PixelLumiDQM.cc

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// -*- C++ -*-

// Package:    PixelLumiDQM
// Class:      PixelLumiDQM

// Author: Amita Raval
// Based on Jeroen Hegeman's code for Pixel Cluster Count Luminosity

#include "PixelLumiDQM.h"

#include "DataFormats/Common/interface/Handle.h"
#include "DataFormats/DetId/interface/DetId.h"
#include "DataFormats/GeometryVector/interface/Pi.h"
#include "DataFormats/GeometryVector/interface/LocalPoint.h"
#include "DataFormats/GeometryVector/interface/GlobalPoint.h"
#include "DataFormats/SiPixelDetId/interface/PixelSubdetector.h"
#include "DataFormats/SiPixelDetId/interface/PixelBarrelName.h"
#include "DataFormats/SiPixelDetId/interface/PixelEndcapName.h"
#include "DataFormats/SiPixelCluster/interface/SiPixelCluster.h"
#include "DQMServices/Core/interface/DQMEDAnalyzer.h"
#include "DQMServices/Core/interface/DQMStore.h"
#include "DQMServices/Core/interface/MonitorElement.h"
#include "FWCore/Framework/interface/ESHandle.h"
#include "FWCore/Framework/interface/Event.h"
#include "FWCore/Framework/interface/EventSetup.h"
#include "FWCore/Framework/interface/LuminosityBlock.h"
#include "FWCore/Framework/interface/MakerMacros.h"
#include "FWCore/Framework/interface/Run.h"
#include "FWCore/ParameterSet/interface/ParameterSet.h"
#include "FWCore/MessageLogger/interface/MessageLogger.h"
#include "FWCore/ServiceRegistry/interface/Service.h"
#include "FWCore/Utilities/interface/EDMException.h"
#include "Geometry/CommonTopologies/interface/PixelTopology.h"
#include "Geometry/Records/interface/TrackerDigiGeometryRecord.h"
#include "Geometry/TrackerGeometryBuilder/interface/PixelGeomDetUnit.h"
#include "Geometry/TrackerGeometryBuilder/interface/TrackerGeometry.h"

#include <fstream>
#include <map>
#include <string>
#include <sys/time.h>
#include <time.h>
#include <vector>

const unsigned int PixelLumiDQM::lastBunchCrossing;

// Constructors and destructor.
PixelLumiDQM::PixelLumiDQM(const edm::ParameterSet& iConfig):
  fPixelClusterLabel(consumes<edmNew::DetSetVector<SiPixelCluster> >(iConfig.getUntrackedParameter<edm::InputTag>("pixelClusterLabel",
                       edm::InputTag("siPixelClusters")))),
  fIncludePixelClusterInfo(iConfig.getUntrackedParameter<bool>("includePixelClusterInfo", true)),
  fIncludePixelQualCheckHistos(iConfig.getUntrackedParameter<bool>("includePixelQualCheckHistos", true)),
  fResetIntervalInLumiSections(iConfig.getUntrackedParameter<int>("resetEveryNLumiSections", 1)),
  fDeadModules(iConfig.getUntrackedParameter<std::vector<uint32_t> >("deadModules", std::vector<uint32_t>())),
  fMinPixelsPerCluster(iConfig.getUntrackedParameter<int>("minNumPixelsPerCluster", 0)),
  fMinClusterCharge(iConfig.getUntrackedParameter<double>("minChargePerCluster", 0)),
  bunchTriggerMask(lastBunchCrossing+1,false),
  filledAndUnmaskedBunches(0),
  useInnerBarrelLayer(iConfig.getUntrackedParameter<bool>("useInnerBarrelLayer", false)),
  fLogFileName_(iConfig.getUntrackedParameter<std::string>("logFileName","/tmp/pixel_lumi.txt"))
{
  edm::LogInfo("Configuration")
    << "PixelLumiDQM looking for pixel clusters in '"
    << iConfig.getUntrackedParameter<edm::InputTag>("pixelClusterLabel",
                       edm::InputTag("siPixelClusters")) << "'";
  edm::LogInfo("Configuration")
    << "PixelLumiDQM storing pixel cluster info? "
    << fIncludePixelClusterInfo;
  edm::LogInfo("Configuration")
    << "PixelLumiDQM storing pixel cluster quality check histograms? "
    << fIncludePixelQualCheckHistos;

  if (!fDeadModules.size()) {
    edm::LogInfo("Configuration")
      << "No pixel modules specified to be ignored";
  } else {
    edm::LogInfo("Configuration")
      << fDeadModules.size() << " pixel modules specified to be ignored:";
    for (std::vector<uint32_t>::const_iterator it = fDeadModules.begin();
         it != fDeadModules.end(); ++it) {
      edm::LogInfo("Configuration")
        << "  " << *it;
    }
  }
  edm::LogInfo("Configuration")
    << "Ignoring pixel clusters with less than "
    << fMinPixelsPerCluster << " pixels";
  edm::LogInfo("Configuration")
    << "Ignoring pixel clusters with charge less than "
    << fMinClusterCharge;
}


