/* ======================================================================== *\
!
! *
! * 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>
!
!   Copyright: MAGIC Software Development, 2000-2004
!
!
\* ======================================================================== */
/////////////////////////////////////////////////////////////////////////////
//
//   MPedCalcPedRun
//
//  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 MPedCalcPedRun)
// 2) The fitted mean pedestal per slice     (from MHPedestalCam)
// 3) The calculated pedestal RMS per slice  (from MPedCalcPedRun)
// 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  =  14
//   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 "MPedCalcPedRun.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(MPedCalcPedRun);

using namespace std;

const Byte_t MPedCalcPedRun::fgHiGainFirst      = 0;
const Byte_t MPedCalcPedRun::fgHiGainLast       = 14;
const Byte_t MPedCalcPedRun::fgLoGainFirst      = 0;
const Byte_t MPedCalcPedRun::fgLoGainLast       = 14;
const Byte_t MPedCalcPedRun::fgHiGainWindowSize = 14;
const Byte_t MPedCalcPedRun::fgLoGainWindowSize = 0;
// --------------------------------------------------------------------------
//
// Default constructor: 
//
// Sets:
// - all pointers to NULL
// - fWindowSizeHiGain to fgHiGainWindowSize
// - fWindowSizeLoGain to fgLoGainWindowSize
//
// Calls: 
// - AddToBranchList("fHiGainPixId");
// - AddToBranchList("fHiGainFadcSamples");
// - SetRange(fgHiGainFirst, fgHiGainLast, fgLoGainFirst, fgLoGainLast)
// - Clear()
//
MPedCalcPedRun::MPedCalcPedRun(const char *name, const char *title)
    : fWindowSizeHiGain(fgHiGainWindowSize), 
      fWindowSizeLoGain(fgLoGainWindowSize), 
      fGeom(NULL),fBad(NULL)
{
  fName  = name  ? name  : "MPedCalcPedRun";
  fTitle = title ? title : "Task to calculate pedestals from pedestal runs raw data";
  
  AddToBranchList("fHiGainPixId");
  AddToBranchList("fHiGainFadcSamples");
  
  SetRange(fgHiGainFirst, fgHiGainLast, fgLoGainFirst, fgLoGainLast);
  Clear();
}

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

  fNumSamplesTot    = 0;

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

// --------------------------------------------------------------------------
//
// SetRange: 
//
// Calls:
// - MExtractor::SetRange(hifirst,hilast,lofirst,lolast);
// - SetWindowSize(fWindowSizeHiGain,fWindowSizeLoGain);
//
void MPedCalcPedRun::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);
  
}


// --------------------------------------------------------------------------
//
// 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 MPedCalcPedRun::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 MPedCalcPedRun::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 MPedCalcPedRun::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;
      fWindowSizeHiGain -= diff;
      fWindowSizeLoGain += diff;
    }


  Int_t npixels  = fPedestals->GetSize();
  Int_t areas    = fPedestals->GetAverageAreas();
  Int_t sectors  = fPedestals->GetAverageSectors();
  
  if (fSumx.GetSize()==0)
    {
      fSumx. Set(npixels);
      fSumx2.Set(npixels);
      
      fAreaSumx. Set(areas);
      fAreaSumx2.Set(areas);
      fAreaValid.Set(areas);
      
      fSectorSumx. Set(sectors);
      fSectorSumx2.Set(sectors);
      fSectorValid.Set(sectors);
      
      fSumx.Reset();
      fSumx2.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 MPedCalcPedRun::Process()
{

  MRawEvtPixelIter pixel(fRawEvt);
  
  while (pixel.Next())
    {

      const UInt_t idx    = pixel.GetPixelId();
      const UInt_t aidx   = (*fGeom)[idx].GetAidx();
      const UInt_t sector = (*fGeom)[idx].GetSector();      

      Byte_t *ptr = pixel.GetHiGainSamples() + fHiGainFirst;
      Byte_t *end = ptr + fWindowSizeHiGain;
      
      UInt_t sum = 0;
      UInt_t sqr = 0;

      do
        {
          sum += *ptr;
          sqr += *ptr * *ptr;
        }
      while (++ptr != end);

      if (fWindowSizeLoGain != 0)
        {
          
          ptr = pixel.GetLoGainSamples() + fLoGainFirst;
          end = ptr + fWindowSizeLoGain;
      
          do
            {
              sum += *ptr;
              sqr += *ptr * *ptr;
            }
          while (++ptr != end);
          
        }
      
      const Float_t msum = (Float_t)sum;
      
