LauSPlot.cc

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/*
Copyright 2006 University of Warwick

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/

/*
Laura++ package authors:
John Back
Paul Harrison
Thomas Latham
*/

/**********************************************************************
 *                                                                    *
 * Copyright (c) 2005 ROOT Foundation,  CERN/PH-SFT                   *
 *                                                                    *
 **********************************************************************/

#include <cfloat>
#include <iostream>
#include <vector>
using std::cout;
using std::cerr;
using std::endl;
using std::vector;

#include "TEventList.h"
#include "TFile.h"
#include "TLeaf.h"
#include "TMath.h"
#include "TObjArray.h"
#include "TSystem.h"
#include "TTree.h"
#include "TVirtualFitter.h"

#include "LauSPlot.hh"

extern void Yields(Int_t &, Double_t *, Double_t &f, Double_t *x, Int_t iflag);

ClassImp(LauSPlot)


LauSPlot::LauSPlot(const TString& fileName, const TString& treeName,
                Int_t firstExpt,
                Int_t nExpt,
                const NameSet& variableNames,
                const NumbMap& freeSpecies,
                const NumbMap& fixdSpecies,
                const TwoDMap& twodimPDFs,
                Bool_t sigSplit,
                Bool_t scfDPSmeared) :
        fileName_(fileName),
        inputTreeName_(treeName),
        cnTreeName_(""),
        sweightTreeName_(""),
        file_(0),
        inputTree_(0),
        cnTree_(0),
        sweightTree_(0),
        eventList_(0),
        variableNames_(variableNames),
        freeSpecies_(freeSpecies),
        fixdSpecies_(fixdSpecies),
        origFreeSpecies_(freeSpecies),
        origFixdSpecies_(fixdSpecies),
        twodimPDFs_(twodimPDFs),
        signalSplit_(sigSplit),
        scfDPSmear_(scfDPSmeared),
        readInput_(kFALSE),
        definedCNBranches_(kFALSE),
        definedSWeightBranches_(kFALSE),
        firstExpt_(firstExpt),
        nExpt_(nExpt),
        iExpt_(0),
        nEvents_(0),
        nDiscVars_(variableNames.size()),
        nFreeSpecies_(freeSpecies.size()),
        nFixdSpecies_(fixdSpecies.size()),
        nSpecies_(freeSpecies.size()+fixdSpecies.size())
{
        this->openInputFileAndTree();
        this->readInputInfo();
        this->createSWeightTree();
        if (nFixdSpecies_>0) {
                this->createCNTree();
        }
}

LauSPlot::~LauSPlot()
{
        // seems that closing the file deletes the tree
        // so only delete if the file is still open
        if (file_ && file_->IsOpen()) {
                delete inputTree_;  inputTree_ = 0;
                delete sweightTree_; sweightTree_ = 0;
                delete cnTree_; cnTree_ = 0;
        }
        delete file_; file_ = 0;
}

void LauSPlot::openInputFileAndTree()
{
        // first check whether we've already opened up the file or not
        if (!file_) {
                // if not, first check the filename and if all ok create the file
                if (fileName_ == "") {
                        cerr<<"ERROR in LauSPlot::createFileAndTree : Bad filename supplied, not creating file or tree."<<endl;
                        return;
                }
                file_ = TFile::Open(fileName_, "update");
                if (!file_ || file_->IsZombie() || !file_->IsWritable()) {
                        cerr<<"ERROR in LauSPlot::createFileAndTree : Problem opening file \""<<fileName_<<"\" for updating, can't do anything."<<endl;
                        return;
                }
        }
        // next open the input tree for reading
        if (!inputTree_) {
                file_->cd();
                inputTree_ = dynamic_cast<TTree*>(file_->Get(inputTreeName_));
                inputTree_->SetDirectory(file_);
        }
}

void LauSPlot::readInputInfo()
{
        // Read the tree and then setup the maps so we know which leaves to
        // read from the tree to get the various PDF values

        Bool_t inputOK = this->readInputLeaves();
        if (!inputOK) {
                this->readInput(inputOK);
                return;
        }

        inputOK = this->checkLeaves();
        this->readInput(inputOK);
        return;
}

Bool_t LauSPlot::readInputLeaves()
{
        // Read all the leaves in the tree and store them in the leaves map

        if (!inputTree_) {
                cerr<<"ERROR in LauSPlot::readInputInfo : Invalid pointer to data tree."<<endl;
                return kFALSE;
        }

        Int_t nBranches = inputTree_ ? static_cast<Int_t>(inputTree_->GetNbranches()) : 0;
        TObjArray* pLeaves = inputTree_->GetListOfLeaves();
        if (!pLeaves) {
                cerr<<"ERROR in LauSPlot::readInputInfo : Problem retrieving leaves from the tree."<<endl;
                return kFALSE;
        }
        TObjArray& leaves = *pLeaves;

        if (nBranches > leaves.GetSize()) {
                cerr<<"ERROR in LauSPlot::readInputInfo : List of leaves is smaller than number of branches - this is strange!"<<endl;
                return kFALSE;
        }

        for (Int_t iLeaf = 0; iLeaf < nBranches; ++iLeaf) {

                TLeaf * leaf = dynamic_cast<TLeaf*>(leaves[iLeaf]);

                // we can't deal with arrays
                Int_t size = leaf->GetNdata();
                if (size != 1) {
                        cerr<<"ERROR in LauSPlot::readInputInfo : Tree has array branches, can't deal with those."<<endl;
                        return kFALSE;
                }

                // find the name of the leaf
                TString name = leaf->GetName();

                // initialise an entry in the maps to hold the value
                leaves_[name] = leaf;
        }

        return kTRUE;
}

Bool_t LauSPlot::checkLeaves() const
{
        // Analyse the names of the leaves to check that we have a leaf for
        // all bits of information we require, i.e. a likelihood value for
        // each combination of variable and species

