This pull request includes fixes

CMakeLists.txt

@@ -56,6 +56,7 @@ SET( ROOT_DICT_INPUT_HEADERS
 		${PROJECT_SOURCE_DIR}/include/testproc.h
 		${PROJECT_SOURCE_DIR}/include/TrackNtuple.h
 		${PROJECT_SOURCE_DIR}/include/VertexMassRecovery.h
+		${PROJECT_SOURCE_DIR}/include/VertexNtuple.h
 		${PROJECT_SOURCE_DIR}/include/LinkDef.h
 )
 SET( ROOT_DICT_INCLUDE_DIRS ${Marlin_INCLUDE_DIRS} )

include/JetFinder.h

@@ -106,7 +106,7 @@ class JetFinder {
   /** Constructor.
   	@param[in] cfg specify the algorithm and the parameters
   	*/
-  JetFinder(const JetConfig& cfg);
+  JetFinder(const JetConfig& cfg, const Vertex* ip = 0);
   /** Destructor. */
   ~JetFinder() {};
   /** Replace JetConfig.
@@ -137,6 +137,7 @@ class JetFinder {
   double (*_Yfunc)(Jet& jet1, Jet& jet2, double Evis2, JetConfig& cfg);
   double (*_YfuncBeam)(Jet& jet1, double Evis2, JetConfig& cfg);
   JetConfig _cfg;
+  const Vertex* _privtx;
 };
 
 /*

include/LinkDef.h

@@ -41,6 +41,7 @@
 #pragma link C++ class lcfiplus::ReadMVA;
 #pragma link C++ class lcfiplus::TrackNtuple;
 #pragma link C++ class lcfiplus::VertexMassRecovery+;
+#pragma link C++ class lcfiplus::VertexNtuple;
 
 #pragma link C++ class lcfiplus::ZHHAlgo;
 #pragma link C++ class lcfiplus::TestAlgo;

include/TrackSelector.h

@@ -66,33 +66,34 @@ class TrackSelectorConfig {
 
 class TrackSelector {
  public:
-  vector<const Track*> operator () (const vector<const Track*>& tracks, TrackSelectorConfig& config) {
+  vector<const Track*> operator () (const vector<const Track*>& tracks, TrackSelectorConfig& config, const Vertex* ip = 0) {
     vector<const Track*> ret;
 
     for (unsigned int i=0; i<tracks.size(); i++) {
-      if (passesCut(tracks[i], config))
+      if (passesCut(tracks[i], config, ip))
         ret.push_back(tracks[i]);
     }
 
     return ret;
   }
 
-  bool passesCut(const Track* trk, const TrackSelectorConfig& cfg) {
+  bool passesCut(const Track* trk, const TrackSelectorConfig& cfg, const Vertex* ip = 0) {
     // AND cuts
 
     if (fabs(trk->getD0()) < cfg.minD0) return false;
     if (fabs(trk->getD0()) > cfg.maxD0) return false;
-    if (trk->getCovMatrix()[tpar::d0d0] < cfg.minD0Err) return false;
-    if (trk->getCovMatrix()[tpar::d0d0] > cfg.maxD0Err) return false;
+    if (sqrt(trk->getCovMatrix()[tpar::d0d0]) < cfg.minD0Err) return false;
+    if (sqrt(trk->getCovMatrix()[tpar::d0d0]) > cfg.maxD0Err) return false;
     double d0sig = fabs(trk->getD0()) / sqrt(trk->getCovMatrix()[tpar::d0d0]);
     if ( d0sig < cfg.minD0Sig) return false;
     if ( d0sig > cfg.maxD0Sig) return false;
 
-    if (fabs(trk->getZ0()) < cfg.minZ0) return false;
-    if (fabs(trk->getZ0()) > cfg.maxZ0) return false;
-    if (trk->getCovMatrix()[tpar::z0z0] < cfg.minZ0Err) return false;
-    if (trk->getCovMatrix()[tpar::z0z0] > cfg.maxZ0Err) return false;
-    double z0sig = fabs(trk->getZ0()) / sqrt(trk->getCovMatrix()[tpar::z0z0]);
+    double z0 = (ip ? fabs(trk->getZ0() - ip->getZ()) : fabs(trk->getZ0()) );
+    if (z0 < cfg.minZ0) return false;
+    if (z0 > cfg.maxZ0) return false;
+    if (sqrt(trk->getCovMatrix()[tpar::z0z0]) < cfg.minZ0Err) return false;
+    if (sqrt(trk->getCovMatrix()[tpar::z0z0]) > cfg.maxZ0Err) return false;
+    double z0sig = z0 / sqrt(trk->getCovMatrix()[tpar::z0z0]);
     if ( z0sig < cfg.minZ0Sig) return false;
     if ( z0sig > cfg.maxZ0Sig) return false;
 

