Njettiness.hh
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	// Nsubjettiness Package
	// Questions/Comments? jthaler@jthaler.net
	//
	// Copyright (c) 2011-13
	// Jesse Thaler, Ken Van Tilburg, and Christopher K. Vermilion
	//
	//----------------------------------------------------------------------
	// This file is part of FastJet contrib.
	//
	// It is free software; you can redistribute it and/or modify it under
	// the terms of the GNU General Public License as published by the
	// Free Software Foundation; either version 2 of the License, or (at
	// your option) any later version.
	//
	// It is distributed in the hope that it will be useful, but WITHOUT
	// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
	// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
	// License for more details.
	//
	// You should have received a copy of the GNU General Public License
	// along with this code. If not, see <http://www.gnu.org/licenses/>.
	//----------------------------------------------------------------------

	#ifndef __FASTJET_CONTRIB_NJETTINESS_HH__
	#define __FASTJET_CONTRIB_NJETTINESS_HH__


	#include "fastjet/PseudoJet.hh"
	#include "fastjet/ClusterSequence.hh"
	#include <cmath>
	#include <vector>
	#include <list>


	FASTJET_BEGIN_NAMESPACE // defined in fastjet/internal/base.hh

	namespace contrib {

	///////
	//
	// Parameter classes
	//
	///////

	inline double sq(double x) {return x*x;}

	// Parameters that define Njettiness
	class NsubParameters {
	private:
	double _beta; // angular weighting exponent
	double _R0; // characteristic jet radius (for normalization)
	double _Rcutoff; // Cutoff scale for cone jet finding (default is large number such that no boundaries are used)

	public:
	NsubParameters(const double mybeta, const double myR0, const double myRcutoff=10000.0) :
	_beta(mybeta), _R0(myR0), _Rcutoff(myRcutoff) {}
	double beta() const {return _beta;}
	double R0() const {return _R0;}
	double Rcutoff() const {return _Rcutoff;}
	};

	// Parameters that define GeometricMeasure
	class NsubGeometricParameters {
	private:
	double _Rcutoff; // Cutoff scale for cone jet finding (default is large number such that no boundaries are used)

	public:
	NsubGeometricParameters(const double myRcutoff=10000.0) : _Rcutoff(myRcutoff) {}
	double Rcutoff() const {return _Rcutoff;}
	};


	// Parameters that change minimization procedure.
	// Set automatically when you choose NsubAxesMode, but can be adjusted manually as well
	class KmeansParameters {
	private:
	int _n_iterations; // Number of iterations to run (0 for no minimization, 1 for one-pass, >>1 for global minimum)
	double _precision; // Desired precision in axes alignment
	int _halt; // maximum number of steps per iteration
	double _noise_range;// noise range for random initialization

	public:
	KmeansParameters() : _n_iterations(0), _precision(0.0), _halt(0), _noise_range(0.0) {}
	KmeansParameters(const int my_n_iterations, double my_precision, int my_halt, double my_noise_range) :
	_n_iterations(my_n_iterations), _precision(my_precision), _halt(my_halt), _noise_range(my_noise_range) {}
	int n_iterations() const { return _n_iterations;}
	double precision() const {return _precision;}
	int halt() const {return _halt;}
	double noise_range() const {return _noise_range;}
	};


	///////
	//
	// Measure Functor
	//
	///////


	class MeasureFunctor {

	protected:
	MeasureFunctor() {}

	public:
	virtual ~MeasureFunctor(){}

	virtual bool doCluster(const fastjet::PseudoJet& particle, const fastjet::PseudoJet& axis) = 0;
	virtual double distance(const fastjet::PseudoJet& particle, const fastjet::PseudoJet& axis) = 0;
	virtual double numerator(const fastjet::PseudoJet& particle, const fastjet::PseudoJet& axis) = 0;
	virtual double denominator(const fastjet::PseudoJet& particle) = 0;

	std::vector<double> subTaus(const std::vector <fastjet::PseudoJet> & particles, const std::vector<fastjet::PseudoJet>& axes);
	double tau(const std::vector <fastjet::PseudoJet>& particles, const std::vector<fastjet::PseudoJet>& axes);

	};

