diff --git a/src/FitBase/Measurement2D.cxx b/src/FitBase/Measurement2D.cxx
index 4c3a6df..33fdd0f 100644
--- a/src/FitBase/Measurement2D.cxx
+++ b/src/FitBase/Measurement2D.cxx
@@ -1,1961 +1,1961 @@
 // 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 "Measurement2D.h"
 #include "TDecompChol.h"
 
 
 //********************************************************************
 Measurement2D::Measurement2D(void) {
 //********************************************************************
 
   covar = NULL;
   fDecomp = NULL;
   fFullCovar = NULL;
 
   fMCHist = NULL;
   fMCFine = NULL;
   fDataHist = NULL;
 
   fMCHist_X = NULL;
   fMCHist_Y = NULL;
   fDataHist_X = NULL;
   fDataHist_Y = NULL;
 
   fMaskHist = NULL;
   fMapHist = NULL;
   fDataOrig = NULL;
   fDataTrue = NULL;
   fMCWeighted = NULL;
 
   fDefaultTypes = "FIX/FULL/CHI2";
   fAllowedTypes =
     "FIX,FREE,SHAPE/FULL,DIAG/CHI2/NORM/ENUCORR/Q2CORR/ENU1D/FITPROJX/"
     "FITPROJY";
 
   fIsFix = false;
   fIsShape = false;
   fIsFree = false;
 
   fIsDiag = false;
   fIsFull = false;
 
   fAddNormPen = false;
   fIsMask = false;
   fIsChi2SVD = false;
 
   fIsRawEvents = false;
   fIsDifXSec = false;
   fIsEnu = false;
 
 
   // XSec Scalings
   fScaleFactor = -1.0;
   fCurrentNorm = 1.0;
 
   // Histograms
   fDataHist = NULL;
   fDataTrue = NULL;
 
   fMCHist = NULL;
   fMCFine = NULL;
   fMCWeighted = NULL;
 
   fMaskHist = NULL;
 
   // Covar
   covar = NULL;
   fFullCovar = NULL;
 
   fCovar  = NULL;
   fInvert = NULL;
   fDecomp = NULL;
 
   // Fake Data
   fFakeDataInput = "";
   fFakeDataFile  = NULL;
 
   // Options
   fDefaultTypes = "FIX/FULL/CHI2";
   fAllowedTypes =
     "FIX,FREE,SHAPE/FULL,DIAG/CHI2/NORM/ENUCORR/Q2CORR/ENU1D/MASK";
 
   fIsFix = false;
   fIsShape = false;
   fIsFree = false;
   fIsDiag = false;
   fIsFull = false;
   fAddNormPen = false;
   fIsMask = false;
   fIsChi2SVD = false;
   fIsRawEvents = false;
   fIsDifXSec = false;
   fIsEnu1D = false;
 
   // Inputs
   fInput = NULL;
   fRW = NULL;
 
   // Extra Histograms
   fMCHist_Modes = NULL;
 
 }
 
 //********************************************************************
 Measurement2D::~Measurement2D(void) {
 //********************************************************************
 
   if (fDataHist)   delete fDataHist;
   if (fDataTrue)   delete fDataTrue;
   if (fMCHist)     delete fMCHist;
   if (fMCFine)     delete fMCFine;
   if (fMCWeighted) delete fMCWeighted;
   if (fMaskHist)   delete fMaskHist;
   if (covar)       delete covar;
   if (fFullCovar)  delete fFullCovar;
   if (fCovar)      delete fCovar;
   if (fInvert)     delete fInvert;
   if (fDecomp)     delete fDecomp;
 
 }
 
 //********************************************************************
 void Measurement2D::FinaliseSampleSettings() {
 //********************************************************************
 
   MeasurementBase::FinaliseSampleSettings();
 
   // Setup naming + renaming
   fName = fSettings.GetName();
   fSettings.SetS("originalname", fName);
   if (fSettings.Has("rename")) {
     fName = fSettings.GetS("rename");
     fSettings.SetS("name", fName);
   }
 
   // Setup all other options
   LOG(SAM) << "Finalising Sample Settings: " << fName << std::endl;
 
   if ((fSettings.GetS("originalname").find("Evt") != std::string::npos)) {
     fIsRawEvents = true;
     LOG(SAM) << "Found event rate measurement but using poisson likelihoods."
              << std::endl;
   }
 
   if (fSettings.GetS("originalname").find("XSec_1DEnu") != std::string::npos) {
     fIsEnu1D = true;
     LOG(SAM) << "::" << fName << "::" << std::endl;
     LOG(SAM) << "Found XSec Enu measurement, applying flux integrated scaling, "
              << "not flux averaged!" << std::endl;
   }
 
   if (fIsEnu1D && fIsRawEvents) {
     LOG(SAM) << "Found 1D Enu XSec distribution AND fIsRawEvents, is this "
              "really correct?!"
              << std::endl;
     LOG(SAM) << "Check experiment constructor for " << fName
              << " and correct this!" << std::endl;
     LOG(SAM) << "I live in " << __FILE__ << ":" << __LINE__ << std::endl;
     exit(-1);
   }
 
   if (!fRW) fRW = FitBase::GetRW();
   if (!fInput) SetupInputs(fSettings.GetS("input"));
 
   // Setup options
   SetFitOptions(fDefaultTypes); // defaults
   SetFitOptions(fSettings.GetS("type")); // user specified
 
   EnuMin = GeneralUtils::StrToDbl(fSettings.GetS("enu_min"));
   EnuMax = GeneralUtils::StrToDbl(fSettings.GetS("enu_max"));
 
   if (fAddNormPen) {
     fNormError = fSettings.GetNormError();
     if (fNormError <= 0.0) {
       ERR(WRN) << "Norm error for class " << fName << " is 0.0!" << std::endl;
       ERR(WRN) << "If you want to use it please add fNormError=VAL" << std::endl;
       throw;
     }
   }
 
 }
 
 void Measurement2D::CreateDataHistogram(int dimx, double* binx, int dimy, double* biny) {
   if (fDataHist) delete fDataHist;
 
   LOG(SAM) << "Creating Data Histogram dim : " << dimx << " " << dimy << std::endl;
 
   fDataHist = new TH2D( (fSettings.GetName() + "_data").c_str(), (fSettings.GetFullTitles()).c_str(),
                         dimx - 1, binx, dimy - 1, biny );
 
 }
 
 void Measurement2D::SetDataFromTextFile(std::string datfile) {
   // fDataHist = PlotUtils::GetTH2DFromTextFile(datfile,"");
 }
 
 void Measurement2D::SetDataFromRootFile(std::string datfile, std::string histname) {
   fDataHist = PlotUtils::GetTH2DFromRootFile(datfile, histname);
 }
 
 void Measurement2D::SetDataValuesFromTextFile(std::string datfile, TH2D* hist) {
 
   LOG(SAM) << "Setting data values from text file" << std::endl;
   if (!hist) hist = fDataHist;
 
   // Read TH2D From textfile
   TH2D* valhist = (TH2D*) hist->Clone();
   valhist->Reset();
   PlotUtils::Set2DHistFromText(datfile, valhist, 1.0, true);
 
   LOG(SAM) << " -> Filling values from read hist." << std::endl;
   for (int i = 0; i < valhist->GetNbinsX(); i++) {
     for (int j = 0; j < valhist->GetNbinsY(); j++) {
       hist->SetBinContent(i + 1, j + 1, valhist->GetBinContent(i + 1, j + 1));
     }
   }
   LOG(SAM) << " --> Done" << std::endl;
 }
 
 void Measurement2D::SetDataErrorsFromTextFile(std::string datfile, TH2D* hist) {
   LOG(SAM) << "Setting data errors from text file" << std::endl;
 
   if (!hist) hist = fDataHist;
 
   // Read TH2D From textfile
   TH2D* valhist = (TH2D*) hist->Clone();
   valhist->Reset();
   PlotUtils::Set2DHistFromText(datfile, valhist, 1.0);
 
   // Fill Errors
   LOG(SAM) << " -> Filling errors from read hist." << std::endl;
 
   for (int i = 0; i < valhist->GetNbinsX(); i++) {
     for (int j = 0; j < valhist->GetNbinsY(); j++) {
       hist->SetBinError(i + 1, j + 1, valhist->GetBinContent(i + 1, j + 1));
     }
   }
   LOG(SAM) << " --> Done" << std::endl;
 