        // If we have 2D PDFs then we have to look for some extra leaves
        for ( TwoDMap::const_iterator twodim_iter = twodimPDFs_.begin(); twodim_iter != twodimPDFs_.end(); ++twodim_iter ) {

                const TString& specName = twodim_iter->first;
                const TString& firstVarName = twodim_iter->second.first;
                const TString& secondVarName = twodim_iter->second.second;

                TString expectedName(specName);
                expectedName += firstVarName;
                expectedName += secondVarName;
                expectedName += "Like";

                Bool_t found(kFALSE);
                for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                        const TString& leafName = leaf_iter->first;
                        const TLeaf* leaf = leaf_iter->second;

                        if ((leafName == expectedName) && (leaf != 0)) {
                                found = kTRUE;
                                break;
                        }
                }

                if (!found) {
                        cerr<<"ERROR in LauSPlot::checkLeaves : Could not find expected leaf \""<<expectedName<<"\"."<<endl;
                        return kFALSE;
                }
        }

        // Search for all other "standard" leaves, i.e. <species><var>Like

        for (NumbMap::const_iterator fixd_iter = fixdSpecies_.begin(); fixd_iter != fixdSpecies_.end(); ++fixd_iter) {

                const TString& specName = fixd_iter->first;

                // if the signal is split we need to do a dedicated search
                // for sigTM and sigSCF, so skip the signal here
                if ( specName == "sig" && this->signalSplit() ) {
                        continue;
                }

                for (NameSet::const_iterator vars_iter = variableNames_.begin(); vars_iter != variableNames_.end(); ++vars_iter) {
                        const TString& varName = (*vars_iter);
                        TString expectedName(specName);
                        expectedName += varName;
                        expectedName += "Like";
                        Bool_t found(kFALSE);
                        for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                const TString& leafName = leaf_iter->first;
                                const TLeaf* leaf = leaf_iter->second;

                                if ((leafName == expectedName) && (leaf != 0)) {
                                        found = kTRUE;
                                        break;
                                }
                        }

                        if (!found) {
                                cerr<<"ERROR in LauSPlot::checkLeaves : Could not find expected leaf \""<<expectedName<<"\"."<<endl;
                                return kFALSE;
                        }
                }
        }

        for (NumbMap::const_iterator free_iter = freeSpecies_.begin(); free_iter != freeSpecies_.end(); ++free_iter) {

                const TString& specName = free_iter->first;

                // if the signal is split we need to do a dedicated search
                // for sigTM and sigSCF, so skip the signal here
                if ( specName == "sig" && this->signalSplit() ) {
                        continue;
                }

                for (NameSet::const_iterator vars_iter = variableNames_.begin(); vars_iter != variableNames_.end(); ++vars_iter) {
                        const TString& varName = (*vars_iter);
                        TString expectedName(specName);
                        expectedName += varName;
                        expectedName += "Like";
                        Bool_t found(kFALSE);
                        for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                const TString& leafName = leaf_iter->first;
                                const TLeaf* leaf = leaf_iter->second;

                                if ((leafName == expectedName) && (leaf != 0)) {
                                        found = kTRUE;
                                        break;
                                }
                        }

                        if (!found) {
                                cerr<<"ERROR in LauSPlot::checkLeaves : Could not find expected leaf \""<<expectedName<<"\"."<<endl;
                                return kFALSE;
                        }
                }
        }

        if ( this->signalSplit() ) {

                // now need to search for the sigTM and sigSCF leaves

                for (NameSet::const_iterator vars_iter = variableNames_.begin(); vars_iter != variableNames_.end(); ++vars_iter) {
                        const TString& varName = (*vars_iter);
                        TString expectedName("sigTM");
                        expectedName += varName;
                        expectedName += "Like";
                        Bool_t found(kFALSE);
                        for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                const TString& leafName = leaf_iter->first;
                                const TLeaf* leaf = leaf_iter->second;

                                if ((leafName == expectedName) && (leaf != 0)) {
                                        found = kTRUE;
                                        break;
                                }
                        }

                        if (!found) {
                                cerr<<"ERROR in LauSPlot::checkLeaves : Could not find expected leaf \""<<expectedName<<"\"."<<endl;
                                return kFALSE;
                        }

                        expectedName = "sigSCF";
                        expectedName += varName;
                        expectedName += "Like";
                        found = kFALSE;
                        for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                const TString& leafName = leaf_iter->first;
                                const TLeaf* leaf = leaf_iter->second;

                                if ((leafName == expectedName) && (leaf != 0)) {
                                        found = kTRUE;
                                        break;
                                }
                        }

                        if (!found) {
                                cerr<<"ERROR in LauSPlot::checkLeaves : Could not find expected leaf \""<<expectedName<<"\"."<<endl;
                                return kFALSE;
                        }

                        expectedName = "sigSCFFrac";
                        found = kFALSE;
                        for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                const TString& leafName = leaf_iter->first;
                                const TLeaf* leaf = leaf_iter->second;

                                if ((leafName == expectedName) && (leaf != 0)) {
                                        found = kTRUE;
                                        break;
                                }
                        }