	// N-subjettiness pieces
	std::vector<double> MeasureFunctor::subTaus(const std::vector <fastjet::PseudoJet> & particles, const std::vector<fastjet::PseudoJet>& axes) {// Returns the sub-tau values, i.e. a std::vector of the contributions to tau_N of each Voronoi region (or region within R_0)

	std::vector<double> tauNum(axes.size(), 0.0), tau(axes.size());

	double tauDen = 0.0;
	for (unsigned i = 0; i < particles.size(); i++) {
	// find minimum distance; start with 0'th axis for reference
	int j_min = 0;
	double minR = distance(particles[i],axes[0]);
	for (unsigned j = 1; j < axes.size(); j++) {
	double tempR = distance(particles[i],axes[j]); // delta R distance
	if (tempR < minR) {minR = tempR; j_min = j;}
	}
	tauNum[j_min] += numerator(particles[i],axes[j_min]);
	tauDen += denominator(particles[i]);
	}
	for (unsigned j = 0; j < axes.size(); j++) {
	tau[j] = tauNum[j]/tauDen;
	}
	return tau;
	}

	double MeasureFunctor::tau(const std::vector <fastjet::PseudoJet>& particles, const std::vector<fastjet::PseudoJet>& axes) {// Calculates tau_N
	std::vector<double> tau_vec = subTaus(particles, axes);
	double tau = 0.0;
	for (unsigned j = 0; j < tau_vec.size(); j++) {tau += tau_vec[j];}
	return tau;
	}

	///Default Measure (includes normalization)
	class DefaultMeasure : public MeasureFunctor {

	private:
	NsubParameters _paraNsub;

	public:
	DefaultMeasure(NsubParameters paraNsub): _paraNsub(paraNsub) {}

	virtual bool doCluster(const fastjet::PseudoJet& particle, const fastjet::PseudoJet& axis) {
	return (distance(particle,axis) <= _paraNsub.Rcutoff());
	}

	virtual double distance(const fastjet::PseudoJet& particle, const fastjet::PseudoJet& axis) {
	return std::sqrt(particle.squared_distance(axis));
	}

	virtual double numerator(const fastjet::PseudoJet& particle, const fastjet::PseudoJet& axis) {
	double deltaR = std::sqrt(particle.squared_distance(axis));
	if (deltaR > _paraNsub.Rcutoff()) deltaR = _paraNsub.Rcutoff();
	return particle.perp() * std::pow(deltaR,_paraNsub.beta());
	}

	virtual double denominator(const fastjet::PseudoJet& particle) {
	return particle.perp() * std::pow(_paraNsub.R0(),_paraNsub.beta());
	}

	};

	///Geometric Measure (includes normalization)
	class GeometricMeasure : public MeasureFunctor {

	private:
	double _Rcutoff;

	// create light-like axis
	fastjet::PseudoJet lightFrom(const fastjet::PseudoJet& input) const {
	double length = sqrt(pow(input.px(),2) + pow(input.py(),2) + pow(input.pz(),2));
	return fastjet::PseudoJet(input.px()/length,input.py()/length,input.pz()/length,1.0);
	}

	// get Q value
	double qValueOf(const fastjet::PseudoJet& input) const {
	return lightFrom(input).pt();
	}

	public:
	GeometricMeasure(double Rcutoff) : _Rcutoff(Rcutoff) {}

	virtual bool doCluster(const fastjet::PseudoJet& particle, const fastjet::PseudoJet& axis) {
	return (distance(particle,axis) <= _Rcutoff);
	}

	virtual double distance(const fastjet::PseudoJet& particle, const fastjet::PseudoJet& axis) {
	double axisValue = 2.0*dot_product(lightFrom(axis),particle)/qValueOf(axis);
	double beamValue = particle.pt();
	double pseudoR = std::sqrt(axisValue/beamValue);
	return pseudoR;
	}

	virtual double numerator(const fastjet::PseudoJet& particle, const fastjet::PseudoJet& axis) {
	double pseudoR = distance(particle,axis);

	if (pseudoR > _Rcutoff) {
	pseudoR = _Rcutoff;
	}
	return particle.pt()*sq(pseudoR);
	}

	virtual double denominator(const fastjet::PseudoJet& particle) {
	return 1.0;
	}
	};



	///////
	//
	// Axes Finder Options
	//
	///////

	class AxesFinder {

	protected:
	AxesFinder() {}

	public:
	virtual ~AxesFinder(){}

	virtual std::vector<fastjet::PseudoJet> getAxes(int n_jets, const std::vector<fastjet::PseudoJet> & inputs, const std::vector<fastjet::PseudoJet>& currentAxes) = 0;

	};