include/VertexFitterSimple.h

@@ -19,19 +19,20 @@ class VertexFitterSimple {
 
     GeometryHandler* gh = GeometryHandler::Instance();
     if (pointConstraint) {
-      Point* ip = new Point(pointConstraint);
+      Point* ip = new Point(pointConstraint,PointBase::PRIVTX);
       vector<PointBase*> tracks;
-      if (!pointInitialOnly)
+      if (!pointInitialOnly) {
         tracks.push_back(ip);
+      }
       int ntracks = 0;
       for (Iterator it = tracksBegin; it != tracksEnd; it++,ntracks++) {
-        tracks.push_back(new Helix(*it));
+        tracks.push_back(new Helix(*it,PointBase::PRIVTX));
       }
       if (verbose)
         cout << "VertexFitterSimple: number of tracks is " << ntracks << endl;
 
       TVector3 initial = pointConstraint->getPos();
-      Point* result = new Point;
+      Point* result = new Point(PointBase::NOTUSED);
       double chi2 = -gh->PointFit(tracks, initial, result);
 
       TVector3 vresult = result->GetPos();
@@ -60,7 +61,7 @@ class VertexFitterSimple {
 
       Vertex* vtx = new Vertex(chi2, TMath::Prob(chi2, ntracks*2-3), vresult.x(), vresult.y(), vresult.z(), cov, false);
       for (Iterator it = tracksBegin; it != tracksEnd; it++,ntracks++) {
-        Helix hel(*it);
+        Helix hel(*it,PointBase::PRIVTX);
         double ll = hel.LogLikelihood(vresult); // need to incorporate vertex error??
 
         if (verbose)
@@ -80,12 +81,12 @@ class VertexFitterSimple {
     vector<Helix*> tracks;
     int ntracks = 0;
     for (Iterator it = tracksBegin; it != tracksEnd; it++,ntracks++) {
-      tracks.push_back(new Helix(*it));
+      tracks.push_back(new Helix(*it,PointBase::SECVTX));
     }
     if (verbose)
       cout << "VertexFitterSimple: number of tracks is " << ntracks << endl;
 
-    Point* result = new Point;
+    Point* result = new Point(PointBase::NOTUSED);
     double chi2 = -gh->HelixPointFit(tracks, result);
 
     TVector3 vresult = result->GetPos();
@@ -104,7 +105,7 @@ class VertexFitterSimple {
 
     Vertex* vtx = new Vertex(chi2, (ntracks > 1 ? TMath::Prob(chi2, ntracks*2-3) : 1), vresult.x(), vresult.y(), vresult.z(), cov, false);
     for (Iterator it = tracksBegin; it != tracksEnd; it++, ntracks++) {
-      Helix hel(*it);
+      Helix hel(*it,PointBase::SECVTX);
       double ll = hel.LogLikelihood(vresult); // need to incorporate vertex error??
       if (verbose)
         cout << "VertexFitterSimple: track loglikelihood is " << ll << endl;
@@ -119,18 +120,18 @@ class VertexFitterSimple {
     return vtx;
   }
 
-  double getChi2(const Vertex* vtx, const Track* trk, int mode=1) {
+  double getChi2(const Vertex* vtx, const Track* trk, int mode=1, PointBase::FITFLAG flag=PointBase::NOTUSED) {
     // 110510 suehara for IPassoc study
     if (mode == 0) {
       // mode 0: no fit at all
-      Helix hel(trk);
+      Helix hel(trk,flag);
       TVector3 v = vtx->getPos();
       return -hel.LogLikelihood(v);
     } else if (mode == 1) {
       // mode 1: vertex treated as errored point
 
-      Point ptVtx(vtx);
-      Helix hel(trk);
+      Point ptVtx(vtx,flag);
+      Helix hel(trk,flag);
 
       vector<PointBase*> vpt;
       vpt.push_back(&ptVtx);
@@ -142,12 +143,12 @@ class VertexFitterSimple {
       // mode 2: vertex treated as track list
       vector<PointBase*> vpt;
       for (unsigned int n=0; n<vtx->getTracks().size(); n++) {
-        vpt.push_back(new Helix(vtx->getTracks()[n]));
+        vpt.push_back(new Helix(vtx->getTracks()[n],flag));
       }
-      vpt.push_back(new Helix(trk));
+      vpt.push_back(new Helix(trk,flag));
 
