[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), 
// fFp(0), 
  fL1Phase(0),
  fAmp(0),
  fTof(0)
{
  //Comment 
  snprintf(fName, 256,"%s", name);
  snprintf(fNameShort,256, "%s", nameshort);
    
  for(int i=0; i < ALTROMAXSAMPLES; i++ )
    {
      fReversed[i] = 0;
    }

  // fFp = fopen("amp2.txt", "w");

}

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 > ALTROMAXSAMPLES  || max > ALTROMAXSAMPLES  )
    {
      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 )
{
  //------------
  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 *data, const int length, const short maxindex, int *const first,  int *const last, const int cut)
{
  //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 =  data[maxindex];
  Double_t prevLast  =  data[maxindex];  
  bool firstJump = false;
  bool lastJump = false;

  while( (tmpfirst >= 0) && (data[tmpfirst] >= cut ) && (!firstJump) ) 
    {
      // jump check:
      if (tmpfirst != maxindex) { // neighbor to maxindex can share peak with maxindex
	if ( data[tmpfirst] >= prevFirst) {
	  firstJump = true;
	}
      }
      prevFirst = data[tmpfirst];
      tmpfirst -- ;
    }
  
  while( (tmplast < length) && (data[tmplast] >=  cut ) && (!lastJump) ) 
    {
      // jump check:
      if (tmplast != maxindex) { // neighbor to maxindex can share peak with maxindex
	if ( data[tmplast] >= prevLast) {
	  lastJump = true;
	}
      }
      prevLast = data[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 )
{
  //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 )
{
  //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, fMaxTimeIndex, fMinTimeIndex) )
	{
	  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 int maxtindx, const int mintindx )
{
  // Ckeck if the index of the max ADC vaue is consistent with trigger.
  if( ( mintindx  < 0 && maxtindx   < 0) ||maxtindx  < 0 )
    {
      return true; 
    }
  return ( maxindex < maxtindx ) && ( maxindex > mintindx  ) ? 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,const int acut )
{ // 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 >= acut ) // 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 >= acut  ) // 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, acut );