	/// Axes From Exclusive Jets

	class AxesFinderFromExclusiveJetDefinition : public AxesFinder {

	private:
	fastjet::JetDefinition _def;

	public:
	AxesFinderFromExclusiveJetDefinition(fastjet::JetDefinition def) : _def(def) {}

	virtual std::vector<fastjet::PseudoJet> getAxes(int n_jets, const std::vector <fastjet::PseudoJet> & inputs, const std::vector<fastjet::PseudoJet>& currentAxes) {
	fastjet::ClusterSequence jet_clust_seq(inputs, _def);
	return jet_clust_seq.exclusive_jets(n_jets);
	}
	};

	class AxesFinderFromKT : public AxesFinderFromExclusiveJetDefinition {
	public:
	AxesFinderFromKT() : AxesFinderFromExclusiveJetDefinition(fastjet::JetDefinition(fastjet::kt_algorithm,M_PI/2.0,fastjet::E_scheme,fastjet::Best)) {}
	};

	class AxesFinderFromCA : public AxesFinderFromExclusiveJetDefinition {
	public:
	AxesFinderFromCA() : AxesFinderFromExclusiveJetDefinition(fastjet::JetDefinition(fastjet::cambridge_algorithm,M_PI/2.0,fastjet::E_scheme,fastjet::Best)) {}
	};


	/// Axes From Hardest Jets

	class AxesFinderFromHardestJetDefinition : public AxesFinder {

	private:
	fastjet::JetDefinition _def;

	public:
	AxesFinderFromHardestJetDefinition(fastjet::JetDefinition def) : _def(def) {}

	virtual std::vector<fastjet::PseudoJet> getAxes(int n_jets, const std::vector <fastjet::PseudoJet> & inputs, const std::vector<fastjet::PseudoJet>& currentAxes) {
	fastjet::ClusterSequence jet_clust_seq(inputs, _def);
	std::vector<fastjet::PseudoJet> myJets = sorted_by_pt(jet_clust_seq.inclusive_jets());
	myJets.resize(n_jets); // only keep n hardest
	return myJets;
	}
	};


	class AxesFinderFromAntiKT : public AxesFinderFromHardestJetDefinition {
	public:
	AxesFinderFromAntiKT(double R0) : AxesFinderFromHardestJetDefinition(fastjet::JetDefinition(fastjet::antikt_algorithm,R0,fastjet::E_scheme,fastjet::Best)) {}
	};


	/// Manual Axes

	class AxesFinderFromUserInput : public AxesFinder {

	public:
	AxesFinderFromUserInput() {}
	~AxesFinderFromUserInput() {}

	virtual std::vector<fastjet::PseudoJet> getAxes(int n_jets, const std::vector <fastjet::PseudoJet> & inputs, const std::vector<fastjet::PseudoJet>& currentAxes) {
	assert(currentAxes.size() == (unsigned int) n_jets);
	return currentAxes;
	}
	};

	/// Minimum Axes

	std::vector<fastjet::PseudoJet> GetMinimumAxes(const std::vector <fastjet::PseudoJet> & seedAxes, const std::vector <fastjet::PseudoJet> & inputJets, KmeansParameters para,
	NsubParameters paraNsub, MeasureFunctor* functor);
	class AxesFinderFromKmeansMinimization : public AxesFinder {

	private:
	AxesFinder* _startingFinder;
	KmeansParameters _paraKmeans;
	NsubParameters _paraNsub;

	MeasureFunctor* _functor;

	public:
	AxesFinderFromKmeansMinimization(AxesFinder* startingFinder, KmeansParameters paraKmeans, NsubParameters paraNsub)
	: _startingFinder(startingFinder), _paraKmeans(paraKmeans), _paraNsub(paraNsub) {
	_functor = new DefaultMeasure(paraNsub);
	}

	~AxesFinderFromKmeansMinimization() {
	delete _startingFinder; //TODO: Convert to smart pointers to avoid this.
	delete _functor;
	}

	virtual std::vector<fastjet::PseudoJet> getAxes(int n_jets, const std::vector <fastjet::PseudoJet> & inputs, const std::vector<fastjet::PseudoJet>& currentAxes) {
	std::vector<fastjet::PseudoJet> seedAxes = _startingFinder->getAxes(n_jets, inputs, currentAxes);
	return GetMinimumAxes(seedAxes, inputs, _paraKmeans, _paraNsub,_functor);
	}
	};


	class AxesFinderFromGeometricMinimization : public AxesFinder {

	private:
	AxesFinder* _startingFinder;
	MeasureFunctor* _functor;
	double _Rcutoff;
	double _nAttempts;
	double _accuracy;


	public:
	AxesFinderFromGeometricMinimization(AxesFinder* startingFinder, double Rcutoff) : _startingFinder(startingFinder), _Rcutoff(Rcutoff) {
	_nAttempts = 100;
	_accuracy = 0.000000001;
	_functor = new GeometricMeasure(_Rcutoff);
	}