       GeometryHandler* gh = GeometryHandler::Instance();
-      Point ret;
+      Point ret(PointBase::NOTUSED);
       double ll = -gh->PointFit(vpt, vtx->getPos(), &ret);
 
       for (unsigned int n=0; n<vpt.size(); n++) {
@@ -156,7 +157,7 @@ class VertexFitterSimple {
       if (mode == 2) {
         return ll;
       } else {
-        Helix hel(trk);
+        Helix hel(trk,flag);
         return -hel.LogLikelihood(ret.GetPos());
       }
     }

include/VertexNtuple.h

@@ -0,0 +1,41 @@
+// VertexNtuple.h
+
+#ifndef VertexNtuple_h
+#define VertexNtuple_h 1
+
+class TFile;
+class TNtuple;
+
+#include "lcfiplus.h"
+
+namespace lcfiplus {
+
+/**
+	Storing the number of tracks associated to vertices..
+
+	@author R.Yonamine, Dept. of Physics, Tohok University
+	@version $Id$
+ */
+
+class VertexNtuple : public Algorithm {
+ public:
+  VertexNtuple() {}
+  virtual ~VertexNtuple() {}
+
+  void init(Parameters* param);
+  void process();
+  void end();
+
+ private:
+  TFile* _file;
+  TNtuple* _tree;
+
+  string _jetcolname;
+  string _primvtxcolname;
+
+  ClassDef(VertexNtuple,1)
+};
+
+}
+
+#endif

include/algoEtc.h

@@ -17,9 +17,11 @@ vector<const Track*> extractTracks(VertexVec& vtx);
 double calcThrust( vector<TVector3>& list, TVector3& taxis );
 
 bool SimpleSecMuonFinder(const Track* tr, double d0sigth, double z0sigth, double maxpos, double mudepmin,
-                         double ecaldepmin, double ecaldepmax, double hcaldepmin, double hcaldepmax, double maxclusterpertrackenergy = 10.);
+                         double ecaldepmin, double ecaldepmax, double hcaldepmin, double hcaldepmax, double maxclusterpertrackenergy = 10.,
+                         const Vertex* ip = 0);
 bool SimpleSecElectronFinder(const Track* tr, double d0sigth, double z0sigth, double maxpos, double emin,
-                             double minfracecal, double minecalpertrackenergy, double maxecalpertrackenergy);
+                             double minfracecal, double minecalpertrackenergy, double maxecalpertrackenergy,
+                             const Vertex* ip = 0);
 
 }
 }

include/flavtag.h

@@ -157,6 +157,13 @@ class FtJProbZ2;
 class FtJProbR25Sigma;
 class FtJProbZ25Sigma;
 
+class FtD0bProb2;
+class FtD0cProb2;
+class FtD0qProb2;
+class FtZ0bProb2;
+class FtZ0cProb2;
+class FtZ0qProb2;
+
 class FtIPProbHolder {
   friend class FtD0bProb;
   friend class FtD0cProb;
@@ -176,6 +183,12 @@ class FtIPProbHolder {
   friend class FtJProbR25Sigma;
   friend class FtJProbZ25Sigma;
 
+  friend class FtD0bProb2;
+  friend class FtD0cProb2;
+  friend class FtD0qProb2;
+  friend class FtZ0bProb2;
+  friend class FtZ0cProb2;
+  friend class FtZ0qProb2;
  public:
   FtIPProbHolder(const char* d0probfile, const char* z0probfile);
   ~FtIPProbHolder();

include/geometry.h

@@ -21,9 +21,13 @@ class PointBase { // pure virtual point-base class
   virtual double LogLikelihood(const TVector3& p)const  = 0;
   virtual void LogLikelihoodDeriv(const TVector3& p,double* output)const  = 0;
   virtual ~PointBase() {}
-
+  enum FITFLAG { NOTUSED, PRIVTX, SECVTX };
  protected:
-  PointBase() {}
+  //PointBase() : _fitflag(DEFAULT) {}
+  PointBase(FITFLAG flag) : _fitflag(flag) {}
+  //void SetFlag(FITFLAG flag) { _fitflag = flag; }
+  FITFLAG GetFlag() const { return _fitflag; }
+  FITFLAG _fitflag;
 };
 
 class Point : public PointBase { // real 3D-point with error
@@ -34,16 +38,20 @@ class Point : public PointBase { // real 3D-point with error
   double LogLikelihood(const TVector3& p)const;
   void LogLikelihoodDeriv(const TVector3& p, double* output)const;
 
