[u/mrichter/AliRoot.git] / EMCAL / AliCaloRawAnalyzer.cxx

// -*- mode: c++ -*-
/**************************************************************************
 * This file is property of and copyright by                              *
 * the Relativistic Heavy Ion Group (RHIG), Yale University, US, 2009     *
 *                                                                        *
 * Primary Author: Per Thomas Hille <perthomas.hille@yale.edu>            *
 *                                                                        *
 * Contributors are mentioned in the code where appropriate.              *
 * Please report bugs to p.t.hille@fys.uio.no                             *
 *                                                                        *
 * 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.                  *
 **************************************************************************/


// Base class for extraction 
// of signal amplitude and peak position
// From CALO Calorimeter RAW data (from the RCU)
// Contains some utilities for preparing / selecting
// Signals suitable for signal extraction
// By derived classes

#include "AliLog.h"
#include "AliCaloRawAnalyzer.h"
#include "AliCaloBunchInfo.h"
#include "AliCaloFitResults.h"
#include "TMath.h"
#include <iostream>
using namespace std;

ClassImp(AliCaloRawAnalyzer)  

AliCaloRawAnalyzer::AliCaloRawAnalyzer(const char *name, const char *nameshort) :  TObject(),
  fMinTimeIndex(-1),
  fMaxTimeIndex(-1),
  fFitArrayCut(5),
  fAmpCut(4),
  fNsampleCut(5),
  fOverflowCut(950),
  fNsamplePed(3),
  fIsZerosupressed( false ),
  fVerbose( false ),
  fAlgo(Algo::kNONE)
{
  //Comment 
  snprintf(fName, 256,"%s", name);
  snprintf(fNameShort,256, "%s", nameshort);
    
  for(int i=0; i < MAXSAMPLES; i++ )
    {
      fReversed[i] = 0;
    }
}

AliCaloRawAnalyzer::~AliCaloRawAnalyzer()
{

}


void 
AliCaloRawAnalyzer::SetTimeConstraint(const int min, const int max ) 
{
  //Require that the bin if the maximum ADC value is between min and max (timebin)
  if(  ( min > max ) || min > MAXSAMPLES  || max > MAXSAMPLES  )
    {
      AliWarning( Form( "Attempt to set Invalid time bin range (Min , Max) = (%d, %d), Ingored",  min, max ) ); 
    }
  else
    {
      fMinTimeIndex  = min;
      fMaxTimeIndex  = max;
    }
}


UShort_t 
AliCaloRawAnalyzer::Max(const UShort_t *data, const int length ) const
{
  //------------
  UShort_t tmpmax  = data[0];

  for(int i=0; i < length; i++)
    {
      if( tmpmax  <  data[i] )
	{
	  tmpmax = data[i];
	}
    }
  return tmpmax;
}


void 
AliCaloRawAnalyzer::SelectSubarray( const Double_t *fData, const int length, const short maxindex, int *const first,  int *const last ) const
{
  //Selection of subset of data from one bunch that will be used for fitting or
  //Peak finding.  Go to the left and right of index of the maximum time bin
  //Until the ADC value is less that fFitArrayCut, or derivative changes sign (data jump)
  int tmpfirst =  maxindex;
  int tmplast  =  maxindex;
  Double_t prevFirst =  fData[maxindex];
  Double_t prevLast  =  fData[maxindex];  
  bool firstJump = false;
  bool lastJump = false;

  while( (tmpfirst >= 0) && (fData[tmpfirst] >= fFitArrayCut) && (!firstJump) ) 
    {
      // jump check:
      if (tmpfirst != maxindex) { // neighbor to maxindex can share peak with maxindex
	if (fData[tmpfirst] >= prevFirst) {
	  firstJump = true;
	}
      }
      prevFirst = fData[tmpfirst];
      tmpfirst -- ;
    }
  
  while( (tmplast < length) && (fData[tmplast] >= fFitArrayCut) && (!lastJump) ) 
    {
      // jump check:
      if (tmplast != maxindex) { // neighbor to maxindex can share peak with maxindex
	if (fData[tmplast] >= prevLast) {
	  lastJump = true;
	}
      }
      prevLast = fData[tmplast];
      tmplast ++;
    }

