Update project structure. Tighten up code, improve syntax, enforce style. Still bugged, but now working from proper environment. Switch back to ROOT as file I/O and data management

CMakeLists.txt

@@ -8,8 +8,10 @@ set(MASK_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
 
 set(CMAKE_CXX_STANDARD 17)
 
+find_package(ROOT REQUIRED COMPONENTS GenVector)
+
 add_subdirectory(src/vendor/catima)
 add_subdirectory(src/Mask)
 add_subdirectory(src/MaskApp)
 add_subdirectory(src/Detectors)
-add_subdirectory(src/Plotters/ROOT)
+add_subdirectory(src/Plotters)

include/AnasenEfficiency.h

@@ -1,69 +0,0 @@
-#ifndef ANASEN_EFFICIENCY_H
-#define ANASEN_EFFICIENCY_H
-
-#include <string>
-
-#include "DetectorEfficiency.h"
-#include "StripDetector.h"
-#include "QQQDetector.h"
-#include "Target.h"
-#include "Nucleus.h"
-#include "MaskFile.h"
-#include "AnasenDeadChannelMap.h"
-
-struct DetectorResult {
-	bool detectFlag = false;
-	Mask::Vec3 direction;
-	double energy_deposited = 0.0;
-	std::string det_name = "";
-};
-
-class AnasenEfficiency : public DetectorEfficiency {
-public:
-	AnasenEfficiency();
-	~AnasenEfficiency();
-	void CalculateEfficiency(const std::string& inputname, const std::string& outputname, const std::string& statsname) override;
-	void DrawDetectorSystem(const std::string& filename) override;
-	double RunConsistencyCheck() override;
-	inline void SetDeadChannelMap(const std::string& filename) { dmap.LoadMapfile(filename); }
-
-private:
-	DetectorResult IsRing1(Mask::Nucleus& nucleus);
-	DetectorResult IsRing2(Mask::Nucleus& nucleus);
-	DetectorResult IsQQQ(Mask::Nucleus& nucleus);
-	DetectorResult IsAnasen(Mask::Nucleus& nucleus);
-	void CountCoincidences(const Mask::MaskFileData& data, std::vector<int>& counts, Mask::RxnType rxn_type);
-
-	std::vector<StripDetector> m_Ring1, m_Ring2;
-	std::vector<QQQDetector> m_forwardQQQs;
-	std::vector<QQQDetector> m_backwardQQQs;
-
-	Mask::Target det_silicon;
-
-	AnasenDeadChannelMap dmap;
-
-	/**** ANASEN geometry constants *****/
-	const int n_sx3_per_ring = 12;
-	const int n_qqq = 4;
-	const double sx3_length = 0.075;
-	const double sx3_width = 0.04;
-	const double barrel_gap = 0.0254;
-	const double sx3_frame = 0.049; //0.049 is base gap due to frames
-	const double ring1_z = sx3_length/2.0 + sx3_frame + barrel_gap/2.0;
-	const double ring2_z = (-1.0)*(barrel_gap/2.0 + sx3_length/2.0);
-	const double qqq_nom_z = 0.0125 + sx3_length + sx3_frame + barrel_gap/2.0;
-	const double qqq_rinner = 0.0501;
-	const double qqq_router = 0.0990;
-	const double qqq_deltaphi = 1.52119;
-	const double qqq_z[4] = {qqq_nom_z, qqq_nom_z, qqq_nom_z, qqq_nom_z};
-	const double qqq_phi[4] = {5.49779, 0.785398, 2.35619, 3.92699};
-	const double ring_rho[12] = {0.0890601, 0.0889871, 0.0890354, 0.0890247, 0.0890354, 0.0890354, 0.0890247, 0.0890354, 0.0890354, 0.0890247, 0.0890354, 0.0890354};
-	const double ring_phi[12] = {4.97426, 5.49739, 6.02132, 0.261868, 0.785398, 1.30893, 1.83266, 2.35619, 2.87972, 3.40346, 3.92699, 4.45052};
-	/*************************/
-
-	static constexpr double threshold = 0.6; //MeV
-	static constexpr double deg2rad = M_PI/180.0;
-	static constexpr double si_thickness = 1000 * 1e-4 * 2.3926 * 1e6; //thickness in um -> eff thickness in ug/cm^2 for detector
-};
-
-#endif

include/AngularDistribution.h

@@ -1,34 +0,0 @@
-#ifndef ANGULARDISTRIBUTION_H
-#define ANGULARDISTRIBUTION_H
-
-#include <string>
-#include <vector>
-#include <random>
-
-namespace Mask {
-
-	class AngularDistribution {
-	public:
-		AngularDistribution();
-		AngularDistribution(const std::string& file);
-		~AngularDistribution();
-		void ReadDistributionFile(const std::string& file);
-		double GetRandomCosTheta();
-		inline int GetL() { return L; }
-		inline double GetBranchingRatio() { return branchingRatio; }
-	
-	private:
-		inline bool IsIsotropic() { return isoFlag; }
-		
-		std::uniform_real_distribution<double> uniform_cosine_dist;
-		std::uniform_real_distribution<double> uniform_prob_dist;
-	
-		double branchingRatio;
-		int L;
-		std::vector<double> constants;
-		bool isoFlag;
-	};
-
-}
-
-#endif

include/DecaySystem.h

@@ -1,41 +0,0 @@
-#ifndef DECAYSYSTEM_H
-#define DECAYSYSTEM_H
-
-#include "ReactionSystem.h"
-#include "AngularDistribution.h"
-
-namespace Mask {
-
-	class DecaySystem: public ReactionSystem {
-	public:
-		DecaySystem();
-		DecaySystem(std::vector<int>& z, std::vector<int>& a);
-		~DecaySystem();
-	
-		bool SetNuclei(std::vector<int>& z, std::vector<int>& a) override;
-		void RunSystem() override;
-		const std::vector<Nucleus>& GetNuclei() override;
-	
-		inline void SetDecay1Distribution(const std::string& filename) { decay1dist.ReadDistributionFile(filename); }
-	
-		inline const Nucleus& GetTarget() const { return step1.GetTarget(); }
-		inline const Nucleus& GetEjectile() const { return step1.GetEjectile(); }
-		inline const Nucleus& GetResidual() const { return step1.GetResidual(); }
-	
-		inline int GetDecay1AngularMomentum() { return decay1dist.GetL(); }
-		inline double GetDecay1BranchingRatio() { return decay1dist.GetBranchingRatio(); }
-	
-	
-	private:
-		void LinkTarget() override;
-		void SetSystemEquation() override;
-	
-		Reaction step1;
-	
-		AngularDistribution decay1dist;
-		
-	};
-
-}
-
-#endif

include/MaskApp.h

@@ -1,38 +0,0 @@
-#ifndef MASKAPP_H
-#define MASKAPP_H
-
-#include "ReactionSystem.h"
-#include "DecaySystem.h"
-#include "OneStepSystem.h"
-#include "TwoStepSystem.h"
-#include "ThreeStepSystem.h"
-#include "RxnType.h"
-
-namespace Mask {
-
-	class MaskApp {
-	public:
-		MaskApp();
-		~MaskApp();
-		bool LoadConfig(const std::string& filename);
-		bool SaveConfig(const std::string& filename);
-		inline int GetNumberOfSamples() const { return m_nsamples; };
-		inline const std::string GetSystemName() const { return m_sys == nullptr ? "" : m_sys->GetSystemEquation(); };
-		inline const std::string GetOutputName() const { return m_outfile_name; };
-		inline const RxnType GetReactionType() const { return m_rxn_type; };
-		void Run();
-
-	private:
-	
-		ReactionSystem* m_sys;
-	
-		std::string m_outfile_name;
-	
-		RxnType m_rxn_type;
-		int m_nsamples;
-	
-	};
-
-}
-
-#endif

include/Nucleus.h

@@ -1,64 +0,0 @@
-/*
-	Nucleus.h
-	Nucleus is a derived class of Vec4. A nucleus is the kinematics is essentially a 4 vector with the
-	additional properties of the number of total nucleons (A), the number of protons (Z), a ground state mass,
-	an exctitation energy, and an isotopic symbol.
-
-	--GWM Jan 2021
-*/
-#ifndef NUCLEUS_H
-#define NUCLEUS_H
-
-#include "Vec4.h"
-#include <string>
-
-namespace Mask {
-
-class Nucleus : public Vec4 {
-public:
-	Nucleus();
-	Nucleus(int Z, int A);
-	Nucleus(int Z, int A, double px, double py, double pz, double E);
-	virtual ~Nucleus() override;
-	bool SetIsotope(int Z, int A);
-	inline void SetThetaCM(double tcm) { m_theta_cm = tcm; }; //save theta in rxn CM frame
-	inline int GetZ() const { return m_z; };
-	inline int GetA() const { return m_a; };
-	inline double GetExcitationEnergy() const { return GetInvMass() - m_gs_mass; };
-	inline double GetGroundStateMass() const { return m_gs_mass; };
-	inline const char* GetIsotopicSymbol() const { return m_symbol.c_str(); };
-	inline double GetThetaCM() const { return m_theta_cm; };
-	inline void SetDetected() { m_detectFlag = true; };
-	inline void SetNotDetected() { m_detectFlag = false; };
-	inline bool IsDetected() const { return m_detectFlag; };
-
-	inline Nucleus& operator=(const Nucleus& rhs) {
-		SetIsotope(rhs.GetZ(), rhs.GetA());
-		SetVectorCartesian(rhs.GetPx(), rhs.GetPy(), rhs.GetPz(), rhs.GetE());
-		SetThetaCM(rhs.GetThetaCM());
-		return *this;
-	};
-
-	//Conservation of nucleons and momentum
-	inline Nucleus operator+(const Nucleus& daughter) {
-		return Nucleus(GetZ()+daughter.GetZ(), GetA()+daughter.GetA(), GetPx()+daughter.GetPx(), GetPy()+daughter.GetPy(), GetPz()+daughter.GetPz(), GetE()+daughter.GetE()); 
-	};
-	inline Nucleus operator-(const Nucleus& daughter) {
-		return (GetZ() - daughter.GetZ()) <= 0 || (GetA() - daughter.GetA()) <= 0 ? Nucleus() :
-				Nucleus(GetZ()-daughter.GetZ(), GetA() - daughter.GetA(), GetPx()-daughter.GetPx(), GetPy()-daughter.GetPy(), GetPz()-daughter.GetPz(), GetE()-daughter.GetE());
-
-	};
-
-private:
-	int m_z, m_a;
-	double m_gs_mass;
-	double m_theta_cm;
-	std::string m_symbol;
-
-	bool m_detectFlag;
-
-};
-
-};
-
-#endif

include/OneStepSystem.h

@@ -1,34 +0,0 @@
-#ifndef ONESTEPSYSTEM_H
-#define ONESTEPSYSTEM_H
-
-#include "ReactionSystem.h"
-
-namespace Mask {
-
-	class OneStepSystem: public ReactionSystem {
-	public:
-		OneStepSystem();
-		OneStepSystem(std::vector<int>& z, std::vector<int>& a);
-		~OneStepSystem();
-	
-		bool SetNuclei(std::vector<int>& z, std::vector<int>& a) override;
-		void RunSystem() override;
-		const std::vector<Nucleus>& GetNuclei() override;
-	
-		inline void SetReactionThetaType(int type) { step1.SetEjectileThetaType(type); };
-		inline const Nucleus& GetTarget() const { return step1.GetTarget(); };
-		inline const Nucleus& GetProjectile() const { return step1.GetProjectile(); };
-		inline const Nucleus& GetEjectile() const { return step1.GetEjectile(); };
-		inline const Nucleus& GetResidual() const { return step1.GetResidual(); };
-	
-	private:
-		void LinkTarget() override;
-		void SetSystemEquation() override;
-	
-		Reaction step1;
-	
-	};
-
-}
-
-#endif

include/QQQDetector.h

@@ -1,57 +0,0 @@
-/*
-	QQQDetector.h
-	Class implementing geometry for QQQDetector where the detector is perpendicular to the beam axis.
-	Detector is first generated centered on the x-axis (phi=0)
-
-	Coordinate convention : +z is downstream, -z is upstream. +y is vertically down in the lab.
-*/
-#ifndef QQQDETECTOR_H
-#define QQQDETECTOR_H
-
-#include <cmath>
-#include <vector>
-#include <random>
-
-#include "Vec3.h"
-#include "Rotation.h"
-#include "RandomGenerator.h"
-
-class QQQDetector {
-public:
-	QQQDetector(double R_in, double R_out, double deltaPhi, double phiCentral, double z, double x=0, double y=0);
-	~QQQDetector();
-	inline Mask::Vec3 GetRingCoordinates(int ringch, int corner) { return m_ringCoords[ringch][corner]; }
-	inline Mask::Vec3 GetWedgeCoordinates(int wedgech, int corner) { return m_wedgeCoords[wedgech][corner]; }
-	inline Mask::Vec3 GetNorm() { return m_norm; }
-	Mask::Vec3 GetTrajectoryCoordinates(double theta, double phi);
-	std::pair<int, int> GetTrajectoryRingWedge(double theta, double phi);
-	Mask::Vec3 GetHitCoordinates(int ringch, int wedgech);
-	inline void TurnOnRandomizedCoordinates() { rndmFlag = true; }
-	inline void TurnOffRandomizedCoordinates() { rndmFlag = false; }
-
-	inline int GetNumberOfRings() { return nrings; }
-	inline int GetNumberOfWedges() { return nwedges; }
-
-private:
-
-	inline bool CheckChannel(int ch) { return (ch >=0 && ch < nrings); }
-	inline bool CheckCorner(int corner) { return (corner >=0 && corner < 4); }
-
-	void CalculateCorners();
-	Mask::Vec3 TransformCoordinates(Mask::Vec3& vector) { return m_ZRot*vector + m_translation; }
-
-	double m_Rinner, m_Router, m_deltaR, m_deltaPhi, m_deltaPhi_per_wedge, m_phiCentral;
-	std::vector<std::vector<Mask::Vec3>> m_ringCoords, m_wedgeCoords;
-	Mask::Vec3 m_translation;
-	Mask::Vec3 m_norm;
-	Mask::ZRotation m_ZRot;
-
-	std::uniform_real_distribution<double> m_uniform_fraction;
-	bool rndmFlag;
-
-	static constexpr int nrings = 16;
-	static constexpr int nwedges = 16;
-	static constexpr double deg2rad  = M_PI/180.0;
-};
-
-#endif

include/RandomGenerator.h

@@ -1,25 +0,0 @@
-#ifndef RANDOMGENERATOR_H
-#define RANDOMGENERATOR_H
-
-#include <random>
-
-namespace Mask {
-
-	class RandomGenerator {
-	public:
-		~RandomGenerator();
-		inline std::mt19937& GetGenerator() { return rng; }
-
-		inline static RandomGenerator& GetInstance() {
-			static RandomGenerator s_instance;
-			return s_instance;
-		}
-
-	private:
-		RandomGenerator();
-		std::mt19937 rng;
-	};
-
-}
-
-#endif

include/Reaction.h

@@ -1,78 +0,0 @@
-/*
-	Reaction.h
-	Reaction is a class which implements either a decay or scattering reaction. As such it requires either
-	3 (decay) or 4 (scattering) nuclei to perform any calcualtions. I also links together the target, which provides
-	energy loss calculations, with the kinematics. Note that Reaction does not own the LayeredTarget.
-
-	--GWM Jan. 2021
-*/
-#ifndef REACTION_H
-#define REACTION_H
-
-#include "Nucleus.h"
-#include "LayeredTarget.h"
-
-namespace Mask {
-
-	class Reaction {
-	public:
-		Reaction();
-		Reaction(int zt, int at, int zp, int ap, int ze, int ae);
-		~Reaction();
-		bool Calculate();
-		void SetNuclei(int zt, int at, int zp, int ap, int ze, int ae);
-		void SetNuclei(const Nucleus* nucs);
-		void SetBeamKE(double bke);
-		void SetEjectileThetaType(int type);
-	
-		inline void SetLayeredTarget(LayeredTarget* targ) { target = targ; };
-		inline void SetPolarRxnAngle(double theta) { m_theta = theta; };
-		inline void SetAzimRxnAngle(double phi) { m_phi = phi; };
-		inline void SetExcitation(double ex) { m_ex = ex; };
-		inline void SetTarget(const Nucleus& nuc) { reactants[0] = nuc; };
-		inline void SetTarget(int z, int a) { reactants[0] = Nucleus(z, a); };
-		inline void SetProjectile(const Nucleus& nuc) { reactants[1] = nuc; };
-		inline void SetProjectile(int z, int a) { reactants[1] = Nucleus(z, a); };
-		inline void SetEjectile(const Nucleus& nuc) { reactants[2] = nuc; };
-		inline void SetEjectile(int z, int a) { reactants[2] = Nucleus(z, a); };
-		inline void SetResidual(const Nucleus& nuc) { reactants[3] = nuc; };
-		inline void SetResidual(int z, int a) { reactants[3] = Nucleus(z, a); };
-		inline void SetRxnLayer(int layer) { rxnLayer = layer; };
-		inline void TurnOffResidualEloss() { resid_elossFlag = false; };
-		inline void TurnOnResidualEloss() { resid_elossFlag = true; };
-		inline bool IsDecay() { return decayFlag; };
-		inline const Nucleus* GetNuclei() const { return &(reactants[0]); };
-		inline const Nucleus& GetProjectile() const { return reactants[1]; };
-		inline const Nucleus& GetTarget() const { return reactants[0]; };
-		inline const Nucleus& GetEjectile() const { return reactants[2]; };
-		inline const Nucleus& GetResidual() const { return reactants[3]; };
-		inline int GetRxnLayer() { return rxnLayer; };
-		inline void ResetTarget() { reactants[0].SetVectorCartesian(0,0,0, reactants[0].GetGroundStateMass()); }
-		inline void ResetProjectile() { reactants[1].SetVectorCartesian(0,0,0, reactants[1].GetGroundStateMass()); }
-		inline void ResetEjectile() { reactants[2].SetVectorCartesian(0,0,0, reactants[2].GetGroundStateMass()); }
-		inline void ResetResidual() { reactants[3].SetVectorCartesian(0,0,0, reactants[3].GetGroundStateMass()); }
-	
-	private:
-		void CalculateDecay(); //target -> light_decay (eject) + heavy_decay(resid)
-		void CalculateReaction(); //target + project -> eject + resid
-		void CalculateReactionThetaLab();
-		void CalculateReactionThetaCM();
-	
-		Nucleus reactants[4]; //0=target, 1=projectile, 2=ejectile, 3=residual
-		LayeredTarget* target; //not owned by Reaction
-	
-		double m_bke, m_theta, m_phi, m_ex;
-	
-		int rxnLayer;
-		int m_eject_theta_type; 
-	
-		bool decayFlag, nuc_initFlag, resid_elossFlag;
-	
-		static constexpr int lab = 0;
-		static constexpr int center_of_mass = 1;
-	
-	};
-
-}
-
-#endif

include/RootPlotter.h

@@ -1,52 +0,0 @@
-#ifndef ROOTPLOTTER_H
-#define ROOTPLOTTER_H
-
-#include <vector>
-#include <string>
-
-#include "Nucleus.h"
-#include "RxnType.h"
-#include "MaskFile.h"
-
-#include <THashTable.h>
-#include <TH1.h>
-#include <TH2.h>
-#include <TGraph.h>
-
-struct GraphData {
-	std::string name;
-	std::string title;
-	std::vector<double> xvec;
-	std::vector<double> yvec;
-	int color;
-};
-
-class RootPlotter {
-public:
-	RootPlotter();
-	~RootPlotter();
-	inline void ClearTable() { table->Clear(); };
-	inline THashTable* GetTable() {
-		GenerateGraphs(); 
-		return table; 
-	};
-	void FillData(const Mask::Nucleus& nuc, double detKE = 0.0, const std::string& modifier = "");
-	void FillCorrelations(const Mask::MaskFileData& data, Mask::RxnType type);
-	void FillCorrelationsDetected(const Mask::MaskFileData& data, Mask::RxnType type);
-
-private:
-	THashTable* table;
-
-	void GenerateGraphs();
-	void MyFill(const std::string& name, const std::string& title, int bins, float min, float max, double val);
-	void MyFill(const std::string& name, const std::string& title, int binsx, float minx, float maxx, int binsy, float miny, float maxy, double valx, double valy);
-	void MyFill(const std::string& name, const std::string& title, double valx, double valy, int color); //TGraph
-
-	std::vector<TGraph*> garbage_collection;
-	std::vector<GraphData> graphs;
-
-	static constexpr double rad2deg = 180.0/M_PI;
-
-};
-
-#endif

include/SabreDetector.h

@@ -1,177 +0,0 @@
-/*
-
-  Class which represents a single MMM detector in the SABRE array at FSU. Origial code by KGH, re-written by
-  GWM.
-
-  Distances in meters, angles in radians.
-
-  The channel arrays have four points, one for each corner. The corners are
-  as follows, as if looking BACK along beam (i.e. from the target's pov):
-
-  0---------------------1
-  |                     |
-  |                     |      x
-  |                     |      <-----
-  |                     |      		|
-  |                     |      		|
-  3---------------------2      		y
-                               (z is hence positive along beam direction) 
-
-  The channel numbers, also as looking back from target pov, are:
-
-  >> rings are 0 -- 15 from inner to outer:
-
-    15 -------------------
-    14 -------------------
-    13 -------------------
-       .
-       .
-       .
-     2 -------------------
-     1 -------------------
-     0 -------------------
-
-  >> wedges are 0 -- 7 moving counterclockwise:
-
-      7 6 ... 1 0
-     | | |   | | |
-     | | |   | | |
-     | | |   | | |
-     | | |   | | |
-     | | |   | | |
-     | | |   | | |
-
-
-  >> Note that the detector starts centered on the x-axis (central phi = 0) untilted, and then is rotated to wherever the frick
-  	 it is supposed to go; phi = 90 is centered on y axis, pointing down towards the bottom of the scattering chamber
-
-  -- GWM, Dec 2020; based on the og code from kgh
-
-*/
-
-#ifndef SABREDETECTOR_H
-#define SABREDETECTOR_H
-
-#include <vector>
-#include <cmath>
-
-#include "Vec3.h"
-#include "Rotation.h"
-
-class SabreDetector {
-public:
-
-	SabreDetector();
-	SabreDetector(int detID, double Rin, double Rout, double deltaPhi_flat, double phiCentral, double tiltFromVert, double zdist, double xdist=0, double ydist=0);
-	~SabreDetector();
-
-	/*Return coordinates of the corners of each ring/wedge in SABRE*/
-	inline Mask::Vec3 GetRingFlatCoords(int ch, int corner) { return CheckRingLocation(ch, corner) ? m_ringCoords_flat[ch][corner] : Mask::Vec3(); };
-	inline Mask::Vec3 GetWedgeFlatCoords(int ch, int corner) { return CheckWedgeLocation(ch, corner) ? m_wedgeCoords_flat[ch][corner] : Mask::Vec3(); };
-	inline Mask::Vec3 GetRingTiltCoords(int ch, int corner) { return CheckRingLocation(ch, corner) ? m_ringCoords_tilt[ch][corner] : Mask::Vec3(); };
-	inline Mask::Vec3 GetWedgeTiltCoords(int ch, int corner) { return CheckWedgeLocation(ch, corner) ? m_wedgeCoords_tilt[ch][corner] : Mask::Vec3(); };
-
-	Mask::Vec3 GetTrajectoryCoordinates(double theta, double phi);
-	std::pair<int, int> GetTrajectoryRingWedge(double theta, double phi);
-	Mask::Vec3 GetHitCoordinates(int ringch, int wedgech);
-
-	/*Basic getters*/
-	inline int GetNumberOfWedges() { return m_nWedges; };
-	inline int GetNumberOfRings() { return m_nRings; };
-	inline double GetInnerRadius() { return m_Rinner; };
-	inline double GetOuterRadius() { return m_Router; };
-	inline double GetPhiCentral() { return m_phiCentral; };
-	inline double GetTiltAngle() { return m_tilt; };
-	inline Mask::Vec3 GetTranslation() { return m_translation; };
-	inline Mask::Vec3 GetNormTilted() { return TransformToTiltedFrame(m_norm_flat); };
-	int GetDetectorID() { return m_detectorID; }
-
-
-private:
-
-	/*Class constants*/
-	static constexpr int m_nRings = 16;
-	static constexpr int m_nWedges = 8;
-	static constexpr double deg2rad = M_PI/180.0;
-	/*These are implicitly the width of the spacing between detector active strips*/
-	static constexpr double POSITION_TOL = 0.0001; //0.1 mm position tolerance
-	static constexpr double ANGULAR_TOL = 0.1*M_PI/180.0; // 0.1 degree angular tolerance
-
-	void CalculateCorners();
-
-	/*Performs the transformation to the tilted,rotated,translated frame of the SABRE detector*/
-	inline Mask::Vec3 TransformToTiltedFrame(Mask::Vec3& vector) { return (m_ZRot*(m_YRot*vector)) + m_translation; };
-
-	/*Determine if a given channel/corner combo is valid*/
-	inline bool CheckRingChannel(int ch) { return (ch<m_nRings && ch>=0) ? true : false; };
-	inline bool CheckWedgeChannel(int ch) { return (ch<m_nWedges && ch >=0) ? true : false; };
-	inline bool CheckCorner(int corner) { return (corner < 4 && corner >=0) ? true : false; };
-	inline bool CheckRingLocation(int ch, int corner) { return CheckRingChannel(ch) && CheckCorner(corner); };
-	inline bool CheckWedgeLocation(int ch, int corner) { return CheckWedgeChannel(ch) && CheckCorner(corner); };
-
-	/*
-		For all of the calculations, need a limit precision to determine if values are actually equal or not
-		Here the approx. size of the strip spacing is used as the precision.
-	*/
-	inline bool CheckPositionEqual(double val1,double val2) { return fabs(val1-val2) > POSITION_TOL ? false : true; };
-	inline bool CheckAngleEqual(double val1,double val2) { return fabs(val1-val2) > ANGULAR_TOL ? false : true; };
-
-	/*Determine if a hit is within the bulk detector*/
-	inline bool IsInside(double r, double phi) { 
-		double phi_1 = m_deltaPhi_flat/2.0;
-		double phi_2 = M_PI*2.0 - m_deltaPhi_flat/2.0;
-		return (((r > m_Rinner && r < m_Router) || CheckPositionEqual(r, m_Rinner) || CheckPositionEqual(r, m_Router)) && (phi > phi_2 || phi < phi_1 || CheckAngleEqual(phi, phi_1) || CheckAngleEqual(phi, phi_2)));
-	};
-
-	/*
-		For a given radius/phi are you inside of a given ring/wedge channel,
-		or are you on the spacing between these channels
-	*/
-	inline bool IsRing(double r, int ringch) {
-		double ringtop = m_Rinner + m_deltaR_flat_ring*(ringch + 1);
-		double ringbottom = m_Rinner + m_deltaR_flat_ring*(ringch);
-		return (r>ringbottom && r<ringtop); 
-	};
-
-	inline bool IsRingTopEdge(double r, int ringch) {
-		double ringtop = m_Rinner + m_deltaR_flat_ring*(ringch + 1);
-		return CheckPositionEqual(r, ringtop); 
-	};
-
-	inline bool IsRingBottomEdge(double r, int ringch) {
-		double ringbottom = m_Rinner + m_deltaR_flat_ring*(ringch);
-		return CheckPositionEqual(r, ringbottom); 
-	};
-
-	inline bool IsWedge(double phi, int wedgech) {
-		double wedgetop = -m_deltaPhi_flat/2.0 + m_deltaPhi_flat_wedge*(wedgech+1);
-		double wedgebottom = -m_deltaPhi_flat/2.0 + m_deltaPhi_flat_wedge*(wedgech);
-		return ((phi>wedgebottom && phi<wedgetop));
-	};
-
-	inline bool IsWedgeTopEdge(double phi, int wedgech) {
-		double wedgetop = -m_deltaPhi_flat/2.0 + m_deltaPhi_flat_wedge*(wedgech+1);
-		return CheckAngleEqual(phi, wedgetop);
-	}
-
-	inline bool IsWedgeBottomEdge(double phi, int wedgech) {
-		double wedgebottom = -m_deltaPhi_flat/2.0 + m_deltaPhi_flat_wedge*(wedgech);
-		return CheckAngleEqual(phi, wedgebottom);
-	}
-
-	/*Class data*/
-	double m_Router, m_Rinner, m_deltaPhi_flat, m_phiCentral, m_tilt;
-	Mask::Vec3 m_translation;
-	Mask::YRotation m_YRot;
-	Mask::ZRotation m_ZRot;
-	double m_deltaR_flat, m_deltaR_flat_ring, m_deltaPhi_flat_wedge;
-	Mask::Vec3 m_norm_flat;
-	int m_detectorID;
-
-	std::vector<std::vector<Mask::Vec3>> m_ringCoords_flat, m_wedgeCoords_flat;
-	std::vector<std::vector<Mask::Vec3>> m_ringCoords_tilt, m_wedgeCoords_tilt;
-
-};
-
-
-#endif

include/SabreEfficiency.h

@@ -1,51 +0,0 @@
-#ifndef SABREEFFICIENCY_H
-#define SABREEFFICIENCY_H
-
-#include "MaskFile.h"
-#include "DetectorEfficiency.h"
-#include "SabreDetector.h"
-#include "Target.h"
-#include "SabreDeadChannelMap.h"
-#include "Nucleus.h"
-
-class SabreEfficiency : public DetectorEfficiency {
-public:
-	SabreEfficiency();
-	~SabreEfficiency();
-    void SetDeadChannelMap(std::string& filename) { dmap.LoadMapfile(filename); };
-	void CalculateEfficiency(const std::string& inputname, const std::string& outputname, const std::string& statsname) override;
-    void DrawDetectorSystem(const std::string& filename) override;
-    double RunConsistencyCheck() override;
-
-private:
-	std::pair<bool,double> IsSabre(Mask::Nucleus& nucleus);
-    void CountCoincidences(const Mask::MaskFileData& data, std::vector<int>& counts, Mask::RxnType rxn_type);
-
-	std::vector<SabreDetector> detectors;
-    
-	Mask::Target deadlayer;
-    Mask::Target sabre_eloss;
-    Mask::Target degrader;
-    SabreDeadChannelMap dmap;
-
-	//Sabre constants
-	const double INNER_R = 0.0326;
-    const double OUTER_R = 0.1351;
-    const double TILT = 40.0;
-    const double DIST_2_TARG = -0.1245;
-    const double PHI_COVERAGE = 54.4; //delta phi for each det
-    const double PHI0 = 306.0; //center phi values for each det in array
-    const double PHI1 = 18.0; //# is equal to detID in channel map
-    const double PHI2 = 234.0;
-    const double PHI3 = 162.0;
-    const double PHI4 = 90.0;
-    const double DEG2RAD = M_PI/180.0;
-    static constexpr double DEADLAYER_THIN = 50 * 1e-7 * 2.3296 * 1e6; // ug/cm^2 (50 nm thick * density)
-    static constexpr double SABRE_THICKNESS = 500 * 1e-4 * 2.3926 * 1e6; // ug/cm^2 (500 um thick * density)
-    static constexpr double DEGRADER_THICKNESS = 70.0 * 1.0e-4 * 16.69 * 1e6; //tantalum degrader (70 um thick) 
-
-    const double ENERGY_THRESHOLD = 0.25; //in MeV
-
-};
-
-#endif

include/Stopwatch.h

@@ -1,30 +0,0 @@
-/*
-	Stopwatch.h
-	Simple class designed to provide timing info on parts of the process.
-	Only for use in development.
-
-	Written by G.W. McCann Oct. 2020
-*/
-#ifndef STOPWATCH_H
-#define STOPWATCH_H
-
-#include <chrono>
-
-class Stopwatch {
-
-public:
-	Stopwatch();
-	~Stopwatch();
-	void Start();
-	void Stop();
-	double GetElapsedSeconds();
-	double GetElapsedMilliseconds();
-
-private:
-	using Time = std::chrono::high_resolution_clock::time_point;
-	using Clock = std::chrono::high_resolution_clock;
-
-	Time start_time, stop_time;
-};
-
-#endif

include/StripDetector.h

@@ -1,76 +0,0 @@
-#ifndef __STRIP_DETECTOR_H
-#define __STRIP_DETECTOR_H
-
-// +z is along beam axis
-// +y is vertically "downward" in the lab frame
-
-//angles must be in radians, but distances can be whatever
-//PROVIDED all input distances are the same
-
-//Front strips from largest y to smallest y
-
-//Back strips from lowest z to highest z
-
-#include <cmath>
-#include <vector>
-#include <random>
-
-#include "Vec3.h"
-#include "Rotation.h"
-#include "RandomGenerator.h"
-
-struct StripHit
-{
-	int front_strip_index=-1;
-	int back_strip_index=-1;
-	double front_ratio=0.0;
-};
-
-class StripDetector {
-public:
-  
-	StripDetector(int ns, double len, double wid, double cphi, double cz, double crho);
-	~StripDetector();
-	inline Mask::Vec3 GetFrontStripCoordinates(int stripch, int corner) { return front_strip_coords[stripch][corner]; }
-	inline Mask::Vec3 GetBackStripCoordinates(int stripch, int corner) { return back_strip_coords[stripch][corner]; }
-	inline Mask::Vec3 GetRotatedFrontStripCoordinates(int stripch, int corner) { return rotated_front_strip_coords[stripch][corner]; }
-	inline Mask::Vec3 GetRotatedBackStripCoordinates(int stripch, int corner) { return rotated_back_strip_coords[stripch][corner]; }
-	inline Mask::Vec3 GetNormRotated() { return zRot*m_norm_unrot; }
-
-	inline void TurnOnRandomizedCoordinates() { rndmFlag = true; }
-	inline void TurnOffRandomizedCoordinates() { rndmFlag = false; }
-
-	Mask::Vec3 GetHitCoordinates(int front_stripch, double front_strip_ratio);
-	StripHit GetChannelRatio(double theta, double phi);
-
-private:
-	inline bool ValidChannel(int f) { return ((f >= 0 && f < num_strips) ? true : false); };
-	inline bool ValidRatio(double r) { return ((r >= -1 && r <= 1) ? true : false); };
-	void CalculateCorners();
-
-	int num_strips;
-	static constexpr int num_corners = 4;
-
-	double length; //common to all strips, hence total
-	double total_width;
-	double front_strip_width; //assuming equal widths
-	double back_strip_length; //assuming equal widths
-
-	double center_phi; //assuming det centered above x-axis (corresponds to zero phi)
-	double center_z;
-	double center_rho; //perpendicular radius from axis
-
-	std::vector<std::vector<Mask::Vec3>> front_strip_coords, back_strip_coords;
-	std::vector<std::vector<Mask::Vec3>> rotated_front_strip_coords, rotated_back_strip_coords;
-
-	Mask::Vec3 m_norm_unrot;
-
-	Mask::ZRotation zRot;
-
-	std::uniform_real_distribution<double> m_uniform_fraction;
-
-	bool rndmFlag;
-
-};
-
-#endif

include/ThreeStepSystem.h

@@ -1,50 +0,0 @@
-#ifndef THREESTEPSYSTEM_H
-#define THREESTEPSYSTEM_H
-
-#include "ReactionSystem.h"
-#include "AngularDistribution.h"
-
-namespace Mask {
-
-	class ThreeStepSystem : public ReactionSystem {
-	public:
-		ThreeStepSystem();
-		ThreeStepSystem(std::vector<int>& z, std::vector<int>& a);
-		~ThreeStepSystem();
-		bool SetNuclei(std::vector<int>& z, std::vector<int>& a) override;
-		void RunSystem() override;
-		const std::vector<Nucleus>& GetNuclei() override;
-	
-		inline void SetDecay1Distribution(const std::string& filename) { decay1dist.ReadDistributionFile(filename); };
-		inline void SetDecay2Distribution(const std::string& filename) { decay2dist.ReadDistributionFile(filename); };
-	
-		inline void SetReactionThetaType(int type) { step1.SetEjectileThetaType(type); };
-		inline const Nucleus& GetTarget() const { return step1.GetTarget(); };
-		inline const Nucleus& GetProjectile() const { return step1.GetProjectile(); };
-		inline const Nucleus& GetEjectile() const { return step1.GetEjectile(); };
-		inline const Nucleus& GetResidual() const { return step1.GetResidual(); };
-		inline const Nucleus& GetBreakup1() const { return step2.GetEjectile(); };
-		inline const Nucleus& GetBreakup2() const { return step2.GetResidual(); };
-		inline const Nucleus& GetBreakup3() const { return step3.GetEjectile(); };
-		inline const Nucleus& GetBreakup4() const { return step3.GetResidual(); };
-	
-		inline int GetDecay1AngularMomentum() { return decay1dist.GetL(); };
-		inline int GetDecay2AngularMomentum(){ return decay2dist.GetL(); };
-		inline double GetDecay1BranchingRatio() { return decay1dist.GetBranchingRatio(); };
-		inline double GetDecay2BranchingRatio(){ return decay2dist.GetBranchingRatio(); };
-	
-	protected:
-		void LinkTarget() override;
-		void SetSystemEquation() override;
-
-		std::uniform_real_distribution<double> m_phi2Range;
-	
-		Reaction step1, step2, step3;
-	
-		AngularDistribution decay1dist, decay2dist;
-	
-	};
-
-}
-
-#endif

include/TwoStepSystem.h

@@ -1,45 +0,0 @@
-#ifndef TWOSTEPSYSTEM_H
-#define TWOSTEPSYSTEM_H
-
-#include "ReactionSystem.h"
-#include "AngularDistribution.h"
-
-namespace Mask {
-
-	class TwoStepSystem : public ReactionSystem {
-	public:
-		TwoStepSystem();
-		TwoStepSystem(std::vector<int>& z, std::vector<int>& a);
-		~TwoStepSystem();
-		bool SetNuclei(std::vector<int>& z, std::vector<int>& a) override;
-		void RunSystem() override;
-		const std::vector<Nucleus>& GetNuclei() override;
-	
-		inline void SetDecay1Distribution(const std::string& filename) { decay1dist.ReadDistributionFile(filename); };
-	
-		inline void SetReactionThetaType(int type) { step1.SetEjectileThetaType(type); };
-		inline const Nucleus& GetTarget() const { return step1.GetTarget(); };
-		inline const Nucleus& GetProjectile() const { return step1.GetProjectile(); };
-		inline const Nucleus& GetEjectile() const { return step1.GetEjectile(); };
-		inline const Nucleus& GetResidual() const { return step1.GetResidual(); };
-		inline const Nucleus& GetBreakup1() const { return step2.GetEjectile(); };
-		inline const Nucleus& GetBreakup2() const { return step2.GetResidual(); };
-	
-		inline int GetDecay1AngularMomentum() { return decay1dist.GetL(); };
-		inline double GetDecay1BranchingRatio() { return decay1dist.GetBranchingRatio(); };
-	
-	private:
-		void LinkTarget() override;
-		void SetSystemEquation() override;
-
-		std::uniform_real_distribution<double> m_phi2Range;
-		
-		Reaction step1, step2;
-	
-		AngularDistribution decay1dist;
-	
-	};
-
-}
-
-#endif

input.txt

@@ -1,28 +1,26 @@
 ----------Data Information----------
-OutputFile: /data1/gwm17/7BeNov2021/sim/7Bedp_1100keV_beam_50CD2.mask
+OutputFile: /media/data/gwm17/mask_tests/10B3Hea_test.root
 ----------Reaction Information----------
-ReactionType: TwoStepRxn
+ReactionType: OneStepRxn
 Z	A (order is target, projectile, ejectile, break1, break3(if pure decay is target, ejectile))
-1	2
+5	10
-4	7
+2	3
-1	1
 2	4
 ----------Target Information----------
 NumberOfLayers: 1
 begin_layer
 	Thickness(ug/cm^2): 50
 	begin_elements (Z, A, Stoich.)
-		element	1 2 2
+		element	5 10 1
-		element	6 12 1
 	end_elements
 end_layer
 ----------Sampling Information----------
-NumberOfSamples: 100000
+NumberOfSamples: 1000
-BeamMeanEnergy(MeV): 1.1 BeamEnergySigma(MeV): 0.0
+BeamMeanEnergy(MeV): 24.0 BeamEnergySigma(MeV): 0.0
 EjectileThetaType(0=Lab,1=CM): 1
 EjectileThetaMin(deg): 0.0 EjectileThetaMax(deg): 180.0
 EjectilePhiMin(deg): 0.0 EjectilePhiMax(deg): 360.0
-ResidualExMean(MeV): 0.0 ResidualExSigma(MeV): 0.0
+ResidualExMean(MeV): 16.8 ResidualExSigma(MeV): 0.023
 Decay1_DistributionFile: ./etc/isotropic_dist.txt
 Decay2_DistributionFile: ./etc/isotropic_dist.txt
 --------------------------------------

src/Detectors/AnasenDeadChannelMap.h

@@ -25,7 +25,7 @@ public:
 	AnasenDeadChannelMap(const std::string& filename);
 	~AnasenDeadChannelMap();
 	void LoadMapfile(const std::string& filename);
-	inline const bool IsValid() const { return valid_flag; }
+	const bool IsValid() const { return valid_flag; }
 	const bool IsDead(AnasenDetectorType type, int detIndex, int channel, AnasenDetectorSide side) const;
 private:
 	void InitMap();

src/Detectors/AnasenEfficiency.cpp

@@ -3,194 +3,221 @@
 #include <iomanip>
 #include <iostream>
 
+#include "TFile.h"
+#include "TTree.h"
+
 AnasenEfficiency::AnasenEfficiency() :
-	DetectorEfficiency(), det_silicon(si_thickness)
+	DetectorEfficiency(), m_detectorEloss({14}, {28}, {1}, s_detectorThickness)
 {
-	for(int i=0; i<n_sx3_per_ring; i++) {
+	for(int i=0; i<s_nSX3PerBarrel; i++)
-		m_Ring1.emplace_back(4, sx3_length, sx3_width, ring_phi[i], ring1_z, ring_rho[i]);
+	{
-		m_Ring1[i].TurnOnRandomizedCoordinates();
+		m_Ring1.emplace_back(4, s_sx3Length, s_sx3Width, s_barrelPhiList[i], s_barrel1Z, s_barrelRhoList[i]);
-		m_Ring2.emplace_back(4, sx3_length, sx3_width, ring_phi[i], ring2_z, ring_rho[i]);
+		m_Ring1[i].SetPixelSmearing(true);
-		m_Ring2[i].TurnOnRandomizedCoordinates();
+		m_Ring2.emplace_back(4, s_sx3Length, s_sx3Width, s_barrelPhiList[i], s_barrel2Z, s_barrelRhoList[i]);
+		m_Ring2[i].SetPixelSmearing(true);
 	}
-	for(int i=0; i<n_qqq; i++) {
+	for(int i=0; i<s_nQQQ; i++)
-		m_forwardQQQs.emplace_back(qqq_rinner, qqq_router, qqq_deltaphi, qqq_phi[i], qqq_z[i]);
+	{
-		m_forwardQQQs[i].TurnOnRandomizedCoordinates();
+		m_forwardQQQs.emplace_back(s_qqqInnerR, s_qqqOuterR, s_qqqDeltaPhi, s_qqqPhiList[i], s_qqqZList[i]);
-		m_backwardQQQs.emplace_back(qqq_rinner, qqq_router, qqq_deltaphi, qqq_phi[i], (-1.0)*qqq_z[i]);
+		m_forwardQQQs[i].SetSmearing(true);
-		m_backwardQQQs[i].TurnOnRandomizedCoordinates();
+		m_backwardQQQs.emplace_back(s_qqqInnerR, s_qqqOuterR, s_qqqDeltaPhi, s_qqqPhiList[i], (-1.0)*s_qqqZList[i]);
+		m_backwardQQQs[i].SetSmearing(true);
 	}
-
-	std::vector<int> det_z = {14};
-	std::vector<int> det_a = {28};
-	std::vector<int> det_stoich = {1};
-	det_silicon.SetElements(det_z, det_a, det_stoich);
-
 }
 