PixelLumiDQM::~PixelLumiDQM()
{
}


void
PixelLumiDQM::fillDescriptions(edm::ConfigurationDescriptions& descriptions) {
  edm::ParameterSetDescription desc;
  desc.setUnknown();
  descriptions.addDefault(desc);
}


void
PixelLumiDQM::analyze(const edm::Event& iEvent,
              const edm::EventSetup& iSetup)
{
  // Collect all bookkeeping information.
  fRunNo = iEvent.id().run();
  fEvtNo = iEvent.id().event();
  fLSNo = iEvent.getLuminosityBlock().luminosityBlock();
  fBXNo = iEvent.bunchCrossing();
  fTimestamp = iEvent.time().unixTime();
  fHistBunchCrossings->Fill(float(fBXNo)); 
  fHistBunchCrossingsLastLumi->Fill(float(fBXNo)); 
  // This serves as event counter to compute luminosity from cluster counts.
  std::map<int, PixelClusterCount>::iterator it = fNumPixelClusters.find(fBXNo);
  if(it==fNumPixelClusters.end()) fNumPixelClusters[fBXNo] = PixelClusterCount();

  if (fIncludePixelClusterInfo) {
    // Find tracker geometry.
    edm::ESHandle<TrackerGeometry> trackerGeo;
    iSetup.get<TrackerDigiGeometryRecord>().get(trackerGeo);
    
    // Find pixel clusters.
    edm::Handle<edmNew::DetSetVector<SiPixelCluster> > pixelClusters;
    iEvent.getByToken(fPixelClusterLabel, pixelClusters);
    
    // Loop over entire tracker geometry.
    for (TrackerGeometry::DetContainer::const_iterator
           i = trackerGeo->dets().begin();
         i != trackerGeo->dets().end(); ++i) {
      // See if this is a pixel unit(?).
         
      if ( GeomDetEnumerators::isTrackerPixel((*i)->subDetector())) {
        DetId detId = (*i)->geographicalId();
        // Find all clusters on this detector module.
        edmNew::DetSetVector<SiPixelCluster>::const_iterator iSearch =
          pixelClusters->find(detId);
        if (iSearch != pixelClusters->end()) {
      
          // Count the number of clusters with at least a minimum
          // number of pixels per cluster and at least a minimum charge.
          size_t numClusters = 0;
          for (edmNew::DetSet<SiPixelCluster>::const_iterator
                 itClus = iSearch->begin();
               itClus != iSearch->end(); ++itClus) {
            if ((itClus->size() >= fMinPixelsPerCluster) &&
                (itClus->charge() >= fMinClusterCharge)) {
              ++numClusters;
            }
          }
            // DEBUG DEBUG DEBUG
          assert(numClusters <= iSearch->size());
          // DEBUG DEBUG DEBUG end
      
          // Add up the cluster count based on the position of this detector element.
          if (detId.subdetId() == PixelSubdetector::PixelBarrel) {
            PixelBarrelName detName = PixelBarrelName(detId);
            int layer = detName.layerName();
            fNumPixelClusters[fBXNo].numB.at(layer - 1) += numClusters;
            fNumPixelClusters[fBXNo].dnumB.at(layer - 1) += sqrt(numClusters);
          } else {
            // DEBUG DEBUG DEBUG
            assert(detId.subdetId() == PixelSubdetector::PixelEndcap);
            // DEBUG DEBUG DEBUG end
        
            PixelEndcapName detName = PixelEndcapName(detId);
            PixelEndcapName::HalfCylinder halfCylinder = detName.halfCylinder();
            int disk = detName.diskName();
            switch (halfCylinder) {
              case PixelEndcapName::mO:
              case PixelEndcapName::mI:
                fNumPixelClusters[fBXNo].numFM.at(disk - 1) += numClusters;
                fNumPixelClusters[fBXNo].dnumFM.at(disk - 1) += sqrt(numClusters);
                break;
              case PixelEndcapName::pO:
              case PixelEndcapName::pI:
                fNumPixelClusters[fBXNo].numFP.at(disk - 1) += numClusters;
                fNumPixelClusters[fBXNo].dnumFP.at(disk - 1) += sqrt(numClusters);
                break;
              default:
                assert(false);
                break;
            }
          }
        }
      }
    }
  }
  // ----------