	  // 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 ),
92d9f317	48	fAlgo(Algo::kNONE),
	49	// fFp(0),
	50	fL1Phase(0),
	51	fAmp(0),
	52	fTof(0)
d655d7dd	53	{
e37e3c84	54	//Comment
a51e676d	55	snprintf(fName, 256,"%s", name);
a51e676d	56	snprintf(fNameShort,256, "%s", nameshort);
48a2e3eb	57
92d9f317	58	for(int i=0; i < ALTROMAXSAMPLES; i++ )
d655d7dd	59	{
	60	fReversed[i] = 0;
	61	}
92d9f317	62
	63	// fFp = fopen("amp2.txt", "w");
	64
d655d7dd	65	}
d655d7dd	66
57839add	67	AliCaloRawAnalyzer::~AliCaloRawAnalyzer()
d655d7dd	68	{
	69
	70	}
	71
	72
	73	void
57839add	74	AliCaloRawAnalyzer::SetTimeConstraint(const int min, const int max )
d655d7dd	75	{
d655d7dd	76	//Require that the bin if the maximum ADC value is between min and max (timebin)
92d9f317	77	if( ( min > max ) \|\| min > ALTROMAXSAMPLES \|\| max > ALTROMAXSAMPLES )
d655d7dd	78	{
	79	AliWarning( Form( "Attempt to set Invalid time bin range (Min , Max) = (%d, %d), Ingored", min, max ) );
	80	}
	81	else
	82	{
	83	fMinTimeIndex = min;
	84	fMaxTimeIndex = max;
	85	}
	86	}
	87
	88
	89	UShort_t
92d9f317	90	AliCaloRawAnalyzer::Max(const UShort_t *data, const int length )
d655d7dd	91	{
	92	//------------
	93	UShort_t tmpmax = data[0];
	94
	95	for(int i=0; i < length; i++)
	96	{
	97	if( tmpmax < data[i] )
	98	{
	99	tmpmax = data[i];
	100	}
	101	}
	102	return tmpmax;
	103	}
	104
	105
	106	void
92d9f317	107	AliCaloRawAnalyzer::SelectSubarray( const Double_t data, const int length, const short maxindex, int const first, int *const last, const int cut)
d655d7dd	108	{
	109	//Selection of subset of data from one bunch that will be used for fitting or
	110	//Peak finding. Go to the left and right of index of the maximum time bin
e7acbc37	111	//Until the ADC value is less that fFitArrayCut, or derivative changes sign (data jump)
d655d7dd	112	int tmpfirst = maxindex;
d655d7dd	113	int tmplast = maxindex;
92d9f317	114	Double_t prevFirst = data[maxindex];
92d9f317	115	Double_t prevLast = data[maxindex];
947c8e28	116	bool firstJump = false;
	117	bool lastJump = false;
	118
92d9f317	119	while( (tmpfirst >= 0) && (data[tmpfirst] >= cut ) && (!firstJump) )
d655d7dd	120	{
947c8e28	121	// jump check:
947c8e28	122	if (tmpfirst != maxindex) { // neighbor to maxindex can share peak with maxindex
92d9f317	123	if ( data[tmpfirst] >= prevFirst) {
947c8e28	124	firstJump = true;
	125	}
	126	}
92d9f317	127	prevFirst = data[tmpfirst];
d655d7dd	128	tmpfirst -- ;
	129	}
	130
92d9f317	131	while( (tmplast < length) && (data[tmplast] >= cut ) && (!lastJump) )
d655d7dd	132	{
947c8e28	133	// jump check:
947c8e28	134	if (tmplast != maxindex) { // neighbor to maxindex can share peak with maxindex
92d9f317	135	if ( data[tmplast] >= prevLast) {
947c8e28	136	lastJump = true;
	137	}
	138	}
92d9f317	139	prevLast = data[tmplast];
d655d7dd	140	tmplast ++;
d655d7dd	141	}
f57baa2d	142
947c8e28	143	// we keep one pre- or post- sample if we can (as in online)
	144	// check though if we ended up on a 'jump', or out of bounds: if so, back up
	145	if (firstJump \|\| tmpfirst<0) tmpfirst ++;
	146	if (lastJump \|\| tmplast>=length) tmplast --;
	147
	148	*first = tmpfirst;
	149	*last = tmplast;
e7acbc37	150	return;
d655d7dd	151	}
	152
	153
	154
	155	Float_t
57839add	156	AliCaloRawAnalyzer::ReverseAndSubtractPed( const AliCaloBunchInfo bunch, const UInt_t /altrocfg1/, const UInt_t /altrocfg2/, double outarray ) const
d655d7dd	157	{
	158	//Time sample comes in reversed order, revers them back
	159	//Subtract the baseline based on content of altrocfg1 and altrocfg2.
	160	Int_t length = bunch->GetLength();
	161	const UShort_t *sig = bunch->GetData();
	162
57839add	163	double ped = EvaluatePedestal( sig , length);
	164
	165	for( int i=0; i < length; i++ )
	166	{
	167	outarray[i] = sig[length -i -1] - ped;
	168	}
	169
	170	return ped;
	171	}
	172
	173
	174
	175	Float_t
	176	AliCaloRawAnalyzer::EvaluatePedestal(const UShort_t * const data, const int /length/ ) const
	177	{
	178	// double ped = 0;
d655d7dd	179	double tmp = 0;
	180
	181	if( fIsZerosupressed == false )
	182	{
f57baa2d	183	for(int i=0; i < fNsamplePed; i++ )
d655d7dd	184	{
57839add	185	tmp += data[i];
d655d7dd	186	}
f57baa2d	187	}
e37e3c84	188
f57baa2d	189	return tmp/fNsamplePed;
f57baa2d	190	}
d655d7dd	191
	192
	193	short
92d9f317	194	AliCaloRawAnalyzer::Max( const AliCaloBunchInfo const bunch , int const maxindex )