	~AxesFinderFromGeometricMinimization() {
	delete _startingFinder; //TODO: Convert to smart pointers to avoid this.
	delete _functor;
	}

	virtual std::vector<fastjet::PseudoJet> getAxes(int n_jets, const std::vector <fastjet::PseudoJet> & particles, const std::vector<fastjet::PseudoJet>& currentAxes) {

	std::vector<fastjet::PseudoJet> seedAxes = _startingFinder->getAxes(n_jets, particles, currentAxes);
	double seedTau = _functor->tau(particles,seedAxes);

	for (int i = 0; i < _nAttempts; i++) {

	std::vector<fastjet::PseudoJet> newAxes(seedAxes.size(),fastjet::PseudoJet(0,0,0,0));

	for (unsigned int i = 0; i < particles.size(); i++) {
	double minDist = 100000000.0; //large number
	int minJ = -1; //bad ref
	for (unsigned int j = 0; j < seedAxes.size(); j++) {
	double tempDist = _functor->distance(particles[i],seedAxes[j]);
	if (tempDist < minDist) {
	minDist = tempDist;
	minJ = j;
	}
	}

	if (_functor->doCluster(particles[i],seedAxes[minJ])) {
	newAxes[minJ] += particles[i];
	}
	}

	seedAxes = newAxes;


	double tempTau = _functor->tau(particles,newAxes);

	if (fabs(tempTau - seedTau) < _accuracy) break;
	seedTau = tempTau;
	}

	return seedAxes;
	}
	};


	// Helper class for minimization
	class LightLikeAxis {
	private:
	double _rap, _phi, _weight, _mom;

	double DistanceSq(double rap2, double phi2) const {
	double rap1 = _rap;
	double phi1 = _phi;

	double distRap = rap1-rap2;
	double distPhi = std::fabs(phi1-phi2);
	if (distPhi > M_PI) {distPhi = 2.0*M_PI - distPhi;}
	return sq(distRap) + sq(distPhi);
	}

	double Distance(double rap2, double phi2) const {
	return std::sqrt(DistanceSq(rap2,phi2));
	}


	public:
	LightLikeAxis() : _rap(0.0), _phi(0.0), _weight(0.0), _mom(0.0) {}
	LightLikeAxis(double my_rap, double my_phi, double my_weight, double my_mom) :
	_rap(my_rap), _phi(my_phi), _weight(my_weight), _mom(my_mom) {}
	double rap() const {return _rap;}
	double phi() const {return _phi;}
	double weight() const {return _weight;}
	double mom() const {return _mom;}
	void set_rap(double my_set_rap) {_rap = my_set_rap;}
	void set_phi(double my_set_phi) {_phi = my_set_phi;}
	void set_weight(double my_set_weight) {_weight = my_set_weight;}
	void set_mom(double my_set_mom) {_mom = my_set_mom;}
	void reset(double my_rap, double my_phi, double my_weight, double my_mom) {_rap=my_rap; _phi=my_phi; _weight=my_weight; _mom=my_mom;}



	double DistanceSq(const fastjet::PseudoJet& input) const {
	return DistanceSq(input.rap(),input.phi());
	}

	double Distance(const fastjet::PseudoJet& input) const {
	return std::sqrt(DistanceSq(input));
	}

	double DistanceSq(const LightLikeAxis& input) const {
	return DistanceSq(input.rap(),input.phi());
	}

	double Distance(const LightLikeAxis& input) const {
	return std::sqrt(DistanceSq(input));
	}

	};

	///////
	//
	// Functions for minimization.
	// TODO: Wrap these in N-subjettiness class
	//
	///////


	// Given starting axes, update to find better axes
	template <int N>
	std::vector<LightLikeAxis> UpdateAxesFast(const std::vector <LightLikeAxis> & old_axes,
	const std::vector <fastjet::PseudoJet> & inputJets,
	NsubParameters paraNsub, double precision) {
	assert(old_axes.size() == N);

