ClusterSearcher and RecoCluster (#365)

* -Updated DigitBuilder to be more consistent with, but independent of ClusterFinder's corresponding functions
--Added some extra features, such as hit LAPPD count and strip-by-strip LAPPD hits.
-Added ClusterSearcher to replace ClusterFinder using RecoDigit and RecoCluster classes
-Updated RecoDigit and RecoCluster classes for corresponding use and new features, such as various cluster parameters
-Added NeutronCheck tool as output for RecoCluster information
-Added sample toolchain configfolder for using the new tools

* Update to previous commit in accordance with feedback:
-Changed RecoCluster and RecoDigit lists in several tools to be vectors of objects, rather than vectors of pointers, to avoid memory complications
-removed unused convex hull function from RecoCluster class
-simplified CalcAS function in RecoCluster class by consolidating for loops
-removed several instances of commented-out code from older versions
-removed several debug outputs
-altered hard-coded time window values in several instances to rely on configuration input
-added use of the true Q2 value from the GenieInfo store to NeutronCheck's output.
-removed several uncontrolled cout lines, and replaced useful ones with Log.
-Tidied the Instance() function of ClusterSearcher
-Added vertex information to NeutronCheck

* Removed ClusterCA from NeutronCheck to fix bug.

* Modified HitCleaner for non-pointer Digits list.

* Update/fix to ClusterSearcher sample toolchain.

* Removed HitCleaner::FilterByClusters because it is neither functional nor memory-safe with recent changes to RecoDigit storage.

* -removed unused configvariable ArgonFV from ClusterSearcher/EventSelectorConfig
-removed unhelpful forced loop end from single-pe gains extraction in ClusterSearcher::Initialize()
-changed Genie version in ClusterSearcher/LoadGenieEventConfig to 1

* Fixed memory leak caused by double-pointing to the same object
-replaced all instances of fClusterList with fRecoClusters in ClusterSearcher
-changed ClusterSearcher::RecoClusters() to a void function, since it was returning a member pointer to itself
-removed ClusterSearcher::SelectByClusters(), which is not used

* Pointer cleanup in RecoClusterClass

Author: flemmons

DataModel/RecoCluster.cpp

@@ -3,7 +3,15 @@
 #ifndef RECOCLUSTER_H
 #define RECOCLUSTER_H
 #include "RecoDigit.h"
+#include "Position.h"
 #include<SerialisableObject.h>
+#include "TVector3.h"
+#include "TMatrixDSym.h"
+#include "TMatrixDSymEigen.h"
+#include "TVectorD.h"
+#include "TMath.h"
+#include "TF1.h"
+#include "Math/IFunction.h"
 
 class RecoCluster : public SerialisableObject {
 
@@ -16,19 +24,96 @@ class RecoCluster : public SerialisableObject {
   void Reset();
   void SortCluster();
 
-  void AddDigit(RecoDigit* digit);
+  void AddDigit(RecoDigit digit);
+  inline void SetDigits(vector<RecoDigit> indigits){fDigitList=indigits;}
 
-  RecoDigit* GetDigit(int n);
+  RecoDigit GetDigit(int n);
+  
+  void SetClusterMode(int cmode);
+  
+  int GetClusterMode();
+  
+  std::vector<RecoDigit> GetDigitList() {return fDigitList;}
+  
   int GetNDigits();
 
   bool Print() {
 		cout<<"Number of digits in this cluster : "<<GetNDigits()<<endl;
+		cout<<"Clustering mode : "<<GetClusterMode()<<endl;
 		return true;
 	}
 
