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	diff --git a/src/Utils/PlotUtils.cxx b/src/Utils/PlotUtils.cxx
	index 24f1c60..a42fa3c 100644
	--- a/src/Utils/PlotUtils.cxx
	+++ b/src/Utils/PlotUtils.cxx
	@@ -1,1033 +1,1162 @@
	// Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret

	/*******************************************************************************
	* This file is part of NUISANCE.
	*
	* NUISANCE 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 3 of the License, or
	* (at your option) any later version.
	*
	* NUISANCE 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 NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	*******************************************************************************/

	#include "PlotUtils.h"
	#include "FitEvent.h"
	#include "StatUtils.h"

	// MOVE TO MB UTILS!
	// This function is intended to be modified to enforce a consistent masking for
	// all models.
	TH2D* PlotUtils::SetMaskHist(std::string type, TH2D* data) {
	TH2D* fMaskHist = (TH2D*)data->Clone("fMaskHist");

	for (int xBin = 0; xBin < fMaskHist->GetNbinsX(); ++xBin) {
	for (int yBin = 0; yBin < fMaskHist->GetNbinsY(); ++yBin) {
	if (data->GetBinContent(xBin + 1, yBin + 1) == 0)
	fMaskHist->SetBinContent(xBin + 1, yBin + 1, 0);
	else
	fMaskHist->SetBinContent(xBin + 1, yBin + 1, 0.5);

	if (!type.compare("MB_numu_2D")) {
	if (yBin == 19 && xBin < 8)
	fMaskHist->SetBinContent(xBin + 1, yBin + 1, 1.0);
	} else {
	if (yBin == 19 && xBin < 11)
	fMaskHist->SetBinContent(xBin + 1, yBin + 1, 1.0);
	}
	if (yBin == 18 && xBin < 3)
	fMaskHist->SetBinContent(xBin + 1, yBin + 1, 1.0);
	if (yBin == 17 && xBin < 2)
	fMaskHist->SetBinContent(xBin + 1, yBin + 1, 1.0);
	if (yBin == 16 && xBin < 1)
	fMaskHist->SetBinContent(xBin + 1, yBin + 1, 1.0);
	}
	}

	return fMaskHist;
	};

	// MOVE TO GENERAL UTILS?
	bool PlotUtils::CheckObjectWithName(TFile* inFile, std::string substring) {
	TIter nextkey(inFile->GetListOfKeys());
	TKey* key;

	while ((key = (TKey*)nextkey())) {
	std::string test(key->GetName());
	if (test.find(substring) != std::string::npos) return true;
	}
	return false;
	};

	// MOVE TO GENERAL UTILS?
	std::string PlotUtils::GetObjectWithName(TFile* inFile, std::string substring) {
	TIter nextkey(inFile->GetListOfKeys());
	TKey* key;
	std::string output = "";

	while ((key = (TKey*)nextkey())) {
	std::string test(key->GetName());
	if (test.find(substring) != std::string::npos) output = test;
	}

	return output;
	};

	void PlotUtils::CreateNeutModeArray(TH1* hist, TH1* neutarray[]) {
	for (int i = 0; i < 60; i++) {
	neutarray[i] = (TH1*)hist->Clone(Form("%s_NMODE_%i", hist->GetName(), i));
	}
	return;
	};

	void PlotUtils::DeleteNeutModeArray(TH1* neutarray[]) {
	for (int i = 0; i < 60; i++) {
	delete neutarray[i];
	}
	return;
	};

	void PlotUtils::FillNeutModeArray(TH1D* hist[], int mode, double xval,
	double weight) {
	if (abs(mode) > 60) return;
	hist[abs(mode)]->Fill(xval, weight);
	return;
	};

	void PlotUtils::FillNeutModeArray(TH2D* hist[], int mode, double xval,
	double yval, double weight) {
	if (abs(mode) > 60) return;
	hist[abs(mode)]->Fill(xval, yval, weight);
	return;
	};

	THStack PlotUtils::GetNeutModeStack(std::string title, TH1* ModeStack[],
	int option) {
	(void)option;
	THStack allmodes = THStack(title.c_str(), title.c_str());

	for (int i = 0; i < 60; i++) {
	allmodes.Add(ModeStack[i]);
	}

	// Credit to Clarence for copying all this out.

	// CC
	ModeStack[1]->SetTitle("CCQE");
	ModeStack[1]->SetFillColor(kBlue);
	// ModeStack[1]->SetFillStyle(3444);
	ModeStack[1]->SetLineColor(kBlue);
	ModeStack[2]->SetTitle("2p/2h Nieves");
	ModeStack[2]->SetFillColor(kRed);
	// ModeStack[2]->SetFillStyle(3344);
	ModeStack[2]->SetLineColor(kRed);

	// ModeStack[11]->SetTitle("#it{#nu + p #rightarrow l^{-} + p + #pi^{+}}");
	ModeStack[11]->SetTitle("CC1#pi^{+} on p");
	ModeStack[11]->SetFillColor(kGreen);
	// ModeStack[11]->SetFillStyle(3004);
	ModeStack[11]->SetLineColor(kGreen);
	// ModeStack[12]->SetTitle("#it{#nu + n #rightarrow l^{-} + p + #pi^{0}}");
	ModeStack[12]->SetTitle("CC1#pi^{0} on n");
	ModeStack[12]->SetFillColor(kGreen + 3);
	// ModeStack[12]->SetFillStyle(3005);
	ModeStack[12]->SetLineColor(kGreen);
	// ModeStack[13]->SetTitle("#it{#nu + n #rightarrow l^{-} + n + #pi^{+}}");
	ModeStack[13]->SetTitle("CC1#pi^{+} on n");
	ModeStack[13]->SetFillColor(kGreen - 2);
	// ModeStack[13]->SetFillStyle(3004);
	ModeStack[13]->SetLineColor(kGreen);

	ModeStack[16]->SetTitle("CC coherent");
	ModeStack[16]->SetFillColor(kBlue);
	// ModeStack[16]->SetFillStyle(3644);
	ModeStack[16]->SetLineColor(kBlue);

	// ModeStack[17]->SetTitle("#it{#nu + n #rightarrow l^{-} + p + #gamma}");
	ModeStack[17]->SetTitle("CC1#gamma");
	ModeStack[17]->SetFillColor(kMagenta);
	// ModeStack[17]->SetFillStyle(3001);
	ModeStack[17]->SetLineColor(kMagenta);

	ModeStack[21]->SetTitle("Multi #pi (1.3 < W < 2.0)");
	ModeStack[21]->SetFillColor(kYellow);
	// ModeStack[21]->SetFillStyle(3005);
	ModeStack[21]->SetLineColor(kYellow);

	// ModeStack[22]->SetTitle("#it{#nu + n #rightarrow l^{-} + p + #eta^{0}}");
	ModeStack[22]->SetTitle("CC1#eta^{0} on n");
	ModeStack[22]->SetFillColor(kYellow - 2);
	// ModeStack[22]->SetFillStyle(3013);
	ModeStack[22]->SetLineColor(kYellow - 2);
	// ModeStack[23]->SetTitle("#it{#nu + n #rightarrow l^{-} + #Lambda +
	// K^{+}}");
	ModeStack[23]->SetTitle("CC1#Labda1K^{+}");
	ModeStack[23]->SetFillColor(kYellow - 6);
	// ModeStack[23]->SetFillStyle(3013);
	ModeStack[23]->SetLineColor(kYellow - 6);

