/* ======================================================================== *\
!
! *
! * This file is part of MARS, the MAGIC Analysis and Reconstruction
! * Software. It is distributed to you in the hope that it can be a useful
! * and timesaving tool in analysing Data of imaging Cerenkov telescopes.
! * It is distributed WITHOUT ANY WARRANTY.
! *
! * Permission to use, copy, modify and distribute this software and its
! * documentation for any purpose is hereby granted without fee,
! * provided that the above copyright notice appear in all copies and
! * that both that copyright notice and this permission notice appear
! * in supporting documentation. It is provided "as is" without express
! * or implied warranty.
! *
!
!
!   Author(s): Josep Flix 04/2001 <mailto:jflix@ifae.es>
!   Author(s): Thomas Bretz 05/2001 <mailto:tbretz@astro.uni-wuerzburg.de>
!   Author(s): Sebastian Commichau 12/2003 
!   Author(s): Javier Rico 01/2004 <mailto:jrico@ifae.es>
!   Author(s): Markus Gaug 01/2004 <mailto:markus@ifae.es>
!   Author(s): Florian Goebel 06/2004 <mailto:fgoebel@mppmu.mpg.de>
!
!   Copyright: MAGIC Software Development, 2000-2004
!
!
\* ======================================================================== */
/////////////////////////////////////////////////////////////////////////////
//
//   MPedCalcLoGain
//
//
//  This task is devide form MPedCalcPedRun, described below. However, It 
//  calculates the pedstals using the low gain slices, whenever the difference 
//  between the highest and the lowest slice in the high gain
//  slices is below a given threshold (SetMaxHiGainVar). In this case the receiver
//  boards do not switch to lo gain and the so called lo gain slices are actually
//  high gain slices. 
//
//  MPedCalcLoGain also fills the ABoffset in MPedestalPix which allows to correct 
//  the 150 MHz clock noise.
//
//  This task takes a pedestal run file and fills MPedestalCam during
//  the Process() with the pedestal and rms computed in an event basis.
//  In the PostProcess() MPedestalCam is finally filled with the pedestal
//  mean and rms computed in a run basis.
//  More than one run (file) can be merged
//
//  MPedCalcPedRun applies the following formula (1):
// 
//  Pedestal per slice = sum(x_i) / n / slices
//  PedRMS per slice   = Sqrt(  ( sum(x_i^2) - sum(x_i)^2/n ) / n-1 / slices )
// 
//  where x_i is the sum of "slices" FADC slices and sum means the sum over all
//  events. "n" is the number of events, "slices" is the number of summed FADC samples.
// 
//  Note that the slice-to-slice fluctuations are not Gaussian, but Poissonian, thus 
//  asymmetric and they are correlated.
// 
//  It is important to know that the Pedestal per slice and PedRMS per slice depend 
//  on the number of used FADC slices, as seen in the following plots:
//
//Begin_Html
/*
<img src="images/PedestalStudyInner.gif">
*/
//End_Html
//
//Begin_Html
/*
<img src="images/PedestalStudyOuter.gif">
*/
//
// The plots show the inner and outer pixels, respectivly and have the following meaning:
// 
// 1) The calculated mean pedestal per slice (from MPedCalcFromLoGain)
// 2) The fitted mean pedestal per slice     (from MHPedestalCam)
// 3) The calculated pedestal RMS per slice  (from MPedCalcFromLoGain)
// 4) The fitted sigma of the pedestal distribution per slice
//                                           (from MHPedestalCam)
// 5) The relative difference between calculation and histogram fit
//    for the mean
// 6) The relative difference between calculation and histogram fit
//    for the sigma or RMS, respectively.
// 
// The calculated means do not change significantly except for the case of 2 slices, 
// however the RMS changes from 5.7 per slice in the case of 2 extracted slices 
// to 8.3 per slice in the case of 26 extracted slices. This change is very significant.
// 
// The plots have been produced on run 20123. You can reproduce them using
// the macro pedestalstudies.C
// 
//  Usage of this class: 
//  ====================
// 
//  Call: SetRange(higainfirst, higainlast, logainfirst, logainlast) 
//  to modify the ranges in which the window is allowed to move. 
//  Defaults are: 
// 
//   fHiGainFirst =  fgHiGainFirst =  0 
//   fHiGainLast  =  fgHiGainLast  =  29
//   fLoGainFirst =  fgLoGainFirst =  0 
//   fLoGainLast  =  fgLoGainLast  =  14
//
//  Call: SetWindowSize(windowhigain, windowlogain) 
//  to modify the sliding window widths. Windows have to be an even number. 
//  In case of odd numbers, the window will be modified.
//
//  Defaults are:
//
//   fHiGainWindowSize = fgHiGainWindowSize = 14
//   fLoGainWindowSize = fgLoGainWindowSize = 0
//
//  Input Containers:
//   MRawEvtData
//   MRawRunHeader
//   MGeomCam
//
//  Output Containers:
//   MPedestalCam
//
//  See also: MPedestalCam, MPedestalPix, MHPedestalCam, MExtractor
//
/////////////////////////////////////////////////////////////////////////////
#include "MPedCalcFromLoGain.h"
#include "MExtractor.h"