                        if (!found) {
                                cerr<<"ERROR in LauSPlot::checkLeaves : Could not find expected leaf \""<<expectedName<<"\"."<<endl;
                                return kFALSE;
                        }
                }
        }

        return kTRUE;
}

void LauSPlot::createCNTree()
{
        // check whether we've already created the tree
        if (!cnTree_) {
                // if not change to the file's directory and create the tree
                cnTreeName_ = inputTreeName_;
                cnTreeName_ += "_cNCoeffs";
                file_->cd();
                cnTree_ = new TTree(cnTreeName_, cnTreeName_);
                cnTree_->SetDirectory(file_);
                this->definedCNBranches(kFALSE);
        }
}

void LauSPlot::createSWeightTree()
{
        // check whether we've already created the tree
        if (!sweightTree_) {
                // if not change to the file's directory and create the tree
                sweightTreeName_ = inputTreeName_;
                sweightTreeName_ += "_sWeights";
                file_->cd();
                sweightTree_ = new TTree(sweightTreeName_, sweightTreeName_);
                sweightTree_->SetDirectory(file_);
                this->definedSWeightBranches(kFALSE);
        }
}

void LauSPlot::defineCNBranches()
{
        if (this->definedCNBranches()) {
                cerr<<"ERROR in LauSPlot::defineCNBranches : Already defined branches, not doing it again."<<endl;
                return;
        }
        if (cN_.empty()) {
                cerr<<"ERROR in LauSPlot::defineCNBranches : No entries in the cN container, can't define branches."<<endl;
                return;
        }
        if (!cnTree_) {
                cerr<<"ERROR in LauSPlot::defineCNBranches : Invalid pointer to the tree, can't define branches."<<endl;
                return;
        }

        // In the cN tree there is one entry per experiment, so need to know the experiment number.
        cnTree_->Branch("iExpt", &iExpt_, "iExpt/I");

        for (std::map<TString,NumbMap>::iterator excl_iter = cN_.begin(); excl_iter != cN_.end(); ++excl_iter) {
                const TString& exclName = excl_iter->first;
                NumbMap& species = excl_iter->second;
                for (NumbMap::iterator spec_iter = species.begin(); spec_iter != species.end(); ++spec_iter) {
                        const TString& specName = spec_iter->first;
                        Double_t * pointer = &(spec_iter->second);
                        TString name(specName); name += "_cN";
                        if (exclName == "none") {
                                name += "_all";
                        } else {
                                name += "_no";
                                name += exclName;
                        }
                        TString thirdPart(name);  thirdPart += "/D";
                        cnTree_->Branch(name, pointer, thirdPart);
                }
        }
        this->definedCNBranches(kTRUE);
}

void LauSPlot::defineSWeightBranches()
{
        if (this->definedSWeightBranches()) {
                cerr<<"ERROR in LauSPlot::defineSWeightBranches : Already defined branches, not doing it again."<<endl;
                return;
        }
        if (sWeights_.empty()) {
                cerr<<"ERROR in LauSPlot::defineSWeightBranches : No entries in the sWeights container, can't define branches."<<endl;
                return;
        }
        if (!sweightTree_) {
                cerr<<"ERROR in LauSPlot::defineSWeightBranches : Invalid pointer to the tree, can't define branches."<<endl;
                return;
        }

        for (std::map<TString,NumbMap>::iterator excl_iter = sWeightsCurrent_.begin(); excl_iter != sWeightsCurrent_.end(); ++excl_iter) {
                const TString& exclName = excl_iter->first;
                NumbMap& species = excl_iter->second;
                for (NumbMap::iterator spec_iter = species.begin(); spec_iter != species.end(); ++spec_iter) {
                        const TString& specName = spec_iter->first;
                        Double_t * pointer = &(spec_iter->second);
                        TString name(specName); name += "_sWeight";
                        if (exclName == "none") {
                                name += "_all";
                        } else {
                                name += "_no";
                                name += exclName;
                        }
                        TString thirdPart(name);  thirdPart += "/D";
                        sweightTree_->Branch(name, pointer, thirdPart);
                }
        }
        this->definedSWeightBranches(kTRUE);
}

void LauSPlot::setExperiment(Int_t iExpt)
{
        if (!inputTree_) {
                cerr<<"ERROR in LauSPlot::setExperiment : Invalid pointer to data tree."<<endl;
                return;
        }

        // create the event list if we haven't already done so
        if (!eventList_) {
                eventList_ = new TEventList("splotelist","splotelist");
                eventList_->SetDirectory(file_);
        }

        // fill the event list with this experiment's events
        TString listName(eventList_->GetName());
        listName.Prepend(">>");
        TString selection("iExpt==");
        selection += iExpt;
        cout<<"LauSPlot::setExperiment : Setting tree to experiment number "<<iExpt<<"."<<endl;
        inputTree_->Draw(listName,selection);

        // find how many events there are
        nEvents_ = eventList_->GetN();
        cout<<"                          Found "<<nEvents_<<" events."<<endl;

        // make sure we have enough space in the per-event value vectors
        pdfTot_.clear(); pdfTot_.resize(nEvents_);
        discPdf_.clear(); discPdf_.resize(nEvents_);
        scfFrac_.clear(); scfFrac_.resize(nEvents_);
        sWeights_.clear(); sWeights_.resize(nEvents_);

        // read the info for this experiment
        this->readExpt();
}

void LauSPlot::readExpt()
{
        for (Int_t iEvt(0); iEvt < nEvents_; ++iEvt) {
                // Find which entry from the full tree contains the requested event
                Long64_t iEntry = eventList_ ? eventList_->GetEntry(iEvt) : iEvt;
                if (iEntry<0) { // this shouldn't happen, but just in case...
                        cerr<<"ERROR in LauSPlot::readExpt : Problem retrieving event."<<endl;
                        gSystem->Exit(EXIT_FAILURE);
                }

                // Then retrieve that entry from the tree
                inputTree_->GetEntry(iEntry);

                // If needed retrieve the SCF fraction values
                if ( this->signalSplit() ) {
                        for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                const TString& leafName = leaf_iter->first;
                                const TLeaf* leaf = leaf_iter->second;
                                if ((leafName == "sigSCFFrac") && (leaf != 0)) {
                                        scfFrac_[iEvt] = leaf->GetValue();
                                        break;
                                }
                        }
                }

                // Copy the leaf values into discPdf_
                for ( TwoDMap::const_iterator twodim_iter = twodimPDFs_.begin(); twodim_iter != twodimPDFs_.end(); ++twodim_iter ) {
                        const TString& specName = twodim_iter->first;
                        const TString& firstVarName = twodim_iter->second.first;
                        const TString& secondVarName = twodim_iter->second.second;