 AnasenEfficiency::~AnasenEfficiency() {}
 
 
-void AnasenEfficiency::DrawDetectorSystem(const std::string& filename) {
+void AnasenEfficiency::DrawDetectorSystem(const std::string& filename)
+{
 	std::ofstream output(filename);
 
 	std::vector<double> x, y, z;
 	std::vector<double> cx, cy, cz;
-	Mask::Vec3 coords;
+	ROOT::Math::XYZPoint coords;
-	for(int i=0; i<n_sx3_per_ring; i++) {
+	for(int i=0; i<s_nSX3PerBarrel; i++)
-		for(int j=0; j<4; j++) {
+	{
-			for(int k=0; k<4; k++) {
+		for(int j=0; j<4; j++)
+		{
+			for(int k=0; k<4; k++)
+			{
 				coords = m_Ring1[i].GetRotatedFrontStripCoordinates(j, k);
-				x.push_back(coords.GetX());
+				x.push_back(coords.X());
-				y.push_back(coords.GetY());
+				y.push_back(coords.Y());
-				z.push_back(coords.GetZ());
+				z.push_back(coords.Z());
 				coords = m_Ring1[i].GetRotatedBackStripCoordinates(j, k);
-				x.push_back(coords.GetX());
+				x.push_back(coords.X());
-				y.push_back(coords.GetY());
+				y.push_back(coords.Y());
-				z.push_back(coords.GetZ());
+				z.push_back(coords.Z());
 			}
 			coords = m_Ring1[i].GetHitCoordinates(j, 0);
-			cx.push_back(coords.GetX());
+			cx.push_back(coords.X());
-			cy.push_back(coords.GetY());
+			cy.push_back(coords.Y());
-			cz.push_back(coords.GetZ());
+			cz.push_back(coords.Z());
 		}
 	}
-	for(int i=0; i<n_sx3_per_ring; i++) {
+	for(int i=0; i<s_nSX3PerBarrel; i++)
-		for(int j=0; j<4; j++) {
+	{
-			for(int k=0; k<4; k++) {
+		for(int j=0; j<4; j++)
+		{
+			for(int k=0; k<4; k++)
+			{
 				coords = m_Ring2[i].GetRotatedFrontStripCoordinates(j, k);
-				x.push_back(coords.GetX());
+				x.push_back(coords.X());
-				y.push_back(coords.GetY());
+				y.push_back(coords.Y());
-				z.push_back(coords.GetZ());
+				z.push_back(coords.Z());
 				coords = m_Ring2[i].GetRotatedBackStripCoordinates(j, k);
-				x.push_back(coords.GetX());
+				x.push_back(coords.X());
-				y.push_back(coords.GetY());
+				y.push_back(coords.Y());
-				z.push_back(coords.GetZ());
+				z.push_back(coords.Z());
 			}
 			coords = m_Ring2[i].GetHitCoordinates(j, 0);
-			cx.push_back(coords.GetX());
+			cx.push_back(coords.X());
-			cy.push_back(coords.GetY());
+			cy.push_back(coords.Y());
-			cz.push_back(coords.GetZ());
+			cz.push_back(coords.Z());
 		}
 	}
-	for(int i=0; i<n_qqq; i++) {
+	for(int i=0; i<s_nQQQ; i++)
-		for(int j=0; j<16; j++) {
+	{
-			for(int k=0; k<4; k++) {
+		for(int j=0; j<16; j++)
+		{
+			for(int k=0; k<4; k++)
+			{
 				coords = m_forwardQQQs[i].GetRingCoordinates(j, k);
-				x.push_back(coords.GetX());
+				x.push_back(coords.X());
-				y.push_back(coords.GetY());
+				y.push_back(coords.Y());
-				z.push_back(coords.GetZ());
+				z.push_back(coords.Z());
 				coords = m_forwardQQQs[i].GetWedgeCoordinates(j, k);
-				x.push_back(coords.GetX());
+				x.push_back(coords.X());
-				y.push_back(coords.GetY());
+				y.push_back(coords.Y());
-				z.push_back(coords.GetZ());
+				z.push_back(coords.Z());
 			}
-			for(int k=0; k<16; k++) {
+			for(int k=0; k<16; k++)
+			{
 				coords = m_forwardQQQs[i].GetHitCoordinates(j, k);
-				cx.push_back(coords.GetX());
+				cx.push_back(coords.X());
-				cy.push_back(coords.GetY());
+				cy.push_back(coords.Y());
-				cz.push_back(coords.GetZ());
+				cz.push_back(coords.Z());
 			}
 		}
 	}
-	for(int i=0; i<n_qqq; i++) {
+	for(int i=0; i<s_nQQQ; i++)
-		for(int j=0; j<16; j++) {
+	{
-			for(int k=0; k<4; k++) {
+		for(int j=0; j<16; j++)
+		{
+			for(int k=0; k<4; k++)
+			{
 				coords = m_backwardQQQs[i].GetRingCoordinates(j, k);
-				x.push_back(coords.GetX());
+				x.push_back(coords.X());
-				y.push_back(coords.GetY());
+				y.push_back(coords.Y());
-				z.push_back(coords.GetZ());
+				z.push_back(coords.Z());
 				coords = m_backwardQQQs[i].GetWedgeCoordinates(j, k);
-				x.push_back(coords.GetX());
+				x.push_back(coords.X());
-				y.push_back(coords.GetY());
+				y.push_back(coords.Y());
-				z.push_back(coords.GetZ());
+				z.push_back(coords.Z());
 			}
-			for(int k=0; k<16; k++) {
+			for(int k=0; k<16; k++)
+			{
 				coords = m_backwardQQQs[i].GetHitCoordinates(j, k);
-				cx.push_back(coords.GetX());
+				cx.push_back(coords.X());
-				cy.push_back(coords.GetY());
+				cy.push_back(coords.Y());
-				cz.push_back(coords.GetZ());
+				cz.push_back(coords.Z());
 			}
 		}
 	}
 
 	output<<"ANASEN Geometry File -- Coordinates for Detectors"<<std::endl;
-	for(unsigned int i=0; i<x.size(); i++) {
+	for(std::size_t i=0; i<x.size(); i++)
 		output<<x[i]<<" "<<y[i]<<" "<<z[i]<<std::endl;
-	}
+	for(std::size_t i=0; i<cx.size(); i++)
-	for(unsigned int i=0; i<cx.size(); i++) {
 		output<<cx[i]<<" "<<cy[i]<<" "<<cz[i]<<std::endl;
-	}
 
 	output.close();
 }
 
-double AnasenEfficiency::RunConsistencyCheck() {
+double AnasenEfficiency::RunConsistencyCheck()
-	std::vector<Mask::Vec3> r1_points;
+{
-	std::vector<Mask::Vec3> r2_points;
+	std::vector<ROOT::Math::XYZPoint> r1_points;
-	std::vector<Mask::Vec3> fqqq_points;
+	std::vector<ROOT::Math::XYZPoint> r2_points;
-	std::vector<Mask::Vec3> bqqq_points;
+	std::vector<ROOT::Math::XYZPoint> fqqq_points;
-	for(int i=0; i<n_sx3_per_ring; i++) {
+	std::vector<ROOT::Math::XYZPoint> bqqq_points;
-		for(int j=0; j<4; j++) {
+	for(int i=0; i<s_nSX3PerBarrel; i++)
+	{
+		for(int j=0; j<4; j++)
 			r1_points.push_back(m_Ring1[i].GetHitCoordinates(j, 0));
-		}
 	}
-	for(int i=0; i<n_sx3_per_ring; i++) {
+	for(int i=0; i<s_nSX3PerBarrel; i++)
-		for(int j=0; j<4; j++) {
+	{
+		for(int j=0; j<4; j++)
 			r2_points.push_back(m_Ring2[i].GetHitCoordinates(j, 0));
-		}
 	}
-	for(int i=0; i<n_qqq; i++) {
+	for(int i=0; i<s_nQQQ; i++)
-		for(int j=0; j<16; j++) {
+	{
-			for(int k=0; k<16; k++) {
+		for(int j=0; j<16; j++)
+		{
+			for(int k=0; k<16; k++)
 				fqqq_points.push_back(m_forwardQQQs[i].GetHitCoordinates(j, k));
-			}
 		}
 	}
-	for(int i=0; i<n_qqq; i++) {
+	for(int i=0; i<s_nQQQ; i++)
-		for(int j=0; j<16; j++) {
+	{
-			for(int k=0; k<16; k++) {
+		for(int j=0; j<16; j++)
+		{
+			for(int k=0; k<16; k++)
 				bqqq_points.push_back(m_backwardQQQs[i].GetHitCoordinates(j, k));
-			}
 		}
 	}
 
-	int npoints = r1_points.size() + r2_points.size() + fqqq_points.size() + bqqq_points.size();
+	std::size_t npoints = r1_points.size() + r2_points.size() + fqqq_points.size() + bqqq_points.size();
-	int count = 0;
+	std::size_t count = 0;
-	Mask::Vec3 coords;
+	ROOT::Math::XYZPoint coords;
-	for(auto& point : r1_points) {
+	for(auto& point : r1_points)
-		for(auto& sx3 : m_Ring1) {
+	{
-			auto result = sx3.GetChannelRatio(point.GetTheta(), point.GetPhi());
+		for(auto& sx3 : m_Ring1)
+		{
+			auto result = sx3.GetChannelRatio(point.Theta(), point.Phi());
 			coords = sx3.GetHitCoordinates(result.front_strip_index, result.front_ratio);
-			if(IsDoubleEqual(point.GetX(), coords.GetX()) && IsDoubleEqual(point.GetY(), coords.GetY()) && IsDoubleEqual(point.GetZ(), coords.GetZ())) {
+			if(IsDoubleEqual(point.X(), coords.X()) && IsDoubleEqual(point.Y(), coords.Y()) && IsDoubleEqual(point.Z(), coords.Z()))
+			{
 				count++;
 				break;
 			}
 		}
 	}
-	for(auto& point : r2_points) {
+	for(auto& point : r2_points)
-		for(auto& sx3 : m_Ring2) {
+	{
-			auto result = sx3.GetChannelRatio(point.GetTheta(), point.GetPhi());
+		for(auto& sx3 : m_Ring2)
+		{
+			auto result = sx3.GetChannelRatio(point.Theta(), point.Phi());
 			coords = sx3.GetHitCoordinates(result.front_strip_index, result.front_ratio);
-			if(IsDoubleEqual(point.GetX(), coords.GetX()) && IsDoubleEqual(point.GetY(), coords.GetY()) && IsDoubleEqual(point.GetZ(), coords.GetZ())) {
+			if(IsDoubleEqual(point.X(), coords.X()) && IsDoubleEqual(point.Y(), coords.Y()) && IsDoubleEqual(point.Z(), coords.Z()))
+			{
 				count++;
 				break;
 			}
 		}
 	}
-	for(auto& point : fqqq_points) {
+	for(auto& point : fqqq_points)
-		for(auto& qqq : m_forwardQQQs) {
+	{
-			auto result = qqq.GetTrajectoryRingWedge(point.GetTheta(), point.GetPhi());
+		for(auto& qqq : m_forwardQQQs)
+		{
+			auto result = qqq.GetTrajectoryRingWedge(point.Theta(), point.Phi());
 			coords = qqq.GetHitCoordinates(result.first, result.second);
-			if(IsDoubleEqual(point.GetX(), coords.GetX()) && IsDoubleEqual(point.GetY(), coords.GetY()) && IsDoubleEqual(point.GetZ(), coords.GetZ())) {
+			if(IsDoubleEqual(point.X(), coords.X()) && IsDoubleEqual(point.Y(), coords.Y()) && IsDoubleEqual(point.Z(), coords.Z()))
+			{
 				count++;
 				break;
 			}
 		}
 	}
-	for(auto& point : bqqq_points) {
+	for(auto& point : bqqq_points)
-		for(auto& qqq : m_backwardQQQs) {
+	{
-			auto result = qqq.GetTrajectoryRingWedge(point.GetTheta(), point.GetPhi());
+		for(auto& qqq : m_backwardQQQs)
+		{
+			auto result = qqq.GetTrajectoryRingWedge(point.Theta(), point.Phi());
 			coords = qqq.GetHitCoordinates(result.first, result.second);
-			if(IsDoubleEqual(point.GetX(), coords.GetX()) && IsDoubleEqual(point.GetY(), coords.GetY()) && IsDoubleEqual(point.GetZ(), coords.GetZ())) {
+			if(IsDoubleEqual(point.X(), coords.X()) && IsDoubleEqual(point.Y(), coords.Y()) && IsDoubleEqual(point.Z(), coords.Z()))
+			{
 				count++;
 				break;
 			}
@@ -203,22 +230,23 @@ double AnasenEfficiency::RunConsistencyCheck() {
 
 }
 
-DetectorResult AnasenEfficiency::IsRing1(Mask::Nucleus& nucleus) {
+DetectorResult AnasenEfficiency::IsRing1(Mask::Nucleus& nucleus)
-
+{
 	DetectorResult observation;
 	double thetaIncident;
-	for(int i=0; i<n_sx3_per_ring; i++) {
+	for(int i=0; i<s_nSX3PerBarrel; i++)
-		auto result = m_Ring1[i].GetChannelRatio(nucleus.GetTheta(), nucleus.GetPhi());
+	{
+		auto result = m_Ring1[i].GetChannelRatio(nucleus.vec4.Theta(), nucleus.vec4.Phi());
 		if(result.front_strip_index != -1 /*&& !dmap.IsDead(AnasenDetectorType::Barrel1, i, result.front_strip_index, AnasenDetectorSide::Front)*/
 			&& !dmap.IsDead(AnasenDetectorType::Barrel1, i, result.back_strip_index, AnasenDetectorSide::Back)) 
 		{
 			observation.detectFlag = true;
 			observation.direction = m_Ring1[i].GetHitCoordinates(result.front_strip_index, result.front_ratio);
-			thetaIncident = std::acos(observation.direction.Dot(m_Ring1[i].GetNormRotated())/observation.direction.GetR());
+			thetaIncident = std::acos(observation.direction.Dot(m_Ring1[i].GetNormRotated())/observation.direction.R());
 			if(thetaIncident > M_PI/2.0)
 				thetaIncident = M_PI - thetaIncident;
 
-			observation.energy_deposited = det_silicon.GetEnergyLossTotal(nucleus.GetZ(), nucleus.GetA(), nucleus.GetKE(), thetaIncident);
+			observation.energy_deposited = m_detectorEloss.GetEnergyLossTotal(nucleus.Z, nucleus.A, nucleus.GetKE(), thetaIncident);
 			observation.det_name = "R1";
 			return observation;
 		}
@@ -227,22 +255,23 @@ DetectorResult AnasenEfficiency::IsRing1(Mask::Nucleus& nucleus) {
 	return observation;
 }
 
-DetectorResult AnasenEfficiency::IsRing2(Mask::Nucleus& nucleus) {
+DetectorResult AnasenEfficiency::IsRing2(Mask::Nucleus& nucleus)
-
+{
 	DetectorResult observation;
 	double thetaIncident;
-	for(int i=0; i<n_sx3_per_ring; i++) {
+	for(int i=0; i<s_nSX3PerBarrel; i++)
-		auto result = m_Ring2[i].GetChannelRatio(nucleus.GetTheta(), nucleus.GetPhi());
+	{
+		auto result = m_Ring2[i].GetChannelRatio(nucleus.vec4.Theta(), nucleus.vec4.Phi());
 		if(result.front_strip_index != -1 /*&& !dmap.IsDead(AnasenDetectorType::Barrel2, i, result.front_strip_index, AnasenDetectorSide::Front)*/
 			&& !dmap.IsDead(AnasenDetectorType::Barrel2, i, result.back_strip_index, AnasenDetectorSide::Back)) 
 		{
 			observation.detectFlag = true;
 			observation.direction = m_Ring2[i].GetHitCoordinates(result.front_strip_index, result.front_ratio);
-			thetaIncident = std::acos(observation.direction.Dot(m_Ring2[i].GetNormRotated())/observation.direction.GetR());
+			thetaIncident = std::acos(observation.direction.Dot(m_Ring2[i].GetNormRotated())/observation.direction.R());
 			if(thetaIncident > M_PI/2.0)
 				thetaIncident = M_PI - thetaIncident;
 
-			observation.energy_deposited = det_silicon.GetEnergyLossTotal(nucleus.GetZ(), nucleus.GetA(), nucleus.GetKE(), thetaIncident);
+			observation.energy_deposited = m_detectorEloss.GetEnergyLossTotal(nucleus.Z, nucleus.A, nucleus.GetKE(), thetaIncident);
 			observation.det_name = "R2";
 			return observation;
 		}
@@ -251,40 +280,42 @@ DetectorResult AnasenEfficiency::IsRing2(Mask::Nucleus& nucleus) {
 	return observation;
 }
 
-DetectorResult AnasenEfficiency::IsQQQ(Mask::Nucleus& nucleus) {
+DetectorResult AnasenEfficiency::IsQQQ(Mask::Nucleus& nucleus)
-
+{
 	DetectorResult observation;
 	double thetaIncident;
-	for(int i=0; i<n_qqq; i++) {
+	for(int i=0; i<s_nQQQ; i++)
-		auto result = m_forwardQQQs[i].GetTrajectoryRingWedge(nucleus.GetTheta(), nucleus.GetPhi());
+	{
+		auto result = m_forwardQQQs[i].GetTrajectoryRingWedge(nucleus.vec4.Theta(), nucleus.vec4.Phi());
 		if(result.first != -1 /*&& !dmap.IsDead(AnasenDetectorType::FQQQ, i, result.first, AnasenDetectorSide::Front)*/ &&
 			!dmap.IsDead(AnasenDetectorType::FQQQ, i, result.second, AnasenDetectorSide::Back)) 
 		{
 			observation.detectFlag = true;
 			observation.direction = m_forwardQQQs[i].GetHitCoordinates(result.first, result.second);
-			thetaIncident = std::acos(observation.direction.Dot(m_forwardQQQs[i].GetNorm())/observation.direction.GetR());
+			thetaIncident = std::acos(observation.direction.Dot(m_forwardQQQs[i].GetNorm())/observation.direction.R());
 			if(thetaIncident > M_PI/2.0)
 				thetaIncident = M_PI - thetaIncident;
 
-			observation.energy_deposited = det_silicon.GetEnergyLossTotal(nucleus.GetZ(), nucleus.GetA(), nucleus.GetKE(), thetaIncident);
+			observation.energy_deposited = m_detectorEloss.GetEnergyLossTotal(nucleus.Z, nucleus.A, nucleus.GetKE(), thetaIncident);
 			observation.det_name = "FQQQ";
 			return observation;
 		}
 	}
 
 	
-	for(int i=0; i<n_qqq; i++) {
+	for(int i=0; i<s_nQQQ; i++)
-		auto result = m_backwardQQQs[i].GetTrajectoryRingWedge(nucleus.GetTheta(), nucleus.GetPhi());
+	{
+		auto result = m_backwardQQQs[i].GetTrajectoryRingWedge(nucleus.vec4.Theta(), nucleus.vec4.Phi());
 		if(result.first != -1 /*&& !dmap.IsDead(AnasenDetectorType::BQQQ, i, result.first, AnasenDetectorSide::Front)*/ &&
 			!dmap.IsDead(AnasenDetectorType::BQQQ, i, result.second, AnasenDetectorSide::Back)) 
 		{
 			observation.detectFlag = true;
 			observation.direction = m_backwardQQQs[i].GetHitCoordinates(result.first, result.second);
-			thetaIncident = std::acos(observation.direction.Dot(m_backwardQQQs[i].GetNorm())/observation.direction.GetR());
+			thetaIncident = std::acos(observation.direction.Dot(m_backwardQQQs[i].GetNorm())/observation.direction.R());
 			if(thetaIncident > M_PI/2.0)
 				thetaIncident = M_PI - thetaIncident;
 
-			observation.energy_deposited = det_silicon.GetEnergyLossTotal(nucleus.GetZ(), nucleus.GetA(), nucleus.GetKE(), thetaIncident);
+			observation.energy_deposited = m_detectorEloss.GetEnergyLossTotal(nucleus.Z, nucleus.A, nucleus.GetKE(), thetaIncident);
 			observation.det_name = "BQQQ";
 			return observation;
 		}
@@ -293,95 +324,93 @@ DetectorResult AnasenEfficiency::IsQQQ(Mask::Nucleus& nucleus) {
 	return observation;
 }
 
-DetectorResult AnasenEfficiency::IsAnasen(Mask::Nucleus& nucleus) {
+DetectorResult AnasenEfficiency::IsAnasen(Mask::Nucleus& nucleus)
+{
 	DetectorResult result;
-	if(nucleus.GetKE() <= threshold)
+	if(nucleus.GetKE() <= s_energyThreshold)
 		return result;
 
-	if(!result.detectFlag) {
+	if(!result.detectFlag)
 		result = IsRing1(nucleus);
-	}
+	if(!result.detectFlag)
-	if(!result.detectFlag) {
 		result = IsRing2(nucleus);
-	}
+	if(!result.detectFlag)
-	if(!result.detectFlag) {
 		result = IsQQQ(nucleus);
-	}
-
 	return result;
 }
 
-void AnasenEfficiency::CountCoincidences(const Mask::MaskFileData& data, std::vector<int>& counts, Mask::RxnType rxn_type) {
+void AnasenEfficiency::CountCoincidences(const std::vector<Mask::Nucleus>& data, std::vector<int>& counts)
-	if (rxn_type == Mask::RxnType::PureDecay && data.detect_flag[1] && data.detect_flag[2])
+{
+	if (data.size() == 3 && data[1].isDetected && data[2].isDetected)
 	{
 		counts[0]++;
 	}
-	else if (rxn_type == Mask::RxnType::OneStepRxn && data.detect_flag[2] && data.detect_flag[3])
+	else if (data.size() == 4 && data[2].isDetected && data[3].isDetected)
 	{
 		counts[0]++;
 	}
-	else if(rxn_type == Mask::RxnType::TwoStepRxn)
+	else if(data.size() == 6)
 	{
-		if(data.detect_flag[2] && data.detect_flag[4]) 
+		if(data[2].isDetected && data[4].isDetected) 
 		{
 			counts[0]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[5])
+		if(data[2].isDetected && data[5].isDetected)
 		{
 			counts[1]++;
 		}
-		if(data.detect_flag[4] && data.detect_flag[5])
+		if(data[4].isDetected && data[5].isDetected)
 		{
 			counts[2]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[4] && data.detect_flag[5])
+		if(data[2].isDetected && data[4].isDetected && data[5].isDetected)
 		{
 			counts[3]++;
 		}
 	}
-	else if(rxn_type == Mask::RxnType::ThreeStepRxn)
+	else if(data.size() == 8)
 	{
-		if(data.detect_flag[2] && data.detect_flag[4]) 
+		if(data[2].isDetected && data[4].isDetected) 
 		{
 			counts[0]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[6])
+		if(data[2].isDetected && data[6].isDetected)
 		{
 			counts[1]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[7])
+		if(data[2].isDetected && data[7].isDetected)
 		{
 			counts[2]++;
 		}
-		if(data.detect_flag[4] && data.detect_flag[6])
+		if(data[4].isDetected && data[6].isDetected)
 		{
 			counts[3]++;
 		}
-		if(data.detect_flag[4] && data.detect_flag[7])
+		if(data[4].isDetected && data[7].isDetected)
 		{
 			counts[4]++;
 		}
-		if(data.detect_flag[6] && data.detect_flag[7])
+		if(data[6].isDetected && data[7].isDetected)
 		{
 			counts[5]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[4] && data.detect_flag[6])
+		if(data[2].isDetected && data[4].isDetected && data[6].isDetected)
 		{
 			counts[6]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[4] && data.detect_flag[7])
+		if(data[2].isDetected && data[4].isDetected && data[7].isDetected)
 		{
 			counts[7]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[6] && data.detect_flag[7])
+		if(data[2].isDetected && data[6].isDetected && data[7].isDetected)
 		{
 			counts[8]++;
 		}
-		if(data.detect_flag[4] && data.detect_flag[6] && data.detect_flag[7])
+		if(data[4].isDetected && data[6].isDetected && data[7].isDetected)
 		{
 			counts[9]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[4] && data.detect_flag[6] && data.detect_flag[7])
+		if(data[2].isDetected && data[4].isDetected && data[6].isDetected && data[7].isDetected)
 		{
 			counts[10]++;
 		}
@@ -401,141 +430,138 @@ void AnasenEfficiency::CalculateEfficiency(const std::string& inputname, const s
 	std::cout<<"Loading in output from kinematics simulation: "<<inputname<<std::endl;
 	std::cout<<"Running efficiency calculation..."<<std::endl;
 
-	Mask::MaskFile input(inputname, Mask::MaskFile::FileType::read);
+	TFile* input = TFile::Open(inputname.c_str(), "READ");
-	Mask::MaskFile output(outputname, Mask::MaskFile::FileType::write);
+	TFile* output = TFile::Open(outputname.c_str(), "RECREATE");
 	std::ofstream stats(statsname);
 	stats<<std::setprecision(5);
 
-	Mask::MaskFileHeader header = input.ReadHeader();
+	TTree* intree = (TTree*) input->Get("SimTree");
-	output.WriteHeader(header.rxn_type, header.nsamples);
+	std::vector<Mask::Nucleus>* dataHandle = new std::vector<Mask::Nucleus>();
+	intree->SetBranchAddress("nuclei", &dataHandle);
+
+	output->cd();
+	TTree* outtree = new TTree("SimTree", "SimTree");
+	outtree->Branch("nuclei", dataHandle);
+
+	input->cd();
+
 	stats<<"Efficiency statistics for data from "<<inputname<<" using the ANASEN geometry"<<std::endl;
 	stats<<"Given in order of target=0, projectile=1, ejectile=2, residual=3, .... etc."<<std::endl;
 
-	Mask::MaskFileData data;
+	intree->GetEntry(1);
-
 	std::vector<int> counts;
 	std::vector<int> coinc_counts;
-	switch(header.rxn_type) {
+	counts.resize(dataHandle->size());
-		case Mask::RxnType::PureDecay:
+	switch(counts.size())
-			counts.resize(3, 0);
+	{
-			coinc_counts.resize(1, 0);
+		case 3: coinc_counts.resize(1, 0); break;
-			break;
+		case 4: coinc_counts.resize(1, 0); break;
-		case Mask::RxnType::OneStepRxn:
+		case 6: coinc_counts.resize(4, 0); break;
-			counts.resize(4, 0);
+		case 8: coinc_counts.resize(11, 0); break;
-			coinc_counts.resize(1, 0);
-			break;
-		case Mask::RxnType::TwoStepRxn:
-			counts.resize(6, 0);
-			coinc_counts.resize(4, 0);
-			break;
-		case Mask::RxnType::ThreeStepRxn:
-			counts.resize(8, 0);
-			coinc_counts.resize(11, 0);
-			break;
 		default:
 		{
-			std::cerr<<"Bad reaction type at AnasenEfficiency::CalculateEfficiency (given value: "<<GetStringFromRxnType(header.rxn_type)<<"). Quiting..."<<std::endl;
+			std::cerr<<"Bad reaction type at AnasenEfficiency::CalculateEfficiency (given value: "<<counts.size()<<"). Quiting..."<<std::endl;
-			input.Close();
+			input->Close();
-			output.Close();
+			output->Close();
 			stats.close();
 			return;
 		}
 	}
 
-	int percent5 = header.nsamples*0.05;
+	uint64_t nentries = intree->GetEntries();
-	int count = 0;
+	uint64_t percent5 = nentries*0.05;
-	int npercent = 0;
+	uint64_t count = 0;
+	uint64_t npercent = 0;
 
 	Mask::Nucleus nucleus;
-	int index=0;
+	for(uint64_t i=0; i<nentries; i++)
-	while(true) {
+	{
-		if(++count == percent5) {//Show progress every 5%
+		intree->GetEntry(i);
+		if(++count == percent5)
+		{//Show progress every 5%
 			npercent++;
 			count = 0;
 			std::cout<<"\rPercent completed: "<<npercent*5<<"%"<<std::flush;
 		}
 
-		data = input.ReadData();
+		for(std::size_t j=0; j<dataHandle->size(); j++)
-		if(data.eof)
+		{
-			break;
+			Mask::Nucleus& nucleus = (*dataHandle)[j];
-
+			DetectorResult result = IsAnasen(nucleus);
-		for(unsigned int i=0; i<data.Z.size(); i++) {
+			if(result.detectFlag)
-			nucleus.SetIsotope(data.Z[i], data.A[i]);
+			{
-			nucleus.SetVectorSpherical(data.theta[i], data.phi[i], data.p[i], data.E[i]);
+				nucleus.isDetected = true;
-			auto result = IsAnasen(nucleus);
+				nucleus.detectedKE = result.energy_deposited;
-			if(result.detectFlag) {
+				nucleus.detectedTheta = result.direction.Theta();
-				data.detect_flag[i] = true;
+				nucleus.detectedPhi = result.direction.Phi();
-				data.KE[i] = result.energy_deposited;
+				counts[j]++;
-				data.theta[i] = result.direction.GetTheta();
-				data.phi[i] = result.direction.GetPhi();
-				counts[i]++;
-			} else if(data.detect_flag[i] == true) {
-				data.detect_flag[i] = false;
 			}
 		}
 
-		CountCoincidences(data, coinc_counts, header.rxn_type);
+		CountCoincidences(*dataHandle, coinc_counts);
 
-		output.WriteData(data);
+		outtree->Fill();
-
-		index++;
 	}
+	input->Close();
+	output->cd();
+	outtree->Write(outtree->GetName(), TObject::kOverwrite);
+	output->Close();
 
-	input.Close();
+	delete dataHandle;
-	output.Close();
 
 	stats<<std::setw(10)<<"Index"<<"|"<<std::setw(10)<<"Efficiency"<<std::endl;
 	stats<<"---------------------"<<std::endl;
-	for(unsigned int i=0; i<counts.size(); i++) {
+	for(unsigned int i=0; i<counts.size(); i++)
-		stats<<std::setw(10)<<i<<"|"<<std::setw(10)<<((double)counts[i]/header.nsamples)<<std::endl;
+	{
+		stats<<std::setw(10)<<i<<"|"<<std::setw(10)<<((double)counts[i]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
 	stats<<"Coincidence Efficiency"<<std::endl;
 	stats<<"---------------------"<<std::endl;
-	if(header.rxn_type == Mask::RxnType::PureDecay)
+	if(dataHandle->size() == 3)
 	{
-		stats<<std::setw(10)<<"1 + 2"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"1 + 2"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
-	else if(header.rxn_type == Mask::RxnType::OneStepRxn)
+	else if(dataHandle->size() == 4)
 	{
-		stats<<std::setw(10)<<"2 + 3"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 3"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
-	else if(header.rxn_type == Mask::RxnType::TwoStepRxn)
+	else if(dataHandle->size() == 6)
 	{
-		stats<<std::setw(10)<<"2 + 4"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[1]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[1]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"4 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[2]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"4 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[2]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 4 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[3]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[3]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
-	else if(header.rxn_type == Mask::RxnType::ThreeStepRxn)
+	else if(dataHandle->size() == 8)
 	{
-		stats<<std::setw(10)<<"2 + 4"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[1]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[1]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[2]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[2]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"4 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[3]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"4 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[3]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"4 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[4]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"4 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[4]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[5]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[5]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 4 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[6]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[6]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 4 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[7]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[7]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[8]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[8]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"4 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[9]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"4 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[9]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 4 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[10]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[10]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
 	stats.close();

src/Detectors/AnasenEfficiency.h

@@ -0,0 +1,64 @@
+#ifndef ANASEN_EFFICIENCY_H
+#define ANASEN_EFFICIENCY_H
+
+#include <string>
+
+#include "DetectorEfficiency.h"
+#include "StripDetector.h"
+#include "QQQDetector.h"
+#include "Target.h"
+#include "Nucleus.h"
+#include "AnasenDeadChannelMap.h"
+
+class AnasenEfficiency : public DetectorEfficiency
+{
+public:
+	AnasenEfficiency();
+	~AnasenEfficiency();
+	void CalculateEfficiency(const std::string& inputname, const std::string& outputname, const std::string& statsname) override;
+	void DrawDetectorSystem(const std::string& filename) override;
+	double RunConsistencyCheck() override;
+	inline void SetDeadChannelMap(const std::string& filename) { dmap.LoadMapfile(filename); }
+
+private:
+	DetectorResult IsRing1(Mask::Nucleus& nucleus);
+	DetectorResult IsRing2(Mask::Nucleus& nucleus);
+	DetectorResult IsQQQ(Mask::Nucleus& nucleus);
+	DetectorResult IsAnasen(Mask::Nucleus& nucleus);
+	void CountCoincidences(const std::vector<Mask::Nucleus>& data, std::vector<int>& counts);
+
+	std::vector<StripDetector> m_Ring1, m_Ring2;
+	std::vector<QQQDetector> m_forwardQQQs;
+	std::vector<QQQDetector> m_backwardQQQs;
+
+	Mask::Target m_detectorEloss;
+
+	AnasenDeadChannelMap dmap;
+
+	/**** ANASEN geometry constants *****/
+	static constexpr int s_nSX3PerBarrel = 12;
+	static constexpr int s_nQQQ = 4;
+	static constexpr double s_sx3Length = 0.075;
+	static constexpr double s_sx3Width = 0.04;
+	static constexpr double s_barrelGap = 0.0254;
+	static constexpr double s_sx3FrameGap = 0.049; //0.049 is base gap due to frames
+	static constexpr double s_barrel1Z = s_sx3Length/2.0 + s_sx3FrameGap + s_barrelGap/2.0;
+	static constexpr double s_barrel2Z = (-1.0)*(s_barrelGap/2.0 + s_sx3Length/2.0);
+	static constexpr double s_qqqZ = 0.0125 + s_sx3Length + s_sx3FrameGap + s_barrelGap/2.0;
+	static constexpr double s_qqqInnerR = 0.0501;
+	static constexpr double s_qqqOuterR = 0.0990;
+	static constexpr double s_qqqDeltaPhi = 1.52119;
+	static constexpr double s_qqqZList[4] = {s_qqqZ, s_qqqZ, s_qqqZ, s_qqqZ};
+	static constexpr double s_qqqPhiList[4] = {5.49779, 0.785398, 2.35619, 3.92699};
+	static constexpr double s_barrelRhoList[12] = {0.0890601, 0.0889871, 0.0890354, 0.0890247, 0.0890354, 0.0890354, 0.0890247,
+												 0.0890354, 0.0890354, 0.0890247, 0.0890354, 0.0890354};
+	static constexpr double s_barrelPhiList[12] = {4.97426, 5.49739, 6.02132, 0.261868, 0.785398, 1.30893, 1.83266, 2.35619, 2.87972, 
+												   3.40346, 3.92699, 4.45052};
+	/*************************/
+
+	static constexpr double s_energyThreshold = 0.6; //MeV
+	static constexpr double s_deg2rad = M_PI/180.0;
+	static constexpr double s_detectorThickness = 1000 * 1e-4 * 2.3926 * 1e6; //thickness in um -> eff thickness in ug/cm^2 for detector
+};
+
+#endif

src/Detectors/CMakeLists.txt

@@ -1,18 +1,27 @@
 add_executable(DetectEff)
-target_include_directories(DetectEff PUBLIC ${MASK_INCLUDE_DIR})
+target_include_directories(DetectEff PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/..)
 
