A specific threshold-based pixel clustering algorithm. More...

#include <PixelThresholdClusterizer.h>

Inheritance diagram for PixelThresholdClusterizer:

Public Member Functions
void	clusterizeDetUnit (const edm::DetSet< PixelDigi > &input, const PixelGeomDetUnit pixDet, const TrackerTopology tTopo, const std::vector< short > &badChannels, edmNew::DetSetVector< SiPixelCluster >::FastFiller &output)

void	clusterizeDetUnit (const edmNew::DetSet< SiPixelCluster > &input, const PixelGeomDetUnit pixDet, const TrackerTopology tTopo, const std::vector< short > &badChannels, edmNew::DetSetVector< SiPixelCluster >::FastFiller &output)

	PixelThresholdClusterizer (edm::ParameterSet const &conf)

	~PixelThresholdClusterizer ()

Public Member Functions inherited from PixelClusterizerBase
void	setSiPixelGainCalibrationService (SiPixelGainCalibrationServiceBase *in)

virtual	~PixelClusterizerBase ()

Static Public Member Functions
static void	fillDescriptions (edm::ConfigurationDescriptions &descriptions)

Private Member Functions
int	calibrate (int adc, int col, int row)

void	clear_buffer (DigiIterator begin, DigiIterator end)
	Clear the internal buffer array. More...

void	clear_buffer (ClusterIterator begin, ClusterIterator end)

template<typename T >
void	clusterizeDetUnitT (const T &input, const PixelGeomDetUnit pixDet, const TrackerTopology tTopo, const std::vector< short > &badChannels, edmNew::DetSetVector< SiPixelCluster >::FastFiller &output)
	Cluster pixels. This method operates on a matrix of pixels and finds the largest contiguous cluster around each seed pixel. Input and output data stored in DetSet. More...

void	copy_to_buffer (DigiIterator begin, DigiIterator end)
	Copy adc counts from PixelDigis into the buffer, identify seeds. More...

void	copy_to_buffer (ClusterIterator begin, ClusterIterator end)

SiPixelCluster	make_cluster (const SiPixelCluster::PixelPos &pix, edmNew::DetSetVector< SiPixelCluster >::FastFiller &output)
	The actual clustering algorithm: group the neighboring pixels around the seed. More...

bool	setup (const PixelGeomDetUnit *pixDet)
	Private helper methods: More...

Private Attributes
bool	bufferAlreadySet

bool	dead_flag

uint32_t	detid_

const bool	doMissCalibrate

const bool	doSplitClusters

int	layer_

SiPixelArrayBuffer	theBuffer
	Data storage. More...

std::vector< SiPixelCluster >	theClusters

const int	theClusterThreshold

const int	theClusterThreshold_L1

float	theClusterThresholdInNoiseUnits

const int	theConversionFactor

const int	theConversionFactor_L1

const double	theElectronPerADCGain_

const int	theFirstStack_

int	theNumOfCols

int	theNumOfRows
	Geometry-related information. More...

const int	theOffset

const int	theOffset_L1

const int	thePixelThreshold

float	thePixelThresholdInNoiseUnits
	Clustering-related quantities: More...

std::vector< SiPixelCluster::PixelPos >	theSeeds

const int	theSeedThreshold

float	theSeedThresholdInNoiseUnits

const int	theStackADC_

Additional Inherited Members
Public Types inherited from PixelClusterizerBase
typedef edmNew::DetSet< SiPixelCluster >::const_iterator	ClusterIterator

typedef edm::DetSet< PixelDigi >::const_iterator	DigiIterator

Protected Attributes inherited from PixelClusterizerBase
SiPixelGainCalibrationServiceBase *	theSiPixelGainCalibrationService_

Detailed Description

A specific threshold-based pixel clustering algorithm.

An explicit threshold-based clustering algorithm.

General logic of PixelThresholdClusterizer:

The clusterization is performed on a matrix with size equal to the size of the pixel detector, each cell containing the ADC count of the corresponding pixel. The matrix is reset after each clusterization.

The search starts from seed pixels, i.e. pixels with sufficiently large amplitudes, found at the time of filling of the matrix and stored in a SiPixelArrayBuffer.

Translate the pixel charge to electrons, we are suppose to do the calibrations ADC->electrons here. Modify the thresholds to be in electrons, convert adc to electrons. d.k. 20/3/06 Get rid of the noiseVector. d.k. 28/3/06

A threshold-based clustering algorithm which clusters SiPixelDigis into SiPixelClusters for each DetUnit. The algorithm is straightforward and purely topological: the clustering process starts with seed pixels and continues by adding adjacent pixels above the pixel threshold. Once the cluster is made, it has to be above the cluster threshold as well.

The clusterization is performed on a matrix with size equal to the size of the pixel detector, each cell containing the ADC count of the corresponding pixel. The matrix is reset after each clusterization.

The search starts from seed pixels, i.e. pixels with sufficiently large amplitudes, found at the time of filling of the matrix and stored in a

At this point the noise and dead channels are ignored, but soon they won't be.

SiPixelCluster contains a barrycenter, but it should be noted that that information is largely useless. One must use a PositionEstimator class to compute the RecHit position and its error for every given cluster.