  // Fill some pixel cluster quality check histograms if requested.
  if (fIncludePixelQualCheckHistos) {
    
    // Find tracker geometry.
    edm::ESHandle<TrackerGeometry> trackerGeo;
    iSetup.get<TrackerDigiGeometryRecord>().get(trackerGeo);
    
    // Find pixel clusters.
    edm::Handle<edmNew::DetSetVector<SiPixelCluster> > pixelClusters;
    iEvent.getByToken(fPixelClusterLabel, pixelClusters);
    
    bool filterDeadModules = (fDeadModules.size() > 0);
    std::vector<uint32_t>::const_iterator deadModulesBegin = fDeadModules.begin();
    std::vector<uint32_t>::const_iterator deadModulesEnd = fDeadModules.end();
    
    // Loop over entire tracker geometry.
    for (TrackerGeometry::DetContainer::const_iterator
           i = trackerGeo->dets().begin();
         i != trackerGeo->dets().end(); ++i) {
      
      // See if this is a pixel module.
      if ( GeomDetEnumerators::isTrackerPixel((*i)->subDetector())) {
        DetId detId = (*i)->geographicalId();
    
        // Skip this module if it's on the list of modules to be ignored.
        if (filterDeadModules &&
            find(deadModulesBegin, deadModulesEnd, detId()) != deadModulesEnd) {
          continue;
        }
    
        // Find all clusters in this module.
        edmNew::DetSetVector<SiPixelCluster>::const_iterator iSearch =
          pixelClusters->find(detId);
    
        // Loop over all clusters in this module.
        if (iSearch != pixelClusters->end()) {
          for (edmNew::DetSet<SiPixelCluster>::const_iterator clus = iSearch->begin();
               clus != iSearch->end(); ++clus) {
        
            if ((clus->size() >= fMinPixelsPerCluster) &&
                (clus->charge() >= fMinClusterCharge)) {
          
              PixelGeomDetUnit const* theGeomDet =
                dynamic_cast<PixelGeomDetUnit const*>(trackerGeo->idToDet(detId));
              PixelTopology const* topol = &(theGeomDet->specificTopology());
              double x = clus->x();
              double y = clus->y();
              LocalPoint clustLP = topol->localPosition(MeasurementPoint(x, y));
              GlobalPoint clustGP = theGeomDet->surface().toGlobal(clustLP);
              double charge = clus->charge() / 1.e3;
              int size = clus->size();
          
              if (detId.subdetId() == PixelSubdetector::PixelBarrel) {
                PixelBarrelName detName = PixelBarrelName(detId);
                int layer = detName.layerName();
                switch (layer) {
                case 1:
                  fHistContainerThisRun["clusPosBarrel1"]->Fill(clustGP.z(), clustGP.phi());
                  fHistContainerThisRun["clusChargeBarrel1"]->Fill(iEvent.bunchCrossing(), charge);
                  fHistContainerThisRun["clusSizeBarrel1"]->Fill(iEvent.bunchCrossing(), size);
                  break;
                case 2:
                  fHistContainerThisRun["clusPosBarrel2"]->Fill(clustGP.z(), clustGP.phi());
                  fHistContainerThisRun["clusChargeBarrel2"]->Fill(iEvent.bunchCrossing(), charge);
                  fHistContainerThisRun["clusSizeBarrel2"]->Fill(iEvent.bunchCrossing(), size);
                  break;
                case 3:
                  fHistContainerThisRun["clusPosBarrel3"]->Fill(clustGP.z(), clustGP.phi());
                  fHistContainerThisRun["clusChargeBarrel3"]->Fill(iEvent.bunchCrossing(), charge);
                  fHistContainerThisRun["clusSizeBarrel3"]->Fill(iEvent.bunchCrossing(), size);
                  break;
                default:
                  assert(false);
                  break;
                }
              } else {
                
                // DEBUG DEBUG DEBUG
                assert(detId.subdetId() == PixelSubdetector::PixelEndcap);
                // DEBUG DEBUG DEBUG end
                