	// some storage, declared static to save allocation/re-allocation costs
	static LightLikeAxis new_axes[N];
	static fastjet::PseudoJet new_jets[N];
	for (int n = 0; n < N; ++n) {
	new_axes[n].reset(0.0,0.0,0.0,0.0);
	#ifdef FASTJET2
	new_jets[n].reset(0.0,0.0,0.0,0.0);
	#else
	// use cheaper reset if available
	new_jets[n].reset_momentum(0.0,0.0,0.0,0.0);
	#endif
	}


	double beta = paraNsub.beta();
	double Rcutoff = paraNsub.Rcutoff();

	/////////////// Assignment Step //////////////////////////////////////////////////////////
	std::vector<int> assignment_index(inputJets.size());
	int k_assign = -1;

	for (unsigned i = 0; i < inputJets.size(); i++){
	double smallestDist = 1000000.0;
	for (int k = 0; k < N; k++) {
	double thisDist = old_axes[k].DistanceSq(inputJets[i]);
	if (thisDist < smallestDist) {
	smallestDist = thisDist;
	k_assign = k;
	}
	}
	if (smallestDist > sq(Rcutoff)) {k_assign = -1;}
	assignment_index[i] = k_assign;
	}

	//////////////// Update Step /////////////////////////////////////////////////////////////
	double distPhi, old_dist;
	for (unsigned i = 0; i < inputJets.size(); i++) {
	int old_jet_i = assignment_index[i];
	if (old_jet_i == -1) {continue;}

	const fastjet::PseudoJet& inputJet_i = inputJets[i];
	LightLikeAxis& new_axis_i = new_axes[old_jet_i];
	double inputPhi_i = inputJet_i.phi();
	double inputRap_i = inputJet_i.rap();

	// optimize pow() call
	// add noise (the precision term) to make sure we don't divide by zero
	if (beta == 1.0) {
	double DR = std::sqrt(sq(precision) + old_axes[old_jet_i].DistanceSq(inputJet_i));
	old_dist = 1.0/DR;
	} else if (beta == 2.0) {
	old_dist = 1.0;
	} else if (beta == 0.0) {
	double DRSq = sq(precision) + old_axes[old_jet_i].DistanceSq(inputJet_i);
	old_dist = 1.0/DRSq;
	} else {
	old_dist = sq(precision) + old_axes[old_jet_i].DistanceSq(inputJet_i);
	old_dist = std::pow(old_dist, (0.5*beta-1.0));
	}

	// TODO: Put some of these addition functions into light-like axes
	// rapidity sum
	new_axis_i.set_rap(new_axis_i.rap() + inputJet_i.perp() * inputRap_i * old_dist);
	// phi sum
	distPhi = inputPhi_i - old_axes[old_jet_i].phi();
	if (fabs(distPhi) <= M_PI){
	new_axis_i.set_phi( new_axis_i.phi() + inputJet_i.perp() * inputPhi_i * old_dist );
	} else if (distPhi > M_PI) {
	new_axis_i.set_phi( new_axis_i.phi() + inputJet_i.perp() * (-2M_PI + inputPhi_i) old_dist );
	} else if (distPhi < -M_PI) {
	new_axis_i.set_phi( new_axis_i.phi() + inputJet_i.perp() * (+2M_PI + inputPhi_i) old_dist );
	}
	// weights sum
	new_axis_i.set_weight( new_axis_i.weight() + inputJet_i.perp() * old_dist );
	// momentum magnitude sum
	new_jets[old_jet_i] += inputJet_i;
	}
	// normalize sums
	for (int k = 0; k < N; k++) {
	if (new_axes[k].weight() == 0) {
	// no particles were closest to this axis! Return to old axis instead of (0,0,0,0)
	new_axes[k] = old_axes[k];
	} else {
	new_axes[k].set_rap( new_axes[k].rap() / new_axes[k].weight() );
	new_axes[k].set_phi( new_axes[k].phi() / new_axes[k].weight() );
	new_axes[k].set_phi( std::fmod(new_axes[k].phi() + 2M_PI, 2M_PI) );
	new_axes[k].set_mom( std::sqrt(new_jets[k].modp2()) );
	}
	}
	std::vector<LightLikeAxis> new_axes_vec(N);
	for (unsigned k = 0; k < N; ++k) new_axes_vec[k] = new_axes[k];
	return new_axes_vec;
	}