                        TString varName = firstVarName + secondVarName;

                        TString expectedName(specName);
                        expectedName += varName;
                        expectedName += "Like";

                        for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                const TString& leafName = leaf_iter->first;
                                const TLeaf* leaf = leaf_iter->second;
                                if ((leafName == expectedName) && (leaf != 0)) {
                                        discPdf_[iEvt][specName][varName] = leaf->GetValue();
                                        break;
                                }
                        }
                }

                Bool_t needSignalSearch(kFALSE);
                for (NumbMap::const_iterator fixd_iter = fixdSpecies_.begin(); fixd_iter != fixdSpecies_.end(); ++fixd_iter) {
                        const TString& specName = fixd_iter->first;

                        // if the signal is split we need to do a dedicated search
                        // for sigTM and sigSCF, so skip the signal here
                        if ( specName == "sig" && this->signalSplit() ) {
                                needSignalSearch = kTRUE;
                                continue;
                        }

                        for (NameSet::const_iterator vars_iter = variableNames_.begin(); vars_iter != variableNames_.end(); ++vars_iter) {
                                const TString& varName = (*vars_iter);
                                TString expectedName(specName);
                                expectedName += varName;
                                expectedName += "Like";
                                for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                        const TString& leafName = leaf_iter->first;
                                        const TLeaf* leaf = leaf_iter->second;
                                        if ((leafName == expectedName) && (leaf != 0)) {
                                                discPdf_[iEvt][specName][varName] = leaf->GetValue();
                                                break;
                                        }
                                }
                        }
                }

                for (NumbMap::const_iterator free_iter = freeSpecies_.begin(); free_iter != freeSpecies_.end(); ++free_iter) {
                        const TString& specName = free_iter->first;

                        // if the signal is split we need to do a dedicated search
                        // for sigTM and sigSCF, so skip the signal here
                        if ( specName == "sig" && this->signalSplit() ) {
                                needSignalSearch = kTRUE;
                                continue;
                        }

                        for (NameSet::const_iterator vars_iter = variableNames_.begin(); vars_iter != variableNames_.end(); ++vars_iter) {
                                const TString& varName = (*vars_iter);
                                TString expectedName(specName);
                                expectedName += varName;
                                expectedName += "Like";
                                for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                        const TString& leafName = leaf_iter->first;
                                        const TLeaf* leaf = leaf_iter->second;
                                        if ((leafName == expectedName) && (leaf != 0)) {
                                                discPdf_[iEvt][specName][varName] = leaf->GetValue();
                                                break;
                                        }
                                }
                        }
                }

                if ( needSignalSearch ) {
                        for (NameSet::const_iterator vars_iter = variableNames_.begin(); vars_iter != variableNames_.end(); ++vars_iter) {
                                const TString& varName = (*vars_iter);
                                TString specName("sigTM");
                                TString expectedName(specName);
                                expectedName += varName;
                                expectedName += "Like";
                                for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                        const TString& leafName = leaf_iter->first;
                                        const TLeaf* leaf = leaf_iter->second;
                                        if ((leafName == expectedName) && (leaf != 0)) {
                                                discPdf_[iEvt][specName][varName] = leaf->GetValue();
                                                break;
                                        }
                                }
                                specName = "sigSCF";
                                expectedName = specName;
                                expectedName += varName;
                                expectedName += "Like";
                                for (LeafMap::const_iterator leaf_iter = leaves_.begin(); leaf_iter != leaves_.end(); ++leaf_iter) {
                                        const TString& leafName = leaf_iter->first;
                                        const TLeaf* leaf = leaf_iter->second;
                                        if ((leafName == expectedName) && (leaf != 0)) {
                                                discPdf_[iEvt][specName][varName] = leaf->GetValue();
                                                break;
                                        }
                                }
                        }
                }
        }
}

void LauSPlot::runCalculations(const TString& option)
{
        // Calculates the sWeights and cN coeffs
        // The option controls the print level:
        // "Q" - no print out (default)
        // "V" - prints the estimated # of events in species
        // "VV" - as "V" + the MINUIT printing + sums of weights for control

        if (!this->readInput()) {
                cerr<<"ERROR in LauSPlot::runCalculations : The input ntuple has not been successfully read, can't calculate anything."<<endl;
                return;
        }

        if (freeSpecies_.empty()) {
                cerr<<"ERROR in LauSPlot::runCalculations : Numbers of events in species have not been set."<<endl;
                return;
        }

        TString opt(option);
        opt.ToUpper();
        opt.ReplaceAll("VV", "W");

        // Make sure that global fitter is MINUIT
        this->checkFitter();

        // Loop over experiments
        for (iExpt_ = firstExpt_; iExpt_ < (firstExpt_+nExpt_); ++iExpt_) {

                this->setExperiment(iExpt_);

                if (nEvents_ < 1) {
                        cerr<<"ERROR in LauSPlot::runCalculations : Zero events in experiment "<<iExpt_<<", skipping..."<<endl;
                        continue;
                }

                // Now loop over the PDFs to exclude, including the case where none are to be excluded.
                NameSet excludePdf;
                if (variableNames_.size()<2) {
                        excludePdf.insert("none");
                } else {
                        excludePdf = variableNames_;
                        excludePdf.insert("none");
                }

                for (NameSet::const_iterator excl_iter = excludePdf.begin(); excl_iter != excludePdf.end(); ++excl_iter) {

                        const TString& exclName = (*excl_iter);

                        cout<<"LauSPlot::runCalculations : Calculating sWeights, excluding PDF: "<<exclName<<"."<<endl;

                        // Calculate the per-event total PDF values for each species.
                        this->calcTotPDFValues(exclName);

                        // Reset the fitter
                        this->initialiseFitter(opt);

                        // Set the parameters to their initial values
                        this->setFitParameters();

                        // Run the fit
                        this->runFit();