                PixelEndcapName detName = PixelEndcapName(detId);
                PixelEndcapName::HalfCylinder halfCylinder = detName.halfCylinder();
                int disk = detName.diskName();
                switch (halfCylinder) {
                  case PixelEndcapName::mO:
                  case PixelEndcapName::mI:
                    switch (disk) {
                      case 1:
                        fHistContainerThisRun["clusPosEndCapM1"]->Fill(clustGP.x(), clustGP.y());
                        fHistContainerThisRun["clusChargeEndCapM1"]->Fill(iEvent.bunchCrossing(), charge);
                        fHistContainerThisRun["clusSizeEndCapM1"]->Fill(iEvent.bunchCrossing(), size);
                        break;
                      case 2:
                        fHistContainerThisRun["clusPosEndCapM2"]->Fill(clustGP.x(), clustGP.y());
                        fHistContainerThisRun["clusChargeEndCapM2"]->Fill(iEvent.bunchCrossing(), charge);
                        fHistContainerThisRun["clusSizeEndCapM2"]->Fill(iEvent.bunchCrossing(), size);
                        break;
                      default:
                        assert(false);
                        break;
                    }
                    break;
                  case PixelEndcapName::pO:
                  case PixelEndcapName::pI:
                    switch (disk) {
                      case 1:
                        fHistContainerThisRun["clusPosEndCapP1"]->Fill(clustGP.x(), clustGP.y());
                        fHistContainerThisRun["clusChargeEndCapP1"]->Fill(iEvent.bunchCrossing(), charge);
                        fHistContainerThisRun["clusSizeEndCapP1"]->Fill(iEvent.bunchCrossing(), size);
                        break;
                      case 2:
                        fHistContainerThisRun["clusPosEndCapP2"]->Fill(clustGP.x(), clustGP.y());
                        fHistContainerThisRun["clusChargeEndCapP2"]->Fill(iEvent.bunchCrossing(), charge);
                        fHistContainerThisRun["clusSizeEndCapP2"]->Fill(iEvent.bunchCrossing(), size);
                        break;
                      default:
                        assert(false);
                        break;
                    }
                    break;
                  default:
                    assert(false);
                    break;
                }
              }
            }
          }
        }
      }
    }
  }
} 

void
PixelLumiDQM::bookHistograms(DQMStore::IBooker & ibooker, 
                                  edm::Run const & run,
                                  edm::EventSetup const & /* iSetup */)
{
  edm::LogInfo("Status") << "Starting processing of run #" << run.id().run();

  // Top folder containing high-level information about pixel and HF lumi.  
  std::string folder = "PixelLumi/";
  ibooker.setCurrentFolder(folder);
  
  fHistTotalRecordedLumiByLS = ibooker.book1D("totalPixelLumiByLS","Pixel Lumi in nb vs LS",8000,0.5,8000.5);
  fHistRecordedByBxCumulative = ibooker.book1D("PXLumiByBXsum","Pixel Lumi in nb by BX Cumulative vs LS",lastBunchCrossing,
                         0.5,float(lastBunchCrossing)+0.5);

  std::string subfolder = folder + "lastLS/";
  ibooker.setCurrentFolder(subfolder);
  fHistRecordedByBxLastLumi = ibooker.book1D("PXByBXLastLumi","Pixel By BX Last Lumi",lastBunchCrossing+1,
                       -0.5,float(lastBunchCrossing)+0.5);

  subfolder = folder+"ClusterCountingDetails/";
  ibooker.setCurrentFolder(subfolder);

  fHistnBClusVsLS[0] = ibooker.book1D("nBClusVsLS_0","Fraction of Clusters vs LS Barrel layer 0",8000,0.5,8000.5);
  fHistnBClusVsLS[1] = ibooker.book1D("nBClusVsLS_1","Fraction of Clusters vs LS Barrel layer 1",8000,0.5,8000.5);
  fHistnBClusVsLS[2] = ibooker.book1D("nBClusVsLS_2","Fraction of Clusters vs LS Barrel layer 2",8000,0.5,8000.5);
  fHistnFPClusVsLS[0] = ibooker.book1D("nFPClusVsLS_0","Fraction of Clusters vs LS Barrel layer 0",8000,0.5,8000.5);
  fHistnFPClusVsLS[1] = ibooker.book1D("nFPClusVsLS_1","Fraction of Clusters vs LS Barrel layer 1",8000,0.5,8000.5);
  fHistnFMClusVsLS[0] = ibooker.book1D("nFMClusVsLS_0","Fraction of Clusters vs LS Barrel layer 0",8000,0.5,8000.5);
  fHistnFMClusVsLS[1] = ibooker.book1D("nFMClusVsLS_1","Fraction of Clusters vs LS Barrel layer 1",8000,0.5,8000.5);
  fHistBunchCrossings = ibooker.book1D("BunchCrossings","Cumulative Bunch Crossings",lastBunchCrossing,
                 0.5,float(lastBunchCrossing)+0.5);
  fHistBunchCrossingsLastLumi = ibooker.book1D("BunchCrossingsLL","Bunch Crossings Last Lumi",lastBunchCrossing,
                     0.5,float(lastBunchCrossing)+0.5);
  fHistClusterCountByBxLastLumi = ibooker.book1D("ClusterCountByBxLL","Cluster Count by BX Last Lumi",lastBunchCrossing,
                     0.5,float(lastBunchCrossing)+0.5);
  fHistClusterCountByBxCumulative = ibooker.book1D("ClusterCountByBxSum","Cluster Count by BX Cumulative",lastBunchCrossing,
                     0.5,float(lastBunchCrossing)+0.5);
  fHistClusByLS = ibooker.book1D("totalClusByLS","Number of Clusters all dets vs LS",8000,0.5,8000.5);