	ModeStack[26]->SetTitle("DIS (W > 2.0)");
	ModeStack[26]->SetFillColor(kRed);
	// ModeStack[26]->SetFillStyle(3006);
	ModeStack[26]->SetLineColor(kRed);

	// NC
	// ModeStack[31]->SetTitle("#it{#nu + n #rightarrow #nu + n + #pi^{0}}");
	ModeStack[31]->SetTitle("NC1#pi^{0} on n");
	ModeStack[31]->SetFillColor(kBlue);
	// ModeStack[31]->SetFillStyle(3004);
	ModeStack[31]->SetLineColor(kBlue);
	// ModeStack[32]->SetTitle("#it{#nu + p #rightarrow #nu + p + #pi^{0}}");
	ModeStack[32]->SetTitle("NC1#pi^{0} on p");
	ModeStack[32]->SetFillColor(kBlue + 3);
	// ModeStack[32]->SetFillStyle(3004);
	ModeStack[32]->SetLineColor(kBlue + 3);
	// ModeStack[33]->SetTitle("#it{#nu + n #rightarrow #nu + p + #pi^{-}}");
	ModeStack[33]->SetTitle("NC1#pi^{-} on n");
	ModeStack[33]->SetFillColor(kBlue - 2);
	// ModeStack[33]->SetFillStyle(3005);
	ModeStack[33]->SetLineColor(kBlue - 2);
	// ModeStack[34]->SetTitle("#it{#nu + p #rightarrow #nu + n + #pi^{+}}");
	ModeStack[34]->SetTitle("NC1#pi^{+} on p");
	ModeStack[34]->SetFillColor(kBlue - 8);
	// ModeStack[34]->SetFillStyle(3005);
	ModeStack[34]->SetLineColor(kBlue - 8);

	ModeStack[36]->SetTitle("NC Coherent");
	ModeStack[36]->SetFillColor(kBlue + 8);
	// ModeStack[36]->SetFillStyle(3644);
	ModeStack[36]->SetLineColor(kBlue + 8);

	// ModeStack[38]->SetTitle("#it{#nu + n #rightarrow #nu + n + #gamma}");
	ModeStack[38]->SetTitle("NC1#gamma on n");
	ModeStack[38]->SetFillColor(kMagenta);
	// ModeStack[38]->SetFillStyle(3001);
	ModeStack[38]->SetLineColor(kMagenta);
	// ModeStack[39]->SetTitle("#it{#nu + p #rightarrow #nu + p + #gamma}");
	ModeStack[39]->SetTitle("NC1#gamma on p");
	ModeStack[39]->SetFillColor(kMagenta - 10);
	// ModeStack[39]->SetFillStyle(3001);
	ModeStack[39]->SetLineColor(kMagenta - 10);

	ModeStack[41]->SetTitle("Multi #pi (1.3 < W < 2.0)");
	ModeStack[41]->SetFillColor(kBlue - 10);
	// ModeStack[41]->SetFillStyle(3005);
	ModeStack[41]->SetLineColor(kBlue - 10);

	// ModeStack[42]->SetTitle("#it{#nu + n #rightarrow #nu + n + #eta^{0}}");
	ModeStack[42]->SetTitle("NC1#eta^{0} on n");
	ModeStack[42]->SetFillColor(kYellow - 2);
	// ModeStack[42]->SetFillStyle(3013);
	ModeStack[42]->SetLineColor(kYellow - 2);
	// ModeStack[43]->SetTitle("#it{#nu + p #rightarrow #nu + p + #eta^{0}}");
	ModeStack[43]->SetTitle("NC1#eta^{0} on p");
	ModeStack[43]->SetFillColor(kYellow - 4);
	// ModeStack[43]->SetFillStyle(3013);
	ModeStack[43]->SetLineColor(kYellow - 4);

	// ModeStack[44]->SetTitle("#it{#nu + n #rightarrow #nu + #Lambda + K^{0}}");
	ModeStack[44]->SetTitle("NC1#Lambda1K^{0} on n");
	ModeStack[44]->SetFillColor(kYellow - 6);
	// ModeStack[44]->SetFillStyle(3014);
	ModeStack[44]->SetLineColor(kYellow - 6);
	// ModeStack[45]->SetTitle("#it{#nu + p #rightarrow #nu + #Lambda + K^{+}}");
	ModeStack[45]->SetTitle("NC1#Lambda1K^{+}");
	ModeStack[45]->SetFillColor(kYellow - 10);
	// ModeStack[45]->SetFillStyle(3014);
	ModeStack[45]->SetLineColor(kYellow - 10);

	ModeStack[46]->SetTitle("DIS (W > 2.0)");
	ModeStack[46]->SetFillColor(kRed);
	// ModeStack[46]->SetFillStyle(3006);
	ModeStack[46]->SetLineColor(kRed);

	// ModeStack[51]->SetTitle("#it{#nu + p #rightarrow #nu + p}");
	ModeStack[51]->SetTitle("NC on p");
	ModeStack[51]->SetFillColor(kBlack);
	// ModeStack[51]->SetFillStyle(3444);
	ModeStack[51]->SetLineColor(kBlack);
	// ModeStack[52]->SetTitle("#it{#nu + n #rightarrow #nu + n}");
	ModeStack[52]->SetTitle("NC on n");
	ModeStack[52]->SetFillColor(kGray);
	// ModeStack[52]->SetFillStyle(3444);
	ModeStack[52]->SetLineColor(kGray);

	return allmodes;
	};

	TLegend PlotUtils::GenerateStackLegend(THStack stack, int xlow, int ylow,
	int xhigh, int yhigh) {
	TLegend leg = TLegend(xlow, ylow, xhigh, yhigh);

	TObjArray* histarray = stack.GetStack();

	int nhist = histarray->GetEntries();
	for (int i = 0; i < nhist; i++) {
	TH1* hist = (TH1*)(histarray->At(i));
	leg.AddEntry((hist), ((TH1*)histarray->At(i))->GetTitle(), "fl");
	}

	leg.SetName(Form("%s_LEG", stack.GetName()));

	return leg;
	};

	void PlotUtils::ScaleNeutModeArray(TH1* hist[], double factor,
	std::string option) {
	for (int i = 0; i < 60; i++) {
	if (hist[i]) hist[i]->Scale(factor, option.c_str());
	}

	return;
	};

	void PlotUtils::ResetNeutModeArray(TH1* hist[]) {
	for (int i = 0; i < 60; i++) {
	if (hist[i]) hist[i]->Reset();
	}

	return;
	};

	//********************************************************************
	// This assumes the Enu axis is the x axis, as is the case for MiniBooNE 2D
	// distributions
	void PlotUtils::FluxUnfoldedScaling(TH2D* fMCHist, TH1D* fhist, TH1D* ehist,
	double scalefactor) {
	//********************************************************************

	// Make clones to avoid changing stuff
	TH1D* eventhist = (TH1D*)ehist->Clone();
	TH1D* fFluxHist = (TH1D*)fhist->Clone();

	// Undo width integral in SF
	fMCHist->Scale(scalefactor /
	eventhist->Integral(1, eventhist->GetNbinsX() + 1, "width"));

	// Standardise The Flux
	eventhist->Scale(1.0 / fFluxHist->Integral());
	fFluxHist->Scale(1.0 / fFluxHist->Integral());

	// Do interpolation for 2D plots?
	// fFluxHist = PlotUtils::InterpolateFineHistogram(fFluxHist,100,"width");
	// eventhist = PlotUtils::InterpolateFineHistogram(eventhist,100,"width");

	// eventhist->Scale(1.0/fFluxHist->Integral());
	// fFluxHist->Scale(1.0/fFluxHist->Integral());