                        // Get the fitted parameter values back
                        this->retrieveFittedParameters(opt);

                        // Get the covariance matrix
                        Bool_t covMatOK = this->calcCovMatrix();
                        Double_t * covmat(0);
                        if (!covMatOK) {
                                TVirtualFitter * fitter = TVirtualFitter::GetFitter();
                                covmat = fitter->GetCovarianceMatrix();
                        }
                        if (opt.Contains("W")) {
                                this->printCovMatrixElements(covmat);
                        }

                        // calculate the cN and sWeights from the covariance matrix
                        if (nFixdSpecies_ > 0) {
                                this->calcCNCoeffs(exclName, covmat);
                        }
                        this->calcSWeights(exclName, covmat);

                        // print verbose info if required
                        if (opt.Contains("W")) {
                                this->printSumOfWeights(exclName);
                        }
                }

                // Finally fill all the branches for this experiment
                if (nFixdSpecies_ > 0) {
                        this->fillCNBranches();
                }
                this->fillSWeightBranches();
        }
}

void LauSPlot::checkFitter() const
{
        TString minuitName("TFitter");
        TVirtualFitter * fitter = TVirtualFitter::GetFitter();
        if (fitter) {
                TString fitterName(fitter->IsA()->GetName());
                if (fitterName != minuitName) {
                        delete fitter; fitter = 0;
                }
        }
        fitter = TVirtualFitter::Fitter(0);
}

void LauSPlot::initialiseFitter(const TString& opt)
{
        TVirtualFitter * fitter = TVirtualFitter::GetFitter();
        fitter->Clear();
        fitter->SetFCN(Yields);
        fitter->SetObjectFit(this);

        // Set the print level
        Double_t arglist[10];
        if (opt.Contains("Q")) {
                arglist[0]=-1;
        }
        if (opt.Contains("V")) {
                arglist[0]=0;
        }
        if (opt.Contains("W")) {
                arglist[0]=1;
        }
        fitter->ExecuteCommand("SET PRINT", arglist, 1);

        // Need to set the "SET ERR" command to +0.5 for +/-1 sigma errors
        // for maximum likelihood fit.
        arglist[0] = 0.5;
        fitter->ExecuteCommand("SET ERR", arglist, 1);
}

void LauSPlot::setFitParameters() const
{
        TVirtualFitter * fitter = TVirtualFitter::GetFitter();

        // must add the parameters in the same order as they are stored in pdfTot_
        Int_t ispecies(0);
        const NumbMap& species = pdfTot_.front();

        for (NumbMap::const_iterator spec_iter = species.begin(); spec_iter != species.end(); ++spec_iter) {
                const TString& name(spec_iter->first);

                // starting parameters should be the original values,
                // not those that came out of the last fit
                NumbMap::const_iterator free_iter = origFreeSpecies_.find(name);
                NumbMap::const_iterator fixd_iter = origFixdSpecies_.find(name);
                Bool_t fixed = fixd_iter != origFixdSpecies_.end();

                Double_t value(0.0);
                if (fixed) {
                        value = fixd_iter->second;
                } else {
                        value = free_iter->second;
                }
                fitter->SetParameter(ispecies, name, value, 1, 0, 0);
                if (fixed) {
                        fitter->FixParameter(ispecies);
                }
                ++ispecies;
        }
}

void LauSPlot::runFit()
{
        TVirtualFitter * fitter = TVirtualFitter::GetFitter();

        Double_t arglist[10];
        arglist[0] = 1000*nFreeSpecies_; // maximum iterations
        arglist[1] = 0.05;               // tolerance : min EDM = 0.001*tolerance

        // Execute MIGRAD
        Int_t fitStatus = fitter->ExecuteCommand("MIGRAD", arglist, 2);

        if (fitStatus != 0) {
                cerr<<"ERROR in LauSPlot::runFit : Error during MIGRAD minimisation."<<endl;
        } else {
                // Execute HESSE
                fitStatus = fitter->ExecuteCommand("HESSE", arglist, 1);
                if (fitStatus != 0) {
                        cerr<<"ERROR in LauSPlot::runFit : Error during HESSE error calculation."<<endl;
                }
        }
}

void LauSPlot::printCovMatrixElements(const Double_t * covmat) const
{
        Int_t a(0);
        cout<<endl;
        for (NumbMap::const_iterator iter_a = freeSpecies_.begin(); iter_a != freeSpecies_.end(); ++iter_a) {
                Int_t b(0);
                for (NumbMap::const_iterator iter_b = freeSpecies_.begin(); iter_b != freeSpecies_.end(); ++iter_b) {
                        if (covmat) {
                                cout<<"CovMat Elem: ["<<iter_a->first<<","<<iter_b->first<<"] = "<<covmat[a*nSpecies_+b]<<endl;
                        } else {
                                cout<<"CovMat Elem: ["<<iter_a->first<<","<<iter_b->first<<"] = "<<covMat_(a,b)<<endl;
                        }
                        ++b;
                }
                ++a;
        }
        cout<<endl;

        if (!covmat) {
                covMat_.Print();
        }
}

void LauSPlot::retrieveFittedParameters(const TString& opt)
{
        TVirtualFitter * fitter = TVirtualFitter::GetFitter();

