HBHEPhase1Reconstructor.cc

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// -*- C++ -*-
//
// Package:    RecoLocalCalo/HcalRecProducers
// Class:      HBHEPhase1Reconstructor
// 
//
// Original Author:  Igor Volobouev
//         Created:  Tue, 21 Jun 2016 00:56:40 GMT
//
//


// system include files
#include <cmath>
#include <utility>
#include <algorithm>

// user include files
#include "FWCore/Framework/interface/Frameworkfwd.h"
#include "FWCore/Framework/interface/stream/EDProducer.h"
#include "FWCore/Framework/interface/ESHandle.h"
#include "FWCore/Framework/interface/Event.h"
#include "FWCore/Framework/interface/MakerMacros.h"
#include "FWCore/Utilities/interface/Exception.h"

#include "FWCore/ParameterSet/interface/ParameterSet.h"
#include "FWCore/Utilities/interface/StreamID.h"

#include "DataFormats/HcalDetId/interface/HcalGenericDetId.h"
#include "DataFormats/HcalDigi/interface/HcalDigiCollections.h"
#include "DataFormats/HcalRecHit/interface/HcalRecHitCollections.h"
#include "DataFormats/METReco/interface/HcalPhase1FlagLabels.h"

#include "CalibFormats/HcalObjects/interface/HcalDbService.h"
#include "CalibFormats/HcalObjects/interface/HcalDbRecord.h"
#include "CalibFormats/HcalObjects/interface/HcalCoderDb.h"

#include "CalibFormats/CaloObjects/interface/CaloSamples.h"

#include "CalibCalorimetry/HcalAlgos/interface/HcalSiPMnonlinearity.h"

#include "RecoLocalCalo/HcalRecAlgos/interface/HcalSeverityLevelComputer.h"
#include "RecoLocalCalo/HcalRecAlgos/interface/HcalSeverityLevelComputerRcd.h"
#include "RecoLocalCalo/HcalRecAlgos/interface/HBHEStatusBitSetter.h"
#include "RecoLocalCalo/HcalRecAlgos/interface/HBHEPulseShapeFlag.h"

#include "CondFormats/HcalObjects/interface/HBHENegativeEFilter.h"
#include "CondFormats/DataRecord/interface/HBHENegativeEFilterRcd.h"

// Parser for Phase 1 HB/HE reco algorithms
#include "RecoLocalCalo/HcalRecAlgos/interface/parseHBHEPhase1AlgoDescription.h"

// Fetcher for reco algorithm data
#include "RecoLocalCalo/HcalRecAlgos/interface/fetchHcalAlgoData.h"

// Some helper functions
namespace {
    // Class for making SiPM/QIE11 look like HPD/QIE8. HPD/QIE8
    // needs only pedestal and gain to convert charge into energy.
    // Due to nonlinearities, response of SiPM/QIE11 is substantially
    // more complicated. It is possible to calculate all necessary
    // quantities from the charge and the info stored in the DB every
    // time the raw charge is needed. However, it does not make sense
    // to retrieve DB contents stored by channel for every time slice.
    // Because of this, we look things up only once, in the constructor.
    template<class DFrame>
    class RawChargeFromSample
    {
    public:
        inline RawChargeFromSample(const int sipmQTSShift,
                                   const int sipmQNTStoSum,
                                   const HcalDbService& cond,
                                   const HcalDetId id,
                                   const CaloSamples& cs,
                                   const int soi,
                                   const DFrame& frame,
                                   const int maxTS) {}

        inline double getRawCharge(const double decodedCharge,
                                   const double pedestal) const
            {return decodedCharge;}
    };

    template<>
    class RawChargeFromSample<QIE11DataFrame>
    {
    public:
        inline RawChargeFromSample(const int sipmQTSShift,
                                   const int sipmQNTStoSum,
                                   const HcalDbService& cond,
                                   const HcalDetId id,
                                   const CaloSamples& cs,
                                   const int soi,
                                   const QIE11DataFrame& frame,
                                   const int maxTS)
            : siPMParameter_(*cond.getHcalSiPMParameter(id)),
              fcByPE_(siPMParameter_.getFCByPE()),
              corr_(cond.getHcalSiPMCharacteristics()->getNonLinearities(siPMParameter_.getType()))
        {
            if (fcByPE_ <= 0.0)
                throw cms::Exception("HBHEPhase1BadDB")
                    << "Invalid fC/PE conversion factor for SiPM " << id
                    << std::endl;