 target_sources(DetectEff PUBLIC
     AnasenDeadChannelMap.cpp
+    AnasenDeadChannelMap.h
     AnasenEfficiency.cpp
-    DetectorEfficiency.cpp
+    AnasenEfficiency.h
+    main.cpp
+    DetectorEfficiency.h
     QQQDetector.cpp
+    QQQDetector.h
     SabreDeadChannelMap.cpp
+    SabreDeadChannelMap.h
     SabreDetector.cpp
+    SabreDetector.h
     SabreEfficiency.cpp
+    SabreEfficiency.h
     StripDetector.cpp
+    StripDetector.h
 )
 
 target_link_libraries(DetectEff
+    MaskDict
     Mask
     catima
 )

src/Detectors/DetectorEfficiency.h

@@ -4,7 +4,18 @@
 #include <string>
 #include <cmath>
 
-class DetectorEfficiency {
+#include "Math/Point3D.h"
+
+struct DetectorResult
+{
+	bool detectFlag = false;
+	ROOT::Math::XYZPoint direction;
+	double energy_deposited = 0.0;
+	std::string det_name = "";
+};
+
+class DetectorEfficiency
+{
 public:
 	DetectorEfficiency() {};
 	virtual ~DetectorEfficiency() {};
@@ -14,9 +25,9 @@ public:
 	virtual double RunConsistencyCheck() = 0;
 
 protected:
-	inline bool IsDoubleEqual(double x, double y) { return std::fabs(x-y) < epsilon ? true : false; };
+	inline bool IsDoubleEqual(double x, double y) { return std::fabs(x-y) < s_epsilon ? true : false; };
 
-	static constexpr double epsilon = 1.0e-6;
+	static constexpr double s_epsilon = 1.0e-6;
 };
 
 #endif

src/Detectors/QQQDetector.cpp

@@ -1,107 +1,116 @@
 #include "QQQDetector.h"
 
 QQQDetector::QQQDetector(double R_in, double R_out, double deltaPhi, double phiCentral, double z, double x, double y) :
-	m_Rinner(R_in), m_Router(R_out), m_deltaPhi(deltaPhi), m_phiCentral(phiCentral), m_translation(x,y,z), m_norm(0.0,0.0,1.0), m_uniform_fraction(0.0, 1.0), rndmFlag(false)
+	m_innerR(R_in), m_outerR(R_out), m_deltaPhi(deltaPhi), m_centralPhi(phiCentral), m_translation(x,y,z), m_norm(0.0,0.0,1.0),
+	m_uniformFraction(0.0, 1.0), m_isSmearing(false)
 {
-	m_deltaR = (m_Router - m_Rinner)/nrings;
+	m_deltaR = (m_outerR - m_innerR)/s_nRings;
-	m_deltaPhi_per_wedge = m_deltaPhi/nwedges;
+	m_deltaPhiWedge = m_deltaPhi/s_nWedges;
-	m_ZRot.SetAngle(m_phiCentral);
+	m_zRotation.SetAngle(m_centralPhi);
-	m_ringCoords.resize(nrings);
+	m_ringCoords.resize(s_nRings);
-	m_wedgeCoords.resize(nwedges);
+	m_wedgeCoords.resize(s_nWedges);
-	for(auto& ring : m_ringCoords) {
+	for(auto& ring : m_ringCoords)
 		ring.resize(4);
-	}
+	for(auto& wedge : m_wedgeCoords)
-	for(auto& wedge : m_wedgeCoords) {
 		wedge.resize(4);
-	}
 
 	CalculateCorners();
 }
 
 QQQDetector::~QQQDetector() {}
 
-void QQQDetector::CalculateCorners() {
+void QQQDetector::CalculateCorners()
+{
 	double x0, x1, x2, x3;
 	double y0, y1, y2, y3;
 	double z0, z1, z2, z3;
 
 	//Generate flat ring corner coordinates
-	for(int i=0; i<nrings; i++) {
+	for(int i=0; i<s_nRings; i++)
-		x0 = (m_Rinner + m_deltaR*(i+1))*std::cos(-m_deltaPhi/2.0);
+	{
-		y0 = (m_Rinner + m_deltaR*(i+1))*std::sin(-m_deltaPhi/2.0);
+		x0 = (m_innerR + m_deltaR*(i+1))*std::cos(-m_deltaPhi/2.0);
+		y0 = (m_innerR + m_deltaR*(i+1))*std::sin(-m_deltaPhi/2.0);
 		z0 = 0.0;
-		m_ringCoords[i][0].SetVectorCartesian(x0, y0, z0);
+		m_ringCoords[i][0].SetXYZ(x0, y0, z0);
 
-		x1 = (m_Rinner + m_deltaR*(i))*std::cos(-m_deltaPhi/2.0);
+		x1 = (m_innerR + m_deltaR*(i))*std::cos(-m_deltaPhi/2.0);
-		y1 = (m_Rinner + m_deltaR*(i))*std::sin(-m_deltaPhi/2.0);
+		y1 = (m_innerR + m_deltaR*(i))*std::sin(-m_deltaPhi/2.0);
 		z1 = 0.0;
-		m_ringCoords[i][1].SetVectorCartesian(x1, y1, z1);
+		m_ringCoords[i][1].SetXYZ(x1, y1, z1);
 
-		x2 = (m_Rinner + m_deltaR*(i))*std::cos(m_deltaPhi/2.0);
+		x2 = (m_innerR + m_deltaR*(i))*std::cos(m_deltaPhi/2.0);
-		y2 = (m_Rinner + m_deltaR*(i))*std::sin(m_deltaPhi/2.0);
+		y2 = (m_innerR + m_deltaR*(i))*std::sin(m_deltaPhi/2.0);
 		z2 = 0.0;
-		m_ringCoords[i][2].SetVectorCartesian(x2, y2, z2);
+		m_ringCoords[i][2].SetXYZ(x2, y2, z2);
 
-		x3 = (m_Rinner + m_deltaR*(i+1))*std::cos(m_deltaPhi/2.0);
+		x3 = (m_innerR + m_deltaR*(i+1))*std::cos(m_deltaPhi/2.0);
-		y3 = (m_Rinner + m_deltaR*(i+1))*std::sin(m_deltaPhi/2.0);
+		y3 = (m_innerR + m_deltaR*(i+1))*std::sin(m_deltaPhi/2.0);
 		z3 = 0.0;
-		m_ringCoords[i][3].SetVectorCartesian(x3, y3, z3);
+		m_ringCoords[i][3].SetXYZ(x3, y3, z3);
 	}
 
 	//Generate flat wedge corner coordinates
-	for(int i=0; i<nwedges; i++) {
+	for(int i=0; i<s_nWedges; i++)
-		x0 = m_Router * std::cos(-m_deltaPhi/2.0 + i*m_deltaPhi_per_wedge);
+	{
-		y0 = m_Router * std::sin(-m_deltaPhi/2.0 + i*m_deltaPhi_per_wedge);
+		x0 = m_outerR * std::cos(-m_deltaPhi/2.0 + i*m_deltaPhiWedge);
+		y0 = m_outerR * std::sin(-m_deltaPhi/2.0 + i*m_deltaPhiWedge);
 		z0 = 0.0;
-		m_wedgeCoords[i][0].SetVectorCartesian(x0, y0, z0);
+		m_wedgeCoords[i][0].SetXYZ(x0, y0, z0);
 
-		x1 = m_Rinner * std::cos(-m_deltaPhi/2.0 + i*m_deltaPhi_per_wedge);
+		x1 = m_innerR * std::cos(-m_deltaPhi/2.0 + i*m_deltaPhiWedge);
-		y1 = m_Rinner * std::sin(-m_deltaPhi/2.0 + i*m_deltaPhi_per_wedge);
+		y1 = m_innerR * std::sin(-m_deltaPhi/2.0 + i*m_deltaPhiWedge);
 		z1 = 0.0;
-		m_wedgeCoords[i][1].SetVectorCartesian(x1, y1, z1);
+		m_wedgeCoords[i][1].SetXYZ(x1, y1, z1);
 
-		x2 = m_Rinner * std::cos(-m_deltaPhi/2.0 + (i+1)*m_deltaPhi_per_wedge);
+		x2 = m_innerR * std::cos(-m_deltaPhi/2.0 + (i+1)*m_deltaPhiWedge);
-		y2 = m_Rinner * std::sin(-m_deltaPhi/2.0 + (i+1)*m_deltaPhi_per_wedge);
+		y2 = m_innerR * std::sin(-m_deltaPhi/2.0 + (i+1)*m_deltaPhiWedge);
 		z2 = 0.0;
-		m_wedgeCoords[i][2].SetVectorCartesian(x2, y2, z2);
+		m_wedgeCoords[i][2].SetXYZ(x2, y2, z2);
 
-		x3 = m_Router * std::cos(-m_deltaPhi/2.0 + (i+1)*m_deltaPhi_per_wedge);
+		x3 = m_outerR * std::cos(-m_deltaPhi/2.0 + (i+1)*m_deltaPhiWedge);
-		y3 = m_Router * std::sin(-m_deltaPhi/2.0 + (i+1)*m_deltaPhi_per_wedge);
+		y3 = m_outerR * std::sin(-m_deltaPhi/2.0 + (i+1)*m_deltaPhiWedge);
 		z3 = 0.0;
-		m_wedgeCoords[i][3].SetVectorCartesian(x3, y3, z3);
+		m_wedgeCoords[i][3].SetXYZ(x3, y3, z3);
 	}
 
-	for(int i=0; i<nrings; i++) {
+	for(int i=0; i<s_nRings; i++)
-		for(int j=0; j<4; j++) {
+	{
+		for(int j=0; j<4; j++)
 			m_ringCoords[i][j] = TransformCoordinates(m_ringCoords[i][j]);
-		}
 	}
 
-	for(int i=0; i<nwedges; i++) {
+	for(int i=0; i<s_nWedges; i++)
-		for(int j=0; j<4; j++) {
+	{
+		for(int j=0; j<4; j++)
 			m_wedgeCoords[i][j] = TransformCoordinates(m_wedgeCoords[i][j]);
-		}
 	}
 
 }
 
-Mask::Vec3 QQQDetector::GetTrajectoryCoordinates(double theta, double phi) {
+ROOT::Math::XYZPoint QQQDetector::GetTrajectoryCoordinates(double theta, double phi)
-	double z_to_detector = m_translation.GetZ();
+{
+	double z_to_detector = m_translation.Vect().Z();
 	double rho_traj = z_to_detector*std::tan(theta);
 	double r_traj = std::sqrt(rho_traj*rho_traj + z_to_detector*z_to_detector);
 	double min_rho, max_rho, min_phi, max_phi;
 
-	Mask::Vec3 result;
+	ROOT::Math::XYZPoint result;
 
-	for(auto& ring : m_ringCoords) {
+	for(auto& ring : m_ringCoords)
-		min_rho = ring[1].GetRho();
+	{
-		max_rho = ring[0].GetRho();
+		min_rho = ring[1].Rho();
-		if(rho_traj < max_rho && rho_traj > min_rho) {
+		max_rho = ring[0].Rho();
-			for(auto& wedge : m_wedgeCoords) {
+		if(rho_traj < max_rho && rho_traj > min_rho)
-				min_phi = wedge[0].GetPhi();
+		{
-				max_phi = wedge[3].GetPhi();
+			for(auto& wedge : m_wedgeCoords)
-				if(phi < min_phi && phi < max_phi) {
+			{
-					result.SetVectorSpherical(r_traj, theta, phi);
+				min_phi = wedge[0].Phi();
+				max_phi = wedge[3].Phi();
+				if(phi < min_phi && phi < max_phi)
+				{
+					result.SetXYZ(std::sin(theta)*std::cos(phi)*r_traj, 
+								  std::sin(theta)*std::sin(phi)*r_traj, 
+								  std::cos(theta)*r_traj);
 					break;
 				}
 			}
@@ -109,55 +118,57 @@ Mask::Vec3 QQQDetector::GetTrajectoryCoordinates(double theta, double phi) {
 	}
 	
 	return result;
-
 }
 
-std::pair<int,int> QQQDetector::GetTrajectoryRingWedge(double theta, double phi) {
+std::pair<int,int> QQQDetector::GetTrajectoryRingWedge(double theta, double phi)
-	double z_to_detector = m_translation.GetZ();
+{
+	double z_to_detector = m_translation.Vect().Z();
 	double rho_traj = z_to_detector*std::tan(theta);
 	double min_rho, max_rho, min_phi, max_phi;
 
 
-	for(int r=0; r<nrings; r++) {
+	for(int r=0; r<s_nRings; r++)
+	{
 		auto& ring = m_ringCoords[r];
-		min_rho = ring[1].GetRho();
+		min_rho = ring[1].Rho();
-		max_rho = ring[0].GetRho();
+		max_rho = ring[0].Rho();
-		if(rho_traj < max_rho && rho_traj > min_rho) {
+		if(rho_traj < max_rho && rho_traj > min_rho)
-			for(int w=0; w<nwedges; w++) {
+		{
+			for(int w=0; w<s_nWedges; w++)
+			{
 				auto& wedge = m_wedgeCoords[w];
-				min_phi = wedge[0].GetPhi();
+				min_phi = wedge[0].Phi();
-				max_phi = wedge[3].GetPhi();
+				max_phi = wedge[3].Phi();
-				if(phi > min_phi && phi < max_phi) {
+				if(phi > min_phi && phi < max_phi)
 					return std::make_pair(r, w);
-				}
 			}
 		}
 	}
 	
 	return std::make_pair(-1, -1);
-
 }
 
-Mask::Vec3 QQQDetector::GetHitCoordinates(int ringch, int wedgech) {
+ROOT::Math::XYZPoint QQQDetector::GetHitCoordinates(int ringch, int wedgech)
+{
 	if(!CheckChannel(ringch) || !CheckChannel(wedgech))
-		return Mask::Vec3();
+		return ROOT::Math::XYZPoint();
 
 	double r_center, phi_center;
-	if(rndmFlag)
+	if(m_isSmearing)
 	{
-		r_center  = m_Rinner + (m_uniform_fraction(Mask::RandomGenerator::GetInstance().GetGenerator())+ringch)*m_deltaR;
+		r_center  = m_innerR + (m_uniformFraction(Mask::RandomGenerator::GetInstance().GetGenerator())+ringch)*m_deltaR;
-		phi_center = -m_deltaPhi/2.0 + (m_uniform_fraction(Mask::RandomGenerator::GetInstance().GetGenerator())+wedgech)*m_deltaPhi_per_wedge;
+		phi_center = -m_deltaPhi/2.0 + (m_uniformFraction(Mask::RandomGenerator::GetInstance().GetGenerator())+wedgech)*m_deltaPhiWedge;
 	}
 	else
 	{
-		r_center  = m_Rinner + (0.5+ringch)*m_deltaR;
+		r_center  = m_innerR + (0.5+ringch)*m_deltaR;
-		phi_center = -m_deltaPhi/2.0 + (0.5+wedgech)*m_deltaPhi_per_wedge;
+		phi_center = -m_deltaPhi/2.0 + (0.5+wedgech)*m_deltaPhiWedge;
 	}
 	double x = r_center*std::cos(phi_center);
 	double y = r_center*std::sin(phi_center);
 	double z = 0;
 
-	Mask::Vec3 hit(x, y, z);
+	ROOT::Math::XYZPoint hit(x, y, z);
 
 	return TransformCoordinates(hit);
 }

src/Detectors/QQQDetector.h

@@ -0,0 +1,65 @@
+/*
+	QQQDetector.h
+	Class implementing geometry for QQQDetector where the detector is perpendicular to the beam axis.
+	Detector is first generated centered on the x-axis (phi=0)
+
+	Coordinate convention : +z is downstream, -z is upstream. +y is vertically down in the lab.
+*/
+#ifndef QQQDETECTOR_H
+#define QQQDETECTOR_H
+
+#include <cmath>
+#include <vector>
+
+#include "RandomGenerator.h"
+#include "Math/Point3D.h"
+#include "Math/Vector3D.h"
+#include "Math/RotationZ.h"
+#include "Math/Translation3D.h"
+
+class QQQDetector
+{
+public:
+	QQQDetector(double R_in, double R_out, double deltaPhi, double phiCentral, double z, double x=0, double y=0);
+	~QQQDetector();
+	const ROOT::Math::XYZPoint& GetRingCoordinates(int ringch, int corner) { return m_ringCoords[ringch][corner]; }
+	const ROOT::Math::XYZPoint& GetWedgeCoordinates(int wedgech, int corner) { return m_wedgeCoords[wedgech][corner]; }
+	const ROOT::Math::XYZVector& GetNorm() { return m_norm; }
+	ROOT::Math::XYZPoint GetTrajectoryCoordinates(double theta, double phi);
+	std::pair<int, int> GetTrajectoryRingWedge(double theta, double phi);
+	ROOT::Math::XYZPoint GetHitCoordinates(int ringch, int wedgech);
+	
+	void SetSmearing(bool isSmearing) { m_isSmearing = isSmearing; }
+
+	int GetNumberOfRings() { return s_nRings; }
+	int GetNumberOfWedges() { return s_nWedges; }
+
+private:
+
+	bool CheckChannel(int ch) { return (ch >=0 && ch < s_nRings); }
+	bool CheckCorner(int corner) { return (corner >=0 && corner < 4); }
+
+	void CalculateCorners();
+	ROOT::Math::XYZPoint TransformCoordinates(ROOT::Math::XYZPoint& vector) { return m_translation * (m_zRotation * vector) ; }
+
+	double m_innerR;
+	double m_outerR;
+	double m_deltaR;
+	double m_deltaPhi;
+	double m_deltaPhiWedge;
+	double m_centralPhi;
+
+	std::vector<std::vector<ROOT::Math::XYZPoint>> m_ringCoords, m_wedgeCoords;
+	ROOT::Math::Translation3D m_translation;
+	ROOT::Math::XYZVector m_norm;
+	ROOT::Math::RotationZ m_zRotation;
+
+	std::uniform_real_distribution<double> m_uniformFraction;
+	bool m_isSmearing;
+
+	static constexpr int s_nRings = 16;
+	static constexpr int s_nWedges = 16;
+	static constexpr double s_deg2rad  = M_PI/180.0;
+};
+
+#endif

src/Detectors/SabreDetector.cpp

@@ -53,126 +53,133 @@
 #include "SabreDetector.h"
 
 SabreDetector::SabreDetector() :
-m_Router(0.1351), m_Rinner(0.0326), m_deltaPhi_flat(54.4*deg2rad), m_phiCentral(0.0), m_tilt(0.0), m_translation(0.,0.,0.), m_norm_flat(0,0,1.0),
+m_outerR(0.1351), m_innerR(0.0326), m_deltaPhiFlat(54.4*s_deg2rad), m_centerPhi(0.0), m_tilt(0.0), 
-m_detectorID(-1)
+	m_translation(0.,0.,0.), m_norm(0,0,1.0), m_detectorID(-1)
 {
-	m_YRot.SetAngle(m_tilt);
+	m_yRotation.SetAngle(m_tilt);
-	m_ZRot.SetAngle(m_phiCentral);
+	m_zRotation.SetAngle(m_centerPhi);
 
 	//Initialize the coordinate arrays
-	m_ringCoords_flat.resize(m_nRings);
+	m_flatRingCoords.resize(s_nRings);
-	m_ringCoords_tilt.resize(m_nRings);
+	m_tiltRingCoords.resize(s_nRings);
-	m_wedgeCoords_flat.resize(m_nWedges);
+	m_flatWedgeCoords.resize(s_nWedges);
-	m_wedgeCoords_tilt.resize(m_nWedges);
+	m_tiltWedgeCoords.resize(s_nWedges);
-	for(int i=0; i<m_nRings; i++) {
+	for(int i=0; i<s_nRings; i++) {
-		m_ringCoords_flat[i].resize(4);
+		m_flatRingCoords[i].resize(4);
-		m_ringCoords_tilt[i].resize(4);
+		m_tiltRingCoords[i].resize(4);
 	}
-	for(int i=0; i<m_nWedges; i++) {
+	for(int i=0; i<s_nWedges; i++) {
-		m_wedgeCoords_flat[i].resize(4);
+		m_flatWedgeCoords[i].resize(4);
-		m_wedgeCoords_tilt[i].resize(4);
+		m_tiltWedgeCoords[i].resize(4);
 	}
 
-	m_deltaR_flat = m_Router - m_Rinner;
+	m_deltaRFlat = m_outerR - m_innerR;
-	m_deltaR_flat_ring = m_deltaR_flat/m_nRings;
+	m_deltaRFlatRing = m_deltaRFlat/s_nRings;
+	m_deltaPhiFlatWedge = m_deltaPhiFlat/s_nWedges;
 
 	CalculateCorners();
 }
 
-SabreDetector::SabreDetector(int detID, double Rin, double Rout, double deltaPhi_flat, double phiCentral, double tiltFromVert, double zdist, double xdist, double ydist) :
+SabreDetector::SabreDetector(int detID, double Rin, double Rout, double deltaPhi_flat, double phiCentral, 
-m_Router(Rout), m_Rinner(Rin), m_deltaPhi_flat(deltaPhi_flat), m_phiCentral(phiCentral), m_tilt(tiltFromVert), m_translation(xdist, ydist, zdist), m_norm_flat(0,0,1.0),
+							 double tiltFromVert, double zdist, double xdist, double ydist) :
-m_detectorID(detID)
+	m_outerR(Rout), m_innerR(Rin), m_deltaPhiFlat(deltaPhi_flat), m_centerPhi(phiCentral), m_tilt(tiltFromVert), 
+	m_translation(xdist, ydist, zdist), m_norm(0,0,1.0), m_detectorID(detID)
 {
-	m_YRot.SetAngle(m_tilt);
+	m_yRotation.SetAngle(m_tilt);
-	m_ZRot.SetAngle(m_phiCentral);
+	m_zRotation.SetAngle(m_centerPhi);
 
 	//Initialize coordinate arrays
-	m_ringCoords_flat.resize(m_nRings);
+	m_flatRingCoords.resize(s_nRings);
-	m_ringCoords_tilt.resize(m_nRings);
+	m_tiltRingCoords.resize(s_nRings);
-	m_wedgeCoords_flat.resize(m_nWedges);
+	m_flatWedgeCoords.resize(s_nWedges);
-	m_wedgeCoords_tilt.resize(m_nWedges);
+	m_tiltWedgeCoords.resize(s_nWedges);
-	for(int i=0; i<m_nRings; i++) {
+	for(int i=0; i<s_nRings; i++)
-		m_ringCoords_flat[i].resize(4);
+	{
-		m_ringCoords_tilt[i].resize(4);
+		m_flatRingCoords[i].resize(4);
+		m_tiltRingCoords[i].resize(4);
 	}
-	for(int i=0; i<m_nWedges; i++) {
+	for(int i=0; i<s_nWedges; i++)
-		m_wedgeCoords_flat[i].resize(4);
+	{
-		m_wedgeCoords_tilt[i].resize(4);
+		m_flatWedgeCoords[i].resize(4);
+		m_tiltWedgeCoords[i].resize(4);
 	}
 
-	m_deltaR_flat = m_Router - m_Rinner;
+	m_deltaRFlat = m_outerR - m_innerR;
-	m_deltaR_flat_ring = m_deltaR_flat/m_nRings;
+	m_deltaRFlatRing = m_deltaRFlat/s_nRings;
-	m_deltaPhi_flat_wedge = m_deltaPhi_flat/m_nWedges;
+	m_deltaPhiFlatWedge = m_deltaPhiFlat/s_nWedges;
 
 	CalculateCorners();
 }
 
 SabreDetector::~SabreDetector() {}
 
-void SabreDetector::CalculateCorners() {
+void SabreDetector::CalculateCorners()
+{
 
 	double x0, x1, x2, x3;
 	double y0, y1, y2, y3;
 	double z0, z1, z2, z3;
 
 	//Generate flat ring corner coordinates
-	for(int i=0; i<m_nRings; i++) {
+	for(int i=0; i<s_nRings; i++)
-		x0 = (m_Rinner + m_deltaR_flat_ring*(i+1))*std::cos(-m_deltaPhi_flat/2.0);
+	{
-		y0 = (m_Rinner + m_deltaR_flat_ring*(i+1))*std::sin(-m_deltaPhi_flat/2.0);
+		x0 = (m_innerR + m_deltaRFlatRing*(i+1))*std::cos(-m_deltaPhiFlat/2.0);
+		y0 = (m_innerR + m_deltaRFlatRing*(i+1))*std::sin(-m_deltaPhiFlat/2.0);
 		z0 = 0.0;
-		m_ringCoords_flat[i][0].SetVectorCartesian(x0, y0, z0);
+		m_flatRingCoords[i][0].SetXYZ(x0, y0, z0);
 
-		x1 = (m_Rinner + m_deltaR_flat_ring*(i))*std::cos(-m_deltaPhi_flat/2.0);
+		x1 = (m_innerR + m_deltaRFlatRing*(i))*std::cos(-m_deltaPhiFlat/2.0);
-		y1 = (m_Rinner + m_deltaR_flat_ring*(i))*std::sin(-m_deltaPhi_flat/2.0);
+		y1 = (m_innerR + m_deltaRFlatRing*(i))*std::sin(-m_deltaPhiFlat/2.0);
 		z1 = 0.0;
-		m_ringCoords_flat[i][1].SetVectorCartesian(x1, y1, z1);
+		m_flatRingCoords[i][1].SetXYZ(x1, y1, z1);
 
-		x2 = (m_Rinner + m_deltaR_flat_ring*(i))*std::cos(m_deltaPhi_flat/2.0);
+		x2 = (m_innerR + m_deltaRFlatRing*(i))*std::cos(m_deltaPhiFlat/2.0);
-		y2 = (m_Rinner + m_deltaR_flat_ring*(i))*std::sin(m_deltaPhi_flat/2.0);
+		y2 = (m_innerR + m_deltaRFlatRing*(i))*std::sin(m_deltaPhiFlat/2.0);
 		z2 = 0.0;
-		m_ringCoords_flat[i][2].SetVectorCartesian(x2, y2, z2);
+		m_flatRingCoords[i][2].SetXYZ(x2, y2, z2);
 
-		x3 = (m_Rinner + m_deltaR_flat_ring*(i+1))*std::cos(m_deltaPhi_flat/2.0);
+		x3 = (m_innerR + m_deltaRFlatRing*(i+1))*std::cos(m_deltaPhiFlat/2.0);
-		y3 = (m_Rinner + m_deltaR_flat_ring*(i+1))*std::sin(m_deltaPhi_flat/2.0);
+		y3 = (m_innerR + m_deltaRFlatRing*(i+1))*std::sin(m_deltaPhiFlat/2.0);
 		z3 = 0.0;
-		m_ringCoords_flat[i][3].SetVectorCartesian(x3, y3, z3);
+		m_flatRingCoords[i][3].SetXYZ(x3, y3, z3);
 	}
 
 	//Generate flat wedge corner coordinates
-	for(int i=0; i<m_nWedges; i++) {
+	for(int i=0; i<s_nWedges; i++)
-		x0 = m_Router * std::cos(-m_deltaPhi_flat/2.0 + i*m_deltaPhi_flat_wedge);
+	{
-		y0 = m_Router * std::sin(-m_deltaPhi_flat/2.0 + i*m_deltaPhi_flat_wedge);
+		x0 = m_outerR * std::cos(-m_deltaPhiFlat/2.0 + i*m_deltaPhiFlatWedge);
+		y0 = m_outerR * std::sin(-m_deltaPhiFlat/2.0 + i*m_deltaPhiFlatWedge);
 		z0 = 0.0;
-		m_wedgeCoords_flat[i][0].SetVectorCartesian(x0, y0, z0);
+		m_flatWedgeCoords[i][0].SetXYZ(x0, y0, z0);
 
-		x1 = m_Rinner * std::cos(-m_deltaPhi_flat/2.0 + i*m_deltaPhi_flat_wedge);
+		x1 = m_innerR * std::cos(-m_deltaPhiFlat/2.0 + i*m_deltaPhiFlatWedge);
-		y1 = m_Rinner * std::sin(-m_deltaPhi_flat/2.0 + i*m_deltaPhi_flat_wedge);
+		y1 = m_innerR * std::sin(-m_deltaPhiFlat/2.0 + i*m_deltaPhiFlatWedge);
 		z1 = 0.0;
-		m_wedgeCoords_flat[i][1].SetVectorCartesian(x1, y1, z1);
+		m_flatWedgeCoords[i][1].SetXYZ(x1, y1, z1);
 
-		x2 = m_Rinner * std::cos(-m_deltaPhi_flat/2.0 + (i+1)*m_deltaPhi_flat_wedge);
+		x2 = m_innerR * std::cos(-m_deltaPhiFlat/2.0 + (i+1)*m_deltaPhiFlatWedge);
-		y2 = m_Rinner * std::sin(-m_deltaPhi_flat/2.0 + (i+1)*m_deltaPhi_flat_wedge);
+		y2 = m_innerR * std::sin(-m_deltaPhiFlat/2.0 + (i+1)*m_deltaPhiFlatWedge);
 		z2 = 0.0;
-		m_wedgeCoords_flat[i][2].SetVectorCartesian(x2, y2, z2);
+		m_flatWedgeCoords[i][2].SetXYZ(x2, y2, z2);
 
-		x3 = m_Router * std::cos(-m_deltaPhi_flat/2.0 + (i+1)*m_deltaPhi_flat_wedge);
+		x3 = m_outerR * std::cos(-m_deltaPhiFlat/2.0 + (i+1)*m_deltaPhiFlatWedge);
-		y3 = m_Router * std::sin(-m_deltaPhi_flat/2.0 + (i+1)*m_deltaPhi_flat_wedge);
+		y3 = m_outerR * std::sin(-m_deltaPhiFlat/2.0 + (i+1)*m_deltaPhiFlatWedge);
 		z3 = 0.0;
-		m_wedgeCoords_flat[i][3].SetVectorCartesian(x3, y3, z3);
+		m_flatWedgeCoords[i][3].SetXYZ(x3, y3, z3);
 	}
 
 	//Generate tilted rings
-	for(int i=0; i<m_nRings; i++) {
+	for(int i=0; i<s_nRings; i++)
-		for(int j=0; j<4; j++) {
+	{
-			m_ringCoords_tilt[i][j] = TransformToTiltedFrame(m_ringCoords_flat[i][j]);
+		for(int j=0; j<4; j++)
-		}
+			m_tiltRingCoords[i][j] = Transform(m_flatRingCoords[i][j]);
 	}
 
 	//Generate tilted wedges
-	for(int i=0; i<m_nWedges; i++) {
+	for(int i=0; i<s_nWedges; i++)
-		for(int j=0; j<4; j++) {
+	{
-			m_wedgeCoords_tilt[i][j] = TransformToTiltedFrame(m_wedgeCoords_flat[i][j]);
+		for(int j=0; j<4; j++)
-		}
+			m_tiltWedgeCoords[i][j] = Transform(m_flatWedgeCoords[i][j]);
 	}
 }
 
@@ -193,35 +200,37 @@ void SabreDetector::CalculateCorners() {
 	!NOTE: This currently only applies to a configuration where there is no translation in x & y. The math becomes significantly messier in these cases.
 	Also, don't use tan(). It's behavior near PI/2 makes it basically useless for these.
 */
-Mask::Vec3 SabreDetector::GetTrajectoryCoordinates(double theta, double phi) {
+ROOT::Math::XYZPoint SabreDetector::GetTrajectoryCoordinates(double theta, double phi)
-	if(m_translation.GetX() != 0.0 || m_translation.GetY() != 0.0) {
+{
-		return Mask::Vec3();
+	if(m_translation.Vect().X() != 0.0 || m_translation.Vect().Y() != 0.0)
-	}
+		return ROOT::Math::XYZPoint();
 
 	//Calculate the *potential* phi in the flat detector
-	double phi_numerator = std::cos(m_tilt)*(std::sin(phi)*std::cos(m_phiCentral) - std::sin(m_phiCentral)*std::cos(phi));
+	double phi_numerator = std::cos(m_tilt)*(std::sin(phi)*std::cos(m_centerPhi) - std::sin(m_centerPhi)*std::cos(phi));
-	double phi_denominator = std::cos(m_phiCentral)*std::cos(phi) + std::sin(m_phiCentral)*std::sin(phi);
+	double phi_denominator = std::cos(m_centerPhi)*std::cos(phi) + std::sin(m_centerPhi)*std::sin(phi);
 	double phi_flat = std::atan2(phi_numerator, phi_denominator);
-	if(phi_flat < 0) phi_flat += M_PI*2.0;
+	if(phi_flat < 0)
+		phi_flat += M_PI*2.0;
 
 	//Calculate the *potential* R in the flat detector
-	double r_numerator = m_translation.GetZ()*std::cos(phi)*std::sin(theta);
+	double r_numerator = m_translation.Vect().Z()*std::cos(phi)*std::sin(theta);
-	double r_denominator = std::cos(phi_flat)*std::cos(m_phiCentral)*std::cos(m_tilt)*std::cos(theta) - std::sin(phi_flat)*std::sin(m_phiCentral)*std::cos(theta) - std::cos(phi_flat)*std::sin(m_tilt)*std::cos(phi)*std::sin(theta);
+	double r_denominator = std::cos(phi_flat)*std::cos(m_centerPhi)*std::cos(m_tilt)*std::cos(theta) -
+						   std::sin(phi_flat)*std::sin(m_centerPhi)*std::cos(theta) -
+						   std::cos(phi_flat)*std::sin(m_tilt)*std::cos(phi)*std::sin(theta);
 	double r_flat = r_numerator/r_denominator;
 
 	//Calculate the distance from the origin to the hit on the detector
-	double R_to_detector = (r_flat*std::cos(phi_flat)*std::sin(m_tilt) + m_translation.GetZ())/std::cos(theta);
+	double R_to_detector = (r_flat*std::cos(phi_flat)*std::sin(m_tilt) + m_translation.Vect().Z())/std::cos(theta);
 	double xhit = R_to_detector*std::sin(theta)*std::cos(phi);
 	double yhit = R_to_detector*std::sin(theta)*std::sin(phi);
 	double zhit = R_to_detector*std::cos(theta);
 
 
 	//Check to see if our flat coords fall inside the flat detector
-	if(IsInside(r_flat, phi_flat)) {
+	if(IsInside(r_flat, phi_flat))
-		return Mask::Vec3(xhit, yhit, zhit);
+		return ROOT::Math::XYZPoint(xhit, yhit, zhit);
-	} else {
+	else
-		return Mask::Vec3();
+		return ROOT::Math::XYZPoint();
-	}
 }
 
 /*
@@ -241,20 +250,23 @@ Mask::Vec3 SabreDetector::GetTrajectoryCoordinates(double theta, double phi) {
 	!NOTE: This currently only applies to a configuration where there is no translation in x & y. The math becomes significantly messier in these cases.
 	Also, don't use tan(). It's behavior near PI/2 makes it basically useless for these.
 */
-std::pair<int, int> SabreDetector::GetTrajectoryRingWedge(double theta, double phi) {
+std::pair<int, int> SabreDetector::GetTrajectoryRingWedge(double theta, double phi)
-	if(m_translation.GetX() != 0.0 || m_translation.GetY() != 0.0) {
+{
+	if(m_translation.Vect().X() != 0.0 || m_translation.Vect().Y() != 0.0)
 		return std::make_pair(-1, -1);
-	}
 
 	//Calculate the *potential* phi in the flat detector
-	double phi_numerator = std::cos(m_tilt)*(std::sin(phi)*std::cos(m_phiCentral) - std::sin(m_phiCentral)*std::cos(phi));
+	double phi_numerator = std::cos(m_tilt)*(std::sin(phi)*std::cos(m_centerPhi) - std::sin(m_centerPhi)*std::cos(phi));
-	double phi_denominator = std::cos(m_phiCentral)*std::cos(phi) + std::sin(m_phiCentral)*std::sin(phi);
+	double phi_denominator = std::cos(m_centerPhi)*std::cos(phi) + std::sin(m_centerPhi)*std::sin(phi);
 	double phi_flat = std::atan2(phi_numerator, phi_denominator);
-	if(phi_flat < 0) phi_flat += M_PI*2.0;
+	if(phi_flat < 0)
+		phi_flat += M_PI*2.0;
 
 	//Calculate the *potential* R in the flat detector
-	double r_numerator = m_translation.GetZ()*std::cos(phi)*std::sin(theta);
+	double r_numerator = m_translation.Vect().Z()*std::cos(phi)*std::sin(theta);
-	double r_denominator = std::cos(phi_flat)*std::cos(m_phiCentral)*std::cos(m_tilt)*std::cos(theta) - std::sin(phi_flat)*std::sin(m_phiCentral)*std::cos(theta) - std::cos(phi_flat)*std::sin(m_tilt)*std::cos(phi)*std::sin(theta);
+	double r_denominator = std::cos(phi_flat)*std::cos(m_centerPhi)*std::cos(m_tilt)*std::cos(theta) -
+						   std::sin(phi_flat)*std::sin(m_centerPhi)*std::cos(theta) -
+						   std::cos(phi_flat)*std::sin(m_tilt)*std::cos(phi)*std::sin(theta);
 	double r_flat = r_numerator/r_denominator;
 
 	//Calculate the distance from the origin to the hit on the detector
@@ -262,31 +274,41 @@ std::pair<int, int> SabreDetector::GetTrajectoryRingWedge(double theta, double p
 
