PixelThresholdClusterizer.cc

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//----------------------------------------------------------------------------
//----------------------------------------------------------------------------

// Our own includes
#include "PixelThresholdClusterizer.h"
#include "SiPixelArrayBuffer.h"
#include "CondFormats/SiPixelObjects/interface/SiPixelGainCalibrationOffline.h"
// Geometry
#include "Geometry/TrackerGeometryBuilder/interface/PixelGeomDetUnit.h"
#include "Geometry/CommonTopologies/interface/PixelTopology.h"
//#include "Geometry/CommonTopologies/RectangularPixelTopology.h"

// STL
#include <stack>
#include <vector>
#include <iostream>
#include <atomic>
using namespace std;

//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
PixelThresholdClusterizer::PixelThresholdClusterizer
  (edm::ParameterSet const& conf) :
    // Get thresholds in electrons
    thePixelThreshold( conf.getParameter<int>("ChannelThreshold") ),
    theSeedThreshold( conf.getParameter<int>("SeedThreshold") ),
    theClusterThreshold( conf.getParameter<int>("ClusterThreshold") ),
    theClusterThreshold_L1( conf.getParameter<int>("ClusterThreshold_L1") ),
    theConversionFactor( conf.getParameter<int>("VCaltoElectronGain") ),
    theConversionFactor_L1( conf.getParameter<int>("VCaltoElectronGain_L1") ),
    theOffset( conf.getParameter<int>("VCaltoElectronOffset") ),
    theOffset_L1( conf.getParameter<int>("VCaltoElectronOffset_L1") ),
    theElectronPerADCGain( conf.getParameter<double>("ElectronPerADCGain") ),
    doPhase2Calibration( conf.getParameter<bool>("Phase2Calibration") ),
    thePhase2ReadoutMode( conf.getParameter<int>("Phase2ReadoutMode") ),
    thePhase2DigiBaseline( conf.getParameter<double>("Phase2DigiBaseline") ),
    thePhase2KinkADC( conf.getParameter<int>("Phase2KinkADC") ),
    theNumOfRows(0), theNumOfCols(0), theDetid(0),
    // Get the constants for the miss-calibration studies
    doMissCalibrate( conf.getParameter<bool>("MissCalibrate") ),
    doSplitClusters( conf.getParameter<bool>("SplitClusters") )
{
  theBuffer.setSize( theNumOfRows, theNumOfCols );
}
PixelThresholdClusterizer::~PixelThresholdClusterizer() {}


// Configuration descriptions
void
PixelThresholdClusterizer::fillPSetDescription(edm::ParameterSetDescription& desc) {
  desc.add<int>("ChannelThreshold", 1000);
  desc.add<bool>("MissCalibrate", true);
  desc.add<bool>("SplitClusters", false);
  desc.add<int>("VCaltoElectronGain", 65);
  desc.add<int>("VCaltoElectronGain_L1", 65);
  desc.add<int>("VCaltoElectronOffset", -414);
  desc.add<int>("VCaltoElectronOffset_L1", -414);
  desc.add<int>("SeedThreshold", 1000);
  desc.add<int>("ClusterThreshold_L1", 4000);
  desc.add<int>("ClusterThreshold", 4000);
  desc.add<double>("ElectronPerADCGain", 135.);
  desc.add<bool>("Phase2Calibration", false);
  desc.add<int>("Phase2ReadoutMode", -1);
  desc.add<double>("Phase2DigiBaseline", 1200.);
  desc.add<int>("Phase2KinkADC", 8);
}

//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
bool PixelThresholdClusterizer::setup(const PixelGeomDetUnit * pixDet) 
{
  // Cache the topology.
  const PixelTopology & topol = pixDet->specificTopology();
  