        // remember fit parameters are in same order as in pdfTot_
        Int_t ispecies(0);
        const NumbMap& species = pdfTot_.front();

        for (NumbMap::const_iterator spec_iter = species.begin(); spec_iter != species.end(); ++spec_iter) {
                const TString& name(spec_iter->first);
                NumbMap::iterator free_iter = freeSpecies_.find(name);
                if (free_iter != freeSpecies_.end()) {
                        free_iter->second = fitter->GetParameter(ispecies);
                        if (!opt.Contains("Q")) {
                                cout<<"Estimated # of events in species "<<name<<" = "<<free_iter->second<<endl;
                        }
                }
                ++ispecies;
        }
        if (!opt.Contains("Q")) {cout<<endl;}
}

void LauSPlot::printSumOfWeights(const TString& exclName) const
{
        for (NumbMap::const_iterator spec_iter = freeSpecies_.begin(); spec_iter != freeSpecies_.end(); ++spec_iter) {
                const TString& specName = spec_iter->first;
                Double_t sumweight(0.0);
                for (Int_t iEvt(0); iEvt < nEvents_; ++iEvt) {
                        const NumbMap& specWeightMap = sWeights_[iEvt].find(exclName)->second;
                        Double_t weight = specWeightMap.find(specName)->second;
                        sumweight += weight;
                }
                cout<<"Sum of sWeights for species \""<<specName<<"\" = "<<sumweight<<endl;
        }
        cout<<endl;
}

Bool_t LauSPlot::calcCovMatrix()
{
        // Calculate our inverse covariance matrix from the various PDFs

        TMatrixD invMatrix(nFreeSpecies_,nFreeSpecies_);

        // First calculate the denominator, which is common to all elements
        vector<Double_t> denominator(nEvents_);
        for (Int_t iEvt(0); iEvt<nEvents_; ++iEvt) {
                denominator[iEvt] = 0.0;
                for (NumbMap::const_iterator spec_iter = freeSpecies_.begin(); spec_iter != freeSpecies_.end(); ++spec_iter) {
                        const TString& specName = spec_iter->first;
                        Double_t specNumEvents = spec_iter->second;
                        denominator[iEvt] += specNumEvents * pdfTot_[iEvt][specName];
                }
                for (NumbMap::const_iterator spec_iter = fixdSpecies_.begin(); spec_iter != fixdSpecies_.end(); ++spec_iter) {
                        const TString& specName = spec_iter->first;
                        Double_t specNumEvents = spec_iter->second;
                        denominator[iEvt] += specNumEvents * pdfTot_[iEvt][specName];
                }
                // Square to get the final denominator
                denominator[iEvt] *= denominator[iEvt];
        }

        // Then calculate each element
        Int_t i(0);
        for (NumbMap::const_iterator spec_iter_i = freeSpecies_.begin(); spec_iter_i != freeSpecies_.end(); ++spec_iter_i) {
                const TString& specName_i = spec_iter_i->first;
                Int_t j(0);
                for (NumbMap::const_iterator spec_iter_j = freeSpecies_.begin(); spec_iter_j != freeSpecies_.end(); ++spec_iter_j) {
                        const TString& specName_j = spec_iter_j->first;
                        invMatrix(i,j) = 0.0;
                        for (Int_t iEvt(0); iEvt<nEvents_; ++iEvt) {
                                Double_t numerator = pdfTot_[iEvt][specName_i] * pdfTot_[iEvt][specName_j];
                                invMatrix(i,j) += numerator/denominator[iEvt];
                        }
                        ++j;
                }
                ++i;
        }

        // Check for a singular matrix
        if (invMatrix.Determinant() < 1e-15) {
                cerr<<"ERROR in LauSPlot::calcCovMatrix : Calculated inverse covariance matrix is singular, can't invert it."<<endl;
                return kFALSE;
        }

        // Invert and store in the covariance matrix
        covMat_.ResizeTo(nFreeSpecies_,nFreeSpecies_);
        covMat_ = TMatrixD(TMatrixD::kInverted, invMatrix);

        return kTRUE;
}

void LauSPlot::calcTotPDFValues(const TString& exclName)
{
        for (Int_t iEvt(0); iEvt<nEvents_; iEvt++) {

                Bool_t needSignalSearch(kFALSE);

                for (NumbMap::const_iterator spec_iter = fixdSpecies_.begin(); spec_iter != fixdSpecies_.end(); ++spec_iter) {
                        const TString& specName = spec_iter->first;

                        // if the signal is split we need to do a dedicated search
                        // for sigTM and sigSCF, so skip the signal here
                        if ( specName == "sig" && this->signalSplit() ) {
                                needSignalSearch = kTRUE;
                                continue;
                        }

                        pdfTot_[iEvt][specName] = 1.0;

                        // loop through the 2D histo list
                        NameSet skipList;
                        for ( TwoDMap::const_iterator twodim_iter = twodimPDFs_.begin(); twodim_iter != twodimPDFs_.end(); ++twodim_iter ) {
                                // if the entry doesn't refer to this
                                // species then skip on
                                if ( specName != twodim_iter->first ) {
                                        continue;
                                }

                                // retrieve the two variable names
                                const TString& firstVarName = twodim_iter->second.first;
                                const TString& secondVarName = twodim_iter->second.second;
                                if ( firstVarName != exclName && secondVarName != exclName ) {
                                        // if neither name is the one being excluded then...
                                        // add them both to the skip list
                                        skipList.insert( firstVarName );
                                        skipList.insert( secondVarName );
                                        // and multiply the total by the combined PDF value
                                        TString varName = firstVarName + secondVarName;
                                        pdfTot_[iEvt][specName] *= discPdf_[iEvt][specName][varName];
                                }
                        }

                        // loop through all the variables
                        for (NameSet::const_iterator var_iter = variableNames_.begin(); var_iter != variableNames_.end(); ++var_iter) {
                                const TString& varName = (*var_iter);
                                // if the variable isn't the one being excluded
                                if (exclName != varName) {
                                        // and it's not involved in a 2D PDF
                                        if ( skipList.find(varName) == skipList.end() ) {
                                                // multiply the total by its PDF value
                                                pdfTot_[iEvt][specName] *= discPdf_[iEvt][specName][varName];
                                        }
                                }
                        }
                }

                for (NumbMap::const_iterator spec_iter = freeSpecies_.begin(); spec_iter != freeSpecies_.end(); ++spec_iter) {
                        const TString& specName = spec_iter->first;