            const HcalCalibrations& calib = cond.getHcalCalibrations(id);
            const int firstTS = std::max(soi + sipmQTSShift, 0);
            const int lastTS = std::min(firstTS + sipmQNTStoSum, maxTS);
            double sipmQ = 0.0;

            for (int ts = firstTS; ts < lastTS; ++ts)
            {
                const double pedestal = calib.pedestal(frame[ts].capid());
                sipmQ += (cs[ts] - pedestal);
            }

            const double effectivePixelsFired = sipmQ/fcByPE_;
            factor_ = corr_.getRecoCorrectionFactor(effectivePixelsFired);
        }

        inline double getRawCharge(const double decodedCharge,
                                   const double pedestal) const
        {
            return (decodedCharge - pedestal)*factor_ + pedestal;

            // Old version of TS-by-TS corrections looked as follows:
            // const double sipmQ = decodedCharge - pedestal;
            // const double nPixelsFired = sipmQ/fcByPE_;
            // return sipmQ*corr_.getRecoCorrectionFactor(nPixelsFired) + pedestal;
       }

    private:
        const HcalSiPMParameter& siPMParameter_;
        double fcByPE_;
        HcalSiPMnonlinearity corr_;
        double factor_;
    };

    float getTDCTimeFromSample(const QIE11DataFrame::Sample& s)
    {
        return HcalSpecialTimes::getTDCTime(s.tdc());
    }

    float getTDCTimeFromSample(const HcalQIESample&)
    {
        return HcalSpecialTimes::UNKNOWN_T_NOTDC;
    }

    float getDifferentialChargeGain(const HcalQIECoder& coder,
                                    const HcalQIEShape& shape,
                                    const unsigned adc,
                                    const unsigned capid,
                                    const bool isQIE11)
    {
        // We have 5-bit ADC mantissa in QIE8 and 6-bit in QIE11
        static const unsigned mantissaMaskQIE8 = 0x1f;
        static const unsigned mantissaMaskQIE11 = 0x3f;

        const float q = coder.charge(shape, adc, capid);
        const unsigned mantissaMask = isQIE11 ? mantissaMaskQIE11 : mantissaMaskQIE8;
        const unsigned mantissa = adc & mantissaMask;

        // First, check if we are in the two lowest or two highest ADC
        // values for this range. Assume that they have the lowest and
        // the highest gain in the range, respectively.
        if (mantissa == 0U || mantissa == mantissaMask - 1U)
            return coder.charge(shape, adc+1U, capid) - q;
        else if (mantissa == 1U || mantissa == mantissaMask)
            return q - coder.charge(shape, adc-1U, capid);
        else
        {
            const float qup = coder.charge(shape, adc+1U, capid);
            const float qdown = coder.charge(shape, adc-1U, capid);
            const float upGain = qup - q;
            const float downGain = q - qdown;
            const float averageGain = (qup - qdown)/2.f;
            if (std::abs(upGain - downGain) < 0.01f*averageGain)
                return averageGain;
            else
            {
                // We are in the gain transition region.
                // Need to determine if we are in the lower
                // gain ADC count or in the higher one.
                // This can be done by figuring out if the
                // "up" gain is more consistent then the
                // "down" gain.
                const float q2up = coder.charge(shape, adc+2U, capid);
                const float q2down = coder.charge(shape, adc-2U, capid);
                const float upGain2 = q2up - qup;
                const float downGain2 = qdown - q2down;
                if (std::abs(upGain2 - upGain) < std::abs(downGain2 - downGain))
                    return upGain;
                else
                    return downGain;
            }
        }
    }