  // Get the new sizes.
  int nrows = topol.nrows();      // rows in x
  int ncols = topol.ncolumns();   // cols in y
  
  theNumOfRows = nrows;  // Set new sizes
  theNumOfCols = ncols;
  
  if ( nrows > theBuffer.rows() || 
       ncols > theBuffer.columns() ) 
    { // change only when a larger is needed
      //if( nrows != theNumOfRows || ncols != theNumOfCols ) {
      //cout << " PixelThresholdClusterizer: pixel buffer redefined to " 
      // << nrows << " * " << ncols << endl;      
      //theNumOfRows = nrows;  // Set new sizes
      //theNumOfCols = ncols;
      // Resize the buffer
      theBuffer.setSize(nrows,ncols);  // Modify
    }
  
  return true;   
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
template<typename T>
void PixelThresholdClusterizer::clusterizeDetUnitT( const T & input,
                           const PixelGeomDetUnit * pixDet,
                           const TrackerTopology* tTopo,
                           const std::vector<short>& badChannels,
                                                   edmNew::DetSetVector<SiPixelCluster>::FastFiller& output) {
  
  typename T::const_iterator begin = input.begin();
  typename T::const_iterator end   = input.end();
  
  // Do not bother for empty detectors
  //if (begin == end) cout << " PixelThresholdClusterizer::clusterizeDetUnit - No digis to clusterize";
  
  //  Set up the clusterization on this DetId.
  if ( !setup(pixDet) ) 
    return;
  
  theDetid = input.detId();
  
  // Set separate cluster threshold for L1 (needed for phase1)
  auto clusterThreshold = theClusterThreshold;
  theLayer = (DetId(theDetid).subdetId()==1) ? tTopo->pxbLayer(theDetid) : 0;
  if (theLayer==1) clusterThreshold = theClusterThreshold_L1;
  
  //  Copy PixelDigis to the buffer array; select the seed pixels
  //  on the way, and store them in theSeeds.
  copy_to_buffer(begin, end);
  
  assert(output.empty());
  //  Loop over all seeds.  TO DO: wouldn't using iterators be faster?
  //  edm::LogError("PixelThresholdClusterizer") <<  "Starting clusterizing" << endl;
  for (unsigned int i = 0; i < theSeeds.size(); i++) 
    {
      
      // Gavril : The charge of seeds that were already inlcuded in clusters is set to 1 electron
      // so we don't want to call "make_cluster" for these cases 
      if ( theBuffer(theSeeds[i]) >= theSeedThreshold ) 
    {  // Is this seed still valid?
      //  Make a cluster around this seed
      SiPixelCluster && cluster = make_cluster( theSeeds[i] , output);
      
      //  Check if the cluster is above threshold  
      // (TO DO: one is signed, other unsigned, gcc warns...)
      if ( cluster.charge() >= clusterThreshold) 
        {
          // std::cout << "putting in this cluster " << i << " " << cluster.charge() << " " << cluster.pixelADC().size() << endl;
              // sort by row (x)
          output.push_back( std::move(cluster) ); 
              std::push_heap(output.begin(),output.end(),[](SiPixelCluster const & cl1,SiPixelCluster const & cl2) { return cl1.minPixelRow() < cl2.minPixelRow();});
        }
    }
    }
  // sort by row (x)   maybe sorting the seed would suffice....
  std::sort_heap(output.begin(),output.end(),[](SiPixelCluster const & cl1,SiPixelCluster const & cl2) { return cl1.minPixelRow() < cl2.minPixelRow();});

  // Erase the seeds.
  theSeeds.clear();
  
  //  Need to clean unused pixels from the buffer array.
  clear_buffer(begin, end);
  
}

//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void PixelThresholdClusterizer::clear_buffer( DigiIterator begin, DigiIterator end ) 
{
  for(DigiIterator di = begin; di != end; ++di ) 
    {
      theBuffer.set_adc( di->row(), di->column(), 0 );   // reset pixel adc to 0
    }
}

void PixelThresholdClusterizer::clear_buffer( ClusterIterator begin, ClusterIterator end )
{
  for(ClusterIterator ci = begin; ci != end; ++ci )
    {
      for(int i = 0; i < ci->size(); ++i)
        {
          const SiPixelCluster::Pixel pixel = ci->pixel(i);

          theBuffer.set_adc( pixel.x, pixel.y, 0 );   // reset pixel adc to 0
        }
    }
}