+  inline double GetTime() { return clusterTime; }
+  inline double GetCharge() { return clusterCharge; }
+
+  void CalcTime();
+  void CalcCharge();
+
+  inline double GetCB() { return clusterCB; }
+  inline Position GetCV() {return ChargeVector; }
+
+  void CalcCB();
+  void CalcAS();
+  void CalcCV();
+  void CalcAMD();
+  void CalcSA();
+  void CalcAW();
+  void CalcPlanaritySphericity();
+  double CalcBeta(int order);
+  void CalcTR();
+  void CalcParameters();
+  int calcBestParent();
+  double GetAS(int mode);
+  inline double GetASC(){return ASC;}
+  inline double GetAMD(){return AMD;}
+  inline Position GetSA(){return SpatialAverage;}
+  inline double GetAW(){return AngularWidth;}
+  inline double GetPlanarity(){return Planarity;}
+  inline double GetSphericity(){return Sphericity;}
+  double GetBeta(int order);
+  inline double GetTimeRangeT() {return TRTotal;}
+  inline double GetTimeRangeQ() {return TRQ;}
+  inline double GetTimeRangeC() {return TRCluster;}
+  inline double GetTRRTQ(){return TRRatioTQ;}
+  inline double GetTRRTC() { return TRRatioTC; }
+  inline double GetTRRQC() { return TRRatioQC; }
+
+  void SetParticle(int pID,int pPDG, double eff, double pur);
+  inline int GetBestParent(){return bestParticleID;}
+  inline void SetPDG(int pPDG) {bestParticlePDG=pPDG;}
+  inline int GetPDG(){return bestParticlePDG;}
+  inline double Efficiency(){return efficiency;}
+  inline double Purity(){return purity;}
+
+  bool CheckFilter();
+  inline bool GetFilterStatus(){return fIsFiltered;}
+  //void CleanDigits();
+
   private:
+	  double clusterTime;
+	  double clusterCharge;
+	  double clusterCB;
+	  double AS0, AS1, ASC;
+	  double AMD;
+	  Position ChargeVector;
+	  Position SpatialAverage;
+	  double AngularWidth;
+	  double Planarity=-999;
+	  double Sphericity=-999;
+	  std::map<int,double> BetaParameters;
+	  double TRTotal, TRQ, TRCluster;
+	  double TRRatioTQ, TRRatioTC,TRRatioQC;
+	  int bestParticleID;
+	  int bestParticlePDG;
+	  double efficiency;
+	  double purity;
+	  bool fIsFiltered=0;
+
+  
+  int fClusterMode = -999;
+  std::vector<RecoDigit> fDigitList;
+  Position TwoDCenter;
 
-  std::vector<RecoDigit*> fDigitList;
 
   protected:
   template<class Archive> void serialize(Archive & ar, const unsigned int version){

DataModel/RecoCluster.h

@@ -33,15 +33,32 @@ class RecoDigit : public SerialisableObject{
 			fIsFiltered = 1;
 			ANNIERecoObjectTable::Instance()->NewDigit();
 		}
+	RecoDigit(RecoDigit* origin) {
+		serialise=true;
+		fRegion=origin->GetRegion();
+		fPosition = origin->GetPosition();
+		fCalTime = origin->GetCalTime();
+		fCalCharge=origin->GetCalCharge();
+		fDigitType=origin->GetDigitType();
+		fDetectorID=origin->GetDetectorID();
+		fIsFiltered=origin->GetFilterStatus();
+
+	}
 	~RecoDigit() {/*ANNIERecoObjectTable::Instance()->DeleteDigit();*/}
 
+	bool operator<(const RecoDigit other) const {
+		return (fPosition.X() == other.GetPosition().X()) ? fPosition.Y() < other.GetPosition().Y() : fPosition.X() < other.GetPosition().X();
+	}
+
 	inline int                 GetRegion() const {return fRegion;}
 	inline Position						 GetPosition() const {return fPosition;}
 	inline double              GetCalTime() const {return fCalTime;}
 	inline double              GetCalCharge() const {return fCalCharge;}
 	inline bool                GetFilterStatus() const {return fIsFiltered;}
+	inline vector<int>		GetClusteredModes() { return fClusterMode; }
 	inline int         				 GetDigitType() const {return fDigitType;}
 	inline int         				 GetDetectorID() const {return fDetectorID;}
+	inline std::vector<int> GetParents() const {return Parents;}
 
 	inline void                SetRegion(int reg) {fRegion = reg;}
 	inline void                SetPosition(Position pos){fPosition = pos;}
@@ -52,6 +69,9 @@ class RecoDigit : public SerialisableObject{
 	inline void                SetFilter(bool pass = 1) { fIsFiltered = pass;}
   inline void                ResetFilter() {SetFilter(0);}
   inline void                PassFilter() {SetFilter(1);}
+  inline void				AddCluster(int InClusterMode) {fClusterMode.push_back(InClusterMode); }
+  inline void				UnCluster(){fClusterMode.pop_back(); }
+  inline void SetParents(std::vector<int> parentsin) { Parents = parentsin; }
 
 	bool Print() {
 		cout<<"Region : "<<fRegion<<endl;
@@ -70,8 +90,10 @@ class RecoDigit : public SerialisableObject{
   double fCalTime;
   double fCalCharge; 
   bool fIsFiltered;
+  vector<int> fClusterMode;
   int fDigitType;
   int fDetectorID;
+  std::vector<int> Parents;
 
 	template<class Archive> void serialize(Archive & ar, const unsigned int version){
 		if(serialise){