Take switched off super modules into account

[u/mrichter/AliRoot.git] / TRD / AliTRDclusterizerV1.cxx

/**************************************************************************
 * Copyright(c) 1998-1999, ALICE Experiment at CERN, All rights reserved. *
 *                                                                        *
 * Author: The ALICE Off-line Project.                                    *
 * Contributors are mentioned in the code where appropriate.              *
 *                                                                        *
 * Permission to use, copy, modify and distribute this software and its   *
 * documentation strictly for non-commercial purposes is hereby granted   *
 * without fee, provided that the above copyright notice appears in all   *
 * copies and that both the copyright notice and this permission notice   *
 * appear in the supporting documentation. The authors make no claims     *
 * about the suitability of this software for any purpose. It is          *
 * provided "as is" without express or implied warranty.                  *
 **************************************************************************/

/* $Id$ */

///////////////////////////////////////////////////////////////////////////////
//                                                                           //
// TRD cluster finder                                                        //
//                                                                           //
///////////////////////////////////////////////////////////////////////////////

#include <TF1.h>
#include <TTree.h>
#include <TH1.h>
#include <TFile.h>

#include "AliRun.h"
#include "AliRunLoader.h"
#include "AliLoader.h"
#include "AliRawReader.h"
#include "AliLog.h"

#include "AliTRDclusterizerV1.h"
#include "AliTRDgeometry.h"
#include "AliTRDdataArrayF.h"
#include "AliTRDdataArrayI.h"
#include "AliTRDdigitsManager.h"
#include "AliTRDpadPlane.h"
#include "AliTRDrawData.h"
#include "AliTRDcalibDB.h"
#include "AliTRDSimParam.h"
#include "AliTRDRecParam.h"
#include "AliTRDCommonParam.h"
#include "AliTRDcluster.h"

ClassImp(AliTRDclusterizerV1)

//_____________________________________________________________________________
AliTRDclusterizerV1::AliTRDclusterizerV1()
  :AliTRDclusterizer()
  ,fDigitsManager(NULL)
{
  //
  // AliTRDclusterizerV1 default constructor
  //

}

//_____________________________________________________________________________
AliTRDclusterizerV1::AliTRDclusterizerV1(const Text_t* name, const Text_t* title)
  :AliTRDclusterizer(name,title)
  ,fDigitsManager(new AliTRDdigitsManager())
{
  //
  // AliTRDclusterizerV1 constructor
  //

  fDigitsManager->CreateArrays();

}

//_____________________________________________________________________________
AliTRDclusterizerV1::AliTRDclusterizerV1(const AliTRDclusterizerV1 &c)
  :AliTRDclusterizer(c)
  ,fDigitsManager(NULL)
{
  //
  // AliTRDclusterizerV1 copy constructor
  //

}

//_____________________________________________________________________________
AliTRDclusterizerV1::~AliTRDclusterizerV1()
{
  //
  // AliTRDclusterizerV1 destructor
  //

  if (fDigitsManager) {
    delete fDigitsManager;
    fDigitsManager = NULL;
  }

}

//_____________________________________________________________________________
AliTRDclusterizerV1 &AliTRDclusterizerV1::operator=(const AliTRDclusterizerV1 &c)
{
  //
  // Assignment operator
  //

  if (this != &c) ((AliTRDclusterizerV1 &) c).Copy(*this);
  return *this;

}

//_____________________________________________________________________________
void AliTRDclusterizerV1::Copy(TObject &c) const
{
  //
  // Copy function
  //

  ((AliTRDclusterizerV1 &) c).fDigitsManager = 0;

  AliTRDclusterizer::Copy(c);

}

//_____________________________________________________________________________
Bool_t AliTRDclusterizerV1::ReadDigits()
{
  //
  // Reads the digits arrays from the input aliroot file
  //

  if (!fRunLoader) {
    AliError("No run loader available");
    return kFALSE;
  }

  AliLoader* loader = fRunLoader->GetLoader("TRDLoader");
  if (!loader->TreeD()) {
    loader->LoadDigits();
  }

  // Read in the digit arrays
  return (fDigitsManager->ReadDigits(loader->TreeD()));