#include "MParList.h"

#include "MLog.h"
#include "MLogManip.h"

#include "MRawRunHeader.h"  
#include "MRawEvtPixelIter.h"
#include "MRawEvtData.h"

#include "MPedestalPix.h"
#include "MPedestalCam.h"

#include "MGeomPix.h"
#include "MGeomCam.h"

#include "MBadPixelsPix.h"
#include "MBadPixelsCam.h"

#include "MGeomCamMagic.h"

ClassImp(MPedCalcFromLoGain);

using namespace std;

const Byte_t MPedCalcFromLoGain::fgHiGainFirst      = 0;
const Byte_t MPedCalcFromLoGain::fgHiGainLast       = 11;
const Byte_t MPedCalcFromLoGain::fgLoGainFirst      = 1;
const Byte_t MPedCalcFromLoGain::fgLoGainLast       = 14;
const Byte_t MPedCalcFromLoGain::fgHiGainWindowSize = 12;
const Byte_t MPedCalcFromLoGain::fgLoGainWindowSize = 14;
const Byte_t MPedCalcFromLoGain::fgMaxHiGainVar     = 20;

// --------------------------------------------------------------------------
//
// Default constructor: 
//
// Sets:
// - all pointers to NULL
// - fWindowSizeHiGain to fgHiGainWindowSize
// - fWindowSizeLoGain to fgLoGainWindowSize
//
// Calls: 
// - AddToBranchList("fHiGainPixId");
// - AddToBranchList("fHiGainFadcSamples");
// - SetRange(fgHiGainFirst, fgHiGainLast, fgLoGainFirst, fgLoGainLast)
// - Clear()
//
MPedCalcFromLoGain::MPedCalcFromLoGain(const char *name, const char *title)
    : fWindowSizeHiGain(fgHiGainWindowSize), 
      fWindowSizeLoGain(fgLoGainWindowSize), 
      fGeom(NULL),fBad(NULL)
{
  fName  = name  ? name  : "MPedCalcFromLoGain";
  fTitle = title ? title : "Task to calculate pedestals from pedestal runs raw data";
  
  AddToBranchList("fHiGainPixId");
  AddToBranchList("fHiGainFadcSamples");
  
  SetRange(fgHiGainFirst, fgHiGainLast, fgLoGainFirst, fgLoGainLast);

  SetMaxHiGainVar(fgMaxHiGainVar);
  SetPedestalUpdate(kTRUE);
  Clear();
}

// --------------------------------------------------------------------------
//
// Sets:
// - fNumSamplesTot to 0
// - fRawEvt to NULL
// - fRunHeader to NULL
// - fPedestals to NULL
//
void MPedCalcFromLoGain::Clear(const Option_t *o)
{

  fRawEvt    = NULL;
  fRunHeader = NULL;
  fPedestals = NULL;
}

// --------------------------------------------------------------------------
//
// SetRange: 
//
// Calls:
// - MExtractor::SetRange(hifirst,hilast,lofirst,lolast);
// - SetWindowSize(fWindowSizeHiGain,fWindowSizeLoGain);
//
void MPedCalcFromLoGain::SetRange(Byte_t hifirst, Byte_t hilast, Byte_t lofirst, Byte_t lolast)
{