d655d7dd	195	{
	196	//comment
	197	short tmpmax = -1;
	198	int tmpindex = -1;
	199	const UShort_t *sig = bunch->GetData();
	200
	201	for(int i=0; i < bunch->GetLength(); i++ )
	202	{
	203	if( sig[i] > tmpmax )
	204	{
	205	tmpmax = sig[i];
	206	tmpindex = i;
	207	}
	208	}
	209
	210	if(maxindex != 0 )
	211	{
48a2e3eb	212	// *maxindex = bunch->GetLength() -1 - tmpindex + bunch->GetStartBin();
48a2e3eb	213	*maxindex = bunch->GetLength() -1 - tmpindex + bunch->GetStartBin();
d655d7dd	214	}
	215
	216	return tmpmax;
	217	}
	218
	219
507751ce	220	bool
	221	AliCaloRawAnalyzer::CheckBunchEdgesForMax( const AliCaloBunchInfo *const bunch ) const
	222	{
	223	// a bunch is considered invalid if the maximum is in the first or last time-bin
	224	short tmpmax = -1;
	225	int tmpindex = -1;
	226	const UShort_t *sig = bunch->GetData();
	227
	228	for(int i=0; i < bunch->GetLength(); i++ )
	229	{
	230	if( sig[i] > tmpmax )
	231	{
	232	tmpmax = sig[i];
	233	tmpindex = i;
	234	}
	235	}
	236
	237	bool bunchOK = true;
	238	if (tmpindex == 0 \|\| tmpindex == (bunch->GetLength()-1) )
	239	{
	240	bunchOK = false;
	241	}
	242
	243	return bunchOK;
	244	}
	245
	246
d655d7dd	247	int
92d9f317	248	AliCaloRawAnalyzer::SelectBunch( const vector<AliCaloBunchInfo> &bunchvector,short const maxampbin, short const maxamplitude )
d655d7dd	249	{
	250	//We select the bunch with the highest amplitude unless any time constraints is set
	251	short max = -1;
	252	short bunchindex = -1;
	253	short maxall = -1;
	254	int indx = -1;
	255
	256	for(unsigned int i=0; i < bunchvector.size(); i++ )
	257	{
48a2e3eb	258	max = Max( &bunchvector.at(i), &indx ); // CRAP PTH, bug fix, trouble if more than one bunches
92d9f317	259	if( IsInTimeRange( indx, fMaxTimeIndex, fMinTimeIndex) )
d655d7dd	260	{
	261	if( max > maxall )
	262	{
	263	maxall = max;
	264	bunchindex = i;
48a2e3eb	265	*maxampbin = indx;
48a2e3eb	266	*maxamplitude = max;
d655d7dd	267	}
	268	}
	269	}
	270
507751ce	271	if (bunchindex >= 0) {
	272	bool bunchOK = CheckBunchEdgesForMax( &bunchvector.at(bunchindex) );
	273	if (! bunchOK) {
	274	bunchindex = -1;
	275	}
	276	}
	277
d655d7dd	278	return bunchindex;
	279	}
	280
	281
	282	bool
92d9f317	283	AliCaloRawAnalyzer::IsInTimeRange( const int maxindex, const int maxtindx, const int mintindx )
d655d7dd	284	{
d655d7dd	285	// Ckeck if the index of the max ADC vaue is consistent with trigger.
92d9f317	286	if( ( mintindx < 0 && maxtindx < 0) \|\|maxtindx < 0 )
d655d7dd	287	{
	288	return true;
	289	}
92d9f317	290	return ( maxindex < maxtindx ) && ( maxindex > mintindx ) ? true : false;
d655d7dd	291	}
	292
	293
	294	void
57839add	295	AliCaloRawAnalyzer::PrintBunches( const vector<AliCaloBunchInfo> &bvctr ) const
d655d7dd	296	{
	297	//comment
	298	cout << __FILE__ << __LINE__<< "************* Printing Bunches *****************" << endl;
	299	cout << __FILE__ << __LINE__<< "*** There are " << bvctr.size() << ", bunches" << endl;
	300
	301	for(unsigned int i=0; i < bvctr.size() ; i++ )
	302	{
	303	PrintBunch( bvctr.at(i) );
	304	cout << " bunch = " << i << endl;
	305	}
	306	cout << __FILE__ << __LINE__<< "************* Done ... *****************" << endl;
	307	}
	308
	309
	310	void
57839add	311	AliCaloRawAnalyzer::PrintBunch( const AliCaloBunchInfo &bunch ) const
d655d7dd	312	{
	313	//comment
	314	cout << __FILE__ << ":" << __LINE__ << endl;
	315	cout << __FILE__ << __LINE__ << ", startimebin = " << bunch.GetStartBin() << ", length =" << bunch.GetLength() << endl;
	316	const UShort_t *sig = bunch.GetData();
	317
	318	for ( Int_t j = 0; j < bunch.GetLength(); j++)
	319	{
	320	printf("%d\t", sig[j] );
	321	}
	322	cout << endl;
	323	}
	324
48a2e3eb	325
947c8e28	326	Double_t
	327	AliCaloRawAnalyzer::CalculateChi2(const Double_t amp, const Double_t time,
	328	const Int_t first, const Int_t last,
	329	const Double_t adcErr,
	330	const Double_t tau)
	331	{
	332	// Input:
	333	// amp - max amplitude;
	334	// time - time of max amplitude;
	335	// first, last - sample array indices to be used
	336	// adcErr - nominal error of amplitude measurement (one value for all channels)
	337	// if adcErr<0 that mean adcErr=1.
	338	// tau - filter time response (in timebin units)
	339	// Output:
	340	// chi2 - chi2
	341
	342	if (first == last \|\| first<0 ) { // signal consists of single sample, chi2 estimate (0) not too well defined..
