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HPS-SVN  March 2016

HPS-SVN March 2016

Subject:

r4328 - /java/trunk/recon/src/main/java/org/hps/recon/vertexing/BilliorVertexer.java

From:

[log in to unmask]

Reply-To:

Notification of commits to the hps svn repository <[log in to unmask]>

Date:

Thu, 24 Mar 2016 01:20:30 -0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (716 lines)

Author: [log in to unmask]
Date: Wed Mar 23 18:20:27 2016
New Revision: 4328

Log:
fix bug in residual calculation

Modified:
    java/trunk/recon/src/main/java/org/hps/recon/vertexing/BilliorVertexer.java

Modified: java/trunk/recon/src/main/java/org/hps/recon/vertexing/BilliorVertexer.java
 =============================================================================
--- java/trunk/recon/src/main/java/org/hps/recon/vertexing/BilliorVertexer.java	(original)
+++ java/trunk/recon/src/main/java/org/hps/recon/vertexing/BilliorVertexer.java	Wed Mar 23 18:20:27 2016
@@ -24,40 +24,25 @@
     // default is a constant field along the z axis
 
     private boolean _debug = false;
-    private double _bField;
-    private boolean _beamspotConstraint = true;
-    private boolean _targetConstraint = false;
-    private double[] _beamSize = {0.001, 0.01, 0.01}; //10um in y and z
+    private final double _bField;
+    private boolean _beamspotConstraint;
+    private boolean _targetConstraint;
+    private String _constraintType;
+    private final double[] _beamSize = {0.001, 0.01, 0.01}; //10um in y and z
+    private final double[] _beamPosition = {0.0, 0.0, 0.0}; //origin
     private int _ntracks;
-    private List<Matrix> paramList = new ArrayList<Matrix>();
-    private List<Matrix> WList = new ArrayList<Matrix>();
-    private List<Matrix> DList = new ArrayList<Matrix>();
-    private List<Matrix> EList = new ArrayList<Matrix>();
-    private Matrix A;
-    private Matrix T;
-    private List<Matrix> BList = new ArrayList<Matrix>();
-    private List<Matrix> CinvList = new ArrayList<Matrix>();
-    private List<Matrix> CList = new ArrayList<Matrix>();
-    private List<Matrix> UList = new ArrayList<Matrix>();
-    private List<Matrix> dqList = new ArrayList<Matrix>();
-    private double[] _v0 = {0.0, 0.0, 0.0};
+    private double[] _v0 = {0.0, 0.0, 0.0}; //initial guess for unconstrained vertex fit
 //    private double[] _vertexPosition = {0., 0.0, 0.0};
-    private Matrix _vertexPosition = new BasicMatrix(3, 1);
-    private Matrix _covVtx = new BasicMatrix(3, 3);
-    private List<Matrix> _pFit = new ArrayList<Matrix>();
+    private Matrix _vertexPosition;
+    private Matrix _covVtx;
+    private List<Matrix> _pFit;
 
     ;//theta,phi_v,rho
-    private List<Matrix> covVtxMomList = new ArrayList<Matrix>();
-    private Matrix[][] covMomList = new Matrix[2][2];//max 2 tracks...just make this bigger for more
+    private List<Matrix> covVtxMomList;
+    private Matrix[][] covMomList;//max 2 tracks...just make this bigger for more
     private Matrix _constrainedFit;
     private Matrix _constrainedCov;
     private double _chiSq;
-    private String _constraintType = "Unspecified";
-
-    // constructor
-
-    public BilliorVertexer() {
-    }
 
     public BilliorVertexer(double bField) {
         _bField = bField;
@@ -89,9 +74,9 @@
         _ntracks = tracks.size();
         follow1985Paper(tracks);
         if (_beamspotConstraint) {
-            addV0fromBSConstraint(true);
+            applyBSconstraint(true);
         } else if (_targetConstraint) {
-            addV0fromBSConstraint(false);
+            applyBSconstraint(false);
         }
         Map<Integer, Hep3Vector> pFitMap = new HashMap<Integer, Hep3Vector>();
         for (int i = 0; i < tracks.size(); i++) {
@@ -104,309 +89,15 @@
         return new BilliorVertex(vertDet, covVtxDet, _chiSq, getInvMass(), pFitMap, _constraintType);
     }
 