  // Add some pixel cluster quality check histograms (in a subfolder).
  subfolder = folder+"qualityChecks/";
  ibooker.setCurrentFolder(subfolder);
  
  if (fIncludePixelQualCheckHistos) {
    // Create histograms for this run if not already present in our list.
    edm::LogInfo("Status") << "Creating histograms for run #" << run.id().run();
    
    // Pixel cluster positions in the barrel - (z, phi).
    for (size_t i = 1; i <= kNumLayers; ++i) {
      std::stringstream key;
      key << "clusPosBarrel" << i;
      std::stringstream name;
      name << key.str() << "_" << run.run();
      std::stringstream title;
      title << "Pixel cluster position - barrel layer " << i;
      fHistContainerThisRun[key.str()] = ibooker.book2D(name.str().c_str(),
                        title.str().c_str(),
                        100, -30., 30.,
                        64, -Geom::pi(), Geom::pi());
    }
    
    // Pixel cluster positions in the endcaps (x, y).
    std::vector<std::string> sides;
    sides.push_back("M");
    sides.push_back("P");
    for (std::vector<std::string>::const_iterator side = sides.begin();
         side != sides.end(); ++side) {
      for (size_t i = 1; i <= kNumDisks; ++i) {
        std::stringstream key;
        key << "clusPosEndCap" << *side << i;
        std::stringstream name;
        name << key.str() << "_" << run.run();
        std::stringstream title;
        title << "Pixel cluster position - endcap disk " << i;
        fHistContainerThisRun[key.str()] = ibooker.book2D(name.str().c_str(),
                          title.str().c_str(),
                          100, -20., 20.,
                          100, -20., 20.);
      }
    }
    
    // Pixel cluster charge in the barrel, per bx.
    for (size_t i = 1; i <= kNumLayers; ++i) {
      std::stringstream key;
      key << "clusChargeBarrel" << i;
      std::stringstream name;
      name << key.str() << "_" << run.run();
      std::stringstream title;
      title << "Pixel cluster charge - barrel layer " << i;
      fHistContainerThisRun[key.str()] = ibooker.book2D(name.str().c_str(),
                        title.str().c_str(),
                        3564, .5, 3564.5,
                        100, 0., 100.);
    }

    // Pixel cluster charge in the endcaps, per bx.
    for (std::vector<std::string>::const_iterator side = sides.begin();
         side != sides.end(); ++side) {
      for (size_t i = 1; i <= kNumDisks; ++i) {
        std::stringstream key;
        key << "clusChargeEndCap" << *side << i;
        std::stringstream name;
        name << key.str() << "_" << run.run();
        std::stringstream title;
        title << "Pixel cluster charge - endcap disk " << i;
        fHistContainerThisRun[key.str()] = ibooker.book2D(name.str().c_str(),
                                    title.str().c_str(),
                                    3564, .5, 3564.5,
                                    100, 0., 100.);
      }
    }

    // Pixel cluster size in the barrel, per bx.
    for (size_t i = 1; i <= kNumLayers; ++i) {
      std::stringstream key;
      key << "clusSizeBarrel" << i;
      std::stringstream name;
      name << key.str() << "_" << run.run();
      std::stringstream title;
      title << "Pixel cluster size - barrel layer " << i;
      fHistContainerThisRun[key.str()] = ibooker.book2D(name.str().c_str(),
                                  title.str().c_str(),
                                  3564, .5, 3564.5,
                                  100, 0., 100.);
    }