}

//_____________________________________________________________________________
Bool_t AliTRDclusterizerV1::ReadDigits(AliRawReader* rawReader)
{
  //
  // Reads the digits arrays from the ddl file
  //

  AliTRDrawData raw;
  fDigitsManager = raw.Raw2Digits(rawReader);

  return kTRUE;

}

//_____________________________________________________________________________
Bool_t AliTRDclusterizerV1::MakeClusters()
{
  //
  // Generates the cluster.
  //

  Int_t row   = 0;
  Int_t col   = 0;
  Int_t time  = 0;
  Int_t icham = 0;
  Int_t iplan = 0;
  Int_t isect = 0;
  Int_t iPad  = 0;
    
  AliTRDdataArrayI *digitsIn;
  AliTRDdataArrayI *track0;
  AliTRDdataArrayI *track1;
  AliTRDdataArrayI *track2; 

  // Get the geometry
  AliTRDgeometry *geo            = AliTRDgeometry::GetGeometry(fRunLoader);  
  AliTRDcalibDB  *calibration    = AliTRDcalibDB::Instance();
  if (!calibration) {
    AliError("No AliTRDcalibDB instance available\n");
    return kFALSE;  
  }
  
  AliTRDSimParam *simParam       = AliTRDSimParam::Instance();
  if (!simParam) {
    AliError("No AliTRDSimParam instance available\n");
    return kFALSE;  
  }
  
  AliTRDRecParam *recParam       = AliTRDRecParam::Instance();
  if (!recParam) {
    AliError("No AliTRDRecParam instance available\n");
    return kFALSE;  
  }
  
  AliTRDCommonParam *commonParam = AliTRDCommonParam::Instance();
  if (!commonParam) {
    AliError("Could not get common parameters\n");
    return kFALSE;
  }

  // ADC threshols
  Float_t ADCthreshold = simParam->GetADCthreshold();
  // Threshold value for the maximum
  Float_t maxThresh    = recParam->GetClusMaxThresh();
  // Threshold value for the digit signal
  Float_t sigThresh    = recParam->GetClusSigThresh();

  // Iteration limit for unfolding procedure
  const Float_t kEpsilon = 0.01;             
  const Int_t   kNclus   = 3;  
  const Int_t   kNsig    = 5;
  const Int_t   kNtrack  = 3 * kNclus;

  Int_t    iType         = 0;
  Int_t    iUnfold       = 0;  
  Double_t ratioLeft     = 1.0;
  Double_t ratioRight    = 1.0;

  Double_t padSignal[kNsig];   
  Double_t clusterSignal[kNclus];
  Double_t clusterPads[kNclus];   
  Int_t    clusterTracks[kNtrack];

  Int_t    chamBeg    = 0;
  Int_t    chamEnd    = AliTRDgeometry::Ncham();
  Int_t    planBeg    = 0;
  Int_t    planEnd    = AliTRDgeometry::Nplan();
  Int_t    sectBeg    = 0;
  Int_t    sectEnd    = AliTRDgeometry::Nsect();
  Int_t    nTimeTotal = calibration->GetNumberOfTimeBins();

  AliDebug(1,Form("Number of Time Bins = %d.\n",nTimeTotal));

  // Start clustering in every chamber
  for (icham = chamBeg; icham < chamEnd; icham++) {
    for (iplan = planBeg; iplan < planEnd; iplan++) {
      for (isect = sectBeg; isect < sectEnd; isect++) {

        Int_t idet    = geo->GetDetector(iplan,icham,isect);

	Int_t nRowMax = commonParam->GetRowMax(iplan,icham,isect);
	Int_t nColMax = commonParam->GetColMax(iplan);

        AliTRDpadPlane *padPlane = commonParam->GetPadPlane(iplan,icham);

        Int_t nClusters      = 0;
        Int_t nClusters2pad  = 0;
        Int_t nClusters3pad  = 0;
        Int_t nClusters4pad  = 0;
        Int_t nClusters5pad  = 0;
        Int_t nClustersLarge = 0;

        AliDebug(1,Form("Analyzing chamber %d, plane %d, sector %d.\n"
		       ,icham,iplan,isect));