 
 }
 
 void Measurement2D::SetMapValuesFromText(std::string dataFile) {
 
   TH2D* hist = fDataHist;
   std::vector<double> edgex;
   std::vector<double> edgey;
 
   for (int i = 0; i <= hist->GetNbinsX(); i++) edgex.push_back(hist->GetXaxis()->GetBinLowEdge(i + 1));
   for (int i = 0; i <= hist->GetNbinsY(); i++) edgey.push_back(hist->GetYaxis()->GetBinLowEdge(i + 1));
 
 
   fMapHist = new TH2I((fName + "_map").c_str(), (fName + fPlotTitles).c_str(),
                       edgex.size() - 1, &edgex[0], edgey.size() - 1, &edgey[0]);
 
   LOG(SAM) << "Reading map from: " << dataFile << std::endl;
   PlotUtils::Set2DHistFromText(dataFile, fMapHist, 1.0);
 
 }
 
 //********************************************************************
 void Measurement2D::SetPoissonErrors() {
 //********************************************************************
 
   if (!fDataHist) {
     ERR(FTL) << "Need a data hist to setup possion errors! " << std::endl;
     ERR(FTL) << "Setup Data First!" << std::endl;
     throw;
   }
 
   for (int i = 0; i < fDataHist->GetNbinsX() + 1; i++) {
     fDataHist->SetBinError(i + 1, sqrt(fDataHist->GetBinContent(i + 1)));
   }
 }
 
 //********************************************************************
 void Measurement2D::SetCovarFromDiagonal(TH2D* data) {
 //********************************************************************
 
   if (!data and fDataHist) {
     data = fDataHist;
   }
 
   if (data) {
     LOG(SAM) << "Setting diagonal covariance for: " << data->GetName() << std::endl;
     fFullCovar = StatUtils::MakeDiagonalCovarMatrix(data);
     covar      = StatUtils::GetInvert(fFullCovar);
     fDecomp    = StatUtils::GetDecomp(fFullCovar);
   } else {
     ERR(FTL) << "No data input provided to set diagonal covar from!" << std::endl;
 
   }
 
   // if (!fIsDiag) {
   //   ERR(FTL) << "SetCovarMatrixFromDiag called for measurement "
   //            << "that is not set as diagonal." << std::endl;
   //   throw;
   // }
 
 }
 
 //********************************************************************
 void Measurement2D::SetCovarFromTextFile(std::string covfile, int dim) {
 //********************************************************************
 
   if (dim == -1) {
     dim = this->GetNDOF();
   }
 
   LOG(SAM) << "Reading covariance from text file: " << covfile << std::endl;
   fFullCovar = StatUtils::GetCovarFromTextFile(covfile, dim);
   covar      = StatUtils::GetInvert(fFullCovar);
   fDecomp    = StatUtils::GetDecomp(fFullCovar);
 
 }
 
 //********************************************************************
 void Measurement2D::SetCovarFromRootFile(std::string covfile, std::string histname) {
 //********************************************************************
 
   LOG(SAM) << "Reading covariance from text file: " << covfile << ";" << histname << std::endl;
   fFullCovar = StatUtils::GetCovarFromRootFile(covfile, histname);
   covar      = StatUtils::GetInvert(fFullCovar);
   fDecomp    = StatUtils::GetDecomp(fFullCovar);
 
 }
 
 //********************************************************************
 void Measurement2D::SetCovarInvertFromTextFile(std::string covfile, int dim) {
 //********************************************************************
 
   if (dim == -1) {
     dim = this->GetNDOF();
   }
 
   LOG(SAM) << "Reading inverted covariance from text file: " << covfile << std::endl;
   covar       = StatUtils::GetCovarFromTextFile(covfile, dim);
   fFullCovar  = StatUtils::GetInvert(covar);
   fDecomp     = StatUtils::GetDecomp(fFullCovar);
 
 }
 
 //********************************************************************
 void Measurement2D::SetCovarInvertFromRootFile(std::string covfile, std::string histname) {
 //********************************************************************
 
   LOG(SAM) << "Reading inverted covariance from text file: " << covfile << ";" << histname << std::endl;
   covar      = StatUtils::GetCovarFromRootFile(covfile, histname);
   fFullCovar = StatUtils::GetInvert(covar);
   fDecomp    = StatUtils::GetDecomp(fFullCovar);
 
 }
 
 //********************************************************************
 void Measurement2D::SetCorrelationFromTextFile(std::string covfile, int dim) {
 //********************************************************************
 
   if (dim == -1) dim = this->GetNDOF();
   LOG(SAM) << "Reading data correlations from text file: " << covfile << ";" << dim << std::endl;
   TMatrixDSym* correlation = StatUtils::GetCovarFromTextFile(covfile, dim);
 
   if (!fDataHist) {
     ERR(FTL) << "Trying to set correlations from text file but there is no data to build it from. \n"
              << "In constructor make sure data is set before SetCorrelationFromTextFile is called. \n" << std::endl;
     throw;
   }
 
   // Fill covar from data errors and correlations
   fFullCovar = new TMatrixDSym(dim);
   for (int i = 0; i < fDataHist->GetNbinsX(); i++) {
     for (int j = 0; j < fDataHist->GetNbinsX(); j++) {
       (*fFullCovar)(i, j) = (*correlation)(i, j) * fDataHist->GetBinError(i + 1) * fDataHist->GetBinError(j + 1) * 1.E76;
     }
   }
 
   // Fill other covars.
   covar   = StatUtils::GetInvert(fFullCovar);
   fDecomp = StatUtils::GetDecomp(fFullCovar);
 
   delete correlation;
 }
 
 //********************************************************************
 void Measurement2D::SetCorrelationFromRootFile(std::string covfile, std::string histname) {
 //********************************************************************
 
   LOG(SAM) << "Reading data correlations from text file: " << covfile << ";" << histname << std::endl;
   TMatrixDSym* correlation = StatUtils::GetCovarFromRootFile(covfile, histname);
 
   if (!fDataHist) {
     ERR(FTL) << "Trying to set correlations from text file but there is no data to build it from. \n"
              << "In constructor make sure data is set before SetCorrelationFromTextFile is called. \n" << std::endl;
     throw;
   }
 
   // Fill covar from data errors and correlations
   fFullCovar = new TMatrixDSym(fDataHist->GetNbinsX());
   for (int i = 0; i < fDataHist->GetNbinsX(); i++) {
     for (int j = 0; j < fDataHist->GetNbinsX(); j++) {
       (*fFullCovar)(i, j) = (*correlation)(i, j) * fDataHist->GetBinError(i + 1) * fDataHist->GetBinError(j + 1) * 1.E76;
     }
   }
 
   // Fill other covars.
   covar   = StatUtils::GetInvert(fFullCovar);
   fDecomp = StatUtils::GetDecomp(fFullCovar);
 
   delete correlation;
 }
 
 
 //********************************************************************
 void Measurement2D::SetCholDecompFromTextFile(std::string covfile, int dim) {
 //********************************************************************
 
   if (dim == -1) {
     dim = this->GetNDOF();
   }
 
   LOG(SAM) << "Reading cholesky from text file: " << covfile << " " << dim << std::endl;
   TMatrixD* temp = StatUtils::GetMatrixFromTextFile(covfile, dim, dim);
 
   TMatrixD* trans = (TMatrixD*)temp->Clone();
   trans->T();
   (*trans) *= (*temp);
 
   fFullCovar  = new TMatrixDSym(dim, trans->GetMatrixArray(), "");
   covar       = StatUtils::GetInvert(fFullCovar);
   fDecomp     = StatUtils::GetDecomp(fFullCovar);
 
   delete temp;
   delete trans;
 
 }
 
 //********************************************************************
 void Measurement2D::SetCholDecompFromRootFile(std::string covfile, std::string histname) {
 //********************************************************************
 
   LOG(SAM) << "Reading cholesky decomp from root file: " << covfile << ";" << histname << std::endl;
   TMatrixD* temp = StatUtils::GetMatrixFromRootFile(covfile, histname);
 
   TMatrixD* trans = (TMatrixD*)temp->Clone();
   trans->T();
   (*trans) *= (*temp);
 
   fFullCovar  = new TMatrixDSym(temp->GetNrows(), trans->GetMatrixArray(), "");
   covar       = StatUtils::GetInvert(fFullCovar);
   fDecomp     = StatUtils::GetDecomp(fFullCovar);
 
   delete temp;
   delete trans;
 }
 
 
 //********************************************************************
 void Measurement2D::ScaleData(double scale) {
 //********************************************************************
   fDataHist->Scale(scale);
 }
 
 
 //********************************************************************
 void Measurement2D::ScaleDataErrors(double scale) {
 //********************************************************************
   for (int i = 0; i < fDataHist->GetNbinsX(); i++) {
     for (int j = 0; j < fDataHist->GetNbinsY(); j++) {
       fDataHist->SetBinError(i + 1, j + 1, fDataHist->GetBinError(i + 1, j + 1) * scale);
     }
   }
 }
 
 
 
