diff -u -r1.2 -r1.3
--- HelicalTrackFitter.java	29 Aug 2006 20:44:26 -0000	1.2
+++ HelicalTrackFitter.java	30 Aug 2006 01:06:54 -0000	1.3
@@ -3,7 +3,7 @@

  *
  * Created on March 25, 2006, 6:11 PM
  *

- * $Id: HelicalTrackFitter.java,v 1.2 2006/08/29 20:44:26 partridge Exp $

+ * $Id: HelicalTrackFitter.java,v 1.3 2006/08/30 01:06:54 partridge Exp $

  */
 
 package org.lcsim.contrib.seedtracker;

@@ -18,7 +18,16 @@

 import org.lcsim.fit.line.SlopeInterceptLineFit;
 import org.lcsim.fit.line.SlopeInterceptLineFitter;
 /**

- *

+ * Fit a helix to a set of space points.  First, a circle is fit to the x-y coordinates.
+ * A straight-line fit is then performed on the s-z coordinates.
+ * 
+ * The r-phi and z coordinate measurements are assumed to be uncorrelated.  A block
+ * diagonal covariance matrix is formed from the results of the circle and s-z fits,
+ * ignoring any correlations between these fits.
+ * 
+ * The resulting track parameters follow the "L3 Convention" adopted by org.lcsim.
+ * 
+ * Modified August 2006 by Richard Partridge

  * @author Norman Graf
  */
 public class HelicalTrackFitter

@@ -30,11 +39,26 @@

     
     private double[] _circleParameters = new double[3];
     

-    /** Creates a new instance of HelicalTrackFitter */

+    /**
+     * Creates a new instance of HelicalTrackFitter.
+     */

     public HelicalTrackFitter()
     {
     }
     

+    /**
+     * Fit a helix to a set of space points.  The space points should be ordered in
+     * increasing track length.  The code will properly handle loopers provided
+     * that the change in direction between successive points is less than pi.
+     * @param x Array of x coordinates
+     * @param y Array of y coordinates
+     * @param z Array of z coordinates
+     * @param drphi Error in r-phi hit position
+     * @param dz Error in z coordinate.  A negative value indicates that this point is to
+     * be excluded in the s-z fit.
+     * @param np Number of points
+     * @return True for successful fit
+     */

     public boolean fit(double[] x, double[] y, double[] z, double[] drphi, double[] dz, int np)
     {
         // fit a circle in the x-y plane

@@ -82,27 +106,6 @@

         if(!success) return false;
         SlopeInterceptLineFit lfit = _lfitter.getFit();
         

-        // TODO convert fit results to track parameters and covariance matrix.
-        // now have the fits, need to assemble the track parameters...
-        
-        // see org.lcsim.event.Track.Parameters
-        // The track parameters for LCD are defined as follows
-        // <table>
-        // <tr><th>Index</th><th>Meaning</th></tr>
-        // <tr><td> 0 </td><td> d0 = XY impact parameter </td><tr>
-        // <tr><td> 1 </td><td> phi0 </td><tr> </td><tr>
-        // <tr><td> 2 </td><td> omega = 1/curv.radius (negative for negative tracks) </td><tr>
-        // <tr><td> 3 </td><td> z0 = z of track origin (z impact parameter) </td><tr>
-        // <tr><td> 4 </td><td> s = tan lambda </td><tr>
-        // </table>
-        
-        // tanlambda = line fit slope
-        // z0 = line fit intercept
-        //TODO should shift s-z line fit to centroid of x-y fit and introduce covariance terms to be correct.
-        
-        
-//        System.out.println("circle fit: "+cfit);
-//        System.out.println("line fit: "+lfit);;

         double[] pars = new double[5];
         double[][] cov = new double[5][5];
         double[] chisq = new double[2];

@@ -114,7 +117,7 @@

         ndf[1] = lfit.ndf();
         ndf[0] = np - 3;
         

-        // d0, xy impact parameter.

+        // d0, xy impact parameter.  Note: - sign due to opposite sign convention in CircleFitter

         pars[0] = -cfit.dca();
         // phi0
         pars[1] =  cfit.phi();

@@ -127,9 +130,9 @@

         
         // fill in covariance matrix
         cov[0][0] = cfit.cov()[0];

-        cov[0][1] = -cfit.cov()[1];

+        cov[0][1] = -cfit.cov()[1];  // Need - sign due to sign convention in CircleFitter

         cov[1][1] = cfit.cov()[2];

-        cov[0][2] = -cfit.cov()[3];

+        cov[0][2] = -cfit.cov()[3];  // Need - sign due to sign convention in CircleFitter

         cov[1][2] = cfit.cov()[4];
         cov[2][2] = cfit.cov()[5];
         cov[0][3] = 0.;

@@ -146,20 +149,24 @@

                 cov[j][i] = cov[i][j];
             }
         }

-//        for(int i=0; i<5; ++i)
-//        {
-//            System.out.println("pars["+i+"]= "+pars[i]);
-//        }

         _fit = new HelicalTrackFit(pars, cov, chisq, ndf);
         _fit.setCircleParameters(_circleParameters);
         return true;
     }
     

+    /**
+     * Get the results of the most recent fit.
+     * @return HelicalTrackFit corresponding to most recent fit
+     */

     public HelicalTrackFit getFit()
     {
         return _fit;
     }
     

+    /**
+     * Get the circle paramaters (xc, yc, R) from the most recent fit.
+     * @return Circle parameters (xc, yc, R)
+     */

     public double[] getCircleParameters()
     {
         return _circleParameters;

@@ -168,9 +175,7 @@

     double s(double radius, double xcenter, double ycenter, double x1, double y1, double x2, double y2)
     {
         double phi1 = atan2( (y1-ycenter), (x1-xcenter) );

-        if (phi1<0) phi1 += 2*PI;

         double phi2 = atan2( (y2-ycenter), (x2-xcenter) );

-        if (phi2<0) phi2 += 2*PI;

         double dphi = abs(phi1-phi2);
         if(dphi>PI) dphi = 2.*PI-dphi;
         return abs(radius)*dphi;