	// Scale fMCHist by eventhist integral
	fMCHist->Scale(eventhist->Integral(1, eventhist->GetNbinsX() + 1));

	+ // Find which axis is the Enu axis
	+ bool EnuOnXaxis = false;
	+ std::string xaxis = fMCHist->GetXaxis()->GetTitle();
	+ if (xaxis.find("E") != std::string::npos && xaxis.find("nu" != std::string::npos)) EnuOnXaxis = true;
	+ std::string yaxis = fMCHist->GetYaxis()->GetTitle();
	+ if (yaxis.find("E") != std::string::npos && xaxis.find("nu" != std::string::npos)) {
	+ // First check that xaxis didn't also find Enu
	+ if (EnuOnXaxis) {
	+ ERR(FTL) << fMCHist->GetTitle() << " error:" << std::endl;
	+ ERR(FTL) << "Found Enu in xaxis title: " << xaxis << std::endl;
	+ ERR(FTL) << "AND" << std::endl;
	+ ERR(FTL) << "Found Enu in yaxis title: " << yaxis << std::endl;
	+ ERR(FTL) << "Enu on x and Enu on y flux unfolded scaling isn't implemented, please modify " << __FILE__ << ":" << __LINE__ << std::endl;
	+ throw;
	+ }
	+ EnuOnXaxis = false;
	+ }
	+
	// Now Get a flux PDF assuming X axis is Enu
	- TH1D* pdfflux = (TH1D*)fMCHist->ProjectionX()->Clone();
	+ TH1D* pdfflux = NULL;
	+
	+ // If xaxis is Enu
	+ if (EnuOnXaxis) pdfflux = (TH1D*)fMCHist->ProjectionX()->Clone();
	+ // If yaxis is Enu
	+ else pdfflux = (TH1D*)fMCHist->ProjectionY()->Clone();
	// pdfflux->Write( (std::string(fMCHist->GetName()) + "_PROJX").c_str());
	pdfflux->Reset();

	// Awful MiniBooNE Check for the time being
	- bool ismb =
	- std::string(fMCHist->GetName()).find("MiniBooNE") != std::string::npos;
	+ // Needed because the flux is in GeV whereas the measurement is in MeV
	+ bool ismb = std::string(fMCHist->GetName()).find("MiniBooNE") != std::string::npos;

	for (int i = 0; i < pdfflux->GetNbinsX(); i++) {
	double Ml = pdfflux->GetXaxis()->GetBinLowEdge(i + 1);
	double Mh = pdfflux->GetXaxis()->GetBinLowEdge(i + 2);
	// double Mc = pdfflux->GetXaxis()->GetBinCenter(i+1);
	// double Mw = pdfflux->GetBinWidth(i+1);
	double fluxint = 0.0;

	// Scaling to match flux for MB
	if (ismb) {
	Ml /= 1.E3;
	Mh /= 1.E3;
	// Mc /= 1.E3;
	// Mw /= 1.E3;
	}

	for (int j = 0; j < fFluxHist->GetNbinsX(); j++) {
	// double Fc = fFluxHist->GetXaxis()->GetBinCenter(j+1);
	double Fl = fFluxHist->GetXaxis()->GetBinLowEdge(j + 1);
	double Fh = fFluxHist->GetXaxis()->GetBinLowEdge(j + 2);
	double Fe = fFluxHist->GetBinContent(j + 1);
	double Fw = fFluxHist->GetXaxis()->GetBinWidth(j + 1);

	if (Fl >= Ml and Fh <= Mh) {
	fluxint += Fe;
	} else if (Fl < Ml and Fl < Mh and Fh > Ml and Fh < Mh) {
	fluxint += Fe * (Fh - Ml) / Fw;
	} else if (Fh > Mh and Fl < Mh and Fh > Ml and Fl > Ml) {
	fluxint += Fe * (Mh - Fl) / Fw;
	} else if (Ml >= Fl and Mh <= Fh) {
	fluxint += Fe * (Mh - Ml) / Fw;
	} else {
	continue;
	}
	}
	-
	pdfflux->SetBinContent(i + 1, fluxint);
	}

	+ // Then finally divide by the bin-width in
	for (int i = 0; i < fMCHist->GetNbinsX(); i++) {
	for (int j = 0; j < fMCHist->GetNbinsY(); j++) {
	if (pdfflux->GetBinContent(i + 1) == 0.0) continue;

	- double binWidth = fMCHist->GetYaxis()->GetBinLowEdge(j + 2) -
	- fMCHist->GetYaxis()->GetBinLowEdge(j + 1);
	+ // Different scaling depending on if Enu is on x or y axis
	+ double scaling = 1.0;
	+ // If Enu is on the x-axis, we want the ith entry of the flux
	+ // And to divide by the bin width of the jth bin
	+ if (EnuOnXaxis) {
	+ double binWidth = fMCHist->GetYaxis()->GetBinLowEdge(j + 2) -
	+ fMCHist->GetYaxis()->GetBinLowEdge(j + 1);
	+ scaling = pdfflux->GetBinContent(i+1)*binWidth;
	+ } else {
	+ double binWidth = fMCHist->GetXaxis()->GetBinLowEdge(i + 2) -
	+ fMCHist->GetXaxis()->GetBinLowEdge(i + 1);
	+ scaling = pdfflux->GetBinContent(j+1)*binWidth;
	+ }
	+ //fMCHist->SetBinContent(i + 1, j + 1,
	+ //fMCHist->GetBinContent(i + 1, j + 1) /
	+ //pdfflux->GetBinContent(i + 1) / binWidth);
	+ //fMCHist->SetBinError(i + 1, j + 1, fMCHist->GetBinError(i + 1, j + 1) /
	+ //pdfflux->GetBinContent(i + 1) /
	+ //binWidth);
	fMCHist->SetBinContent(i + 1, j + 1,
	fMCHist->GetBinContent(i + 1, j + 1) /
	- pdfflux->GetBinContent(i + 1) / binWidth);
	+ scaling);
	fMCHist->SetBinError(i + 1, j + 1, fMCHist->GetBinError(i + 1, j + 1) /
	- pdfflux->GetBinContent(i + 1) /
	- binWidth);
	+ scaling);
	}
	}

	delete eventhist;
	delete fFluxHist;
	-
	- return;
	};

	TH1D* PlotUtils::InterpolateFineHistogram(TH1D* hist, int res,
	std::string opt) {
	int nbins = hist->GetNbinsX();
	double elow = hist->GetXaxis()->GetBinLowEdge(1);
	double ehigh = hist->GetXaxis()->GetBinLowEdge(nbins + 1);
	bool width = true; // opt.find("width") != std::string::npos;

	TH1D* fine = new TH1D("fine", "fine", nbins * res, elow, ehigh);

	TGraph* temp = new TGraph();

	for (int i = 0; i < nbins; i++) {
	double E = hist->GetXaxis()->GetBinCenter(i + 1);
	double C = hist->GetBinContent(i + 1);
	double W = hist->GetXaxis()->GetBinWidth(i + 1);
	if (!width) W = 1.0;

	if (W != 0.0) temp->SetPoint(temp->GetN(), E, C / W);
	}

	for (int i = 0; i < fine->GetNbinsX(); i++) {
	double E = fine->GetXaxis()->GetBinCenter(i + 1);
	double W = fine->GetBinWidth(i + 1);
	if (!width) W = 1.0;

	fine->SetBinContent(i + 1, temp->Eval(E, 0, "S") * W);
	}

	fine->Scale(hist->Integral(1, hist->GetNbinsX() + 1) /
	fine->Integral(1, fine->GetNbinsX() + 1));
	//std::cout << "Interpolation Difference = "
	//<< fine->Integral(1, fine->GetNbinsX() + 1) << "/"
	//<< hist->Integral(1, hist->GetNbinsX() + 1) << std::endl;

	return fine;
	}

	//********************************************************************
	// This interpolates the flux by a TGraph instead of requiring the flux and MC
	// flux to have the same binning
	void PlotUtils::FluxUnfoldedScaling(TH1D* mcHist, TH1D* fhist, TH1D* ehist,
	double scalefactor, int nevents) {
	//********************************************************************