  // we keep one pre- or post- sample if we can (as in online)
  // check though if we ended up on a 'jump', or out of bounds: if so, back up
  if (firstJump || tmpfirst<0) tmpfirst ++;
  if (lastJump || tmplast>=length) tmplast --;

  *first = tmpfirst;
  *last =  tmplast;
  return;
}


Float_t 
AliCaloRawAnalyzer::ReverseAndSubtractPed( const AliCaloBunchInfo *bunch, const UInt_t /*altrocfg1*/,  const UInt_t /*altrocfg2*/, double *outarray ) const
{
  //Time sample comes in reversed order, revers them back
  //Subtract the baseline based on content of altrocfg1 and altrocfg2.
  Int_t length =  bunch->GetLength(); 
  const UShort_t *sig = bunch->GetData();

  double ped = EvaluatePedestal( sig , length);

  for( int i=0; i < length; i++ )
    {
      outarray[i] = sig[length -i -1] - ped;
    }

  return ped;
}


Float_t 
AliCaloRawAnalyzer::EvaluatePedestal(const UShort_t * const data, const int /*length*/ ) const
{
  //  double ped = 0;
  double tmp = 0;

  if( fIsZerosupressed == false ) 
    {
      for(int i=0; i < fNsamplePed; i++ )
	{
	  tmp += data[i];
	}
   }

  return  tmp/fNsamplePed;
 }


short  
AliCaloRawAnalyzer::Max( const AliCaloBunchInfo *const bunch , int *const maxindex ) const
{
  //comment
  short tmpmax = -1;
  int tmpindex = -1;
  const UShort_t *sig = bunch->GetData();

  for(int i=0; i < bunch->GetLength(); i++ )
    {
      if( sig[i] > tmpmax )
	{
	  tmpmax   =  sig[i];
	  tmpindex =  i; 
	}
    }
  
  if(maxindex != 0 )
    {
      //   *maxindex =  bunch->GetLength() -1 - tmpindex + bunch->GetStartBin(); 
       *maxindex =  bunch->GetLength() -1 - tmpindex + bunch->GetStartBin(); 
    }
  
  return  tmpmax;
}


bool  
AliCaloRawAnalyzer::CheckBunchEdgesForMax( const AliCaloBunchInfo *const bunch ) const
{
  // a bunch is considered invalid if the maximum is in the first or last time-bin
  short tmpmax = -1;
  int tmpindex = -1;
  const UShort_t *sig = bunch->GetData();

  for(int i=0; i < bunch->GetLength(); i++ )
    {
      if( sig[i] > tmpmax )
	{
	  tmpmax   =  sig[i];
	  tmpindex =  i; 
	}
    }
  
  bool bunchOK = true;
  if (tmpindex == 0 || tmpindex == (bunch->GetLength()-1) )
    {
      bunchOK = false;
    }
  
  return  bunchOK;
}


int 
AliCaloRawAnalyzer::SelectBunch( const vector<AliCaloBunchInfo> &bunchvector,short *const maxampbin, short *const maxamplitude ) const
{
  //We select the bunch with the highest amplitude unless any time constraints is set
  short max = -1;
  short bunchindex = -1;
  short maxall = -1;
  int indx = -1;

  for(unsigned int i=0; i < bunchvector.size(); i++ )
    {
      max = Max(  &bunchvector.at(i), &indx ); // CRAP PTH, bug fix, trouble if more than one bunches  
      if( IsInTimeRange( indx) )
	{
	  if( max > maxall )
	    {
	      maxall = max;
	      bunchindex = i;
	      *maxampbin     = indx;
	      *maxamplitude  = max;
	    }
	}
    }
 
  if (bunchindex >= 0) {
    bool bunchOK = CheckBunchEdgesForMax( &bunchvector.at(bunchindex) );
    if (! bunchOK) { 
      bunchindex = -1; 
    }
  }

  return  bunchindex;
}


bool 
AliCaloRawAnalyzer::IsInTimeRange( const int maxindex  ) const
{
  // Ckeck if the index of the max ADC vaue is consistent with trigger.
  if( ( fMinTimeIndex  < 0 && fMaxTimeIndex  < 0) ||fMaxTimeIndex  < 0 )
    {
      return true; 
    }
  return ( maxindex < fMaxTimeIndex ) && ( maxindex > fMinTimeIndex  ) ? true : false;
}