Author: Largely copied from NewPixelClusterizer in ORCA written by Danek Kotlinski (PSI). Ported to CMSSW by Petar Maksimovic (JHU). DetSetVector data container implemented by V.Chiochia (Uni Zurich)

Sets the PixelArrayBuffer dimensions and pixel thresholds. Makes clusters and stores them in theCache if the option useCache has been set.

Definition at line 59 of file PixelThresholdClusterizer.h.

Constructor & Destructor Documentation

PixelThresholdClusterizer::PixelThresholdClusterizer ( edm::ParameterSet const & conf )

Constructor: Initilize the buffer to hold pixels from a detector module. This is a vector of 44k ints, stays valid all the time.

Definition at line 44 of file PixelThresholdClusterizer.cc.

                                 :
     bufferAlreadySet(false),
     // 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") ),
     theStackADC_( conf.exists("AdcFullScaleStack") ? conf.getParameter<int>("AdcFullScaleStack") : 255 ),
     theFirstStack_( conf.exists("FirstStackLayer") ? conf.getParameter<int>("FirstStackLayer") : 5 ),
     theElectronPerADCGain_( conf.exists("ElectronPerADCGain") ? conf.getParameter<double>("ElectronPerADCGain") : 135. ),
     theNumOfRows(0), theNumOfCols(0), detid_(0),
     // 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 ( )

Definition at line 66 of file PixelThresholdClusterizer.cc.

66 {}

Member Function Documentation

int PixelThresholdClusterizer::calibrate	(	int	adc,
		int	col,
		int	row
	)

private

Definition at line 306 of file PixelThresholdClusterizer.cc.

References genericTrackCleaner_cfi::electrons, muonCSCDigis_cfi::gain, createfilelist::int, sistrip::layer_, and muonCSCDigis_cfi::pedestal.

 {
   int electrons = 0;
 
   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;
       
       if (layer_==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);
       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 = theElectronPerADCGain_; // default: 1 ADC = 135 electrons
         electrons = int((adc-1) * gain * 255/float(theStackADC_-1));
       }
       }
     }
   
   return electrons;
 }

void PixelThresholdClusterizer::clear_buffer	(	DigiIterator	begin,
		DigiIterator	end
	)

private

Clear the internal buffer array.

Pixels which are not part of recognized clusters are NOT ERASED during the cluster finding. Erase them now.

TO DO: ask Danek... wouldn't it be faster to simply memcopy() zeros into the whole buffer array?

Definition at line 200 of file PixelThresholdClusterizer.cc.

References 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
	)

private

Definition at line 208 of file PixelThresholdClusterizer.cc.

References end, mps_fire::i, digi_MixPreMix_cfi::pixel, SiPixelCluster::Pixel::x, and SiPixelCluster::Pixel::y.

 {
   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::clusterizeDetUnit	(	const edm::DetSet< PixelDigi > &	input,
		const PixelGeomDetUnit *	pixDet,
		const TrackerTopology *	tTopo,
		const std::vector< short > &	badChannels,
		edmNew::DetSetVector< SiPixelCluster >::FastFiller &	output
	)

inlinevirtual

Implements PixelClusterizerBase.

Definition at line 66 of file PixelThresholdClusterizer.h.

70 { clusterizeDetUnitT(input, pixDet, tTopo, badChannels, output); }

PixelThresholdClusterizer::clusterizeDetUnitT

void clusterizeDetUnitT(const T &input, const PixelGeomDetUnit *pixDet, const TrackerTopology *tTopo, const std::vector< short > &badChannels, edmNew::DetSetVector< SiPixelCluster >::FastFiller &output)

Cluster pixels. This method operates on a matrix of pixels and finds the largest contiguous cluster a...

Definition: PixelThresholdClusterizer.cc:129

void PixelThresholdClusterizer::clusterizeDetUnit	(	const edmNew::DetSet< SiPixelCluster > &	input,
		const PixelGeomDetUnit *	pixDet,
		const TrackerTopology *	tTopo,
		const std::vector< short > &	badChannels,
		edmNew::DetSetVector< SiPixelCluster >::FastFiller &	output
	)

inlinevirtual

Implements PixelClusterizerBase.

Definition at line 71 of file PixelThresholdClusterizer.h.

References input, and convertSQLitetoXML_cfg::output.

75 { clusterizeDetUnitT(input, pixDet, tTopo, badChannels, output); }

PixelThresholdClusterizer::clusterizeDetUnitT

void clusterizeDetUnitT(const T &input, const PixelGeomDetUnit *pixDet, const TrackerTopology *tTopo, const std::vector< short > &badChannels, edmNew::DetSetVector< SiPixelCluster >::FastFiller &output)

Cluster pixels. This method operates on a matrix of pixels and finds the largest contiguous cluster a...

Definition: PixelThresholdClusterizer.cc:129

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
	)

private

Cluster pixels. This method operates on a matrix of pixels and finds the largest contiguous cluster around each seed pixel. Input and output data stored in DetSet.

Definition at line 129 of file PixelThresholdClusterizer.cc.