  MExtractor::SetRange(hifirst,hilast,lofirst,lolast);

  //
  // Redo the checks if the window is still inside the ranges
  //
  SetWindowSize(fWindowSizeHiGain,fWindowSizeLoGain);
  
}


// --------------------------------------------------------------------------
//
void MPedCalcFromLoGain::SetMaxHiGainVar(Byte_t maxvar) {
  fMaxHiGainVar = maxvar;
}


// --------------------------------------------------------------------------
//
// Checks:
// - if a window is odd, subtract one
// - if a window is bigger than the one defined by the ranges, set it to the available range
// - if a window is smaller than 2, set it to 2
// 
// Sets:
// - fNumHiGainSamples to: (Float_t)fWindowSizeHiGain
// - fNumLoGainSamples to: (Float_t)fWindowSizeLoGain
// - fSqrtHiGainSamples to: TMath::Sqrt(fNumHiGainSamples)
// - fSqrtLoGainSamples to: TMath::Sqrt(fNumLoGainSamples)  
//  
void MPedCalcFromLoGain::SetWindowSize(Byte_t windowh, Byte_t windowl)
{
  
  fWindowSizeHiGain = windowh & ~1;
  fWindowSizeLoGain = windowl & ~1;

  if (fWindowSizeHiGain != windowh)
    *fLog << warn << GetDescriptor() << ": Hi Gain window size has to be even, set to: " 
          << int(fWindowSizeHiGain) << " samples " << endl;
  
  if (fWindowSizeLoGain != windowl)
    *fLog << warn << GetDescriptor() << ": Lo Gain window size has to be even, set to: " 
          << int(fWindowSizeLoGain) << " samples " << endl;
    
  const Byte_t availhirange = (fHiGainLast-fHiGainFirst+1) & ~1;
  const Byte_t availlorange = (fLoGainLast-fLoGainFirst+1) & ~1;

  if (fWindowSizeHiGain > availhirange)
    {
      *fLog << warn << GetDescriptor() 
            << Form("%s%2i%s%2i%s%2i%s",": Hi Gain window size: ",(int)fWindowSizeHiGain,
                    " is bigger than available range: [",(int)fHiGainFirst,",",(int)fHiGainLast,"]") << endl;
      *fLog << warn << GetDescriptor() 
            << ": Will set window size to: " << (int)availhirange << endl;
      fWindowSizeHiGain = availhirange;
    }
  
  if (fWindowSizeLoGain > availlorange)
    {
      *fLog << warn << GetDescriptor() 
            << Form("%s%2i%s%2i%s%2i%s",": Lo Gain window size: ",(int)fWindowSizeLoGain,
                    " is bigger than available range: [",(int)fLoGainFirst,",",(int)fLoGainLast,"]") << endl;
      *fLog << warn << GetDescriptor() 
            << ": Will set window size to: " << (int)availlorange << endl;
      fWindowSizeLoGain = availlorange;
    }
  
  
  fNumHiGainSamples = (Float_t)fWindowSizeHiGain;
  fNumLoGainSamples = (Float_t)fWindowSizeLoGain;
  
  fSqrtHiGainSamples = TMath::Sqrt(fNumHiGainSamples);
  fSqrtLoGainSamples = TMath::Sqrt(fNumLoGainSamples);

}

  
    
// --------------------------------------------------------------------------
//
// Look for the following input containers:
//
//  - MRawEvtData
//  - MRawRunHeader
//  - MGeomCam
//  - MBadPixelsCam
// 
// The following output containers are also searched and created if
// they were not found:
//
//  - MPedestalCam
//
Int_t MPedCalcFromLoGain::PreProcess( MParList *pList )
{