    // Pixel cluster size in the endcaps, per bx.
    for (std::vector<std::string>::const_iterator side = sides.begin();
         side != sides.end(); ++side) {
      for (size_t i = 1; i <= kNumDisks; ++i) {
        std::stringstream key;
        key << "clusSizeEndCap" << *side << i;
        std::stringstream name;
        name << key.str() << "_" << run.run();
        std::stringstream title;
        title << "Pixel cluster size - endcap disk " << i;
        fHistContainerThisRun[key.str()] = ibooker.book2D(name.str().c_str(),
                                    title.str().c_str(),
                                    3564, .5, 3564.5,
                                    100, 0., 100.);
      }
    }
  }
}

// ------------ Method called when ending the processing of a run.  ------------
void
PixelLumiDQM::dqmBeginRun(edm::Run const&, edm::EventSetup const&)
{
}

// ------------ Method called when ending the processing of a run.  ------------
void
PixelLumiDQM::endRun(edm::Run const&, edm::EventSetup const&)
{
}


// ------------ Method called when starting to process a luminosity block.  ------------
void
PixelLumiDQM::beginLuminosityBlock(edm::LuminosityBlock const&lumiBlock,
                   edm::EventSetup const&)
{
  // Only reset and fill every fResetIntervalInLumiSections (default is 1 LS)
  // Return unless the PREVIOUS LS was at the right modulo value 
  // (e.g. is resetinterval = 5 the rest will only be executed at LS=6
  // NB: reset is done here so the histograms by LS are sent before resetting.
  // NB: not being used for now since default is 1 LS. There is a bug here.

  unsigned int ls = lumiBlock.luminosityBlockAuxiliary().luminosityBlock();

  if((ls-1)%fResetIntervalInLumiSections==0){
    fHistBunchCrossingsLastLumi->Reset();
    fHistClusterCountByBxLastLumi->Reset();
    fHistRecordedByBxLastLumi->Reset();
  }
}


// ------------ Method called when ending the processing of a luminosity block.  ------------
void
PixelLumiDQM::endLuminosityBlock(edm::LuminosityBlock const& lumiBlock,
                 edm::EventSetup const&es)
{
  
  unsigned int ls = lumiBlock.luminosityBlockAuxiliary().luminosityBlock();
  
  // Only fill every fResetIntervalInLumiSections (default is 1 LS)
  if(ls%fResetIntervalInLumiSections!=0) return;
  
  printf("Lumi Block = %d\n",ls);

  if((ls-1)%fResetIntervalInLumiSections==0){
  }
  
  unsigned int nBClus[3] = {0,0,0};
  unsigned int nFPClus[2] = {0, 0};
  unsigned int nFMClus[2] = {0, 0};
  
  double total_recorded = 0.;
  double total_recorded_unc_square = 0.;
  
  // Obtain bunch-by-bunch cluster counts and compute totals for lumi calculation.
  double totalcounts = 0.0;
  double etotalcounts = 0.0;
  double totalevents = 0.0;
  double lumi_factor_per_bx = 0.0;
  if(useInnerBarrelLayer) 
    lumi_factor_per_bx = FREQ_ORBIT * SECONDS_PER_LS * fResetIntervalInLumiSections / XSEC_PIXEL_CLUSTER  ;
  else
    lumi_factor_per_bx = FREQ_ORBIT * SECONDS_PER_LS * fResetIntervalInLumiSections / rXSEC_PIXEL_CLUSTER  ;
  
  for(std::map<int, PixelClusterCount>::iterator it = fNumPixelClusters.begin();
      it != fNumPixelClusters.end(); it++) {
    
    // Sum all clusters for this BX.
    unsigned int total = (*it).second.numB.at(1)+
      (*it).second.numB.at(2)+(*it).second.numFP.at(0)+(*it).second.numFP.at(1)+
      (*it).second.numFM.at(0)+(*it).second.numFM.at(1);
    if(useInnerBarrelLayer) total+=(*it).second.numB.at(0);
    totalcounts += total;
    double etotal = (*it).second.dnumB.at(1)+
      (*it).second.dnumB.at(2)+(*it).second.dnumFP.at(0)+(*it).second.dnumFP.at(1)+
      (*it).second.dnumFM.at(0)+(*it).second.dnumFM.at(1);
    if(useInnerBarrelLayer) etotal = (*it).second.dnumB.at(0);
    etotalcounts += etotal;
    etotal = sqrt(etotal);