void 
AliCaloRawAnalyzer::PrintBunches( const vector<AliCaloBunchInfo> &bvctr ) const
{
  //comment
  cout << __FILE__ << __LINE__<< "*************** Printing Bunches *******************" << endl;
  cout << __FILE__ << __LINE__<< "*** There are " << bvctr.size() << ", bunches" << endl;

  for(unsigned int i=0; i < bvctr.size() ; i++ )
    {
      PrintBunch( bvctr.at(i) );
      cout << " bunch = "  <<  i  << endl;
    }
  cout << __FILE__ << __LINE__<< "*************** Done ... *******************" << endl;
}


void 
AliCaloRawAnalyzer::PrintBunch( const AliCaloBunchInfo &bunch ) const
{
  //comment
  cout << __FILE__ << ":" << __LINE__ << endl;
  cout << __FILE__ << __LINE__   << ", startimebin = " << bunch.GetStartBin() << ", length =" <<  bunch.GetLength() << endl;
  const UShort_t *sig =  bunch.GetData();  
  
  for ( Int_t j = 0; j <  bunch.GetLength();  j++) 
    {
      printf("%d\t", sig[j] );
    }
  cout << endl; 
}


Double_t
AliCaloRawAnalyzer::CalculateChi2(const Double_t amp, const Double_t time,
				  const Int_t first, const Int_t last,
				  const Double_t adcErr, 
				  const Double_t tau)
{
  //   Input:
  //   amp   - max amplitude;
  //   time    - time of max amplitude; 
  //   first, last - sample array indices to be used
  //   adcErr   - nominal error of amplitude measurement (one value for all channels)
  //           if adcErr<0 that mean adcErr=1.
  //   tau   - filter time response (in timebin units)
  // Output:
  //   chi2 - chi2

  if (first == last || first<0 ) { // signal consists of single sample, chi2 estimate (0) not too well defined.. 
    // or, first is negative, the indices are not valid
    return Ret::kDummy;
  }

  int nsamples =  last - first + 1;
  // printf(" AliCaloRawAnalyzer::CalculateChi2 : first %i last %i : nsamples %i : amp %3.2f time %3.2f \n", first, last, nsamples, amp, time); 

  Int_t x = 0;
  Double_t chi2 = 0;
  Double_t dy = 0.0, xx = 0.0, f=0.0;

  for (Int_t i=0; i<nsamples; i++) {
    x     = first + i; // timebin
    xx    = (x - time + tau) / tau; // help variable
    f     = 0;
    if (xx > 0) {
      f = amp * xx*xx * TMath::Exp(2 * (1 - xx )) ;
    }
    dy    = fReversed[x] - f; 
    chi2 += dy*dy;
    // printf(" AliCaloRawAnalyzer::CalculateChi2 : %i : y %f -> f %f : dy %f \n", i, fReversed[first+i], f, dy); 
  }

  if (adcErr>0.0) { // weight chi2
    chi2 /= (adcErr*adcErr);
  }
  return chi2;
}


void
AliCaloRawAnalyzer::CalculateMeanAndRMS(const Int_t first, const Int_t last,
					Double_t & mean, Double_t & rms)
{
  //   Input:
  //   first, last - sample array indices to be used
  // Output:
  //   mean and RMS of samples 
  //
  // To possibly be used to differentiate good signals from bad before fitting
  // 
  mean = Ret::kDummy;
  rms =  Ret::kDummy;

  if (first == last || first<0 ) { // signal consists of single sample, chi2 estimate (0) not too well defined.. 
    // or, first is negative, the indices are not valid
    return;
  }

  int nsamples =  last - first + 1;
  //  printf(" AliCaloRawAnalyzer::CalculateMeanAndRMS : first %i last %i : nsamples %i \n", first, last, nsamples); 

  int x = 0;
  Double_t sampleSum = 0; // sum of samples
  Double_t squaredSampleSum = 0; // sum of samples squared

  for (Int_t i=0; i<nsamples; i++) {
    x = first + i;
    sampleSum += fReversed[x];
    squaredSampleSum += (fReversed[x] * fReversed[x]);
  }

