SVDNNShapeReconstructorModule.cc

/**************************************************************************
 * basf2 (Belle II Analysis Software Framework)                           *
 * Author: The Belle II Collaboration                                     *
 *                                                                        *
 * See git log for contributors and copyright holders.                    *
 * This file is licensed under LGPL-3.0, see LICENSE.md.                  *
 **************************************************************************/
 
#include <svd/modules/svdReconstruction/SVDNNShapeReconstructorModule.h>
 
#include <framework/datastore/DataStore.h>
#include <framework/datastore/StoreArray.h>
#include <framework/logging/Logger.h>
 
#include <mdst/dataobjects/MCParticle.h>
#include <svd/dataobjects/SVDTrueHit.h>
#include <svd/dataobjects/SVDShaperDigit.h>
#include <svd/dataobjects/SVDRecoDigit.h>
#include <mva/dataobjects/DatabaseRepresentationOfWeightfile.h>
 
#include <svd/reconstruction/NNWaveFitTool.h>
 
#include <algorithm>
#include <functional>
 
using namespace std;
using namespace Belle2;
using namespace Belle2::SVD;
 
//-----------------------------------------------------------------
//                 Register the Module
//-----------------------------------------------------------------
REG_MODULE(SVDNNShapeReconstructor);
 
//-----------------------------------------------------------------
//                 Implementation
//-----------------------------------------------------------------
 
SVDNNShapeReconstructorModule::SVDNNShapeReconstructorModule() : Module()
{
  B2DEBUG(200, "Now in SVDNNShapeReconstructorModule ctor");
  //Set module properties
  setDescription("Reconstruct signals on SVD strips.");
  setPropertyFlags(c_ParallelProcessingCertified);
 
  // 1. Collections.
  addParam("Digits", m_storeShaperDigitsName,
           "Shaperdigits collection name", string(""));
  addParam("RecoDigits", m_storeRecoDigitsName,
           "RecoDigits collection name", string(""));
  addParam("TrueHits", m_storeTrueHitsName,
           "TrueHits collection name", string(""));
  addParam("MCParticles", m_storeMCParticlesName,
           "MCParticles collection name", string(""));
  addParam("WriteRecoDigits", m_writeRecoDigits,
           "Write RecoDigits to output?", m_writeRecoDigits);
  addParam("SVDEventInfo", m_svdEventInfoName,
           "SVDEventInfo name", string(""));
  // 2. Calibration and time fitter sources
  addParam("TimeFitterName", m_timeFitterName,
           "Name of time fitter data file", string("SVDTimeNet_6samples"));
  addParam("CalibratePeak", m_calibratePeak, "Use calibrattion (vs. default) for peak widths and positions", bool(false));
  // 3. Zero suppression
  addParam("ZeroSuppressionCut", m_cutAdjacent, "Zero-suppression cut on digits",
           m_cutAdjacent);
}
 
void SVDNNShapeReconstructorModule::initialize()
{
  //Register collections
  StoreArray<SVDRecoDigit> storeRecoDigits(m_storeRecoDigitsName);
  StoreArray<SVDShaperDigit> storeShaperDigits(m_storeShaperDigitsName);
  StoreArray<SVDTrueHit> storeTrueHits(m_storeTrueHitsName);
  StoreArray<MCParticle> storeMCParticles(m_storeMCParticlesName);
 
  if (!m_writeRecoDigits)
    storeRecoDigits.registerInDataStore(DataStore::c_DontWriteOut);
  else
    storeRecoDigits.registerInDataStore();
 
  storeShaperDigits.isRequired();
  storeTrueHits.isOptional();
  storeMCParticles.isOptional();
  m_storeSVDEvtInfo.isRequired();
 
  if (!m_storeSVDEvtInfo.isOptional(m_svdEventInfoName)) m_svdEventInfoName = "SVDEventInfoSim";
  m_storeSVDEvtInfo.isRequired(m_svdEventInfoName);
 