-    public BilliorVertex fitFastVertex(List<BilliorTrack> tracks) {
-        _ntracks = tracks.size();
-        fastVertex(tracks);
-        Hep3Vector vert = new BasicHep3Vector(_vertexPosition.e(0, 0), _vertexPosition.e(1, 0), _vertexPosition.e(2, 0));
-        return new BilliorVertex((Hep3Vector) _vertexPosition, _covVtx, _chiSq, getInvMass());
-    }
-
-//    private void calculateCovariance() {
-//        for (int i = 0; i < _ntracks; i++) {
-//            BasicMatrix b = (BasicMatrix) BList.get(i);
-//            BasicMatrix cinv = (BasicMatrix) CinvList.get(i);
-//            BasicMatrix bt = (BasicMatrix) MatrixOp.transposed(b);
-//            covVtxMomList.add((MatrixOp.mult(-1, MatrixOp.mult(_covVtx, MatrixOp.mult(b, cinv)))));
-//            for (int j = 0; j < _ntracks; j++) {
-//                BasicMatrix bj = (BasicMatrix) BList.get(j);
-//                BasicMatrix cjinv = (BasicMatrix) CinvList.get(j);
-//                BasicMatrix tmp = (BasicMatrix) MatrixOp.mult(cinv, MatrixOp.mult(bt, MatrixOp.mult(_covVtx, MatrixOp.mult(bj, cjinv))));
-//                if (i == j)
-//                    tmp = (BasicMatrix) MatrixOp.add(tmp, cinv);
-//                covMomList[i][j] = tmp;
-//            }
-//        }
-//    }
-//
-//    private void calculateMomenta() {
-//
-//        for (int i = 0; i < _ntracks; i++) {
-//            BasicMatrix params = (BasicMatrix) paramList.get(i);
-//            BasicMatrix b = (BasicMatrix) BList.get(i);
-//            BasicMatrix cinv = (BasicMatrix) CinvList.get(i);
-//            BasicMatrix u = (BasicMatrix) UList.get(i);
-//            //not sure following line is correct...mg 10/21/10
-//            BasicMatrix CinvU = (BasicMatrix) MatrixOp.mult(cinv, u);
-//            BasicMatrix CinvBTdV = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(cinv, MatrixOp.mult(MatrixOp.transposed(b), _vertexPosition)));
-////            if(_debug)System.out.println(" B = "+b.toString());
-////            if(_debug)System.out.println(" cinv = "+cinv.toString());
-////            if(_debug)System.out.println(" u = "+u.toString());
-////            if(_debug)System.out.println(" CinvU = "+CinvU.toString());
-////            if(_debug)System.out.println(" CinvBTdV = "+CinvBTdV.toString());
-//            BasicMatrix tmpP = (BasicMatrix) MatrixOp.add(CinvBTdV, CinvU);
-//            tmpP.setElement(0, 0, tmpP.e(0, 0) + params.e(2, 0));
-//            tmpP.setElement(1, 0, tmpP.e(1, 0) + params.e(3, 0));
-//            tmpP.setElement(2, 0, tmpP.e(2, 0) + params.e(4, 0));
-//            _pFit.add(tmpP);
-////            if(_debug)System.out.println("Track "+i+" orig parameters  = "+params);
-////            if(_debug)System.out.println("Track "+i+" deltaP  = "+MatrixOp.add(CinvBTdV, CinvU));
-////            if(_debug)System.out.println("Track " + i + " _pFit  = " + tmpP);
-//        }
-//    }
-//
-//    private void calculateVertexPosition() {
-//        BasicMatrix tmpcov = new BasicMatrix(3, 3);
-//        BasicMatrix tmp = new BasicMatrix(3, 1);
-//        for (int i = 0; i < _ntracks; i++) {
-//            BasicMatrix b = (BasicMatrix) BList.get(i);
-//            BasicMatrix cinv = (BasicMatrix) CinvList.get(i);
-//            BasicMatrix u = (BasicMatrix) UList.get(i);
-////            if(_debug)System.out.println("Cinv matrix " + cinv.toString());
-////            if(_debug)System.out.println("B matrix " + b.toString());
-////            if(_debug)System.out.println("U matrix " + u.toString());
-//            BasicMatrix bt = (BasicMatrix) MatrixOp.transposed(b);
-//            //           if(_debug)System.out.println("Adding this to tmpcov : " + MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, bt))));
-//            if (i == 0) {
-//                tmpcov = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, bt)));
-//                tmp = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, u)));
-//            } else {
-//                tmpcov = (BasicMatrix) MatrixOp.add(tmpcov, MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, bt))));