	TH1D* eventhist = (TH1D*)ehist->Clone();
	TH1D* fFluxHist = (TH1D*)fhist->Clone();

	if (FitPar::Config().GetParB("save_flux_debug")) {
	std::string name = std::string(mcHist->GetName());

	mcHist->Write((name + "_UNF_MC").c_str());
	fFluxHist->Write((name + "_UNF_FLUX").c_str());
	eventhist->Write((name + "_UNF_EVT").c_str());

	TH1D* scalehist = new TH1D("scalehist", "scalehist", 1, 0.0, 1.0);
	scalehist->SetBinContent(1, scalefactor);
	scalehist->SetBinContent(2, nevents);

	scalehist->Write((name + "_UNF_SCALE").c_str());
	}

	// Undo width integral in SF
	mcHist->Scale(scalefactor /
	eventhist->Integral(1, eventhist->GetNbinsX() + 1, "width"));

	// Standardise The Flux
	eventhist->Scale(1.0 / fFluxHist->Integral());
	fFluxHist->Scale(1.0 / fFluxHist->Integral());

	// Scale mcHist by eventhist integral
	mcHist->Scale(eventhist->Integral(1, eventhist->GetNbinsX() + 1));

	// Now Get a flux PDF
	TH1D* pdfflux = (TH1D*)mcHist->Clone();
	pdfflux->Reset();

	for (int i = 0; i < mcHist->GetNbinsX(); i++) {
	double Ml = mcHist->GetXaxis()->GetBinLowEdge(i + 1);
	double Mh = mcHist->GetXaxis()->GetBinLowEdge(i + 2);
	// double Mc = mcHist->GetXaxis()->GetBinCenter(i+1);
	// double Me = mcHist->GetBinContent(i+1);
	// double Mw = mcHist->GetBinWidth(i+1);
	double fluxint = 0.0;

	for (int j = 0; j < fFluxHist->GetNbinsX(); j++) {
	// double Fc = fFluxHist->GetXaxis()->GetBinCenter(j+1);
	double Fl = fFluxHist->GetXaxis()->GetBinLowEdge(j + 1);
	double Fh = fFluxHist->GetXaxis()->GetBinLowEdge(j + 2);
	double Fe = fFluxHist->GetBinContent(j + 1);
	double Fw = fFluxHist->GetXaxis()->GetBinWidth(j + 1);

	if (Fl >= Ml and Fh <= Mh) {
	fluxint += Fe;
	} else if (Fl < Ml and Fl < Mh and Fh > Ml and Fh < Mh) {
	fluxint += Fe * (Fh - Ml) / Fw;
	} else if (Fh > Mh and Fl < Mh and Fh > Ml and Fl > Ml) {
	fluxint += Fe * (Mh - Fl) / Fw;
	} else if (Ml >= Fl and Mh <= Fh) {
	fluxint += Fe * (Mh - Ml) / Fw;
	} else {
	continue;
	}
	}

	pdfflux->SetBinContent(i + 1, fluxint);
	}

	// Scale MC hist by pdfflux
	for (int i = 0; i < mcHist->GetNbinsX(); i++) {
	if (pdfflux->GetBinContent(i + 1) == 0.0) continue;

	mcHist->SetBinContent(
	i + 1, mcHist->GetBinContent(i + 1) / pdfflux->GetBinContent(i + 1));
	mcHist->SetBinError(
	i + 1, mcHist->GetBinError(i + 1) / pdfflux->GetBinContent(i + 1));
	}

	delete eventhist;
	delete fFluxHist;
	-
	- return;
	};

	// MOVE TO GENERAL UTILS
	//********************************************************************
	void PlotUtils::Set2DHistFromText(std::string dataFile, TH2* hist, double norm,
	bool skipbins) {
	//********************************************************************

	std::string line;
	std::ifstream data(dataFile.c_str(), std::ifstream::in);

	int yBin = 0;
	while (std::getline(data >> std::ws, line, '\n')) {
	std::vector<double> entries = GeneralUtils::ParseToDbl(line, " ");

	// Loop over entries and insert them into the histogram
	for (uint xBin = 0; xBin < entries.size(); xBin++) {
	- if (!skipbins or entries[xBin] != -1.0)
	+ if (!skipbins \|\| entries[xBin] != -1.0)
	hist->SetBinContent(xBin + 1, yBin + 1, entries[xBin] * norm);
	}
	yBin++;
	}

	return;
	}

	// MOVE TO GENERAL UTILS
	TH1D* PlotUtils::GetTH1DFromFile(std::string dataFile, std::string title,
	std::string fPlotTitles,
	std::string alt_name) {
	TH1D* tempPlot;

	// If format is a root file
	if (dataFile.find(".root") != std::string::npos) {
	TFile* temp_infile = new TFile(dataFile.c_str(), "READ");
	tempPlot = (TH1D*)temp_infile->Get(title.c_str());
	tempPlot->SetDirectory(0);

	temp_infile->Close();
	delete temp_infile;

	// Else its a space seperated txt file
	} else {
	// Make a TGraph Errors
	TGraphErrors* gr = new TGraphErrors(dataFile.c_str(), "%lg %lg %lg");
	if (gr->IsZombie()) {
	THROW(dataFile << " is a zombie and could not be read. Are you sure it exists?" << std::endl);
	}
	double* bins = gr->GetX();
	double* values = gr->GetY();
	double* errors = gr->GetEY();
	int npoints = gr->GetN();

	// Fill the histogram from it
	tempPlot = new TH1D(title.c_str(), title.c_str(), npoints - 1, bins);

	for (int i = 0; i < npoints; ++i) {
	tempPlot->SetBinContent(i + 1, values[i]);

	// If only two columns are present in the input file, use the sqrt(values) as the error
	// equivalent to assuming that the error is statistical. Also check that we're looking at an event rate rather than a cross section
	if (!errors[i] && values[i] > 1E-30) {
	tempPlot->SetBinError(i + 1, sqrt(values[i]));
	} else {
	tempPlot->SetBinError(i + 1, errors[i]);
	}
	}

	delete gr;
	}

	// Allow alternate naming for root files
	if (!alt_name.empty()) {
	tempPlot->SetNameTitle(alt_name.c_str(), alt_name.c_str());
	}

	// Allow alternate axis titles
	if (!fPlotTitles.empty()) {
	tempPlot->SetNameTitle(
	tempPlot->GetName(),
	(std::string(tempPlot->GetTitle()) + fPlotTitles).c_str());
	}

	return tempPlot;
	};

	TH1D* PlotUtils::GetRatioPlot(TH1D* hist1, TH1D* hist2) {
	// make copy of first hist
	TH1D* new_hist = (TH1D*)hist1->Clone();