  Clear();
  
  fRawEvt = (MRawEvtData*)pList->FindObject("MRawEvtData");
  if (!fRawEvt)
    {
      *fLog << err << "MRawEvtData not found... aborting." << endl;
      return kFALSE;
    }
  
  fRunHeader = (MRawRunHeader*)pList->FindObject(AddSerialNumber("MRawRunHeader"));
  if (!fRunHeader)
    {
      *fLog << err << AddSerialNumber("MRawRunHeader") << " not found... aborting." << endl;
      return kFALSE;
    }

  fGeom   =  (MGeomCam*)pList->FindObject("MGeomCam");
  if (!fGeom)
    {
      *fLog << err << "MGeomCam not found... aborting." << endl;
      return kFALSE;
    }

  fPedestals = (MPedestalCam*)pList->FindCreateObj("MPedestalCam");
  if (!fPedestals)
    return kFALSE;

  fBad       =  (MBadPixelsCam*)pList->FindObject("MBadPixelsCam");

  return kTRUE;
}

// --------------------------------------------------------------------------
//
// The ReInit searches for:
// -  MRawRunHeader::GetNumSamplesHiGain()
// -  MRawRunHeader::GetNumSamplesLoGain()
//
// In case that the variables fHiGainLast and fLoGainLast are smaller than 
// the even part of the number of samples obtained from the run header, a
// warning is given an the range is set back accordingly. A call to:  
// - SetRange(fHiGainFirst, fHiGainLast-diff, fLoGainFirst, fLoGainLast) or 
// - SetRange(fHiGainFirst, fHiGainLast, fLoGainFirst, fLoGainLast-diff) 
// is performed in that case. The variable diff means here the difference 
// between the requested range (fHiGainLast) and the available one. Note that 
// the functions SetRange() are mostly overloaded and perform more checks, 
// modifying the ranges again, if necessary.
//
// A loop over the MBadPixelsCam is performed and bad pixels are set
// to MPedestalPix::SetValid(kFALSE);
//
Bool_t MPedCalcFromLoGain::ReInit(MParList *pList)
{
      
  Int_t lastdesired   = (Int_t)fLoGainLast;
  Int_t lastavailable = (Int_t)fRunHeader->GetNumSamplesLoGain()-1;
  
  if (lastdesired > lastavailable)
    {
      const Int_t diff = lastdesired - lastavailable;
      *fLog << endl; 
      *fLog << warn << GetDescriptor()
            << Form("%s%2i%s%2i%s%2i%s",": Selected Lo Gain FADC Window [",
                    (int)fLoGainFirst,",",lastdesired,
                    "] ranges out of the available limits: [0,",lastavailable,"].") << endl;
      *fLog << GetDescriptor() << ": Will reduce the upper edge to " << (int)(fLoGainLast - diff) << endl;
      SetRange(fHiGainFirst, fHiGainLast, fLoGainFirst, fLoGainLast-diff);
    }

  lastdesired   = (Int_t)fHiGainLast;
  lastavailable = (Int_t)fRunHeader->GetNumSamplesHiGain()-1;
  
  if (lastdesired > lastavailable)
    {
      const Int_t diff = lastdesired - lastavailable;
      *fLog << endl;
      *fLog << warn << GetDescriptor()
            << Form("%s%2i%s%2i%s%2i%s",": Selected Hi Gain Range [",
                    (int)fHiGainFirst,",",lastdesired,
                    "] ranges out of the available limits: [0,",lastavailable,"].") << endl;
      *fLog << warn << GetDescriptor() 
            << Form("%s%2i%s",": Will possibly use ",diff," samples from the Low-Gain for the High-Gain range")
            << endl;
      fHiGainLast -= diff;
      fHiLoLast    = diff;
    }

  lastdesired   = (Int_t)fHiGainFirst+fWindowSizeHiGain-1;
  lastavailable = (Int_t)fRunHeader->GetNumSamplesHiGain()-1;
  