-//                tmp = (BasicMatrix) MatrixOp.add(tmp, MatrixOp.mult(-1, MatrixOp.mult(b, MatrixOp.mult(cinv, u))));
-//            }
-////            if(_debug)System.out.println("tmpCov matrix " + tmpcov.toString());
-////            if(_debug)System.out.println("tmp matrix " + tmp.toString());
-//        }
-////
-////        if(_debug)System.out.println("A matrix " + A.toString());
-////        if(_debug)System.out.println("tmpCov matrix " + tmpcov.toString());
-////        if(_debug)System.out.println("sum of A and tmpCov = " + MatrixOp.add(A, tmpcov).toString());
-//        _covVtx = MatrixOp.inverse(MatrixOp.add(A, tmpcov));
-////        if(_debug)System.out.println("_covVtx matrix " + _covVtx.toString());
-////        if(_debug)System.out.println("T matrix " + T.toString());
-//        _vertexPosition = (BasicMatrix) MatrixOp.mult(_covVtx, MatrixOp.add(T, tmp));
-//
-//    }
-//
-//    private void makeOtherMatrices() {
-//        BasicMatrix tmpA = new BasicMatrix(3, 3);
-//        BasicMatrix tmpT = new BasicMatrix(3, 1);
-//
-//        for (int i = 0; i < _ntracks; i++) {
-//            BasicMatrix tmpD = (BasicMatrix) DList.get(i);
-//            BasicMatrix tmpE = (BasicMatrix) EList.get(i);
-//            BasicMatrix dq = (BasicMatrix) dqList.get(i);
-//            BasicMatrix tmpW = (BasicMatrix) WList.get(i);
-//
-//            if (i == 0) {
-//                tmpA = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpD));
-//                tmpT = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, dq));
-//            } else {
-//                tmpT = (BasicMatrix) MatrixOp.add(tmpT, MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, dq)));
-//                tmpA = (BasicMatrix) MatrixOp.add(tmpA, MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpD)));
-//            }
-//            BList.add(MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpE)));
-//            BasicMatrix tmpC = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpE), MatrixOp.mult(tmpW, tmpE));
-//            CList.add(tmpC);
-//            CinvList.add(MatrixOp.inverse(tmpC));
-//            UList.add(MatrixOp.mult(MatrixOp.transposed(tmpE), MatrixOp.mult(tmpW, dq)));
-//
-//        }
-//        A = tmpA;
-//        T = tmpT;
-//    }
-//
-//    private void calculateChisq() {
-//        _chiSq = 0;
-//        for (int i = 0; i < _ntracks; i++) {
-//            BasicMatrix params = (BasicMatrix) paramList.get(i);
-//            BasicMatrix d = (BasicMatrix) DList.get(i);
-//            BasicMatrix e = (BasicMatrix) EList.get(i);
-//            BasicMatrix w = (BasicMatrix) WList.get(i);
-//            BasicMatrix pi = (BasicMatrix) _pFit.get(i);
-//            BasicMatrix Vtilde = (BasicMatrix) MatrixOp.mult(d, _vertexPosition);
-//            BasicMatrix Trtilde = (BasicMatrix) MatrixOp.mult(e, pi);
-//            BasicMatrix ptilde = (BasicMatrix) MatrixOp.add(Vtilde, Trtilde);
-//            //          if(_debug)System.out.println("Vtilde = "+Vtilde);
-//            //          if(_debug)System.out.println("Trtilde = "+Trtilde);
-//            BasicMatrix resid = (BasicMatrix) MatrixOp.add(params, MatrixOp.mult(-1, ptilde));
-//            BasicMatrix residT = (BasicMatrix) MatrixOp.transposed(resid);
-////            if(_debug)System.out.println("ptilde = "+ptilde);
-////              if(_debug)System.out.println("params = "+params);
-////            if(_debug)System.out.println("resid = "+resid);
-////            if(_debug)System.out.println("Covariance = "+MatrixOp.inverse(w));
-////             if(_debug)System.out.println("Weight = "+w);
-//            _chiSq = _chiSq + (MatrixOp.mult(residT, MatrixOp.mult(w, resid))).e(0, 0);
-////            if(_debug)System.out.println("_chiSq = "+_chiSq);
-//        }
-//    }
-    private void fastVertex(List<BilliorTrack> tracks) {
-        boolean firstTrack = true;
-        BasicMatrix sumwi = new BasicMatrix(3, 3);
-        BasicMatrix sumwiXi = new BasicMatrix(3, 1);
-        BasicMatrix dX = new BasicMatrix(3, 1);
-
-        for (BilliorTrack bt : tracks) {