	// Do bins and errors ourselves as scales can go awkward
	for (int i = 0; i < new_hist->GetNbinsX(); i++) {
	if (hist2->GetBinContent(i + 1) == 0.0) {
	new_hist->SetBinContent(i + 1, 0.0);
	}

	new_hist->SetBinContent(
	i + 1, hist1->GetBinContent(i + 1) / hist2->GetBinContent(i + 1));
	new_hist->SetBinError(
	i + 1, hist1->GetBinError(i + 1) / hist2->GetBinContent(i + 1));
	}

	return new_hist;
	};

	TH1D* PlotUtils::GetRenormalisedPlot(TH1D* hist1, TH1D* hist2) {
	// make copy of first hist
	TH1D* new_hist = (TH1D*)hist1->Clone();

	if (hist1->Integral("width") == 0 or hist2->Integral("width") == 0) {
	new_hist->Reset();
	return new_hist;
	}

	Double_t scaleF = hist2->Integral("width") / hist1->Integral("width");
	new_hist->Scale(scaleF);

	return new_hist;
	};

	TH1D* PlotUtils::GetShapePlot(TH1D* hist1) {
	// make copy of first hist
	TH1D* new_hist = (TH1D*)hist1->Clone();

	if (hist1->Integral("width") == 0) {
	new_hist->Reset();
	return new_hist;
	}

	Double_t scaleF1 = 1.0 / hist1->Integral("width");

	new_hist->Scale(scaleF1);

	return new_hist;
	};

	TH1D* PlotUtils::GetShapeRatio(TH1D* hist1, TH1D* hist2) {
	TH1D* new_hist1 = GetShapePlot(hist1);
	TH1D* new_hist2 = GetShapePlot(hist2);

	// Do bins and errors ourselves as scales can go awkward
	for (int i = 0; i < new_hist1->GetNbinsX(); i++) {
	if (hist2->GetBinContent(i + 1) == 0) {
	new_hist1->SetBinContent(i + 1, 0.0);
	}

	new_hist1->SetBinContent(i + 1, new_hist1->GetBinContent(i + 1) /
	new_hist2->GetBinContent(i + 1));
	new_hist1->SetBinError(
	i + 1, new_hist1->GetBinError(i + 1) / new_hist2->GetBinContent(i + 1));
	}

	delete new_hist2;

	return new_hist1;
	};

	TH2D* PlotUtils::GetCovarPlot(TMatrixDSym* cov, std::string name,
	std::string title) {
	TH2D* CovarPlot;

	if (cov)
	CovarPlot = new TH2D((*cov));
	else
	CovarPlot = new TH2D(name.c_str(), title.c_str(), 1, 0, 1, 1, 0, 1);

	CovarPlot->SetName(name.c_str());
	CovarPlot->SetTitle(title.c_str());

	return CovarPlot;
	}

	TH2D* PlotUtils::GetFullCovarPlot(TMatrixDSym* cov, std::string name) {
	return PlotUtils::GetCovarPlot(
	cov, name + "_COV", name + "_COV;Bins;Bins;Covariance (#times10^{-76})");
	}

	TH2D* PlotUtils::GetInvCovarPlot(TMatrixDSym* cov, std::string name) {
	return PlotUtils::GetCovarPlot(
	cov, name + "_INVCOV",
	name + "_INVCOV;Bins;Bins;Inv. Covariance (#times10^{-76})");
	}

	TH2D* PlotUtils::GetDecompCovarPlot(TMatrixDSym* cov, std::string name) {
	return PlotUtils::GetCovarPlot(
	cov, name + "_DECCOV",
	name + "_DECCOV;Bins;Bins;Decomp Covariance (#times10^{-76})");
	}

	TH1D* PlotUtils::GetTH1DFromRootFile(std::string file, std::string name) {
	if (name.empty()) {
	std::vector<std::string> tempfile = GeneralUtils::ParseToStr(file, ";");
	file = tempfile[0];
	name = tempfile[1];
	}

	TFile* rootHistFile = new TFile(file.c_str(), "READ");
	TH1D* tempHist = (TH1D*)rootHistFile->Get(name.c_str())->Clone();
	if (tempHist == NULL) {
	ERR(FTL) << "Could not find distribution " << name << " in file " << file << std::endl;
	throw;
	}
	tempHist->SetDirectory(0);

	rootHistFile->Close();

	return tempHist;
	}

	TH2D* PlotUtils::GetTH2DFromRootFile(std::string file, std::string name) {
	if (name.empty()) {
	std::vector<std::string> tempfile = GeneralUtils::ParseToStr(file, ";");
	file = tempfile[0];
	name = tempfile[1];
	}

	TFile* rootHistFile = new TFile(file.c_str(), "READ");
	TH2D* tempHist = (TH2D*)rootHistFile->Get(name.c_str())->Clone();
	tempHist->SetDirectory(0);

	rootHistFile->Close();
	delete rootHistFile;

	return tempHist;
	}

	TH1* PlotUtils::GetTH1FromRootFile(std::string file, std::string name) {
	if (name.empty()) {
	std::vector<std::string> tempfile = GeneralUtils::ParseToStr(file, ";");
	file = tempfile[0];
	name = tempfile[1];
	}

	TFile* rootHistFile = new TFile(file.c_str(), "READ");
	if (!rootHistFile \|\| rootHistFile->IsZombie()) {
	THROW("Couldn't open root file: \"" << file << "\".");
	}
	TH1* tempHist = dynamic_cast<TH1*>(rootHistFile->Get(name.c_str())->Clone());
	if (!tempHist) {
	THROW("Couldn't retrieve: \"" << name << "\" from root file: \"" << file
	<< "\".");
	}
	tempHist->SetDirectory(0);

	rootHistFile->Close();
	delete rootHistFile;

	return tempHist;
	}

	TGraph* PlotUtils::GetTGraphFromRootFile(std::string file, std::string name) {
	if (name.empty()) {
	std::vector<std::string> tempfile = GeneralUtils::ParseToStr(file, ";");
	file = tempfile[0];
	name = tempfile[1];
	}

	TDirectory* olddir = gDirectory;

	TFile* rootHistFile = new TFile(file.c_str(), "READ");
	if (!rootHistFile \|\| rootHistFile->IsZombie()) {
	THROW("Couldn't open root file: \"" << file << "\".");
	}
	TDirectory* newdir = gDirectory;

	TGraph* temp = dynamic_cast<TGraph*>(rootHistFile->Get(name.c_str())->Clone());
	if (!temp) {
	THROW("Couldn't retrieve: \"" << name << "\" from root file: \"" << file
	<< "\".");
	}
	newdir->Remove(temp);
	olddir->Append(temp);
	rootHistFile->Close();
	olddir->cd();
	return temp;
	}


	/// Returns a vector of named TH1*s found in a single input file.
	///
	/// Expects a descriptor like: file.root[hist1\|hist2\|...]
	std::vector<TH1*> PlotUtils::GetTH1sFromRootFile(
	std::string const& descriptor) {
	std::vector<std::string> descriptors =
	GeneralUtils::ParseToStr(descriptor, ",");

	std::vector<TH1*> hists;
	for (size_t d_it = 0; d_it < descriptors.size(); ++d_it) {
	std::string& d = descriptors[d_it];

	std::vector<std::string> fname = GeneralUtils::ParseToStr(d, "[");
	if (!fname.size() \|\| !fname[0].length()) {
	THROW("Couldn't find input file when attempting to parse : \""
	<< d << "\". Expected input.root[hist1\|hist2\|...].");
	}

	if (fname[1][fname[1].length() - 1] == ']') {
	fname[1] = fname[1].substr(0, fname[1].length() - 1);
	}
	std::vector<std::string> histnames =
	GeneralUtils::ParseToStr(fname[1], "\|");
	if (!histnames.size()) {
	THROW(
	"Couldn't find any histogram name specifiers when attempting to "
	"parse "
	": \""
	<< fname[1] << "\". Expected hist1\|hist2\|...");
	}