  if (lastdesired > lastavailable)
    {
      const Int_t diff = lastdesired - lastavailable;
      *fLog << endl;
      *fLog << warn << GetDescriptor()
            << Form("%s%2i%s%2i%s",": Selected Hi Gain FADC Window size ",
                    (int)fWindowSizeHiGain,
                    " ranges out of the available limits: [0,",lastavailable,"].") << endl;
      *fLog << warn << GetDescriptor() 
            << Form("%s%2i%s",": Will use ",diff," samples from the Low-Gain for the High-Gain extraction")
            << endl;

      if ((Int_t)fWindowSizeHiGain > diff)
        {
          fWindowSizeHiGain -= diff;
          fWindowSizeLoGain += diff;
        }
      else
        {
          fWindowSizeLoGain += fWindowSizeHiGain;
          fLoGainFirst       = diff-fWindowSizeHiGain;
          fWindowSizeHiGain  = 0;
        }
    }


  Int_t npixels  = fPedestals->GetSize();
  
  if (fSumx.GetSize()==0)
    {
      fSumx. Set(npixels);
      fSumx2.Set(npixels);
      fSumAB0.Set(npixels);
      fSumAB1.Set(npixels);
      fNumEventsUsed.Set(npixels);
      fTotalCounter.Set(npixels);
      
      fSumx.Reset();
      fSumx2.Reset();
      fSumAB0.Reset();
      fSumAB1.Reset();
      fNumEventsUsed.Reset();
      fTotalCounter.Reset();
    }
  
  if (fWindowSizeHiGain == 0 && fWindowSizeLoGain == 0)
    {
      *fLog << err << GetDescriptor() 
            << ": Number of extracted Slices is 0, abort ... " << endl;
      return kFALSE;
    }
  
  
  *fLog << endl;
  *fLog << inf << GetDescriptor() << ": Taking " << (int)fWindowSizeHiGain
        << " HiGain FADC samples starting with slice: " << (int)fHiGainFirst << endl;
  *fLog << inf << GetDescriptor() << ": Taking " << (int)fWindowSizeLoGain
        << " LoGain FADC samples starting with slice: " << (int)fLoGainFirst << endl;
  
  
  if (fBad)
    {
      const Int_t nbads = fBad->GetSize();
      for (Int_t i=0; i<(nbads>npixels?npixels:nbads);i++)
        if ((*fBad)[i].IsBad())
          (*fPedestals)[i].SetValid(kFALSE);
    }
  
  return kTRUE;
      
}
// --------------------------------------------------------------------------
//
// Fill the MPedestalCam container with the signal mean and rms for the event.
// Store the measured signal in arrays fSumx and fSumx2 so that we can 
// calculate the overall mean and rms in the PostProcess()
//
Int_t MPedCalcFromLoGain::Process()
{

  MRawEvtPixelIter pixel(fRawEvt);
  
  //   cout << "fHiGainFirst: " << (Int_t)fHiGainFirst << " fWindowSizeHiGain: " << (Int_t)fWindowSizeHiGain << " fLoGainFirst: " << (Int_t)fLoGainFirst << " fWindowSizeLoGain: " << (Int_t)fWindowSizeLoGain << endl;


  while (pixel.Next()) {
    
    const UInt_t idx    = pixel.GetPixelId();
    
    Byte_t *ptr = pixel.GetHiGainSamples() + fHiGainFirst;
    Byte_t *end = ptr + fWindowSizeHiGain;

    UInt_t sum = 0;
    UInt_t sqr = 0;
    
    UInt_t max = 0;
    UInt_t min = 255;
    
    // Find the maximum and minimum signal per slice in the high gain window
    do {
      if (*ptr > max) {
	max = *ptr;
      }
      if (*ptr < min) {
	min = *ptr;
      }
    } while (++ptr != end);
    
    // If the maximum in the high gain window is smaller than 
    if ((max-min < fMaxHiGainVar) && (max < 255)) {
      