  mean = sampleSum / nsamples; 	 
  Double_t squaredMean = squaredSampleSum / nsamples; 	 
  // The variance (rms squared) is equal to the mean of the squares minus the square of the mean.. 	 
  rms = sqrt(squaredMean - mean*mean);

  return;
}


// AliCaloFitResults
// AliCaloRawAnalyzer::Evaluate( const vector<AliCaloBunchInfo>  &/*bunchvector*/, const UInt_t /*altrocfg1*/,  const UInt_t /*altrocfg2*/)
// { // method to do the selection of what should possibly be fitted
//   // not implemented for base class
//   cout << __FILE__ << ":" << __LINE__ << " " << endl;
  
//   return AliCaloFitResults( 0, 0 );
// }


int
AliCaloRawAnalyzer::PreFitEvaluateSamples( const vector<AliCaloBunchInfo>  &bunchvector, const UInt_t altrocfg1,  const UInt_t altrocfg2, Int_t & index, Float_t & maxf, short & maxamp, short & maxrev, Float_t & ped, int & first, int & last)
{ // method to do the selection of what should possibly be fitted
  int nsamples  = 0;
  short maxampindex = 0;
  index = SelectBunch( bunchvector,  &maxampindex,  &maxamp ); // select the bunch with the highest amplitude unless any time constraints is set

  
  if( index >= 0 && maxamp >= fAmpCut) // something valid was found, and non-zero amplitude
    {
      // use more convenient numbering and possibly subtract pedestal
      ped  = ReverseAndSubtractPed( &(bunchvector.at(index)),  altrocfg1, altrocfg2, fReversed  );
      maxf = TMath::MaxElement( bunchvector.at(index).GetLength(),  fReversed );
      
      if ( maxf >= fAmpCut ) // possibly significant signal
	{
	  // select array around max to possibly be used in fit
	  maxrev = maxampindex - bunchvector.at(index).GetStartBin(); 
	  SelectSubarray( fReversed,  bunchvector.at(index).GetLength(),  maxrev, &first, &last);

	  // sanity check: maximum should not be in first or last bin
	  // if we should do a fit
	  if (first!=maxrev && last!=maxrev) {
	    // calculate how many samples we have 
	    nsamples =  last - first + 1;	  
	  }
	}
    }