        // Get the digits
        digitsIn = fDigitsManager->GetDigits(idet);
	// This is to take care of switched off super modules
        if (digitsIn->GetNtime() == 0) {
          continue;
	}
        digitsIn->Expand();
        track0   = fDigitsManager->GetDictionary(idet,0);
        track0->Expand();
        track1   = fDigitsManager->GetDictionary(idet,1);
        track1->Expand();
        track2   = fDigitsManager->GetDictionary(idet,2); 
        track2->Expand();

        AliTRDdataArrayF *digitsOut = new AliTRDdataArrayF(digitsIn->GetNrow()
                                                          ,digitsIn->GetNcol()
                                                          ,digitsIn->GetNtime());
        Transform(digitsIn, digitsOut,idet,nRowMax,nColMax,nTimeTotal,ADCthreshold);

        // Loop through the chamber and find the maxima 
        for ( row = 0;  row <  nRowMax;    row++) {
	  for ( col = 2;  col <  nColMax;    col++) {
            for (time = 0; time < nTimeTotal; time++) {

              Float_t signalL = TMath::Abs(digitsOut->GetDataUnchecked(row,col  ,time));
              Float_t signalM = TMath::Abs(digitsOut->GetDataUnchecked(row,col-1,time));
              Float_t signalR = TMath::Abs(digitsOut->GetDataUnchecked(row,col-2,time));
 
	      // Look for the maximum
              if (signalM >= maxThresh) {
                if ((TMath::Abs(signalL) <= signalM) && 
                    (TMath::Abs(signalR) <= signalM) && 
		    ((TMath::Abs(signalL) + TMath::Abs(signalR)) > sigThresh)) {
                  // Maximum found, mark the position by a negative signal
                  digitsOut->SetDataUnchecked(row,col-1,time,-signalM);
		}
	      }

            }
          }
        }

        // Now check the maxima and calculate the cluster position
        for ( row = 0;  row <  nRowMax  ;  row++) {
          for (time = 0; time < nTimeTotal; time++) {
            for ( col = 1;  col <  nColMax-1;  col++) {

              // Maximum found ?             
              if (digitsOut->GetDataUnchecked(row,col,time) < 0) {

                for (iPad = 0; iPad < kNclus; iPad++) {
                  Int_t iPadCol = col - 1 + iPad;
                  clusterSignal[iPad]     = TMath::Abs(digitsOut->GetDataUnchecked(row
                                                                                  ,iPadCol
                                                                                   ,time));
                  clusterTracks[3*iPad  ] = track0->GetDataUnchecked(row,iPadCol,time) - 1;
		  clusterTracks[3*iPad+1] = track1->GetDataUnchecked(row,iPadCol,time) - 1;
		  clusterTracks[3*iPad+2] = track2->GetDataUnchecked(row,iPadCol,time) - 1;
                }

		// Count the number of pads in the cluster
                Int_t nPadCount = 0;
                Int_t ii        = 0;
                while (TMath::Abs(digitsOut->GetDataUnchecked(row,col-ii  ,time)) >= sigThresh) {
                  nPadCount++;
                  ii++;
                  if (col-ii   <        0) break;
		}
                ii = 0;
                while (TMath::Abs(digitsOut->GetDataUnchecked(row,col+ii+1,time)) >= sigThresh) {
                  nPadCount++;
                  ii++;
                  if (col+ii+1 >= nColMax) break;
		}

                nClusters++;
                switch (nPadCount) {
                case 2:
                  iType = 0;
                  nClusters2pad++;
                  break;
                case 3:
                  iType = 1;
                  nClusters3pad++;
                  break;
                case 4:
                  iType = 2;
                  nClusters4pad++;
                  break;
                case 5:
                  iType = 3;
                  nClusters5pad++;
                  break;
                default:
                  iType = 4;
                  nClustersLarge++;
                  break;
		};

		// Look for 5 pad cluster with minimum in the middle
                Bool_t fivePadCluster = kFALSE;
                if (col < (nColMax - 3)) {
                  if (digitsOut->GetDataUnchecked(row,col+2,time) < 0) {
                    fivePadCluster = kTRUE;
	  	  }
                  if ((fivePadCluster) && (col < (nColMax - 5))) {
                    if (digitsOut->GetDataUnchecked(row,col+4,time) >= sigThresh) {
                      fivePadCluster = kFALSE;
		    }
		  }
                  if ((fivePadCluster) && (col >             1)) {
                    if (digitsOut->GetDataUnchecked(row,col-2,time) >= sigThresh) {
                      fivePadCluster = kFALSE;
		    }
		  }
		}