    // The first element of the pair indicates presence of optical
    // link errors. The second indicated presence of capid errors.
    std::pair<bool,bool> findHWErrors(const HBHEDataFrame& df,
                                      const unsigned len)
    {
        bool linkErr = false;
        bool capidErr = false;
        if (len)
        {
            int expectedCapid = df[0].capid();
            for (unsigned i=0; i<len; ++i)
            {
                if (df[i].er())
                    linkErr = true;
                if (df[i].capid() != expectedCapid)
                    capidErr = true;
                expectedCapid = (expectedCapid + 1) % 4;
            }
        }
        return std::pair<bool,bool>(linkErr, capidErr);
    }

    std::pair<bool,bool> findHWErrors(const QIE11DataFrame& df,
                                      const unsigned /* len */)
    {
        return std::pair<bool,bool>(df.linkError(), df.capidError());
    }

    std::unique_ptr<HBHEStatusBitSetter> parse_HBHEStatusBitSetter(
        const edm::ParameterSet& psdigi)
    {
        return std::make_unique<HBHEStatusBitSetter>(
            psdigi.getParameter<double>("nominalPedestal"),
            psdigi.getParameter<double>("hitEnergyMinimum"),
            psdigi.getParameter<int>("hitMultiplicityThreshold"),
            psdigi.getParameter<std::vector<edm::ParameterSet> >("pulseShapeParameterSets"));
    }

    std::unique_ptr<HBHEPulseShapeFlagSetter> parse_HBHEPulseShapeFlagSetter(
        const edm::ParameterSet& psPulseShape, const bool setLegacyFlags)
    {
        return std::make_unique<HBHEPulseShapeFlagSetter>(
            psPulseShape.getParameter<double>("MinimumChargeThreshold"),
            psPulseShape.getParameter<double>("TS4TS5ChargeThreshold"),
            psPulseShape.getParameter<double>("TS3TS4ChargeThreshold"),
            psPulseShape.getParameter<double>("TS3TS4UpperChargeThreshold"),
            psPulseShape.getParameter<double>("TS5TS6ChargeThreshold"),
            psPulseShape.getParameter<double>("TS5TS6UpperChargeThreshold"),
            psPulseShape.getParameter<double>("R45PlusOneRange"),
            psPulseShape.getParameter<double>("R45MinusOneRange"),
            psPulseShape.getParameter<unsigned int>("TrianglePeakTS"),
            psPulseShape.getParameter<std::vector<double> >("LinearThreshold"),
            psPulseShape.getParameter<std::vector<double> >("LinearCut"),
            psPulseShape.getParameter<std::vector<double> >("RMS8MaxThreshold"),
            psPulseShape.getParameter<std::vector<double> >("RMS8MaxCut"),
            psPulseShape.getParameter<std::vector<double> >("LeftSlopeThreshold"),
            psPulseShape.getParameter<std::vector<double> >("LeftSlopeCut"),
            psPulseShape.getParameter<std::vector<double> >("RightSlopeThreshold"),
            psPulseShape.getParameter<std::vector<double> >("RightSlopeCut"),
            psPulseShape.getParameter<std::vector<double> >("RightSlopeSmallThreshold"),
            psPulseShape.getParameter<std::vector<double> >("RightSlopeSmallCut"),
            psPulseShape.getParameter<std::vector<double> >("TS4TS5LowerThreshold"),
            psPulseShape.getParameter<std::vector<double> >("TS4TS5LowerCut"),
            psPulseShape.getParameter<std::vector<double> >("TS4TS5UpperThreshold"),
            psPulseShape.getParameter<std::vector<double> >("TS4TS5UpperCut"),
            psPulseShape.getParameter<bool>("UseDualFit"),
            psPulseShape.getParameter<bool>("TriangleIgnoreSlow"),
            setLegacyFlags);
    }
}


//
// class declaration
//
class HBHEPhase1Reconstructor : public edm::stream::EDProducer<>
{
public:
    explicit HBHEPhase1Reconstructor(const edm::ParameterSet&);
    ~HBHEPhase1Reconstructor() override;

    static void fillDescriptions(edm::ConfigurationDescriptions& descriptions);

private:
    void beginRun(edm::Run const&, edm::EventSetup const&) override;
    void endRun(edm::Run const&, edm::EventSetup const&) override;
    void produce(edm::Event&, const edm::EventSetup&) override;

    // Configuration parameters
    std::string algoConfigClass_;
    bool processQIE8_;
    bool processQIE11_;
    bool saveInfos_;
    bool saveDroppedInfos_;
    bool makeRecHits_;
    bool dropZSmarkedPassed_;
    bool tsFromDB_;
    bool recoParamsFromDB_;
    bool saveEffectivePedestal_;
    int sipmQTSShift_;
    int sipmQNTStoSum_;