-            double[] par = bt.parameters();
-//            if(_debug)System.out.println("Track parameters = (" + par[0] + ", " + par[1] + ", " + par[2] + ", " + par[3] + ", " + par[4] + ")");
-            double cotth = 1. / tan(par[2]);
-            double phiv = par[3];
-            double cosf = cos(phiv);
-            double sinf = sin(phiv);
-
-            double xi = par[0] * sin(par[3]);
-            double yi = -par[0] * cos(par[3]);
-            double zi = par[1];
-
-            dX.setElement(0, 0, xi);
-            dX.setElement(1, 0, yi);
-            dX.setElement(2, 0, zi);
-
-            BasicMatrix tmpD = new BasicMatrix(2, 3);
-            tmpD.setElement(0, 0, sinf);
-            tmpD.setElement(0, 1, -cosf);
-            tmpD.setElement(1, 0, -cotth * cosf);
-            tmpD.setElement(1, 1, -cotth * sinf);
-            tmpD.setElement(1, 2, 1);
-            BasicMatrix trkCov = new BasicMatrix(2, 2);
-            trkCov.setElement(0, 0, bt.covariance().e(0, 0));
-            trkCov.setElement(0, 1, bt.covariance().e(0, 1));
-            trkCov.setElement(1, 0, bt.covariance().e(1, 0));
-            trkCov.setElement(1, 1, bt.covariance().e(1, 1));
-            BasicMatrix tmpW = (BasicMatrix) MatrixOp.inverse(trkCov);
-            BasicMatrix wi = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpD));
-            if (firstTrack) {
-                sumwi = wi;
-                sumwiXi = (BasicMatrix) MatrixOp.mult(wi, dX);
-            } else {
-                sumwi = (BasicMatrix) MatrixOp.add(sumwi, wi);
-                sumwiXi = (BasicMatrix) MatrixOp.add(sumwiXi, MatrixOp.mult(wi, dX));
-            }
-            firstTrack = false;
-        }
-        _covVtx = MatrixOp.inverse(sumwi);
-        if (_debug) {
-            System.out.println("fastVertex::_covVtx matrix " + _covVtx.toString());
-        }
-        _vertexPosition = (BasicMatrix) MatrixOp.mult(_covVtx, sumwiXi);
-        _chiSq = 0;
-        //get the chisq
-        for (BilliorTrack bt : tracks) {
-            double[] par = bt.parameters();
-//            if(_debug)System.out.println("Track parameters = (" + par[0] + ", " + par[1] + ", " + par[2] + ", " + par[3] + ", " + par[4] + ")");
-            double cotth = 1. / tan(par[2]);
-            double phiv = par[3];
-            double cosf = cos(phiv);
-            double sinf = sin(phiv);
-
-            double xi = par[0] * sin(par[3]);
-            double yi = -par[0] * cos(par[3]);
-            double zi = par[1];
-            //this is xi - fitted vertex now
-            dX.setElement(0, 0, xi - _vertexPosition.e(0, 0));
-            dX.setElement(1, 0, yi - _vertexPosition.e(1, 0));
-            dX.setElement(2, 0, zi - _vertexPosition.e(2, 0));
-
-            BasicMatrix tmpD = new BasicMatrix(2, 3);
-            tmpD.setElement(0, 0, sinf);
-            tmpD.setElement(0, 1, -cosf);
-            tmpD.setElement(1, 0, -cotth * cosf);
-            tmpD.setElement(1, 1, -cotth * sinf);
-            tmpD.setElement(1, 2, 1);
-            BasicMatrix trkCov = new BasicMatrix(2, 2);
-            trkCov.setElement(0, 0, bt.covariance().e(0, 0));
-            trkCov.setElement(0, 1, bt.covariance().e(0, 1));
-            trkCov.setElement(1, 0, bt.covariance().e(1, 0));
-            trkCov.setElement(1, 1, bt.covariance().e(1, 1));
-            BasicMatrix tmpW = (BasicMatrix) MatrixOp.inverse(trkCov);
-            BasicMatrix wi = (BasicMatrix) MatrixOp.mult(MatrixOp.transposed(tmpD), MatrixOp.mult(tmpW, tmpD));
-            _chiSq += MatrixOp.mult(MatrixOp.transposed(dX), MatrixOp.mult(wi, dX)).e(0, 0);
-        }
-    }
-
-//    private void makeDerivativeMatrices(List<BilliorTrack> tracks) {
-//
-//        //DList.clear();
-//        //EList.clear();
-//        //paramList.clear();
-//        //dqList.clear();
-//        //WList.clear();
-//        BasicMatrix dq = new BasicMatrix(5, 1);
-//        BasicMatrix tmpW = new BasicMatrix(5, 5);
-//        for (BilliorTrack bt : tracks) {
-//            double[] par = bt.parameters();
-//            BasicMatrix tmpPar = new BasicMatrix(5, 1);