  RelationArray relRecoDigitShaperDigits(storeRecoDigits, storeShaperDigits);
  RelationArray relRecoDigitTrueHits(storeRecoDigits, storeTrueHits);
  RelationArray relRecoDigitMCParticles(storeRecoDigits, storeMCParticles);
  RelationArray relShaperDigitTrueHits(storeShaperDigits, storeTrueHits);
  RelationArray relShaperDigitMCParticles(storeShaperDigits, storeMCParticles);
 
  if (!m_writeRecoDigits)
    relRecoDigitShaperDigits.registerInDataStore(DataStore::c_DontWriteOut);
  else
    relRecoDigitShaperDigits.registerInDataStore();
  //Relations to simulation objects only if the ancestor relations exist
  if (relShaperDigitTrueHits.isOptional())
    relRecoDigitTrueHits.registerInDataStore();
  if (relShaperDigitMCParticles.isOptional())
    relRecoDigitMCParticles.registerInDataStore();
 
  //Store names to speed up creation later
  m_storeRecoDigitsName = storeRecoDigits.getName();
  m_storeShaperDigitsName = storeShaperDigits.getName();
  m_storeTrueHitsName = storeTrueHits.getName();
  m_storeMCParticlesName = storeMCParticles.getName();
 
  m_relRecoDigitShaperDigitName = relRecoDigitShaperDigits.getName();
  m_relRecoDigitTrueHitName = relRecoDigitTrueHits.getName();
  m_relRecoDigitMCParticleName = relRecoDigitMCParticles.getName();
  m_relShaperDigitTrueHitName = relShaperDigitTrueHits.getName();
  m_relShaperDigitMCParticleName = relShaperDigitMCParticles.getName();
 
  B2INFO(" 1. COLLECTIONS:");
  B2INFO(" -->  MCParticles:        " << m_storeMCParticlesName);
  B2INFO(" -->  Digits:             " << m_storeShaperDigitsName);
  B2INFO(" -->  RecoDigits:           " << m_storeRecoDigitsName);
  B2INFO(" -->  TrueHits:           " << m_storeTrueHitsName);
  B2INFO(" -->  DigitMCRel:         " << m_relShaperDigitMCParticleName);
  B2INFO(" -->  RecoDigitMCRel:       " << m_relRecoDigitMCParticleName);
  B2INFO(" -->  RecoDigitDigitRel:    " << m_relRecoDigitShaperDigitName);
  B2INFO(" -->  DigitTrueRel:       " << m_relShaperDigitTrueHitName);
  B2INFO(" -->  RecoDigitTrueRel:     " << m_relRecoDigitTrueHitName);
  B2INFO(" -->  Save RecoDigits?    " << (m_writeRecoDigits ? "Y" : "N"));
  B2INFO(" 2. CALIBRATION:");
  B2INFO(" -->  Time NN:            " << m_timeFitterName);
 
  // Properly initialize the NN time fitter
  // FIXME: Should be moved to beginRun
  // FIXME: No support for 3/6 sample switching within a run/event
  DBObjPtr<DatabaseRepresentationOfWeightfile> dbXml(m_timeFitterName);
  m_fitter.setNetwrok(dbXml->m_data);
}
 
void SVDNNShapeReconstructorModule::createRelationLookup(const RelationArray& relation,
                                                         RelationLookup& lookup, size_t digits)
{
  lookup.clear();
  //If we don't have a relation we don't build a lookuptable
  if (!relation) return;
  //Resize to number of digits and set all values
  lookup.resize(digits);
  for (const auto& element : relation) {
    lookup[element.getFromIndex()] = &element;
  }
}
 
void SVDNNShapeReconstructorModule::fillRelationMap(const RelationLookup& lookup,
                                                    std::map<unsigned int, float>& relation, unsigned int index)
{
  //If the lookup table is not empty and the element is set
  if (!lookup.empty() && lookup[index]) {
    const RelationElement& element = *lookup[index];
    const unsigned int size = element.getSize();
    //Add all Relations to the map
    for (unsigned int i = 0; i < size; ++i) {
      //negative weights are from ignored particles, we don't like them and
      //thus ignore them :D
      if (element.getWeight(i) < 0) continue;
      relation[element.getToIndex(i)] += element.getWeight(i);
    }
  }
}
 
void SVDNNShapeReconstructorModule::event()
{
 
  const StoreArray<SVDShaperDigit> storeShaperDigits(m_storeShaperDigitsName);
  // If no digits or no SVDEventInfo, nothing to do
  if (!storeShaperDigits || !storeShaperDigits.getEntries() || !m_storeSVDEvtInfo.isValid()) return;
 
  SVDModeByte modeByte = m_storeSVDEvtInfo->getModeByte();
 
  size_t nDigits = storeShaperDigits.getEntries();
  B2DEBUG(90, "Initial size of StoreDigits array: " << nDigits);
 
  const StoreArray<MCParticle> storeMCParticles(m_storeMCParticlesName);
  const StoreArray<SVDTrueHit> storeTrueHits(m_storeTrueHitsName);
 