  return nsamples;
}
Commit	Line	Data
168c7b3c	1	// -- mode: c++ --
d655d7dd	2	/**************************************************************************
	3	* This file is property of and copyright by *
	4	* the Relativistic Heavy Ion Group (RHIG), Yale University, US, 2009 *
	5	* *
e37e3c84	6	* Primary Author: Per Thomas Hille <perthomas.hille@yale.edu> *
d655d7dd	7	* *
	8	* Contributors are mentioned in the code where appropriate. *
	9	* Please report bugs to p.t.hille@fys.uio.no *
	10	* *
	11	* Permission to use, copy, modify and distribute this software and its *
	12	* documentation strictly for non-commercial purposes is hereby granted *
	13	* without fee, provided that the above copyright notice appears in all *
	14	* copies and that both the copyright notice and this permission notice *
	15	* appear in the supporting documentation. The authors make no claims *
	16	* about the suitability of this software for any purpose. It is *
	17	* provided "as is" without express or implied warranty. *
	18	**************************************************************************/
	19
	20
	21	// Base class for extraction
	22	// of signal amplitude and peak position
57839add	23	// From CALO Calorimeter RAW data (from the RCU)
d655d7dd	24	// Contains some utilities for preparing / selecting
	25	// Signals suitable for signal extraction
	26	// By derived classes
	27
	28	#include "AliLog.h"
57839add	29	#include "AliCaloRawAnalyzer.h"
	30	#include "AliCaloBunchInfo.h"
	31	#include "AliCaloFitResults.h"
	32	#include "TMath.h"
d655d7dd	33	#include <iostream>
	34	using namespace std;
	35
ce95bae9	36	ClassImp(AliCaloRawAnalyzer)
48a2e3eb	37
48a2e3eb	38	AliCaloRawAnalyzer::AliCaloRawAnalyzer(const char name, const char nameshort) : TObject(),
168c7b3c	39	fMinTimeIndex(-1),
	40	fMaxTimeIndex(-1),
	41	fFitArrayCut(5),
	42	fAmpCut(4),
	43	fNsampleCut(5),
	44	fOverflowCut(950),
	45	fNsamplePed(3),
	46	fIsZerosupressed( false ),
	47	fVerbose( false ),
	48	fAlgo(Algo::kNONE)
d655d7dd	49	{
e37e3c84	50	//Comment
a51e676d	51	snprintf(fName, 256,"%s", name);
a51e676d	52	snprintf(fNameShort,256, "%s", nameshort);
48a2e3eb	53
d655d7dd	54	for(int i=0; i < MAXSAMPLES; i++ )
	55	{
	56	fReversed[i] = 0;
	57	}
	58	}
	59
57839add	60	AliCaloRawAnalyzer::~AliCaloRawAnalyzer()
d655d7dd	61	{
	62
	63	}
	64
	65
	66	void
57839add	67	AliCaloRawAnalyzer::SetTimeConstraint(const int min, const int max )
d655d7dd	68	{
	69	//Require that the bin if the maximum ADC value is between min and max (timebin)
	70	if( ( min > max ) \|\| min > MAXSAMPLES \|\| max > MAXSAMPLES )
	71	{
	72	AliWarning( Form( "Attempt to set Invalid time bin range (Min , Max) = (%d, %d), Ingored", min, max ) );
	73	}
	74	else
	75	{
	76	fMinTimeIndex = min;
	77	fMaxTimeIndex = max;
	78	}
	79	}
	80
	81
	82	UShort_t
57839add	83	AliCaloRawAnalyzer::Max(const UShort_t *data, const int length ) const
d655d7dd	84	{
	85	//------------
	86	UShort_t tmpmax = data[0];
	87
	88	for(int i=0; i < length; i++)
	89	{
	90	if( tmpmax < data[i] )
	91	{
	92	tmpmax = data[i];
	93	}
	94	}
	95	return tmpmax;
	96	}
	97
	98
	99	void
57839add	100	AliCaloRawAnalyzer::SelectSubarray( const Double_t fData, const int length, const short maxindex, int const first, int *const last ) const
d655d7dd	101	{
	102	//Selection of subset of data from one bunch that will be used for fitting or
	103	//Peak finding. Go to the left and right of index of the maximum time bin
e7acbc37	104	//Until the ADC value is less that fFitArrayCut, or derivative changes sign (data jump)
d655d7dd	105	int tmpfirst = maxindex;
d655d7dd	106	int tmplast = maxindex;
947c8e28	107	Double_t prevFirst = fData[maxindex];
