/afs/cern.ch/work/a/aaltunda/public/www/CMSSW_6_2_5/src/RecoLocalTracker/SiPixelClusterizer/src/PixelThresholdClusterizer.cc

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

// Our own includes
#include "RecoLocalTracker/SiPixelClusterizer/interface/PixelThresholdClusterizer.h"
#include "RecoLocalTracker/SiPixelClusterizer/interface/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"
#include "DataFormats/SiPixelDetId/interface/PXBDetId.h"

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

//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
PixelThresholdClusterizer::PixelThresholdClusterizer
  (edm::ParameterSet const& conf) :
    conf_(conf), bufferAlreadySet(false), theNumOfRows(0), theNumOfCols(0), detid_(0) 
{
  // Get thresholds in electrons
  thePixelThreshold   = 
    conf_.getParameter<int>("ChannelThreshold");
  theSeedThreshold    = 
    conf_.getParameter<int>("SeedThreshold");
  theClusterThreshold = 
    conf_.getParameter<double>("ClusterThreshold");
  theConversionFactor = 
    conf_.getParameter<int>("VCaltoElectronGain");
  theOffset = 
    conf_.getParameter<int>("VCaltoElectronOffset");
  if ( conf_.exists("AdcFullScaleStack") ) theStackADC_=conf_.getParameter<int>("AdcFullScaleStack");
  else 
    theStackADC_=255;
  if ( conf_.exists("FirstStackLayer") ) theFirstStack_=conf_.getParameter<int>("FirstStackLayer");
  else
    theFirstStack_=5;
  
  // Get the constants for the miss-calibration studies
  doMissCalibrate=conf_.getUntrackedParameter<bool>("MissCalibrate",true); 
  doSplitClusters = conf.getParameter<bool>("SplitClusters");
  theBuffer.setSize( theNumOfRows, theNumOfCols );
}
PixelThresholdClusterizer::~PixelThresholdClusterizer() {}

//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
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
      bufferAlreadySet = true;
    }
  
  return true;   
}
//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
void PixelThresholdClusterizer::clusterizeDetUnit( const edm::DetSet<PixelDigi> & input,
                                                   const PixelGeomDetUnit * pixDet,
                                                   const std::vector<short>& badChannels,
                                                   edmNew::DetSetVector<SiPixelCluster>::FastFiller& output) {
  
  DigiIterator begin = input.begin();
  DigiIterator 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;
  
  detid_ = input.detId();
  
  //  Copy PixelDigis to the buffer array; select the seed pixels
  //  on the way, and store them in theSeeds.
  copy_to_buffer(begin, end);
  
  //  At this point we know the number of seeds on this DetUnit, and thus
  //  also the maximal number of possible clusters, so resize theClusters
  //  in order to make vector<>::push_back() efficient.
  // output.reserve ( theSeeds.size() ); //GPetruc: It is better *not* to reserve, with the new DetSetVector!
  
  
  //  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() >= theClusterThreshold) 
            {
              //        cout << "putting in this cluster" << endl;
              output.push_back( cluster );
            }
        }
    }
  
  // 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::copy_to_buffer( DigiIterator begin, DigiIterator end ) 
{
  for(DigiIterator di = begin; di != end; ++di) 
    {
      int row = di->row();
      int col = di->column();
      int adc = calibrate(di->adc(),col,row); // convert ADC -> electrons
      if ( adc >= thePixelThreshold) 
        {
          theBuffer.set_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;
  int layer= 0;
  if (DetId(detid_).subdetId()==1){ layer = PXBDetId(detid_).layer();}

  if ( doMissCalibrate ) 
    {
      // do not perform calibration if pixel is dead!
      
      if ( !theSiPixelGainCalibrationService_->isDead(detid_,col,row) && 
           !theSiPixelGainCalibrationService_->isNoisy(detid_,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(detid_, col, row);
          float DBpedestal = theSiPixelGainCalibrationService_->getPedestal(detid_, col, row) * 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;
          
          electrons = int( vcal * theConversionFactor + theOffset); 
        }
    }
  else 
    { // No misscalibration in the digitizer
      // Simple (default) linear gain 
      const float gain = 135.; // 1 ADC = 135 electrons
      const float pedestal = 0.; //
      electrons = int(adc * gain + pedestal);
      if (layer>=theFirstStack_) {
        if (theStackADC_==1&&adc==1)
          {
            electrons = int(255*135); // Arbitrarily use overflow value.
          }
        if (theStackADC_>1&&theStackADC_!=255&&adc>=1)
          {
            const float gain = 135.; // 1 ADC = 135 electrons
            electrons = int((adc-1) * gain * 255/float(theStackADC_-1));
          }
      }
    }
  
  return electrons;
}


namespace {

  struct AccretionCluster {
    typedef unsigned short UShort;
    static constexpr UShort MAXSIZE = 256;
    UShort adc[256];
    UShort x[256];
    UShort y[256];
    UShort xmin=16000;
    UShort ymin=16000;
    unsigned int isize=0;
    unsigned int curr=0;

    // stack interface (unsafe ok for use below)
    UShort top() const { return curr;}
    void pop() { ++curr;}   
    bool empty() { return curr==isize;}

    bool add(SiPixelCluster::PixelPos const & p, UShort const iadc) {
      if (isize==MAXSIZE) return false;
      xmin=std::min(xmin,(unsigned short)(p.row()));
      ymin=std::min(ymin,(unsigned short)(p.col()));
      adc[isize]=iadc;
      x[isize]=p.row();
      y[isize++]=p.col();
      return true;
    }
  };

}

//----------------------------------------------------------------------------
//----------------------------------------------------------------------------
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.

  if ( doMissCalibrate &&
       (theSiPixelGainCalibrationService_->isDead(detid_,pix.col(),pix.row()) || 
        theSiPixelGainCalibrationService_->isNoisy(detid_,pix.col(),pix.row())) )
    {
      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 r = acluster.x[curInd]-1; r <= acluster.x[curInd]+1; ++r) 
        {
          for ( auto c = acluster.y[curInd]-1; c <= acluster.y[curInd]+1; ++c) 
            {
              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(detid_,c,r) || theSiPixelGainCalibrationService_->isNoisy(detid_,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 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() >= theClusterThreshold && 
               first_cluster.charge() >= theClusterThreshold )
            {
              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() >= theClusterThreshold && have_second_cluster) 
        {
          output.push_back( first_cluster );
        }
    }
  
  return cluster;
}