PHG4TruthEventAction.cc

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#include "PHG4TruthEventAction.h"

#include "PHG4Hit.h"
#include "PHG4HitContainer.h"
#include "PHG4HitDefs.h"   // for keytype
#include "PHG4Particle.h"  // for PHG4Particle
#include "PHG4Shower.h"
#include "PHG4TruthInfoContainer.h"
#include "PHG4UserPrimaryParticleInformation.h"

#include <phool/PHCompositeNode.h>
#include <phool/PHIODataNode.h>  // for PHIODataNode
#include <phool/PHNode.h>
#include <phool/PHNodeIterator.h>  // for PHNodeIterator
#include <phool/PHPointerListIterator.h>
#include <phool/getClass.h>
#include <phool/phool.h>  // for PHWHERE

#include <Geant4/G4Event.hh>
#include <Geant4/G4PrimaryParticle.hh>                  // for G4PrimaryPart...
#include <Geant4/G4PrimaryVertex.hh>                    // for G4PrimaryVertex
#include <Geant4/G4VUserPrimaryParticleInformation.hh>  // for G4VUserPrimar...

#include <Eigen/Dense>

#include <cmath>     // for isnan
#include <cstdlib>   // for abs
#include <iostream>  // for operator<<, endl
#include <iterator>  // for reverse_iterator
#include <map>
#include <string>   // for operator==
#include <utility>  // for swap, pair
#include <vector>   // for vector, vecto...

class PHG4VtxPoint;

using namespace std;

//___________________________________________________
PHG4TruthEventAction::PHG4TruthEventAction()
  : m_TruthInfoContainer(nullptr)
  , m_LowerKeyPrevExist(0)
  , m_UpperKeyPrevExist(0)
{
}

//___________________________________________________
void PHG4TruthEventAction::BeginOfEventAction(const G4Event* /*evt*/)
{
  // if we do not find the node we need to make it.
  if (!m_TruthInfoContainer)
  {
    std::cout << "PHG4TruthEventAction::EndOfEventAction - unable to find G4TruthInfo node" << std::endl;
    return;
  }

  const PHG4TruthInfoContainer::Map& map = m_TruthInfoContainer->GetMap();
  if (!map.empty())
  {
    m_LowerKeyPrevExist = map.begin()->first;
    m_UpperKeyPrevExist = map.rbegin()->first;
  }
}

//___________________________________________________
void PHG4TruthEventAction::EndOfEventAction(const G4Event* evt)
{
  // if we do not find the node we need to make it.
  if (!m_TruthInfoContainer)
  {
    std::cout << "PHG4TruthEventAction::EndOfEventAction - unable to find G4TruthInfo node" << std::endl;
    return;
  }
  // First deal with the showers - they do need the info which
  // is removed from the maps in the subsequent cleanup to reduce the
  // output file size
  PruneShowers();
  ProcessShowers();
  // construct a list of track ids to preserve in the the output that includes any
  // track designated in the m_WriteSet during processing or its ancestry chain

  std::set<int> savelist;
  std::set<int> savevtxlist;

  for (std::set<int>::const_iterator write_iter = m_WriteSet.begin();
       write_iter != m_WriteSet.end();
       ++write_iter)
  {
    std::vector<int> wrttracks;
    std::vector<int> wrtvtx;

    // usertrackid
    int mytrkid = *write_iter;
    PHG4Particle* particle = m_TruthInfoContainer->GetParticle(mytrkid);

    // if track is already in save list, nothing needs to be done
    if (savelist.find(mytrkid) != savelist.end())
    {
      continue;
    }
    else
    {
      wrttracks.push_back(mytrkid);
      wrtvtx.push_back(particle->get_vtx_id());
    }

    // now crawl up the truth info and add parents until we hit
    // a track which is already being saved
    int parentid = particle->get_parent_id();
    while (savelist.find(parentid) == savelist.end() && parentid != 0)
    {
      particle = m_TruthInfoContainer->GetParticle(parentid);
      wrttracks.push_back(parentid);
      wrtvtx.push_back(particle->get_vtx_id());
      parentid = particle->get_parent_id();
    }

    // now fill the new tracks into the save list
    // while emptying the write lists
    while (wrttracks.begin() != wrttracks.end())
    {
      savelist.insert(wrttracks.back());
      wrttracks.pop_back();
    }

    while (wrtvtx.begin() != wrtvtx.end())
    {
      savevtxlist.insert(wrtvtx.back());
      wrtvtx.pop_back();
    }
  }