	108	Double_t prevLast = fData[maxindex];
	109	bool firstJump = false;
	110	bool lastJump = false;
	111
	112	while( (tmpfirst >= 0) && (fData[tmpfirst] >= fFitArrayCut) && (!firstJump) )
d655d7dd	113	{
947c8e28	114	// jump check:
	115	if (tmpfirst != maxindex) { // neighbor to maxindex can share peak with maxindex
	116	if (fData[tmpfirst] >= prevFirst) {
	117	firstJump = true;
	118	}
	119	}
	120	prevFirst = fData[tmpfirst];
d655d7dd	121	tmpfirst -- ;
	122	}
	123
947c8e28	124	while( (tmplast < length) && (fData[tmplast] >= fFitArrayCut) && (!lastJump) )
d655d7dd	125	{
947c8e28	126	// jump check:
	127	if (tmplast != maxindex) { // neighbor to maxindex can share peak with maxindex
	128	if (fData[tmplast] >= prevLast) {
	129	lastJump = true;
	130	}
	131	}
	132	prevLast = fData[tmplast];
d655d7dd	133	tmplast ++;
d655d7dd	134	}
f57baa2d	135
947c8e28	136	// we keep one pre- or post- sample if we can (as in online)
	137	// check though if we ended up on a 'jump', or out of bounds: if so, back up
	138	if (firstJump \|\| tmpfirst<0) tmpfirst ++;
	139	if (lastJump \|\| tmplast>=length) tmplast --;
	140
	141	*first = tmpfirst;
	142	*last = tmplast;
e7acbc37	143	return;
d655d7dd	144	}
	145
	146
	147
	148	Float_t
57839add	149	AliCaloRawAnalyzer::ReverseAndSubtractPed( const AliCaloBunchInfo bunch, const UInt_t /altrocfg1/, const UInt_t /altrocfg2/, double outarray ) const
d655d7dd	150	{
	151	//Time sample comes in reversed order, revers them back
	152	//Subtract the baseline based on content of altrocfg1 and altrocfg2.
	153	Int_t length = bunch->GetLength();
	154	const UShort_t *sig = bunch->GetData();
	155
57839add	156	double ped = EvaluatePedestal( sig , length);
	157
	158	for( int i=0; i < length; i++ )
	159	{
	160	outarray[i] = sig[length -i -1] - ped;
	161	}
	162
	163	return ped;
	164	}
	165
	166
	167
	168	Float_t
	169	AliCaloRawAnalyzer::EvaluatePedestal(const UShort_t * const data, const int /length/ ) const
	170	{
	171	// double ped = 0;
d655d7dd	172	double tmp = 0;
	173
	174	if( fIsZerosupressed == false )
	175	{
f57baa2d	176	for(int i=0; i < fNsamplePed; i++ )
d655d7dd	177	{
57839add	178	tmp += data[i];
d655d7dd	179	}
f57baa2d	180	}
e37e3c84	181
f57baa2d	182	return tmp/fNsamplePed;
f57baa2d	183	}
d655d7dd	184
	185
	186	short
57839add	187	AliCaloRawAnalyzer::Max( const AliCaloBunchInfo const bunch , int const maxindex ) const
d655d7dd	188	{
	189	//comment
	190	short tmpmax = -1;
	191	int tmpindex = -1;
	192	const UShort_t *sig = bunch->GetData();
	193
	194	for(int i=0; i < bunch->GetLength(); i++ )
	195	{
	196	if( sig[i] > tmpmax )
	197	{
	198	tmpmax = sig[i];
	199	tmpindex = i;
	200	}
	201	}
	202
	203	if(maxindex != 0 )
	204	{
48a2e3eb	205	// *maxindex = bunch->GetLength() -1 - tmpindex + bunch->GetStartBin();
48a2e3eb	206	*maxindex = bunch->GetLength() -1 - tmpindex + bunch->GetStartBin();
d655d7dd	207	}
	208
	209	return tmpmax;
	210	}
	211
	212
507751ce	213	bool
	214	AliCaloRawAnalyzer::CheckBunchEdgesForMax( const AliCaloBunchInfo *const bunch ) const
	215	{
	216	// a bunch is considered invalid if the maximum is in the first or last time-bin
	217	short tmpmax = -1;
	218	int tmpindex = -1;
	219	const UShort_t *sig = bunch->GetData();
	220
	221	for(int i=0; i < bunch->GetLength(); i++ )
	222	{
	223	if( sig[i] > tmpmax )
	224	{
	225	tmpmax = sig[i];
	226	tmpindex = i;
	227	}
	228	}
	229
	230	bool bunchOK = true;
	231	if (tmpindex == 0 \|\| tmpindex == (bunch->GetLength()-1) )
	232	{
	233	bunchOK = false;
	234	}
	235
	236	return bunchOK;
	237	}
	238
	239
d655d7dd	240	int
57839add	241	AliCaloRawAnalyzer::SelectBunch( const vector<AliCaloBunchInfo> &bunchvector,short const maxampbin, short const maxamplitude ) const