 
 	//Check to see if our flat coords fall inside the flat detector
-	if(IsInside(r_flat, phi_flat)) {
+	if(IsInside(r_flat, phi_flat))
+	{
 		int ringch, wedgech;
-		if(phi_flat > M_PI) phi_flat -= 2.0*M_PI; //Need phi in terms of [-deltaPhi_flat/2, deltaPhi_flat/2]
+		if(phi_flat > M_PI)
-		for(int i=0; i<m_nRings; i++) {
+			phi_flat -= 2.0*M_PI; //Need phi in terms of [-deltaPhi_flat/2, deltaPhi_flat/2]
-			if(IsRingTopEdge(r_flat, i) || IsRingBottomEdge(r_flat, i)) { //If it falls in the interstrip spacing, kill it
+		for(int i=0; i<s_nRings; i++)
+		{
+			if(IsRingTopEdge(r_flat, i) || IsRingBottomEdge(r_flat, i))
+			{ //If it falls in the interstrip spacing, kill it
 				ringch = -1;
 				break;
-			} else if(IsRing(r_flat, i)) {
+			}
+			else if(IsRing(r_flat, i))
+			{
 				ringch = i;
 				break;
 			}
 		}
-		for(int i=0; i<m_nWedges; i++) {
+		for(int i=0; i<s_nWedges; i++)
-			if(IsWedgeTopEdge(phi_flat, i) || IsWedgeBottomEdge(phi_flat, i)){ //If it falls in the interstrip spacing, kill it
+		{
+			if(IsWedgeTopEdge(phi_flat, i) || IsWedgeBottomEdge(phi_flat, i))
+			{ //If it falls in the interstrip spacing, kill it
 				wedgech = -1;
 				break;
-			} else if(IsWedge(phi_flat, i)) {
+			}
+			else if(IsWedge(phi_flat, i))
+			{
 				wedgech = i;
 				break;
 			}
 		}
 		return std::make_pair(ringch, wedgech);
-	} else {
-		return std::make_pair(-1,-1);
 	}
+	else
+		return std::make_pair(-1,-1);
 }
 
 /*
@@ -295,18 +317,18 @@ std::pair<int, int> SabreDetector::GetTrajectoryRingWedge(double theta, double p
 	randomly wiggle the point within the pixel. Method intended for use with data, or
 	to smear out simulated data to mimic real data.
 */
-Mask::Vec3 SabreDetector::GetHitCoordinates(int ringch, int wedgech) {
+ROOT::Math::XYZPoint SabreDetector::GetHitCoordinates(int ringch, int wedgech)
-	if(!CheckRingChannel(ringch) || !CheckWedgeChannel(wedgech)) {
+{
-		return Mask::Vec3();
+	if(!CheckRingChannel(ringch) || !CheckWedgeChannel(wedgech))
-	}
+		return ROOT::Math::XYZPoint();
 
-	double r_center  = m_Rinner + (0.5+ringch)*m_deltaR_flat_ring;
+	double r_center  = m_innerR + (0.5+ringch)*m_deltaRFlatRing;
-	double phi_center = -m_deltaPhi_flat/2.0 + (0.5+wedgech)*m_deltaPhi_flat_wedge;
+	double phi_center = -m_deltaPhiFlat/2.0 + (0.5+wedgech)*m_deltaPhiFlatWedge;
 	double x = r_center*std::cos(phi_center);
 	double y = r_center*std::sin(phi_center);
 	double z = 0;
 
-	Mask::Vec3 hit(x, y, z);
+	ROOT::Math::XYZPoint hit(x, y, z);
 
-	return TransformToTiltedFrame(hit);
+	return Transform(hit);
 }

src/Detectors/SabreDetector.h

@@ -0,0 +1,189 @@
+/*
+
+  Class which represents a single MMM detector in the SABRE array at FSU. Origial code by KGH, re-written by
+  GWM.
+
+  Distances in meters, angles in radians.
+
+  The channel arrays have four points, one for each corner. The corners are
+  as follows, as if looking BACK along beam (i.e. from the target's pov):
+
+  0---------------------1
+  |                     |
+  |                     |      x
+  |                     |      <-----
+  |                     |      		|
+  |                     |      		|
+  3---------------------2      		y
+                               (z is hence positive along beam direction) 
+
+  The channel numbers, also as looking back from target pov, are:
+
+  >> rings are 0 -- 15 from inner to outer:
+
+    15 -------------------
+    14 -------------------
+    13 -------------------
+       .
+       .
+       .
+     2 -------------------
+     1 -------------------
+     0 -------------------
+
+  >> wedges are 0 -- 7 moving counterclockwise:
+
+      7 6 ... 1 0
+     | | |   | | |
+     | | |   | | |
+     | | |   | | |
+     | | |   | | |
+     | | |   | | |
+     | | |   | | |
+
+
+  >> Note that the detector starts centered on the x-axis (central phi = 0) untilted, and then is rotated to wherever the frick
+  	 it is supposed to go; phi = 90 is centered on y axis, pointing down towards the bottom of the scattering chamber
+
+  -- GWM, Dec 2020; based on the og code from kgh
+
+*/
+
+#ifndef SABREDETECTOR_H
+#define SABREDETECTOR_H
+
+#include <vector>
+#include <cmath>
+
+#include "Math/Point3D.h"
+#include "Math/Vector3D.h"
+#include "Math/RotationZ.h"
+#include "Math/RotationY.h"
+#include "Math/Translation3D.h"
+
+class SabreDetector {
+public:
+
+	SabreDetector();
+	SabreDetector(int detID, double Rin, double Rout, double deltaPhi_flat, double phiCentral, double tiltFromVert, double zdist, double xdist=0, double ydist=0);
+	~SabreDetector();
+
+	/*Return coordinates of the corners of each ring/wedge in SABRE*/
+	const ROOT::Math::XYZPoint& GetRingFlatCoords(int ch, int corner) const { return m_flatRingCoords[ch][corner]; }
+	const ROOT::Math::XYZPoint& GetWedgeFlatCoords(int ch, int corner) const { return m_flatWedgeCoords[ch][corner]; }
+	const ROOT::Math::XYZPoint& GetRingTiltCoords(int ch, int corner) const { return m_tiltRingCoords[ch][corner]; }
+	const ROOT::Math::XYZPoint& GetWedgeTiltCoords(int ch, int corner) const { return m_tiltWedgeCoords[ch][corner]; }
+
+	ROOT::Math::XYZPoint GetTrajectoryCoordinates(double theta, double phi);
+	std::pair<int, int> GetTrajectoryRingWedge(double theta, double phi);
+	ROOT::Math::XYZPoint GetHitCoordinates(int ringch, int wedgech);
+
+	int GetNumberOfWedges() { return s_nWedges; }
+	int GetNumberOfRings() { return s_nRings; }
+	ROOT::Math::XYZVector GetNormTilted() { return m_zRotation*(m_yRotation*m_norm); }
+	int GetDetectorID() { return m_detectorID; }
+
+private:
+
+	
+
+	void CalculateCorners();
+
+	/*Performs the transformation to the tilted,rotated,translated frame of the SABRE detector*/
+	ROOT::Math::XYZPoint Transform(const ROOT::Math::XYZPoint& vector) { return m_translation*(m_zRotation*(m_yRotation*vector)); };
+
+	/*Determine if a given channel/corner combo is valid*/
+	bool CheckRingChannel(int ch) { return (ch<s_nRings && ch>=0) ? true : false; };
+	bool CheckWedgeChannel(int ch) { return (ch<s_nWedges && ch >=0) ? true : false; };
+	bool CheckCorner(int corner) { return (corner < 4 && corner >=0) ? true : false; };
+	bool CheckRingLocation(int ch, int corner) { return CheckRingChannel(ch) && CheckCorner(corner); };
+	bool CheckWedgeLocation(int ch, int corner) { return CheckWedgeChannel(ch) && CheckCorner(corner); };
+
+	/*
+		For all of the calculations, need a limit precision to determine if values are actually equal or not
+		Here the approx. size of the strip spacing is used as the precision.
+	*/
+	bool CheckPositionEqual(double val1,double val2) { return fabs(val1-val2) > s_positionTol ? false : true; };
+	bool CheckAngleEqual(double val1,double val2) { return fabs(val1-val2) > s_angularTol ? false : true; };
+
+	/*Determine if a hit is within the bulk detector*/
+	bool IsInside(double r, double phi)
+	{ 
+		double phi_1 = m_deltaPhiFlat/2.0;
+		double phi_2 = M_PI*2.0 - m_deltaPhiFlat/2.0;
+		return (((r > m_innerR && r < m_outerR) || CheckPositionEqual(r, m_innerR) || CheckPositionEqual(r, m_outerR)) 
+				&& (phi > phi_2 || phi < phi_1 || CheckAngleEqual(phi, phi_1) || CheckAngleEqual(phi, phi_2)));
+	};
+
+	/*
+		For a given radius/phi are you inside of a given ring/wedge channel,
+		or are you on the spacing between these channels
+	*/
+	bool IsRing(double r, int ringch)
+	{
+		double ringtop = m_innerR + m_deltaRFlatRing*(ringch + 1);
+		double ringbottom = m_innerR + m_deltaRFlatRing*(ringch);
+		return (r>ringbottom && r<ringtop); 
+	};
+
+	inline bool IsRingTopEdge(double r, int ringch)
+	{
+		double ringtop = m_innerR + m_deltaRFlatRing*(ringch + 1);
+		return CheckPositionEqual(r, ringtop); 
+	};
+
+	inline bool IsRingBottomEdge(double r, int ringch)
+	{
+		double ringbottom = m_innerR + m_deltaRFlatRing*(ringch);
+		return CheckPositionEqual(r, ringbottom); 
+	};
+
+	inline bool IsWedge(double phi, int wedgech)
+	{
+		double wedgetop = -m_deltaPhiFlat/2.0 + m_deltaPhiFlatWedge*(wedgech+1);
+		double wedgebottom = -m_deltaPhiFlat/2.0 + m_deltaPhiFlatWedge*(wedgech);
+		return ((phi>wedgebottom && phi<wedgetop));
+	};
+
+	inline bool IsWedgeTopEdge(double phi, int wedgech)
+	{
+		double wedgetop = -m_deltaPhiFlat/2.0 + m_deltaPhiFlatWedge*(wedgech+1);
+		return CheckAngleEqual(phi, wedgetop);
+	}
+
+	inline bool IsWedgeBottomEdge(double phi, int wedgech)
+	{
+		double wedgebottom = -m_deltaPhiFlat/2.0 + m_deltaPhiFlatWedge*(wedgech);
+		return CheckAngleEqual(phi, wedgebottom);
+	}
+
+	/*Class constants*/
+	static constexpr int s_nRings = 16;
+	static constexpr int s_nWedges = 8;
+	static constexpr double s_deg2rad = M_PI/180.0;
+	/*These are implicitly the width of the spacing between detector active strips*/
+	static constexpr double s_positionTol = 0.0001; //0.1 mm position tolerance
+	static constexpr double s_angularTol = 0.1*M_PI/180.0; // 0.1 degree angular tolerance
+
+	/*Class data*/
+	double m_outerR;
+	double m_innerR;
+	double m_deltaRFlat;
+	double m_deltaRFlatRing;
+	double m_deltaPhiFlat;
+	double m_deltaPhiFlatWedge;
+	double m_centerPhi;
+	double m_tilt;
+	ROOT::Math::Translation3D m_translation;
+	ROOT::Math::RotationY m_yRotation;
+	ROOT::Math::RotationZ m_zRotation;
+	ROOT::Math::XYZVector m_norm;
+	int m_detectorID;
+
+	std::vector<std::vector<ROOT::Math::XYZPoint>> m_flatRingCoords, m_flatWedgeCoords;
+	std::vector<std::vector<ROOT::Math::XYZPoint>> m_tiltRingCoords, m_tiltWedgeCoords;
+
+};
+
+
+#endif

src/Detectors/SabreEfficiency.cpp

@@ -1,40 +1,44 @@
 #include "SabreEfficiency.h"
-#include "MaskFile.h"
 #include <fstream>
 #include <iostream>
 #include <iomanip>
 
+#include "TFile.h"
+#include "TTree.h"
+
 
 SabreEfficiency::SabreEfficiency() : 
-	DetectorEfficiency(), deadlayer(DEADLAYER_THIN), sabre_eloss(SABRE_THICKNESS), degrader(DEGRADER_THICKNESS)
+	DetectorEfficiency(), m_deadlayerEloss({14}, {28}, {1}, s_deadlayerThickness), 
+	m_detectorEloss({14}, {28}, {1}, s_detectorThickness), m_degraderEloss({73}, {181}, {1}, s_degraderThickness)
 {
+
+	for(int i=0; i<s_nDets; i++)
+		m_detectors.emplace_back(i, s_innerR, s_outerR, s_deltaPhi*s_deg2rad, s_centerPhiList[i]*s_deg2rad, s_tilt*s_deg2rad, s_zOffset);
 	//Only 0, 1, 4 valid in degrader land
-	//detectors.emplace_back(0, INNER_R,OUTER_R,PHI_COVERAGE*DEG2RAD,PHI0*DEG2RAD,TILT*DEG2RAD,DIST_2_TARG);
+	m_degradedDetectors[0] = true;
-	//detectors.emplace_back(1, INNER_R,OUTER_R,PHI_COVERAGE*DEG2RAD,PHI1*DEG2RAD,TILT*DEG2RAD,DIST_2_TARG);
+	m_degradedDetectors[1] = true;
- 	detectors.emplace_back(2, INNER_R,OUTER_R,PHI_COVERAGE*DEG2RAD,PHI2*DEG2RAD,TILT*DEG2RAD,DIST_2_TARG);
+	m_degradedDetectors[2] = false;
- 	detectors.emplace_back(3, INNER_R,OUTER_R,PHI_COVERAGE*DEG2RAD,PHI3*DEG2RAD,TILT*DEG2RAD,DIST_2_TARG);
+	m_degradedDetectors[3] = false;
- 	//detectors.emplace_back(4, INNER_R,OUTER_R,PHI_COVERAGE*DEG2RAD,PHI4*DEG2RAD,TILT*DEG2RAD,DIST_2_TARG);
+	m_degradedDetectors[4] = true;
 
- 	
+	//Choose who to look at right now. Usually switch on or off degraded/non-degraded.
-	std::vector<int> dead_z = {14};
+	m_activeDetectors[0] = false;
-	std::vector<int> dead_a = {28};
+	m_activeDetectors[1] = false;
-	std::vector<int> dead_stoich = {1};
+	m_activeDetectors[2] = true;
-	deadlayer.SetElements(dead_z, dead_a, dead_stoich);
+	m_activeDetectors[3] = true;
-	sabre_eloss.SetElements(dead_z, dead_a, dead_stoich);
+	m_activeDetectors[4] = false;
-	std::vector<int> deg_z = {73};
-	std::vector<int> deg_a = {181};
-	std::vector<int> deg_s = {1};
-	degrader.SetElements(deg_z, deg_a, deg_s);
 }
 
 SabreEfficiency::~SabreEfficiency() {}
 
-void SabreEfficiency::CalculateEfficiency(const std::string& inputname, const std::string& outputname, const std::string& statsname) {
+void SabreEfficiency::CalculateEfficiency(const std::string& inputname, const std::string& outputname, const std::string& statsname)
+{
 	std::cout<<"----------SABRE Efficiency Calculation----------"<<std::endl;
 	std::cout<<"Loading in output from kinematics simulation: "<<inputname<<std::endl;
 	std::cout<<"Running efficiency calculation..."<<std::endl;
 
-	if(!dmap.IsValid()) {
+	if(!m_deadMap.IsValid())
+	{
 		std::cerr<<"Unable to run SABRE Efficiency without a dead channel map."<<std::endl;
 		std::cerr<<"If you have no dead channels, simply make a file that's empty"<<std::endl;
 		std::cerr<<"Exiting."<<std::endl;
@@ -42,137 +46,137 @@ void SabreEfficiency::CalculateEfficiency(const std::string& inputname, const st
 	}
 
 
-	Mask::MaskFile input(inputname, Mask::MaskFile::FileType::read);
+	TFile* input = TFile::Open(inputname.c_str(), "READ");
-	Mask::MaskFile output(outputname, Mask::MaskFile::FileType::write);
+	TFile* output = TFile::Open(outputname.c_str(), "RECREATE");
 	std::ofstream stats(statsname);
 	stats<<std::setprecision(5);
 
-	Mask::MaskFileHeader header = input.ReadHeader();
+	TTree* intree = (TTree*) input->Get("SimTree");
-	output.WriteHeader(header.rxn_type, header.nsamples);
+	std::vector<Mask::Nucleus>* dataHandle = new std::vector<Mask::Nucleus>();
-	stats<<"Efficiency statistics for data from "<<inputname<<" using the SPS-SABRE geometry"<<std::endl;
+	intree->SetBranchAddress("nuclei", &dataHandle);
+
+	output->cd();
+	TTree* outtree = new TTree("SimTree", "SimTree");
+	outtree->Branch("nuclei", dataHandle);
+
+	input->cd();
+
+	stats<<"Efficiency statistics for data from "<<inputname<<" using the ANASEN geometry"<<std::endl;
 	stats<<"Given in order of target=0, projectile=1, ejectile=2, residual=3, .... etc."<<std::endl;
 
-	Mask::MaskFileData data;
+	intree->GetEntry(1);
-	Mask::Nucleus nucleus;
-
 	std::vector<int> counts;
 	std::vector<int> coinc_counts;
-	switch(header.rxn_type) {
+	counts.resize(dataHandle->size());
-		case Mask::RxnType::PureDecay:
+	switch(counts.size())
-			counts.resize(3, 0);
+	{
-			coinc_counts.resize(1, 0);
+		case 3: coinc_counts.resize(1, 0); break;
-			break;
+		case 4: coinc_counts.resize(1, 0); break;
-		case Mask::RxnType::OneStepRxn:
+		case 6: coinc_counts.resize(4, 0); break;
-			counts.resize(4, 0);
+		case 8: coinc_counts.resize(11, 0); break;
-			coinc_counts.resize(1, 0);
-			break;
-		case Mask::RxnType::TwoStepRxn:
-			counts.resize(6, 0);
-			coinc_counts.resize(4, 0);
-			break;
-		case Mask::RxnType::ThreeStepRxn:
-			counts.resize(8, 0);
-			coinc_counts.resize(11, 0);
-			break;
 		default:
 		{
-			std::cerr<<"Bad reaction type at AnasenEfficiency::CalculateEfficiency (given value: "<<GetStringFromRxnType(header.rxn_type)<<"). Quiting..."<<std::endl;
+			std::cerr<<"Bad reaction type at AnasenEfficiency::CalculateEfficiency (given value: "<<counts.size()<<"). Quiting..."<<std::endl;
-			input.Close();
+			input->Close();
-			output.Close();
+			output->Close();
 			stats.close();
 			return;
 		}
 	}
 
-	int percent5 = header.nsamples*0.05;
+	uint64_t nentries = intree->GetEntries();
-	int count = 0;
+	uint64_t percent5 = nentries*0.05;
-	int npercent = 0;
+	uint64_t count = 0;
+	uint64_t npercent = 0;
 
-	while(true) {
+	Mask::Nucleus nucleus;
-		if(++count == percent5) {//Show progress every 5%
+	for(uint64_t i=0; i<nentries; i++)
+	{
+		intree->GetEntry(i);
+		if(++count == percent5)
+		{//Show progress every 5%
 			npercent++;
 			count = 0;
 			std::cout<<"\rPercent completed: "<<npercent*5<<"%"<<std::flush;
 		}
 
-		data = input.ReadData();
+		for(std::size_t j=0; j<dataHandle->size(); j++)
-		if(data.eof)
+		{
-			break;
+			Mask::Nucleus& nucleus = (*dataHandle)[j];
-
+			DetectorResult result = IsSabre(nucleus);
-		for(unsigned int i=0; i<data.Z.size(); i++) {
+			if(result.detectFlag)
-			nucleus.SetIsotope(data.Z[i], data.A[i]);
+			{
-			nucleus.SetVectorSpherical(data.theta[i], data.phi[i], data.p[i], data.E[i]);
+				nucleus.isDetected = true;
-			
+				nucleus.detectedKE = result.energy_deposited;
-			auto result = IsSabre(nucleus);
+				nucleus.detectedTheta = result.direction.Theta();
-			if(result.first) {
+				nucleus.detectedPhi = result.direction.Phi();
-				data.detect_flag[i] = true;
+				counts[j]++;
-				data.KE[i] = result.second;
-				counts[i]++;
-			} else if(data.detect_flag[i] == true) {
-				data.detect_flag[i] = false;
 			}
 		}
 
-		CountCoincidences(data, coinc_counts, header.rxn_type);
+		CountCoincidences(*dataHandle, coinc_counts);
 
-		output.WriteData(data);
+		outtree->Fill();
 	}
+	input->Close();
+	output->cd();
+	outtree->Write(outtree->GetName(), TObject::kOverwrite);
+	output->Close();
 
-	input.Close();
+	delete dataHandle;
-	output.Close();
 
 	stats<<std::setw(10)<<"Index"<<"|"<<std::setw(10)<<"Efficiency"<<std::endl;
 	stats<<"---------------------"<<std::endl;
 	for(unsigned int i=0; i<counts.size(); i++) {
-		stats<<std::setw(10)<<i<<"|"<<std::setw(10)<<((double)counts[i]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<i<<"|"<<std::setw(10)<<((double)counts[i]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
 	stats<<"Coincidence Efficiency"<<std::endl;
 	stats<<"---------------------"<<std::endl;
-	if(header.rxn_type == Mask::RxnType::PureDecay)
+	if(counts.size() == 3)
 	{
-		stats<<std::setw(10)<<"1 + 2"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"1 + 2"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
-	else if(header.rxn_type == Mask::RxnType::OneStepRxn)
+	else if(counts.size() == 4)
 	{
-		stats<<std::setw(10)<<"2 + 3"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 3"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
-	else if(header.rxn_type == Mask::RxnType::TwoStepRxn)
+	else if(counts.size() == 6)
 	{
-		stats<<std::setw(10)<<"2 + 4"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[1]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[1]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"4 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[2]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"4 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[2]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 4 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[3]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4 + 5"<<"|"<<std::setw(10)<<((double)coinc_counts[3]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
-	else if(header.rxn_type == Mask::RxnType::ThreeStepRxn)
+	else if(counts.size() == 8)
 	{
-		stats<<std::setw(10)<<"2 + 4"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4"<<"|"<<std::setw(10)<<((double)coinc_counts[0]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[1]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[1]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[2]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[2]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"4 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[3]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"4 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[3]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"4 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[4]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"4 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[4]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[5]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[5]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 4 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[6]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4 + 6"<<"|"<<std::setw(10)<<((double)coinc_counts[6]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 4 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[7]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[7]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[8]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[8]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"4 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[9]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"4 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[9]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
-		stats<<std::setw(10)<<"2 + 4 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[10]/header.nsamples)<<std::endl;
+		stats<<std::setw(10)<<"2 + 4 + 6 + 7"<<"|"<<std::setw(10)<<((double)coinc_counts[10]/nentries)<<std::endl;
 		stats<<"---------------------"<<std::endl;
 	}
 	stats.close();
@@ -182,58 +186,69 @@ void SabreEfficiency::CalculateEfficiency(const std::string& inputname, const st
 	std::cout<<"---------------------------------------------"<<std::endl;
 }
 
-void SabreEfficiency::DrawDetectorSystem(const std::string& filename) {
+void SabreEfficiency::DrawDetectorSystem(const std::string& filename)
+{
 	std::ofstream output(filename);
 
 	std::vector<double> ringxs, ringys, ringzs;
     std::vector<double> wedgexs, wedgeys, wedgezs;
-	Mask::Vec3 coords;
+	ROOT::Math::XYZPoint coords;
- 	for(int i=0; i<5; i++) {
+ 	for(int i=0; i<s_nDets; i++)
- 		for(int j=0; j<detectors[i].GetNumberOfRings(); j++) {
+	{
- 			for(int k=0; k<4; k++) {
+ 		for(int j=0; j<m_detectors[i].GetNumberOfRings(); j++)
- 				coords = detectors[i].GetRingTiltCoords(j, k);
+		{
- 				ringxs.push_back(coords.GetX());
+ 			for(int k=0; k<4; k++)
- 				ringys.push_back(coords.GetY());
+			{
- 				ringzs.push_back(coords.GetZ());
+ 				coords = m_detectors[i].GetRingTiltCoords(j, k);
+ 				ringxs.push_back(coords.X());
+ 				ringys.push_back(coords.Y());
+ 				ringzs.push_back(coords.Z());
  			}
  		}
  	}
 
- 	for(int i=0; i<5; i++) {
+ 	for(int i=0; i<s_nDets; i++)
- 		for(int j=0; j<detectors[i].GetNumberOfWedges(); j++) {
+	{
- 			for(int k=0; k<4; k++) {
+ 		for(int j=0; j<m_detectors[i].GetNumberOfWedges(); j++)
- 				coords = detectors[i].GetWedgeTiltCoords(j, k);
+		{
- 				wedgexs.push_back(coords.GetX());
+ 			for(int k=0; k<4; k++)
- 				wedgeys.push_back(coords.GetY());
+			{
- 				wedgezs.push_back(coords.GetZ());
+ 				coords = m_detectors[i].GetWedgeTiltCoords(j, k);
+ 				wedgexs.push_back(coords.X());
+ 				wedgeys.push_back(coords.Y());
+ 				wedgezs.push_back(coords.Z());
  			}
  		}
  	}
 
  	output<<"SABRE Geometry File -- Coordinates for Detectors"<<std::endl;
 	output<<"Edges: x y z"<<std::endl;
-	for(unsigned int i=0; i<ringxs.size(); i++) {
+	for(unsigned int i=0; i<ringxs.size(); i++)
 		output<<ringxs[i]<<" "<<ringys[i]<<" "<<ringzs[i]<<std::endl;
-	}
+	for(unsigned int i=0; i<wedgexs.size(); i++)
-	for(unsigned int i=0; i<wedgexs.size(); i++) {
 		output<<wedgexs[i]<<" "<<wedgeys[i]<<" "<<wedgezs[i]<<std::endl;
-	}
 
  	output.close();
 }
 
-double SabreEfficiency::RunConsistencyCheck() {
+double SabreEfficiency::RunConsistencyCheck()
+{
 	double theta, phi;
 	double npoints = 5.0*16.0*4.0;
 	int count=0;
- 	for(int h=0; h<5; h++) {
+	ROOT::Math::XYZPoint corner;
- 		for(int j=0; j<16; j++) {
+ 	for(auto& detector : m_detectors)
- 			for(int k=0; k<4; k ++) {
+	{
- 				theta  = detectors[h].GetRingTiltCoords(j, k).GetTheta();
+ 		for(int j=0; j<detector.GetNumberOfRings(); j++)
- 				phi = detectors[h].GetRingTiltCoords(j, k).GetPhi();
+		{
- 				for(int i=0; i<5; i++) {
+ 			for(int k=0; k<4; k ++) //Check corners
- 					auto channels = detectors[i].GetTrajectoryRingWedge(theta, phi);
+			{
- 					if(channels.first != -1) {
+				corner = detector.GetRingTiltCoords(j, k);
+ 				for(int i=0; i<5; i++)
+				{
+ 					auto channels = m_detectors[i].GetTrajectoryRingWedge(corner.Theta(), corner.Phi());
+ 					if(channels.first != -1)
+					{
  						count++;
  					}
  				}
@@ -245,105 +260,118 @@ double SabreEfficiency::RunConsistencyCheck() {
 }
 
 /*Returns if detected, as well as total energy deposited in SABRE*/
-std::pair<bool,double> SabreEfficiency::IsSabre(Mask::Nucleus& nucleus) {
+DetectorResult SabreEfficiency::IsSabre(Mask::Nucleus& nucleus)
-	if(nucleus.GetKE() <= ENERGY_THRESHOLD) {
+{
-		return std::make_pair(false, 0.0);
+	DetectorResult observation;
-	}
+	if(nucleus.GetKE() <= s_energyThreshold)
+		return observation;
 
-	Mask::Vec3 coords;
+	double thetaIncident;
-	double thetaIncident, eloss, e_deposited;
 	double ke = 0.0;
-	for(auto& detector : detectors) {
+	for(auto& detector : m_detectors)
-		auto chan = detector.GetTrajectoryRingWedge(nucleus.GetTheta(), nucleus.GetPhi());
+	{
-		if(chan.first != -1 && chan.second != -1) {
+		if(!m_activeDetectors[detector.GetDetectorID()])
-			if(dmap.IsDead(detector.GetDetectorID(), chan.first, 0) || dmap.IsDead(detector.GetDetectorID(), chan.second, 1)) break; //dead channel check
+			continue;
-			coords = detector.GetTrajectoryCoordinates(nucleus.GetTheta(), nucleus.GetPhi());
+
-			thetaIncident = std::acos(coords.Dot(detector.GetNormTilted())/(coords.GetR()));
+		auto channel = detector.GetTrajectoryRingWedge(nucleus.vec4.Theta(), nucleus.vec4.Phi());
-			//eloss = degrader.GetEnergyLossTotal(nucleus.GetZ(), nucleus.GetA(), nucleus.GetKE(), thetaIncident);
+		if(channel.first == -1 || channel.second == -1)
-			//ke = nucleus.GetKE() - eloss;
+			continue;
-			eloss = deadlayer.GetEnergyLossTotal(nucleus.GetZ(), nucleus.GetA(), ke, M_PI - thetaIncident);
+		if(m_deadMap.IsDead(detector.GetDetectorID(), channel.first, 0) || m_deadMap.IsDead(detector.GetDetectorID(), channel.second, 1))
-			ke = nucleus.GetKE() - eloss;
+				break; //dead channel check
-			//ke -= eloss;
+
-			if(ke <= ENERGY_THRESHOLD) break; //deadlayer check
+		observation.detectFlag = true;
-			e_deposited = sabre_eloss.GetEnergyLossTotal(nucleus.GetZ(), nucleus.GetA(), ke, M_PI - thetaIncident);
+		observation.direction = detector.GetTrajectoryCoordinates(nucleus.vec4.Theta(), nucleus.vec4.Phi());
-			return std::make_pair(true, e_deposited);
+		thetaIncident = std::acos(observation.direction.Dot(detector.GetNormTilted())/(observation.direction.R()));
-		}
+
+		//Energy loss
+		ke = nucleus.GetKE();
+		if(m_degradedDetectors[detector.GetDetectorID()])
+			ke -= m_degraderEloss.GetEnergyLossTotal(nucleus.Z, nucleus.A, ke, M_PI - thetaIncident);
+		ke -= m_deadlayerEloss.GetEnergyLossTotal(nucleus.Z, nucleus.A, ke, M_PI - thetaIncident);
+		if(ke <= s_energyThreshold)
+			break;
+
+		observation.det_name = "SABRE"+std::to_string(detector.GetDetectorID());
+		observation.energy_deposited = m_detectorEloss.GetEnergyLossTotal(nucleus.Z, nucleus.A, ke, M_PI - thetaIncident);
+		return observation;
 	}
 
-	return std::make_pair(false,0.0);
+	observation.detectFlag = false;
+	return observation;
 }
 
-void SabreEfficiency::CountCoincidences(const Mask::MaskFileData& data, std::vector<int>& counts, Mask::RxnType rxn_type) {
+void SabreEfficiency::CountCoincidences(const std::vector<Mask::Nucleus>& data, std::vector<int>& counts)
-	if (rxn_type == Mask::RxnType::PureDecay && data.detect_flag[1] && data.detect_flag[2])
+{
+	if (data.size() == 3 && data[1].isDetected && data[2].isDetected)
 	{
 		counts[0]++;
 	}
-	else if (rxn_type == Mask::RxnType::OneStepRxn && data.detect_flag[2] && data.detect_flag[3])
+	else if (data.size() == 4 && data[2].isDetected && data[3].isDetected)
 	{
 		counts[0]++;
 	}
-	else if(rxn_type == Mask::RxnType::TwoStepRxn)
+	else if(data.size() == 6)
 	{
-		if(data.detect_flag[2] && data.detect_flag[4]) 
+		if(data[2].isDetected && data[4].isDetected) 
 		{
 			counts[0]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[5])
+		if(data[2].isDetected && data[5].isDetected)
 		{
 			counts[1]++;
 		}
-		if(data.detect_flag[4] && data.detect_flag[5])
+		if(data[4].isDetected && data[5].isDetected)
 		{
 			counts[2]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[4] && data.detect_flag[5])
+		if(data[2].isDetected && data[4].isDetected && data[5].isDetected)
 		{
 			counts[3]++;
 		}
 	}
-	else if(rxn_type == Mask::RxnType::ThreeStepRxn)
+	else if(data.size() == 8)
 	{
-		if(data.detect_flag[2] && data.detect_flag[4]) 
+		if(data[2].isDetected && data[4].isDetected) 
 		{
 			counts[0]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[6])
+		if(data[2].isDetected && data[6].isDetected)
 		{
 			counts[1]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[7])
+		if(data[2].isDetected && data[7].isDetected)
 		{
 			counts[2]++;
 		}
-		if(data.detect_flag[4] && data.detect_flag[6])
+		if(data[4].isDetected && data[6].isDetected)
 		{
 			counts[3]++;
 		}
-		if(data.detect_flag[4] && data.detect_flag[7])
+		if(data[4].isDetected && data[7].isDetected)
 		{
 			counts[4]++;
 		}
-		if(data.detect_flag[6] && data.detect_flag[7])
+		if(data[6].isDetected && data[7].isDetected)
 		{
 			counts[5]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[4] && data.detect_flag[6])
+		if(data[2].isDetected && data[4].isDetected && data[6].isDetected)
 		{
 			counts[6]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[4] && data.detect_flag[7])
+		if(data[2].isDetected && data[4].isDetected && data[7].isDetected)
 		{
 			counts[7]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[6] && data.detect_flag[7])
+		if(data[2].isDetected && data[6].isDetected && data[7].isDetected)
 		{
 			counts[8]++;
 		}
-		if(data.detect_flag[4] && data.detect_flag[6] && data.detect_flag[7])
+		if(data[4].isDetected && data[6].isDetected && data[7].isDetected)
 		{
 			counts[9]++;
 		}
-		if(data.detect_flag[2] && data.detect_flag[4] && data.detect_flag[6] && data.detect_flag[7])
+		if(data[2].isDetected && data[4].isDetected && data[6].isDetected && data[7].isDetected)
 		{
 			counts[10]++;
 		}

src/Detectors/SabreEfficiency.h

@@ -0,0 +1,51 @@
+#ifndef SABREEFFICIENCY_H
+#define SABREEFFICIENCY_H
+
+#include "DetectorEfficiency.h"
+#include "SabreDetector.h"
+#include "Target.h"
+#include "SabreDeadChannelMap.h"
+#include "Mask/Nucleus.h"
+
+class SabreEfficiency : public DetectorEfficiency
+{
+public:
+	SabreEfficiency();
+	~SabreEfficiency();
+    void SetDeadChannelMap(const std::string& filename) { m_deadMap.LoadMapfile(filename); };
+	void CalculateEfficiency(const std::string& inputname, const std::string& outputname, const std::string& statsname) override;
+    void DrawDetectorSystem(const std::string& filename) override;
+    double RunConsistencyCheck() override;
+
+private:
+	DetectorResult IsSabre(Mask::Nucleus& nucleus);
+    void CountCoincidences(const std::vector<Mask::Nucleus>& data, std::vector<int>& counts);
+
+	std::vector<SabreDetector> m_detectors;
+    
+	Mask::Target m_deadlayerEloss;
+    Mask::Target m_detectorEloss;
+    Mask::Target m_degraderEloss;
+    SabreDeadChannelMap m_deadMap;
+
+    bool m_activeDetectors[5];
+    bool m_degradedDetectors[5];
+
+	//Sabre constants
+	static constexpr double s_innerR = 0.0326;
+    static constexpr double s_outerR = 0.1351;
+    static constexpr double s_tilt = 40.0;
+    static constexpr double s_zOffset = -0.1245;
+    static constexpr double s_deltaPhi = 54.4; //delta phi for each det
+    static constexpr int s_nDets = 5;
+    static constexpr double s_centerPhiList[s_nDets] = {306.0, 18.0, 234.0, 162.0, 90.0};
+    static constexpr double s_deg2rad = M_PI/180.0;
+    static constexpr double s_deadlayerThickness = 50 * 1e-7 * 2.3296 * 1e6; // ug/cm^2 (50 nm thick * density)
+    static constexpr double s_detectorThickness = 500 * 1e-4 * 2.3926 * 1e6; // ug/cm^2 (500 um thick * density)
+    static constexpr double s_degraderThickness = 70.0 * 1.0e-4 * 16.69 * 1e6; //tantalum degrader (70 um thick) 
+
+    static constexpr double s_energyThreshold = 0.25; //in MeV
+
+};
+
+#endif

src/Detectors/StripDetector.cpp

@@ -17,32 +17,34 @@
 */
 
 StripDetector::StripDetector(int ns, double len, double wid, double cphi, double cz, double crho) :
-	m_norm_unrot(1.0,0.0,0.0), m_uniform_fraction(0.0, 1.0), rndmFlag(false)
+	m_norm(1.0,0.0,0.0), m_uniformFraction(0.0, 1.0), m_isSmearing(false)
 {
 
-	num_strips = ns;
+	m_nStrips = ns;
 	
-	length = std::fabs(len);
+	m_stripLength = std::fabs(len);
-	total_width = std::fabs(wid);
+	m_totalWidth = std::fabs(wid);
-	front_strip_width = total_width/num_strips;
+	m_frontStripWidth = m_totalWidth/m_nStrips;
-	back_strip_length = length/num_strips;
+	m_backStripLength = m_stripLength/m_nStrips;
 
-	while (cphi < 0) cphi += 2*M_PI;
+	while (cphi < 0)
-	center_phi = cphi;
+		cphi += 2*M_PI;
-	center_z   = cz;
+	m_centerPhi = cphi;
-	center_rho = std::fabs(crho);
+	m_centerZ   = cz;
+	m_centerRho = std::fabs(crho);
 
-	zRot.SetAngle(center_phi);
+	m_zRotation.SetAngle(m_centerPhi);
 
-	front_strip_coords.resize(num_strips);
+	m_frontStripCoords.resize(m_nStrips);
-	back_strip_coords.resize(num_strips);
+	m_backStripCoords.resize(m_nStrips);
-	rotated_front_strip_coords.resize(num_strips);
+	m_rotFrontStripCoords.resize(m_nStrips);
-	rotated_back_strip_coords.resize(num_strips);
+	m_rotBackStripCoords.resize(m_nStrips);
-	for(int i=0; i<num_strips; i++) {
+	for(int i=0; i<m_nStrips; i++)
-		front_strip_coords[i].resize(num_corners);
+	{
-		back_strip_coords[i].resize(num_corners);
+		m_frontStripCoords[i].resize(s_nCorners);
-		rotated_front_strip_coords[i].resize(num_corners);
+		m_backStripCoords[i].resize(s_nCorners);
-		rotated_back_strip_coords[i].resize(num_corners);
+		m_rotFrontStripCoords[i].resize(s_nCorners);
+		m_rotBackStripCoords[i].resize(s_nCorners);
 	}
 	CalculateCorners();
 	