 //********************************************************************
 void Measurement2D::ScaleCovar(double scale) {
 //********************************************************************
   (*fFullCovar) *= scale;
   (*covar) *= 1.0 / scale;
   (*fDecomp) *= sqrt(scale);
 }
 
 
 //********************************************************************
 void Measurement2D::SetBinMask(std::string maskfile) {
 //********************************************************************
 
   if (!fIsMask) return;
   LOG(SAM) << "Reading bin mask from file: " << maskfile << std::endl;
 
   // Create a mask histogram with dim of data
   int nbinsx = fDataHist->GetNbinsX();
   int nbinxy = fDataHist->GetNbinsY();
   fMaskHist =
     new TH2I((fSettings.GetName() + "_BINMASK").c_str(),
              (fSettings.GetName() + "_BINMASK; Bin; Mask?").c_str(), nbinsx, 0, nbinsx, nbinxy, 0, nbinxy);
   std::string line;
   std::ifstream mask(maskfile.c_str(), ifstream::in);
 
   if (!mask.is_open()) {
     LOG(FTL) << " Cannot find mask file." << std::endl;
     throw;
   }
 
   while (std::getline(mask >> std::ws, line, '\n')) {
     std::vector<int> entries = GeneralUtils::ParseToInt(line, " ");
 
     // Skip lines with poorly formatted lines
     if (entries.size() < 2) {
       LOG(WRN) << "Measurement2D::SetBinMask(), couldn't parse line: " << line
                << std::endl;
       continue;
     }
 
     // The first index should be the bin number, the second should be the mask
     // value.
     int val = 0;
     if (entries[2] > 0) val = 1;
     fMaskHist->SetBinContent(entries[0], entries[1], val);
   }
 
   // Apply masking by setting masked data bins to zero
   PlotUtils::MaskBins(fDataHist, fMaskHist);
 
 
   return;
 }
 
 
 
 //********************************************************************
 void Measurement2D::FinaliseMeasurement() {
 //********************************************************************
 
   LOG(SAM) << "Finalising Measurement: " << fName << std::endl;
   if (fSettings.GetB("onlymc")) {
     if (fDataHist) delete fDataHist;
     fDataHist = new TH2D("empty_data", "empty_data", 1, 0.0, 1.0,1,0.0,1.0);
   }
   // Make sure data is setup
   if (!fDataHist) {
     ERR(FTL) << "No data has been setup inside " << fName << " constructor!" << std::endl;
     throw;
   }
 
   // Make sure covariances are setup
   if (!fFullCovar) {
     fIsDiag = true;
     SetCovarFromDiagonal(fDataHist);
   }
 
   if (!covar) {
     covar = StatUtils::GetInvert(fFullCovar);
   }
 
   if (!fDecomp) {
     fDecomp = StatUtils::GetDecomp(fFullCovar);
   }
 
   // Setup fMCHist from data
   fMCHist = (TH2D*)fDataHist->Clone();
   fMCHist->SetNameTitle((fSettings.GetName() + "_MC").c_str(),
                         (fSettings.GetFullTitles()).c_str());
   fMCHist->Reset();
 
   // Setup fMCFine
   fMCFine = new TH2D("mcfine", "mcfine", fDataHist->GetNbinsX() * 6,
                      fMCHist->GetXaxis()->GetBinLowEdge(1),
                      fMCHist->GetXaxis()->GetBinLowEdge(fDataHist->GetNbinsX() + 1),
                      fDataHist->GetNbinsY() * 6,
                      fMCHist->GetYaxis()->GetBinLowEdge(1),
                      fMCHist->GetYaxis()->GetBinLowEdge(fDataHist->GetNbinsY() + 1));
 
   fMCFine->SetNameTitle((fSettings.GetName() + "_MC_FINE").c_str(),
                         (fSettings.GetFullTitles()).c_str());
   fMCFine->Reset();
 
   // Setup MC Stat
   fMCStat = (TH2D*)fMCHist->Clone();
   fMCStat->Reset();
 
   // Search drawopts for possible types to include by default
   std::string drawopts = FitPar::Config().GetParS("drawopts");
   if (drawopts.find("MODES") != std::string::npos) {
     fMCHist_Modes = new TrueModeStack( (fSettings.GetName() + "_MODES").c_str(),
                                        ("True Channels"), fMCHist);
     SetAutoProcessTH1(fMCHist_Modes);
   }
 
   // Setup bin masks using sample name
   if (fIsMask) {
 
     std::string curname  = fName;
     std::string origname = fSettings.GetS("originalname");
 
     // Check rename.mask
     std::string maskloc = FitPar::Config().GetParDIR(curname + ".mask");
 
     // Check origname.mask
     if (maskloc.empty()) maskloc = FitPar::Config().GetParDIR(origname + ".mask");
 
     // Check database
     if (maskloc.empty()) {
       maskloc = FitPar::GetDataBase() + "/masks/" + origname + ".mask";
     }
 
     // Setup Bin Mask
     SetBinMask(maskloc);
   }
 
   if (fScaleFactor < 0) {
     ERR(FTL) << "I found a negative fScaleFactor in " << __FILE__ << ":" << __LINE__ << std::endl;
     ERR(FTL) << "fScaleFactor = " << fScaleFactor << std::endl;
     ERR(FTL) << "EXITING" << std::endl;
     throw;
   }
 
   // Create and fill Weighted Histogram
   if (!fMCWeighted) {
 
     fMCWeighted = (TH2D*)fMCHist->Clone();
     fMCWeighted->SetNameTitle((fName + "_MCWGHTS").c_str(),
                               (fName + "_MCWGHTS" + fPlotTitles).c_str());
     fMCWeighted->GetYaxis()->SetTitle("Weighted Events");
 
   }
 
 
 }
 
 //********************************************************************
 void Measurement2D::SetFitOptions(std::string opt) {
 //********************************************************************
 
   // Do nothing if default given
   if (opt == "DEFAULT") return;
 
   // CHECK Conflicting Fit Options
   std::vector<std::string> fit_option_allow =
     GeneralUtils::ParseToStr(fAllowedTypes, "/");
 
   for (UInt_t i = 0; i < fit_option_allow.size(); i++) {
     std::vector<std::string> fit_option_section =
       GeneralUtils::ParseToStr(fit_option_allow.at(i), ",");
 
     bool found_option = false;
 
     for (UInt_t j = 0; j < fit_option_section.size(); j++) {
       std::string av_opt = fit_option_section.at(j);
 
       if (!found_option and opt.find(av_opt) != std::string::npos) {
         found_option = true;
 
       } else if (found_option and opt.find(av_opt) != std::string::npos) {
         ERR(FTL) << "ERROR: Conflicting fit options provided: "
                  << opt << std::endl
                  << "Conflicting group = " << fit_option_section.at(i) << std::endl
                  << "You should only supply one of these options in card file." << std::endl;
         throw;
       }
     }
   }
 
   // Check all options are allowed
   std::vector<std::string> fit_options_input =
     GeneralUtils::ParseToStr(opt, "/");
   for (UInt_t i = 0; i < fit_options_input.size(); i++) {
     if (fAllowedTypes.find(fit_options_input.at(i)) == std::string::npos) {
       ERR(FTL) << "ERROR: Fit Option '" << fit_options_input.at(i)
                << "' Provided is not allowed for this measurement."
                << std::endl;
       ERR(FTL) << "Fit Options should be provided as a '/' seperated list "
                "(e.g. FREE/DIAG/NORM)"
                << std::endl;
       ERR(FTL) << "Available options for " << fName << " are '" << fAllowedTypes
                << "'" << std::endl;
 
       throw;
     }
   }
 
   // Set TYPE
   fFitType = opt;
 
   // FIX,SHAPE,FREE
   if (opt.find("FIX") != std::string::npos) {
     fIsFree = fIsShape = false;
     fIsFix = true;
   } else if (opt.find("SHAPE") != std::string::npos) {
     fIsFree = fIsFix = false;
     fIsShape = true;
   } else if (opt.find("FREE") != std::string::npos) {
     fIsFix = fIsShape = false;
     fIsFree = true;
   }
 
   // DIAG,FULL (or default to full)
   if (opt.find("DIAG") != std::string::npos) {
     fIsDiag = true;
     fIsFull = false;
   } else if (opt.find("FULL") != std::string::npos) {
     fIsDiag = false;
     fIsFull = true;
   }
 
   // CHI2/LL (OTHERS?)
   if (opt.find("LOG") != std::string::npos) {
     fIsChi2 = false;
 
     ERR(FTL) << "No other LIKELIHOODS properly supported!" << std::endl;
     ERR(FTL) << "Try to use a chi2!" << std::endl;
     throw;
 