		// 5 pad cluster
                // Modify the signal of the overlapping pad for the left part 
		// of the cluster which remains from a previous unfolding
                if (iUnfold) {
                  clusterSignal[0] *= ratioLeft;
                  iType   = 5;
                  iUnfold = 0;
		}

		// Unfold the 5 pad cluster
                if (fivePadCluster) {
                  for (iPad = 0; iPad < kNsig; iPad++) {
                    padSignal[iPad] = TMath::Abs(digitsOut->GetDataUnchecked(row
									     ,col-1+iPad
									     ,time));
                  }
                  // Unfold the two maxima and set the signal on 
                  // the overlapping pad to the ratio
                  ratioRight        = Unfold(kEpsilon,iplan,padSignal);
                  ratioLeft         = 1.0 - ratioRight; 
                  clusterSignal[2] *= ratioRight;
                  iType   = 5;
                  iUnfold = 1;
                }

                Double_t clusterCharge = clusterSignal[0]
                                       + clusterSignal[1]
                                       + clusterSignal[2];
                
		// The position of the cluster
                clusterPads[0] = row + 0.5;
		// Take the shift of the additional time bins into account
                clusterPads[2] = time + 0.5;

                if (recParam->LUTOn()) {
  		  // Calculate the position of the cluster by using the
		  // lookup table method
                  clusterPads[1] = recParam->LUTposition(iplan,clusterSignal[0]
                                                              ,clusterSignal[1]
                                                              ,clusterSignal[2]);
		}
		else {
  		  // Calculate the position of the cluster by using the
		  // center of gravity method
		  for (Int_t i = 0; i < 5; i++) {
                    padSignal[i] = 0;
		  }
		  padSignal[2] = TMath::Abs(digitsOut->GetDataUnchecked(row,col  ,time)); // central  pad
		  padSignal[1] = TMath::Abs(digitsOut->GetDataUnchecked(row,col-1,time)); // left     pad
		  padSignal[3] = TMath::Abs(digitsOut->GetDataUnchecked(row,col+1,time)); // right    pad
		  if ((col >           2) && 
                      (TMath::Abs(digitsOut->GetDataUnchecked(row,col-2,time)) < padSignal[1])) {
		    padSignal[0] = TMath::Abs(digitsOut->GetDataUnchecked(row,col-2,time));
		  }
		  if ((col < nColMax - 3) &&
                      (TMath::Abs(digitsOut->GetDataUnchecked(row,col+2,time)) < padSignal[3])) {
		    padSignal[4] = TMath::Abs(digitsOut->GetDataUnchecked(row,col+2,time));
		  }		  
		  clusterPads[1] = GetCOG(padSignal);
		}

                Double_t q0 = clusterSignal[0];
		Double_t q1 = clusterSignal[1];
                Double_t q2 = clusterSignal[2];
                Double_t clusterSigmaY2 = (q1*(q0+q2)+4*q0*q2) /
                                          (clusterCharge*clusterCharge);

		//
                // Calculate the position and the error
		//		

                // Correct for t0
		Int_t    clusterTimeBin = TMath::Nint(time - calibration->GetT0(idet, col, row));

                Double_t colSize        = padPlane->GetColSize(col);
                Double_t rowSize        = padPlane->GetRowSize(row);

                Double_t clusterPos[3];
		clusterPos[0] = padPlane->GetColPos(col) - (clusterPads[1]+0.5)*colSize;
		clusterPos[1] = padPlane->GetRowPos(row) - 0.5*rowSize;
                clusterPos[2] = CalcXposFromTimebin(clusterPads[2],idet,col,row);
                Double_t clusterSig[2];
                clusterSig[0] = (clusterSigmaY2 + 1./12.) * colSize*colSize;
                clusterSig[1] = rowSize * rowSize / 12.;                                       
                