-  Point() {}
-  Point(const SVector3& pos, const SMatrixSym3& err) {
+  //Point() {}
+  Point(FITFLAG flag) : PointBase(flag) {}
+  //Point(const SVector3& pos, const SMatrixSym3& err) {
+  Point(const SVector3& pos, const SMatrixSym3& err, FITFLAG flag) : PointBase(flag) {
     _pos = pos;
     _err = err;
   }
-  Point(const Point& ref) {
+  //Point(const Point& ref) {
+  Point(const Point& ref, FITFLAG flag) : PointBase(flag) {
     _pos = ref._pos;
     _err = ref._err;
   }
-  Point(const Vertex* vtx);
+  Point(const Vertex* vtx, FITFLAG flag) ;
+  //Point(const Vertex* vtx, FITFLAG flag);
   ~Point() {}
 
   void SetPosErr(const SVector3& pos, const SMatrixSym3& err) {
@@ -133,13 +141,13 @@ class Helix : public PointBase { // parametrized point for helix
 
   double LongitudinalDeviation(const Vertex* ip, const Vertex* sec);
 
-  Helix() {}
-  Helix(const SVector5& hel, const SMatrixSym5& err, int charge) {
+  Helix(FITFLAG flag) : PointBase(flag) {}
+  Helix(const SVector5& hel, const SMatrixSym5& err, int charge, FITFLAG flag) : PointBase(flag) {
     _hel = hel, _err = err;
     _charge = charge;
   }
-  Helix(const Track* trk);
-  Helix(const Helix& ref) {
+  Helix(const Track* trk, FITFLAG flag) ;
+  Helix(const Helix& ref, FITFLAG flag) : PointBase(flag) {
     _hel = ref._hel;
     _err = ref._err;
     _charge = ref._charge;
@@ -186,14 +194,14 @@ class VertexLine : public PointBase { // line with error for IP-vertex line
   void LogLikelihoodDeriv(const TVector3& p, double* output)const;
   double Variance(const TVector3& p, double t)const;		// t-fixed version, internally used
 
-  VertexLine() {}
-  VertexLine(const Vertex* ip, const Vertex* secvtx) {
+  VertexLine(FITFLAG flag) : PointBase(flag) {}
+  VertexLine(const Vertex* ip, const Vertex* secvtx, FITFLAG flag) : PointBase(flag) {
     _ip = ip;
     _vertex = secvtx;
     _origin = _vertex->getPos();
     _unit = (_origin - _ip->getPos()).Unit();
   }
-  VertexLine(const TVector3& origin, const TVector3& dir) {
+  VertexLine(const TVector3& origin, const TVector3& dir, FITFLAG flag) : PointBase(flag) {
     _origin = origin;
     _unit = dir.Unit();
     _ip = 0;

include/lcfiplus.h

@@ -178,10 +178,10 @@ class Parameters {
     } else if (_map.find(key)->second.first == &typeid(T))ret = *(T*)(_map.find(key)->second.second);
     else if (_allowstring && _map.find(key)->second.first == &typeid(string)) {
       istringstream str(*(string*)_map.find(key)->second.second);
-      str >> ret;
+      str >> boolalpha >> ret;
     } else if (_allowstring && _map.find(key)->second.first == &typeid(vector<string>)) {
       istringstream str((*(const vector<string>*)_map.find(key)->second.second)[0]);
-      str >> ret;
+      str >> boolalpha >> ret;
     } else {
       cout << "Parameter type invalid: key = " << key << ", type = " << _map.find(key)->second.first->name() << " vs " << typeid(T).name() << endl;
       throw (Exception("Parameter type invalid."));

include/process.h

@@ -31,7 +31,7 @@ class PrimaryVertexFinder : public Algorithm {
   bool _beamspotSmearing;
 
   // track cut parameters
-  TrackSelectorConfig* _secVtxCfg; //!
+  TrackSelectorConfig* _priVtxCfg; //!
 };
 
 class BuildUpVertex : public Algorithm {
@@ -109,7 +109,8 @@ class JetClustering : public Algorithm {
   double _vsMaxDist;
   double _vsK0MassWidth;
   bool _outputVertexStoresVertex;
-  string _vcolname;
+  string _vpricolname;
+  string _vseccolname;
   int _maxYth;
 
   double _yaddVV;