//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void PixelThresholdClusterizer::copy_to_buffer( DigiIterator begin, DigiIterator end ) 
{
#ifdef PIXELREGRESSION
  static std::atomic<int> s_ic=0;
  in ic = ++s_ic;
  if (ic==1) {
    // std::cout << (doMissCalibrate ? "VI from db" : "VI linear") << std::endl;
  }
#endif
  int electron[end-begin]; // pixel charge in electrons 
  memset(electron, 0, sizeof(electron));

  if (doPhase2Calibration) {
    int i = 0;
    for(DigiIterator di = begin; di != end; ++di) {
      electron[i] = calibrate(di->adc(), di->column(), di->row());
      i++;
    }
    assert(i==(end-begin));
  }

  else {
    if ( doMissCalibrate ) {
      if (theLayer==1) {
        (*theSiPixelGainCalibrationService_).calibrate(theDetid,begin,end,theConversionFactor_L1, theOffset_L1,electron);
      } else {
        (*theSiPixelGainCalibrationService_).calibrate(theDetid,begin,end,theConversionFactor,    theOffset,  electron);
      }
    } else {
      int i=0;
      const float gain = theElectronPerADCGain; // default: 1 ADC = 135 electrons
      for(DigiIterator di = begin; di != end; ++di) {
        auto adc = di->adc();
        const float pedestal = 0.; //
        electron[i] = int(adc * gain + pedestal);
        ++i;
      }
      assert(i==(end-begin));
    }
  }

  int i=0;
#ifdef PIXELREGRESSION
  static std::atomic<int> eqD=0;
#endif
  for(DigiIterator di = begin; di != end; ++di) {
    int row = di->row();
    int col = di->column();
    int adc = electron[i++]; // this is in electrons 

#ifdef PIXELREGRESSION
    int adcOld = calibrate(di->adc(),col,row);
    //assert(adc==adcOld);
    if (adc!=adcOld) std::cout << "VI " << eqD  <<' '<< ic  <<' '<< end-begin <<' '<< i <<' '<< di->adc() <<' ' << adc <<' '<< adcOld << std::endl; else ++eqD;
#endif

    if(adc<100) adc=100; // put all negative pixel charges into the 100 elec bin 
    /* This is semi-random good number. The exact number (in place of 100) is irrelevant from the point 
       of view of the final cluster charge since these are typically >= 20000.
    */

    if ( adc >= thePixelThreshold) {
      theBuffer.set_adc( row, col, adc);
      if ( adc >= theSeedThreshold) theSeeds.push_back( SiPixelCluster::PixelPos(row,col) );
    }
  }
  assert(i==(end-begin));

}

void PixelThresholdClusterizer::copy_to_buffer( ClusterIterator begin, ClusterIterator end )
{
  // loop over clusters
  for(ClusterIterator ci = begin; ci != end; ++ci) {
    // loop over pixels
    for(int i = 0; i < ci->size(); ++i) {
      const SiPixelCluster::Pixel pixel = ci->pixel(i);

      int row = pixel.x;
      int col = pixel.y;
      int adc = pixel.adc;
      if ( adc >= thePixelThreshold) {
        theBuffer.add_adc( row, col, adc);
        if ( adc >= theSeedThreshold) theSeeds.push_back( SiPixelCluster::PixelPos(row,col) );
      }
    }
  }
}

//----------------------------------------------------------------------------
// Calibrate adc counts to electrons
//-----------------------------------------------------------------
int PixelThresholdClusterizer::calibrate(int adc, int col, int row) 
{
  int electrons = 0;

  if (doPhase2Calibration) {

    const float gain = theElectronPerADCGain;
    int p2rm = (thePhase2ReadoutMode < -1 ? -1 : thePhase2ReadoutMode);

    if (p2rm == -1) {
        electrons = int(adc * gain);
    }
    else {
        if (adc < thePhase2KinkADC) {
            electrons = int((adc - 0.5) * gain);
        }
        else {
            const int dualslopeparam = (thePhase2ReadoutMode < 10 ? thePhase2ReadoutMode : 10);
            const int dualslope = int(dualslopeparam <= 1 ? 1. : pow(2, dualslopeparam-1));
            adc -= (thePhase2KinkADC-1);
            adc *= dualslope;
            adc += (thePhase2KinkADC-1);
            electrons = int((adc - 0.5 * dualslope) * gain);
        } 
        electrons += int(thePhase2DigiBaseline);
    }

    return electrons;