@@ -50,99 +52,107 @@ StripDetector::StripDetector(int ns, double len, double wid, double cphi, double
 
 StripDetector::~StripDetector() {}
 
-void StripDetector::CalculateCorners() {
+void StripDetector::CalculateCorners()
+{
 	double y_min, y_max, z_min, z_max; 
-	for (int s=0; s<num_strips; s++) {
+	for (int s=0; s<m_nStrips; s++)
-		y_max = total_width/2.0 - front_strip_width*s;
+	{
-		y_min = total_width/2.0 - front_strip_width*(s+1);
+		y_max = m_totalWidth/2.0 - m_frontStripWidth*s;
-		z_max = center_z + length/2.0;
+		y_min = m_totalWidth/2.0 - m_frontStripWidth*(s+1);
-		z_min = center_z - length/2.0;
+		z_max = m_centerZ + m_stripLength/2.0;
-		front_strip_coords[s][2] = Mask::Vec3(center_rho, y_max, z_max);
+		z_min = m_centerZ - m_stripLength/2.0;
-		front_strip_coords[s][3] = Mask::Vec3(center_rho, y_max, z_min);
+		m_frontStripCoords[s][2].SetXYZ(m_centerRho, y_max, z_max);
-		front_strip_coords[s][0] = Mask::Vec3(center_rho, y_min, z_max);
+		m_frontStripCoords[s][3].SetXYZ(m_centerRho, y_max, z_min);
-		front_strip_coords[s][1] = Mask::Vec3(center_rho, y_min, z_min);
+		m_frontStripCoords[s][0].SetXYZ(m_centerRho, y_min, z_max);
+		m_frontStripCoords[s][1].SetXYZ(m_centerRho, y_min, z_min);
 
-		z_max = (center_z - length/2.0) + (s+1)*back_strip_length;
+		z_max = (m_centerZ - m_stripLength/2.0) + (s+1)*m_backStripLength;
-		z_min = (center_z - length/2.0) + (s)*back_strip_length;
+		z_min = (m_centerZ - m_stripLength/2.0) + (s)*m_backStripLength;
-		y_max = total_width/2.0;
+		y_max = m_totalWidth/2.0;
-		y_min = -total_width/2.0;
+		y_min = -m_totalWidth/2.0;
-		back_strip_coords[s][2] = Mask::Vec3(center_rho, y_max, z_max);
+		m_backStripCoords[s][2].SetXYZ(m_centerRho, y_max, z_max);
-		back_strip_coords[s][3] = Mask::Vec3(center_rho, y_max, z_min);
+		m_backStripCoords[s][3].SetXYZ(m_centerRho, y_max, z_min);
-		back_strip_coords[s][0] = Mask::Vec3(center_rho, y_min, z_max);
+		m_backStripCoords[s][0].SetXYZ(m_centerRho, y_min, z_max);
-		back_strip_coords[s][1] = Mask::Vec3(center_rho, y_min, z_min);
+		m_backStripCoords[s][1].SetXYZ(m_centerRho, y_min, z_min);
 	}
 
-	for(int s=0; s<num_strips; s++) {
+	for(int s=0; s<m_nStrips; s++)
-		rotated_front_strip_coords[s][0] = zRot*front_strip_coords[s][0];
+	{
-		rotated_front_strip_coords[s][1] = zRot*front_strip_coords[s][1];
+		m_rotFrontStripCoords[s][0] = m_zRotation*m_frontStripCoords[s][0];
-		rotated_front_strip_coords[s][2] = zRot*front_strip_coords[s][2];
+		m_rotFrontStripCoords[s][1] = m_zRotation*m_frontStripCoords[s][1];
-		rotated_front_strip_coords[s][3] = zRot*front_strip_coords[s][3];
+		m_rotFrontStripCoords[s][2] = m_zRotation*m_frontStripCoords[s][2];
+		m_rotFrontStripCoords[s][3] = m_zRotation*m_frontStripCoords[s][3];
 
-		rotated_back_strip_coords[s][0] = zRot*back_strip_coords[s][0];
+		m_rotBackStripCoords[s][0] = m_zRotation*m_backStripCoords[s][0];
-		rotated_back_strip_coords[s][1] = zRot*back_strip_coords[s][1];
+		m_rotBackStripCoords[s][1] = m_zRotation*m_backStripCoords[s][1];
-		rotated_back_strip_coords[s][2] = zRot*back_strip_coords[s][2];
+		m_rotBackStripCoords[s][2] = m_zRotation*m_backStripCoords[s][2];
-		rotated_back_strip_coords[s][3] = zRot*back_strip_coords[s][3];
+		m_rotBackStripCoords[s][3] = m_zRotation*m_backStripCoords[s][3];
 	}
 }
 
-Mask::Vec3 StripDetector::GetHitCoordinates(int front_stripch, double front_strip_ratio) {
+ROOT::Math::XYZPoint StripDetector::GetHitCoordinates(int front_stripch, double front_strip_ratio)
+{
 
-	if (!ValidChannel(front_stripch) || !ValidRatio(front_strip_ratio)) return Mask::Vec3(0,0,0);
+	if (!ValidChannel(front_stripch) || !ValidRatio(front_strip_ratio))
+		return ROOT::Math::XYZPoint(0,0,0);
 
 	double y;
-	if(rndmFlag) {
+	if(m_isSmearing)
-		y = -total_width/2.0 + (front_stripch + m_uniform_fraction(Mask::RandomGenerator::GetInstance().GetGenerator()))*front_strip_width;
+		y = -m_totalWidth/2.0 + (front_stripch + m_uniformFraction(Mask::RandomGenerator::GetInstance().GetGenerator()))*m_frontStripWidth;
-	} else {
+	else
-		y = -total_width/2.0 + (front_stripch+0.5)*front_strip_width;
+		y = -m_totalWidth/2.0 + (front_stripch+0.5)*m_frontStripWidth;
-	}
 
 	//recall we're still assuming phi=0 det:
-	Mask::Vec3 coords(center_rho, y, front_strip_ratio*(length/2) + center_z);
+	ROOT::Math::XYZPoint coords(m_centerRho, y, front_strip_ratio*(m_stripLength/2) + m_centerZ);
   
 	//NOW rotate by appropriate phi
-	return zRot*coords;
+	return m_zRotation*coords;
 
 }
 
-StripHit StripDetector::GetChannelRatio(double theta, double phi) {
+StripHit StripDetector::GetChannelRatio(double theta, double phi)
+{
 
 	StripHit hit;
-	while (phi < 0) phi += 2*M_PI;
+	while (phi < 0)
+		phi += 2*M_PI;
 
 	//to make the math easier (and the same for each det), rotate the input phi
 	//BACKWARD by the phi of the det, s.t. we are looking along x-axis
-	phi -= center_phi;
+	phi -= m_centerPhi;
 
-	if (phi > M_PI) phi -= 2*M_PI;
+	if (phi > M_PI)
+		phi -= 2*M_PI;
 
 	//then we can check easily whether it even hit the detector in phi
-	double det_max_phi = atan2(total_width/2,center_rho);
+	double det_max_phi = std::atan2(m_totalWidth/2,m_centerRho);
 	double det_min_phi = -det_max_phi;
   
-	if (phi < det_min_phi || phi > det_max_phi) return hit;
+	if (phi < det_min_phi || phi > det_max_phi)
+		return hit;
 
 	//for theta it's not so simple, so we have to go through the typical plane-intersect method
 	//first thing's first: we have a fixed x for the entire detector plane:
-	double xhit = center_rho;
+	double xhit = m_centerRho;
 	//thus we find the corresponding y and z for that fixed x, given the input theta and phi:
 	double yhit = xhit*tan(phi);
 	double zhit = sqrt(xhit*xhit+yhit*yhit)/tan(theta);
 
-	for (int s=0; s<num_strips; s++) {
+	for (int s=0; s<m_nStrips; s++) {
-		if (xhit >= front_strip_coords[s][0].GetX() && xhit <= front_strip_coords[s][0].GetX() && //Check min and max x (constant in flat)
+		if (xhit >=m_frontStripCoords[s][0].X() && xhit <=m_frontStripCoords[s][0].X() && //Check min and max x (constant in flat)
-			yhit >= front_strip_coords[s][1].GetY() && yhit <= front_strip_coords[s][2].GetY() && //Check min and max y
+			yhit >=m_frontStripCoords[s][1].Y() && yhit <=m_frontStripCoords[s][2].Y() && //Check min and max y
-			zhit >= front_strip_coords[s][1].GetZ() && zhit <= front_strip_coords[s][0].GetZ()) //Check min and max z
+			zhit >=m_frontStripCoords[s][1].Z() && zhit <=m_frontStripCoords[s][0].Z()) //Check min and max z
 		{
 			hit.front_strip_index = s;
-			hit.front_ratio = (zhit-center_z)/(length/2);
+			hit.front_ratio = (zhit-m_centerZ)/(m_stripLength/2);
 			break;
 		}
 	}
 
-	for (int s=0; s<num_strips; s++) {
+	for (int s=0; s<m_nStrips; s++) {
-		if (xhit >= back_strip_coords[s][0].GetX() && xhit <= back_strip_coords[s][0].GetX() && //Check min and max x (constant in flat)
+		if (xhit >= m_backStripCoords[s][0].X() && xhit <= m_backStripCoords[s][0].X() && //Check min and max x (constant in flat)
-			yhit >= back_strip_coords[s][1].GetY() && yhit <= back_strip_coords[s][2].GetY() && //Check min and max y
+			yhit >= m_backStripCoords[s][1].Y() && yhit <= m_backStripCoords[s][2].Y() && //Check min and max y
-			zhit >= back_strip_coords[s][1].GetZ() && zhit <= back_strip_coords[s][0].GetZ()) //Check min and max z
+			zhit >= m_backStripCoords[s][1].Z() && zhit <= m_backStripCoords[s][0].Z()) //Check min and max z
 		{
 			hit.back_strip_index = s;
 			break;

src/Detectors/StripDetector.h

@@ -0,0 +1,82 @@
+#ifndef STRIP_DETECTOR_H
+#define STRIP_DETECTOR_H
+
+// +z is along beam axis
+// +y is vertically "downward" in the lab frame
+
+//angles must be in radians, but distances can be whatever
+//PROVIDED all input distances are the same
+
+//Front strips from largest y to smallest y
+
+//Back strips from lowest z to highest z
+
+#include <cmath>
+#include <vector>
+
+#include "Math/Point3D.h"
+#include "Math/Vector3D.h"
+#include "Math/RotationZ.h"
+#include "Mask/RandomGenerator.h"
+
+struct StripHit
+{
+	int front_strip_index=-1;
+	int back_strip_index=-1;
+	double front_ratio=0.0;
+};
+
+class StripDetector
+{
+public:
+  
+	StripDetector(int ns, double len, double wid, double cphi, double cz, double crho);
+	~StripDetector();
+	const ROOT::Math::XYZPoint& GetFrontStripCoordinates(int stripch, int corner) const { return m_frontStripCoords[stripch][corner]; }
+	const ROOT::Math::XYZPoint& GetBackStripCoordinates(int stripch, int corner) const { return m_backStripCoords[stripch][corner]; }
+	const ROOT::Math::XYZPoint& GetRotatedFrontStripCoordinates(int stripch, int corner) const 
+	{ 
+		return m_rotFrontStripCoords[stripch][corner];
+	}
+	const ROOT::Math::XYZPoint& GetRotatedBackStripCoordinates(int stripch, int corner) const 
+	{ 
+		return m_rotBackStripCoords[stripch][corner];
+	}
+	ROOT::Math::XYZVector GetNormRotated() const { return m_zRotation * m_norm; }
+
+	void SetPixelSmearing(bool isSmearing) { m_isSmearing = isSmearing; }
+
+	ROOT::Math::XYZPoint GetHitCoordinates(int front_stripch, double front_strip_ratio);
+	StripHit GetChannelRatio(double theta, double phi);
+
+private:
+	bool ValidChannel(int f) { return ((f >= 0 && f < m_nStrips) ? true : false); };
+	bool ValidRatio(double r) { return ((r >= -1 && r <= 1) ? true : false); };
+	void CalculateCorners();
+
+	int m_nStrips;
+	static constexpr int s_nCorners = 4;
+
+	double m_stripLength; //common to all strips, hence total
+	double m_totalWidth;
+	double m_frontStripWidth; //assuming equal widths
+	double m_backStripLength; //assuming equal widths
+
+	double m_centerPhi; //assuming det centered above x-axis (corresponds to zero phi)
+	double m_centerZ;
+	double m_centerRho; //perpendicular radius from axis
+
+	std::vector<std::vector<ROOT::Math::XYZPoint>> m_frontStripCoords, m_backStripCoords;
+	std::vector<std::vector<ROOT::Math::XYZPoint>> m_rotFrontStripCoords, m_rotBackStripCoords;
+
+	ROOT::Math::XYZVector m_norm;
+
+	ROOT::Math::RotationZ m_zRotation;
+
+	std::uniform_real_distribution<double> m_uniformFraction;
+
+	bool m_isSmearing;
+
+};
+
+#endif

src/Detectors/main.cpp

@@ -4,9 +4,11 @@
 #include <iostream>
 #include <string>
 
-int main(int argc, char** argv) {
+int main(int argc, char** argv)
+{
 
-	if(argc != 4) {
+	if(argc != 4)
+	{
 		std::cerr<<"Incorrect number of commandline arguments! Returning."<<std::endl;
 		return 1;
 	}
@@ -25,18 +27,12 @@ int main(int argc, char** argv) {
 	
 
 	/*
-	try {
+ 	AnasenEfficiency anasen;
- 		AnasenEfficiency anasen;
+ 	std::string mapfile = "./etc/AnasenDeadChannels.txt";
- 		std::string mapfile = "./etc/AnasenDeadChannels.txt";
+ 	anasen.SetDeadChannelMap(mapfile);
- 		anasen.SetDeadChannelMap(mapfile);
+ 	anasen.CalculateEfficiency(inputname, outputname, statsname);
- 		anasen.CalculateEfficiency(inputname, outputname, statsname);
  	//std::cout<<"Running consistency check(1=success): "<<anasen.RunConsistencyCheck()<<std::endl;
  	//anasen.DrawDetectorSystem("/data1/gwm17/TRIUMF_7Bed/simulation/ANASENGeo_centered_target_targetGap_BackQQQ_fixedZ.txt");
-	} catch(const std::exception& e) {
-		std::cerr<<"Error: "<<e.what()<<std::endl;
-		std::cerr<<"Terminating."<<std::endl;
-		return 1;
-	}
 	*/
 	return 0;
 }

src/Mask/AngularDistribution.cpp

@@ -8,26 +8,28 @@
 namespace Mask {
 
 	AngularDistribution::AngularDistribution() :
-		uniform_cosine_dist(-1.0, 1.0), uniform_prob_dist(0.0, 1.0), branchingRatio(1.0), L(0), isoFlag(true)
+		m_uniformCosineDist(-1.0, 1.0), m_uniformProbDist(0.0, 1.0), m_branchingRatio(1.0), m_L(0), m_isIsotropic(true)
 	{
 	}
 	
 	AngularDistribution::AngularDistribution(const std::string& file) :
-		branchingRatio(1.0), L(0), isoFlag(true)
+		m_branchingRatio(1.0), m_L(0), m_isIsotropic(true)
 	{
 		ReadDistributionFile(file);
 	}
 	
 	AngularDistribution::~AngularDistribution() {}
 	
-	void AngularDistribution::ReadDistributionFile(const std::string& file) {
+	void AngularDistribution::ReadDistributionFile(const std::string& file)
+	{
 	
-		if(file == "none" || file == "") {
+		if(file == "none" || file == "")
-			L=0;
+		{
-			branchingRatio=1.0;
+			m_L=0;
-			constants.clear();
+			m_branchingRatio=1.0;
-			constants.push_back(0.5);
+			m_constants.clear();
-			isoFlag = true;
+			m_constants.push_back(0.5);
+			m_isIsotropic = true;
 			return;
 		}
 	
@@ -36,67 +38,76 @@ namespace Mask {
 		int l;
 		double par;
 	
-		if(!input.is_open()) {
+		if(!input.is_open())
+		{
 			std::cerr<<"Unable to open distribution file. All values reset to default."<<std::endl;
-			L=0;
+			m_L=0;
-			branchingRatio=1.0;
+			m_branchingRatio=1.0;
-			constants.clear();
+			m_constants.clear();
-			constants.push_back(0.5);
+			m_constants.push_back(0.5);
-			isoFlag = true;
+			m_isIsotropic = true;
 			return;
 		}
 	
 		input>>junk>>l;
-		while(input>>junk) {
+		while(input>>junk)
+		{
 			input>>par;
-			constants.push_back(par);
+			m_constants.push_back(par);
 		}
 		input.close();
 	
-		if(constants.size() != ((unsigned int) l+1)) {
+		if(m_constants.size() != ((std::size_t) l+1))
-			std::cerr<<"Unexpected number of constants for given angular momentum! Expected "<<l+1<<" and given "<<constants.size()<<std::endl;
+		{
+			std::cerr<<"Unexpected number of constants for given angular momentum! Expected "<<l+1<<" and given "<<m_constants.size()<<std::endl;
 			std::cerr<<"Setting all values to default."<<std::endl;
-			branchingRatio=1.0;
+			m_L=0;
-			constants.clear();
+			m_branchingRatio=1.0;
-			constants.push_back(0.5);
+			m_constants.clear();
-			isoFlag = true;
+			m_constants.push_back(0.5);
+			m_isIsotropic = true;
 			return;
 		}
 	
 		//Total branching ratio
-		branchingRatio = constants[0]*2.0;
+		m_branchingRatio = m_constants[0]*2.0;
-		L = l;
+		m_L = l;
 	
 		//Renormalize distribution such that total prob is 1.0.
 		//Test branching ratio to see if we "make" a decay particle,
 		//then use re-normalized distribution to pick an angle. 
-		if(constants[0] < 0.5) {
+		if(m_constants[0] < 0.5)
-			double norm = 0.5/constants[0];
+		{
-			for(auto& value : constants)
+			double norm = 0.5/m_constants[0];
+			for(auto& value : m_constants)
 				value *= norm;
 		}
 	
-		isoFlag = false;
+		m_isIsotropic = false;
 	
 	}
 	
-	double AngularDistribution::GetRandomCosTheta() {
+	double AngularDistribution::GetRandomCosTheta()
-		if(isoFlag) 
+	{
-			return uniform_cosine_dist(RandomGenerator::GetInstance().GetGenerator());
+		if(m_isIsotropic) 
+			return m_uniformCosineDist(RandomGenerator::GetInstance().GetGenerator());
 	
 		double test, probability;
 		double costheta;
 	
-		test = uniform_prob_dist(RandomGenerator::GetInstance().GetGenerator());
+		test = m_uniformProbDist(RandomGenerator::GetInstance().GetGenerator());
-		if(test > branchingRatio) return -10;
+		if(test > m_branchingRatio)
+			return -10;
 	
-		do {
+		do
+		{
 			probability = 0.0;
-			costheta = uniform_cosine_dist(RandomGenerator::GetInstance().GetGenerator());
+			costheta = m_uniformCosineDist(RandomGenerator::GetInstance().GetGenerator());
-			test = uniform_prob_dist(RandomGenerator::GetInstance().GetGenerator());
+			test = m_uniformProbDist(RandomGenerator::GetInstance().GetGenerator());
-			for(unsigned int i=0; i<constants.size(); i++)
+			for(std::size_t i=0; i<m_constants.size(); i++)
-				probability += constants[i]*P_l(i*2, costheta);
+				probability += m_constants[i]*P_l(i*2, costheta);
-		} while(test > probability);
+		}
+		while(test > probability);
 	
 		return costheta;
 	}

src/Mask/AngularDistribution.h

@@ -0,0 +1,35 @@
+#ifndef ANGULARDISTRIBUTION_H
+#define ANGULARDISTRIBUTION_H
+
+#include <string>
+#include <vector>
+#include <random>
+
+namespace Mask {
+
+	class AngularDistribution
+	{
+	public:
+		AngularDistribution();
+		AngularDistribution(const std::string& file);
+		~AngularDistribution();
+		void ReadDistributionFile(const std::string& file);
+		double GetRandomCosTheta();
+		int GetL() { return m_L; }
+		double GetBranchingRatio() { return m_branchingRatio; }
+	
+	private:
+		bool IsIsotropic() { return m_isIsotropic; }
+		
+		std::uniform_real_distribution<double> m_uniformCosineDist;
+		std::uniform_real_distribution<double> m_uniformProbDist;
+	
+		double m_branchingRatio;
+		int m_L;
+		std::vector<double> m_constants;
+		bool m_isIsotropic;
+	};
+
+}
+
+#endif

src/Mask/CMakeLists.txt

@@ -1,30 +1,56 @@
+add_library(MaskDict SHARED)
+target_include_directories(MaskDict
+    PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}
+    SYSTEM PUBLIC ${ROOT_INCLUDE_DIRS}
+)
+
+ROOT_GENERATE_DICTIONARY(mask_dict Nucleus.h LINKDEF LinkDef_Nucleus.h MODULE MaskDict)
+
+target_sources(MaskDict PRIVATE Nucleus.h Nucleus.cpp MassLookup.h MassLookup.cpp)
+target_link_libraries(MaskDict ${ROOT_LIBRARIES})
+set_target_properties(MaskDict PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${MASK_LIBRARY_DIR})
+add_custom_command(TARGET MaskDict POST_BUILD
+	COMMAND ${CMAKE_COMMAND} -E copy
+	${CMAKE_CURRENT_BINARY_DIR}/libMaskDict_rdict.pcm
+	${MASK_LIBRARY_DIR}/libMaskDict_rdict.pcm
+	)
+
 add_library(Mask STATIC)
 target_include_directories(Mask 
     PUBLIC ${MASK_INCLUDE_DIR}
+    ${ROOT_INCLUDE_DIRS}
 )
 
 target_sources(Mask PRIVATE
     AngularDistribution.cpp
+    AngularDistribution.h
     DecaySystem.cpp
-    EnergyLoss.cpp
+    DecaySystem.h
     LayeredTarget.cpp
+    LayeredTarget.h
     LegendrePoly.cpp
+    LegendrePoly.h
     MaskApp.cpp
-    MaskFile.cpp
+    MaskApp.h
     MassLookup.cpp
-    Nucleus.cpp
+    MassLookup.h
     OneStepSystem.cpp
+    OneStepSystem.h
     RandomGenerator.cpp
+    RandomGenerator.h
     Reaction.cpp
+    Reaction.h
     ReactionSystem.cpp
-    Rotation.cpp
+    ReactionSystem.h
     Stopwatch.cpp
+    Stopwatch.h
     Target.cpp
+    Target.h
     ThreeStepSystem.cpp
+    ThreeStepSystem.h
     TwoStepSystem.cpp
-    Vec3.cpp
+    TwoStepSystem.h
-    Vec4.cpp
 )
 
-target_link_libraries(Mask catima)
+target_link_libraries(Mask catima MaskDict ${ROOT_LIBRARIES})
-set_target_properties(Mask PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${MASK_LIBRARY_DIR})
+set_target_properties(Mask PROPERTIES ARCHIVE_OUTPUT_DIRECTORY ${MASK_LIBRARY_DIR})

src/Mask/DecaySystem.cpp

@@ -1,76 +1,81 @@
 #include "DecaySystem.h"
 #include "RandomGenerator.h"
 
+#include <sstream>
+
 namespace Mask {
 
 	DecaySystem::DecaySystem() :
 		ReactionSystem()
 	{
-		nuclei.resize(3);
+		m_nuclei.resize(3);
 	}
 	
-	DecaySystem::DecaySystem(std::vector<int>& z, std::vector<int>& a) :
+	DecaySystem::DecaySystem(const std::vector<int>& z, const std::vector<int>& a) :
 		ReactionSystem()
 	{
-		nuclei.resize(3);
+		m_nuclei.resize(3);
 		SetNuclei(z, a);
 	}
 	
 	DecaySystem::~DecaySystem() {}
 	
-	bool DecaySystem::SetNuclei(std::vector<int>& z, std::vector<int>& a) {
+	bool DecaySystem::SetNuclei(const std::vector<int>& z, const std::vector<int>& a)
-		if(z.size() != a.size() || z.size() != 2) {
+	{
+		if(z.size() != a.size() || z.size() != 2)
 			return false;
-		}
 
-		step1.SetNuclei(z[0], a[0], 0, 0, z[1], a[1]);
+		int zr = z[0] - z[1];
+		int ar = a[0] - a[1];
+
+		m_nuclei[0] = CreateNucleus(z[0], a[0]); //target
+		m_nuclei[1] = CreateNucleus(z[1], a[1]); //breakup1
+		m_nuclei[2] = CreateNucleus(zr, ar); //breakup2
+
+		m_step1.BindNuclei(&(m_nuclei[0]), nullptr, &(m_nuclei[1]), &(m_nuclei[2]));
 		SetSystemEquation();
 		return true;
 	}
 
-	const std::vector<Nucleus>& DecaySystem::GetNuclei()
+	std::vector<Nucleus>* DecaySystem::GetNuclei()
 	{
-		nuclei[0] = step1.GetTarget();
+		return &m_nuclei;
-		nuclei[1] = step1.GetEjectile();
-		nuclei[2] = step1.GetResidual();
-
-		return nuclei;
 	}
 	
 	void DecaySystem::LinkTarget() {
-		step1.SetLayeredTarget(&target);
+		m_step1.SetLayeredTarget(&m_target);
 	
-		rxnLayer = target.FindLayerContaining(step1.GetTarget().GetZ(), step1.GetTarget().GetA());
+		m_rxnLayer = m_target.FindLayerContaining(m_nuclei[0].Z, m_nuclei[0].A);
-		if(rxnLayer != -1) {
+		if(m_rxnLayer != m_target.GetNumberOfLayers())
-			step1.SetRxnLayer(rxnLayer);
+		{
-			target_set_flag = true;
+			m_step1.SetRxnLayer(m_rxnLayer);
-		} else {
+			m_isTargetSet = true;
+		}
+		else
 			throw ReactionLayerException();
-		}
 	}
 	
-	void DecaySystem::SetSystemEquation() {
+	void DecaySystem::SetSystemEquation()
-		m_sys_equation = step1.GetTarget().GetIsotopicSymbol();
+	{
-		m_sys_equation += "-> ";
+		std::stringstream stream;
-		m_sys_equation += step1.GetEjectile().GetIsotopicSymbol();
+		stream << m_nuclei[0].isotopicSymbol << "->"
-		m_sys_equation += "+";
+			   << m_nuclei[1].isotopicSymbol << "+"
-		m_sys_equation += step1.GetResidual().GetIsotopicSymbol();
+			   << m_nuclei[2].isotopicSymbol;
+		m_sysEquation = stream.str();
 	}
 	
-	void DecaySystem::RunSystem() {
+	void DecaySystem::RunSystem()
+	{
 		//Link up the target if it hasn't been done yet
-		if(!target_set_flag) {
+		if(!m_isTargetSet)
 			LinkTarget();
-		}
 	
-		double rxnTheta = std::acos(decay1dist.GetRandomCosTheta());
+		double rxnTheta = std::acos(m_step1Distribution.GetRandomCosTheta());
 		double rxnPhi = (*m_phi1Range)(RandomGenerator::GetInstance().GetGenerator());
-		step1.SetPolarRxnAngle(rxnTheta);
+		m_step1.SetPolarRxnAngle(rxnTheta);
-		step1.SetAzimRxnAngle(rxnPhi);
+		m_step1.SetAzimRxnAngle(rxnPhi);
-	
+		m_step1.SetResidualEnergyLoss(true);
-		step1.TurnOnResidualEloss();
+		m_step1.Calculate();
-		step1.Calculate();
-
 	}
 
 }

src/Mask/DecaySystem.h

@@ -0,0 +1,36 @@
+#ifndef DECAYSYSTEM_H
+#define DECAYSYSTEM_H
+
+#include "ReactionSystem.h"
+#include "AngularDistribution.h"
+
+namespace Mask {
+
+	class DecaySystem: public ReactionSystem {
+	public:
+		DecaySystem();
+		DecaySystem(const std::vector<int>& z, const std::vector<int>& a);
+		~DecaySystem();
+	
+		bool SetNuclei(const std::vector<int>& z, const std::vector<int>& a) override;
+		void RunSystem() override;
+		std::vector<Nucleus>*GetNuclei() override;
+	
+		void SetDecay1Distribution(const std::string& filename) { m_step1Distribution.ReadDistributionFile(filename); }
+	
+		int GetDecay1AngularMomentum() { return m_step1Distribution.GetL(); }
+		double GetDecay1BranchingRatio() { return m_step1Distribution.GetBranchingRatio(); }
+	
+	private:
+		void LinkTarget() override;
+		void SetSystemEquation() override;
+	
+		Reaction m_step1;
+	
+		AngularDistribution m_step1Distribution;
+		
+	};
+
+}
+
+#endif

src/Mask/LayeredTarget.cpp

@@ -16,17 +16,16 @@ Written by G.W. McCann Aug. 2020
 namespace Mask {
 
 	LayeredTarget::LayeredTarget() :
-		name(""), m_fractional_depth_dist(0.0, 1.0)
+		m_name(""), m_fractionalDepthDistribution(0.0, 1.0)
 	{
 	}
 	
 	LayeredTarget::~LayeredTarget() {}
 	
 	/*Add in a Target made of a compound defined by a set of Zs, As, Ss, and a thickness*/
-	void LayeredTarget::AddLayer(std::vector<int>& Z, std::vector<int>& A, std::vector<int>& stoich, double thickness) {
+	void LayeredTarget::AddLayer(const std::vector<int>& Z, const std::vector<int>& A, const std::vector<int>& stoich, double thickness)
-		Target t(thickness);
+	{
-		t.SetElements(Z, A, stoich);
+		m_layers.emplace_back(Z, A, stoich, thickness);
-		layers.push_back(t);
 	}
 	
 	/*
@@ -34,9 +33,10 @@ namespace Mask {
 	  Calculates energy loss assuming that the reaction occurs in the middle of the target layer
 	  Note that the layer order can matter!
 	*/
-	double LayeredTarget::GetProjectileEnergyLoss(int zp, int ap, double startEnergy, int rxnLayer, double angle) {
+	double LayeredTarget::GetProjectileEnergyLoss(int zp, int ap, double startEnergy, std::size_t rxnLayer, double angle)
-	
+	{
-		if(rxnLayer < 0 || ((unsigned int) rxnLayer) > layers.size()) {
+		if(rxnLayer > m_layers.size())
+		{
 			std::cerr<<"Reaction layer in eloss calculation is not in range! Returning 0"<<std::endl;
 			return 0.0;
 		}
@@ -44,13 +44,17 @@ namespace Mask {
 		double eloss = 0.0;
 		double newEnergy = startEnergy;
 		double frac;
-		for(int i=0; i<=rxnLayer; i++) {
+		for(std::size_t i=0; i<=rxnLayer; i++)
-			if(i == rxnLayer) {
+		{
-				frac = m_fractional_depth_dist(RandomGenerator::GetInstance().GetGenerator());
+			if(i == rxnLayer)
-				eloss += layers[i].GetEnergyLossFractionalDepth(zp, ap, newEnergy, angle, frac);
+			{
+				frac = m_fractionalDepthDistribution(RandomGenerator::GetInstance().GetGenerator());
+				eloss += m_layers[i].GetEnergyLossFractionalDepth(zp, ap, newEnergy, angle, frac);
 				newEnergy = startEnergy - eloss;
-			} else {
+			}
-				eloss += layers[i].GetEnergyLossTotal(zp, ap, newEnergy, angle);
+			else
+			{
+				eloss += m_layers[i].GetEnergyLossTotal(zp, ap, newEnergy, angle);
 				newEnergy = startEnergy-eloss;
 			}
 		}
@@ -63,83 +67,96 @@ namespace Mask {
 	  Calculates energy loss assuming that the reaction occurs in the middle of the target
 	  Note that the layer order can matter!
 	*/
-	double LayeredTarget::GetEjectileEnergyLoss(int ze, int ae, double startEnergy, int rxnLayer, double angle) {
+	double LayeredTarget::GetEjectileEnergyLoss(int ze, int ae, double startEnergy, std::size_t rxnLayer, double angle) {
 	
-		if(rxnLayer < 0 || ((unsigned int) rxnLayer) > layers.size()) {
+		if(rxnLayer > m_layers.size())
+		{
 			std::cerr<<"Reaction layer in eloss calculation is not in range! Returning 0"<<std::endl;
 			return 0.0;
 		}
 	
 		double eloss = 0.0;
-		if(angle < M_PI/2.0) {
+		RandomGenerator& gen = RandomGenerator::GetInstance();
+		if(angle < M_PI/2.0)
+		{
 			double newEnergy = startEnergy;
-			for(unsigned int i=rxnLayer; i<layers.size(); i++) {
+			eloss += m_layers[rxnLayer].GetEnergyLossFractionalDepth(ze, ae, newEnergy, angle, m_fractionalDepthDistribution(gen.GetGenerator()));
-				if(i == ((unsigned int)rxnLayer)) {
+			newEnergy = startEnergy - eloss;
-					eloss += layers[i].GetEnergyLossFractionalDepth(ze, ae, newEnergy, angle, m_fractional_depth_dist(RandomGenerator::GetInstance().GetGenerator()));
+			if(rxnLayer == m_layers.size())
-					newEnergy = startEnergy - eloss;
+				return eloss;
-				} else {
+
-					eloss += layers[i].GetEnergyLossTotal(ze, ae, newEnergy, angle);
+			for(std::size_t i=rxnLayer; i<m_layers.size(); i++)
-					newEnergy = startEnergy - eloss;
+			{
-				}
+				eloss += m_layers[i].GetEnergyLossTotal(ze, ae, newEnergy, angle);
+				newEnergy = startEnergy - eloss;
 			}
-		} else { //Travelling backwards through target
+		}
+		else
+		{ //Travelling backwards through target
 			double newEnergy = startEnergy;
-			for(int i=rxnLayer; i>=0; i--) {
+			eloss += m_layers[rxnLayer].GetEnergyLossFractionalDepth(ze, ae, newEnergy, angle, m_fractionalDepthDistribution(gen.GetGenerator()));
-				if(i == ((unsigned int)rxnLayer)) {
+			newEnergy = startEnergy - eloss;
-					eloss += layers[i].GetEnergyLossFractionalDepth(ze, ae, newEnergy, angle, m_fractional_depth_dist(RandomGenerator::GetInstance().GetGenerator()));
+			if(rxnLayer == 0)
-					newEnergy = startEnergy - eloss;
+				return eloss;
-				} else {
+
-					eloss += layers[i].GetEnergyLossTotal(ze, ae, newEnergy, angle);
+			for(std::size_t i=rxnLayer-1; i>0; i--) //unsigned ints cant be less than 0
-					newEnergy = startEnergy - eloss;
+			{
-				}
+				eloss += m_layers[i].GetEnergyLossTotal(ze, ae, newEnergy, angle);
+				newEnergy = startEnergy - eloss;
 			}
+			eloss += m_layers[0].GetEnergyLossTotal(ze, ae, newEnergy, angle);
+			newEnergy = startEnergy - eloss;
 		}
 	
 		return eloss;
 	}
 	
 	/*ReverseEnergyLoss version of GetEjectileEnergyLoss*/
-	double LayeredTarget::GetEjectileReverseEnergyLoss(int ze, int ae, double startEnergy, int rxnLayer, double angle) {
+	double LayeredTarget::GetEjectileReverseEnergyLoss(int ze, int ae, double startEnergy, std::size_t rxnLayer, double angle)
-	
+	{
-		if(rxnLayer < 0 || ((unsigned int) rxnLayer) > layers.size()) {
+		if(rxnLayer > m_layers.size())
+		{
 			std::cerr<<"Reaction layer in eloss calculation is not in range! Returning 0"<<std::endl;
 			return 0.0;
 		}	
 	
 		double eloss = 0.0;
-		if(angle < M_PI/2.0) {
+		RandomGenerator& gen = RandomGenerator::GetInstance();
+		if(angle < M_PI/2.0)
+		{
 			double newEnergy = startEnergy;
-			for(int i=(layers.size()-1); i>=rxnLayer; i--) {
+			for(std::size_t i=(m_layers.size()-1); i>rxnLayer; i--)
-				if(i == rxnLayer) {
+			{
-					eloss += layers[i].GetReverseEnergyLossFractionalDepth(ze, ae, newEnergy, angle, m_fractional_depth_dist(RandomGenerator::GetInstance().GetGenerator()));
+				eloss += m_layers[i].GetReverseEnergyLossTotal(ze, ae, newEnergy, angle);
-					newEnergy = startEnergy + eloss;
+				newEnergy = startEnergy + eloss;
-				} else {
-					eloss += layers[i].GetReverseEnergyLossTotal(ze, ae, newEnergy, angle);
-					newEnergy = startEnergy + eloss;
-				}
 			}
-		} else {
+			eloss += m_layers[rxnLayer].GetReverseEnergyLossFractionalDepth(ze, ae, newEnergy, angle, m_fractionalDepthDistribution(gen.GetGenerator()));
+			newEnergy = startEnergy + eloss;
+		}
+		else
+		{
 			double newEnergy = startEnergy;
-			for(int i=0; i <= rxnLayer; i++) {
+			for(std::size_t i=0; i < rxnLayer; i++)
-				if(i == rxnLayer) {
+			{
-					eloss += layers[i].GetReverseEnergyLossFractionalDepth(ze, ae, newEnergy, angle, m_fractional_depth_dist(RandomGenerator::GetInstance().GetGenerator()));
+				eloss += m_layers[i].GetReverseEnergyLossTotal(ze, ae, newEnergy, angle);
-					newEnergy = startEnergy + eloss;
+				newEnergy = startEnergy + eloss;
-				} else {
-					eloss += layers[i].GetReverseEnergyLossTotal(ze, ae, newEnergy, angle);
-					newEnergy = startEnergy + eloss;
-				}
 			}
+			eloss += m_layers[rxnLayer].GetReverseEnergyLossFractionalDepth(ze, ae, newEnergy, angle, m_fractionalDepthDistribution(gen.GetGenerator()));
+			newEnergy = startEnergy + eloss;
 		}
 	
 		return eloss;
 	}
 	
-	int LayeredTarget::FindLayerContaining(int Z, int A) {
+	std::size_t LayeredTarget::FindLayerContaining(int Z, int A)
-		for(unsigned int i=0; i<layers.size(); i++)
+	{
-			if(layers[i].ContainsElement(Z, A)) 
+		for(std::size_t i=0; i<m_layers.size(); i++)
+		{
+			if(m_layers[i].ContainsElement(Z, A)) 
 				return i;
+		}
 