  RelationArray relShaperDigitMCParticle(storeShaperDigits, storeMCParticles, m_relShaperDigitMCParticleName);
  RelationArray relShaperDigitTrueHit(storeShaperDigits, storeTrueHits, m_relShaperDigitTrueHitName);
 
  StoreArray<SVDRecoDigit> storeRecoDigits(m_storeRecoDigitsName);
  storeRecoDigits.clear();
 
  RelationArray relRecoDigitMCParticle(storeRecoDigits, storeMCParticles,
                                       m_relRecoDigitMCParticleName);
  if (relRecoDigitMCParticle) relRecoDigitMCParticle.clear();
 
  RelationArray relRecoDigitShaperDigit(storeRecoDigits, storeShaperDigits,
                                        m_relRecoDigitShaperDigitName);
  if (relRecoDigitShaperDigit) relRecoDigitShaperDigit.clear();
 
  RelationArray relRecoDigitTrueHit(storeRecoDigits, storeTrueHits,
                                    m_relRecoDigitTrueHitName);
  if (relRecoDigitTrueHit) relRecoDigitTrueHit.clear();
 
  //Build lookup tables for relations
  createRelationLookup(relShaperDigitMCParticle, m_mcRelation, nDigits);
  createRelationLookup(relShaperDigitTrueHit, m_trueRelation, nDigits);
 
  // Create fit tool object
  NNWaveFitTool fitTool = m_fitter.getFitTool();
 
  // I. Group digits by sensor/side.
  vector<pair<unsigned short, unsigned short> > sensorDigits;
  VxdID lastSensorID(0);
  size_t firstSensorDigit = 0;
  for (size_t iDigit = 0; iDigit < nDigits; ++iDigit) {
    const SVDShaperDigit& digit = *storeShaperDigits[iDigit];
    VxdID sensorID = digit.getSensorID();
    sensorID.setSegmentNumber(digit.isUStrip() ? 1 : 0);
    if (sensorID != lastSensorID) { // we have a new sensor side
      sensorDigits.push_back(make_pair(firstSensorDigit, iDigit));
      firstSensorDigit = iDigit;
      lastSensorID = sensorID;
    }
  }
  // save last VxdID
  sensorDigits.push_back(make_pair(firstSensorDigit, nDigits));
 
  // ICYCLE OVER SENSORS
  for (auto id_indices : sensorDigits) {
    // Retrieve parameters from sensorDigits
    unsigned int firstDigit = id_indices.first;
    unsigned int lastDigit = id_indices.second;
    // Get VXDID and side from the first digit
    const SVDShaperDigit& exampleDigit = *storeShaperDigits[firstDigit];
    VxdID sensorID = exampleDigit.getSensorID();
    bool isU = exampleDigit.isUStrip();
 
    // 2. Cycle through digits and form recodigits on the way.
 
    B2DEBUG(300, "Reconstructing digits " << firstDigit << " to " << lastDigit);
    for (size_t iDigit = firstDigit; iDigit < lastDigit; ++iDigit) {
 
      const SVDShaperDigit& shaperDigit = *storeShaperDigits[iDigit];
      unsigned short stripNo = shaperDigit.getCellID();
      bool validDigit = true; // FIXME: We don't care about local run bad strips for now.
      const double triggerBinSep = 4 * 1.96516; //in ns
      double apvPhase = triggerBinSep * (0.5 + static_cast<int>(modeByte.getTriggerBin()));
      // Get things from the database.
      // Noise is good as it comes.
      float stripNoiseADU = m_noiseCal.getNoise(sensorID, isU, stripNo);
      // Some calibrations magic.
      // FIXME: Only use calibration on real data. Until simulations correspond to
      // default calibrtion, we cannot use it.
      double stripSignalWidth = 270;
      double stripT0 = isU ? 2.5 : -2.2;
      if (m_calibratePeak) {
        stripSignalWidth = 1.988 * m_pulseShapeCal.getWidth(sensorID, isU, stripNo);
        stripT0 = m_pulseShapeCal.getPeakTime(sensorID, isU, stripNo)
                  - 0.25 * stripSignalWidth;
      }
 