d655d7dd	242	{
	243	//We select the bunch with the highest amplitude unless any time constraints is set
	244	short max = -1;
	245	short bunchindex = -1;
	246	short maxall = -1;
	247	int indx = -1;
	248
	249	for(unsigned int i=0; i < bunchvector.size(); i++ )
	250	{
48a2e3eb	251	max = Max( &bunchvector.at(i), &indx ); // CRAP PTH, bug fix, trouble if more than one bunches
d655d7dd	252	if( IsInTimeRange( indx) )
	253	{
	254	if( max > maxall )
	255	{
	256	maxall = max;
	257	bunchindex = i;
48a2e3eb	258	*maxampbin = indx;
48a2e3eb	259	*maxamplitude = max;
d655d7dd	260	}
	261	}
	262	}
	263
507751ce	264	if (bunchindex >= 0) {
	265	bool bunchOK = CheckBunchEdgesForMax( &bunchvector.at(bunchindex) );
	266	if (! bunchOK) {
	267	bunchindex = -1;
	268	}
	269	}
	270
d655d7dd	271	return bunchindex;
	272	}
	273
	274
	275	bool
57839add	276	AliCaloRawAnalyzer::IsInTimeRange( const int maxindex ) const
d655d7dd	277	{
	278	// Ckeck if the index of the max ADC vaue is consistent with trigger.
	279	if( ( fMinTimeIndex < 0 && fMaxTimeIndex < 0) \|\|fMaxTimeIndex < 0 )
	280	{
	281	return true;
	282	}
	283	return ( maxindex < fMaxTimeIndex ) && ( maxindex > fMinTimeIndex ) ? true : false;
	284	}
	285
	286
	287	void
57839add	288	AliCaloRawAnalyzer::PrintBunches( const vector<AliCaloBunchInfo> &bvctr ) const
d655d7dd	289	{
	290	//comment
	291	cout << __FILE__ << __LINE__<< "************* Printing Bunches *****************" << endl;
	292	cout << __FILE__ << __LINE__<< "*** There are " << bvctr.size() << ", bunches" << endl;
	293
	294	for(unsigned int i=0; i < bvctr.size() ; i++ )
	295	{
	296	PrintBunch( bvctr.at(i) );
	297	cout << " bunch = " << i << endl;
	298	}
	299	cout << __FILE__ << __LINE__<< "************* Done ... *****************" << endl;
	300	}
	301
	302
	303	void
57839add	304	AliCaloRawAnalyzer::PrintBunch( const AliCaloBunchInfo &bunch ) const
d655d7dd	305	{
	306	//comment
	307	cout << __FILE__ << ":" << __LINE__ << endl;
	308	cout << __FILE__ << __LINE__ << ", startimebin = " << bunch.GetStartBin() << ", length =" << bunch.GetLength() << endl;
	309	const UShort_t *sig = bunch.GetData();
	310
	311	for ( Int_t j = 0; j < bunch.GetLength(); j++)
	312	{
	313	printf("%d\t", sig[j] );
	314	}
	315	cout << endl;
	316	}
	317
48a2e3eb	318
947c8e28	319	Double_t
	320	AliCaloRawAnalyzer::CalculateChi2(const Double_t amp, const Double_t time,
	321	const Int_t first, const Int_t last,
	322	const Double_t adcErr,
	323	const Double_t tau)
	324	{
	325	// Input:
	326	// amp - max amplitude;
	327	// time - time of max amplitude;
	328	// first, last - sample array indices to be used
	329	// adcErr - nominal error of amplitude measurement (one value for all channels)
	330	// if adcErr<0 that mean adcErr=1.
	331	// tau - filter time response (in timebin units)
	332	// Output:
	333	// chi2 - chi2
	334
	335	if (first == last \|\| first<0 ) { // signal consists of single sample, chi2 estimate (0) not too well defined..
	336	// or, first is negative, the indices are not valid
168c7b3c	337	return Ret::kDummy;
947c8e28	338	}
	339
	340	int nsamples = last - first + 1;
2cd0ffda	341	// printf(" AliCaloRawAnalyzer::CalculateChi2 : first %i last %i : nsamples %i : amp %3.2f time %3.2f \n", first, last, nsamples, amp, time);
947c8e28	342
	343	Int_t x = 0;
	344	Double_t chi2 = 0;
	345	Double_t dy = 0.0, xx = 0.0, f=0.0;
	346
	347	for (Int_t i=0; i<nsamples; i++) {
	348	x = first + i; // timebin
	349	xx = (x - time + tau) / tau; // help variable
	350	f = 0;
	351	if (xx > 0) {
	352	f = amp * xxxx TMath::Exp(2 * (1 - xx )) ;
	353	}
	354	dy = fReversed[x] - f;