  // the save lists are filled now, except primary track which never
  // made it into any active volume and their vertex

  // loop over particles in truth list and remove them if they are not
  // in the save list and are not primary particles (parent_id == 0)

  int removed[4] = {0};
  PHG4TruthInfoContainer::Range truth_range = m_TruthInfoContainer->GetParticleRange();
  PHG4TruthInfoContainer::Iterator truthiter = truth_range.first;
  while (truthiter != truth_range.second)
  {
    removed[0]++;
    int trackid = truthiter->first;
    if (savelist.find(trackid) == savelist.end())
    {
      // track not in save list

      // check if particle below offset
      // primary particles had parentid = 0
      // for embedding: particles from initial sim do not have their keep flag set, we want to keep particles with trkid <= trackidoffset
      // tracks from a previous geant pass will not be recorded as leaving
      // hit in the sim, so we exclude this range from the removal
      // for regular sims, that range is zero to zero
      if (((trackid < m_LowerKeyPrevExist) || (trackid > m_UpperKeyPrevExist)) && ((truthiter->second)->get_parent_id() != 0))
      {
        m_TruthInfoContainer->delete_particle(truthiter++);
        removed[1]++;
      }
      else
      {
        // save vertex id for primary particle which leaves no hit
        // in active area
        savevtxlist.insert((truthiter->second)->get_vtx_id());
        ++truthiter;
      }
    }
    else
    {
      // track was in save list, move on
      ++truthiter;
    }
  }

  PHG4TruthInfoContainer::VtxRange vtxrange = m_TruthInfoContainer->GetVtxRange();
  PHG4TruthInfoContainer::VtxIterator vtxiter = vtxrange.first;
  while (vtxiter != vtxrange.second)
  {
    removed[2]++;
    if (savevtxlist.find(vtxiter->first) == savevtxlist.end())
    {
      m_TruthInfoContainer->delete_vtx(vtxiter++);
      removed[3]++;
    }
    else
    {
      ++vtxiter;
    }
  }

  // loop over all input particles and fish out the ones which have the embed flag set
  // and store their geant track ids in truthinfo container
  G4PrimaryVertex* pvtx = evt->GetPrimaryVertex();
  while (pvtx)
  {
    G4PrimaryParticle* part = pvtx->GetPrimary();
    while (part)
    {
      PHG4UserPrimaryParticleInformation* userdata = dynamic_cast<PHG4UserPrimaryParticleInformation*>(part->GetUserInformation());
      if (userdata)
      {
        if (userdata->get_embed())
        {
          m_TruthInfoContainer->AddEmbededTrkId(userdata->get_user_track_id(), userdata->get_embed());
          m_TruthInfoContainer->AddEmbededVtxId(userdata->get_user_vtx_id(), userdata->get_embed());
        }
      }
      part = part->GetNext();
    }
    pvtx = pvtx->GetNext();
  }

  return;
}

//___________________________________________________
void PHG4TruthEventAction::AddTrackidToWritelist(const int trackid)
{
  m_WriteSet.insert(trackid);
}

//___________________________________________________
void PHG4TruthEventAction::SetInterfacePointers(PHCompositeNode* topNode)
{
  //now look for the map and grab a pointer to it.
  m_TruthInfoContainer = findNode::getClass<PHG4TruthInfoContainer>(topNode, "G4TruthInfo");

  // if we do not find the node we need to make it.
  if (!m_TruthInfoContainer)
  {
    std::cout << "PHG4TruthEventAction::SetInterfacePointers - unable to find G4TruthInfo" << std::endl;
  }

  SearchNode(topNode);
}

void PHG4TruthEventAction::SearchNode(PHCompositeNode* top)
{
  // fill a lookup map between the g4hit container ids and the containers themselves
  // without knowing what the container names are in advance, only that they
  // begin G4HIT_*