-//            tmpPar.setElement(0, 0, par[0]);
-//            tmpPar.setElement(1, 0, par[1]);
-//            tmpPar.setElement(2, 0, par[2]);
-//            tmpPar.setElement(3, 0, par[3]);
-//            tmpPar.setElement(4, 0, par[4]);
-//            paramList.add(tmpPar);
-//            double cotth = 1. / tan(par[2]);
-//            double uu = _v0[0] * cos(par[3]) + _v0[1] * sin(par[3]);//Q
-//            double vv = _v0[1] * cos(par[3]) - _v0[0] * sin(par[3]);//R
-//            double eps = -vv - .5 * uu * uu * par[4];
-//            double zp = _v0[2] - uu * (1 - vv * par[4]) * cotth;
-//            // * phi at vertex with these parameters
-//            double phiv = par[3] + uu * par[4];
-//            double cosf = cos(phiv);
-//            double sinf = sin(phiv);
-//
-//            BasicMatrix tmpD = new BasicMatrix(5, 3);
-//            tmpD.setElement(0, 0, sinf);
-//            tmpD.setElement(0, 1, -cosf);
-//            tmpD.setElement(1, 0, -cotth * cosf);
-//            tmpD.setElement(1, 1, -cotth * sinf);
-//            tmpD.setElement(1, 2, 1);
-//            tmpD.setElement(3, 0, -par[4] * cosf);
-//            tmpD.setElement(3, 1, -par[4] * sinf);
-//
-//            BasicMatrix tmpE = new BasicMatrix(5, 3);
-//            tmpE.setElement(0, 1, uu);
-//            tmpE.setElement(0, 2, -uu * uu / 2);
-//            tmpE.setElement(1, 0, uu * (1 + cotth * cotth));
-//            tmpE.setElement(1, 1, -vv * cotth);
-//            tmpE.setElement(1, 2, uu * vv * cotth);
-//            tmpE.setElement(3, 1, 1);
-//            tmpE.setElement(3, 2, -uu);
-//            tmpE.setElement(2, 0, 1);  //partial(theta)/dtheta
-//            tmpE.setElement(4, 2, 1); //partial (rho)/drho
-//            DList.add(tmpD);
-//            EList.add(tmpE);
-//
-//            double deps = par[0] - eps;
-//            double dzp = par[1] - zp;
-//            double dphi = par[3] - phiv;
-//
-//            dq.setElement(0, 0, deps);
-//            dq.setElement(1, 0, dzp);
-//            dq.setElement(3, 0, dphi);
-//            dqList.add(dq);
-//            tmpW = (BasicMatrix) MatrixOp.inverse(bt.covariance());
-//            WList.add(tmpW);
-//
-//            if (_debug)
-//                System.out.println("makeDerivativeMatrices::Params = \n" + tmpPar);
-//            if (_debug)
-//                System.out.println("D = \n" + tmpD);
-//            if (_debug)
-//                System.out.println("E = \n" + tmpE);
-//            if (_debug)
-//                System.out.println("dq = \n" + dq);
-//            if (_debug)
-//                System.out.println("W = \n" + tmpW);
-//        }
-//
-//    }
-
-    /*  Add the constraint that V0 points back to beamspot
+    /*  Add the constraint that V0 is at/points back to beamspot
      *  this method is based on progressive least squares fit
      *  using the unconstrained fit result as the (k-1) fit
      *
      *  all notation is taken from:
      * W. Hulsbergen, NIM 552 (2005) 566-575
      */
-    private void addV0fromBSConstraint(boolean bscon) {
-        String methodName = bscon ? "addV0fromBSConstraint" : "constrainV0toBS";
+    private void applyBSconstraint(boolean pointback) {
+        String methodName = pointback ? "constrainV0toBS" : "constrainV0toTarget";
         BasicMatrix Ckm1 = new BasicMatrix(3 * (_ntracks + 1), 3 * (_ntracks + 1));
         BasicMatrix Xkm1 = new BasicMatrix(3 * (_ntracks + 1), 1);
         MatrixOp.setSubMatrix(Ckm1, _covVtx, 0, 0);
@@ -457,9 +148,15 @@
             pztot += pz;
         }
         //calculate the position of the A' at X=0
-        BasicMatrix rk = makeRk(Vx, Vy, Vz, pxtot, pytot, pztot, bscon);
-
-        BasicMatrix Hk = makeHk(_ntracks, pxtot, pytot, pztot, bscon);
+        BasicMatrix rk = makeRk(Vx, Vy, Vz, pxtot, pytot, pztot, pointback);
+        if (_debug) {
+            System.out.println(methodName + "::rk = " + rk);
+        }
+
+        BasicMatrix Hk = makeHk(_ntracks, pxtot, pytot, pztot, pointback);
+        if (_debug) {
+            System.out.println(methodName + "::Hk = " + Hk);
+        }
 