    // Parameters for turning status bit setters on/off
    bool setNegativeFlagsQIE8_;
    bool setNegativeFlagsQIE11_;
    bool setNoiseFlagsQIE8_;
    bool setNoiseFlagsQIE11_;
    bool setPulseShapeFlagsQIE8_;
    bool setPulseShapeFlagsQIE11_;

    // Other members
    edm::EDGetTokenT<HBHEDigiCollection> tok_qie8_;
    edm::EDGetTokenT<QIE11DigiCollection> tok_qie11_;
    std::unique_ptr<AbsHBHEPhase1Algo> reco_;
    std::unique_ptr<AbsHcalAlgoData> recoConfig_;
    std::unique_ptr<HcalRecoParams> paramTS_;

    // Status bit setters
    const HBHENegativeEFilter* negEFilter_;    // We don't manage this pointer
    std::unique_ptr<HBHEStatusBitSetter> hbheFlagSetterQIE8_;
    std::unique_ptr<HBHEStatusBitSetter> hbheFlagSetterQIE11_;
    std::unique_ptr<HBHEPulseShapeFlagSetter> hbhePulseShapeFlagSetterQIE8_;
    std::unique_ptr<HBHEPulseShapeFlagSetter> hbhePulseShapeFlagSetterQIE11_;

    // For the function below, arguments "infoColl" and/or "rechits"
    // are allowed to be null.
    template<class DataFrame, class Collection>
    void processData(const Collection& coll,
                     const HcalDbService& cond,
                     const HcalChannelQuality& qual,
                     const HcalSeverityLevelComputer& severity,
                     const bool isRealData,
                     HBHEChannelInfo* info,
                     HBHEChannelInfoCollection* infoColl,
                     HBHERecHitCollection* rechits);

    // Methods for setting rechit status bits
    void setAsicSpecificBits(const HBHEDataFrame& frame, const HcalCoder& coder,
                             const HBHEChannelInfo& info, const HcalCalibrations& calib,
                             HBHERecHit* rh);
    void setAsicSpecificBits(const QIE11DataFrame& frame, const HcalCoder& coder,
                             const HBHEChannelInfo& info, const HcalCalibrations& calib,
                             HBHERecHit* rh);
    void setCommonStatusBits(const HBHEChannelInfo& info, const HcalCalibrations& calib,
                             HBHERecHit* rh);

    void runHBHENegativeEFilter(const HBHEChannelInfo& info, HBHERecHit* rh);
};

//
// constructors and destructor
//
HBHEPhase1Reconstructor::HBHEPhase1Reconstructor(const edm::ParameterSet& conf)
    : algoConfigClass_(conf.getParameter<std::string>("algoConfigClass")),
      processQIE8_(conf.getParameter<bool>("processQIE8")),
      processQIE11_(conf.getParameter<bool>("processQIE11")),
      saveInfos_(conf.getParameter<bool>("saveInfos")),
      saveDroppedInfos_(conf.getParameter<bool>("saveDroppedInfos")),
      makeRecHits_(conf.getParameter<bool>("makeRecHits")),
      dropZSmarkedPassed_(conf.getParameter<bool>("dropZSmarkedPassed")),
      tsFromDB_(conf.getParameter<bool>("tsFromDB")),
      recoParamsFromDB_(conf.getParameter<bool>("recoParamsFromDB")),
      saveEffectivePedestal_(conf.getParameter<bool>("saveEffectivePedestal")),
      sipmQTSShift_(conf.getParameter<int>("sipmQTSShift")),
      sipmQNTStoSum_(conf.getParameter<int>("sipmQNTStoSum")),
      setNegativeFlagsQIE8_(conf.getParameter<bool>("setNegativeFlagsQIE8")),
      setNegativeFlagsQIE11_(conf.getParameter<bool>("setNegativeFlagsQIE11")),
      setNoiseFlagsQIE8_(conf.getParameter<bool>("setNoiseFlagsQIE8")),
      setNoiseFlagsQIE11_(conf.getParameter<bool>("setNoiseFlagsQIE11")),
      setPulseShapeFlagsQIE8_(conf.getParameter<bool>("setPulseShapeFlagsQIE8")),
      setPulseShapeFlagsQIE11_(conf.getParameter<bool>("setPulseShapeFlagsQIE11")),
      reco_(parseHBHEPhase1AlgoDescription(conf.getParameter<edm::ParameterSet>("algorithm"))),
      negEFilter_(nullptr)
{
    // Check that the reco algorithm has been successfully configured
    if (!reco_.get())
        throw cms::Exception("HBHEPhase1BadConfig")
            << "Invalid HBHEPhase1Algo algorithm configuration"
            << std::endl;