-		return -1;
+		return m_layers.size();
 	}
     
     

src/Mask/LayeredTarget.h

@@ -21,25 +21,25 @@ Written by G.W. McCann Aug. 2020
 
 namespace Mask {
 
-	class LayeredTarget {
+	class LayeredTarget
-	  
+	{
 	public:
 		LayeredTarget();
 		~LayeredTarget();
-		void AddLayer(std::vector<int>& Z, std::vector<int>& A, std::vector<int>& stoich, double thickness);
+		void AddLayer(const std::vector<int>& Z, const std::vector<int>& A, const std::vector<int>& stoich, double thickness);
-		double GetProjectileEnergyLoss(int zp, int ap, double startEnergy, int rxnLayer, double angle);
+		double GetProjectileEnergyLoss(int zp, int ap, double startEnergy, std::size_t rxnLayer, double angle);
-		double GetEjectileEnergyLoss(int ze, int ae, double startEnergy, int rxnLayer, double angle);
+		double GetEjectileEnergyLoss(int ze, int ae, double startEnergy, std::size_t rxnLayer, double angle);
-		double GetEjectileReverseEnergyLoss(int ze, int ae, double startEnergy, int rxnLayer, double angle);
+		double GetEjectileReverseEnergyLoss(int ze, int ae, double startEnergy, std::size_t rxnLayer, double angle);
-		int FindLayerContaining(int Z, int A);
+		std::size_t FindLayerContaining(int Z, int A);
-		inline int GetNumberOfLayers() { return layers.size(); }
+		std::size_t GetNumberOfLayers() { return m_layers.size(); }
-		inline void SetName(std::string& n) { name = n; }
+		void SetName(std::string& n) { m_name = n; }
-		inline const Target& GetLayerInfo(int index) { return layers[index]; }
+		const Target& GetLayerInfo(int index) { return m_layers[index]; }
-		inline const std::string& GetName() { return name; }
+		const std::string& GetName() { return m_name; }
 	
 	private:
-		std::vector<Target> layers;
+		std::vector<Target> m_layers;
-		std::string name;
+		std::string m_name;
-		std::uniform_real_distribution<double> m_fractional_depth_dist;
+		std::uniform_real_distribution<double> m_fractionalDepthDistribution;
 	};
 
 }

src/Mask/LegendrePoly.cpp

@@ -3,33 +3,38 @@
 
 namespace Mask {
 
-	double P_l(int l, double x) {
+	double P_l(int l, double x)
-		if(l == 0) {
+	{
+		if(l == 0)
 			return 1.0;
-		} else if (l == 1) {
+		else if (l == 1)
 			return x;
-		} else {
+		else
 			return (2.0*l - 1.0)/l*x*P_l(l-1, x) - (l-1.0)/l*P_l(l-2, x);
-		}
 	}
 	
-	double Normed_P_l_sq(int l, double x) {
+	double Normed_P_l_sq(int l, double x)
+	{
 		return (2.0*l+1.0)/2.0*std::pow(P_l(l, x), 2.0);
 	}
 	
-	double P_0(double x) {
+	double P_0(double x)
+	{
 		return 1.0;
 	}
 	
-	double P_1(double x) {
+	double P_1(double x)
+	{
 		return x;
 	}
 	
-	double P_2(double x) {
+	double P_2(double x)
+	{
 		return 0.5*(3.0*x*x -1.0);
 	}
 	
-	double P_l_ROOT(double* x, double* pars) {
+	double P_l_ROOT(double* x, double* pars)
+	{
 		return P_l(pars[0], x[0]);
 	}
 

src/Mask/LegendrePoly.h

@@ -4,7 +4,7 @@
 namespace Mask {
 
 	double P_l(int l, double x);
-	double P_l_ROOT(double* x, double* pars);
+	double P_l_ROOT(double* x, double* pars); //Only for use with ROOT cern in plotting
 	double Normed_P_l_sq(int l, double x);
 	
 	double P_0(double x);

src/Mask/LinkDef_Nucleus.h

@@ -0,0 +1,7 @@
+#ifdef __CLING__
+
+#pragma link C++ struct Mask::Nucleus+;
+#pragma link C++ class std::vector<Mask::Nucleus>+;
+#pragma link C++ class std::string+;
+
+#endif

src/Mask/MaskApp.cpp

@@ -1,19 +1,21 @@
 #include "MaskApp.h"
-#include "MaskFile.h"
 #include <fstream>
 #include <iostream>
 
+#include "TFile.h"
+#include "TTree.h"
+
 namespace Mask {
 
 	MaskApp::MaskApp() :
-		m_sys(nullptr)
+		m_system(nullptr)
 	{
 		std::cout<<"----------GWM Kinematics Simulation----------"<<std::endl;
 	}
 	
 	MaskApp::~MaskApp() 
 	{
-		if(m_sys) delete m_sys;
+		delete m_system;
 	}
 	
 	bool MaskApp::LoadConfig(const std::string& filename) 
@@ -28,23 +30,23 @@ namespace Mask {
 	
 		std::string junk;
 		getline(input, junk);
-		input>>junk>>m_outfile_name;
+		input>>junk>>m_outputName;
 	
 		std::vector<int> avec, zvec, svec;
 		int z, a, s;
 		getline(input, junk);
 		getline(input, junk);
 		input>>junk>>junk;
-		m_rxn_type = GetRxnTypeFromString(junk);
+		m_rxnType = GetRxnTypeFromString(junk);
 		getline(input, junk);
 		getline(input, junk);
-		switch(m_rxn_type) 
+		switch(m_rxnType) 
 		{
 			case RxnType::PureDecay:
 			{
-				m_sys = new DecaySystem();
+				m_system = new DecaySystem();
-				m_rxn_type = RxnType::PureDecay;
+				for(int i=0; i<2; i++)
-				for(int i=0; i<2; i++) {
+				{
 					input>>z>>a;
 					avec.push_back(a);
 					zvec.push_back(z);
@@ -53,20 +55,21 @@ namespace Mask {
 			}
 			case RxnType::OneStepRxn:
 			{
-				m_sys = new OneStepSystem();
+				m_system = new OneStepSystem();
-				m_rxn_type = RxnType::OneStepRxn;
+				for(int i=0; i<3; i++)
-				for(int i=0; i<3; i++) {
+				{
 					input>>z>>a;
 					avec.push_back(a);
 					zvec.push_back(z);
 				}
+				std::cout<<"here"<<std::endl;
 				break;
 			}
 			case RxnType::TwoStepRxn:
 			{
-				m_sys = new TwoStepSystem();
+				m_system = new TwoStepSystem();
-				m_rxn_type = RxnType::TwoStepRxn;
+				for(int i=0; i<4; i++)
-				for(int i=0; i<4; i++) {
+				{
 					input>>z>>a;
 					avec.push_back(a);
 					zvec.push_back(z);
@@ -75,9 +78,9 @@ namespace Mask {
 			}
 			case RxnType::ThreeStepRxn:
 			{
-				m_sys = new ThreeStepSystem();
+				m_system = new ThreeStepSystem();
-				m_rxn_type = RxnType::ThreeStepRxn;
+				for(int i=0; i<5; i++)
-				for(int i=0; i<5; i++) {
+				{
 					input>>z>>a;
 					avec.push_back(a);
 					zvec.push_back(z);
@@ -87,7 +90,7 @@ namespace Mask {
 			default:
 				return false;
 		}
-		m_sys->SetNuclei(zvec, avec);
+		m_system->SetNuclei(zvec, avec);
 	
 		int nlayers;
 		double thickness;
@@ -110,7 +113,7 @@ namespace Mask {
 				input>>z>>a>>s;
 				zvec.push_back(z); avec.push_back(a); svec.push_back(s);
 			}
-			m_sys->AddTargetLayer(zvec, avec, svec, thickness);
+			m_system->AddTargetLayer(zvec, avec, svec, thickness);
 			input>>junk;
 		}
 		std::cout<<"Reaction equation: "<<GetSystemName()<<std::endl;
@@ -122,51 +125,51 @@ namespace Mask {
 	
 		input>>junk>>m_nsamples;
 		input>>junk>>par1>>junk>>par2;
-		m_sys->SetBeamDistro(par1, par2);
+		m_system->SetBeamDistro(par1, par2);
 		input>>junk>>par1;
-		switch(m_rxn_type) 
+		switch(m_rxnType) 
 		{
 			case RxnType::PureDecay : break;
 			case RxnType::None : break;
 			case RxnType::OneStepRxn :
 			{
-				dynamic_cast<OneStepSystem*>(m_sys)->SetReactionThetaType(par1);
+				dynamic_cast<OneStepSystem*>(m_system)->SetReactionThetaType(par1);
 				break;
 			}
 			case RxnType::TwoStepRxn :
 			{
-				dynamic_cast<TwoStepSystem*>(m_sys)->SetReactionThetaType(par1);
+				dynamic_cast<TwoStepSystem*>(m_system)->SetReactionThetaType(par1);
 				break;
 			}
 			case RxnType::ThreeStepRxn :
 			{
-				dynamic_cast<ThreeStepSystem*>(m_sys)->SetReactionThetaType(par1);
+				dynamic_cast<ThreeStepSystem*>(m_system)->SetReactionThetaType(par1);
 				break;
 			}
 		}
 		input>>junk>>par1>>junk>>par2;
-		m_sys->SetTheta1Range(par1, par2);
+		m_system->SetTheta1Range(par1, par2);
 		input>>junk>>par1>>junk>>par2;
-		m_sys->SetPhi1Range(par1, par2);
+		m_system->SetPhi1Range(par1, par2);
 		input>>junk>>par1>>junk>>par2;
-		m_sys->SetExcitationDistro(par1, par2);
+		m_system->SetExcitationDistro(par1, par2);
 		input>>junk>>dfile1;
 		input>>junk>>dfile2;
-		switch(m_rxn_type) 
+		switch(m_rxnType) 
 		{
-			case RxnType::PureDecay : break;
+			case RxnType::PureDecay :
-			case RxnType::None : break;
-			case RxnType::OneStepRxn :
 			{
-				DecaySystem* this_sys = dynamic_cast<DecaySystem*>(m_sys);
+				DecaySystem* this_sys = dynamic_cast<DecaySystem*>(m_system);
 				this_sys->SetDecay1Distribution(dfile1);
 				std::cout<<"Decay1 angular momentum: "<<this_sys->GetDecay1AngularMomentum()<<std::endl;
 				std::cout<<"Decay1 total branching ratio: "<<this_sys->GetDecay1BranchingRatio()<<std::endl;
 				break;
 			}
+			case RxnType::None : break;
+			case RxnType::OneStepRxn : break;
 			case RxnType::TwoStepRxn :
 			{
-				TwoStepSystem* this_sys = dynamic_cast<TwoStepSystem*>(m_sys);
+				TwoStepSystem* this_sys = dynamic_cast<TwoStepSystem*>(m_system);
 				this_sys->SetDecay1Distribution(dfile1);
 				std::cout<<"Decay1 angular momentum: "<<this_sys->GetDecay1AngularMomentum()<<std::endl;
 				std::cout<<"Decay1 total branching ratio: "<<this_sys->GetDecay1BranchingRatio()<<std::endl;
@@ -174,7 +177,7 @@ namespace Mask {
 			}
 			case RxnType::ThreeStepRxn :
 			{
-				ThreeStepSystem* this_sys = dynamic_cast<ThreeStepSystem*>(m_sys);
+				ThreeStepSystem* this_sys = dynamic_cast<ThreeStepSystem*>(m_system);
 				this_sys->SetDecay1Distribution(dfile1);
 				this_sys->SetDecay2Distribution(dfile2);
 				std::cout<<"Decay1 angular momentum: "<<this_sys->GetDecay1AngularMomentum()<<" Decay2 angular momentum: "<<this_sys->GetDecay2AngularMomentum()<<std::endl;
@@ -192,13 +195,14 @@ namespace Mask {
 	
 	void MaskApp::Run() {
 		std::cout<<"Running simulation..."<<std::endl;
-		if(m_sys == nullptr) 
+		if(m_system == nullptr) 
 		{
 			return;
 		}
 	
-		MaskFile output(m_outfile_name, MaskFile::FileType::write);
+		TFile* output = TFile::Open(m_outputName.c_str(), "RECREATE");
-		output.WriteHeader(m_rxn_type, m_nsamples);
+		TTree* tree = new TTree("SimTree", "SimTree");
+		tree->Branch("nuclei", m_system->GetNuclei());
 	
 		//For progress tracking
 		uint32_t percent5 = 0.05*m_nsamples;
@@ -214,11 +218,12 @@ namespace Mask {
 				std::cout<<"\rPercent complete: "<<npercent*5<<"%"<<std::flush;
 			}
 	
-			m_sys->RunSystem();
+			m_system->RunSystem();
-			output.WriteData(m_sys->GetNuclei());
+			tree->Fill();
 		}
 	
-		output.Close();
+		tree->Write(tree->GetName(), TObject::kOverwrite);
+		output->Close();
 		
 		std::cout<<std::endl;
 		std::cout<<"Complete."<<std::endl;

src/Mask/MaskApp.h

@@ -0,0 +1,37 @@
+#ifndef MASKAPP_H
+#define MASKAPP_H
+
+#include "ReactionSystem.h"
+#include "DecaySystem.h"
+#include "OneStepSystem.h"
+#include "TwoStepSystem.h"
+#include "ThreeStepSystem.h"
+#include "RxnType.h"
+
+namespace Mask {
+
+	class MaskApp
+	{
+	public:
+		MaskApp();
+		~MaskApp();
+		bool LoadConfig(const std::string& filename);
+		bool SaveConfig(const std::string& filename);
+		int GetNumberOfSamples() const { return m_nsamples; }
+		const std::string GetSystemName() const { return m_system == nullptr ? "Invalid System" : m_system->GetSystemEquation(); }
+		const std::string GetOutputName() const { return m_outputName; }
+		const RxnType GetReactionType() const { return m_rxnType; }
+
+		void Run();
+
+	private:
+		ReactionSystem* m_system;
+		std::string m_outputName;
+		RxnType m_rxnType;
+		int m_nsamples;
+	
+	};
+
+}
+
+#endif

src/Mask/MassLookup.cpp

@@ -10,38 +10,41 @@ Written by G.W. McCann Aug. 2020
 */
 #include "MassLookup.h"
 #include "KinematicsExceptions.h"
+#include <sstream>
 
 namespace Mask {
 
+	MassLookup* MassLookup::s_instance = new MassLookup();
 
-	MassLookup::MassLookup() {
+	MassLookup::MassLookup()
-	
+	{
 		std::ifstream massfile("etc/mass.txt");
-		if(massfile.is_open()) {
+		KeyPair key;
-			std::string junk, A, element;
+		if(massfile.is_open())
-			int Z;
+		{
+			std::string junk, element;
 			double atomicMassBig, atomicMassSmall, isotopicMass;
 			getline(massfile,junk);
 			getline(massfile,junk);
-			while(massfile>>junk) {
+			while(massfile>>junk)
-				massfile>>Z>>A>>element>>atomicMassBig>>atomicMassSmall;
+			{
-				isotopicMass = (atomicMassBig + atomicMassSmall*1e-6 - Z*electron_mass)*u_to_mev;
+				massfile>>key.Z>>key.A>>element>>atomicMassBig>>atomicMassSmall;
-				std::string key = "("+std::to_string(Z)+","+A+")";
+				isotopicMass = (atomicMassBig + atomicMassSmall*1e-6 - key.Z*electron_mass)*u_to_mev;
-				massTable[key] = isotopicMass;
+				massTable[key.GetID()] = isotopicMass;
-				elementTable[Z] = element;
+				elementTable[key.GetID()] = std::to_string(key.A) + element;
 			}
-		} else {
-			throw MassFileException();
 		}
+		else
+			throw MassFileException();
 	}
 	
-	MassLookup::~MassLookup() {
+	MassLookup::~MassLookup() {}
-	}
 	
 	//Returns nuclear mass in MeV
-	double MassLookup::FindMass(int Z, int A) {
+	double MassLookup::FindMass(int Z, int A)
-		std::string key = "("+std::to_string(Z)+","+std::to_string(A)+")";
+	{
-		auto data = massTable.find(key);
+		KeyPair key({Z, A});
+		auto data = massTable.find(key.GetID());
 		if(data == massTable.end())
 			throw MassException();
 	
@@ -49,13 +52,14 @@ namespace Mask {
 	}
 	
 	//returns element symbol
-	std::string MassLookup::FindSymbol(int Z, int A) {
+	std::string MassLookup::FindSymbol(int Z, int A)
-		auto data = elementTable.find(Z);
+	{
+		KeyPair key({Z, A});
+		auto data = elementTable.find(key.GetID());
 		if(data == elementTable.end())
 			throw MassException();
 	
-		std::string fullsymbol = std::to_string(A) + data->second;
+		return data->second;
-		return fullsymbol;
 	}
 
 }

src/Mask/MassLookup.h

@@ -18,22 +18,35 @@ Converted to true singleton to simplify usage -- Aug. 2021 GWM
 
 namespace Mask {
 
-	class MassLookup {
+	class MassLookup
+	{
 	public:
+
+		struct KeyPair
+		{
+			uint32_t Z;
+			uint32_t A;
+
+			//Use szudzik pairing method to make unqiue key out of two unsigned ints. Use size_t as extra safety.
+			std::size_t GetID()
+			{
+				return Z >= A ? Z*Z + Z + A : A*A + Z;
+			}
+		};
+
 		~MassLookup();
 		double FindMass(int Z, int A);
 		double FindMassU(int Z, int A) { return FindMass(Z, A)/u_to_mev; }
 		std::string FindSymbol(int Z, int A);
 	
-		static MassLookup& GetInstance() {
+		static MassLookup& GetInstance() { return *s_instance; }
-			static MassLookup s_instance;
-			return s_instance;
-		}
 	
 	private:
 		MassLookup();
-		std::unordered_map<std::string, double> massTable;
+
-		std::unordered_map<int, std::string> elementTable;
+		static MassLookup* s_instance;
+		std::unordered_map<std::size_t, double> massTable;
+		std::unordered_map<std::size_t, std::string> elementTable;
 	
 		//constants
 		static constexpr double u_to_mev = 931.4940954;

src/Mask/Nucleus.cpp

@@ -0,0 +1,17 @@
+#include "Nucleus.h"
+
+namespace Mask {
+
+    Nucleus CreateNucleus(int z, int a)
+    {
+        Nucleus nuc;
+        nuc.Z = z;
+        nuc.A = a;
+        nuc.groundStateMass = MassLookup::GetInstance().FindMass(z, a);
+		nuc.isotopicSymbol = MassLookup::GetInstance().FindSymbol(z, a);
+		nuc.vec4 = ROOT::Math::PxPyPzEVector(0., 0., 0., nuc.groundStateMass);
+        return nuc;
+    }
+
+    bool EnforceDictionaryLinked() { return true; }
+}

src/Mask/Nucleus.h

@@ -0,0 +1,59 @@
+/*
+	Nucleus.h
+	Nucleus is a derived class of Vec4. A nucleus is the kinematics is essentially a 4 vector with the
+	additional properties of the number of total nucleons (A), the number of protons (Z), a ground state mass,
+	an exctitation energy, and an isotopic symbol.
+
+	--GWM Jan 2021
+*/
+#ifndef NUCLEUS_H
+#define NUCLEUS_H
+
+#include <string>
+#include <vector>
+#include "Math/Vector4D.h"
+#include "MassLookup.h"
+
+namespace Mask {
+
+	struct Nucleus
+	{
+		void SetVec4Spherical(double theta, double phi, double p, double E)
+		{
+			vec4.SetPxPyPzE(std::sin(theta)*std::cos(phi)*p,
+							std::sin(theta)*std::sin(phi)*p,
+							std::cos(theta)*p,
+							E
+						   );
+		}
+
+		double GetKE() const
+		{
+			return vec4.E() - vec4.M();
+		}
+
+		double GetExcitationEnergy() const
+		{
+			return vec4.M() - groundStateMass;
+		}
+
+		int Z = 0; 
+		int A = 0;
+		double groundStateMass = 0.0;
+		std::string isotopicSymbol = "";
+		double thetaCM = 0.0;
+		ROOT::Math::PxPyPzEVector vec4;
+
+		bool isDetected = false;
+		double detectedKE = 0.0;
+		double detectedTheta = 0.0;
+		double detectedPhi = 0.0;
+	};
+
+	Nucleus CreateNucleus(int z, int a);
+
+	bool EnforceDictionaryLinked();
+
+};
+
+#endif

src/Mask/OneStepSystem.cpp

@@ -1,68 +1,76 @@
 #include "OneStepSystem.h"
 #include "RandomGenerator.h"
 
+#include <sstream>
+
 namespace Mask {
 
 	OneStepSystem::OneStepSystem() :
 		ReactionSystem()
 	{
-		nuclei.resize(4);
+		m_nuclei.resize(4);
 	}
 	
-	OneStepSystem::OneStepSystem(std::vector<int>& z, std::vector<int>& a) :
+	OneStepSystem::OneStepSystem(const std::vector<int>& z, const std::vector<int>& a) :
 		ReactionSystem()
 	{
-		nuclei.resize(4);
+		m_nuclei.resize(4);
 		SetNuclei(z, a);
 	}
 	
 	OneStepSystem::~OneStepSystem() {}
 	
-	bool OneStepSystem::SetNuclei(std::vector<int>& z, std::vector<int>& a) {
+	bool OneStepSystem::SetNuclei(const std::vector<int>& z, const std::vector<int>& a)
-		if(z.size() != a.size() || z.size() != 3) {
+	{
+		if(z.size() != a.size() || z.size() != 3)
 			return false;
-		}
 
-		step1.SetNuclei(z[0], a[0], z[1], a[1], z[2], a[2]);
+		int zr = z[0] + z[1] - z[2];
+		int ar = a[0] + a[1] - a[2];
+
+		m_nuclei[0] = CreateNucleus(z[0], a[0]); //target
+		m_nuclei[1] = CreateNucleus(z[1], a[1]); //projectile
+		m_nuclei[2] = CreateNucleus(z[2], a[2]); //ejectile
+		m_nuclei[3] = CreateNucleus(zr, ar); //residual
+
+		m_step1.BindNuclei(&(m_nuclei[0]), &(m_nuclei[1]), &(m_nuclei[2]), &(m_nuclei[3]));
 		SetSystemEquation();
 		return true;
 	}
 
-	const std::vector<Nucleus>& OneStepSystem::GetNuclei()
+	std::vector<Nucleus>* OneStepSystem::GetNuclei()
 	{
-		nuclei[0] = step1.GetTarget();
+		return &m_nuclei;
-		nuclei[1] = step1.GetProjectile();
-		nuclei[2] = step1.GetEjectile();
-		nuclei[3] = step1.GetResidual();
-
-		return nuclei;
 	}
 	
-	void OneStepSystem::LinkTarget() {
+	void OneStepSystem::LinkTarget()
-		step1.SetLayeredTarget(&target);
+	{
+		m_step1.SetLayeredTarget(&m_target);
 	
-		rxnLayer = target.FindLayerContaining(step1.GetTarget().GetZ(), step1.GetTarget().GetA());
+		m_rxnLayer = m_target.FindLayerContaining(m_nuclei[0].Z, m_nuclei[0].A);
-		if(rxnLayer != -1) {
+		if(m_rxnLayer != m_target.GetNumberOfLayers())
-			step1.SetRxnLayer(rxnLayer);
+		{
-			target_set_flag = true;
+			m_step1.SetRxnLayer(m_rxnLayer);
-		} else {
+			m_isTargetSet = true;
-			throw ReactionLayerException();
 		}
+		else
+			throw ReactionLayerException();
 	}
 	
-	void OneStepSystem::SetSystemEquation() {
+	void OneStepSystem::SetSystemEquation()
-		m_sys_equation = step1.GetTarget().GetIsotopicSymbol();
+	{
-		m_sys_equation += "(";
+		std::stringstream stream;
-		m_sys_equation += step1.GetProjectile().GetIsotopicSymbol();
+		stream << m_nuclei[0].isotopicSymbol << "("
-		m_sys_equation += ", ";
+			   << m_nuclei[1].isotopicSymbol << ", "
-		m_sys_equation += step1.GetEjectile().GetIsotopicSymbol();
+			   << m_nuclei[2].isotopicSymbol << ")"
-		m_sys_equation += ")";
+			   << m_nuclei[3].isotopicSymbol;
-		m_sys_equation += step1.GetResidual().GetIsotopicSymbol();
+		m_sysEquation = stream.str();
 	}
 	
 	void OneStepSystem::RunSystem() {
 		//Link up the target if it hasn't been done yet
-		if(!target_set_flag) {
+		if(!m_isTargetSet)
+		{
 			LinkTarget();
 		}
 	
@@ -72,13 +80,13 @@ namespace Mask {
 		double rxnPhi = (*m_phi1Range)(RandomGenerator::GetInstance().GetGenerator());
 		double residEx = (*m_exDist)(RandomGenerator::GetInstance().GetGenerator());
 		
-		step1.SetBeamKE(bke);
+		m_step1.SetBeamKE(bke);
-		step1.SetPolarRxnAngle(rxnTheta);
+		m_step1.SetPolarRxnAngle(rxnTheta);
-		step1.SetAzimRxnAngle(rxnPhi);
+		m_step1.SetAzimRxnAngle(rxnPhi);
-		step1.SetExcitation(residEx);
+		m_step1.SetExcitation(residEx);
 		
-		step1.TurnOnResidualEloss();
+		m_step1.SetResidualEnergyLoss(true);
-		step1.Calculate();
+		m_step1.Calculate();
 	}
 
 }

src/Mask/OneStepSystem.h

@@ -0,0 +1,30 @@
+#ifndef ONESTEPSYSTEM_H
+#define ONESTEPSYSTEM_H
+
+#include "ReactionSystem.h"
+
+namespace Mask {
+
+	class OneStepSystem: public ReactionSystem {
+	public:
+		OneStepSystem();
+		OneStepSystem(const std::vector<int>& z, const std::vector<int>& a);
+		~OneStepSystem();
+	
+		bool SetNuclei(const std::vector<int>& z, const std::vector<int>& a) override;
+		void RunSystem() override;
+		std::vector<Nucleus>* GetNuclei() override;
+	
+		void SetReactionThetaType(int type) { m_step1.SetEjectileThetaType(type); };
+	
+	private:
+		void LinkTarget() override;
+		void SetSystemEquation() override;
+	
+		Reaction m_step1;
+	
+	};
+
+}
+
+#endif

src/Mask/RandomGenerator.cpp

@@ -1,11 +1,13 @@
 #include "RandomGenerator.h"
 
 namespace Mask {
-	RandomGenerator::RandomGenerator() {
+	RandomGenerator* RandomGenerator::s_instance = new RandomGenerator();
+
+	RandomGenerator::RandomGenerator()
+	{
 		std::random_device rd;
 		rng.seed(rd());
 	}
 
-	RandomGenerator::~RandomGenerator() {
+	RandomGenerator::~RandomGenerator() {}
-	}
 }

src/Mask/RandomGenerator.h

@@ -0,0 +1,24 @@
+#ifndef RANDOMGENERATOR_H
+#define RANDOMGENERATOR_H
+
+#include <random>
+
+namespace Mask {
+
+	class RandomGenerator
+	{
+	public:
+		~RandomGenerator();
+		std::mt19937& GetGenerator() { return rng; }
+		static RandomGenerator& GetInstance() { return *s_instance; }
+
+	private:
+		RandomGenerator();
+		
+		static RandomGenerator* s_instance;
+		std::mt19937 rng;
+	};
+
+}
+
+#endif

src/Mask/Reaction.cpp

@@ -1,4 +1,4 @@
-/*
+/*ayer
 	Reaction.cpp
 	Reaction is a class which implements either a decay or scattering reaction. As such it requires either
 	3 (decay) or 4 (scattering) nuclei to perform any calcualtions. I also links together the target, which provides
@@ -9,29 +9,33 @@
 #include "Reaction.h"
 #include "KinematicsExceptions.h"
 
+#include "Math/Boost.h"
+
 namespace Mask {
 
 	Reaction::Reaction() :
-		target(nullptr), m_bke(0), m_theta(0), m_phi(0), m_ex(0), rxnLayer(0), m_eject_theta_type(lab), nuc_initFlag(false), resid_elossFlag(false)
+		m_target(nullptr), m_projectile(nullptr), m_ejectile(nullptr), m_residual(nullptr), m_layeredTarget(nullptr), 
+		m_bke(0), m_theta(0), m_phi(0), m_ex(0), m_rxnLayer(0), m_ejectThetaType(s_lab), m_isInit(false), m_isResidEloss(false)
 	{
 	}
 	
-	Reaction::Reaction(int zt, int at, int zp, int ap, int ze, int ae) :
+	Reaction::Reaction(Nucleus* target, Nucleus* projectile, Nucleus* ejectile, Nucleus* residual) :
-		target(nullptr), m_bke(0), m_theta(0), m_phi(0), m_ex(0), rxnLayer(0), m_eject_theta_type(lab), resid_elossFlag(false)
+		m_target(nullptr), m_projectile(nullptr), m_ejectile(nullptr), m_residual(nullptr),
+		m_layeredTarget(nullptr), m_bke(0), m_theta(0), m_phi(0), m_ex(0), m_rxnLayer(0), m_ejectThetaType(s_lab), m_isResidEloss(false)
 	{
-		SetNuclei(zt, at, zp, ap, ze, ae);
+		BindNuclei(target, projectile, ejectile, residual);
 	}
 	
 	Reaction::~Reaction()
 	{
 	}
 	
-	bool Reaction::Calculate() {
+	bool Reaction::Calculate()
-	
+	{
-		if(!nuc_initFlag) 
+		if(!m_isInit) 
 			return false;
 	
-		if(decayFlag) {
+		if(m_isDecay) {
 			CalculateDecay();
 			return true;
 		} else {
@@ -40,203 +44,184 @@ namespace Mask {
 		}
 	}
 	
-	//Deep copy of nucleus array
+	void Reaction::BindNuclei(Nucleus* target, Nucleus* projectile, Nucleus* ejectile, Nucleus* residual)
-	void Reaction::SetNuclei(const Nucleus* nucs) {
+	{
-		reactants[0] = nucs[0];
+		m_target = target;
-		reactants[1] = nucs[1];
+		m_projectile = projectile;
-		reactants[2] = nucs[2];
+		m_ejectile = ejectile;
-		reactants[3] = nucs[3];
+		m_residual = residual;
-		nuc_initFlag = true;
+
+		if(m_projectile == nullptr)
+			m_isDecay = true;
+		else
+			m_isDecay = false;
+
+		if(m_target == nullptr || m_ejectile ==  nullptr || m_residual == nullptr)
+			m_isInit = false;
+		else
+			m_isInit = true;
 	}
 	
-	void Reaction::SetNuclei(int zt, int at, int zp, int ap, int ze, int ae) {
+	void Reaction::SetBeamKE(double bke)
-		int zr, ar;
+	{
-		reactants[0] = Nucleus(zt, at);
+		if(!m_isInit || m_isDecay) 
-		reactants[2] = Nucleus(ze, ae);
-		if(ap == 0) {
-			decayFlag = true;
-			zr = zt - ze;
-			ar = at - ae;
-		} else {
-			reactants[1] = Nucleus(zp, ap);
-			decayFlag = false;
-			zr = zt + zp - ze;
-			ar = at + ap - ae;
-		}
-	
-		if(zr < 0 || ar <= 0) {
-			nuc_initFlag = false;
-		} else {
-			reactants[3] = Nucleus(zr, ar);
-			nuc_initFlag = true;
-		}
-	}
-	
-	void Reaction::SetBeamKE(double bke) {
-		if(!nuc_initFlag || decayFlag) 
 			return;
 	
-		m_bke = bke - target->GetProjectileEnergyLoss(reactants[1].GetZ(), reactants[1].GetA(), bke, rxnLayer, 0);
+		m_bke = bke - m_layeredTarget->GetProjectileEnergyLoss(m_projectile->Z, m_projectile->A, bke, m_rxnLayer, 0);
 	}
 	
-	void Reaction::SetEjectileThetaType(int type) {
+	void Reaction::SetEjectileThetaType(int type)
-		if(decayFlag) return;
+	{
-		if(type != center_of_mass && type != lab) return;
+		if(m_isDecay)
+			return;
+		if(type != s_centerOfMass && type != s_lab)
+			return;
 	
-		m_eject_theta_type = type;
+		m_ejectThetaType = type;
 	}
 	
 	//Methods given by Iliadis in Nuclear Physics of Stars, Appendix C
 	//For use with lab frame restricted angles. May not give appropriate disribution for ejectile
-	void Reaction::CalculateReactionThetaLab() {
+	void Reaction::CalculateReactionThetaLab()
-		reactants[0].SetVectorCartesian(0.,0.,0.,reactants[0].GetGroundStateMass());
+	{
-		double beam_pz = std::sqrt(m_bke*(m_bke + 2.0 * reactants[1].GetGroundStateMass()));
+		m_target->vec4.SetPxPyPzE(0.,0.,0.,m_target->groundStateMass);
-		double beam_E = m_bke + reactants[1].GetGroundStateMass();
+		double beam_pz = std::sqrt(m_bke*(m_bke + 2.0 * m_projectile->groundStateMass));
-		reactants[1].SetVectorCartesian(0.,0.,beam_pz,beam_E);
+		double beam_E = m_bke + m_projectile->groundStateMass;
+		m_projectile->vec4.SetPxPyPzE(0.,0.,beam_pz,beam_E);
 	
-		double Q = reactants[0].GetGroundStateMass() + reactants[1].GetGroundStateMass() - (reactants[2].GetGroundStateMass() + reactants[3].GetGroundStateMass() + m_ex);
+		double Q = m_target->groundStateMass + m_projectile->groundStateMass - (m_ejectile->groundStateMass + m_residual->groundStateMass + m_ex);
 	
-		double Ethresh = -Q*(reactants[2].GetGroundStateMass()+reactants[3].GetGroundStateMass())/(reactants[2].GetGroundStateMass() + reactants[3].GetGroundStateMass() - reactants[1].GetGroundStateMass());
+		double Ethresh = -Q*(m_ejectile->groundStateMass+m_residual->groundStateMass) / 
-		if(m_bke < Ethresh) {
+						 (m_ejectile->groundStateMass + m_residual->groundStateMass - m_projectile->groundStateMass);
+		if(m_bke < Ethresh)
 			throw EnergyThresholdException();
-		}
 	
-		double term1 = sqrt(reactants[1].GetGroundStateMass()*reactants[2].GetGroundStateMass()*m_bke)/(reactants[2].GetGroundStateMass()+reactants[3].GetGroundStateMass())*cos(m_theta);
+		double term1 = std::sqrt(m_projectile->groundStateMass * m_ejectile->groundStateMass * m_bke)/
-		double term2 = (m_bke*(reactants[3].GetGroundStateMass() - reactants[1].GetGroundStateMass()) + reactants[3].GetGroundStateMass()*Q)/(reactants[3].GetGroundStateMass() + reactants[2].GetGroundStateMass());
+					   (m_ejectile->groundStateMass + m_residual->groundStateMass) * std::cos(m_theta);
-		double sqrt_pos_ejectKE = term1 + sqrt(term1*term1 + term2);
+		double term2 = (m_bke * (m_residual->groundStateMass - m_projectile->groundStateMass) + m_residual->groundStateMass*Q) / 
-		double sqrt_neg_ejectKE = term1 - sqrt(term1*term1 + term2);
+					   (m_residual->groundStateMass + m_ejectile->groundStateMass);
+		double sqrt_pos_ejectKE = term1 + std::sqrt(term1*term1 + term2);
+		double sqrt_neg_ejectKE = term1 - std::sqrt(term1*term1 + term2);
 		double ejectKE;
-		if(sqrt_pos_ejectKE > 0) {
+		if(sqrt_pos_ejectKE > 0)
 			ejectKE = sqrt_pos_ejectKE*sqrt_pos_ejectKE;
-		} else {
+		else
 			ejectKE = sqrt_neg_ejectKE*sqrt_neg_ejectKE;
-		}
-		double ejectP = std::sqrt(ejectKE*(ejectKE + 2.0 * reactants[2].GetGroundStateMass()));
-		double ejectE = ejectKE + reactants[2].GetGroundStateMass();
 
-		reactants[2].SetVectorSpherical(m_theta, m_phi, ejectP, ejectE);
+		double ejectP = std::sqrt(ejectKE * (ejectKE + 2.0 * m_ejectile->groundStateMass));
+		double ejectE = ejectKE + m_ejectile->groundStateMass;
 	
-		reactants[3] = reactants[0] + reactants[1] - reactants[2];
+		m_ejectile->SetVec4Spherical(m_theta, m_phi, ejectP, ejectE);
 	
-		ejectKE -= target->GetEjectileEnergyLoss(reactants[2].GetZ(), reactants[2].GetA(), ejectKE, rxnLayer, m_theta);
+		m_residual->vec4 = m_target->vec4 + m_projectile->vec4 - m_ejectile->vec4;
-		ejectP = std::sqrt(ejectKE*(ejectKE + 2.0 * reactants[2].GetGroundStateMass()));
-		ejectE = ejectKE + reactants[2].GetGroundStateMass();
-		reactants[2].SetVectorSpherical(m_theta, m_phi, ejectP, ejectE);
 	
-		if(resid_elossFlag) {
+		ejectKE -= m_layeredTarget->GetEjectileEnergyLoss(m_ejectile->Z, m_ejectile->A, ejectKE, m_rxnLayer, m_theta);
-			double residKE = reactants[3].GetKE() - target->GetEjectileEnergyLoss(reactants[3].GetZ(), reactants[3].GetA(), reactants[3].GetKE(), rxnLayer, reactants[3].GetTheta());
+		ejectP = std::sqrt(ejectKE*(ejectKE + 2.0 * m_ejectile->groundStateMass));
-			double residP = std::sqrt(residKE*(residKE + 2.0*reactants[3].GetInvMass()));
+		ejectE = ejectKE + m_ejectile->groundStateMass;
-			double residE = residKE + reactants[3].GetInvMass();
+		m_ejectile->SetVec4Spherical(m_theta, m_phi, ejectP, ejectE);
-			reactants[3].SetVectorSpherical(reactants[3].GetTheta(), reactants[3].GetPhi(), residP, residE);
+	
+		if(m_isResidEloss) {
+			double residKE = m_residual->GetKE() - m_layeredTarget->GetEjectileEnergyLoss(m_residual->Z, m_residual->A, m_residual->GetKE(), 
+																						  m_rxnLayer, m_residual->vec4.Theta());
+			double residP = std::sqrt(residKE*(residKE + 2.0*m_residual->vec4.M()));
+			double residE = residKE + m_residual->vec4.M();
+			m_residual->SetVec4Spherical(m_residual->vec4.Theta(), m_residual->vec4.Phi(), residP, residE);
 		}
 	}
 	