	TFile* rootHistFile = new TFile(fname[0].c_str(), "READ");
	if (!rootHistFile \|\| rootHistFile->IsZombie()) {
	THROW("Couldn't open root file: \"" << fname[0] << "\".");
	}

	for (size_t i = 0; i < histnames.size(); ++i) {
	TH1* tempHist =
	dynamic_cast<TH1*>(rootHistFile->Get(histnames[i].c_str())->Clone());
	if (!tempHist) {
	THROW("Couldn't retrieve: \"" << histnames[i] << "\" from root file: \""
	<< fname[0] << "\".");
	}
	tempHist->SetDirectory(0);
	hists.push_back(tempHist);
	}
	rootHistFile->Close();
	}

	return hists;
	}

	-TH2D* PlotUtils::GetTH2DFromTextFile(std::string file) {
	- /// Contents should be
	- /// Low Edfe
	+// Create an array from an input file
	+std::vector<double> PlotUtils::GetArrayFromTextFile(std::string DataFile) {
	+ std::string line;
	+ std::ifstream data(DataFile.c_str(), std::ifstream::in);
	+ // Get first line
	+ std::getline(data >> std::ws, line, '\n');
	+ // Convert from a string into a vector of double
	+ std::vector<double> entries = GeneralUtils::ParseToDbl(line, " ");
	+ return entries;
	+}
	+
	+// Get a 2D array from a text file
	+std::vector<std::vector<double> > PlotUtils::Get2DArrayFromTextFile(std::string DataFile) {
	+ std::string line;
	+ std::vector<std::vector<double> > DataArray;
	+ std::ifstream data(DataFile.c_str(), std::ifstream::in);
	+ while (std::getline(data >> std::ws, line, '\n')) {
	+ std::vector<double> entries = GeneralUtils::ParseToDbl(line, " ");
	+ DataArray.push_back(entries);
	+ }
	+ return DataArray;
	+}
	+
	+TH2D* PlotUtils::GetTH2DFromTextFile(std::string data, std::string binx, std::string biny) {
	+
	+ // First read in the binning
	+ // Array of x binning
	+ std::vector<double> xbins = GetArrayFromTextFile(binx);
	+
	+ // Array of y binning
	+ std::vector<double> ybins = GetArrayFromTextFile(biny);
	+
	+ // Read in the data
	+ std::vector<std::vector<double> > Data = Get2DArrayFromTextFile(data);
	+
	+ // And finally fill the data
	+ TH2D* DataPlot = new TH2D("TempHist", "TempHist", xbins.size()-1, &xbins[0], ybins.size()-1, &ybins[0]);
	+ int nBinsX = 0;
	+ int nBinsY = 0;
	+ for (std::vector<std::vector<double> >::iterator it = Data.begin();
	+ it != Data.end(); ++it) {
	+ nBinsX++;
	+ // Get the inner vector
	+ std::vector<double> temp = *it;
	+
	+ // Save the previous number[of bins to make sure it's uniform binning
	+ int oldBinsY = nBinsY;
	+ // Reset the counter
	+ nBinsY = 0;
	+ for (std::vector<double>::iterator jt = temp.begin();
	+ jt != temp.end(); ++jt) {
	+ nBinsY++;
	+ DataPlot->SetBinContent(nBinsX, nBinsY, *jt);
	+ DataPlot->SetBinError(nBinsX, nBinsY, 0.0);
	+ }
	+ if (oldBinsY > 0 && oldBinsY != nBinsY) {
	+ ERR(FTL) << "Found non-uniform y-binning in " << data << std::endl;
	+ ERR(FTL) << "Previous slice: " << oldBinsY << std::endl;
	+ ERR(FTL) << "Current slice: " << nBinsY << std::endl;
	+ ERR(FTL) << "Non-uniform binning is not supported in PlotUtils::GetTH2DFromTextFile" << std::endl;
	+ throw;
	+ }
	+ }
	+
	+ // Check x bins
	+ if (size_t(nBinsX+1) != xbins.size()) {
	+ ERR(FTL) << "Number of x bins in data histogram does not match the binning histogram!" << std::endl;
	+ ERR(FTL) << "Are they the wrong way around (i.e. xbinning should be ybinning)?" << std::endl;
	+ ERR(FTL) << "Data: " << nBinsX << std::endl;
	+ ERR(FTL) << "From " << binx << " binning: " << xbins.size() << std::endl;
	+ throw;
	+ }
	+
	+ // Check y bins
	+ if (size_t(nBinsY+1) != ybins.size()) {
	+ ERR(FTL) << "Number of y bins in data histogram does not match the binning histogram!" << std::endl;
	+ ERR(FTL) << "Are they the wrong way around (i.e. xbinning should be ybinning)?" << std::endl;
	+ ERR(FTL) << "Data: " << nBinsY << std::endl;
	+ ERR(FTL) << "From " << biny << " binning: " << ybins.size() << std::endl;
	+ throw;
	+ }
	+
	+ return DataPlot;
	+}
	+
	+TH1D* PlotUtils::GetSliceY(TH2D *Hist, int SliceNo) {
	+ TH1D *Slice = Hist->ProjectionX(Form("%s_SLICEY%i", Hist->GetName(), SliceNo), SliceNo, SliceNo, "e");
	+ Slice->SetTitle(Form("%s, %.2f-%.2f", Hist->GetYaxis()->GetTitle(), Hist->GetYaxis()->GetBinLowEdge(SliceNo), Hist->GetYaxis()->GetBinLowEdge(SliceNo+1)));
	+ Slice->GetYaxis()->SetTitle(Hist->GetZaxis()->GetTitle());
	+ return Slice;
	+}

	- return NULL;
	+TH1D* PlotUtils::GetSliceX(TH2D *Hist, int SliceNo) {
	+ TH1D *Slice = Hist->ProjectionY(Form("%s_SLICEX%i", Hist->GetName(), SliceNo), SliceNo, SliceNo, "e");
	+ Slice->SetTitle(Form("%s, %.2f-%.2f", Hist->GetXaxis()->GetTitle(), Hist->GetXaxis()->GetBinLowEdge(SliceNo), Hist->GetXaxis()->GetBinLowEdge(SliceNo+1)));
	+ Slice->GetYaxis()->SetTitle(Hist->GetZaxis()->GetTitle());
	+ return Slice;
	}

	void PlotUtils::AddNeutModeArray(TH1D* hist1[], TH1D* hist2[], double scaling) {
	for (int i = 0; i < 60; i++) {
	if (!hist2[i]) continue;
	if (!hist1[i]) continue;
	hist1[i]->Add(hist2[i], scaling);
	}
	return;
	}

	void PlotUtils::ScaleToData(TH1D* data, TH1D* mc, TH1I* mask) {
	double scaleF = GetDataMCRatio(data, mc, mask);
	mc->Scale(scaleF);

	return;
	}

	void PlotUtils::MaskBins(TH1D* hist, TH1I* mask) {
	for (int i = 0; i < hist->GetNbinsX(); i++) {
	if (mask->GetBinContent(i + 1) <= 0.5) continue;

	hist->SetBinContent(i + 1, 0.0);
	hist->SetBinError(i + 1, 0.0);