   } else {
     fIsChi2 = true;
   }
 
   // EXTRAS
   if (opt.find("RAW") != std::string::npos) fIsRawEvents = true;
   if (opt.find("DIF") != std::string::npos) fIsDifXSec = true;
   if (opt.find("ENU1D") != std::string::npos) fIsEnu1D = true;
   if (opt.find("NORM") != std::string::npos) fAddNormPen = true;
   if (opt.find("MASK") != std::string::npos) fIsMask = true;
 
   // Set TYPE
   fFitType = opt;
 
   // FIX,SHAPE,FREE
   if (opt.find("FIX") != std::string::npos) {
     fIsFree = fIsShape = false;
     fIsFix = true;
   } else if (opt.find("SHAPE") != std::string::npos) {
     fIsFree = fIsFix = false;
     fIsShape = true;
   } else if (opt.find("FREE") != std::string::npos) {
     fIsFix = fIsShape = false;
     fIsFree = true;
   }
 
   // DIAG,FULL (or default to full)
   if (opt.find("DIAG") != std::string::npos) {
     fIsDiag = true;
     fIsFull = false;
   } else if (opt.find("FULL") != std::string::npos) {
     fIsDiag = false;
     fIsFull = true;
   }
 
   // CHI2/LL (OTHERS?)
   if (opt.find("LOG") != std::string::npos)
     fIsChi2 = false;
   else
     fIsChi2 = true;
 
   // EXTRAS
   if (opt.find("RAW") != std::string::npos) fIsRawEvents = true;
   if (opt.find("DIF") != std::string::npos) fIsDifXSec = true;
   if (opt.find("ENU1D") != std::string::npos) fIsEnu = true;
   if (opt.find("NORM") != std::string::npos) fAddNormPen = true;
   if (opt.find("MASK") != std::string::npos) fIsMask = true;
 
   fIsProjFitX = (opt.find("FITPROJX") != std::string::npos);
   fIsProjFitY = (opt.find("FITPROJY") != std::string::npos);
 
   return;
 };
 
 
 /*
    Reconfigure LOOP
 */
 //********************************************************************
 void Measurement2D::ResetAll() {
 //********************************************************************
 
   fMCHist->Reset();
   fMCFine->Reset();
   fMCStat->Reset();
 
   return;
 };
 
 //********************************************************************
 void Measurement2D::FillHistograms() {
   //********************************************************************
 
   if (Signal) {
     fMCHist->Fill(fXVar, fYVar, Weight);
     fMCFine->Fill(fXVar, fYVar, Weight);
     fMCStat->Fill(fXVar, fYVar, 1.0);
 
     if (fMCHist_Modes) fMCHist_Modes->Fill(Mode, fXVar, fYVar, Weight);
   }
 
   return;
 };
 
 //********************************************************************
 void Measurement2D::ScaleEvents() {
 //********************************************************************
 
   // Fill MCWeighted;
   // for (int i = 0; i < fMCHist->GetNbinsX(); i++) {
   // fMCWeighted->SetBinContent(i + 1, fMCHist->GetBinContent(i + 1));
   // fMCWeighted->SetBinError(i + 1,   fMCHist->GetBinError(i + 1));
   // }
 
 
   // Setup Stat ratios for MC and MC Fine
   double* statratio     = new double[fMCHist->GetNbinsX()];
   for (int i = 0; i < fMCHist->GetNbinsX(); i++) {
     if (fMCHist->GetBinContent(i + 1) != 0) {
       statratio[i] = fMCHist->GetBinError(i + 1) / fMCHist->GetBinContent(i + 1);
     } else {
       statratio[i] = 0.0;
     }
   }
 
   double* statratiofine = new double[fMCFine->GetNbinsX()];
   for (int i = 0; i < fMCFine->GetNbinsX(); i++) {
     if (fMCFine->GetBinContent(i + 1) != 0) {
       statratiofine[i] = fMCFine->GetBinError(i + 1) / fMCFine->GetBinContent(i + 1);
     } else {
       statratiofine[i] = 0.0;
     }
   }
 
 
   // Scaling for raw event rates
   if (fIsRawEvents) {
     double datamcratio = fDataHist->Integral() / fMCHist->Integral();
 
     fMCHist->Scale(datamcratio);
     fMCFine->Scale(datamcratio);
 
     if (fMCHist_Modes) fMCHist_Modes->Scale(datamcratio);
 
     // Scaling for XSec as function of Enu
   } else if (fIsEnu1D) {
 
     PlotUtils::FluxUnfoldedScaling(fMCHist, GetFluxHistogram(),
                                    GetEventHistogram(), fScaleFactor);
 
     PlotUtils::FluxUnfoldedScaling(fMCFine, GetFluxHistogram(),
                                    GetEventHistogram(), fScaleFactor);
 
 
     // if (fMCHist_Modes) {
     // PlotUtils::FluxUnfoldedScaling(fMCHist_Modes, GetFluxHistogram(),
     // GetEventHistogram(), fScaleFactor,
     // fNEvents);
     // }
 
     // Any other differential scaling
   } else {
     fMCHist->Scale(fScaleFactor, "width");
     fMCFine->Scale(fScaleFactor, "width");
 
     // if (fMCHist_Modes) fMCHist_Modes->Scale(fScaleFactor, "width");
   }
 
 
   // Proper error scaling - ROOT Freaks out with xsec weights sometimes
   for (int i = 0; i < fMCStat->GetNbinsX(); i++) {
     fMCHist->SetBinError(i + 1, fMCHist->GetBinContent(i + 1) * statratio[i]);
   }
 
   for (int i = 0; i < fMCFine->GetNbinsX(); i++) {
     fMCFine->SetBinError(i + 1, fMCFine->GetBinContent(i + 1) * statratiofine[i]);
   }
 
 
   // Clean up
   delete statratio;
   delete statratiofine;
 
   return;
 };
 
 //********************************************************************
 void Measurement2D::ApplyNormScale(double norm) {
 //********************************************************************
 
   fCurrentNorm = norm;
 
   fMCHist->Scale(1.0 / norm);
   fMCFine->Scale(1.0 / norm);
 
   return;
 };
 
 
 
 /*
    Statistic Functions - Outsources to StatUtils
 */
 
 //********************************************************************
 int Measurement2D::GetNDOF() {
 //********************************************************************
 
   
   // Just incase it has gone...
   if (!fDataHist) return -1;
 
   int nDOF = 0;
 
   // If datahist has no errors make sure we don't include those bins as they are
   // not data points
   for (int xBin = 0; xBin < fDataHist->GetNbinsX() + 1; ++xBin) {
     for (int yBin = 0; yBin < fDataHist->GetNbinsY() + 1; ++yBin) {
       if (fDataHist->GetBinError(xBin, yBin) != 0)
         ++nDOF;
     }
   }
   
   // Account for possible bin masking
   int nMasked = 0;
   if (fMaskHist and fIsMask)
     if (fMaskHist->Integral() > 0)
       for (int xBin = 0; xBin < fMaskHist->GetNbinsX() + 1; ++xBin)
         for (int yBin = 0; yBin < fMaskHist->GetNbinsY() + 1; ++yBin)
           if (fMaskHist->GetBinContent(xBin, yBin) > 0.5) ++nMasked;
 
   // Take away those masked DOF
   if (fIsMask) {
     nDOF -= nMasked;
   }
   
   return nDOF;
 }
 
 //********************************************************************
 double Measurement2D::GetLikelihood() {
 //********************************************************************
 
   // If this is for a ratio, there is no data histogram to compare to!
   if (fNoData || !fDataHist) return 0.;
 
   // Fix weird masking bug
   if (!fIsMask) {
     if (fMaskHist) {
       fMaskHist = NULL;
     }
   } else {
     if (fMaskHist) {
       PlotUtils::MaskBins(fMCHist, fMaskHist);
     }
   }
 
   //  if (fIsProjFitX or fIsProjFitY) return GetProjectedChi2();
 
   // Scale up the results to match each other (Not using width might be
   // inconsistent with Meas1D)
   double scaleF = fDataHist->Integral() / fMCHist->Integral();
   if (fIsShape) {
     fMCHist->Scale(scaleF);
     fMCFine->Scale(scaleF);
-    PlotUtils::ScaleNeutModeArray((TH1**)fMCHist_PDG, scaleF);
+    //PlotUtils::ScaleNeutModeArray((TH1**)fMCHist_PDG, scaleF);
   }
 
   if (!fMapHist) {
     fMapHist = StatUtils::GenerateMap(fDataHist);
   }
 
   // Get the chi2 from either covar or diagonals
   double chi2 = 0.0;
 
   if (fIsChi2) {
     if (fIsDiag) {
       chi2 =
         StatUtils::GetChi2FromDiag(fDataHist, fMCHist, fMapHist, fMaskHist);
     } else {
       chi2 = StatUtils::GetChi2FromCov(fDataHist, fMCHist, covar, fMapHist,
                                        fMaskHist);
     }
   }
 