  PHNodeIterator nodeiter(top);
  PHPointerListIterator<PHNode> iter(nodeiter.ls());
  PHNode* thisNode;
  while ((thisNode = iter()))
  {
    if (thisNode->getType() == "PHCompositeNode")
    {
      SearchNode(static_cast<PHCompositeNode*>(thisNode));
    }
    else if (thisNode->getType() == "PHIODataNode")
    {
      if (thisNode->getName().find("G4HIT_") == 0)
      {
        PHIODataNode<PHG4HitContainer>* DNode = static_cast<PHIODataNode<PHG4HitContainer>*>(thisNode);
        if (DNode)
        {
          PHG4HitContainer* object = dynamic_cast<PHG4HitContainer*>(DNode->getData());
          if (object)
          {
            m_HitContainerMap[object->GetID()] = object;
          }
        }
      }
    }
  }
}

int PHG4TruthEventAction::ResetEvent(PHCompositeNode*)
{
  m_WriteSet.clear();
  return 0;
}

void PHG4TruthEventAction::PruneShowers()
{
  PHG4TruthInfoContainer::ShowerRange range = m_TruthInfoContainer->GetShowerRange();
  for (PHG4TruthInfoContainer::ShowerIterator iter = range.first;
       iter != range.second;
       ++iter)
  {
    PHG4Shower* shower = iter->second;

    std::set<int> remove_ids;
    for (PHG4Shower::ParticleIdIter jter = shower->begin_g4particle_id();
         jter != shower->end_g4particle_id();
         ++jter)
    {
      int g4particle_id = *jter;
      PHG4Particle* particle = m_TruthInfoContainer->GetParticle(g4particle_id);
      if (!particle)
      {
        remove_ids.insert(g4particle_id);
        continue;
      }
    }

    for (std::set<int>::iterator jter = remove_ids.begin();
         jter != remove_ids.end();
         ++jter)
    {
      shower->remove_g4particle_id(*jter);
    }

    std::set<int> remove_more_ids;
    for (std::map<int, std::set<PHG4HitDefs::keytype> >::iterator jter = shower->begin_g4hit_id();
         jter != shower->end_g4hit_id();
         ++jter)
    {
      int g4hitmap_id = jter->first;
      std::map<int, PHG4HitContainer*>::iterator mapiter = m_HitContainerMap.find(g4hitmap_id);
      if (mapiter == m_HitContainerMap.end())
      {
        continue;
      }

      // get the g4hits from this particle in this volume
      for (std::set<PHG4HitDefs::keytype>::iterator kter = jter->second.begin();
           kter != jter->second.end();)
      {
        PHG4HitDefs::keytype g4hit_id = *kter;

        PHG4Hit* g4hit = mapiter->second->findHit(g4hit_id);
        if (!g4hit)
        {
          // some zero edep g4hits have been removed already
          jter->second.erase(kter++);
          continue;
        }
        else
        {
          ++kter;
        }
      }

      if (jter->second.empty())
      {
        remove_more_ids.insert(g4hitmap_id);
      }
    }

    for (std::set<int>::iterator jter = remove_more_ids.begin();
         jter != remove_more_ids.end();
         ++jter)
    {
      shower->remove_g4hit_volume(*jter);
    }
  }

  range = m_TruthInfoContainer->GetShowerRange();
  for (PHG4TruthInfoContainer::ShowerIterator iter = range.first;
       iter != range.second;)
  {
    PHG4Shower* shower = iter->second;

    if (shower->empty_g4particle_id() && shower->empty_g4hit_id())
    {
      if (shower->get_edep() == 0)  // check whether this shower has already been processed in the previous simulation cycles
      {
        m_TruthInfoContainer->delete_shower(iter++);
        continue;
      }
    }

    ++iter;
  }
}

void PHG4TruthEventAction::ProcessShowers()
{
  PHG4TruthInfoContainer::ShowerRange range = m_TruthInfoContainer->GetShowerRange();
  for (PHG4TruthInfoContainer::ShowerIterator shwiter = range.first;
       shwiter != range.second;
       ++shwiter)
  {
    PHG4Shower* shower = shwiter->second;

    // Data structures to hold weighted pca
    std::vector<std::vector<float> > points;
    std::vector<float> weights;
    float sumw = 0.0;
    float sumw2 = 0.0;

    for (std::map<int, std::set<PHG4HitDefs::keytype> >::iterator iter = shower->begin_g4hit_id();
         iter != shower->end_g4hit_id();
         ++iter)
    {
      int g4hitmap_id = iter->first;
      std::map<int, PHG4HitContainer*>::iterator mapiter = m_HitContainerMap.find(g4hitmap_id);
      if (mapiter == m_HitContainerMap.end())
      {
        continue;
      }

      PHG4HitContainer* hits = mapiter->second;

      unsigned int nhits = 0;
      float edep = 0.0;
      float eion = 0.0;
      float light_yield = 0.0;
      float edep_e = 0.0;
      float edep_h = 0.0;