	LOG(REC) << "MaskBins: Set " << hist->GetName() << " Bin " << i + 1
	<< " to 0.0 +- 0.0" << std::endl;
	}

	return;
	}

	void PlotUtils::MaskBins(TH2D* hist, TH2I* mask) {
	for (int i = 0; i < hist->GetNbinsX(); i++) {
	for (int j = 0; j < hist->GetNbinsY(); j++) {
	if (mask->GetBinContent(i + 1, j + 1) <= 0.5) continue;

	hist->SetBinContent(i + 1, j + 1, 0.0);
	hist->SetBinError(i + 1, j + 1, 0.0);

	LOG(REC) << "MaskBins: Set " << hist->GetName() << " Bin " << i + 1 << " "
	<< j + 1 << " to 0.0 +- 0.0" << std::endl;
	}
	}
	return;
	}

	double PlotUtils::GetDataMCRatio(TH1D* data, TH1D* mc, TH1I* mask) {
	double rat = 1.0;

	TH1D* newmc = (TH1D*)mc->Clone();
	TH1D* newdt = (TH1D*)data->Clone();

	if (mask) {
	MaskBins(newmc, mask);
	MaskBins(newdt, mask);
	}

	rat = newdt->Integral() / newmc->Integral();

	return rat;
	}

	TH2D* PlotUtils::GetCorrelationPlot(TH2D* cov, std::string name) {
	TH2D* cor = (TH2D*)cov->Clone();
	cor->Reset();

	for (int i = 0; i < cov->GetNbinsX(); i++) {
	for (int j = 0; j < cov->GetNbinsY(); j++) {
	if (cov->GetBinContent(i + 1, i + 1) != 0.0 and
	cov->GetBinContent(j + 1, j + 1) != 0.0)
	cor->SetBinContent(i + 1, j + 1,
	cov->GetBinContent(i + 1, j + 1) /
	(sqrt(cov->GetBinContent(i + 1, i + 1) *
	cov->GetBinContent(j + 1, j + 1))));
	}
	}

	if (!name.empty()) {
	cor->SetNameTitle(name.c_str(), (name + ";;correlation").c_str());
	}

	cor->SetMinimum(-1);
	cor->SetMaximum(1);

	return cor;
	}

	TH2D* PlotUtils::GetDecompPlot(TH2D* cov, std::string name) {
	TMatrixDSym* covarmat = new TMatrixDSym(cov->GetNbinsX());

	for (int i = 0; i < cov->GetNbinsX(); i++)
	for (int j = 0; j < cov->GetNbinsY(); j++)
	(*covarmat)(i, j) = cov->GetBinContent(i + 1, j + 1);

	TMatrixDSym* decompmat = StatUtils::GetDecomp(covarmat);

	TH2D* dec = (TH2D*)cov->Clone();
	for (int i = 0; i < cov->GetNbinsX(); i++)
	for (int j = 0; j < cov->GetNbinsY(); j++)
	dec->SetBinContent(i + 1, j + 1, (*decompmat)(i, j));

	delete covarmat;
	delete decompmat;

	dec->SetNameTitle(name.c_str(), (name + ";;;decomposition").c_str());

	return dec;
	}

	TH2D* PlotUtils::MergeIntoTH2D(TH1D* xhist, TH1D* yhist, std::string zname) {
	std::vector<double> xedges, yedges;
	for (int i = 0; i < xhist->GetNbinsX() + 2; i++) {
	xedges.push_back(xhist->GetXaxis()->GetBinLowEdge(i + 1));
	}
	for (int i = 0; i < yhist->GetNbinsX() + 2; i++) {
	yedges.push_back(yhist->GetXaxis()->GetBinLowEdge(i + 1));
	}

	int nbinsx = xhist->GetNbinsX();
	int nbinsy = yhist->GetNbinsX();

	std::string name =
	std::string(xhist->GetName()) + "_vs_" + std::string(yhist->GetName());
	std::string titles = ";" + std::string(xhist->GetXaxis()->GetTitle()) + ";" +
	std::string(yhist->GetXaxis()->GetTitle()) + ";" + zname;

	TH2D* newplot = new TH2D(name.c_str(), (name + titles).c_str(), nbinsx,
	&xedges[0], nbinsy, &yedges[0]);

	return newplot;
	}

	//***************************************************
	void PlotUtils::MatchEmptyBins(TH1D* data, TH1D* mc) {
	//**************************************************

	for (int i = 0; i < data->GetNbinsX(); i++) {
	if (data->GetBinContent(i + 1) == 0.0 or data->GetBinError(i + 1) == 0.0)
	mc->SetBinContent(i + 1, 0.0);
	}

	return;
	}

	//***************************************************
	void PlotUtils::MatchEmptyBins(TH2D* data, TH2D* mc) {
	//**************************************************

	for (int i = 0; i < data->GetNbinsX(); i++) {
	for (int j = 0; j < data->GetNbinsY(); j++) {
	if (data->GetBinContent(i + 1, j + 1) == 0.0 or
	data->GetBinError(i + 1, j + 1) == 0.0)
	mc->SetBinContent(i + 1, j + 1, 0.0);
	}
	}

	return;
	}

	//***************************************************
	TH1D* PlotUtils::GetProjectionX(TH2D* hist, TH2I* mask) {
	//***************************************************

	TH2D* maskedhist = StatUtils::ApplyHistogramMasking(hist, mask);

	+ // This includes the underflow/overflow
	TH1D* hist_X = maskedhist->ProjectionX();

	delete maskedhist;
	return hist_X;
	}

	//***************************************************
	TH1D* PlotUtils::GetProjectionY(TH2D* hist, TH2I* mask) {
	//***************************************************

	TH2D* maskedhist = StatUtils::ApplyHistogramMasking(hist, mask);

	+ // This includes the underflow/overflow
	TH1D* hist_Y = maskedhist->ProjectionY();

	delete maskedhist;
	return hist_Y;
	}
	diff --git a/src/Utils/PlotUtils.h b/src/Utils/PlotUtils.h
	index 38955e3..981c986 100644
	--- a/src/Utils/PlotUtils.h
	+++ b/src/Utils/PlotUtils.h
	@@ -1,243 +1,251 @@
	// Copyright 2016 L. Pickering, P Stowell, R. Terri, C. Wilkinson, C. Wret

	/*******************************************************************************
	* This file is part of NUISANCE.
	*
	* NUISANCE 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 3 of the License, or
	* (at your option) any later version.
	*
	* NUISANCE 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 NUISANCE. If not, see <http://www.gnu.org/licenses/>.
	*******************************************************************************/

	#ifndef PLOTUTILS_H_SEEN
	#define PLOTUTILS_H_SEEN

	#include "TF1.h"
	#include "TFile.h"
	#include "TH1.h"
	#include "TMatrixD.h"
	#include "TProfile.h"
	#include "TSystem.h"
	#include "TVectorD.h"

	#include <cstring>
	#include <iostream>
	#include <sstream>
	#include <string>
	#include <vector>

	// C Includes
	#include <math.h>
	#include <stdlib.h>
	#include <unistd.h>
	#include <cstring>
	#include <iostream>
	#include <iostream>
	#include <numeric>
	#include <sstream>
	#include <string>
	#include <vector>

	// ROOT includes
	#include <TChain.h>
	#include <TFile.h>
	#include <TH1D.h>
	#include <TH2D.h>
	#include <THStack.h>
	#include <TKey.h>
	#include <TLegend.h>
	#include <TList.h>
	#include <TLorentzVector.h>
	#include <TObjArray.h>
	#include <TROOT.h>
	#include <TRandom3.h>
	#include <TTree.h>
	#include <ctime>
	#include "TGraphErrors.h"
	#include "TH2Poly.h"
	#include "TMatrixDSym.h"