   // Add a normal penalty term
   if (fAddNormPen) {
     chi2 +=
       (1 - (fCurrentNorm)) * (1 - (fCurrentNorm)) / (fNormError * fNormError);
     LOG(REC) << "Norm penalty = "
              << (1 - (fCurrentNorm)) * (1 - (fCurrentNorm)) /
              (fNormError * fNormError)
              << std::endl;
   }
 
   // Adjust the shape back to where it was.
   if (fIsShape and !FitPar::Config().GetParB("saveshapescaling")) {
     fMCHist->Scale(1. / scaleF);
     fMCFine->Scale(1. / scaleF);
   }
 
   fLikelihood = chi2;
 
   return chi2;
 }
 
 
 /*
   Fake Data Functions
 */
 //********************************************************************
 void Measurement2D::SetFakeDataValues(std::string fakeOption) {
 //********************************************************************
 
   // Setup original/datatrue
   TH2D* tempdata = (TH2D*) fDataHist->Clone();
 
   if (!fIsFakeData) {
     fIsFakeData = true;
 
     // Make a copy of the original data histogram.
     if (!fDataOrig) fDataOrig = (TH2D*)fDataHist->Clone((fName + "_data_original").c_str());
 
   } else {
     ResetFakeData();
 
   }
 
   // Setup Inputs
   fFakeDataInput = fakeOption;
   LOG(SAM) << "Setting fake data from : " << fFakeDataInput << std::endl;
 
   // From MC
   if (fFakeDataInput.compare("MC") == 0) {
     fDataHist = (TH2D*)fMCHist->Clone((fName + "_MC").c_str());
 
     // Fake File
   } else {
     if (!fFakeDataFile) fFakeDataFile = new TFile(fFakeDataInput.c_str(), "READ");
     fDataHist = (TH2D*)fFakeDataFile->Get((fName + "_MC").c_str());
 
   }
 
   // Setup Data Hist
   fDataHist->SetNameTitle((fName + "_FAKE").c_str(),
                           (fName + fPlotTitles).c_str());
 
   // Replace Data True
   if (fDataTrue) delete fDataTrue;
   fDataTrue = (TH2D*)fDataHist->Clone();
   fDataTrue->SetNameTitle((fName + "_FAKE_TRUE").c_str(),
                           (fName + fPlotTitles).c_str());
 
 
   // Make a new covariance for fake data hist.
   int nbins = fDataHist->GetNbinsX() * fDataHist->GetNbinsY();
   double alpha_i = 0.0;
   double alpha_j = 0.0;
 
   for (int i = 0; i < nbins; i++) {
     for (int j = 0; j < nbins; j++) {
       if (tempdata->GetBinContent(i + 1) && tempdata->GetBinContent(j + 1)) {
         alpha_i = fDataHist->GetBinContent(i + 1) / tempdata->GetBinContent(i + 1);
         alpha_j = fDataHist->GetBinContent(j + 1) / tempdata->GetBinContent(j + 1);
       } else {
         alpha_i = 0.0;
         alpha_j = 0.0;
       }
 
       (*fFullCovar)(i, j) = alpha_i * alpha_j * (*fFullCovar)(i, j);
     }
   }
 
   // Setup Covariances
   if (covar) delete covar;
   covar   = StatUtils::GetInvert(fFullCovar);
 
   if (fDecomp) delete fDecomp;
   fDecomp = StatUtils::GetInvert(fFullCovar);
 
   delete tempdata;
 
   return;
 };
 
 //********************************************************************
 void Measurement2D::ResetFakeData() {
 //********************************************************************
 
   if (fIsFakeData) {
     if (fDataHist) delete fDataHist;
     fDataHist = (TH2D*)fDataTrue->Clone((fSettings.GetName() + "_FKDAT").c_str());
   }
 
 }
 
 //********************************************************************
 void Measurement2D::ResetData() {
 //********************************************************************
 
   if (fIsFakeData) {
     if (fDataHist) delete fDataHist;
     fDataHist = (TH2D*)fDataOrig->Clone((fSettings.GetName() + "_data").c_str());
   }
 
   fIsFakeData = false;
 }
 
 //********************************************************************
 void Measurement2D::ThrowCovariance() {
 //********************************************************************
 
   // Take a fDecomposition and use it to throw the current dataset.
   // Requires fDataTrue also be set incase used repeatedly.
 
   if (fDataHist) delete fDataHist;
   fDataHist = StatUtils::ThrowHistogram(fDataTrue, fFullCovar);
 
   return;
 };
 
 //********************************************************************
 void Measurement2D::ThrowDataToy() {
   //********************************************************************
   if (!fDataTrue) fDataTrue = (TH2D*) fDataHist->Clone();
   if (fMCHist) delete fMCHist;
   fMCHist = StatUtils::ThrowHistogram(fDataTrue, fFullCovar);
 }
 
 
 /*
    Access Functions
 */
 
 //********************************************************************
 TH2D* Measurement2D::GetMCHistogram() {
 //********************************************************************
 
   if (!fMCHist) return fMCHist;
 
   std::ostringstream chi2;
   chi2 << std::setprecision(5) << this->GetLikelihood();
 
   int linecolor = kRed;
   int linestyle = 1;
   int linewidth = 1;
 
   int fillcolor = 0;
   int fillstyle = 1001;
 
   if (fSettings.Has("linecolor")) linecolor = fSettings.GetI("linecolor");
   if (fSettings.Has("linestyle")) linestyle = fSettings.GetI("linestyle");
   if (fSettings.Has("linewidth")) linewidth = fSettings.GetI("linewidth");
 
   if (fSettings.Has("fillcolor")) fillcolor = fSettings.GetI("fillcolor");
   if (fSettings.Has("fillstyle")) fillstyle = fSettings.GetI("fillstyle");
 
   fMCHist->SetTitle(chi2.str().c_str());
 
   fMCHist->SetLineColor(linecolor);
   fMCHist->SetLineStyle(linestyle);
   fMCHist->SetLineWidth(linewidth);
 
   fMCHist->SetFillColor(fillcolor);
   fMCHist->SetFillStyle(fillstyle);
 
   return fMCHist;
 };
 
 //********************************************************************
 TH2D* Measurement2D::GetDataHistogram() {
 //********************************************************************
 
   if (!fDataHist) return fDataHist;
 
   int datacolor = kBlack;
   int datastyle = 1;
   int datawidth = 1;
 
   if (fSettings.Has("datacolor")) datacolor = fSettings.GetI("datacolor");
   if (fSettings.Has("datastyle")) datastyle = fSettings.GetI("datastyle");
   if (fSettings.Has("datawidth")) datawidth = fSettings.GetI("datawidth");
 
   fDataHist->SetLineColor(datacolor);
   fDataHist->SetLineWidth(datawidth);
   fDataHist->SetMarkerStyle(datastyle);
 
   return fDataHist;
 };
 
 
 /*
    Write Functions
 */
 
 // Save all the histograms at once
 //********************************************************************
 void Measurement2D::Write(std::string drawOpt) {
 //********************************************************************
 
   // Get Draw Options
   drawOpt = FitPar::Config().GetParS("drawopts");
 
   // Write Settigns
   if (drawOpt.find("SETTINGS") != std::string::npos) {
     fSettings.Set("#chi^{2}", fLikelihood);
     fSettings.Set("NDOF", this->GetNDOF() );
     fSettings.Set("#chi^{2}/NDOF", fLikelihood / this->GetNDOF() );
     fSettings.Write();
   }
 
   // Write Data/MC
   GetDataList().at(0)->Write();
   GetMCList().at(0)->Write();
 
   // Write Fine Histogram
   if (drawOpt.find("FINE") != std::string::npos)
     GetFineList().at(0)->Write();
 
   // Write Weighted Histogram
   if (drawOpt.find("WEIGHTS") != std::string::npos && fMCWeighted)
     fMCWeighted->Write();
 
 
   // Save Flux/Evt if no event manager
   if (!FitPar::Config().GetParB("EventManager")) {
 
     if (drawOpt.find("FLUX") != std::string::npos && GetFluxHistogram())
       GetFluxHistogram()->Write();
 
     if (drawOpt.find("EVT") != std::string::npos && GetEventHistogram())
       GetEventHistogram()->Write();
 
     if (drawOpt.find("XSEC") != std::string::npos && GetEventHistogram())
       GetEventHistogram()->Write();
 
   }
 
   // Write Mask
   if (fIsMask && (drawOpt.find("MASK") != std::string::npos)) {
     fMaskHist->Write();
   }
 