      //
      // These three lines have been uncommented by Markus Gaug
      // If anybody needs them, please contact me!!
      //
      //	const Float_t higainped = msum/fNumHiGainSlices;
      //	const Float_t higainrms = TMath::Sqrt((msqr-msum*msum/fNumHiGainSlices)/(fNumHiGainSlices-1.));
      //	(*fPedestals)[idx].Set(higainped, higainrms);
      
      fSumx[idx]          += msum;
      fAreaSumx[aidx]     += msum;
      fSectorSumx[sector] += msum;      
      //
      // The old version:
      //
      //       const Float_t msqr = (Float_t)sqr;
      //	fSumx2[idx] += msqr;
      //
      // The new version:
      //
      const Float_t sqrsum  = msum*msum;
      fSumx2[idx]          += sqrsum;
      fAreaSumx2[aidx]     += sqrsum;
      fSectorSumx2[sector] += sqrsum;      
    }
  
  fPedestals->SetReadyToSave();
  fNumSamplesTot += fWindowSizeHiGain + fWindowSizeLoGain;

  return kTRUE;
}

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

  // Compute pedestals and rms from the whole run
  const ULong_t n     = fNumSamplesTot;
  const ULong_t nevts = GetNumExecutions();

  MRawEvtPixelIter pixel(fRawEvt);
  
  while (pixel.Next())
    {

      const Int_t  pixid  = pixel.GetPixelId();
      const UInt_t aidx   = (*fGeom)[pixid].GetAidx();
      const UInt_t sector = (*fGeom)[pixid].GetSector();      
      
      fAreaValid  [aidx]++;
      fSectorValid[sector]++;

      const Float_t sum  = fSumx.At(pixid);
      const Float_t sum2 = fSumx2.At(pixid);
      const Float_t higainped = sum/n;
      //
      // The old version:
      //
      //      const Float_t higainrms = TMath::Sqrt((sum2-sum*sum/n)/(n-1.));
      //
      // The new version:
      //
      // 1. Calculate the Variance of the sums:
      Float_t higainVar = (sum2-sum*sum/nevts)/(nevts-1.);
      // 2. Scale the variance to the number of slices:
      higainVar /= (Float_t)(fWindowSizeHiGain+fWindowSizeLoGain);
      // 3. Calculate the RMS from the Variance:
      (*fPedestals)[pixid].Set(higainped, higainVar < 0 ? 0. : TMath::Sqrt(higainVar));

    }

  //
  // Loop over the (two) area indices to get the averaged pedestal per aidx
  //
  for (Int_t aidx=0; aidx<fAreaValid.GetSize(); aidx++)
    {
      
      const Int_t   napix = fAreaValid.At(aidx);
      const Float_t sum   = fAreaSumx.At(aidx);
      const Float_t sum2  = fAreaSumx2.At(aidx);
      const ULong_t an    = napix * n;
      const ULong_t aevts = napix * nevts;
      
      const Float_t higainped = sum/an;

      // 1. Calculate the Variance of the sums:
      Float_t higainVar = (sum2-sum*sum/aevts)/(aevts-1.);
      // 2. Scale the variance to the number of slices:
      higainVar /= fWindowSizeHiGain+fWindowSizeLoGain;
      // 3. Calculate the RMS from the Variance:
      Float_t higainrms = TMath::Sqrt(higainVar);
      // 4. Re-scale it with the square root of the number of involved pixels 
      //    in order to be comparable to the mean of pedRMS of that area
      higainrms *= TMath::Sqrt((Float_t)napix);

      fPedestals->GetAverageArea(aidx).Set(higainped, higainrms);
    }
  
  //
  // Loop over the (six) sector indices to get the averaged pedestal per sector
  //
  for (Int_t sector=0; sector<fSectorValid.GetSize(); sector++)
    {
      
      const Int_t   nspix = fSectorValid.At(sector);
      const Float_t sum   = fSectorSumx.At(sector);
      const Float_t sum2  = fSectorSumx2.At(sector);
      const ULong_t sn    = nspix * n;
      const ULong_t sevts = nspix * nevts;
      
      const Float_t higainped = sum/sn;

      // 1. Calculate the Variance of the sums:
      Float_t higainVar = (sum2-sum*sum/sevts)/(sevts-1.);
      // 2. Scale the variance to the number of slices:
      higainVar /= fWindowSizeHiGain+fWindowSizeLoGain;
      // 3. Calculate the RMS from the Variance:
      Float_t higainrms = TMath::Sqrt(higainVar);
      // 4. Re-scale it with the square root of the number of involved pixels 
      //    in order to be comparable to the mean of pedRMS of that sector
      higainrms *= TMath::Sqrt((Float_t)nspix);

      fPedestals->GetAverageSector(sector).Set(higainped, higainrms);
    }
  
  fPedestals->SetTotalEntries(fNumSamplesTot);
  fPedestals->SetReadyToSave();

  return kTRUE;
}