  }

  if ( doMissCalibrate ) 
    {
      // do not perform calibration if pixel is dead!
      
      if ( !theSiPixelGainCalibrationService_->isDead(theDetid,col,row) && 
       !theSiPixelGainCalibrationService_->isNoisy(theDetid,col,row) )
    {
      
      // Linear approximation of the TANH response
      // Pixel(0,0,0)
      //const float gain = 2.95; // 1 ADC = 2.95 VCALs (1/0.339)
      //const float pedestal = -83.; // -28/0.339
      // Roc-0 average
      //const float gain = 1./0.357; // 1 ADC = 2.80 VCALs 
      //const float pedestal = -28.2 * gain; // -79.
      
      float DBgain     = theSiPixelGainCalibrationService_->getGain(theDetid, col, row);
      float pedestal   = theSiPixelGainCalibrationService_->getPedestal(theDetid, col, row);
      float DBpedestal = pedestal * DBgain;
      
      // Roc-6 average
      //const float gain = 1./0.313; // 1 ADC = 3.19 VCALs 
      //const float pedestal = -6.2 * gain; // -19.8
      // 
      float vcal = adc * DBgain - DBpedestal;
      
      // atanh calibration 
      // Roc-6 average
      //const float p0 = 0.00492;
      //const float p1 = 1.998;
      //const float p2 = 90.6;
      //const float p3 = 134.1; 
      // Roc-6 average
      //const float p0 = 0.00382;
      //const float p1 = 0.886;
      //const float p2 = 112.7;
      //const float p3 = 113.0; 
      //float vcal = ( atanh( (adc-p3)/p2) + p1)/p0;
      
      if (theLayer==1) {
        electrons = int( vcal * theConversionFactor_L1 + theOffset_L1); 
      } else {
        electrons = int( vcal * theConversionFactor + theOffset); 
      }

    }
    }
  else 
    { // No misscalibration in the digitizer
      // Simple (default) linear gain 
      const float gain = theElectronPerADCGain; // default: 1 ADC = 135 electrons
      const float pedestal = 0.; //
      electrons = int(adc * gain + pedestal);
    }
  
  return electrons;
}

//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
SiPixelCluster 
PixelThresholdClusterizer::make_cluster( const SiPixelCluster::PixelPos& pix, 
                     edmNew::DetSetVector<SiPixelCluster>::FastFiller& output) 
{
  
  //First we acquire the seeds for the clusters
  int seed_adc;
  stack<SiPixelCluster::PixelPos, vector<SiPixelCluster::PixelPos> > dead_pixel_stack;
  
  //The individual modules have been loaded into a buffer.
  //After each pixel has been considered by the clusterizer, we set the adc count to 1
  //to mark that we have already considered it.
  //The only difference between dead/noisy pixels and standard ones is that for dead/noisy pixels,
  //We consider the charge of the pixel to always be zero.

  /*  this is not possible as dead and noisy pixel cannot make it into a seed...
  if ( doMissCalibrate &&
       (theSiPixelGainCalibrationService_->isDead(theDetid,pix.col(),pix.row()) || 
    theSiPixelGainCalibrationService_->isNoisy(theDetid,pix.col(),pix.row())) )
    {
      std::cout << "IMPOSSIBLE" << std::endl;
      seed_adc = 0;
      theBuffer.set_adc(pix, 1);
    }
    else {
  */
  seed_adc = theBuffer(pix.row(), pix.col());
  theBuffer.set_adc( pix, 1);
      //  }
  
  AccretionCluster acluster;
  acluster.add(pix, seed_adc);
  