                
                // Add the cluster to the output array 
                AliTRDcluster * cluster = AddCluster(clusterPos
                                                    ,clusterTimeBin
                                                    ,idet
			                            ,clusterCharge
			                            ,clusterTracks
			                            ,clusterSig
			                            ,iType
                                                    ,clusterPads[1]);

                printf("Add a cluster: q=%f, det=%d, x=%f, y=%f, z=%f\n",clusterCharge
		       ,idet,clusterPos[0],clusterPos[1],clusterPos[2]);

		Short_t signals[7]={ 0, 0, 0, 0, 0, 0, 0 };
		for (Int_t jPad = col-3; jPad <= col+3; jPad++) {
		  if ((jPad < 0) || (jPad >= nColMax-1)) {
                    continue;
		  }
		  signals[jPad-col+3] = TMath::Nint(TMath::Abs(digitsOut->GetDataUnchecked(row,jPad,time)));
		}
		cluster->SetSignals(signals);

              }

            } 
          }   
        }

        delete digitsOut;

        // Compress the arrays
        track0->Compress(1,0);
	track1->Compress(1,0);
        track2->Compress(1,0);

        // Write the cluster and reset the array
	WriteClusters(idet);
	ResetRecPoints();

      }    
    }      
  }        

  return kTRUE;

}

//_____________________________________________________________________________
Double_t AliTRDclusterizerV1::GetCOG(Double_t signal[5])
{
  //
  // Get COG position
  // Used for clusters with more than 3 pads - where LUT not applicable
  //

  Double_t sum = signal[0]+signal[1]+signal[2]+signal[3]+signal[4];
  Double_t res = (0.0*(-signal[0]+signal[4])+(-signal[1]+signal[3]))/sum;

  return res;		  

}

//_____________________________________________________________________________
Double_t AliTRDclusterizerV1::Unfold(Double_t eps, Int_t plane, Double_t* padSignal)
{
  //
  // Method to unfold neighbouring maxima.
  // The charge ratio on the overlapping pad is calculated
  // until there is no more change within the range given by eps.
  // The resulting ratio is then returned to the calling method.
  //

  AliTRDcalibDB* calibration = AliTRDcalibDB::Instance();
  if (!calibration) {
    AliError("No AliTRDcalibDB instance available\n");
    return kFALSE;  
  }
  
  Int_t   irc                = 0;
  Int_t   itStep             = 0;      // Count iteration steps

  Double_t ratio             = 0.5;    // Start value for ratio
  Double_t prevRatio         = 0;      // Store previous ratio

  Double_t newLeftSignal[3]  = {0};    // Array to store left cluster signal
  Double_t newRightSignal[3] = {0};    // Array to store right cluster signal
  Double_t newSignal[3]      = {0};

  // Start the iteration
  while ((TMath::Abs(prevRatio - ratio) > eps) && (itStep < 10)) {

    itStep++;
    prevRatio = ratio;

    // Cluster position according to charge ratio
    Double_t maxLeft  = (ratio*padSignal[2] - padSignal[0]) 
                      / (padSignal[0] + padSignal[1] + ratio*padSignal[2]);
    Double_t maxRight = (padSignal[4] - (1-ratio)*padSignal[2]) 
                      / ((1-ratio)*padSignal[2] + padSignal[3] + padSignal[4]);

    // Set cluster charge ratio
    irc = calibration->PadResponse(1.0,maxLeft ,plane,newSignal);
    Double_t ampLeft  = padSignal[1] / newSignal[1];
    irc = calibration->PadResponse(1.0,maxRight,plane,newSignal);
    Double_t ampRight = padSignal[3] / newSignal[1];

    // Apply pad response to parameters
    irc = calibration->PadResponse(ampLeft ,maxLeft ,plane,newLeftSignal );
    irc = calibration->PadResponse(ampRight,maxRight,plane,newRightSignal);

    // Calculate new overlapping ratio
    ratio = TMath::Min((Double_t)1.0,newLeftSignal[2] / 
                          (newLeftSignal[2] + newRightSignal[0]));

  }

  return ratio;