	355	chi2 += dy*dy;
2cd0ffda	356	// printf(" AliCaloRawAnalyzer::CalculateChi2 : %i : y %f -> f %f : dy %f \n", i, fReversed[first+i], f, dy);
947c8e28	357	}
	358
	359	if (adcErr>0.0) { // weight chi2
	360	chi2 /= (adcErr*adcErr);
	361	}
	362	return chi2;
	363	}
	364
	365
	366	void
	367	AliCaloRawAnalyzer::CalculateMeanAndRMS(const Int_t first, const Int_t last,
	368	Double_t & mean, Double_t & rms)
	369	{
	370	// Input:
	371	// first, last - sample array indices to be used
	372	// Output:
	373	// mean and RMS of samples
	374	//
	375	// To possibly be used to differentiate good signals from bad before fitting
	376	//
168c7b3c	377	mean = Ret::kDummy;
168c7b3c	378	rms = Ret::kDummy;
947c8e28	379
	380	if (first == last \|\| first<0 ) { // signal consists of single sample, chi2 estimate (0) not too well defined..
	381	// or, first is negative, the indices are not valid
	382	return;
	383	}
	384
	385	int nsamples = last - first + 1;
	386	// printf(" AliCaloRawAnalyzer::CalculateMeanAndRMS : first %i last %i : nsamples %i \n", first, last, nsamples);
	387
	388	int x = 0;
	389	Double_t sampleSum = 0; // sum of samples
	390	Double_t squaredSampleSum = 0; // sum of samples squared
	391
	392	for (Int_t i=0; i<nsamples; i++) {
	393	x = first + i;
	394	sampleSum += fReversed[x];
	395	squaredSampleSum += (fReversed[x] * fReversed[x]);
	396	}
	397
	398	mean = sampleSum / nsamples;
	399	Double_t squaredMean = squaredSampleSum / nsamples;
	400	// The variance (rms squared) is equal to the mean of the squares minus the square of the mean..
	401	rms = sqrt(squaredMean - mean*mean);
	402
	403	return;
	404	}
	405
168c7b3c	406
	407
	408	// AliCaloFitResults
	409	// AliCaloRawAnalyzer::Evaluate( const vector<AliCaloBunchInfo> &/bunchvector/, const UInt_t /altrocfg1/, const UInt_t /altrocfg2/)
	410	// { // method to do the selection of what should possibly be fitted
	411	// // not implemented for base class
	412	// cout << __FILE__ << ":" << __LINE__ << " " << endl;
	413
	414	// return AliCaloFitResults( 0, 0 );
	415	// }
	416
57839add	417
48a2e3eb	418
57839add	419	int
f57baa2d	420	AliCaloRawAnalyzer::PreFitEvaluateSamples( const vector<AliCaloBunchInfo> &bunchvector, const UInt_t altrocfg1, const UInt_t altrocfg2, Int_t & index, Float_t & maxf, short & maxamp, short & maxrev, Float_t & ped, int & first, int & last)
57839add	421	{ // method to do the selection of what should possibly be fitted
57839add	422	int nsamples = 0;
f57baa2d	423	short maxampindex = 0;
57839add	424	index = SelectBunch( bunchvector, &maxampindex, &maxamp ); // select the bunch with the highest amplitude unless any time constraints is set
	425
	426
1afbf4b1	427	if( index >= 0 && maxamp >= fAmpCut) // something valid was found, and non-zero amplitude
57839add	428	{
	429	// use more convenient numbering and possibly subtract pedestal
	430	ped = ReverseAndSubtractPed( &(bunchvector.at(index)), altrocfg1, altrocfg2, fReversed );
	431	maxf = TMath::MaxElement( bunchvector.at(index).GetLength(), fReversed );
	432
1afbf4b1	433	if ( maxf >= fAmpCut ) // possibly significant signal
57839add	434	{
57839add	435	// select array around max to possibly be used in fit
f57baa2d	436	maxrev = maxampindex - bunchvector.at(index).GetStartBin();
f57baa2d	437	SelectSubarray( fReversed, bunchvector.at(index).GetLength(), maxrev, &first, &last);
57839add	438
	439	// sanity check: maximum should not be in first or last bin
	440	// if we should do a fit
f57baa2d	441	if (first!=maxrev && last!=maxrev) {
57839add	442	// calculate how many samples we have
	443	nsamples = last - first + 1;
	444	}
	445	}
	446	}
	447
	448	return nsamples;
	449	}
	450