  //Here we search all pixels adjacent to all pixels in the cluster.
  bool dead_flag = false;
  while ( ! acluster.empty()) 
    {
      //This is the standard algorithm to find and add a pixel
      auto curInd = acluster.top(); acluster.pop();
      for ( auto c = std::max(0,int(acluster.y[curInd])-1); c < std::min(int(acluster.y[curInd])+2,theBuffer.columns()) ; ++c) {
    for ( auto r = std::max(0,int(acluster.x[curInd])-1); r < std::min(int(acluster.x[curInd])+2,theBuffer.rows()); ++r)  {
      if ( theBuffer(r,c) >= thePixelThreshold) {
        SiPixelCluster::PixelPos newpix(r,c);
        if (!acluster.add( newpix, theBuffer(r,c))) goto endClus;
        theBuffer.set_adc( newpix, 1);
      }
         

          /* //Commenting out the addition of dead pixels to the cluster until further testing -- dfehling 06/09
          //Check on the bounds of the module; this is to keep the isDead and isNoisy modules from returning errors 
          else if(r>= 0 && c >= 0 && (r <= (theNumOfRows-1.)) && (c <= (theNumOfCols-1.))){ 
          //Check for dead/noisy pixels check that the buffer is not -1 (already considered).  Check whether we want to split clusters separated by dead pixels or not.
          if((theSiPixelGainCalibrationService_->isDead(theDetid,c,r) || theSiPixelGainCalibrationService_->isNoisy(theDetid,c,r)) && theBuffer(r,c) != 1){
          
          //If a pixel is dead or noisy, check to see if we want to split the clusters or not.  
          //Push it into a dead pixel stack in case we want to split the clusters.  Otherwise add it to the cluster.
          //If we are splitting the clusters, we will iterate over the dead pixel stack later.
          
          SiPixelCluster::PixelPos newpix(r,c);
          if(!doSplitClusters){
          
          cluster.add(newpix, theBuffer(r,c));}
          else if(doSplitClusters){
          dead_pixel_stack.push(newpix);
          dead_flag = true;}
          
          theBuffer.set_adc(newpix, 1);
          } 
          
          }
          */
        


        }
    }
      
    }  // while accretion
 endClus:
  SiPixelCluster cluster(acluster.isize,acluster.adc, acluster.x,acluster.y, acluster.xmin,acluster.ymin);
  //Here we split the cluster, if the flag to do so is set and we have found a dead or noisy pixel.
  
  if (dead_flag && doSplitClusters) 
    {
      // Set separate cluster threshold for L1 (needed for phase1)
      auto clusterThreshold = theClusterThreshold;
      if (theLayer==1) clusterThreshold = theClusterThreshold_L1;
      
      //Set the first cluster equal to the existing cluster.
      SiPixelCluster first_cluster = cluster;
      bool have_second_cluster = false;
      while ( !dead_pixel_stack.empty() )
    {
      //consider each found dead pixel
      SiPixelCluster::PixelPos deadpix = dead_pixel_stack.top(); dead_pixel_stack.pop();
      theBuffer.set_adc(deadpix, 1);
     
      //Clusterize the split cluster using the dead pixel as a seed
      SiPixelCluster second_cluster = make_cluster(deadpix, output);
      
      //If both clusters would normally have been found by the clusterizer, put them into output
      if ( second_cluster.charge() >= clusterThreshold && 
           first_cluster.charge() >= clusterThreshold )
        {
          output.push_back( second_cluster );
          have_second_cluster = true;   
        }
      
      //We also want to keep the merged cluster in data and let the RecHit algorithm decide which set to keep
      //This loop adds the second cluster to the first.
      const std::vector<SiPixelCluster::Pixel>& branch_pixels = second_cluster.pixels();
      for ( unsigned int i = 0; i<branch_pixels.size(); i++)
        {
          int temp_x = branch_pixels[i].x;
          int temp_y = branch_pixels[i].y;
          int temp_adc = branch_pixels[i].adc;
          SiPixelCluster::PixelPos newpix(temp_x, temp_y);
          cluster.add(newpix, temp_adc);}
    }
      
      //Remember to also add the first cluster if we added the second one.
      if ( first_cluster.charge() >= clusterThreshold && have_second_cluster) 
    {
      output.push_back( first_cluster );
          std::push_heap(output.begin(),output.end(),[](SiPixelCluster const & cl1,SiPixelCluster const & cl2) { return cl1.minPixelRow() < cl2.minPixelRow();});
    }
    }
  
  return cluster;
}