                        // if the signal is split we need to do a dedicated search
                        // for sigTM and sigSCF, so skip the signal here
                        if ( specName == "sig" && this->signalSplit() ) {
                                needSignalSearch = kTRUE;
                                continue;
                        }

                        pdfTot_[iEvt][specName] = 1.0;

                        // loop through the 2D histo list
                        NameSet skipList;
                        for ( TwoDMap::const_iterator twodim_iter = twodimPDFs_.begin(); twodim_iter != twodimPDFs_.end(); ++twodim_iter ) {
                                // if the entry doesn't refer to this
                                // species then skip on
                                if ( specName != twodim_iter->first ) {
                                        continue;
                                }

                                // retrieve the two variable names
                                const TString& firstVarName = twodim_iter->second.first;
                                const TString& secondVarName = twodim_iter->second.second;
                                if ( firstVarName != exclName && secondVarName != exclName ) {
                                        // if neither name is the one being excluded then...
                                        // add them both to the skip list
                                        skipList.insert( firstVarName );
                                        skipList.insert( secondVarName );
                                        // and multiply the total by the combined PDF value
                                        TString varName = firstVarName + secondVarName;
                                        pdfTot_[iEvt][specName] *= discPdf_[iEvt][specName][varName];
                                }
                        }

                        // loop through all the variables
                        for (NameSet::const_iterator var_iter = variableNames_.begin(); var_iter != variableNames_.end(); ++var_iter) {
                                const TString& varName = (*var_iter);
                                // if the variable isn't the one being excluded
                                if (exclName != varName) {
                                        // and it's not involved in a 2D PDF
                                        if ( skipList.find(varName) == skipList.end() ) {
                                                // multiply the total by its PDF value
                                                pdfTot_[iEvt][specName] *= discPdf_[iEvt][specName][varName];
                                        }
                                }
                        }
                }

                if ( needSignalSearch ) {

                        // loop through the 2D histo list
                        TString specName("sigTM");
                        Double_t tmPDFVal(1.0);
                        NameSet skipList;
                        for ( TwoDMap::const_iterator twodim_iter = twodimPDFs_.begin(); twodim_iter != twodimPDFs_.end(); ++twodim_iter ) {
                                // if the entry doesn't refer to this
                                // species then skip on
                                if ( specName != twodim_iter->first ) {
                                        continue;
                                }

                                // retrieve the two variable names
                                const TString& firstVarName = twodim_iter->second.first;
                                const TString& secondVarName = twodim_iter->second.second;
                                if ( firstVarName != exclName && secondVarName != exclName ) {
                                        // if neither name is the one being excluded then...
                                        // add them both to the skip list
                                        skipList.insert( firstVarName );
                                        skipList.insert( secondVarName );
                                        // and multiply the total by the combined PDF value
                                        TString varName = firstVarName + secondVarName;
                                        tmPDFVal *= discPdf_[iEvt][specName][varName];
                                }
                        }

                        // loop through all the variables
                        for (NameSet::const_iterator var_iter = variableNames_.begin(); var_iter != variableNames_.end(); ++var_iter) {
                                const TString& varName = (*var_iter);
                                // if the variable isn't the one being excluded
                                if (exclName != varName) {
                                        // and it's not involved in a 2D PDF
                                        if ( skipList.find(varName) == skipList.end() ) {
                                                // multiply the total by its PDF value
                                                tmPDFVal *= discPdf_[iEvt][specName][varName];
                                        }
                                }
                        }

                        tmPDFVal *= (1.0 - scfFrac_[iEvt]);


                        // loop through the 2D histo list
                        specName = "sigSCF";
                        Double_t scfPDFVal(1.0);
                        skipList.clear();
                        for ( TwoDMap::const_iterator twodim_iter = twodimPDFs_.begin(); twodim_iter != twodimPDFs_.end(); ++twodim_iter ) {
                                // if the entry doesn't refer to this
                                // species then skip on
                                if ( specName != twodim_iter->first ) {
                                        continue;
                                }

                                // retrieve the two variable names
                                const TString& firstVarName = twodim_iter->second.first;
                                const TString& secondVarName = twodim_iter->second.second;
                                if ( firstVarName != exclName && secondVarName != exclName ) {
                                        // if neither name is the one being excluded then...
                                        // add them both to the skip list
                                        skipList.insert( firstVarName );
                                        skipList.insert( secondVarName );
                                        // and multiply the total by the combined PDF value
                                        TString varName = firstVarName + secondVarName;
                                        scfPDFVal *= discPdf_[iEvt][specName][varName];
                                }
                        }

                        // loop through all the variables
                        for (NameSet::const_iterator var_iter = variableNames_.begin(); var_iter != variableNames_.end(); ++var_iter) {
                                const TString& varName = (*var_iter);
                                // if the variable isn't the one being excluded
                                if (exclName != varName) {
                                        // and it's not involved in a 2D PDF
                                        if ( skipList.find(varName) == skipList.end() ) {
                                                // multiply the total by its PDF value
                                                scfPDFVal *= discPdf_[iEvt][specName][varName];
                                        }
                                }
                        }

                        if ( exclName == "DP" || !this->scfDPSmear() ) {
                                scfPDFVal *= scfFrac_[iEvt];
                        }

                        pdfTot_[iEvt]["sig"] = tmPDFVal + scfPDFVal;
                }
        }
}

void LauSPlot::calcCNCoeffs(const TString& exclName, const Double_t *covmat)
{
        // Computes the cN for the extended sPlots from the covariance matrix

        if (nFixdSpecies_ <= 0) {
                return;
        }

        Int_t species_n(0);
        for (NumbMap::const_iterator iter_n = freeSpecies_.begin(); iter_n != freeSpecies_.end(); ++iter_n) {
                Int_t species_j(0);
                const TString& specName = iter_n->first;
                Double_t value = iter_n->second;
                cN_[exclName][specName] = value;
                for (NumbMap::const_iterator iter_j = freeSpecies_.begin(); iter_j != freeSpecies_.end(); ++iter_j) {
                        if (covmat) {
                                cN_[exclName][specName] -= covmat[species_n*nSpecies_+species_j];
                        } else {
                                cN_[exclName][specName] -= covMat_(species_n,species_j);
                        }
                        ++species_j;
                }
                ++species_n;
        }
}

void LauSPlot::calcSWeights(const TString& exclName, Double_t *covmat)
{
        // Computes the sWeights from the covariance matrix
        // NB for the extended sPlot the sum in the denominator is still over all species,
        // while that in the numerator is only over the free species.
        // Similarly the sWeights can only be calculated for the free species.