    // Configure the status bit setters that have been turned on
    if (setNoiseFlagsQIE8_)
        hbheFlagSetterQIE8_ = parse_HBHEStatusBitSetter(
            conf.getParameter<edm::ParameterSet>("flagParametersQIE8"));

    if (setNoiseFlagsQIE11_)
        hbheFlagSetterQIE11_ = parse_HBHEStatusBitSetter(
            conf.getParameter<edm::ParameterSet>("flagParametersQIE11"));

    if (setPulseShapeFlagsQIE8_)
        hbhePulseShapeFlagSetterQIE8_ = parse_HBHEPulseShapeFlagSetter(
            conf.getParameter<edm::ParameterSet>("pulseShapeParametersQIE8"),
            conf.getParameter<bool>("setLegacyFlagsQIE8"));

    if (setPulseShapeFlagsQIE11_)
        hbhePulseShapeFlagSetterQIE11_ = parse_HBHEPulseShapeFlagSetter(
            conf.getParameter<edm::ParameterSet>("pulseShapeParametersQIE11"),
            conf.getParameter<bool>("setLegacyFlagsQIE11"));

    // Consumes and produces statements
    if (processQIE8_)
        tok_qie8_ = consumes<HBHEDigiCollection>(
            conf.getParameter<edm::InputTag>("digiLabelQIE8"));

    if (processQIE11_)
        tok_qie11_ = consumes<QIE11DigiCollection>(
            conf.getParameter<edm::InputTag>("digiLabelQIE11"));

    if (saveInfos_)
        produces<HBHEChannelInfoCollection>();

    if (makeRecHits_)
        produces<HBHERecHitCollection>();
}


HBHEPhase1Reconstructor::~HBHEPhase1Reconstructor()
{
   // do anything here that needs to be done at destruction time
   // (e.g. close files, deallocate resources etc.)
}


//
// member functions
//
template<class DFrame, class Collection>
void HBHEPhase1Reconstructor::processData(const Collection& coll,
                                          const HcalDbService& cond,
                                          const HcalChannelQuality& qual,
                                          const HcalSeverityLevelComputer& severity,
                                          const bool isRealData,
                                          HBHEChannelInfo* channelInfo,
                                          HBHEChannelInfoCollection* infos,
                                          HBHERecHitCollection* rechits)
{
    // If "saveDroppedInfos_" flag is set, fill the info with something
    // meaningful even if the database tells us to drop this channel.
    // Note that this flag affects only "infos", the rechits are still
    // not going to be constructed from such channels.
    const bool skipDroppedChannels = !(infos && saveDroppedInfos_);

    // Iterate over the input collection
    for (typename Collection::const_iterator it = coll.begin();
         it != coll.end(); ++it)
    {
        const DFrame& frame(*it);
        const HcalDetId cell(frame.id());

        // Protection against calibration channels which are not
        // in the database but can still come in the QIE11DataFrame
        // in the laser calibs, etc.
        const HcalSubdetector subdet = cell.subdet();
        if (!(subdet == HcalSubdetector::HcalBarrel ||
              subdet == HcalSubdetector::HcalEndcap ||
              subdet == HcalSubdetector::HcalOuter))
            continue;

        // Check if the database tells us to drop this channel
        const HcalChannelStatus* mydigistatus = qual.getValues(cell.rawId());
        const bool taggedBadByDb = severity.dropChannel(mydigistatus->getValue());
        if (taggedBadByDb && skipDroppedChannels)
            continue;

        // Check if the channel is zero suppressed
        bool dropByZS = false;
        if (dropZSmarkedPassed_)
            if (frame.zsMarkAndPass())
                dropByZS = true;
        if (dropByZS && skipDroppedChannels)
            continue;

        // Basic ADC decoding tools
        const HcalRecoParam* param_ts = paramTS_->getValues(cell.rawId());
        const HcalCalibrations& calib = cond.getHcalCalibrations(cell);
        const HcalCalibrationWidths& calibWidth = cond.getHcalCalibrationWidths(cell);
        const HcalQIECoder* channelCoder = cond.getHcalCoder(cell);
        const HcalQIEShape* shape = cond.getHcalShape(channelCoder);
        const HcalCoderDb coder(*channelCoder, *shape);