	// Given starting axes, update to find better axes
	// (This is just a wrapper for the templated version above.)
	std::vector<LightLikeAxis> UpdateAxes(const std::vector <LightLikeAxis> & old_axes,
	const std::vector <fastjet::PseudoJet> & inputJets, NsubParameters paraNsub, double precision) {
	int N = old_axes.size();
	switch (N) {
	case 1: return UpdateAxesFast<1>(old_axes, inputJets, paraNsub, precision);
	case 2: return UpdateAxesFast<2>(old_axes, inputJets, paraNsub, precision);
	case 3: return UpdateAxesFast<3>(old_axes, inputJets, paraNsub, precision);
	case 4: return UpdateAxesFast<4>(old_axes, inputJets, paraNsub, precision);
	case 5: return UpdateAxesFast<5>(old_axes, inputJets, paraNsub, precision);
	case 6: return UpdateAxesFast<6>(old_axes, inputJets, paraNsub, precision);
	case 7: return UpdateAxesFast<7>(old_axes, inputJets, paraNsub, precision);
	case 8: return UpdateAxesFast<8>(old_axes, inputJets, paraNsub, precision);
	case 9: return UpdateAxesFast<9>(old_axes, inputJets, paraNsub, precision);
	case 10: return UpdateAxesFast<10>(old_axes, inputJets, paraNsub, precision);
	case 11: return UpdateAxesFast<11>(old_axes, inputJets, paraNsub, precision);
	case 12: return UpdateAxesFast<12>(old_axes, inputJets, paraNsub, precision);
	case 13: return UpdateAxesFast<13>(old_axes, inputJets, paraNsub, precision);
	case 14: return UpdateAxesFast<14>(old_axes, inputJets, paraNsub, precision);
	case 15: return UpdateAxesFast<15>(old_axes, inputJets, paraNsub, precision);
	case 16: return UpdateAxesFast<16>(old_axes, inputJets, paraNsub, precision);
	case 17: return UpdateAxesFast<17>(old_axes, inputJets, paraNsub, precision);
	case 18: return UpdateAxesFast<18>(old_axes, inputJets, paraNsub, precision);
	case 19: return UpdateAxesFast<19>(old_axes, inputJets, paraNsub, precision);
	case 20: return UpdateAxesFast<20>(old_axes, inputJets, paraNsub, precision);
	default: std::cout << "N-jettiness is hard-coded to only allow up to 20 jets!" << std::endl;
	return std::vector<LightLikeAxis>();
	}

	}


	// Go from internal LightLikeAxis to PseudoJet
	// TODO: Make part of LightLikeAxis class.
	std::vector<fastjet::PseudoJet> ConvertToPseudoJet(const std::vector <LightLikeAxis>& axes) {

	int n_jets = axes.size();

	double px, py, pz, E;
	std::vector<fastjet::PseudoJet> FourVecJets;
	for (int k = 0; k < n_jets; k++) {
	E = axes[k].mom();
	pz = (std::exp(2.0axes[k].rap()) - 1.0) / (std::exp(2.0axes[k].rap()) + 1.0) * E;
	px = std::cos(axes[k].phi()) * std::sqrt( std::pow(E,2) - std::pow(pz,2) );
	py = std::sin(axes[k].phi()) * std::sqrt( std::pow(E,2) - std::pow(pz,2) );
	fastjet::PseudoJet temp = fastjet::PseudoJet(px,py,pz,E);
	FourVecJets.push_back(temp);
	}
	return FourVecJets;
	}


	// Get minimization axes
	std::vector<fastjet::PseudoJet> GetMinimumAxes(const std::vector <fastjet::PseudoJet> & seedAxes, const std::vector <fastjet::PseudoJet> & inputJets, KmeansParameters para,
	NsubParameters paraNsub,MeasureFunctor* functor) {
	int n_jets = seedAxes.size();
	double noise = 0, tau = 10000.0, tau_tmp, cmp;
	std::vector< LightLikeAxis > new_axes(n_jets, LightLikeAxis(0,0,0,0)), old_axes(n_jets, LightLikeAxis(0,0,0,0));
	std::vector<fastjet::PseudoJet> tmp_min_axes, min_axes;
	for (int l = 0; l < para.n_iterations(); l++) { // Do minimization procedure multiple times
	// Add noise to guess for the axes
	for (int k = 0; k < n_jets; k++) {
	if ( 0 == l ) { // Don't add noise on first pass
	old_axes[k].set_rap( seedAxes[k].rap() );
	old_axes[k].set_phi( seedAxes[k].phi() );
	} else {
	noise = ((double)rand()/(double)RAND_MAX) * para.noise_range() * 2 - para.noise_range();
	old_axes[k].set_rap( seedAxes[k].rap() + noise );
	noise = ((double)rand()/(double)RAND_MAX) * para.noise_range() * 2 - para.noise_range();
	old_axes[k].set_phi( seedAxes[k].phi() + noise );
	}
	}
	cmp = 100.0; int h = 0;
	while (cmp > para.precision() && h < para.halt()) { // Keep updating axes until near-convergence or too many update steps
	cmp = 0.0; h++;
	new_axes = UpdateAxes(old_axes, inputJets, paraNsub, para.precision()); // Update axes
	for (int k = 0; k < n_jets; k++) {
	cmp += old_axes[k].Distance(new_axes[k]);
	}
	cmp = cmp / ((double) n_jets);
	old_axes = new_axes;
	}
	tmp_min_axes = ConvertToPseudoJet(old_axes); // Convert axes directions into four-std::vectors