 
   // Write Covariances
   if (drawOpt.find("COV") != std::string::npos && fFullCovar) {
     PlotUtils::GetFullCovarPlot(fFullCovar, fSettings.GetName());
   }
 
   if (drawOpt.find("INVCOV") != std::string::npos && covar) {
     PlotUtils::GetInvCovarPlot(covar, fSettings.GetName());
   }
 
   if (drawOpt.find("DECOMP") != std::string::npos && fDecomp) {
     PlotUtils::GetDecompCovarPlot(fDecomp, fSettings.GetName());
   }
 
   // // Likelihood residual plots
   // if (drawOpt.find("RESIDUAL") != std::string::npos) {
   //   WriteResidualPlots();
   // }
 
 
   // // RATIO
   // if (drawOpt.find("CANVMC") != std::string::npos) {
   //   TCanvas* c1 = WriteMCCanvas(fDataHist, fMCHist);
   //   c1->Write();
   //   delete c1;
   // }
 
   // // PDG
   // if (drawOpt.find("CANVPDG") != std::string::npos && fMCHist_Modes) {
   //   TCanvas* c2 = WritePDGCanvas(fDataHist, fMCHist, fMCHist_Modes);
   //   c2->Write();
   //   delete c2;
   // }
 
   // Write Extra Histograms
   AutoWriteExtraTH1();
   WriteExtraHistograms();
 
   /// 2D VERSION
   // If null pointer return
   if (!fMCHist and !fDataHist) {
     LOG(SAM) << fName << "Incomplete histogram set!" << std::endl;
     return;
   }
 
   //  FitPar::Config().out->cd();
 
   // Get Draw Options
   drawOpt = FitPar::Config().GetParS("drawopts");
   bool drawData = (drawOpt.find("DATA") != std::string::npos);
   bool drawNormal = (drawOpt.find("MC") != std::string::npos);
   bool drawEvents = (drawOpt.find("EVT") != std::string::npos);
   bool drawXSec = (drawOpt.find("XSEC") != std::string::npos);
   bool drawFine = (drawOpt.find("FINE") != std::string::npos);
   bool drawRatio = (drawOpt.find("RATIO") != std::string::npos);
   // bool drawModes = (drawOpt.find("MODES") != std::string::npos);
   bool drawShape = (drawOpt.find("SHAPE") != std::string::npos);
   bool residual = (drawOpt.find("RESIDUAL") != std::string::npos);
   bool drawMatrix = (drawOpt.find("MATRIX") != std::string::npos);
   bool drawFlux = (drawOpt.find("FLUX") != std::string::npos);
   bool drawMask = (drawOpt.find("MASK") != std::string::npos);
   bool drawMap = (drawOpt.find("MAP") != std::string::npos);
   bool drawProj = (drawOpt.find("PROJ") != std::string::npos);
   // bool drawCanvPDG = (drawOpt.find("CANVPDG") != std::string::npos);
   bool drawCov = (drawOpt.find("COV") != std::string::npos);
   bool drawSliceCanvYMC = (drawOpt.find("CANVYMC") != std::string::npos);
   bool drawWeighted = (drawOpt.find("WGHT") != std::string::npos);
 
   if (FitPar::Config().GetParB("EventManager")) {
     drawFlux = false;
     drawXSec = false;
     drawEvents = false;
   }
 
   if (fMaskHist) fMaskHist->Write();
 
   // Save standard plots
   if (drawData) this->GetDataList().at(0)->Write();
   if (drawNormal) this->GetMCList().at(0)->Write();
 
   if (drawCov) {
     TH2D(*fFullCovar).Write((fName + "_COV").c_str());
   }
 
   if (drawOpt.find("INVCOV") != std::string::npos) {
     TH2D(*covar).Write((fName + "_INVCOV").c_str());
   }
 
   // Generate a simple map
   if (!fMapHist) fMapHist = StatUtils::GenerateMap(fDataHist);
 
   // Convert to 1D Lists
   TH1D* data_1D = StatUtils::MapToTH1D(fDataHist, fMapHist);
   TH1D* mc_1D = StatUtils::MapToTH1D(fMCHist, fMapHist);
   TH1I* mask_1D = StatUtils::MapToMask(fMaskHist, fMapHist);
 
   data_1D->Write();
   mc_1D->Write();
 
   if (mask_1D) {
     mask_1D->Write();
 
     TMatrixDSym* calc_cov =
       StatUtils::ApplyInvertedMatrixMasking(covar, mask_1D);
     TH1D* calc_data = StatUtils::ApplyHistogramMasking(data_1D, mask_1D);
     TH1D* calc_mc = StatUtils::ApplyHistogramMasking(mc_1D, mask_1D);
 
     TH2D* bin_cov = new TH2D(*calc_cov);
 
     bin_cov->Write();
     calc_data->Write();
     calc_mc->Write();
 
     delete mask_1D;
     delete calc_cov;
     delete calc_data;
     delete calc_mc;
     delete bin_cov;
   }
 
   delete data_1D;
   delete mc_1D;
 
   // Save only mc and data if splines
   if (fEventType == 4 or fEventType == 3) {
     return;
   }
 
   // Draw Extra plots
   if (drawFine) this->GetFineList().at(0)->Write();
   if (drawFlux and GetFluxHistogram()) {
     GetFluxHistogram()->Write();
   }
   if (drawEvents and GetEventHistogram()) {
     GetEventHistogram()->Write();
   }
   if (fIsMask and drawMask) {
     fMaskHist->Write((fName + "_MSK").c_str());  //< save mask
   }
   if (drawMap) fMapHist->Write((fName + "_MAP").c_str());  //< save map
 
   // // Save neut stack
   // if (drawModes) {
   //   THStack combo_fMCHist_PDG = PlotUtils::GetNeutModeStack(
   //                                 (fName + "_MC_PDG").c_str(), (TH1**)fMCHist_PDG, 0);
   //   combo_fMCHist_PDG.Write();
   // }
 
   // Save Matrix plots
   if (drawMatrix and fFullCovar and covar and fDecomp) {
     TH2D cov = TH2D((*fFullCovar));
     cov.SetNameTitle((fName + "_cov").c_str(),
                      (fName + "_cov;Bins; Bins;").c_str());
     cov.Write();
 
     TH2D covinv = TH2D((*this->covar));
     covinv.SetNameTitle((fName + "_covinv").c_str(),
                         (fName + "_cov;Bins; Bins;").c_str());
     covinv.Write();
 
     TH2D covdec = TH2D((*fDecomp));
     covdec.SetNameTitle((fName + "_covdec").c_str(),
                         (fName + "_cov;Bins; Bins;").c_str());
     covdec.Write();
   }
 
   // Save ratio plots if required
   if (drawRatio) {
     // Needed for error bars
     for (int i = 0; i < fMCHist->GetNbinsX() * fMCHist->GetNbinsY(); i++)
       fMCHist->SetBinError(i + 1, 0.0);
 
     fDataHist->GetSumw2();
     fMCHist->GetSumw2();
 
     // Create Ratio Histograms
     TH2D* dataRatio = (TH2D*)fDataHist->Clone((fName + "_data_RATIO").c_str());
     TH2D* mcRatio = (TH2D*)fMCHist->Clone((fName + "_MC_RATIO").c_str());
 
     mcRatio->Divide(fMCHist);
     dataRatio->Divide(fMCHist);
 
     // Cancel bin errors on MC
     for (int i = 0; i < mcRatio->GetNbinsX() * mcRatio->GetNbinsY(); i++) {
       mcRatio->SetBinError(
         i + 1, fMCHist->GetBinError(i + 1) / fMCHist->GetBinContent(i + 1));
     }
 
     mcRatio->SetMinimum(0);
     mcRatio->SetMaximum(2);
     dataRatio->SetMinimum(0);
     dataRatio->SetMaximum(2);
 
     mcRatio->Write();
     dataRatio->Write();
 
     delete mcRatio;
     delete dataRatio;
   }
 
   // Save Shape Plots if required
   if (drawShape) {
     // Create Shape Histogram
     TH2D* mcShape = (TH2D*)fMCHist->Clone((fName + "_MC_SHAPE").c_str());
 
     double shapeScale = 1.0;
     if (fIsRawEvents) {
       shapeScale = fDataHist->Integral() / fMCHist->Integral();
     } else {
       shapeScale = fDataHist->Integral("width") / fMCHist->Integral("width");
     }
 
     mcShape->Scale(shapeScale);
 
     mcShape->SetLineWidth(3);
     mcShape->SetLineStyle(7);  // dashes
 
     mcShape->Write();
 
     // Save shape ratios
     if (drawRatio) {
       // Needed for error bars
       mcShape->GetSumw2();
 
       // Create shape ratio histograms
       TH2D* mcShapeRatio =
         (TH2D*)mcShape->Clone((fName + "_MC_SHAPE_RATIO").c_str());
       TH2D* dataShapeRatio =
         (TH2D*)fDataHist->Clone((fName + "_data_SHAPE_RATIO").c_str());
 