	// Fit includes
	#include "FitEvent.h"
	#include "FitLogger.h"
	#include "GeneralUtils.h"
	#include "StatUtils.h"

	/*!
	* \addtogroup Utils
	* @{
	*/

	//! Functions to handle different TH1s and TFiles
	namespace PlotUtils {

	/*!
	MISC Functions
	*/

	//! Check the root file has an object containing the given substring in its name
	bool CheckObjectWithName(TFile* inFile, std::string substring);

	//! Get object in a TFile that has a matching substring in its name
	std::string GetObjectWithName(TFile* inFile, std::string substring);

	/*!
	Interaction Mode Histogram Handling
	*/

	//! Fill the Histogram Array with 61 new histograms for interaction channels.
	void CreateNeutModeArray(TH1* hist, TH1* neutarray[]);

	//! Call Fill on the relevent Mode 1D Histogram
	void FillNeutModeArray(TH1D* hist[], int mode, double xval,
	double weight = 1.0);

	//! Call Fill on the relevant Mode 2D Histogram
	void FillNeutModeArray(TH2D* hist[], int mode, double xval, double yval,
	double weight = 1.0);

	//! Given two arrays of histograms for the NEUT interaction mode, hist1 = hist1
	//! + scale*hist2
	void AddNeutModeArray(TH1D* hist1[], TH1D* hist2[], double scaling = 1.0);

	//! Generate a legend for the THStack
	TLegend GenerateStackLegend(THStack stack, int xlow, int ylow, int xhigh,
	int yhigh);

	//! Turn the array of TH1 histograms into a stack of Modes
	THStack GetNeutModeStack(std::string title, TH1* ModeStack[], int option);

	+//! Get a slice in Y of a TH2D
	+TH1D* GetSliceY(TH2D*, int);
	+//! Get a slice in X of a TH2D
	+TH1D* GetSliceX(TH2D*, int);
	+
	//! Reset each histogram in the mode array
	void ResetNeutModeArray(TH1* hist[]);

	//! Scale each histogram in the mode array by a single scaling factor, option
	//! can be used to define "width" scaling.
	void ScaleNeutModeArray(TH1* hist[], double factor, std::string option = "");

	//! Free up the memory used by each of the 61 mode histograms
	void DeleteNeutModeArray(TH1* neutarray[]);

	/*!
	Handling Functions
	*/

	//! Fill a mask histogram from a text file
	TH2D* SetMaskHist(std::string type, TH2D* data);

	//! Divide by the flux histogram for Enu Histograms
	void DivideByFlux(TH1D* fMCHist, TH1D* fFluxHist);

	TH1D* InterpolateFineHistogram(TH1D* hist, int res, std::string opt);

	//! Flux unfolded scaling, like DivideByFlux but uses interpolation.
	void FluxUnfoldedScaling(TH1D* plot, TH1D* flux, TH1D* events = NULL,
	double scalefactor = 1.0, int nevents = 1);

	//! Flux unfolded scaling for 2D histograms
	void FluxUnfoldedScaling(TH2D* plot, TH1D* flux, TH1D* events = NULL,
	double scalefactor = 1.0);

	//! Fill a 2D Histogram from a text file
	void Set2DHistFromText(std::string dataFile, TH2* hist, double norm,
	bool skipbins = false);

	//! Fill a 2D Poly Histogram from a text file
	void Set2PolyHistFromText(std::string dataFile, TH2Poly* hist, double norm,
	bool skipbins = false);

	//! Fill a 1D Histogram from a text file
	TH1D* GetTH1DFromFile(std::string dataFile, std::string title = "",
	std::string fPlotTitles = "", std::string alt_name = "");

	TH1* GetTH1FromRootFile(std::string file, std::string name);

	std::vector<TH1*> GetTH1sFromRootFile(std::string const& descriptor);

	//! Grab a 1D Histrogram from a ROOT File
	TH1D* GetTH1DFromRootFile(std::string file, std::string name);

	//! Grab a 2D Histrogram from a ROOT File
	TH2D* GetTH2DFromRootFile(std::string file, std::string name);

	//! Get a TGraph from a ROOT file
	TGraph* GetTGraphFromRootFile(std::string file, std::string name);

	//! Grab a 2D Histrogram from a ROOT File
	-TH2D* GetTH2DFromTextFile(std::string file);
	+TH2D* GetTH2DFromTextFile(std::string data, std::string binx, std::string biny);
	+
	+std::vector<double> GetArrayFromTextFile(std::string file);
	+std::vector<std::vector<double> > Get2DArrayFromTextFile(std::string file);

	//! Scale mc to match data considering empty and masked bins
	void ScaleToData(TH1D* data, TH1D* mc, TH1I* mask);

	//! Apply bin masking (More cosmetic)
	void MaskBins(TH1D* hist, TH1I* mask);

	//! Apply bin masking (More cosmetic)
	void MaskBins(TH2D* hist, TH2I* mask);

	//! Get the data MC ratio considering empty and masked bins
	double GetDataMCRatio(TH1D* data, TH1D* mc, TH1I* mask = NULL);

	/*!
	Formatting Plot Utils
	*/

	//! Create new ratio plot. hist3 = hist1/hist2
	TH1D* GetRatioPlot(TH1D* hist1, TH1D* hist2);

	//! Create new plot of hist2 normalised to hist1. hist2 = hist1 *
	//! (Integral(hist1)/Integral(hist2))
	TH1D* GetRenormalisedPlot(TH1D* hist1, TH1D* hist2);

	//! Normalise histogram to area of unity.
	TH1D* GetShapePlot(TH1D* hist1);

	//! Normalise hist1 and hist2 to unity, before creating a new plot of their
	//! ratio.
	TH1D* GetShapeRatio(TH1D* hist1, TH1D* hist2);

	//! Create a covariance histogram from a TMatrixDSym and add titles given.
	TH2D* GetCovarPlot(TMatrixDSym* cov, std::string name, std::string title);

	//! Wrapper function to create full covariance plot
	TH2D* GetFullCovarPlot(TMatrixDSym* cov, std::string name);

	//! Wrapper function to create inverted covariance plot
	TH2D* GetInvCovarPlot(TMatrixDSym* cov, std::string name);

	//! Wrapper function to create decomposed covariance plot
	TH2D* GetDecompCovarPlot(TMatrixDSym* cov, std::string name);

	//! Given a covariance histogram, divide by errors to form a correlation plot.
	TH2D* GetCorrelationPlot(TH2D* cov, std::string name);

	//! Given a covariance histogram, calculate the decomposed matrix to form a
	//! decomposed plot.
	TH2D* GetDecompPlot(TH2D* cov, std::string name);

	//! Given two 1D histograms create a 2D histogram which uses their bin edges to
	//! define both axes.
	TH2D* MergeIntoTH2D(TH1D* xhist, TH1D* yhist, std::string zname = "");

	//! Given a 1D Histogram, set any empty bins in Data to empty bins in MC
	void MatchEmptyBins(TH1D* data, TH1D* mc);

	//! Given a 2D Histogram, set any empty bins in Data to empty bins in MC
	void MatchEmptyBins(TH2D* data, TH2D* mc);

	//! Return a projection of a 2D Histogram onto X accounting for bin masking
	TH1D* GetProjectionX(TH2D* hist, TH2I* mask);

	//! Return a projection of a 2D Histogram onto Y accounting for bin masking
	TH1D* GetProjectionY(TH2D* hist, TH2I* mask);
	}

	/! @} /
	#endif

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