        // needed for the dark current in the M2
        const HcalSiPMParameter& siPMParameter(*cond.getHcalSiPMParameter(cell));
        const double darkCurrent = siPMParameter.getDarkCurrent();
        const double fcByPE = siPMParameter.getFCByPE();
        const double lambda = cond.getHcalSiPMCharacteristics()->getCrossTalk(siPMParameter.getType());

        // ADC to fC conversion
        CaloSamples cs;
        coder.adc2fC(frame, cs);

        // Prepare to iterate over time slices
        const bool saveEffectivePeds = channelInfo->hasEffectivePedestals();
        const int nRead = cs.size();
        const int maxTS = std::min(nRead, static_cast<int>(HBHEChannelInfo::MAXSAMPLES));
        const int soi = tsFromDB_ ? param_ts->firstSample() : frame.presamples();
        const RawChargeFromSample<DFrame> rcfs(sipmQTSShift_, sipmQNTStoSum_, 
                                               cond, cell, cs, soi, frame, maxTS);
        int soiCapid = 4;

        // Go over time slices and fill the samples
        for (int ts = 0; ts < maxTS; ++ts)
        {
            auto s(frame[ts]);
            const uint8_t adc = s.adc();
            const int capid = s.capid();
            //optionally store "effective" pedestal (measured with bias voltage on)
            // = QIE contribution + SiPM contribution (from dark current + crosstalk)
            const double pedestal = saveEffectivePeds ? calib.effpedestal(capid) : calib.pedestal(capid);
            const double pedestalWidth = saveEffectivePeds ? calibWidth.effpedestal(capid) : calibWidth.pedestal(capid);
            const double gain = calib.respcorrgain(capid);
            const double gainWidth = calibWidth.gain(capid);
            //always use QIE-only pedestal for this computation
            const double rawCharge = rcfs.getRawCharge(cs[ts], calib.pedestal(capid));
            const float t = getTDCTimeFromSample(s);
            const float dfc = getDifferentialChargeGain(*channelCoder, *shape, adc,
                                                        capid, channelInfo->hasTimeInfo());
            channelInfo->setSample(ts, adc, dfc, rawCharge,
                                   pedestal, pedestalWidth,
                                   gain, gainWidth, t);
            if (ts == soi)
                soiCapid = capid;
        }

        // Fill the overall channel info items
        const int pulseShapeID = param_ts->pulseShapeID();
        const std::pair<bool,bool> hwerr = findHWErrors(frame, maxTS);
        channelInfo->setChannelInfo(cell, pulseShapeID, maxTS, soi, soiCapid,
                                    darkCurrent, fcByPE, lambda,
                                    hwerr.first, hwerr.second,
                                    taggedBadByDb || dropByZS);

        // If needed, add the channel info to the output collection
        const bool makeThisRechit = !channelInfo->isDropped();
        if (infos && (saveDroppedInfos_ || makeThisRechit))
            infos->push_back(*channelInfo);

        // Reconstruct the rechit
        if (rechits && makeThisRechit)
        {
            const HcalRecoParam* pptr = nullptr;
            if (recoParamsFromDB_)
                pptr = param_ts;
            HBHERecHit rh = reco_->reconstruct(*channelInfo, pptr, calib, isRealData);
            if (rh.id().rawId())
            {
                setAsicSpecificBits(frame, coder, *channelInfo, calib, &rh);
                setCommonStatusBits(*channelInfo, calib, &rh);
                rechits->push_back(rh);
            }
        }
    }
}

void HBHEPhase1Reconstructor::setCommonStatusBits(
    const HBHEChannelInfo& /* info */, const HcalCalibrations& /* calib */,
    HBHERecHit* /* rh */)
{
}

void HBHEPhase1Reconstructor::setAsicSpecificBits(
    const HBHEDataFrame& frame, const HcalCoder& coder,
    const HBHEChannelInfo& info, const HcalCalibrations& calib,
    HBHERecHit* rh)
{
    if (setNoiseFlagsQIE8_)
        hbheFlagSetterQIE8_->rememberHit(*rh);

    if (setPulseShapeFlagsQIE8_)
        hbhePulseShapeFlagSetterQIE8_->SetPulseShapeFlags(*rh, frame, coder, calib);