    fHistClusterCountByBxLastLumi->setBinContent((*it).first,total);
    fHistClusterCountByBxLastLumi->setBinError((*it).first,etotal);
    fHistClusterCountByBxCumulative->setBinContent((*it).first,fHistClusterCountByBxCumulative->getBinContent((*it).first)+total);
    
    unsigned int events_per_bx = fHistBunchCrossingsLastLumi->getBinContent((*it).first);
    totalevents += events_per_bx;
    double average_cluster_count = events_per_bx !=0 ? double(total)/events_per_bx : 0.;
    double average_cluster_count_unc = events_per_bx!=0 ? etotal/events_per_bx : 0.;
    double pixel_bx_lumi_per_ls =  lumi_factor_per_bx * average_cluster_count / CM2_TO_NANOBARN ;
    double pixel_bx_lumi_per_ls_unc = 0.0;
    if(useInnerBarrelLayer) 
      pixel_bx_lumi_per_ls_unc = sqrt(lumi_factor_per_bx*lumi_factor_per_bx *
                      (average_cluster_count_unc*average_cluster_count_unc +
                       (average_cluster_count*  XSEC_PIXEL_CLUSTER_UNC /
                    XSEC_PIXEL_CLUSTER )*
                       (average_cluster_count*  XSEC_PIXEL_CLUSTER / 
                    XSEC_PIXEL_CLUSTER ))
                      ) / CM2_TO_NANOBARN ;
    else
      pixel_bx_lumi_per_ls_unc = sqrt(lumi_factor_per_bx*lumi_factor_per_bx *
                      (average_cluster_count_unc*average_cluster_count_unc +
                       (average_cluster_count*  rXSEC_PIXEL_CLUSTER_UNC /
                    rXSEC_PIXEL_CLUSTER )*
                       (average_cluster_count*  rXSEC_PIXEL_CLUSTER / 
                    rXSEC_PIXEL_CLUSTER ))
                      ) / CM2_TO_NANOBARN ;
    
    fHistRecordedByBxLastLumi->setBinContent((*it).first,pixel_bx_lumi_per_ls);
    fHistRecordedByBxLastLumi->setBinError((*it).first,pixel_bx_lumi_per_ls_unc);
    
    fHistRecordedByBxCumulative->setBinContent((*it).first,
                           fHistRecordedByBxCumulative->getBinContent((*it).first)+
                           pixel_bx_lumi_per_ls);
    
    /*
      if(fHistRecordedByBxLastLumi->getBinContent((*it).first)!=0.)
      fHistRecordedByBxLastLumi->getBinContent((*it).first));
      if(fHistRecordedByBxCumulative->getBinContent((*it).first)!=0.)
      fHistRecordedByBxCumulative->getBinContent((*it).first));
    */

    nBClus[0] +=(*it).second.numB.at(0);
    nBClus[1] +=(*it).second.numB.at(1);
    nBClus[2] +=(*it).second.numB.at(2);
    nFPClus[0] +=(*it).second.numFP.at(0);
    nFPClus[1] +=(*it).second.numFP.at(1);
    nFMClus[0] +=(*it).second.numFM.at(0);
    nFMClus[1] +=(*it).second.numFM.at(1);
    
    // Reset counters 
    (*it).second.Reset();

    // std::cout << "bx="<< (*it).first << " clusters=" << (*it).second.numB.at(0)) << std::endl; 
  }

  if((filledAndUnmaskedBunches = calculateBunchMask(fHistClusterCountByBxCumulative,bunchTriggerMask))!=0){
    for(unsigned int i = 0; i<= lastBunchCrossing; i++){
      if(bunchTriggerMask[i]){ 
        double err = fHistRecordedByBxLastLumi->getBinError(i);
        total_recorded += fHistRecordedByBxLastLumi->getBinContent(i);
        total_recorded_unc_square += err*err;
      }
    }
    
    // Replace the total obtained by summing over BXs with the average per BX from the total cluster count and rescale 
    
    if(totalevents > 10){
      total_recorded = lumi_factor_per_bx * totalcounts / totalevents / CM2_TO_NANOBARN ;
    }
    else total_recorded = 0.0;
    
    std::cout << " Total recorded " << total_recorded  << std::endl;
    fHistTotalRecordedLumiByLS->setBinContent(ls,total_recorded);
    fHistTotalRecordedLumiByLS->setBinError(ls,
                        sqrt(total_recorded_unc_square));
  }
  // fill cluster counts by detector regions for sanity checks
  unsigned int all_detectors_counts = 0;
  for(unsigned int i = 0; i < 3; i++){
    all_detectors_counts+=nBClus[i];
  }
  for(unsigned int i = 0; i < 2; i++){
    all_detectors_counts+=nFPClus[i];
  }
  for(unsigned int i = 0; i < 2; i++){
    all_detectors_counts+=nFMClus[i];
  }
  