}

//_____________________________________________________________________________
void AliTRDclusterizerV1::Transform(AliTRDdataArrayI* digitsIn,
				    AliTRDdataArrayF* digitsOut,
				    Int_t idet, Int_t nRowMax,
				    Int_t nColMax, Int_t nTimeTotal,
				    Float_t ADCthreshold)
{
  //
  // Apply gain factor
  // Apply tail cancellation: Transform digitsIn to digitsOut
  //

  Int_t iRow  = 0;
  Int_t iCol  = 0;
  Int_t iTime = 0;

  AliTRDRecParam* recParam = AliTRDRecParam::Instance();
  if (!recParam) {
    AliError("No AliTRDRecParam instance available\n");
    return;
  }
  AliTRDcalibDB* calibration = AliTRDcalibDB::Instance();
  if (!calibration) {
    AliError("No AliTRDcalibDB instance available\n");
    return;  
  }

  Double_t *inADC  = new Double_t[nTimeTotal];  // adc data before tail cancellation
  Double_t *outADC = new Double_t[nTimeTotal];  // adc data after tail cancellation

  AliDebug(1,Form("Tail cancellation (nExp = %d) for detector %d.\n"
	         ,recParam->GetTCnexp(),idet));

  for (iRow  = 0; iRow  <  nRowMax;   iRow++ ) {
    for (iCol  = 0; iCol  <  nColMax;   iCol++ ) {
      for (iTime = 0; iTime < nTimeTotal; iTime++) {

	//
	// Add gain
	//
	Double_t gain = calibration->GetGainFactor(idet,iCol,iRow);
	if (gain == 0) {
	  AliError("Not a valid gain\n");
	}
	inADC[iTime]  = digitsIn->GetDataUnchecked(iRow,iCol,iTime);
        inADC[iTime] /= gain;
        outADC[iTime] = inADC[iTime];

      }

      // Apply the tail cancelation via the digital filter
      if (recParam->TCOn()) {
	DeConvExp(inADC,outADC,nTimeTotal,recParam->GetTCnexp());
      }

      for (iTime = 0; iTime < nTimeTotal; iTime++) {

	// Store the amplitude of the digit if above threshold
	if (outADC[iTime] > ADCthreshold) {
	  AliDebug(2,Form("  iRow = %d, iCol = %d, iTime = %d, adc = %f\n"
		         ,iRow,iCol,iTime,outADC[iTime]));
	  digitsOut->SetDataUnchecked(iRow,iCol,iTime,outADC[iTime]);
	}

      }

    }
  }

  delete [] inADC;
  delete [] outADC;

  return;

}

//_____________________________________________________________________________
void AliTRDclusterizerV1::DeConvExp(Double_t *source, Double_t *target,
				    Int_t n, Int_t nexp) 
{
  //
  // Tail cancellation by deconvolution for PASA v4 TRF
  //

  Double_t rates[2];
  Double_t coefficients[2];

  // Initialization (coefficient = alpha, rates = lambda)
  Double_t R1 = 1.0;
  Double_t R2 = 1.0;
  Double_t C1 = 0.5;
  Double_t C2 = 0.5;

  if (nexp == 1) {   // 1 Exponentials
    R1 = 1.156;
    R2 = 0.130;
    C1 = 0.066;
    C2 = 0.000;
  }
  if (nexp == 2) {   // 2 Exponentials
    R1 = 1.156;
    R2 = 0.130;
    C1 = 0.114;
    C2 = 0.624;
  }

  coefficients[0] = C1;
  coefficients[1] = C2;

  Double_t Dt = 0.100;

  rates[0] = TMath::Exp(-Dt/(R1));
  rates[1] = TMath::Exp(-Dt/(R2));
  
  Int_t i = 0;
  Int_t k = 0;

  Double_t reminder[2];
  Double_t correction;
  Double_t result;

  // Attention: computation order is important
  correction = 0.0;
  for (k = 0; k < nexp; k++) {
    reminder[k] = 0.0;
  }
  for (i = 0; i < n; i++) {
    result    = (source[i] - correction);    // no rescaling
    target[i] = result;

    for (k = 0; k < nexp; k++) {
      reminder[k] = rates[k] * (reminder[k] + coefficients[k] * result);
    }
    correction = 0.0;
    for (k = 0; k < nexp; k++) {
      correction += reminder[k];
    }
  }

}