         // the beam covariance
         BasicMatrix Vk = new BasicMatrix(3, 3);
@@ -511,6 +208,10 @@
 //        if(_debug)System.out.println("With Constraint : " + _vertexPosition.toString());
 //        if(_debug)System.out.println("With Constraint : " + _covVtx.toString());
 
+        if (_debug) {
+            System.out.println("Constrained vertex: " + _vertexPosition);
+        }
+
         for (int i = 0; i < _ntracks; i++) {
             BasicMatrix ptmp = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedFit, 3 * (i + 1), 0, 3, 1);
             _pFit.set(i, ptmp);
@@ -519,134 +220,24 @@
 //        if(_debug)System.out.println("Unconstrained chi^2 = "+_chiSq);
         //ok...add to the chi^2
         if (_debug) {
-            System.out.println(MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)));
+            System.out.println("Chisq contribution: " + MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)));
         }
         _chiSq += MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)).e(0, 0);
 //        if(_debug)System.out.println("Constrained chi^2 = "+_chiSq);
     }
 
-//    private void constrainV0toBS() {
-//        BasicMatrix Ckm1 = new BasicMatrix(3 * (_ntracks + 1), 3 * (_ntracks + 1));
-//        BasicMatrix Xkm1 = new BasicMatrix(3 * (_ntracks + 1), 1);
-//        MatrixOp.setSubMatrix(Ckm1, _covVtx, 0, 0);
-//        MatrixOp.setSubMatrix(Xkm1, _vertexPosition, 0, 0);
-//
-//        int n = 1;
-//        for (Matrix covVtxMom : covVtxMomList) {
-//            if (_debug)
-//                System.out.println("constrainV0toBS::Track " + n + "  covVtxMom : " + covVtxMom.toString());
-//            MatrixOp.setSubMatrix(Ckm1, covVtxMom, 0, 3 * n);
-//            MatrixOp.setSubMatrix(Ckm1, MatrixOp.transposed(covVtxMom), 3 * n, 0);
-//            n++;
-//        }
-//        for (int i = 0; i < _ntracks; i++) {
-//            BasicMatrix pi = (BasicMatrix) _pFit.get(i);
-//            MatrixOp.setSubMatrix(Xkm1, pi, 3 * (i + 1), 0);
-//            //           if(_debug)System.out.println("Track "+i+"  p : " + pi.toString());
-//            for (int j = 0; j < _ntracks; j++)
-//                MatrixOp.setSubMatrix(Ckm1, covMomList[i][j], 3 * (i + 1), 3 * (j + 1));
-//        }
-//        //  now calculate the derivative matrix for the beam constraint.
-//        //  the beamspot is assumed to be at bvec=(0,0,0)
-//        //  the V0 production position is Vbvec=(0,0,0)
-//        //  where ptot=sum_i (pi)
-//        //  need derivites wrt to the vertex position and momentum (theta,phi_v,rho)
-//        double Vx = _vertexPosition.e(0, 0);
-//        double Vy = _vertexPosition.e(1, 0);
-//        double Vz = _vertexPosition.e(2, 0);
-//        //first, get the sum of momenta...
-//        double pxtot = 0;
-//        double pytot = 0;
-//        double pztot = 0;
-//        for (int i = 0; i < _ntracks; i++) {
-//            BasicMatrix pi = (BasicMatrix) _pFit.get(i);
-//            double theta = pi.e(0, 0);
-//            double phiv = pi.e(1, 0);
-//            double rho = pi.e(2, 0);
-//            double Pt = Math.abs((1. / rho) * _bField * Constants.fieldConversion);
-//            double px = Pt * Math.cos(phiv);
-//            double py = Pt * Math.sin(phiv);
-//            double pz = Pt * 1 / Math.tan(theta);
-//            pxtot += px;
-//            pytot += py;
-//            pztot += pz;
-//        }
-//        BasicMatrix rk = makeRk(Vx,Vy,Vz,pxtot,pytot,pztot,false);
-////        //calculate the position of the A' at X=0
-////        BasicMatrix rk = new BasicMatrix(3, 1);
-////        //       if(_debug)System.out.println("Vx = " + Vx + "; Vy = " + Vy + "; Vz = " + Vz + "; pxtot = " + pxtot + "; pytot = " + pytot + "; pztot = " + pztot);
-////        rk.setElement(0, 0, -Vx);
-////        rk.setElement(1, 0, -Vy);
-////        rk.setElement(2, 0, -Vz);
-//
-//        BasicMatrix Hk = makeHk(_ntracks,pxtot,pytot,pztot,false);
-//
-//        // the beam covariance
-//        BasicMatrix Vk = new BasicMatrix(3, 3);
-//        Vk.setElement(0, 0, _beamSize[0] * _beamSize[0]);
-//        Vk.setElement(1, 1, _beamSize[1] * _beamSize[1]);
-//        Vk.setElement(2, 2, _beamSize[2] * _beamSize[2]);
-//
-//        //now do the matrix operations to get the constrained parameters
-//        BasicMatrix Hkt = (BasicMatrix) MatrixOp.transposed(Hk);
-////         if(_debug)System.out.println("Ckm1Hk = " + MatrixOp.mult(Ckm1, Hk));
-//
-//        BasicMatrix Rk = (BasicMatrix) MatrixOp.mult(Hkt, MatrixOp.mult(Ckm1, Hk));
-////        if(_debug)System.out.println("Pre Vk:  Rk = " + Rk.toString());
-//        Rk = (BasicMatrix) MatrixOp.add(Rk, Vk);
-//        BasicMatrix Rkinv = (BasicMatrix) MatrixOp.inverse(Rk);
-//        BasicMatrix Kk = (BasicMatrix) MatrixOp.mult(Ckm1, MatrixOp.mult(Hk, Rkinv));
-//
-////        if(_debug)System.out.println("Ckm1 = " + Ckm1.toString());
-////        if(_debug)System.out.println("Hk = " + Hk.toString());
-////        if(_debug)System.out.println("Rk = " + Rk.toString());
-////        if(_debug)System.out.println("Vk = " + Vk.toString());