  fHistClusByLS->setBinContent(ls, all_detectors_counts);
  
  for(unsigned int i = 0; i < 3; i++){
    fHistnBClusVsLS[i]->setBinContent(ls, 
                      float(nBClus[i])/float(all_detectors_counts));
  }
  for(unsigned int i = 0; i < 2; i++){
    fHistnFPClusVsLS[i]->setBinContent(ls, 
                       float(nFPClus[i])/float(all_detectors_counts));
  }
  for(unsigned int i = 0; i < 2; i++){
    fHistnFMClusVsLS[i]->setBinContent(ls, 
                       float(nFMClus[i])/float(all_detectors_counts));
  }
  
  logFile_.open(fLogFileName_.c_str(),std::ios_base::trunc);        

  timeval tv;
  gettimeofday(&tv,0);
  tm *ts = gmtime(&tv.tv_sec);
  char datestring[256];
  strftime(datestring, sizeof(datestring),"%Y.%m.%d %T GMT %s",ts);
  logFile_ << "RunNumber "<< fRunNo << std::endl;
  logFile_ << "EndTimeOfFit " << datestring << std::endl;
  logFile_ << "LumiRange "<< ls << "-" << ls << std::endl;
  logFile_ << "Fill "<< -99 << std::endl;
  logFile_ << "ActiveBunchCrossings "<< filledAndUnmaskedBunches << std::endl;
  logFile_ << "PixelLumi "<< fHistTotalRecordedLumiByLS->getBinContent(ls) * 0.98 << std::endl;
  logFile_ << "HFLumi "<< -99 << std::endl;
  logFile_ << "Ratio " << -99 << std::endl;
  logFile_.close();
}

unsigned int PixelLumiDQM::calculateBunchMask(MonitorElement *e, std::vector<bool> &mask){
  unsigned int nbins = e->getNbinsX();
  std::vector<float> ar(nbins,0.);
  for(unsigned int i = 1; i<= nbins; i++){
    ar[i] = e->getBinContent(i);
  }
  return calculateBunchMask(ar,nbins,mask);
}
unsigned int PixelLumiDQM::calculateBunchMask(std::vector<float> &e, unsigned int nbins, std::vector<bool> &mask){
  // Take the cumulative cluster count histogram and find max and average of non-empty bins.
  unsigned int active_count = 0;
  double maxc = 0.0;
  double ave = 0.0; // Average of non-empty bins
  unsigned int non_empty_bins = 0;
  
  for(unsigned int i = 1; i<= nbins; i++){
    double bin = e[i];
    if(bin !=0.0){
      if(maxc<bin) maxc = bin;
      ave += bin;
      non_empty_bins++;
    }      
  }
  
  ave /= non_empty_bins;
  std::cout << "Bunch mask finder - non empty bins " << non_empty_bins
        << " average of non empty bins " << ave 
        << " max content of one bin " << maxc << std::endl;
  double mean = 0.;
  double sigma = 0.;
  if(non_empty_bins < 50){
    mean = maxc;
    sigma = (maxc)/20;
  }    
  else{
    TH1F dist("dist","dist",500,0.,maxc+(maxc/500.)*20.);
    for(unsigned int i = 1; i<= nbins; i++){
      double bin = e[i];
      dist.Fill(bin);
    }  
    dist.Fit("gaus","","",fmax(0.,ave-(maxc-ave)/5.),maxc);
    TF1 *fit = dist.GetFunction("gaus");
    mean = fit->GetParameter("Mean");
    sigma = fit->GetParameter("Sigma");
  }
  std::cout << "Bunch mask will use mean" << mean << " sigma " << sigma << std::endl;
  // Active BX defined as those which have nclus within fixed standard deviations of peak.
  for(unsigned int i = 1; i<= nbins; i++){
    double bin = e[i];
    if(bin>0. && abs(bin-mean)<5.*(sigma)){ mask[i]=true; active_count++;}
  }
  std::cout << "Bunch mask finds " << active_count << " active bunch crossings " << std::endl;
  //   std::cout << "this is the full bx mask " ;
  //   for(unsigned int i = 1; i<= nbins; i++)
  //     std::cout << ((mask[i]) ? 1:0);
  //   std::cout << std::endl;
  return active_count;
}
// Define this as a CMSSW plug-in.
DEFINE_FWK_MODULE(PixelLumiDQM);