    if (setNegativeFlagsQIE8_)
        runHBHENegativeEFilter(info, rh);
}

void HBHEPhase1Reconstructor::setAsicSpecificBits(
    const QIE11DataFrame& frame, const HcalCoder& coder,
    const HBHEChannelInfo& info, const HcalCalibrations& calib,
    HBHERecHit* rh)
{
    if (setNoiseFlagsQIE11_)
        hbheFlagSetterQIE11_->rememberHit(*rh);

    if (setPulseShapeFlagsQIE11_)
        hbhePulseShapeFlagSetterQIE11_->SetPulseShapeFlags(*rh, frame, coder, calib);

    if (setNegativeFlagsQIE11_)
        runHBHENegativeEFilter(info, rh);
}

void HBHEPhase1Reconstructor::runHBHENegativeEFilter(const HBHEChannelInfo& info,
                                                     HBHERecHit* rh)
{
    double ts[HBHEChannelInfo::MAXSAMPLES];
    const unsigned nRead = info.nSamples();
    for (unsigned i=0; i<nRead; ++i)
        ts[i] = info.tsCharge(i);
    const bool passes = negEFilter_->checkPassFilter(info.id(), &ts[0], nRead);
    if (!passes)
        rh->setFlagField(1, HcalPhase1FlagLabels::HBHENegativeNoise);
}

// ------------ method called to produce the data  ------------
void
HBHEPhase1Reconstructor::produce(edm::Event& e, const edm::EventSetup& eventSetup)
{
    using namespace edm;

    // Get the Hcal topology
    ESHandle<HcalTopology> htopo;
    eventSetup.get<HcalRecNumberingRecord>().get(htopo);
    paramTS_->setTopo(htopo.product());

    // Fetch the calibrations
    ESHandle<HcalDbService> conditions;
    eventSetup.get<HcalDbRecord>().get(conditions);

    ESHandle<HcalChannelQuality> p;
    eventSetup.get<HcalChannelQualityRcd>().get("withTopo", p);
 
    ESHandle<HcalSeverityLevelComputer> mycomputer;
    eventSetup.get<HcalSeverityLevelComputerRcd>().get(mycomputer);

    // Configure the negative energy filter
    ESHandle<HBHENegativeEFilter> negEHandle;
    if (setNegativeFlagsQIE8_ || setNegativeFlagsQIE11_)
    {
        eventSetup.get<HBHENegativeEFilterRcd>().get(negEHandle);
        negEFilter_ = negEHandle.product();
    }

    // Find the input data
    unsigned maxOutputSize = 0;
    Handle<HBHEDigiCollection> hbDigis;
    if (processQIE8_)
    {
        e.getByToken(tok_qie8_, hbDigis);
        maxOutputSize += hbDigis->size();
    }

    Handle<QIE11DigiCollection> heDigis;
    if (processQIE11_)
    {
        e.getByToken(tok_qie11_, heDigis);
        maxOutputSize += heDigis->size();
    }

    // Create new output collections
    std::unique_ptr<HBHEChannelInfoCollection> infos;
    if (saveInfos_)
    {
        infos = std::make_unique<HBHEChannelInfoCollection>();
        infos->reserve(maxOutputSize);
    }

    std::unique_ptr<HBHERecHitCollection> out;
    if (makeRecHits_)
    {
        out = std::make_unique<HBHERecHitCollection>();
        out->reserve(maxOutputSize);
    }

    // Process the input collections, filling the output ones
    const bool isData = e.isRealData();
    if (processQIE8_)
    {
        if (setNoiseFlagsQIE8_)
            hbheFlagSetterQIE8_->Clear();

        HBHEChannelInfo channelInfo(false,false);
        processData<HBHEDataFrame>(*hbDigis, *conditions, *p, *mycomputer,
                                   isData, &channelInfo, infos.get(), out.get());
        if (setNoiseFlagsQIE8_)
            hbheFlagSetterQIE8_->SetFlagsFromRecHits(*out);
    }

    if (processQIE11_)
    {
        if (setNoiseFlagsQIE11_)
            hbheFlagSetterQIE11_->Clear();