-////        if(_debug)System.out.println("rk = " + rk.toString());
-////        if(_debug)System.out.println("Kk = " + Kk.toString());
-//        _constrainedFit = MatrixOp.mult(Kk, rk);
-//        _constrainedFit = MatrixOp.add(_constrainedFit, Xkm1);//Xk
-//
-//        //ok, get the new covariance
-//        BasicMatrix RkKkt = (BasicMatrix) MatrixOp.mult(Rk, MatrixOp.transposed(Kk));
-//        BasicMatrix HkCkm1 = (BasicMatrix) MatrixOp.mult(Hkt, Ckm1);
-//        RkKkt = (BasicMatrix) MatrixOp.mult(1, RkKkt);
-//        HkCkm1 = (BasicMatrix) MatrixOp.mult(-2, HkCkm1);
-//        BasicMatrix sumMatrix = (BasicMatrix) MatrixOp.mult(Kk, MatrixOp.add(HkCkm1, RkKkt));
-//        _constrainedCov = (BasicMatrix) MatrixOp.add(Ckm1, sumMatrix);
-//
-//        //update the regular parameter names to the constrained result
-////        if(_debug)System.out.println("Without Constraint : " + _vertexPosition.toString());
-////        if(_debug)System.out.println("Without Constraint:  x= "+_vertexPosition.e(0,0));
-//        //        if(_debug)System.out.println(_constrainedFit.toString());
-////         if(_debug)System.out.println("Without Constraint : " + _covVtx.toString());
-//        _vertexPosition = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedFit, 0, 0, 3, 1);
-//        _covVtx = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedCov, 0, 0, 3, 3);
-////        if(_debug)System.out.println("With Constraint : " + _vertexPosition.toString());
-////        if(_debug)System.out.println("With Constraint : " + _covVtx.toString());
-//
-//        for (int i = 0; i < _ntracks; i++) {
-//            BasicMatrix ptmp = (BasicMatrix) MatrixOp.getSubMatrix(_constrainedFit, 3 * (i + 1), 0, 3, 1);
-//            _pFit.set(i, ptmp);
-//        }
-//
-////        if(_debug)System.out.println("Unconstrained chi^2 = "+_chiSq);
-//        //ok...add to the chi^2
-//        if (_debug)
-//            System.out.println(MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)));
-//        _chiSq += MatrixOp.mult(MatrixOp.transposed(rk), MatrixOp.mult(Rkinv, rk)).e(0, 0);
-////        if(_debug)System.out.println("Constrained chi^2 = "+_chiSq);
-//    }
     private BasicMatrix makeHk(int ntracks, double pxtot, double pytot, double pztot, boolean bscon) {
         double Vx = _vertexPosition.e(0, 0);
 //        double Vy = _vertexPosition.e(1, 0);
 //        double Vz = _vertexPosition.e(2, 0);
         BasicMatrix Hk = new BasicMatrix(3 * (ntracks + 1), 3);
 //  ok, can set the derivitives wrt to V
-        Hk.setElement(0, 0, 0);
         if (bscon) {
+            Hk.setElement(0, 0, 0);
             Hk.setElement(0, 1, pytot / pxtot);
             Hk.setElement(0, 2, pztot / pxtot);
         } else {
+            Hk.setElement(0, 0, 1);
             Hk.setElement(0, 1, 0);
             Hk.setElement(0, 2, 0);
         }
@@ -670,7 +261,8 @@
             Hk.setElement(3 * (i + 1), 0, 0);
             Hk.setElement(3 * (i + 1), 1, 0);
             if (bscon) {
-                Hk.setElement(3 * (i + 1), 2, -Pt / Math.pow(sin(theta), 2) * Vx);
+                Hk.setElement(3 * (i + 1), 2,
+                        -Pt / Math.pow(sin(theta), 2) * Vx);
             } else {
                 Hk.setElement(3 * (i + 1), 2, 0);
             }
@@ -679,7 +271,8 @@
             if (bscon) {
                 Hk.setElement(3 * (i + 1) + 1, 1,
                         (Pt * Pt * cos(phiv) * sin(phiv) / (pxtot * pxtot)) * Vx);
-                Hk.setElement(3 * (i + 1) + 1, 2, (Pt * sin(phiv) / (pxtot * pxtot)) * Vx * pztot);
+                Hk.setElement(3 * (i + 1) + 1, 2,
+                        (Pt * sin(phiv) / (pxtot * pxtot)) * Vx * pztot);
             } else {
                 Hk.setElement(3 * (i + 1) + 1, 1, 0);
                 Hk.setElement(3 * (i + 1) + 1, 2, 0);
@@ -710,16 +303,16 @@
         //calculate the position of the A' at X=0
         BasicMatrix rk = new BasicMatrix(3, 1);
         if (_debug) {
-            System.out.println("addV0fromBSConstraint::Vx = " + Vx + "; Vy = " + Vy + "; Vz = " + Vz + "; pxtot = " + pxtot + "; pytot = " + pytot + "; pztot = " + pztot);
+            System.out.println("makeRk::Vx = " + Vx + "; Vy = " + Vy + "; Vz = " + Vz + "; pxtot = " + pxtot + "; pytot = " + pytot + "; pztot = " + pztot);
         }
         if (bscon) {
             rk.setElement(0, 0, 0);
-            rk.setElement(1, 0, 0 - (Vy - pytot / pxtot * Vx));
-            rk.setElement(2, 0, 0 - (Vz - pztot / pxtot * Vx));
+            rk.setElement(1, 0, _beamPosition[1] - (Vy - pytot / pxtot * (Vx - _beamPosition[0])));
+            rk.setElement(2, 0, _beamPosition[2] - (Vz - pztot / pxtot * (Vx - _beamPosition[0])));
         } else {
-            rk.setElement(0, 0, -Vx);
-            rk.setElement(1, 0, -Vy);
-            rk.setElement(2, 0, -Vz);
+            rk.setElement(0, 0, _beamPosition[0] - Vx);
+            rk.setElement(1, 0, _beamPosition[1] - Vy);
+            rk.setElement(2, 0, _beamPosition[2] - Vz);
         }
         return rk;
     }
@@ -734,13 +327,21 @@
         _beamSize[2] = bs[2];
     }
 