      B2DEBUG(300, "Strip parameters: stripNoiseADU: " << stripNoiseADU <<
              " Width: " << stripSignalWidth <<
              " T0: " << stripT0);
 
      // If the strip is not masked away, normalize samples (sample/stripNoise)
      apvSamples normedSamples;
      auto samples = shaperDigit.getSamples();
      transform(samples.begin(), samples.end(), normedSamples.begin(),
                bind2nd(divides<float>(), stripNoiseADU));
      // FIXME: This won't work in 3 sample mode, we have no control over the number of non-zero samples.
      validDigit = validDigit && pass3Samples(normedSamples, m_cutAdjacent);
 
      if (validDigit) {
        zeroSuppress(normedSamples, m_cutAdjacent);
      } else // only now we give up on the diigit
        continue;
 
      // 3. Now we create and save the RecoDigit
 
      ostringstream os;
      os << "Input to NNFitter: iDigit = " << iDigit << endl << "Samples: ";
      copy(normedSamples.begin(), normedSamples.end(), ostream_iterator<double>(os, " "));
      os << endl;
      std::shared_ptr<nnFitterBinData> pStrip = m_fitter.getFit(normedSamples, stripSignalWidth);
      os << "Output from NNWaveFitter: " << endl;
      copy(pStrip->begin(), pStrip->end(), ostream_iterator<double>(os, " "));
      os << endl;
      // Apply strip time shift to pdf
      fitTool.shiftInTime(*pStrip, -apvPhase - stripT0);
      B2DEBUG(200, os.str());
      // Calculate time and its error, amplitude and its error, and chi2
      double stripTime, stripTimeError;
      tie(stripTime, stripTimeError) = fitTool.getTimeShift(*pStrip);
      // Now we have the cluster time pdf, so we can calculate amplitudes.
      double stripAmplitude, stripAmplitudeError, stripChi2;
      tie(stripAmplitude, stripAmplitudeError, stripChi2) =
        fitTool.getAmplitudeChi2(normedSamples, stripTime, stripSignalWidth);
      //De-normalize amplitudes and convert to electrons.
      stripAmplitude = m_pulseShapeCal.getChargeFromADC(sensorID, isU, stripNo, stripAmplitude * stripNoiseADU);
      stripAmplitudeError = m_pulseShapeCal.getChargeFromADC(sensorID, isU, stripNo, stripAmplitudeError * stripNoiseADU);
      B2DEBUG(200, "RecoDigit " << iDigit << " Noise: " << m_pulseShapeCal.getChargeFromADC(sensorID, isU, stripNo, stripNoiseADU)
              << " Time: " << stripTime << " +/- " << stripTimeError
              << " Amplitude: " << stripAmplitude << " +/- " << stripAmplitudeError
              << " Chi2: " << stripChi2
             );
 
      // Finally, we save the RecoDigit and its relations.
      map<unsigned int, float> mc_relations;
      map<unsigned int, float> truehit_relations;
      vector<pair<unsigned int, float> > digit_weights;
      digit_weights.reserve(1);
 
      // Store relations to MCParticles and SVDTrueHits
      fillRelationMap(m_mcRelation, mc_relations, iDigit);
      fillRelationMap(m_trueRelation, truehit_relations, iDigit);
      //Add digit to the RecoDigit->ShaperDigit relation list
      digit_weights.emplace_back(iDigit, 1.0);
 
      //Store the RecoDigit into Datastore ...
      int recoDigitIndex = storeRecoDigits.getEntries();
      storeRecoDigits.appendNew(
        SVDRecoDigit(sensorID, isU, shaperDigit.getCellID(), stripAmplitude,
                     stripAmplitudeError, stripTime, stripTimeError, *pStrip, stripChi2)
      );
 
      //Create relations to RecoDigits
      if (!mc_relations.empty()) {
        relRecoDigitMCParticle.add(recoDigitIndex, mc_relations.begin(), mc_relations.end());
      }
      if (!truehit_relations.empty()) {
        relRecoDigitTrueHit.add(recoDigitIndex, truehit_relations.begin(), truehit_relations.end());
      }
      relRecoDigitShaperDigit.add(recoDigitIndex, digit_weights.begin(), digit_weights.end());
    } // CYCLE OVER SHAPERDIGITS
 
  } // CYCLE OVER SENSORS for items in sensorDigits
 
  B2DEBUG(100, "Number of RecoDigits: " << storeRecoDigits.getEntries());
 
} // event()