        HBHEChannelInfo channelInfo(true,saveEffectivePedestal_);
        processData<QIE11DataFrame>(*heDigis, *conditions, *p, *mycomputer,
                                    isData, &channelInfo, infos.get(), out.get());
        if (setNoiseFlagsQIE11_)
            hbheFlagSetterQIE11_->SetFlagsFromRecHits(*out);
    }

    // Add the output collections to the event record
    if (saveInfos_)
        e.put(std::move(infos));
    if (makeRecHits_)
        e.put(std::move(out));
}

// ------------ method called when starting to processes a run  ------------
void
HBHEPhase1Reconstructor::beginRun(edm::Run const& r, edm::EventSetup const& es)
{
    edm::ESHandle<HcalRecoParams> p;
    es.get<HcalRecoParamsRcd>().get(p);
    paramTS_ = std::make_unique<HcalRecoParams>(*p.product());

    if (reco_->isConfigurable())
    {
        recoConfig_ = fetchHcalAlgoData(algoConfigClass_, es);
        if (!recoConfig_.get())
            throw cms::Exception("HBHEPhase1BadConfig")
                << "Invalid HBHEPhase1Reconstructor \"algoConfigClass\" parameter value \""
                << algoConfigClass_ << '"' << std::endl;
        if (!reco_->configure(recoConfig_.get()))
            throw cms::Exception("HBHEPhase1BadConfig")
                << "Failed to configure HBHEPhase1Algo algorithm from EventSetup"
                << std::endl;
    }

    if (setNoiseFlagsQIE8_ || setNoiseFlagsQIE11_)
    {
        edm::ESHandle<HcalFrontEndMap> hfemap;
        es.get<HcalFrontEndMapRcd>().get(hfemap);
        if (hfemap.isValid())
        {
            if (setNoiseFlagsQIE8_)
                hbheFlagSetterQIE8_->SetFrontEndMap(hfemap.product());
            if (setNoiseFlagsQIE11_)
                hbheFlagSetterQIE11_->SetFrontEndMap(hfemap.product());
        }
        else
            edm::LogWarning("EventSetup") <<
                "HBHEPhase1Reconstructor failed to get HcalFrontEndMap!" << std::endl;
    }

    reco_->beginRun(r, es);
}

void
HBHEPhase1Reconstructor::endRun(edm::Run const&, edm::EventSetup const&)
{
    reco_->endRun();
}

#define add_param_set(name)        \
    edm::ParameterSetDescription name; \
    name.setAllowAnything();           \
    desc.add<edm::ParameterSetDescription>(#name, name)

// ------------ method fills 'descriptions' with the allowed parameters for the module  ------------
void
HBHEPhase1Reconstructor::fillDescriptions(edm::ConfigurationDescriptions& descriptions)
{
    edm::ParameterSetDescription desc;

    desc.add<edm::InputTag>("digiLabelQIE8");
    desc.add<edm::InputTag>("digiLabelQIE11");
    desc.add<std::string>("algoConfigClass");
    desc.add<bool>("processQIE8");
    desc.add<bool>("processQIE11");
    desc.add<bool>("saveInfos");
    desc.add<bool>("saveDroppedInfos");
    desc.add<bool>("makeRecHits");
    desc.add<bool>("dropZSmarkedPassed");
    desc.add<bool>("tsFromDB");
    desc.add<bool>("recoParamsFromDB");
    desc.add<bool>("saveEffectivePedestal", false);
    desc.add<int>("sipmQTSShift", 0);
    desc.add<int>("sipmQNTStoSum", 3);
    desc.add<bool>("setNegativeFlagsQIE8");
    desc.add<bool>("setNegativeFlagsQIE11");
    desc.add<bool>("setNoiseFlagsQIE8");
    desc.add<bool>("setNoiseFlagsQIE11");
    desc.add<bool>("setPulseShapeFlagsQIE8");
    desc.add<bool>("setPulseShapeFlagsQIE11");
    desc.add<bool>("setLegacyFlagsQIE8");
    desc.add<bool>("setLegacyFlagsQIE11");

    add_param_set(algorithm);
    add_param_set(flagParametersQIE8);
    add_param_set(flagParametersQIE11);
    add_param_set(pulseShapeParametersQIE8);
    add_param_set(pulseShapeParametersQIE11);
    
    descriptions.addDefault(desc);
}

//define this as a plug-in
DEFINE_FWK_MODULE(HBHEPhase1Reconstructor);