       // Divide the histograms
       mcShapeRatio->Divide(mcShape);
       dataShapeRatio->Divide(mcShape);
 
       // Colour the shape ratio plots
       mcShapeRatio->SetLineWidth(3);
       mcShapeRatio->SetLineStyle(7);  // dashes
 
       mcShapeRatio->Write();
       dataShapeRatio->Write();
 
       delete mcShapeRatio;
       delete dataShapeRatio;
     }
 
     delete mcShape;
   }
 
   // Save residual calculations of what contributed to the chi2 values.
   if (residual) {
   }
 
   if (fIsProjFitX or fIsProjFitY or drawProj) {
     // If not already made, make the projections
     if (!fMCHist_X) {
       PlotUtils::MatchEmptyBins(fDataHist, fMCHist);
 
       fMCHist_X = PlotUtils::GetProjectionX(fMCHist, fMaskHist);
       fMCHist_Y = PlotUtils::GetProjectionY(fMCHist, fMaskHist);
 
       fDataHist_X = PlotUtils::GetProjectionX(fDataHist, fMaskHist);
       fDataHist_Y = PlotUtils::GetProjectionY(fDataHist, fMaskHist);
 
       double chi2X = StatUtils::GetChi2FromDiag(fDataHist_X, fMCHist_X);
       double chi2Y = StatUtils::GetChi2FromDiag(fDataHist_Y, fMCHist_Y);
 
       fMCHist_X->SetTitle(Form("%f", chi2X));
       fMCHist_Y->SetTitle(Form("%f", chi2Y));
     }
 
     // Save the histograms
     fDataHist_X->Write();
     fMCHist_X->Write();
 
     fDataHist_Y->Write();
     fMCHist_Y->Write();
   }
 
   if (drawSliceCanvYMC or true) {
     TCanvas* c1 = new TCanvas((fName + "_MC_CANV_Y").c_str(),
                               (fName + "_MC_CANV_Y").c_str(), 800, 600);
 
     c1->Divide(int(sqrt(fDataHist->GetNbinsY() + 1)),
                int(sqrt(fDataHist->GetNbinsY() + 1)));
     TH2D* mcShape = (TH2D*)fMCHist->Clone((fName + "_MC_SHAPE").c_str());
     double shapeScale =
       fDataHist->Integral("width") / fMCHist->Integral("width");
     mcShape->Scale(shapeScale);
     mcShape->SetLineStyle(7);
 
     c1->cd(1);
     TLegend* leg = new TLegend(0.6, 0.6, 0.9, 0.9);
     leg->AddEntry(fDataHist, (fName + " Data").c_str(), "ep");
     leg->AddEntry(fMCHist, (fName + " MC").c_str(), "l");
     leg->AddEntry(mcShape, (fName + " Shape").c_str(), "l");
     leg->Draw("SAME");
 
     /*
     // Make Y slices
     for (int i = 0; i < fDataHist->GetNbinY(); i++){
 
       c1->cd(i+2);
       TH1D* fDataHist_SliceY = PlotUtils::GetSliceY(fDataHist, i);
       fDataHist_SliceY->Draw("E1");
 
       TH1D* fMCHist_SliceY = PlotUtils::GetSliceY(fMCHist, i);
       fMCHist_SliceY->Draw("SAME HIST C");
 
       TH1D* mcShape_SliceY = PlotUtils::GetSliceY(mcShape, i);
       mcShape_SliceY->Draw("SAME HIST C");
     }
     */
     c1->Write();
   }
 
   if (drawWeighted) {
     fMCWeighted->Write();
   }
 
   // Returning
   LOG(SAM) << "Written Histograms: " << fName << std::endl;
   return;
 
   // Returning
   LOG(SAM) << "Written Histograms: " << fName << std::endl;
   return;
 }
 
 
 
 /*
   Setup Functions
 */
 //********************************************************************
 void Measurement2D::SetupMeasurement(std::string inputfile, std::string type,
                                      FitWeight* rw, std::string fkdt) {
 //********************************************************************
 
   // Check if name contains Evt, indicating that it is a raw number of events
   // measurements and should thus be treated as once
   fIsRawEvents = false;
   if ((fName.find("Evt") != std::string::npos) && fIsRawEvents == false) {
     fIsRawEvents = true;
     LOG(SAM) << "Found event rate measurement but fIsRawEvents == false!"
              << std::endl;
     LOG(SAM) << "Overriding this and setting fIsRawEvents == true!"
              << std::endl;
   }
 
   fIsEnu = false;
   if ((fName.find("XSec") != std::string::npos) &&
       (fName.find("Enu") != std::string::npos)) {
     fIsEnu = true;
     LOG(SAM) << "::" << fName << "::" << std::endl;
     LOG(SAM) << "Found XSec Enu measurement, applying flux integrated scaling, "
              "not flux averaged!"
              << std::endl;
     if (FitPar::Config().GetParB("EventManager")) {
       ERR(FTL) << "Enu Measurements do not yet work with the Event Manager!"
                << std::endl;
       ERR(FTL) << "If you want decent flux unfolded results please run in "
                "series mode (-q EventManager=0)"
                << std::endl;
       sleep(2);
     }
   }
 
   if (fIsEnu && fIsRawEvents) {
     LOG(SAM) << "Found 1D Enu XSec distribution AND fIsRawEvents, is this "
              "really correct?!"
              << std::endl;
     LOG(SAM) << "Check experiment constructor for " << fName
              << " and correct this!" << std::endl;
     LOG(SAM) << "I live in " << __FILE__ << ":" << __LINE__ << std::endl;
     exit(-1);
   }
 
   // Reset everything to NULL
   fRW = rw;
 
   // Setting up 2D Inputs
   this->SetupInputs(inputfile);
 
   // Set Default Options
   SetFitOptions(fDefaultTypes);
 
   // Set Passed Options
   SetFitOptions(type);
 }
 
 //********************************************************************
 void Measurement2D::SetupDefaultHist() {
   //********************************************************************
 
   // Setup fMCHist
   fMCHist = (TH2D*)fDataHist->Clone();
   fMCHist->SetNameTitle((fName + "_MC").c_str(),
                         (fName + "_MC" + fPlotTitles).c_str());
 
   // Setup fMCFine
   Int_t nBinsX = fMCHist->GetNbinsX();
   Int_t nBinsY = fMCHist->GetNbinsY();
   fMCFine = new TH2D((fName + "_MC_FINE").c_str(),
                      (fName + "_MC_FINE" + fPlotTitles).c_str(), nBinsX * 3,
                      fMCHist->GetXaxis()->GetBinLowEdge(1),
                      fMCHist->GetXaxis()->GetBinLowEdge(nBinsX + 1), nBinsY * 3,
                      fMCHist->GetYaxis()->GetBinLowEdge(1),
                      fMCHist->GetYaxis()->GetBinLowEdge(nBinsY + 1));
 
   // Setup MC Stat
   fMCStat = (TH2D*)fMCHist->Clone();
   fMCStat->Reset();
 
 
   // Setup the NEUT Mode Array
-  PlotUtils::CreateNeutModeArray(fMCHist, (TH1**)fMCHist_PDG);
+  //PlotUtils::CreateNeutModeArray(fMCHist, (TH1**)fMCHist_PDG);
 
   // Setup bin masks using sample name
   if (fIsMask) {
     std::string maskloc = FitPar::Config().GetParDIR(fName + ".mask");
     if (maskloc.empty()) {
       maskloc = FitPar::GetDataBase() + "/masks/" + fName + ".mask";
     }
 
     SetBinMask(maskloc);
   }
 
   return;
 }
 
 
 //********************************************************************
 void Measurement2D::SetDataValues(std::string dataFile, std::string TH2Dname) {
   //********************************************************************
 
   if (dataFile.find(".root") == std::string::npos) {
     ERR(FTL) << "Error! " << dataFile << " is not a .root file" << std::endl;
     ERR(FTL) << "Currently only .root file reading is supported (MiniBooNE "
              "CC1pi+ 2D), but implementing .txt should be dirt easy"
              << std::endl;
     ERR(FTL) << "See me at " << __FILE__ << ":" << __LINE__ << std::endl;
     exit(-1);
 
   } else {
     TFile* inFile = new TFile(dataFile.c_str(), "READ");
     fDataHist = (TH2D*)(inFile->Get(TH2Dname.c_str())->Clone());
     fDataHist->SetDirectory(0);
 
     fDataHist->SetNameTitle((fName + "_data").c_str(),
                             (fName + "_MC" + fPlotTitles).c_str());
 
     delete inFile;
   }
 
   return;
 }
 
 //********************************************************************
 void Measurement2D::SetDataValues(std::string dataFile, double dataNorm,
                                   std::string errorFile, double errorNorm) {
   //********************************************************************
 