      Byte_t *firstSlice = pixel.GetLoGainSamples() + fLoGainFirst;
      Byte_t *lastSlice  = firstSlice + fWindowSizeLoGain;
      
      Byte_t *slice = firstSlice;
      do {
	sum += *slice;
	sqr += *slice * *slice;
      } while (++slice != lastSlice);

      const Float_t msum = (Float_t)sum;
      const Float_t sqrsum  = msum*msum;
      
      fSumx[idx]  += msum;
      fSumx2[idx] += sqrsum;
      fNumEventsUsed[idx]++;

      // Calculate the amplitude of the 150MHz "AB" noise

      Int_t abFlag = (fRunHeader->GetNumSamplesHiGain()
		       + fLoGainFirst
		       + pixel.HasABFlag()) & 0x1;
      for (Int_t islice=0; islice<fWindowSizeLoGain; islice+=2) {
	Int_t sliceAB0 = islice + abFlag;
	Int_t sliceAB1 = islice + 1 - abFlag;
	fSumAB0[idx] += firstSlice[sliceAB0];
	fSumAB1[idx] += firstSlice[sliceAB1];
      }

      if (fPedestalUpdate && (fNumEventsUsed[idx] == fNumEventsDump)) {

	const ULong_t n = fNumEventsDump;

	const ULong_t nsamplestot = n*fWindowSizeLoGain;
	
	const Float_t sum  = fSumx.At(idx);
	const Float_t sum2 = fSumx2.At(idx);
	const Float_t ped  = sum/(nsamplestot);
    
	// 1. Calculate the Variance of the sums:
	Float_t var = (sum2-sum*sum/n)/(n-1.);
	
	// 2. Scale the variance to the number of slices:
	var /= (Float_t)(fWindowSizeLoGain);
	
	// 3. Calculate the RMS from the Variance:
	Float_t rms = var < 0 ? 0. : TMath::Sqrt(var);

	// 4. Calculate the amplitude of the 150MHz "AB" noise
	Float_t abOffs = (fSumAB0[idx] - fSumAB1[idx]) / nsamplestot;

	(*fPedestals)[idx].Set(ped, rms, abOffs, n);
	
	fTotalCounter[idx]++;
	fNumEventsUsed[idx]=0;
	fSumx[idx]=0;
	fSumx2[idx]=0;
	fSumAB0[idx]=0;
	fSumAB1[idx]=0;
      }
    }
  }
  
  fPedestals->SetReadyToSave();
  
  return kTRUE;
}

// --------------------------------------------------------------------------
//
// Compute signal mean and rms in the whole run and store it in MPedestalCam
//
Int_t MPedCalcFromLoGain::PostProcess()
{

  // Compute pedestals and rms from the whole run

  if (!fPedestalUpdate) {

    MRawEvtPixelIter pixel(fRawEvt);
    
    while (pixel.Next()) {
      
      const Int_t  idx = pixel.GetPixelId();
      
      const ULong_t n = fNumEventsUsed[idx];
      
      if (n < 2)
	continue;
      
      const ULong_t nsamplestot = n*fWindowSizeLoGain;
      
      const Float_t sum  = fSumx.At(idx);
      const Float_t sum2 = fSumx2.At(idx);
      const Float_t ped  = sum/(nsamplestot);
      
      // 1. Calculate the Variance of the sums:
      Float_t var = (sum2-sum*sum/n)/(n-1.);
      
      // 2. Scale the variance to the number of slices:
      var /= (Float_t)(fWindowSizeLoGain);
      
      // 3. Calculate the RMS from the Variance:
      Float_t rms = var < 0 ? 0. : TMath::Sqrt(var);
      
      // 4. Calculate the amplitude of the 150MHz "AB" noise
      Float_t abOffs = (fSumAB0[idx] - fSumAB1[idx]) / nsamplestot;
      
      (*fPedestals)[idx].Set(ped, rms, abOffs, n);
      
      fTotalCounter[idx]++;
    }

    fPedestals->SetReadyToSave();
  }

  return kTRUE;
}