+    public void setBeamPosition(double[] bp) {
+        _beamPosition[0] = bp[0];
+        _beamPosition[1] = bp[1];
+        _beamPosition[2] = bp[2];
+    }
+
     public void doBeamSpotConstraint(boolean bsconst) {
         _beamspotConstraint = bsconst;
+        _targetConstraint = false;
         _constraintType = "BeamspotConstrained";
 
     }
 
     public void doTargetConstraint(boolean bsconst) {
+        _beamspotConstraint = false;
         _targetConstraint = bsconst;
         _constraintType = "TargetConstrained";
     }
@@ -797,9 +398,10 @@
         }
     }
 
+    @Override
     public String toString() {
-        StringBuffer sb = new StringBuffer("Vertex at : \nx= " + _vertexPosition.e(0, 0) + " +/- " + Math.sqrt(_covVtx.e(0, 0)) + "\ny= " + _vertexPosition.e(1, 0) + " +/- " + Math.sqrt(_covVtx.e(1, 1)) + "\nz= " + _vertexPosition.e(2, 0) + " +/- " + Math.sqrt(_covVtx.e(2, 2)));
-        return sb.toString();
+        String sb = "Vertex at : \nx= " + _vertexPosition.e(0, 0) + " +/- " + Math.sqrt(_covVtx.e(0, 0)) + "\ny= " + _vertexPosition.e(1, 0) + " +/- " + Math.sqrt(_covVtx.e(1, 1)) + "\nz= " + _vertexPosition.e(2, 0) + " +/- " + Math.sqrt(_covVtx.e(2, 2));
+        return sb;
     }
 
     private void follow1985Paper(List<BilliorTrack> tracks) {
@@ -808,8 +410,8 @@
         v0.setElement(0, 0, _v0[0]);
         v0.setElement(1, 0, _v0[1]);
         v0.setElement(2, 0, _v0[2]);
-        List<Matrix> params = new ArrayList<Matrix>();
-        List<Matrix> q0s = new ArrayList<Matrix>();
+//        List<Matrix> params = new ArrayList<Matrix>();
+//        List<Matrix> q0s = new ArrayList<Matrix>();
         List<Matrix> Gs = new ArrayList<Matrix>();
         List<Matrix> Ds = new ArrayList<Matrix>();
         List<Matrix> Es = new ArrayList<Matrix>();
@@ -828,11 +430,11 @@
             tmpPar.setElement(2, 0, par[2]);
             tmpPar.setElement(3, 0, par[3]);
             tmpPar.setElement(4, 0, par[4]);
-            params.add(tmpPar);
+//            params.add(tmpPar);
             double theta = par[2];
-            double phiv = par[3];
+//            double phiv = par[3];
             double rho = par[4];
-            double Pt = Math.abs((1. / rho) * _bField * Constants.fieldConversion);
+//            double Pt = Math.abs((1. / rho) * _bField * Constants.fieldConversion);
 
             double cotth = 1. / tan(par[2]);
             double uu = v0.e(0, 0) * cos(par[3]) + v0.e(1, 0) * sin(par[3]);//Q
@@ -858,7 +460,7 @@
             q0.setElement(0, 0, theta);
             q0.setElement(1, 0, phiVert);
             q0.setElement(2, 0, rho);
-            q0s.add(q0);
+//            q0s.add(q0);
 
             double cosf = cos(phiVert);
             double sinf = sin(phiVert);
@@ -935,8 +537,8 @@
         }
 
         //ok, now the momentum
-        List<Matrix> qtildes = new ArrayList<Matrix>();
-        List<Matrix> ptildes = new ArrayList<Matrix>();
+//        List<Matrix> qtildes = new ArrayList<Matrix>();
+//        List<Matrix> ptildes = new ArrayList<Matrix>();
         List<Matrix> C0j = new ArrayList<Matrix>();
         List<Matrix> pfit = new ArrayList<Matrix>();
         Matrix[][] Cij = new Matrix[2][2];//max 2 tracks...just make this bigger for more
@@ -954,9 +556,9 @@
             BasicMatrix second = (BasicMatrix) MatrixOp.mult(MatrixOp.inverse(e), MatrixOp.mult(MatrixOp.transposed(b), g));
             second = (BasicMatrix) MatrixOp.mult(second, p);
             BasicMatrix qtilde = (BasicMatrix) MatrixOp.add(first, second);
-            qtildes.add(qtilde);
+//            qtildes.add(qtilde);
             BasicMatrix ptilde = (BasicMatrix) MatrixOp.add(MatrixOp.mult(a, xtilde), MatrixOp.mult(b, qtilde));
-            ptildes.add(ptilde);
+//            ptildes.add(ptilde);
             chisq += MatrixOp.mult(MatrixOp.transposed(MatrixOp.add(p, MatrixOp.mult(-1, ptilde))), MatrixOp.mult(g, MatrixOp.add(p, MatrixOp.mult(-1, ptilde)))).e(0, 0);
             if (_debug) {
                 System.out.println("\n\nfollow1985Paper::Track #" + j);
@@ -980,12 +582,12 @@
             BasicMatrix tmpC0j = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(covVtx, MatrixOp.mult(d, MatrixOp.inverse(e))));
             C0j.add(tmpC0j);
             for (int i = 0; i < _ntracks; i++) {
-                BasicMatrix ai = (BasicMatrix) As.get(i);
-                BasicMatrix bi = (BasicMatrix) Bs.get(i);
-                BasicMatrix di = (BasicMatrix) Ds.get(i);
-                BasicMatrix ei = (BasicMatrix) Es.get(i);
-                BasicMatrix gi = (BasicMatrix) Gs.get(i);
-                BasicMatrix pi = (BasicMatrix) pis.get(i);
+//                BasicMatrix ai = (BasicMatrix) As.get(i);
+//                BasicMatrix bi = (BasicMatrix) Bs.get(i);
+//                BasicMatrix di = (BasicMatrix) Ds.get(i);
+//                BasicMatrix ei = (BasicMatrix) Es.get(i);
+//                BasicMatrix gi = (BasicMatrix) Gs.get(i);
+//                BasicMatrix pi = (BasicMatrix) pis.get(i);
                 BasicMatrix tmpCij = (BasicMatrix) MatrixOp.mult(-1, MatrixOp.mult(MatrixOp.inverse(e), MatrixOp.mult(MatrixOp.transposed(d), tmpC0j)));
                 Cij[i][j] = tmpCij;
             }

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