   // Make a counter to track the line number
   int yBin = 0;
 
   std::string line;
   std::ifstream data(dataFile.c_str(), ifstream::in);
 
   fDataHist = new TH2D((fName + "_data").c_str(), (fName + fPlotTitles).c_str(),
                        fNDataPointsX - 1, fXBins, fNDataPointsY - 1, fYBins);
 
   if (data.is_open())
     LOG(SAM) << "Reading data from: " << dataFile.c_str() << std::endl;
 
   while (std::getline(data >> std::ws, line, '\n')) {
     int xBin = 0;
 
     // Loop over entries and insert them into the histogram
     std::vector<double> entries = GeneralUtils::ParseToDbl(line, " ");
     for (std::vector<double>::iterator iter = entries.begin();
          iter != entries.end(); iter++) {
       fDataHist->SetBinContent(xBin + 1, yBin + 1, (*iter) * dataNorm);
       xBin++;
     }
     yBin++;
   }
 
   yBin = 0;
   std::ifstream error(errorFile.c_str(), ifstream::in);
 
   if (error.is_open())
     LOG(SAM) << "Reading errors from: " << errorFile.c_str() << std::endl;
 
   while (std::getline(error >> std::ws, line, '\n')) {
     int xBin = 0;
 
     // Loop over entries and insert them into the histogram
     std::vector<double> entries = GeneralUtils::ParseToDbl(line, " ");
     for (std::vector<double>::iterator iter = entries.begin();
          iter != entries.end(); iter++) {
       fDataHist->SetBinError(xBin + 1, yBin + 1, (*iter) * errorNorm);
       xBin++;
     }
     yBin++;
   }
 
   return;
 };
 
 //********************************************************************
 void Measurement2D::SetDataValuesFromText(std::string dataFile,
     double dataNorm) {
   //********************************************************************
 
   fDataHist = new TH2D((fName + "_data").c_str(), (fName + fPlotTitles).c_str(),
                        fNDataPointsX - 1, fXBins, fNDataPointsY - 1, fYBins);
 
   LOG(SAM) << "Reading data from: " << dataFile << std::endl;
   PlotUtils::Set2DHistFromText(dataFile, fDataHist, dataNorm, true);
 
   return;
 };
 
 //********************************************************************
 void Measurement2D::SetCovarMatrix(std::string covarFile) {
   //********************************************************************
 
   // Used to read a covariance matrix from a root file
   TFile* tempFile = new TFile(covarFile.c_str(), "READ");
 
   // Make plots that we want
   TH2D* covarPlot = new TH2D();
   //  TH2D* decmpPlot = new TH2D();
   TH2D* covarInvPlot = new TH2D();
   TH2D* fFullCovarPlot = new TH2D();
 
   // Get covariance options for fake data studies
   std::string covName = "";
   std::string covOption = FitPar::Config().GetParS("throw_covariance");
 
   // Which matrix to get?
   if (fIsShape || fIsFree) covName = "shp_";
   if (fIsDiag)
     covName += "diag";
   else
     covName += "full";
 
   covarPlot = (TH2D*)tempFile->Get((covName + "cov").c_str());
   covarInvPlot = (TH2D*)tempFile->Get((covName + "covinv").c_str());
 
   // Throw either the sub matrix or the full matrix
   if (!covOption.compare("SUB"))
     fFullCovarPlot = (TH2D*)tempFile->Get((covName + "cov").c_str());
   else if (!covOption.compare("FULL"))
     fFullCovarPlot = (TH2D*)tempFile->Get("fullcov");
   else
     ERR(WRN) << " Incorrect thrown_covariance option in parameters."
              << std::endl;
 
   // Bin masking?
   int dim = int(fDataHist->GetNbinsX());  //-this->masked->Integral());
   int covdim = int(fDataHist->GetNbinsX());
 
   // Make new covars
   this->covar = new TMatrixDSym(dim);
   fFullCovar = new TMatrixDSym(dim);
   fDecomp = new TMatrixDSym(dim);
 
   // Full covariance values
   int row, column = 0;
   row = 0;
   column = 0;
   for (Int_t i = 0; i < covdim; i++) {
     // masking can be dodgy
     // if (this->masked->GetBinContent(i+1) > 0) continue;
     for (Int_t j = 0; j < covdim; j++) {
       //   if (this->masked->GetBinContent(j+1) > 0) continue;
       (*this->covar)(row, column) = covarPlot->GetBinContent(i + 1, j + 1);
       (*fFullCovar)(row, column) = fFullCovarPlot->GetBinContent(i + 1, j + 1);
 
       column++;
     }
     column = 0;
     row++;
   }
 
   // Set bin errors on data
   if (!fIsDiag) {
     for (Int_t i = 0; i < fDataHist->GetNbinsX(); i++) {
       fDataHist->SetBinError(
         i + 1, sqrt((covarPlot->GetBinContent(i + 1, i + 1))) * 1E-38);
     }
   }
 
   TDecompSVD LU = TDecompSVD(*this->covar);
   this->covar = new TMatrixDSym(dim, LU.Invert().GetMatrixArray(), "");
 
   tempFile->Close();
   delete tempFile;
 
   return;
 };
 
 //********************************************************************
 void Measurement2D::SetCovarMatrixFromText(std::string covarFile, int dim) {
   //********************************************************************
 
   // Make a counter to track the line number
   int row = 0;
 
   std::string line;
   std::ifstream covar(covarFile.c_str(), ifstream::in);
 
   this->covar = new TMatrixDSym(dim);
   fFullCovar = new TMatrixDSym(dim);
   if (covar.is_open())
     LOG(SAM) << "Reading covariance matrix from file: " << covarFile
              << std::endl;
 
   while (std::getline(covar >> std::ws, line, '\n')) {
     int column = 0;
 
     // Loop over entries and insert them into matrix
     // Multiply by the errors to get the covariance, rather than the correlation
     // matrix
     std::vector<double> entries = GeneralUtils::ParseToDbl(line, " ");
     for (std::vector<double>::iterator iter = entries.begin();
          iter != entries.end(); iter++) {
       double val = (*iter) * fDataHist->GetBinError(row + 1) * 1E38 *
                    fDataHist->GetBinError(column + 1) * 1E38;
       (*this->covar)(row, column) = val;
       (*fFullCovar)(row, column) = val;
 
       column++;
     }
 
     row++;
   }
 
   // Robust matrix inversion method
   TDecompSVD LU = TDecompSVD(*this->covar);
   this->covar = new TMatrixDSym(dim, LU.Invert().GetMatrixArray(), "");
 
   return;
 };
 
 //********************************************************************
 void Measurement2D::SetCovarMatrixFromChol(std::string covarFile, int dim) {
   //********************************************************************
 
   // Make a counter to track the line number
   int row = 0;
 
   std::string line;
   std::ifstream covarread(covarFile.c_str(), ifstream::in);
 
   TMatrixD* newcov = new TMatrixD(dim, dim);
 
   if (covarread.is_open())
     LOG(SAM) << "Reading covariance matrix from file: " << covarFile
              << std::endl;
   while (std::getline(covarread >> std::ws, line, '\n')) {
     int column = 0;
 
     // Loop over entries and insert them into matrix
     // Multiply by the errors to get the covariance, rather than the correlation
     // matrix
     std::vector<double> entries = GeneralUtils::ParseToDbl(line, " ");
     for (std::vector<double>::iterator iter = entries.begin();
          iter != entries.end(); iter++) {
       (*newcov)(row, column) = *iter;
       column++;
     }
 
     row++;
   }
   covarread.close();
 
   // Form full covariance
   TMatrixD* trans = (TMatrixD*)(newcov)->Clone();
   trans->T();
   (*trans) *= (*newcov);
 
   fFullCovar = new TMatrixDSym(dim, trans->GetMatrixArray(), "");
 
   delete newcov;
   delete trans;
 
   // Robust matrix inversion method
   TDecompChol LU = TDecompChol(*this->fFullCovar);
   this->covar = new TMatrixDSym(dim, LU.Invert().GetMatrixArray(), "");
 
   return;
 };
 
 // //********************************************************************
 // void Measurement2D::SetMapValuesFromText(std::string dataFile) {
 // //********************************************************************
 
 //   fMapHist = new TH2I((fName + "_map").c_str(), (fName + fPlotTitles).c_str(),
 //                       fNDataPointsX - 1, fXBins, fNDataPointsY - 1, fYBins);
 
 //   LOG(SAM) << "Reading map from: " << dataFile << std::endl;
 //   PlotUtils::Set2DHistFromText(dataFile, fMapHist, 1.0);
 
 //   return;
 // };