	343	// or, first is negative, the indices are not valid
168c7b3c	344	return Ret::kDummy;
947c8e28	345	}
	346
	347	int nsamples = last - first + 1;
2cd0ffda	348	// printf(" AliCaloRawAnalyzer::CalculateChi2 : first %i last %i : nsamples %i : amp %3.2f time %3.2f \n", first, last, nsamples, amp, time);
947c8e28	349
	350	Int_t x = 0;
	351	Double_t chi2 = 0;
	352	Double_t dy = 0.0, xx = 0.0, f=0.0;
	353
	354	for (Int_t i=0; i<nsamples; i++) {
	355	x = first + i; // timebin
	356	xx = (x - time + tau) / tau; // help variable
	357	f = 0;
	358	if (xx > 0) {
	359	f = amp * xxxx TMath::Exp(2 * (1 - xx )) ;
	360	}
	361	dy = fReversed[x] - f;
	362	chi2 += dy*dy;
2cd0ffda	363	// printf(" AliCaloRawAnalyzer::CalculateChi2 : %i : y %f -> f %f : dy %f \n", i, fReversed[first+i], f, dy);
947c8e28	364	}
	365
	366	if (adcErr>0.0) { // weight chi2
	367	chi2 /= (adcErr*adcErr);
	368	}
	369	return chi2;
	370	}
	371
	372
	373	void
	374	AliCaloRawAnalyzer::CalculateMeanAndRMS(const Int_t first, const Int_t last,
	375	Double_t & mean, Double_t & rms)
	376	{
	377	// Input:
	378	// first, last - sample array indices to be used
	379	// Output:
	380	// mean and RMS of samples
	381	//
	382	// To possibly be used to differentiate good signals from bad before fitting
	383	//
168c7b3c	384	mean = Ret::kDummy;
168c7b3c	385	rms = Ret::kDummy;
947c8e28	386
	387	if (first == last \|\| first<0 ) { // signal consists of single sample, chi2 estimate (0) not too well defined..
	388	// or, first is negative, the indices are not valid
	389	return;
	390	}
	391
	392	int nsamples = last - first + 1;
	393	// printf(" AliCaloRawAnalyzer::CalculateMeanAndRMS : first %i last %i : nsamples %i \n", first, last, nsamples);
	394
	395	int x = 0;
	396	Double_t sampleSum = 0; // sum of samples
	397	Double_t squaredSampleSum = 0; // sum of samples squared
	398
	399	for (Int_t i=0; i<nsamples; i++) {
	400	x = first + i;
	401	sampleSum += fReversed[x];
	402	squaredSampleSum += (fReversed[x] * fReversed[x]);
	403	}
	404
	405	mean = sampleSum / nsamples;
	406	Double_t squaredMean = squaredSampleSum / nsamples;
	407	// The variance (rms squared) is equal to the mean of the squares minus the square of the mean..
	408	rms = sqrt(squaredMean - mean*mean);
	409
	410	return;
	411	}
	412
168c7b3c	413
	414
	415	// AliCaloFitResults
	416	// AliCaloRawAnalyzer::Evaluate( const vector<AliCaloBunchInfo> &/bunchvector/, const UInt_t /altrocfg1/, const UInt_t /altrocfg2/)
	417	// { // method to do the selection of what should possibly be fitted
	418	// // not implemented for base class
	419	// cout << __FILE__ << ":" << __LINE__ << " " << endl;
	420
	421	// return AliCaloFitResults( 0, 0 );
	422	// }
	423
57839add	424
48a2e3eb	425
57839add	426	int
92d9f317	427	AliCaloRawAnalyzer::PreFitEvaluateSamples( const vector<AliCaloBunchInfo> &bunchvector, const UInt_t altrocfg1,
	428	const UInt_t altrocfg2, Int_t & index, Float_t & maxf, short & maxamp,
	429	short & maxrev, Float_t & ped, int & first, int & last,const int acut )
57839add	430	{ // method to do the selection of what should possibly be fitted
57839add	431	int nsamples = 0;
f57baa2d	432	short maxampindex = 0;
57839add	433	index = SelectBunch( bunchvector, &maxampindex, &maxamp ); // select the bunch with the highest amplitude unless any time constraints is set
	434
	435
92d9f317	436	if( index >= 0 && maxamp >= acut ) // something valid was found, and non-zero amplitude
57839add	437	{
	438	// use more convenient numbering and possibly subtract pedestal
	439	ped = ReverseAndSubtractPed( &(bunchvector.at(index)), altrocfg1, altrocfg2, fReversed );
	440	maxf = TMath::MaxElement( bunchvector.at(index).GetLength(), fReversed );
	441
92d9f317	442	if ( maxf >= acut ) // possibly significant signal
57839add	443	{
57839add	444	// select array around max to possibly be used in fit
f57baa2d	445	maxrev = maxampindex - bunchvector.at(index).GetStartBin();
92d9f317	446	SelectSubarray( fReversed, bunchvector.at(index).GetLength(), maxrev, &first, &last, acut );
57839add	447
	448	// sanity check: maximum should not be in first or last bin
	449	// if we should do a fit
92d9f317	450	if (first!=maxrev && last!=maxrev)
	451	{
	452	// calculate how many samples we have
	453	nsamples = last - first + 1;
	454	}
57839add	455	}
	456	}
	457
	458	return nsamples;
	459	}
	460