References begin, edmNew::DetSetVector< T >::FastFiller::begin(), SiPixelCluster::charge(), GetRecoTauVFromDQM_MC_cff::cl2, edmNew::DetSetVector< T >::FastFiller::empty(), end, edmNew::DetSetVector< T >::FastFiller::end(), mps_fire::i, sistrip::layer_, SiPixelCluster::minPixelRow(), eostools::move(), edmNew::DetSetVector< T >::FastFiller::push_back(), TrackerTopology::pxbLayer(), GeneralSetup::setup(), and DetId::subdetId().

                                                                                                          {
   
   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;
   
   detid_ = input.detId();
   
   // Set separate cluster threshold for L1 (needed for phase1)
   auto clusterThreshold = theClusterThreshold;
   layer_ = (DetId(detid_).subdetId()==1) ? tTopo->pxbLayer(detid_) : 0;
   if (layer_==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::copy_to_buffer	(	DigiIterator	begin,
		DigiIterator	end
	)

private

Copy adc counts from PixelDigis into the buffer, identify seeds.

Definition at line 224 of file PixelThresholdClusterizer.cc.

References ecalMGPA::adc(), begin, cuy::col, gather_cfg::cout, metsig::electron, end, muonCSCDigis_cfi::gain, mps_fire::i, recoMuon::in, createfilelist::int, sistrip::layer_, and muonCSCDigis_cfi::pedestal.

 {
 #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];
   memset(electron, 0, sizeof(electron));
   if ( doMissCalibrate ) {
     if (layer_==1) {
       (*theSiPixelGainCalibrationService_).calibrate(detid_,begin,end,theConversionFactor_L1, theOffset_L1,electron);
     } else {
       (*theSiPixelGainCalibrationService_).calibrate(detid_,begin,end,theConversionFactor,    theOffset,  electron);
     }
   } else {
     int i=0;
     for(DigiIterator di = begin; di != end; ++di) {
       auto adc = di->adc();
       const float gain = theElectronPerADCGain_; // default: 1 ADC = 135 electrons
       const float pedestal = 0.; //
       electron[i] = int(adc * gain + pedestal);
       if (layer_>=theFirstStack_) {
     if (theStackADC_==1&&adc==1) {
       electron[i] = int(255*135); // Arbitrarily use overflow value.
     }
     if (theStackADC_>1&&theStackADC_!=255&&adc>=1){
       const float gain = theElectronPerADCGain_; // default: 1 ADC = 135 electrons
       electron[i] = int((adc-1) * gain * 255/float(theStackADC_-1));
     }
       }
       ++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++];
 #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 >= 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
	)

private

Definition at line 284 of file PixelThresholdClusterizer.cc.

References ecalMGPA::adc(), SiPixelCluster::Pixel::adc, cuy::col, end, mps_fire::i, digi_MixPreMix_cfi::pixel, SiPixelCluster::Pixel::x, and SiPixelCluster::Pixel::y.

 {
   // 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) );
       }
     }
   }
 }

void PixelThresholdClusterizer::fillDescriptions ( edm::ConfigurationDescriptions & descriptions )

static

Definition at line 71 of file PixelThresholdClusterizer.cc.

References edm::ConfigurationDescriptions::add(), edm::ParameterSetDescription::add(), edm::ParameterSetDescription::addUntracked(), and AlCaHLTBitMon_QueryRunRegistry::string.

                                                                                       {
   // siPixelClusters
   edm::ParameterSetDescription desc;
   desc.add<edm::InputTag>("src", edm::InputTag("siPixelDigis"));
   desc.add<int>("ChannelThreshold", 1000);
   desc.addUntracked<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<std::string>("payloadType", "Offline");
   desc.add<int>("SeedThreshold", 1000);
   desc.add<int>("ClusterThreshold_L1", 4000);
   desc.add<int>("ClusterThreshold", 4000);
   desc.add<int>("maxNumberOfClusters", -1);
   descriptions.add("siPixelClusters", desc);
 }

SiPixelCluster PixelThresholdClusterizer::make_cluster	(	const SiPixelCluster::PixelPos &	pix,
		edmNew::DetSetVector< SiPixelCluster >::FastFiller &	output
	)

private

The actual clustering algorithm: group the neighboring pixels around the seed.

Definition at line 382 of file PixelThresholdClusterizer.cc.

 {
   
   //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(detid_,pix.col(),pix.row()) || 
     theSiPixelGainCalibrationService_->isNoisy(detid_,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(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 separate cluster threshold for L1 (needed for phase1)
       auto clusterThreshold = theClusterThreshold;
       if (layer_==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;
 }

bool PixelThresholdClusterizer::setup ( const PixelGeomDetUnit * pixDet )

private

Private helper methods:

Prepare the Clusterizer to work on a particular DetUnit. Re-init the size of the panel/plaquette (so update nrows and ncols),

Definition at line 94 of file PixelThresholdClusterizer.cc.

References trackingPlots::ncols, PixelTopology::ncolumns(), PixelTopology::nrows(), and PixelGeomDetUnit::specificTopology().

 {
   // 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;   
 }