	tau_tmp = functor->tau(inputJets, tmp_min_axes);
	if (tau_tmp < tau) {tau = tau_tmp; min_axes = tmp_min_axes;} // Keep axes and tau only if they are best so far
	}
	return min_axes;
	}

	///////
	//
	// Main Njettiness Class
	//
	///////

	class Njettiness {
	public:
	enum AxesMode {
	kt_axes, // exclusive kt axes
	ca_axes, // exclusive ca axes
	antikt_0p2_axes, // inclusive hardest axes with antikt-0.2
	min_axes, // axes that minimize N-subjettiness (100 passes by default)
	manual_axes, // set your own axes with setAxes()
	onepass_kt_axes, // one-pass minimization from kt starting point
	onepass_ca_axes, // one-pass minimization from ca starting point
	onepass_antikt_0p2_axes, // one-pass minimization from antikt-0.2 starting point
	onepass_manual_axes // one-pass minimization from manual starting point
	};

	private:
	MeasureFunctor* _functor;
	AxesFinder* _axesFinder;

	std::vector<fastjet::PseudoJet> _currentAxes;
	std::vector<double> _currentTaus;
	double _currentTau;

	void establishAxes(unsigned n_jets, const std::vector <fastjet::PseudoJet> & inputs);
	void establishTaus(const std::vector <fastjet::PseudoJet> & inputs);

	public:
	Njettiness(MeasureFunctor* functor, AxesFinder* axesFinder) : _functor(functor), _axesFinder(axesFinder) {}

	Njettiness(AxesMode axes, NsubParameters paraNsub);
	Njettiness(NsubGeometricParameters paraGeo);

	~Njettiness();

	void setMeasureFunctor(MeasureFunctor* newFunctor) {_functor = newFunctor;}
	void setAxesFinder(AxesFinder* newAxesFinder) {_axesFinder = newAxesFinder;}

	// setAxes for Manual mode
	void setAxes(std::vector<fastjet::PseudoJet> myAxes) {
	_currentAxes = myAxes;
	}

	// The value of N-subjettiness
	double getTau(unsigned n_jets, const std::vector<fastjet::PseudoJet> & inputJets) {
	if (inputJets.size() <= n_jets) {
	_currentAxes = inputJets;
	_currentAxes.resize(n_jets,fastjet::PseudoJet(0.0,0.0,0.0,0.0));
	return 0.0;
	}
	establishAxes(n_jets, inputJets); // sets current Axes
	establishTaus(inputJets); // sets current Tau Values

	return _currentTau;
	}

	// get axes used by getTau.
	std::vector<fastjet::PseudoJet> currentAxes() {
	return _currentAxes;
	}

	// get subTau values calculated in getTau.
	std::vector<double> currentTaus() {
	return _currentTaus;
	}

	// get total Tau value calculated in getTau.
	double currentTau() {
	return _currentTau;
	}

	// partition inputs by Voronoi (each vector stores indices corresponding to inputJets)
	std::vector<std::list<int> > getPartition(const std::vector<fastjet::PseudoJet> & inputJets);

	// partition inputs by Voronoi
	std::vector<fastjet::PseudoJet> getJets(const std::vector<fastjet::PseudoJet> & inputJets);

	};

	void Njettiness::establishTaus(const std::vector <fastjet::PseudoJet> & inputs) {
	//subTau values
	_currentTaus = _functor->subTaus(inputs, _currentAxes);

	//totalTau value
	_currentTau = 0.0;
	for (unsigned j = 0; j < _currentTaus.size(); j++) {_currentTau += _currentTaus[j];}
	}



