr,d0,phi0,R), 2) );
-        double C = Math.sqrt( R*R + Math.pow( x - xc(xr,d0,phi0,R), 2) )*dsign_dR(R);
-        return -Math.cos(phi0) + num/den + C;
-    }
-    
-    
-     //-----------------------------------
-    // Derivatives of z 
-
-    
-    public double dz_dd0(double x, double xr, double yr, double d0, double phi0, double slope, double R, double phi) {                
-        return -R*slope*dtmpdphi_dd0(x,  xr,  yr,  d0,  phi0,  R, phi);
-    }
-        
-    public double dz_dz0() {
-        return 1.0;
-    }
-
-    public double dz_dslope(double x, double xr, double yr, double d0, double phi0, double slope, double R, double phi) {        
-        double dphi = get_dphi(x,xr,yr,d0,phi0,R,phi);
-        return -R*dphi;
-    }
-
-    public double dz_ddphi(double x, double xr, double yr, double d0, double phi0, double slope, double R, double phi) {                
-        return -R*slope*dtmpdphi_ddphi(x,  xr,  yr,  d0,  phi0,  R, phi);
-    }
-    
-    public double dz_dR(double x, double xr, double yr, double d0, double phi0, double slope, double R, double phi) {
-        double dphi = get_dphi(x,xr,yr,d0,phi0,R,phi);
-        double derdphi_dR = dtmpdphi_dR(x,xr,yr,d0,phi0,R,phi);
-        return -slope*( dphi + R*derdphi_dR); 
-    }
-
-    
-    
-    
-    

     //-------------------------------------------
     //Helper functions