        Double_t numerator(0.0), denominator(0.0);
        for (Int_t iEvent = 0; iEvent < nEvents_; ++iEvent) {
                denominator = 0.0;
                for (NumbMap::const_iterator free_iter = freeSpecies_.begin(); free_iter != freeSpecies_.end(); ++free_iter) {
                        denominator += free_iter->second * pdfTot_[iEvent][free_iter->first];
                }
                for (NumbMap::const_iterator fixd_iter = fixdSpecies_.begin(); fixd_iter != fixdSpecies_.end(); ++fixd_iter) {
                        denominator += fixd_iter->second * pdfTot_[iEvent][fixd_iter->first];
                }
                Int_t species_n(0);
                for (NumbMap::const_iterator iter_n = freeSpecies_.begin(); iter_n != freeSpecies_.end(); ++iter_n) {
                        numerator = 0.0;
                        Int_t species_j(0);
                        for (NumbMap::const_iterator iter_j = freeSpecies_.begin(); iter_j != freeSpecies_.end(); ++iter_j) {
                                if (covmat) {
                                        numerator += covmat[species_n*nSpecies_+species_j] * pdfTot_[iEvent][iter_j->first];
                                } else {
                                        numerator += covMat_(species_n,species_j) * pdfTot_[iEvent][iter_j->first];
                                }
                                ++species_j;
                        }
                        sWeights_[iEvent][exclName][iter_n->first] = numerator/denominator;
                        ++species_n;
                }
        }
}

void LauSPlot::fillCNBranches()
{
        if (!cnTree_) {
                cerr<<"ERROR in LauSPlot::fillCNBranches : Tree not created, cannot fill branches."<<endl;
                return;
        } else if (!this->definedCNBranches()) {
                this->defineCNBranches();
        }
        cnTree_->Fill();
}

void LauSPlot::fillSWeightBranches()
{
        if (!sweightTree_) {
                cerr<<"ERROR in LauSPlot::fillSWeightBranches : Tree not created, cannot fill branches."<<endl;
                return;
        } else if (sWeights_.empty()) {
                cerr<<"ERROR in LauSPlot::fillSWeightBranches : No sWeights calculated, can't fill branches."<<endl;
                return;
        } else if (!this->definedSWeightBranches()) {
                this->copyEventWeights(0);
                this->defineSWeightBranches();
        }

        for (Int_t iEvent = 0; iEvent < nEvents_; ++iEvent) {
                this->copyEventWeights(iEvent);
                sweightTree_->Fill();
        }
}

void LauSPlot::copyEventWeights(Int_t iEvent)
{
        for (std::map<TString,NumbMap>::const_iterator excl_iter = sWeights_[iEvent].begin(); excl_iter != sWeights_[iEvent].end(); ++excl_iter) {
                const TString& exclName = excl_iter->first;
                const NumbMap& species = excl_iter->second;
                for (NumbMap::const_iterator spec_iter = species.begin(); spec_iter != species.end(); ++spec_iter) {
                        const TString& specName = spec_iter->first;
                        sWeightsCurrent_[exclName][specName] = spec_iter->second;
                }
        }
}

void LauSPlot::writeOutResults()
{
        // write out the results

        // remove the transient objects that we don't want (re-)written to the file
        if (eventList_) {
                delete eventList_; eventList_ = 0;
        }
        if (inputTree_) {
                delete inputTree_; inputTree_ = 0;
        }

        // first add the input tree as a friend of the output tree
        this->addFriendTree();

        // then write everything to the file and clean up
        file_->cd();
        file_->Write();
        file_->Close();
        delete file_; file_ = 0;
}

void LauSPlot::addFriendTree()
{
        if (!sweightTree_) {
                cerr<<"ERROR in LauSPlot::addFriendTree : Tree not created, cannot add friend."<<endl;
                return;
        }
        sweightTree_->AddFriend(inputTreeName_,fileName_);
}

void Yields(Int_t &, Double_t *, Double_t &f, Double_t *x, Int_t /*iflag*/)
{
        // FCN-function for Minuit

        f = 0.0;

        TVirtualFitter *fitter = TVirtualFitter::GetFitter();
        LauSPlot* theModel = dynamic_cast<LauSPlot*>(fitter->GetObjectFit());
        const std::vector<LauSPlot::NumbMap>& pdfTot = theModel->totalPdf();

        Double_t ntot(0.0);
        for (std::vector<LauSPlot::NumbMap>::const_iterator evt_iter = pdfTot.begin(); evt_iter != pdfTot.end(); ++evt_iter) {  // loop over events
                const LauSPlot::NumbMap& species = (*evt_iter);
                Int_t ispecies(0);
                Double_t lik(0.0);
                ntot = 0.0;
                for (LauSPlot::NumbMap::const_iterator spec_iter = species.begin(); spec_iter != species.end(); ++spec_iter) {  // loop over species
                        lik += x[ispecies] * spec_iter->second;
                        ntot += x[ispecies];
                        ++ispecies;
                }
                if (lik < 0.0) {
                        // make f the worst possible value to force MINUIT
                        // out of this region of parameter space
                        f = -DBL_MAX;
                        break;
                } else {
                        f += TMath::Log(lik);
                }
        }

        // extended likelihood
        f = (ntot-f);
}