 	//Methods from original ANASEN. Gives proper distribution for inverse kinematics.
-	void Reaction::CalculateReactionThetaCM() {
+	void Reaction::CalculateReactionThetaCM()
+	{
 		//Target assumed at rest, with 0 excitation energy
-		reactants[0].SetVectorCartesian(0.,0.,0.,reactants[0].GetGroundStateMass());
+		m_target->vec4.SetPxPyPzE(0.,0.,0.,m_target->groundStateMass);
-		double beam_pz = std::sqrt(m_bke*(m_bke + 2.0 * reactants[1].GetGroundStateMass()));
+		double beam_pz = std::sqrt(m_bke*(m_bke + 2.0 * m_projectile->groundStateMass));
-		double beam_E = m_bke + reactants[1].GetGroundStateMass();
+		double beam_E = m_bke + m_projectile->groundStateMass;
-		reactants[1].SetVectorCartesian(0.,0.,beam_pz,beam_E);
+		m_projectile->vec4.SetPxPyPzE(0.,0.,beam_pz,beam_E);
 	
+		double Q = m_target->groundStateMass + m_projectile->groundStateMass - (m_ejectile->groundStateMass + m_residual->groundStateMass + m_ex);
 	
-		double Q = reactants[0].GetGroundStateMass() + reactants[1].GetGroundStateMass() - (reactants[2].GetGroundStateMass() + reactants[3].GetGroundStateMass() + m_ex);
+		double Ethresh = -Q*(m_ejectile->groundStateMass + m_residual->groundStateMass) / 
-	
+						 (m_ejectile->groundStateMass + m_residual->groundStateMass - m_projectile->groundStateMass);
-		double Ethresh = -Q*(reactants[2].GetGroundStateMass()+reactants[3].GetGroundStateMass())/(reactants[2].GetGroundStateMass() + reactants[3].GetGroundStateMass() - reactants[1].GetGroundStateMass());
+		if(m_bke < Ethresh)
-		if(m_bke < Ethresh) {
 			throw EnergyThresholdException();
-		}
 		
-		auto parent = reactants[0] + reactants[1];
+		ROOT::Math::PxPyPzEVector parent = m_target->vec4 + m_projectile->vec4;
-		double boost2lab[3];
+		ROOT::Math::Boost boost(parent.BoostToCM());
-		double boost2cm[3];
+		parent = boost*parent;
-		const double* boost = parent.GetBoost();
+		double ejectE_cm = (std::pow(m_ejectile->groundStateMass, 2.0) - 
-		for(int i=0; i<3; i++) {
+							std::pow(m_residual->groundStateMass + m_ex, 2.0) + std::pow(parent.E(),2.0))/
-			boost2lab[i] = boost[i];
+							(2.0*parent.E());
-			boost2cm[i] = boost[i]*(-1.0);
+		double ejectP_cm = std::sqrt(ejectE_cm*ejectE_cm - std::pow(m_ejectile->groundStateMass, 2.0));
-		}
+		m_ejectile->SetVec4Spherical(m_theta, m_phi, ejectP_cm, ejectE_cm);
-		parent.ApplyBoost(boost2cm);
+		m_ejectile->vec4 = boost.Inverse() * m_ejectile->vec4;
-		double ejectE_cm = (std::pow(reactants[2].GetGroundStateMass(), 2.0) - std::pow(reactants[3].GetGroundStateMass() + m_ex, 2.0) + std::pow(parent.GetE(),2.0))/(2.0*parent.GetE());
+		m_residual->vec4 = m_target->vec4 + m_projectile->vec4 - m_ejectile->vec4;
-		double ejectP_cm = std::sqrt(ejectE_cm*ejectE_cm - std::pow(reactants[2].GetGroundStateMass(), 2.0));
-		reactants[2].SetVectorSpherical(m_theta, m_phi, ejectP_cm, ejectE_cm);
-		reactants[2].ApplyBoost(boost2lab);
-		reactants[3] = reactants[0] + reactants[1] - reactants[2];
 	
-		double ejectKE = reactants[2].GetKE();
+		double ejectKE = m_ejectile->GetKE();
-		double ejectP = reactants[2].GetP();
+		double ejectP = m_ejectile->vec4.P();
-		double ejectE = reactants[2].GetE();
+		double ejectE = m_ejectile->vec4.E();
 		//energy loss for ejectile (after reaction!)
-		ejectKE -= target->GetEjectileEnergyLoss(reactants[2].GetZ(), reactants[2].GetA(), ejectKE, rxnLayer, reactants[2].GetTheta());
+		ejectKE -= m_layeredTarget->GetEjectileEnergyLoss(m_ejectile->Z, m_ejectile->A, ejectKE, m_rxnLayer, m_ejectile->vec4.Theta());
-		ejectP = std::sqrt(ejectKE*(ejectKE + 2.0 * reactants[2].GetGroundStateMass()));
+		ejectP = std::sqrt(ejectKE*(ejectKE + 2.0 * m_ejectile->groundStateMass));
-		ejectE = ejectKE + reactants[2].GetGroundStateMass();
+		ejectE = ejectKE + m_ejectile->groundStateMass;
-		reactants[2].SetVectorSpherical(reactants[2].GetTheta(), reactants[2].GetPhi(), ejectP, ejectE);
+		m_ejectile->SetVec4Spherical(m_ejectile->vec4.Theta(), m_ejectile->vec4.Phi(), ejectP, ejectE);
 	
 		//if on, get eloss for residual (after reaction!)
-		if(resid_elossFlag) {
+		if(m_isResidEloss)
-			double residKE = reactants[3].GetKE() - target->GetEjectileEnergyLoss(reactants[3].GetZ(), reactants[3].GetA(), reactants[3].GetKE(), rxnLayer, reactants[3].GetTheta());
+		{
-			double residP = std::sqrt(residKE*(residKE + 2.0*reactants[3].GetInvMass()));
+			double residKE = m_residual->GetKE() - 
-			double residE = residKE + reactants[3].GetInvMass();
+					m_layeredTarget->GetEjectileEnergyLoss(m_residual->Z, m_residual->A, m_residual->GetKE(), m_rxnLayer, m_residual->vec4.Theta());
-			reactants[3].SetVectorSpherical(reactants[3].GetTheta(), reactants[3].GetPhi(), residP, residE);
+			double residP = std::sqrt(residKE*(residKE + 2.0*m_residual->vec4.M()));
+			double residE = residKE + m_residual->vec4.M();
+			m_residual->SetVec4Spherical(m_residual->vec4.Theta(), m_residual->vec4.Phi(), residP, residE);
 		}
 	}
 	
-	void Reaction::CalculateReaction() {
+	void Reaction::CalculateReaction()
-		switch(m_eject_theta_type) {
+	{
-			case center_of_mass:
+		switch(m_ejectThetaType)
-			{
+		{
-				CalculateReactionThetaCM();
+			case s_centerOfMass: CalculateReactionThetaCM(); break;
-				break;
+			case s_lab: CalculateReactionThetaLab(); break;
-			}
-			case lab:
-			{
-				CalculateReactionThetaLab();
-				break;
-			}
 		}
 	}
 	
 	//Calculate in CM, where decay is isotropic
-	void Reaction::CalculateDecay() {
+	void Reaction::CalculateDecay()
-	
+	{
-		double Q = reactants[0].GetInvMass() - reactants[2].GetGroundStateMass() - reactants[3].GetGroundStateMass();
+		double Q = m_target->vec4.M() - m_ejectile->groundStateMass - m_residual->groundStateMass;
-		if(Q < 0) {
+		if(Q < 0)
 			throw QValueException();
-		}
 	
-		const double* boost = reactants[0].GetBoost();
+		ROOT::Math::Boost boost(m_target->vec4.BoostToCM());
-		double boost2cm[3];
+		m_target->vec4 = boost*m_target->vec4;
-		double boost2lab[3];
+		double ejectE_cm = (m_ejectile->groundStateMass*m_ejectile->groundStateMass - 
-		for(int i=0; i<3; i++) {
+						   m_residual->groundStateMass*m_residual->groundStateMass + m_target->vec4.E()*m_target->vec4.E()) /
-			boost2lab[i] = boost[i];
+					       (2.0*m_target->vec4.E());
-			boost2cm[i] = boost[i]*(-1.0);
+		double ejectP_cm = std::sqrt(ejectE_cm*ejectE_cm - m_ejectile->groundStateMass*m_ejectile->groundStateMass);
-		}
 	
-		reactants[0].ApplyBoost(&(boost2cm[0]));
+		m_ejectile->SetVec4Spherical(m_theta, m_phi, ejectP_cm, ejectE_cm);
-		double ejectE_cm = (reactants[2].GetGroundStateMass()*reactants[2].GetGroundStateMass() - reactants[3].GetGroundStateMass()*reactants[3].GetGroundStateMass() + reactants[0].GetE()*reactants[0].GetE())/
+		m_ejectile->thetaCM = m_theta;
-					(2.0*reactants[0].GetE());
-		double ejectP_cm = std::sqrt(ejectE_cm*ejectE_cm - reactants[2].GetGroundStateMass()*reactants[2].GetGroundStateMass());
 	
-		reactants[2].SetVectorSpherical(m_theta, m_phi, ejectP_cm, ejectE_cm);
+		m_target->vec4 = boost.Inverse() * m_target->vec4;
-		reactants[2].SetThetaCM(m_theta);
+		m_ejectile->vec4 = boost.Inverse() * m_ejectile->vec4;
 	
-		reactants[0].ApplyBoost(boost2lab);
+		m_residual->vec4 = m_target->vec4 - m_ejectile->vec4;
-		reactants[2].ApplyBoost(boost2lab);
-	
-		reactants[3] = reactants[0] - reactants[2];
 	
 		//energy loss for the *light* break up nucleus
-		double ejectKE = reactants[2].GetKE() - target->GetEjectileEnergyLoss(reactants[2].GetZ(), reactants[2].GetA(), reactants[2].GetKE(), rxnLayer, reactants[2].GetTheta());
+		double ejectKE = m_ejectile->GetKE() - 
-		double ejectP = std::sqrt(ejectKE*(ejectKE + 2.0*reactants[2].GetGroundStateMass()));
+					m_layeredTarget->GetEjectileEnergyLoss(m_ejectile->Z, m_ejectile->A, m_ejectile->GetKE(), m_rxnLayer, m_ejectile->vec4.Theta());
-		double ejectE = ejectKE + reactants[2].GetGroundStateMass();
+		double ejectP = std::sqrt(ejectKE*(ejectKE + 2.0*m_ejectile->groundStateMass));
-		reactants[2].SetVectorSpherical(reactants[2].GetTheta(), reactants[2].GetPhi(), ejectP, ejectE);
+		double ejectE = ejectKE + m_ejectile->groundStateMass;
+		m_ejectile->SetVec4Spherical(m_ejectile->vec4.Theta(), m_ejectile->vec4.Phi(), ejectP, ejectE);
 	
 		//if on, get eloss for *heavy* break up nucleus
-		if(resid_elossFlag) {
+		if(m_isResidEloss)
-	
+		{
-			double residKE = reactants[3].GetKE() - target->GetEjectileEnergyLoss(reactants[3].GetZ(), reactants[3].GetA(), reactants[3].GetKE(), rxnLayer, reactants[3].GetTheta());
+			double residKE = m_residual->GetKE() - 
-			double residP = std::sqrt(residKE*(residKE + 2.0*reactants[3].GetInvMass()));
+					m_layeredTarget->GetEjectileEnergyLoss(m_residual->Z, m_residual->A, m_residual->GetKE(), m_rxnLayer, m_residual->vec4.Theta());
-			double residE = residKE + reactants[3].GetInvMass();
+			double residP = std::sqrt(residKE*(residKE + 2.0*m_residual->vec4.M()));
-			reactants[3].SetVectorSpherical(reactants[3].GetTheta(), reactants[3].GetPhi(), residP, residE);
+			double residE = residKE + m_residual->vec4.M();
+			m_residual->SetVec4Spherical(m_residual->vec4.Theta(), m_residual->vec4.Phi(), residP, residE);
 		}
 	}
 

src/Mask/Reaction.h

@@ -0,0 +1,74 @@
+/*
+	Reaction.h
+	Reaction is a class which implements either a decay or scattering reaction. As such it requires either
+	3 (decay) or 4 (scattering) nuclei to perform any calcualtions. I also links together the target, which provides
+	energy loss calculations, with the kinematics. Note that Reaction does not own the LayeredTarget.
+
+	--GWM Jan. 2021
+*/
+#ifndef REACTION_H
+#define REACTION_H
+
+#include "Nucleus.h"
+#include "LayeredTarget.h"
+
+namespace Mask {
+
+	class Reaction
+	{
+	public:
+		Reaction();
+		Reaction(Nucleus* target, Nucleus* projectile, Nucleus* ejectile, Nucleus* residual);
+		~Reaction();
+		bool Calculate(); //do sim
+
+		void BindNuclei(Nucleus* target, Nucleus* projectile, Nucleus* ejectile, Nucleus* residual);
+		void SetBeamKE(double bke);
+		void SetEjectileThetaType(int type);
+	
+		void SetLayeredTarget(LayeredTarget* targ) { m_layeredTarget = targ; };
+
+		void SetPolarRxnAngle(double theta) { m_theta = theta; };
+		void SetAzimRxnAngle(double phi) { m_phi = phi; };
+		void SetExcitation(double ex) { m_ex = ex; };
+
+		void BindTarget(Nucleus* nuc) { m_target = nuc; };
+		void BindProjectile(Nucleus* nuc) { m_projectile = nuc; };
+		void BindEjectile(Nucleus* nuc) { m_ejectile = nuc; };
+		void BindResidual(Nucleus* nuc) { m_residual = nuc; };
+
+		void SetRxnLayer(std::size_t layer) { m_rxnLayer = layer; };
+		void SetResidualEnergyLoss(bool isEloss) { m_isResidEloss = isEloss; };
+
+		bool IsDecay() const { return m_isDecay; };
+
+		std::size_t GetRxnLayer() const { return m_rxnLayer; };
+	
+	private:
+		void CalculateDecay(); //target -> light_decay (eject) + heavy_decay(resid)
+		void CalculateReaction(); //target + project -> eject + resid
+		void CalculateReactionThetaLab();
+		void CalculateReactionThetaCM();
+	
+		//Reactants -> NOT OWNED BY RXN
+		Nucleus* m_target;
+		Nucleus* m_projectile;
+		Nucleus* m_ejectile;
+		Nucleus* m_residual;
+
+		LayeredTarget* m_layeredTarget; //not owned by Reaction
+	
+		double m_bke, m_theta, m_phi, m_ex;
+	
+		int m_rxnLayer;
+		int m_ejectThetaType; 
+	
+		bool m_isDecay, m_isInit, m_isResidEloss;
+	
+		static constexpr int s_lab = 0;
+		static constexpr int s_centerOfMass = 1;
+	};
+
+}
+
+#endif

src/Mask/ReactionSystem.cpp

@@ -5,20 +5,22 @@
 namespace Mask {
 
 	ReactionSystem::ReactionSystem() :
-		m_beamDist(nullptr), m_theta1Range(nullptr), m_phi1Range(nullptr), m_exDist(nullptr), target_set_flag(false),
+		m_beamDist(nullptr), m_theta1Range(nullptr), m_phi1Range(nullptr), m_exDist(nullptr), m_isTargetSet(false),
-		rxnLayer(0), m_sys_equation("")
+		m_rxnLayer(0), m_sysEquation("")
 	{
 	}
 	
-	ReactionSystem::~ReactionSystem() {
+	ReactionSystem::~ReactionSystem()
+	{
 		delete m_beamDist;
 		delete m_theta1Range;
 		delete m_phi1Range;
 		delete m_exDist;
 	}
 	
-	void ReactionSystem::AddTargetLayer(std::vector<int>& zt, std::vector<int>& at, std::vector<int>& stoich, double thickness) {
+	void ReactionSystem::AddTargetLayer(const std::vector<int>& zt, const std::vector<int>& at, const std::vector<int>& stoich, double thickness)
-		target.AddLayer(zt, at, stoich, thickness);
+	{
+		m_target.AddLayer(zt, at, stoich, thickness);
 	}
 
 }

src/Mask/ReactionSystem.h

@@ -16,59 +16,64 @@
 
 namespace Mask {
 
-	class ReactionSystem {
+	class ReactionSystem
+	{
 	public:
 		ReactionSystem();
 		virtual ~ReactionSystem();
 	
-		virtual bool SetNuclei(std::vector<int>& z, std::vector<int>& a) = 0;
+		virtual bool SetNuclei(const std::vector<int>& z, const std::vector<int>& a) = 0;
 		virtual void RunSystem() = 0;
-		virtual const std::vector<Nucleus>& GetNuclei() = 0;
+		virtual std::vector<Nucleus>* GetNuclei() = 0;
 	
-		void AddTargetLayer(std::vector<int>& zt, std::vector<int>& at, std::vector<int>& stoich, double thickness);
+		void AddTargetLayer(const std::vector<int>& zt, const std::vector<int>& at, const std::vector<int>& stoich, double thickness);
 	
 		/*Set sampling parameters*/
-		inline void SetBeamDistro(double mean, double sigma) {
+		void SetBeamDistro(double mean, double sigma)
+		{
 			if(m_beamDist)
 				delete m_beamDist;
 			m_beamDist = new std::normal_distribution<double>(mean, sigma); 
 		}
 	
-		inline void SetTheta1Range(double min, double max) { 
+		void SetTheta1Range(double min, double max)
+		{ 
 			if(m_theta1Range)
 				delete m_theta1Range;
-			m_theta1Range = new std::uniform_real_distribution<double>(std::cos(min*deg2rad), std::cos(max*deg2rad)); 
+			m_theta1Range = new std::uniform_real_distribution<double>(std::cos(min*s_deg2rad), std::cos(max*s_deg2rad)); 
 		}
 	
-		inline void SetPhi1Range(double min, double max) {
+		void SetPhi1Range(double min, double max)
+		{
 			if(m_phi1Range)
 				delete m_phi1Range;
-			m_phi1Range = new std::uniform_real_distribution<double>(min*deg2rad, max*deg2rad); 
+			m_phi1Range = new std::uniform_real_distribution<double>(min*s_deg2rad, max*s_deg2rad); 
 		}
 	
-		inline void SetExcitationDistro(double mean, double sigma) {
+		void SetExcitationDistro(double mean, double sigma)
+		{
 			if(m_exDist)
 				delete m_exDist;
 			m_exDist = new std::normal_distribution<double>(mean, sigma); 
 		}
 	
-		inline const std::string& GetSystemEquation() const { return m_sys_equation; }
+		const std::string& GetSystemEquation() const { return m_sysEquation; }
 	
 	protected:
 		virtual void LinkTarget() = 0;
 		virtual void SetSystemEquation() = 0;
 		
-		LayeredTarget target;
+		LayeredTarget m_target;
 	
 		//Sampling information
 		std::normal_distribution<double> *m_beamDist, *m_exDist;
 		std::uniform_real_distribution<double> *m_theta1Range, *m_phi1Range; 
 	
-		bool target_set_flag, gen_set_flag;
+		bool m_isTargetSet;
-		int rxnLayer;
+		std::size_t m_rxnLayer;
-		std::string m_sys_equation;
+		std::string m_sysEquation;
-		std::vector<Nucleus> nuclei;
+		std::vector<Nucleus> m_nuclei;
-		static constexpr double deg2rad = M_PI/180.0;
+		static constexpr double s_deg2rad = M_PI/180.0;
 	};
 
 }

src/Mask/Stopwatch.cpp

@@ -7,25 +7,34 @@
 */
 #include "Stopwatch.h"
 
-Stopwatch::Stopwatch() {
+namespace Mask {
-	start_time = Clock::now();
-	stop_time = start_time;
-}
 
-Stopwatch::~Stopwatch() {}
+	Stopwatch::Stopwatch()
+	{
+		start_time = Clock::now();
+		stop_time = start_time;
+	}
 
-void Stopwatch::Start() {
+	Stopwatch::~Stopwatch() {}
-	start_time = Clock::now();
-}
 
-void Stopwatch::Stop() {
+	void Stopwatch::Start()
-	stop_time = Clock::now();
+	{
-}
+		start_time = Clock::now();
+	}
 
-double Stopwatch::GetElapsedSeconds() {
+	void Stopwatch::Stop()
-	return std::chrono::duration_cast<std::chrono::duration<double>>(stop_time-start_time).count();
+	{
-}
+		stop_time = Clock::now();
+	}
+
+	double Stopwatch::GetElapsedSeconds()
+	{
+		return std::chrono::duration_cast<std::chrono::duration<double>>(stop_time-start_time).count();
+	}
+
+	double Stopwatch::GetElapsedMilliseconds()
+	{
+		return std::chrono::duration_cast<std::chrono::duration<double>>(stop_time-start_time).count()*1000.0;
+	}
 
-double Stopwatch::GetElapsedMilliseconds() {
-	return std::chrono::duration_cast<std::chrono::duration<double>>(stop_time-start_time).count()*1000.0;
 }

src/Mask/Stopwatch.h

@@ -0,0 +1,32 @@
+/*
+	Stopwatch.h
+	Simple class designed to provide timing info on parts of the process.
+	Only for use in development.
+
+	Written by G.W. McCann Oct. 2020
+*/
+#ifndef STOPWATCH_H
+#define STOPWATCH_H
+
+#include <chrono>
+namespace Mask {
+	
+	class Stopwatch
+	{
+	public:
+		Stopwatch();
+		~Stopwatch();
+		void Start();
+		void Stop();
+		double GetElapsedSeconds();
+		double GetElapsedMilliseconds();
+
+	private:
+		using Time = std::chrono::high_resolution_clock::time_point;
+		using Clock = std::chrono::high_resolution_clock;
+
+		Time start_time, stop_time;
+	};
+
+}
+#endif

src/Mask/Target.cpp

@@ -16,45 +16,50 @@ Written by G.W. McCann Aug. 2020
 namespace Mask {
 
 	/*Targets must be of known thickness*/
-	Target::Target(double thick) {
+	Target::Target(const std::vector<int>& z, const std::vector<int>& a, const std::vector<int>& stoich, double thick) :
-		thickness = thick;
+		m_thickness(thick), m_thickness_gcm2(thick*1.0e-6)
-		thickness_gcm2 = thickness*1.0e-6;
+	{
+		Init(z, a, stoich);
 	}
 	
 	Target::~Target() {}
 	
 	/*Set target elements of given Z, A, S*/
-	void Target::SetElements(std::vector<int>& z, std::vector<int>& a, std::vector<int>& stoich) {
+	void Target::Init(const std::vector<int>& z, const std::vector<int>& a, const std::vector<int>& stoich) 
-		Z = z;
+	{
-		A = a;
+		m_Z = z;
-		Stoich = stoich;
+		m_A = a;
+		m_stoich = stoich;
 		MassLookup& masses = MassLookup::GetInstance();
-		eloss.SetTargetComponents(Z, A, Stoich);
+		for(size_t i=0; i<m_Z.size(); i++)
-		for(size_t i=0; i<Z.size(); i++)
 		{
-			target_material.add_element(masses.FindMassU(Z[i], A[i]), Z[i], Stoich[i]);
+			m_material.add_element(masses.FindMassU(m_Z[i], m_A[i]), m_Z[i], m_stoich[i]);
 		}
 	}
 	
 	/*Element verification*/
-	bool Target::ContainsElement(int z, int a) {
+	bool Target::ContainsElement(int z, int a)
-		for(unsigned int i=0; i<Z.size(); i++)
+	{
-			if( z == Z[i] && a == A[i]) 
+		for(std::size_t i=0; i<m_Z.size(); i++)
+		{
+			if( z == m_Z[i] && a == m_A[i]) 
 				return true;
+		}
 		return false;
 	}
 	
 	/*Calculates energy loss for travelling all the way through the target*/
-	double Target::GetEnergyLossTotal(int zp, int ap, double startEnergy, double theta) {
+	double Target::GetEnergyLossTotal(int zp, int ap, double startEnergy, double theta)
+	{
 		if(theta == M_PI/2.) 
 			return startEnergy;
 		else if (theta > M_PI/2.) 
 			theta = M_PI - theta;
+
 		catima::Projectile proj(MassLookup::GetInstance().FindMassU(zp, ap), zp, 0.0, 0.0);
 		proj.T = startEnergy/proj.A;
-		target_material.thickness(thickness_gcm2/fabs(cos(theta)));
+		m_material.thickness(m_thickness_gcm2/fabs(cos(theta)));
-		return catima::integrate_energyloss(proj, target_material);
+		return catima::integrate_energyloss(proj, m_material);
-		//return eloss.GetEnergyLoss(zp, ap, startEnergy, thickness/fabs(cos(theta)));
 	}
 
 	/*Calculates the energy loss for traveling some fraction through the target*/
@@ -67,13 +72,13 @@ namespace Mask {
 
 		catima::Projectile proj(MassLookup::GetInstance().FindMassU(zp, ap), zp, 0.0, 0.0);
 		proj.T = finalEnergy/proj.A;
-		target_material.thickness(thickness_gcm2*percent_depth/fabs(cos(theta)));
+		m_material.thickness(m_thickness_gcm2*percent_depth/fabs(cos(theta)));
-		return catima::integrate_energyloss(proj, target_material);
+		return catima::integrate_energyloss(proj, m_material);
-		//return eloss.GetEnergyLoss(zp, ap, finalEnergy, thickness*percent_depth/(std::fabs(std::cos(theta))));
 	}
 	
 	/*Calculates reverse energy loss for travelling all the way through the target*/
-	double Target::GetReverseEnergyLossTotal(int zp, int ap, double finalEnergy, double theta) {
+	double Target::GetReverseEnergyLossTotal(int zp, int ap, double finalEnergy, double theta)
+	{
 		if(theta == M_PI/2.) 
 			return finalEnergy;
 		else if (theta > M_PI/2.) 
@@ -81,9 +86,8 @@ namespace Mask {
 
 		catima::Projectile proj(MassLookup::GetInstance().FindMassU(zp, ap), zp, 0.0, 0.0);
 		proj.T = finalEnergy/proj.A;
-		target_material.thickness(thickness_gcm2/fabs(cos(theta)));
+		m_material.thickness(m_thickness_gcm2/fabs(cos(theta)));
-		return catima::reverse_integrate_energyloss(proj, target_material);
+		return catima::reverse_integrate_energyloss(proj, m_material);
-		//return eloss.GetReverseEnergyLoss(zp, ap, finalEnergy, thickness/fabs(cos(theta)));
 	}
 
 	/*Calculates the reverse energy loss for traveling some fraction through the target*/
@@ -95,9 +99,8 @@ namespace Mask {
 			theta = M_PI-theta;
 		catima::Projectile proj(MassLookup::GetInstance().FindMassU(zp, ap), zp, 0.0, 0.0);
 		proj.T = finalEnergy/proj.A;
-		target_material.thickness(thickness_gcm2*percent_depth/fabs(cos(theta)));
+		m_material.thickness(m_thickness_gcm2*percent_depth/fabs(cos(theta)));
-		return catima::reverse_integrate_energyloss(proj, target_material);
+		return catima::reverse_integrate_energyloss(proj, m_material);
-		//return eloss.GetReverseEnergyLoss(zp, ap, finalEnergy, thickness*percent_depth/(std::fabs(std::cos(theta))));
 	}
 
 }

src/Mask/Target.h

@@ -16,7 +16,6 @@ Written by G.W. McCann Aug. 2020
 #include <string>
 #include <vector>
 #include <cmath>
-#include "EnergyLoss.h"
 #include "catima/gwm_integrators.h"
 #include "MassLookup.h"
 
@@ -25,26 +24,26 @@ namespace Mask {
 	class Target {
 	
 	public:
-	 	Target(double thick);
+	 	Target(const std::vector<int>& z, const std::vector<int>& a, const std::vector<int>& stoich, double thick);
 	 	~Target();
-	 	void SetElements(std::vector<int>& z, std::vector<int>& a, std::vector<int>& stoich);
 	 	bool ContainsElement(int z, int a);
 	 	double GetEnergyLossTotal(int zp, int ap, double startEnergy, double angle);
 	 	double GetReverseEnergyLossTotal(int zp, int ap, double finalEnergy, double angle);
 	 	double GetEnergyLossFractionalDepth(int zp, int ap, double startEnergy, double angle, double percent_depth);
 	 	double GetReverseEnergyLossFractionalDepth(int zp, int ap, double finalEnergy, double angle, double percent_depth);
-	 	inline const double& GetThickness() { return thickness; }
+	 	inline const double& GetThickness() { return m_thickness; }
-	 	inline int GetNumberOfElements() { return Z.size(); }
+	 	inline int GetNumberOfElements() { return m_Z.size(); }
-	 	inline int GetElementZ(int index) { return Z[index]; }
+	 	inline int GetElementZ(int index) { return m_Z[index]; }
-	 	inline int GetElementA(int index) { return A[index]; }
+	 	inline int GetElementA(int index) { return m_A[index]; }
-	 	inline int GetElementStoich(int index) { return Stoich[index]; }
+	 	inline int GetElementStoich(int index) { return m_stoich[index]; }
 	
 	private:
-		EnergyLoss eloss;
+	 	void Init(const std::vector<int>& z, const std::vector<int>& a, const std::vector<int>& stoich);
-		catima::Material target_material;
+		
-		double thickness;
+		catima::Material m_material;
-		double thickness_gcm2;
+		double m_thickness;
-		std::vector<int> Z, A, Stoich;
+		double m_thickness_gcm2;
+		std::vector<int> m_Z, m_A, m_stoich;
 	
 	};
 

src/Mask/ThreeStepSystem.cpp

@@ -7,133 +7,131 @@ namespace Mask {
 	ThreeStepSystem::ThreeStepSystem() :
 		ReactionSystem(), m_phi2Range(0, 2.0*M_PI)
 	{
-		nuclei.resize(8);
+		m_nuclei.resize(8);
 	}
 	
-	ThreeStepSystem::ThreeStepSystem(std::vector<int>& z, std::vector<int>& a) :
+	ThreeStepSystem::ThreeStepSystem(const std::vector<int>& z, const std::vector<int>& a) :
 		ReactionSystem(), m_phi2Range(0, 2.0*M_PI)
 	{
-		nuclei.resize(8);
+		m_nuclei.resize(8);
 		SetNuclei(z, a);
 	}
 	
 	ThreeStepSystem::~ThreeStepSystem() {}
 	
-	
+	bool ThreeStepSystem::SetNuclei(const std::vector<int>& z, const std::vector<int>& a)
-	bool ThreeStepSystem::SetNuclei(std::vector<int>&z, std::vector<int>& a) {
+	{
-		if(z.size() != a.size() || z.size() < 5) {
+		if(z.size() != a.size() || z.size() < 5)
 			return false;
-		}
+
 		int zr = z[0] + z[1] - z[2];
 		int zb2 = zr - z[3];
+		int zb4 = zb2 - z[4];
 		int ar = a[0] + a[1] - a[2];
 		int ab2 = ar - a[3];
+		int ab4 = ab2 - a[4];
+
+		m_nuclei[0] = CreateNucleus(z[0], a[0]); //target
+		m_nuclei[1] = CreateNucleus(z[1], a[1]); //projectile
+		m_nuclei[2] = CreateNucleus(z[2], a[2]); //ejectile
+		m_nuclei[3] = CreateNucleus(zr, ar); //residual
+		m_nuclei[4] = CreateNucleus(z[3], a[3]); //breakup1
+		m_nuclei[5] = CreateNucleus(zb2, ab2); //breakup2
+		m_nuclei[5] = CreateNucleus(z[4], a[4]); //breakup3
+		m_nuclei[5] = CreateNucleus(zb4, ab4); //breakup4
+
+		m_step1.BindNuclei(&(m_nuclei[0]), &(m_nuclei[1]), &(m_nuclei[2]), &(m_nuclei[3]));
+		m_step2.BindNuclei(&(m_nuclei[3]), nullptr, &(m_nuclei[4]), &(m_nuclei[5]));
+		m_step3.BindNuclei(&(m_nuclei[5]), nullptr, &(m_nuclei[6]), &(m_nuclei[7]));
 	
-		step1.SetNuclei(z[0], a[0], z[1], a[1], z[2], a[2]);
-		step2.SetNuclei(zr, ar, 0, 0, z[3], a[3]);
-		step3.SetNuclei(zb2, ab2, 0, 0, z[4], a[4]);
 		SetSystemEquation();
 		return true;
 	}
 	
-	const std::vector<Nucleus>& ThreeStepSystem::GetNuclei()
+	std::vector<Nucleus>* ThreeStepSystem::GetNuclei()
 	{
-		nuclei[0] = step1.GetTarget();
+		return &m_nuclei;
-		nuclei[1] = step1.GetProjectile();
-		nuclei[2] = step1.GetEjectile();
-		nuclei[3] = step1.GetResidual();
-		nuclei[4] = step2.GetEjectile();
-		nuclei[5] = step2.GetResidual();
-		nuclei[6] = step3.GetEjectile();
-		nuclei[7] = step3.GetResidual();
-
-		return nuclei;
 	}
 
-	void ThreeStepSystem::LinkTarget() {
+	void ThreeStepSystem::LinkTarget()
-		step1.SetLayeredTarget(&target);
+	{
-		step2.SetLayeredTarget(&target);
+		m_step1.SetLayeredTarget(&m_target);
-		step3.SetLayeredTarget(&target);
+		m_step2.SetLayeredTarget(&m_target);
+		m_step3.SetLayeredTarget(&m_target);
 	
-		rxnLayer = target.FindLayerContaining(step1.GetTarget().GetZ(), step1.GetTarget().GetA());
+		m_rxnLayer = m_target.FindLayerContaining(m_nuclei[0].Z, m_nuclei[0].A);
-		if(rxnLayer != -1) {
+		if(m_rxnLayer != m_target.GetNumberOfLayers())
-			step1.SetRxnLayer(rxnLayer);
+		{
-			step2.SetRxnLayer(rxnLayer);
+			m_step1.SetRxnLayer(m_rxnLayer);
-			step3.SetRxnLayer(rxnLayer);
+			m_step2.SetRxnLayer(m_rxnLayer);
-			target_set_flag = true;
+			m_step3.SetRxnLayer(m_rxnLayer);
-		} else {
+			m_isTargetSet = true;
+		} else
 			throw ReactionLayerException();
-		}
 	}
 	
-	void ThreeStepSystem::SetSystemEquation() {
+	void ThreeStepSystem::SetSystemEquation()
-		m_sys_equation = step1.GetTarget().GetIsotopicSymbol();
+	{
-		m_sys_equation += "(";
+		std::stringstream stream;
-		m_sys_equation += step1.GetProjectile().GetIsotopicSymbol();
+		stream << m_nuclei[0].isotopicSymbol << "("
-		m_sys_equation += ", ";
+			   << m_nuclei[1].isotopicSymbol << ", "
-		m_sys_equation += step1.GetEjectile().GetIsotopicSymbol();
+			   << m_nuclei[2].isotopicSymbol << ")"
-		m_sys_equation += ")";
+			   << m_nuclei[3].isotopicSymbol << "->"
-		m_sys_equation += step1.GetResidual().GetIsotopicSymbol();
+			   << m_nuclei[4].isotopicSymbol << "+"
-		m_sys_equation += "-> ";
+			   << m_nuclei[5].isotopicSymbol << "->"
-		m_sys_equation += step2.GetEjectile().GetIsotopicSymbol();
+			   << m_nuclei[6].isotopicSymbol << "+"
-		m_sys_equation += " + ";
+			   << m_nuclei[7].isotopicSymbol;
-		m_sys_equation += step2.GetResidual().GetIsotopicSymbol();
+		m_sysEquation = stream.str();
-		m_sys_equation += "-> ";
-		m_sys_equation += step3.GetEjectile().GetIsotopicSymbol();
-		m_sys_equation += " + ";
-		m_sys_equation += step3.GetResidual().GetIsotopicSymbol();
 	}
 	
 	void ThreeStepSystem::RunSystem() {
 		//Link up the target if it hasn't been done yet
-		if(!target_set_flag) {
+		if(!m_isTargetSet)
 			LinkTarget();
-		}
 	
 		//Sample parameters
 		double bke = (*m_beamDist)(RandomGenerator::GetInstance().GetGenerator());
 		double rxnTheta = acos((*m_theta1Range)(RandomGenerator::GetInstance().GetGenerator()));
 		double rxnPhi = (*m_phi1Range)(RandomGenerator::GetInstance().GetGenerator());
-		double decay1costheta = decay1dist.GetRandomCosTheta();
+		double decay1costheta = m_step2Distribution.GetRandomCosTheta();
 		double decay1Theta = std::acos(decay1costheta);
 		double decay1Phi = m_phi2Range(RandomGenerator::GetInstance().GetGenerator());
-		double decay2costheta = decay2dist.GetRandomCosTheta();
+		double decay2costheta = m_step3Distribution.GetRandomCosTheta();
 		double decay2Theta = std::acos(decay2costheta);
 		double decay2Phi = m_phi2Range(RandomGenerator::GetInstance().GetGenerator());
 		double residEx = (*m_exDist)(RandomGenerator::GetInstance().GetGenerator());
 	
-		step1.SetBeamKE(bke);
+		m_step1.SetBeamKE(bke);
-		step1.SetPolarRxnAngle(rxnTheta);
+		m_step1.SetPolarRxnAngle(rxnTheta);
-		step1.SetAzimRxnAngle(rxnPhi);
+		m_step1.SetAzimRxnAngle(rxnPhi);
-		step1.SetExcitation(residEx);
+		m_step1.SetExcitation(residEx);
 	
-		step2.SetPolarRxnAngle(decay1Theta);
+		m_step2.SetPolarRxnAngle(decay1Theta);
-		step2.SetAzimRxnAngle(decay1Phi);
+		m_step2.SetAzimRxnAngle(decay1Phi);
 	
-		step3.SetPolarRxnAngle(decay2Theta);
+		m_step3.SetPolarRxnAngle(decay2Theta);
-		step3.SetAzimRxnAngle(decay2Phi);
+		m_step3.SetAzimRxnAngle(decay2Phi);
 	
-		step1.Calculate();
+		m_step1.Calculate();
 	
-		step2.SetTarget(step1.GetResidual());
+		if(decay1costheta == -10)
-		if(decay1costheta == -10) {
+		{
-			step2.ResetEjectile();
+			m_nuclei[4].vec4.SetPxPyPzE(0., 0., 0., m_nuclei[4].groundStateMass);
-			step2.ResetResidual();
+			m_nuclei[5].vec4.SetPxPyPzE(0., 0., 0., m_nuclei[5].groundStateMass);
-			step3.ResetTarget();
+			m_nuclei[6].vec4.SetPxPyPzE(0., 0., 0., m_nuclei[6].groundStateMass);
-			step3.ResetEjectile();
+			m_nuclei[7].vec4.SetPxPyPzE(0., 0., 0., m_nuclei[7].groundStateMass);
-			step3.ResetResidual();
 			return;
 		}
-		step2.Calculate();
+		m_step2.Calculate();
 	