	//Use NsubAxesMode to pick which type of axes to use
	void Njettiness::establishAxes(unsigned int n_jets, const std::vector <fastjet::PseudoJet> & inputs) {
	_currentAxes = _axesFinder->getAxes(n_jets,inputs,_currentAxes);
	}


	Njettiness::Njettiness(NsubGeometricParameters paraGeo) {
	double Rcutoff = paraGeo.Rcutoff();
	_functor = new GeometricMeasure(Rcutoff);
	_axesFinder = new AxesFinderFromGeometricMinimization(new AxesFinderFromKT(),Rcutoff);
	}

	//Constructor sets KmeansParameters from NsubAxesMode input
	Njettiness::Njettiness(AxesMode axes, NsubParameters paraNsub) {

	_functor = new DefaultMeasure(paraNsub); //Is there a way to do this without pointers?

	// memory management note, AxesFinderFromKmeansMinimization is responsible for deleting its subpointer.
	// TODO: convert to smart pointers

	switch (axes) {
	case kt_axes:
	_axesFinder = new AxesFinderFromKT();
	break;
	case ca_axes:
	_axesFinder = new AxesFinderFromCA();
	break;
	case antikt_0p2_axes:
	_axesFinder = new AxesFinderFromAntiKT(0.2);
	break;
	case onepass_kt_axes:
	_axesFinder = new AxesFinderFromKmeansMinimization(new AxesFinderFromKT(),KmeansParameters(1,0.0001,1000,0.8), paraNsub);
	break;
	case onepass_ca_axes:
	_axesFinder = new AxesFinderFromKmeansMinimization(new AxesFinderFromCA(),KmeansParameters(1,0.0001,1000,0.8), paraNsub);
	break;
	case onepass_antikt_0p2_axes:
	_axesFinder = new AxesFinderFromKmeansMinimization(new AxesFinderFromAntiKT(0.2),KmeansParameters(1,0.0001,1000,0.8), paraNsub);
	break;
	case onepass_manual_axes:
	_axesFinder = new AxesFinderFromKmeansMinimization(new AxesFinderFromUserInput(),KmeansParameters(1,0.0001,1000,0.8), paraNsub);
	break;
	case min_axes:
	_axesFinder = new AxesFinderFromKmeansMinimization(new AxesFinderFromKT(),KmeansParameters(100,0.0001,1000,0.8), paraNsub);
	break;
	case manual_axes:
	_axesFinder = new AxesFinderFromUserInput();
	break;
	default:
	assert(false);
	break;
	}

	}

	Njettiness::~Njettiness() {
	delete _functor;
	delete _axesFinder;
	}


	// Partition a list of particles according to which N-jettiness axis they are closest to.
	// Return a vector of length _currentAxes.size() (which should be N).
	// Each vector element is a list of ints corresponding to the indices in
	// particles of the particles belonging to that jet.
	std::vector<std::list<int> > Njettiness::getPartition(const std::vector<fastjet::PseudoJet> & particles) {
	std::vector<std::list<int> > partitions(_currentAxes.size());

	int j_min = -1;
	for (unsigned i = 0; i < particles.size(); i++) {
	// find minimum distance
	double minR = 10000.0; // large number
	for (unsigned j = 0; j < _currentAxes.size(); j++) {
	double tempR = _functor->distance(particles[i],_currentAxes[j]); // delta R distance
	if (tempR < minR) {
	minR = tempR;
	j_min = j;
	}
	}
	if (_functor->doCluster(particles[i],_currentAxes[j_min])) partitions[j_min].push_back(i);
	}
	return partitions;
	}


	// Having found axes, assign each particle in particles to an axis, and return a set of jets.
	// Each jet is the sum of particles closest to an axis (Njet = Naxes).
	std::vector<fastjet::PseudoJet> Njettiness::getJets(const std::vector<fastjet::PseudoJet> & particles) {

	std::vector<fastjet::PseudoJet> jets(_currentAxes.size());

	std::vector<std::list<int> > partition = getPartition(particles);
	for (unsigned j = 0; j < partition.size(); ++j) {
	std::list<int>::const_iterator it, itE;
	for (it = partition[j].begin(), itE = partition[j].end(); it != itE; ++it) {
	jets[j] += particles[*it];
	}
	}
	return jets;
	}

	} // namespace contrib

	FASTJET_END_NAMESPACE

	#endif // __FASTJET_CONTRIB_NJETTINESS_HH__

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