      // get the g4hits from this particle in this volume
      for (std::set<PHG4HitDefs::keytype>::iterator kter = iter->second.begin();
           kter != iter->second.end();
           ++kter)
      {
        PHG4HitDefs::keytype g4hit_id = *kter;

        PHG4Hit* g4hit = hits->findHit(g4hit_id);
        if (!g4hit)
        {
          cout << PHWHERE << " missing g4hit" << endl;
          continue;
        }

        PHG4Particle* particle = m_TruthInfoContainer->GetParticle(g4hit->get_trkid());
        if (!particle)
        {
          cout << PHWHERE << " missing g4particle for track "
               << g4hit->get_trkid() << endl;
          continue;
        }

        PHG4VtxPoint* vtx = m_TruthInfoContainer->GetVtx(particle->get_vtx_id());
        if (!vtx)
        {
          cout << PHWHERE << " missing g4vertex" << endl;
          continue;
        }

        // shower location and shape info

        if (!isnan(g4hit->get_x(0)) &&
            !isnan(g4hit->get_y(0)) &&
            !isnan(g4hit->get_z(0)))
        {
          std::vector<float> entry(3);
          entry[0] = g4hit->get_x(0);
          entry[1] = g4hit->get_y(0);
          entry[2] = g4hit->get_z(0);

          points.push_back(entry);
          float w = g4hit->get_edep();
          weights.push_back(w);
          sumw += w;
          sumw2 += w * w;
        }

        if (!isnan(g4hit->get_x(1)) &&
            !isnan(g4hit->get_y(1)) &&
            !isnan(g4hit->get_z(1)))
        {
          std::vector<float> entry(3);
          entry[0] = g4hit->get_x(1);
          entry[1] = g4hit->get_y(1);
          entry[2] = g4hit->get_z(1);

          points.push_back(entry);
          float w = g4hit->get_edep();
          weights.push_back(w);
          sumw += w;
          sumw2 += w * w;
        }

        // e/h ratio

        if (!isnan(g4hit->get_edep()))
        {
          if (abs(particle->get_pid()) == 11)
          {
            edep_e += g4hit->get_edep();
          }
          else
          {
            edep_h += g4hit->get_edep();
          }
        }

        // summary info

        ++nhits;
        if (!isnan(g4hit->get_edep())) edep += g4hit->get_edep();
        if (!isnan(g4hit->get_eion())) eion += g4hit->get_eion();
        if (!isnan(g4hit->get_light_yield())) light_yield += g4hit->get_light_yield();
      }  // g4hit loop

      // summary info

      if (nhits) shower->set_nhits(g4hitmap_id, nhits);
      if (edep != 0.0) shower->set_edep(g4hitmap_id, edep);
      if (eion != 0.0) shower->set_eion(g4hitmap_id, eion);
      if (light_yield != 0.0) shower->set_light_yield(g4hitmap_id, light_yield);
      if (edep_h != 0.0) shower->set_eh_ratio(g4hitmap_id, edep_e / edep_h);
    }  // volume loop

    // fill Eigen matrices to compute wPCA
    // resizing these non-destructively is expensive
    // so I fill vectors and then copy
    Eigen::Matrix<double, Eigen::Dynamic, 3> X(points.size(), 3);
    Eigen::Matrix<double, Eigen::Dynamic, 1> W(weights.size(), 1);

    for (unsigned int i = 0; i < points.size(); ++i)
    {
      for (unsigned int j = 0; j < 3; ++j)
      {
        X(i, j) = points[i][j];
      }
      W(i, 0) = weights[i];
    }

    // mean value of shower
    double prefactor = 1.0 / sumw;
    Eigen::Matrix<double, 1, 3> mean = prefactor * W.transpose() * X;

    // compute residual relative to the mean
    for (unsigned int i = 0; i < points.size(); ++i)
    {
      for (unsigned int j = 0; j < 3; ++j) X(i, j) = points[i][j] - mean(0, j);
    }

    // weighted covariance matrix
    prefactor = sumw / (sumw*sumw - sumw2);  // effectivelly 1/(N-1) when w_i = 1.0
    Eigen::Matrix<double, 3, 3> covar = prefactor * (X.transpose() * W.asDiagonal() * X);

    shower->set_x(mean(0, 0));
    shower->set_y(mean(0, 1));
    shower->set_z(mean(0, 2));

    for (unsigned int i = 0; i < 3; ++i)
    {
      for (unsigned int j = 0; j <= i; ++j)
      {
        shower->set_covar(i, j, covar(i, j));
      }
    }

    // shower->identify();
  }
}