-		step3.SetTarget(step2.GetResidual());
+		if(decay2costheta == -10)
-		if(decay2costheta == -10) {
+		{
-			step3.ResetEjectile();
+			m_nuclei[6].vec4.SetPxPyPzE(0., 0., 0., m_nuclei[6].groundStateMass);
-			step3.ResetResidual();
+			m_nuclei[7].vec4.SetPxPyPzE(0., 0., 0., m_nuclei[7].groundStateMass);
 			return;
 		}
-		step3.TurnOnResidualEloss();
+		m_step3.SetResidualEnergyLoss(true);
-		step3.Calculate();
+		m_step3.Calculate();
 	
 	}
 

src/Mask/ThreeStepSystem.h

@@ -0,0 +1,42 @@
+#ifndef THREESTEPSYSTEM_H
+#define THREESTEPSYSTEM_H
+
+#include "ReactionSystem.h"
+#include "AngularDistribution.h"
+
+namespace Mask {
+
+	class ThreeStepSystem : public ReactionSystem {
+	public:
+		ThreeStepSystem();
+		ThreeStepSystem(const std::vector<int>& z, const std::vector<int>& a);
+		~ThreeStepSystem();
+		bool SetNuclei(const std::vector<int>& z, const std::vector<int>& a) override;
+		void RunSystem() override;
+		std::vector<Nucleus>* GetNuclei() override;
+	
+		inline void SetDecay1Distribution(const std::string& filename) { m_step2Distribution.ReadDistributionFile(filename); };
+		inline void SetDecay2Distribution(const std::string& filename) { m_step3Distribution.ReadDistributionFile(filename); };
+	
+		void SetReactionThetaType(int type) { m_step1.SetEjectileThetaType(type); };
+	
+		int GetDecay1AngularMomentum() { return m_step2Distribution.GetL(); };
+		int GetDecay2AngularMomentum(){ return m_step3Distribution.GetL(); };
+		double GetDecay1BranchingRatio() { return m_step2Distribution.GetBranchingRatio(); };
+		double GetDecay2BranchingRatio(){ return m_step3Distribution.GetBranchingRatio(); };
+	
+	protected:
+		void LinkTarget() override;
+		void SetSystemEquation() override;
+
+		std::uniform_real_distribution<double> m_phi2Range;
+	
+		Reaction m_step1, m_step2, m_step3;
+	
+		AngularDistribution m_step2Distribution, m_step3Distribution;
+	
+	};
+
+}
+
+#endif

src/Mask/TwoStepSystem.cpp

@@ -2,111 +2,114 @@
 #include "RandomGenerator.h"
 #include "KinematicsExceptions.h"
 
+#include <sstream>
+
 namespace Mask {
 
 	TwoStepSystem::TwoStepSystem() :
 		ReactionSystem(), m_phi2Range(0, 2.0*M_PI)
 	{
-		nuclei.resize(6);
+		m_nuclei.resize(6);
 	}
 	
-	TwoStepSystem::TwoStepSystem(std::vector<int>& z, std::vector<int>& a) :
+	TwoStepSystem::TwoStepSystem(const std::vector<int>& z, const std::vector<int>& a) :
 		ReactionSystem(), m_phi2Range(0, 2.0*M_PI)
 	{
-		nuclei.resize(6);
+		m_nuclei.resize(6);
 		SetNuclei(z, a);
 	}
 	
-	TwoStepSystem::~TwoStepSystem() {
+	TwoStepSystem::~TwoStepSystem() {}
 	
-	}
+	bool TwoStepSystem::SetNuclei(const std::vector<int>&z, const std::vector<int>& a)
-	
+	{
-	bool TwoStepSystem::SetNuclei(std::vector<int>&z, std::vector<int>& a) {
+		if(z.size() != a.size() || z.size() != 4)
-		if(z.size() != a.size() || z.size() != 4) {
 			return false;
-		}
+
 		int zr = z[0] + z[1] - z[2];
 		int ar = a[0] + a[1] - a[2];
+		int zb = zr - z[3];
+		int ab = ar - a[3];
 
-		step1.SetNuclei(z[0], a[0], z[1], a[1], z[2], a[2]);
+		m_nuclei[0] = CreateNucleus(z[0], a[0]); //target
-		step2.SetNuclei(zr, ar, 0, 0, z[3], a[3]);
+		m_nuclei[1] = CreateNucleus(z[1], a[1]); //projectile
+		m_nuclei[2] = CreateNucleus(z[2], a[2]); //ejectile
+		m_nuclei[3] = CreateNucleus(zr, ar); //residual
+		m_nuclei[4] = CreateNucleus(z[3], a[3]); //breakup1
+		m_nuclei[5] = CreateNucleus(zb, ab); //breakup2
+	
+		m_step1.BindNuclei(&(m_nuclei[0]), &(m_nuclei[1]), &(m_nuclei[2]), &(m_nuclei[3]));
+		m_step2.BindNuclei(&(m_nuclei[3]), nullptr, &(m_nuclei[4]), &(m_nuclei[5]));
 		SetSystemEquation();
 		return true;
 	}
 
-	const std::vector<Nucleus>& TwoStepSystem::GetNuclei()
+	std::vector<Nucleus>* TwoStepSystem::GetNuclei()
 	{
-		nuclei[0] = step1.GetTarget();
+		return &m_nuclei;
-		nuclei[1] = step1.GetProjectile();
-		nuclei[2] = step1.GetEjectile();
-		nuclei[3] = step1.GetResidual();
-		nuclei[4] = step2.GetEjectile();
-		nuclei[5] = step2.GetResidual();
-
-		return nuclei;
 	}
 	
-	void TwoStepSystem::LinkTarget() {
+	void TwoStepSystem::LinkTarget()
-		step1.SetLayeredTarget(&target);
+	{
-		step2.SetLayeredTarget(&target);
+		m_step1.SetLayeredTarget(&m_target);
+		m_step2.SetLayeredTarget(&m_target);
 	
-		rxnLayer = target.FindLayerContaining(step1.GetTarget().GetZ(), step1.GetTarget().GetA());
+		m_rxnLayer = m_target.FindLayerContaining(m_nuclei[0].Z, m_nuclei[0].A);
-		if(rxnLayer != -1) {
+		if(m_rxnLayer != m_target.GetNumberOfLayers())
-			step1.SetRxnLayer(rxnLayer);
+		{
-			step2.SetRxnLayer(rxnLayer);
+			m_step1.SetRxnLayer(m_rxnLayer);
-			target_set_flag = true;
+			m_step2.SetRxnLayer(m_rxnLayer);
-		} else {
+			m_isTargetSet = true;
+		}
+		else
 			throw ReactionLayerException();
-		}
 	}
 	
-	void TwoStepSystem::SetSystemEquation() {
+	void TwoStepSystem::SetSystemEquation()
-		m_sys_equation = step1.GetTarget().GetIsotopicSymbol();
+	{
-		m_sys_equation += "(";
+		std::stringstream stream;
-		m_sys_equation += step1.GetProjectile().GetIsotopicSymbol();
+		stream << m_nuclei[0].isotopicSymbol << "("
-		m_sys_equation += ", ";
+			   << m_nuclei[1].isotopicSymbol << ", "
-		m_sys_equation += step1.GetEjectile().GetIsotopicSymbol();
+			   << m_nuclei[2].isotopicSymbol << ")"
-		m_sys_equation += ")";
+			   << m_nuclei[3].isotopicSymbol << "->"
-		m_sys_equation += step1.GetResidual().GetIsotopicSymbol();
+			   << m_nuclei[4].isotopicSymbol << "+"
-		m_sys_equation += "-> ";
+			   << m_nuclei[5].isotopicSymbol;
-		m_sys_equation += step2.GetEjectile().GetIsotopicSymbol();
+		m_sysEquation = stream.str();
-		m_sys_equation += "+";
-		m_sys_equation += step2.GetResidual().GetIsotopicSymbol();
 	}
 	
-	void TwoStepSystem::RunSystem() {
+	void TwoStepSystem::RunSystem()
+	{
 		//Link up the target if it hasn't been done yet
-		if(!target_set_flag) {
+		if(!m_isTargetSet)
 			LinkTarget();
-		}
 	
 		//Sample parameters
 		double bke = (*m_beamDist)(RandomGenerator::GetInstance().GetGenerator());
 		double rxnTheta = acos((*m_theta1Range)(RandomGenerator::GetInstance().GetGenerator()));
 		double rxnPhi = (*m_phi1Range)(RandomGenerator::GetInstance().GetGenerator());
-		double decay1costheta = decay1dist.GetRandomCosTheta();
+		double decay1costheta = m_step2Distribution.GetRandomCosTheta();
 		double decay1Theta = std::acos(decay1costheta);
 		double decay1Phi = m_phi2Range(RandomGenerator::GetInstance().GetGenerator());
 		double residEx = (*m_exDist)(RandomGenerator::GetInstance().GetGenerator());
 	
-		step1.SetBeamKE(bke);
+		m_step1.SetBeamKE(bke);
-		step1.SetPolarRxnAngle(rxnTheta);
+		m_step1.SetPolarRxnAngle(rxnTheta);
-		step1.SetAzimRxnAngle(rxnPhi);
+		m_step1.SetAzimRxnAngle(rxnPhi);
-		step1.SetExcitation(residEx);
+		m_step1.SetExcitation(residEx);
 	
-		step2.SetPolarRxnAngle(decay1Theta);
+		m_step2.SetPolarRxnAngle(decay1Theta);
-		step2.SetAzimRxnAngle(decay1Phi);
+		m_step2.SetAzimRxnAngle(decay1Phi);
 		
-		step1.Calculate();
+		m_step1.Calculate();
 	
-		step2.SetTarget(step1.GetResidual());
+		if(decay1costheta == -10)
-		if(decay1costheta == -10) {
+		{
-			step2.ResetEjectile();
+			m_nuclei[4].vec4.SetPxPyPzE(0., 0., 0., m_nuclei[4].groundStateMass);
-			step2.ResetResidual();
+			m_nuclei[5].vec4.SetPxPyPzE(0., 0., 0., m_nuclei[5].groundStateMass);
 			return;
 		}
-		step2.TurnOnResidualEloss();
+		m_step2.SetResidualEnergyLoss(true);
-		step2.Calculate();
+		m_step2.Calculate();
 	
 	
 	}

src/Mask/TwoStepSystem.h

@@ -0,0 +1,40 @@
+#ifndef TWOSTEPSYSTEM_H
+#define TWOSTEPSYSTEM_H
+
+#include "ReactionSystem.h"
+#include "AngularDistribution.h"
+
+namespace Mask {
+
+	class TwoStepSystem : public ReactionSystem
+	{
+	public:
+		TwoStepSystem();
+		TwoStepSystem(const std::vector<int>& z, const std::vector<int>& a);
+		~TwoStepSystem();
+		bool SetNuclei(const std::vector<int>& z, const std::vector<int>& a) override;
+		void RunSystem() override;
+		std::vector<Nucleus>* GetNuclei() override;
+	
+		void SetDecay1Distribution(const std::string& filename) { m_step2Distribution.ReadDistributionFile(filename); };
+	
+		void SetReactionThetaType(int type) { m_step1.SetEjectileThetaType(type); };
+
+		int GetDecay1AngularMomentum() { return m_step2Distribution.GetL(); };
+		double GetDecay1BranchingRatio() { return m_step2Distribution.GetBranchingRatio(); };
+	
+	private:
+		void LinkTarget() override;
+		void SetSystemEquation() override;
+
+		std::uniform_real_distribution<double> m_phi2Range;
+		
+		Reaction m_step1, m_step2;
+	
+		AngularDistribution m_step2Distribution;
+	
+	};
+
+}
+
+#endif

src/MaskApp/CMakeLists.txt

@@ -1,5 +1,5 @@
 add_executable(MaskApp)
-target_include_directories(MaskApp PUBLIC ${MASK_INCLUDE_DIR})
+target_include_directories(MaskApp PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/..)
 
 target_sources(MaskApp PUBLIC
     main.cpp

src/MaskApp/main.cpp

@@ -1,27 +1,32 @@
 #include <iostream>
 #include <string>
-#include "Stopwatch.h"
+#include "Mask/Stopwatch.h"
-#include "MaskFile.h"
+#include "Mask/MaskApp.h"
-#include "MaskApp.h"
+#include "Mask/KinematicsExceptions.h"
-#include "KinematicsExceptions.h"
 
-int main(int argc, char** argv) {
+int main(int argc, char** argv)
-	if(argc<2) {
+{
+	if(argc<2)
+	{
 		std::cerr<<"Incorrect number of arguments!"<<std::endl;
 		return 1;
 	}
-	Stopwatch sw;
+	Mask::Stopwatch sw;
 
 
 	Mask::MaskApp calculator;
 	sw.Start();
-	try {
+	try
-		if(!calculator.LoadConfig(argv[1])) {
+	{
+		if(!calculator.LoadConfig(argv[1]))
+		{
 			std::cerr<<"Unable to read input file!"<<std::endl;
 			return 1;
 		}
 		calculator.Run();
-	} catch(const std::exception& e) {
+	}
+	catch(const std::exception& e)
+	{
 		std::cerr<<"Exception caught! Information: "<<e.what()<<std::endl;
 		std::cerr<<"Terminating process."<<std::endl;
 		return 1;

src/Plotters/CMakeLists.txt

@@ -1,15 +1,18 @@
-find_package(ROOT REQUIRED)
 add_executable(RootPlot)
 target_include_directories(RootPlot 
-    PUBLIC ${MASK_INCLUDE_DIR}
+    PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}
+           ${CMAKE_CURRENT_SOURCE_DIR}/..
     SYSTEM PUBLIC ${ROOT_INCLUDE_DIRS}
 )
 
 target_sources(RootPlot PUBLIC
     RootPlotter.cpp
+    RootPlotter.h
+    main.cpp
 )
 
 target_link_libraries(RootPlot
+    MaskDict
     Mask
     ${ROOT_LIBRARIES}
 )

src/Plotters/ROOT/RootPlotter.cpp

@@ -1,323 +0,0 @@
-#include "RootPlotter.h"
-#include <TFile.h>
-#include <TVector3.h>
-
-#include <iostream>
-
-RootPlotter::RootPlotter() :
-	table(new THashTable())
-{
-}
-
-RootPlotter::~RootPlotter() {}
-
-void RootPlotter::FillData(const Mask::Nucleus& nuc, double detKE, const std::string& modifier) {
-	std::string sym = nuc.GetIsotopicSymbol();
-	std::string ke_vs_th_name = sym + modifier + "_ke_vs_theta";
-	std::string ke_vs_th_title = ke_vs_th_name + ";#theta_{lab} (degrees);Kinetic Energy (MeV)";
-	std::string ke_vs_ph_name = sym + modifier + "_ke_vs_phi";
-	std::string ke_vs_ph_title = ke_vs_ph_name + ";#phi_{lab} (degrees);Kinetic Energy (MeV)";
-	std::string th_vs_ph_name = sym + modifier + "_theta_vs_phi";
-	std::string th_vs_ph_title = th_vs_ph_name + ";#theta_{lab};#phi_{lab}";
-	std::string ex_name = sym + modifier + "_ex";
-	std::string ex_title = ex_name + ";E_{ex} (MeV);counts";
-	std::string angdist_name = sym + modifier +"_angDist";
-	std::string angdist_title = angdist_name+";cos#right(#theta_{CM}#left);counts";
-	
-	if(detKE == 0.0)
-	{
-		MyFill(ke_vs_th_name.c_str(), ke_vs_th_title.c_str(), nuc.GetTheta()*rad2deg, nuc.GetKE(), 2);
-		MyFill(ke_vs_ph_name.c_str(), ke_vs_ph_title.c_str(), nuc.GetPhi()*rad2deg, nuc.GetKE(), 4);
-		MyFill(th_vs_ph_name.c_str(), th_vs_ph_title.c_str(), nuc.GetTheta()*rad2deg, nuc.GetPhi()*rad2deg, 2);
-		MyFill(ex_name.c_str(),ex_title.c_str(),260,-1.0,25,nuc.GetExcitationEnergy());
-		MyFill(angdist_name.c_str(), angdist_title.c_str(),20,-1.0,1.0,std::cos(nuc.GetThetaCM()));
-	}
-	else
-	{
-		MyFill(ke_vs_th_name.c_str(), ke_vs_th_title.c_str(), nuc.GetTheta()*rad2deg, detKE, 2);
-		MyFill(ke_vs_ph_name.c_str(), ke_vs_ph_title.c_str(), nuc.GetPhi()*rad2deg, detKE, 4);
-		MyFill(th_vs_ph_name.c_str(), th_vs_ph_title.c_str(), nuc.GetTheta()*rad2deg, nuc.GetPhi()*rad2deg, 2);
-		MyFill(ex_name.c_str(),ex_title.c_str(),260,-1.0,25,nuc.GetExcitationEnergy());
-		MyFill(angdist_name.c_str(), angdist_title.c_str(),20,-1.0,1.0,std::cos(nuc.GetThetaCM()));
-	}
-	
-}
-
-void RootPlotter::FillCorrelations(const Mask::MaskFileData& data, Mask::RxnType type)
-{
-	std::string theta_eject_theta_resid_name = "theta_eject_theta_resid_cor";
-	std::string theta_eject_theta_resid_title = theta_eject_theta_resid_name + ";#theta_{lab} Ejectile (deg);#theta_{lab} Residual";
-	if(type == Mask::RxnType::PureDecay)
-	{
-		MyFill(theta_eject_theta_resid_name, theta_eject_theta_resid_title, data.theta[1]*rad2deg, data.theta[2]*rad2deg, 4);
-	}
-	else
-	{
-		MyFill(theta_eject_theta_resid_name, theta_eject_theta_resid_title, data.theta[2]*rad2deg, data.theta[3]*rad2deg, 4);
-	}
-
-	if(type == Mask::RxnType::TwoStepRxn || type == Mask::RxnType::ThreeStepRxn)
-	{
-		TVector3 p1, p2;
-		p1.SetMagThetaPhi(1.0, data.theta[3], data.phi[3]);
-		p2.SetMagThetaPhi(1.0, data.theta[4], data.phi[4]);
-		double theta_resid_break1 = std::acos(p1.Dot(p2));
-		std::string theta_break1_theta_break2_name = "theta_break1_theta_break2_cor";
-		std::string theta_break1_theta_break2_title = theta_break1_theta_break2_name + ";#theta_{lab} Breakup1 (deg);#theta_{lab} Breakup2 (deg)";
-		MyFill(theta_break1_theta_break2_name, theta_break1_theta_break2_title, data.theta[4]*rad2deg, data.theta[5]*rad2deg, 4);
-		std::string theta_resid_theta_break1_name = "theta_resid_theta_break1_cor";
-		std::string theta_resid_theta_break1_title = theta_resid_theta_break1_name + ";#theta_{lab} Residual (deg);#theta_{lab} Breakup1 (deg)";
-		MyFill(theta_resid_theta_break1_name, theta_resid_theta_break1_title, data.theta[3]*rad2deg, data.theta[4]*rad2deg, 4);
-		std::string ke_break1_theta_rel_name = "ke_break1_theta_rel";
-		std::string ke_break1_theta_rel_title = ke_break1_theta_rel_name + ";#theta_{resid-break1};KE_{break1} (MeV)";
-		MyFill(ke_break1_theta_rel_name, ke_break1_theta_rel_title, theta_resid_break1*rad2deg, data.KE[4], 4);
-	}
-	if(type == Mask::RxnType::ThreeStepRxn)
-	{
-		std::string theta_break3_theta_break4_name = "theta_break3_theta_break4_cor";
-		std::string theta_break3_theta_break4_title = theta_break3_theta_break4_name + ";#theta_{lab} Breakup3 (deg);#theta_{lab} Breakup4 (deg)";
-		MyFill(theta_break3_theta_break4_name, theta_break3_theta_break4_title, data.theta[6]*rad2deg, data.theta[7]*rad2deg, 4);
-	}
-}
-
-void RootPlotter::FillCorrelationsDetected(const Mask::MaskFileData& data, Mask::RxnType type)
-{
-	std::string theta_eject_theta_resid_name = "theta_eject_theta_resid_cor_detected";
-	std::string theta_eject_theta_resid_title = theta_eject_theta_resid_name + ";#theta_{lab} Ejectile (deg);#theta_{lab} Residual";
-	if(type == Mask::RxnType::PureDecay && data.detect_flag[1] && data.detect_flag[2])
-	{
-		MyFill(theta_eject_theta_resid_name, theta_eject_theta_resid_title, data.theta[1]*rad2deg, data.theta[2]*rad2deg, 4);
-	}
-	else if(data.detect_flag[2] && data.detect_flag[3])
-	{
-		MyFill(theta_eject_theta_resid_name, theta_eject_theta_resid_title, data.theta[2]*rad2deg, data.theta[3]*rad2deg, 4);
-	}
-	if((type == Mask::RxnType::TwoStepRxn || type == Mask::RxnType::ThreeStepRxn) && data.detect_flag[4])
-	{
-		TVector3 p1, p2;
-		p1.SetMagThetaPhi(1.0, data.theta[3], data.phi[3]);
-		p2.SetMagThetaPhi(1.0, data.theta[4], data.phi[4]);
-		double theta_resid_break1 = std::acos(p1.Dot(p2));
-		std::string theta_resid_theta_break1_name = "theta_resid_theta_break1_cor_detected";
-		std::string theta_resid_theta_break1_title = theta_resid_theta_break1_name + ";#theta_{lab} Residual (deg);#theta_{lab} Breakup1 (deg)";
-		MyFill(theta_resid_theta_break1_name, theta_resid_theta_break1_title, data.theta[3]*rad2deg, data.theta[4]*rad2deg, 4);
-		std::string ke_break1_theta_rel_name = "ke_break1_theta_rel_detected";
-		std::string ke_break1_theta_rel_title = ke_break1_theta_rel_name + ";#theta_{resid-break1};KE_{break1} (MeV)";
-		MyFill(ke_break1_theta_rel_name, ke_break1_theta_rel_title, theta_resid_break1*rad2deg, data.KE[4], 4);
-	}
-
-	if((type == Mask::RxnType::TwoStepRxn || type == Mask::RxnType::ThreeStepRxn) && data.detect_flag[4] && data.detect_flag[5])
-	{
-		std::string theta_break1_theta_break2_name = "theta_break1_theta_break2_cor_detected";
-		std::string theta_break1_theta_break2_title = theta_break1_theta_break2_name + ";#theta_{lab} Breakup1 (deg);#theta_{lab} Breakup2 (deg)";
-		MyFill(theta_break1_theta_break2_name, theta_break1_theta_break2_title, data.theta[4]*rad2deg, data.theta[5]*rad2deg, 4);
-	}
-	if(type == Mask::RxnType::ThreeStepRxn && data.detect_flag[6] && data.detect_flag[7])
-	{
-		std::string theta_break3_theta_break4_name = "theta_break3_theta_break4_cor_detected";
-		std::string theta_break3_theta_break4_title = theta_break3_theta_break4_name + ";#theta_{lab} Breakup3 (deg);#theta_{lab} Breakup4 (deg)";
-		MyFill(theta_break3_theta_break4_name, theta_break3_theta_break4_title, data.theta[6]*rad2deg, data.theta[7]*rad2deg, 4);
-	}
-}
-
-void RootPlotter::MyFill(const std::string& name, const std::string& title, int bins, float min, float max, double val) {
-	TH1F* h = (TH1F*) table->FindObject(name.c_str());
-	if(h) {
-		h->Fill(val);
-	} else {
-		h = new TH1F(name.c_str(), title.c_str(), bins, min, max);
-		h->Fill(val);
-		table->Add(h);
-	}
-}
-
-void RootPlotter::MyFill(const std::string& name, const std::string& title, int binsx, float minx, float maxx, int binsy, float miny, float maxy, double valx, double valy) {
-	TH2F* h = (TH2F*) table->FindObject(name.c_str());
-	if(h) {
-		h->Fill(valx, valy);
-	} else {
-		h = new TH2F(name.c_str(), title.c_str(), binsx, minx, maxx, binsy, miny, maxy);
-		h->Fill(valx, valy);
-		table->Add(h);
-	}
-}
-
-void RootPlotter::MyFill(const std::string& name, const std::string& title, double valx, double valy, int color) {
-	for(auto& g : graphs) {
-		if(g.name == name) {
-			g.xvec.push_back(valx);
-			g.yvec.push_back(valy);
-			return;
-		}
-	}
-
-	GraphData new_g;
-	new_g.name = name;
-	new_g.title = title;
-	new_g.xvec.push_back(valx);
-	new_g.yvec.push_back(valy);
-	new_g.color = color;
-
-	graphs.push_back(new_g);
-}
-
-void RootPlotter::GenerateGraphs() {
-	for(auto& g : graphs) {
-		TGraph* graph = new TGraph(g.xvec.size(), &(g.xvec[0]), &(g.yvec[0]));
-		graph->SetName(g.name.c_str());
-		graph->SetTitle(g.title.c_str());
-		graph->SetMarkerColor(g.color);
-		table->Add(graph);
-		garbage_collection.push_back(graph);
-	}
-}
-
-std::vector<Mask::Nucleus> GetParents(const Mask::MaskFileData& data, Mask::RxnType rxn_type)
-{
-	std::vector<Mask::Nucleus> parents;
-	Mask::Nucleus temp1, temp2, temp3;
-	switch(rxn_type)
-	{
-		case Mask::RxnType::None : break;
-		case Mask::RxnType::PureDecay :
-		{
-			temp1.SetIsotope(data.Z[0], data.A[0]);
-			temp1.SetVectorSpherical(data.theta[0], data.phi[0], data.p[0], data.E[0]);
-			parents.push_back(temp1);
-			return parents;
-		}
-		case Mask::RxnType::OneStepRxn :
-		{
-			temp1.SetIsotope(data.Z[0], data.A[0]);
-			temp1.SetVectorSpherical(data.theta[0], data.phi[0], data.p[0], data.E[0]);
-			temp2.SetIsotope(data.Z[1], data.A[1]);
-			temp2.SetVectorSpherical(data.theta[1], data.phi[1], data.p[1], data.E[1]);
-			temp3 = temp1 + temp2;
-			parents.push_back(temp3);
-			return parents;
-		}
-		case Mask::RxnType::TwoStepRxn :
-		{
-			temp1.SetIsotope(data.Z[0], data.A[0]);
-			temp1.SetVectorSpherical(data.theta[0], data.phi[0], data.p[0], data.E[0]);
-			temp2.SetIsotope(data.Z[1], data.A[1]);
-			temp2.SetVectorSpherical(data.theta[1], data.phi[1], data.p[1], data.E[1]);
-			temp3 = temp1 + temp2;
-			parents.push_back(temp3);
-			temp3.SetIsotope(data.Z[3], data.A[3]);
-			temp3.SetVectorSpherical(data.theta[3], data.phi[3], data.p[3], data.E[3]);
-			parents.push_back(temp3);
-			return parents;
-		}
-		case Mask::RxnType::ThreeStepRxn :
-		{
-			temp1.SetIsotope(data.Z[0], data.A[0]);
-			temp1.SetVectorSpherical(data.theta[0], data.phi[0], data.p[0], data.E[0]);
-			temp2.SetIsotope(data.Z[1], data.A[1]);
-			temp2.SetVectorSpherical(data.theta[1], data.phi[1], data.p[1], data.E[1]);
-			temp3 = temp1 + temp2;
-			parents.push_back(temp3);
-			temp3.SetIsotope(data.Z[3], data.A[3]);
-			temp3.SetVectorSpherical(data.theta[3], data.phi[3], data.p[3], data.E[3]);
-			parents.push_back(temp3);
-			temp3.SetIsotope(data.Z[5], data.A[5]);
-			temp3.SetVectorSpherical(data.theta[5], data.phi[5], data.p[5], data.E[5]);
-			parents.push_back(temp3);
-			return parents;
-		}
-	}
-	return parents;
-}
-
-void SetThetaCM(Mask::Nucleus& daughter, const Mask::Nucleus& parent)
-{
-	const double* boost = parent.GetBoost();
-	double boost2cm[3];
-	double boost2lab[3];
-	for(int i=0; i<3; i++)
-	{
-		boost2lab[i] = boost[i];
-		boost2cm[i] = -1.0*boost[i];
-	}
-
-	daughter.ApplyBoost(boost2cm);
-	daughter.SetThetaCM(daughter.GetTheta());
-	daughter.ApplyBoost(boost2lab);
-}
-
-int main(int argc, char** argv) {
-	if(argc != 3) {
-		std::cout<<"Unable to run ROOT plotting tool with incorrect number of arguments! Expected 2 args, given: "<<argc<<" Exiting."<<std::endl;
-		return 1;
-	}
-
-	std::string inputname = argv[1];
-	std::string outputname = argv[2];
-
-	Mask::MaskFile input(inputname, Mask::MaskFile::FileType::read);
-
-	TFile* root_out = TFile::Open(outputname.c_str(), "RECREATE");
-
-	RootPlotter plotter;
-
-	Mask::MaskFileHeader header = input.ReadHeader();
-
-	std::cout<<"File Header -- rxn type: "<<GetStringFromRxnType(header.rxn_type)<<" nsamples: "<<header.nsamples<<std::endl;
-
-	Mask::MaskFileData data;
-	Mask::Nucleus nucleus;
-	std::vector<Mask::Nucleus> parents; //for use with CM theta calc
-
-	double flush_frac = 0.05;
-	int count = 0, flush_val = flush_frac*header.nsamples, flush_count = 0;
-	while(true) {
-		if(count == flush_val) {
-			count = 0;
-			flush_count++;
-			std::cout<<"\rPercent of file processed: "<<flush_frac*flush_count*100<<"%"<<std::flush;
-		}
-
-		data = input.ReadData();
-		if(data.eof)
-			break;
-
-		parents = GetParents(data, header.rxn_type);
-		for(unsigned int i=0; i<data.Z.size(); i++) {
-			nucleus.SetIsotope(data.Z[i], data.A[i]);
-			nucleus.SetVectorSpherical(data.theta[i], data.phi[i], data.p[i], data.E[i]);
-			/*
-				Little dirty, but works well. Save theta CM using parent from specific rxn step.
-				I.e. ejectile calculated from first parent, break1 from second parent, break3 from third...
-			*/
-			if(i==1 || i==2 || i==3)
-			{
-				SetThetaCM(nucleus, parents[0]);
-			}
-			else if (i==4 || i==5)
-			{
-				SetThetaCM(nucleus, parents[1]);
-			}
-			else if(i==6 || i==7)
-			{
-				SetThetaCM(nucleus, parents[2]);
-			}
-
-			plotter.FillData(nucleus);
-			if(data.detect_flag[i] == true) {
-				plotter.FillData(nucleus, data.KE[i], "detected");
-			}
-		}
-		plotter.FillCorrelations(data, header.rxn_type);
-		plotter.FillCorrelationsDetected(data, header.rxn_type);
-		count++;
-	}
-	std::cout<<std::endl;
-
-	input.Close();
-
-	root_out->cd();
-	plotter.GetTable()->Write();
-	root_out->Close();
-
-	return 0;
-}

src/Plotters/RootPlotter.cpp

@@ -0,0 +1,139 @@
+#include "RootPlotter.h"
+#include <TFile.h>
+#include <TTree.h>
+#include <TVector3.h>
+
+#include <iostream>
+
+RootPlotter::RootPlotter()
+{
+	TH1::AddDirectory(kFALSE);
+	//Enforce dictionary linking
+	if(Mask::EnforceDictionaryLinked())
+	{
+		std::cout<<"Dictionary Linked"<<std::endl;
+	}
+}
+
+RootPlotter::~RootPlotter() {}
+
+void RootPlotter::Run(const std::string& inputname, const std::string& outputname)
+{
+	TFile* input = TFile::Open(inputname.c_str(), "READ");
+	TTree* tree = (TTree*) input->Get("SimTree");
+	std::vector<Mask::Nucleus>* dataHandle = new std::vector<Mask::Nucleus>();
+	tree->SetBranchAddress("nuclei", &dataHandle);
+
+	TFile* output = TFile::Open(outputname.c_str(), "RECREATE");
+
+	double flushFrac = 0.05;
+	uint64_t nentries = tree->GetEntries();
+	uint64_t flushVal = flushFrac*nentries;
+	uint64_t count=0;
+	uint64_t flushCount = 0;
+
+	for(uint64_t i=0; i<nentries; i++)
+	{
+		tree->GetEntry(i);
+		for(Mask::Nucleus& nuc : *(dataHandle))
+		{
+			FillData(nuc);
+		}
+	}
+
+	input->Close();
+	delete dataHandle;
+
+	output->cd();
+	for(auto& obj : m_map)
+		obj.second->Write(obj.second->GetName(), TObject::kOverwrite);
+	output->Close();
+}
+
+void RootPlotter::FillData(const Mask::Nucleus& nuc)
+{
+	std::string modifier = "";
+	if(nuc.isDetected)
+		modifier = "detected";
+
+	std::string sym = nuc.isotopicSymbol;
+	std::string ke_vs_th_name = sym + modifier + "_ke_vs_theta";
+	std::string ke_vs_th_title = ke_vs_th_name + ";#theta_{lab} (degrees);Kinetic Energy (MeV)";
+	std::string ke_vs_ph_name = sym + modifier + "_ke_vs_phi";
+	std::string ke_vs_ph_title = ke_vs_ph_name + ";#phi_{lab} (degrees);Kinetic Energy (MeV)";
+	std::string th_vs_ph_name = sym + modifier + "_theta_vs_phi";
+	std::string th_vs_ph_title = th_vs_ph_name + ";#theta_{lab};#phi_{lab}";
+	std::string ex_name = sym + modifier + "_ex";
+	std::string ex_title = ex_name + ";E_{ex} (MeV);counts";
+	std::string angdist_name = sym + modifier +"_angDist";
+	std::string angdist_title = angdist_name+";cos#right(#theta_{CM}#left);counts";
+	
+	if(nuc.isDetected)
+	{
+		MyFill(ke_vs_th_name.c_str(), ke_vs_th_title.c_str(), nuc.vec4.Theta()*s_rad2deg, nuc.GetKE(), 2);
+		MyFill(ke_vs_ph_name.c_str(), ke_vs_ph_title.c_str(), nuc.vec4.Phi()*s_rad2deg, nuc.GetKE(), 4);
+		MyFill(th_vs_ph_name.c_str(), th_vs_ph_title.c_str(), nuc.vec4.Theta()*s_rad2deg, nuc.vec4.Phi()*s_rad2deg, 2);
+		MyFill(ex_name.c_str(),ex_title.c_str(),260,-1.0,25,nuc.GetExcitationEnergy());
+		MyFill(angdist_name.c_str(), angdist_title.c_str(),20,-1.0,1.0,std::cos(nuc.thetaCM));
+	}
+	else
+	{
+		MyFill(ke_vs_th_name.c_str(), ke_vs_th_title.c_str(), nuc.vec4.Theta()*s_rad2deg, nuc.detectedKE, 2);
+		MyFill(ke_vs_ph_name.c_str(), ke_vs_ph_title.c_str(), nuc.vec4.Phi()*s_rad2deg, nuc.detectedKE, 4);
+		MyFill(th_vs_ph_name.c_str(), th_vs_ph_title.c_str(), nuc.vec4.Theta()*s_rad2deg, nuc.vec4.Phi()*s_rad2deg, 2);
+		MyFill(ex_name.c_str(),ex_title.c_str(),260,-1.0,25,nuc.GetExcitationEnergy());
+		MyFill(angdist_name.c_str(), angdist_title.c_str(),20,-1.0,1.0,std::cos(nuc.thetaCM));
+	}
+	
+}
+
+void RootPlotter::MyFill(const std::string& name, const std::string& title, int bins, float min, float max, double val)
+{
+	auto iter = m_map.find(name);
+	if(iter != m_map.end())
+	{
+		std::shared_ptr<TH1> h = std::static_pointer_cast<TH1>(iter->second);
+		h->Fill(val);
+	}
+	else
+	{
+		std::shared_ptr<TH1F> h = std::make_shared<TH1F>(name.c_str(), title.c_str(), bins, min, max);
+		h->Fill(val);
+		m_map[name] = h;
+	}
+}
+
+void RootPlotter::MyFill(const std::string& name, const std::string& title, int binsx, float minx, float maxx,
+						 int binsy, float miny, float maxy, double valx, double valy)
+{
+	auto iter = m_map.find(name);
+	if(iter != m_map.end())
+	{
+		std::shared_ptr<TH2> h = std::static_pointer_cast<TH2>(iter->second);
+		h->Fill(valx, valy);
+	}
+	else
+	{
+		std::shared_ptr<TH2F> h = std::make_shared<TH2F>(name.c_str(), title.c_str(), binsx, minx, maxx, binsy, miny, maxy);
+		h->Fill(valx, valy);
+		m_map[name] = h;
+	}
+}
+
+void RootPlotter::MyFill(const std::string& name, const std::string& title, double valx, double valy, int color)
+{
+	auto iter = m_map.find(name);
+	if(iter != m_map.end())
+	{
+		std::shared_ptr<TGraph> g = std::static_pointer_cast<TGraph>(iter->second);
+		g->SetPoint(g->GetN(), valx, valy);
+	}
+	else
+	{
+		std::shared_ptr<TGraph> g = std::make_shared<TGraph>(1, &valx, &valy);
+		g->SetName(name.c_str());
+		g->SetTitle(title.c_str());
+		g->SetMarkerColor(color);
+		m_map[name] = g;
+	}
+}

src/Plotters/RootPlotter.h

@@ -0,0 +1,34 @@
+#ifndef ROOTPLOTTER_H
+#define ROOTPLOTTER_H
+
+#include <vector>
+#include <string>
+#include <unordered_map>
+
+#include "Nucleus.h"
+
+#include <TH1.h>
+#include <TH2.h>
+#include <TGraph.h>
+
+class RootPlotter
+{
+public:
+	RootPlotter();
+	~RootPlotter();
+	
+	void Run(const std::string& inputname, const std::string& outputname);
+	
+private:
+	void FillData(const Mask::Nucleus& nuc);
+	void MyFill(const std::string& name, const std::string& title, int bins, float min, float max, double val);
+	void MyFill(const std::string& name, const std::string& title, int binsx, float minx, float maxx, int binsy, float miny, float maxy, 
+				double valx, double valy);
+	void MyFill(const std::string& name, const std::string& title, double valx, double valy, int color); //TGraph
+
+	std::unordered_map<std::string, std::shared_ptr<TObject>> m_map;
+
+	static constexpr double s_rad2deg = 180.0/M_PI;
+};
+
+#endif

src/Plotters/main.cpp

@@ -0,0 +1,14 @@
+#include "RootPlotter.h"
+#include <iostream>
+
+int main(int argc, char** argv)
+{
+    if(argc != 3)
+    {
+        std::cerr<<"Root plotter requires two commandline arguments: path to input file and path to outputfile"<<std::endl;
+        return 1;
+    }
+
+    RootPlotter plotter;
+    plotter.Run(argv[1], argv[2]);
+}