The purpose is to add a call in THcHallCSpectrometer:TrackCalc
to fill variables in THcDC for the golden track.

THcHallCSpectrometer.h
----------------------
1) Add object THcDC* fDC
2) Eliminate object fShower since it was not being used.

THcHallCSpectrometer.cxx
----------------------
1) in ReadDatabase method cast fDC in detector "dc" is defined
2) in FindVertices method add call
    to fDC->SetFocalPlaneBestTrack(hit_gold_track)
    where hit_gold_track is the HaTracks array index
    of the golden track

THcDC.h
-------
1) Add method SetFocalPlaneBestTrack

THcDC.cxx
---------
1) Eliminate filling of best focal plane quantities
   in CoarseTrack which defined "best" by lowest chi2
2) Create method SetFocalPlaneBestTrack
   a)fills the best focal plane quantities using the golden track
   b) fills fResiduals using golden track

THcShowerHit.h and THcShowerHit.cxx
---------------
1) Added fY for horizontal position
2) Added fY to THcShowerHit

THcShower.h
-----------
1) Added variables
2) Added method addY, clY to get the cluster Y position

THcShower.cxx
--------------
1) Added variables to the tree for "layer" detector
    either SHMS preshower or HMS layers
2) Added variables if the SHMS "array" is used
3) Added y position to THcShowerHit in CoarseProcess
4) In FineProcess, if SHMS "array" used then fill X,Y info
     for the Cluster and the "best" track that matched the cluster

THcShowerArray.h and THcShowerArray.cxx
---------------------------------------
1) Added methods to Get the array cluster size, X and Y position
   and block number that has the highest energy in the cluster
2) Added array fBlockClusterID for all blocks. initialized to -1
   for each block for each event and then filled with
   the cluster number if the block is included in the cluster
3) Add variable fNhits and fNgoodhits

Main purpose was to have option for per wire tzero offsets

Modified THcDriftChamberPlane.h
------------------------------
1) added fUsingTzeroPerWire as parameter flag to switch on per wire tzero offsets when parameter equals 1
2) fTzeroWire is array of tzero offsets for each wire in plane

Modified THcDriftChamberPlane.cxx
------------------------------
1) THcDriftChamberPlane::ReadDatabase
    a)set a default value of fUsingTzeroPerWire=0
    b)added to DBRequest list option to read in fUsingTzeroPerWire
    c) if fUsingTzeroPerWire=1 then separate DBRequest to read in fTzeroWire
   d) if fUsingTzeroPerWire=0 then all fTzeroWire=0

2) THcDriftChamberPlane::ProcessHits
------------------------------------
   a) Modify calcualation of drift time to subtract fTzeroWire
Double_t time = -StartTime- rawtdc*fNSperChan + fPlaneTimeZero - fTzeroWire[wireNum-1];

  Then the # tubes of the Aerogel is known.
  Remove MaxNumXXXAeroPmt constants from THcAerogel.h

The line fNpeSum += fNegNpeSum
was basically double counting the fNegNpeSum
Same for fNpeSum += fPosNpeSum
since they were in a loop over Neg and Pos hits.

Just set
fNpeSum = fNegNpeSum + fPosNpeSum
after the two loops over Neg and Pos hits

THcShowerArray
1) in ProcessHits methodfFixed mistake in index of fThresh
   was using padnum instead of padnum-1
2) add parameter pcal_arr_AdcThreshold so that threshold
   can be set by a parameter. Default is zero which gives
   the best resolution.

THcShowerPlane
1) Added the parameter cal_AdcNegThreshold and cal_AdcPosThreshold
   so that the threshold can be set through a parameter
   Previously it was hardcoded.

New parameters are added.  hallc_replay of 3/31/2017 or later is needed.

As of now, the size of the TClonesArray objects are hard-coded in the
respective header files. This is not okay in the long run. Ideally,
the size of the TClonesArrays should be defined by the parameter which
dictates how many readout detectors exist for the respective
detector. I tried doing this in the Init method however, podd
complained regarding the size of the TClonesArrays in the DEF-file
histograms. I was unsuccessful in my first attempt. This should be
addressed in the future even though things work for now.

  Process slot with clock first so that time is available to other slots
  Add option to use data in first scaler event
     (handler->SetUseFirstEvent(Bool_t)) instead of subtracting first event
     from subsequent events

The change was in part of code which calculates the fiducial
 area of the scintillators where the drift chamber should
 have had a track. This sets fGoodScintHits=1 or 0
 Used to calculate the DC track efficiency

1) Eliminate variables fScinShould and fScindid. These will
   be defined in the cuts file.
2) Eliminate code which determined bestXpScin and bestYpScin since
   since these variables were never used.
3) Initialized  fHitSweet1X,fHitSweet1Y,fHitSweet2X and
   fHitSweet2Y to zero.
4) Change so that loops over number of paddles do not
    assume that X (Y) planes for Ch1 and Ch2 have same number
    of paddles.

Main purposes:
1) Add the possibility of multiple ADC hits per channel and
   select best ADC by a time window.
2) Change ProcessHits method in ShowerPlane and ShowerArray to only
    fill "raw" TClonesArrays.
3) Add CoarseProcessHits method to ShowerPlane and ShowerArray
    to fill the "good" data arrays from call in THcShower:CoarseProcess
4) Moved code to fill Track object with energy from FineProcess
   to CoarseProcess so that the Track->Get(Energy) can be used by other
    detectors in their FineProcess.
5) FineProcess loops over Track object add gets Track energy
6) Add AdcErrorFlag TClonesArray to be filled to check for
   problems with FADC




THcShower.h
1) Add methods GetADCMode(),GetAdcTimeWindowMin(),GetAdcTimeWindowMax()
    so that the ShowerPlane can access these parameters
2) Add parameters ADCMode,fAdcTimeWindowMin,fAdcTimeWindowMax
3) Add variables
   fNclustTrack : NUmber of cluster that matches best track
   fXclustTrack : X pos of cluster that matches best track
   fXTrack      : X pos of best track that matches cluster
   fEtrack  : Cluster energy associated with best track
   fEtrackNorm  : Cluster energy/Track momentum associated with best track
THcShower.cxx
1) Add calls to THcShowerPlane and THcShowerArray CoarseProcessHits
    in CoarseProcess
2) Moved filling of Energy in Track object to CoarseProcess
3) In FineProcess get the "best" Track object and match
   Track energy and trajectory to cluster.

THcShowerArray.h and cxx
1)add parameters fADCMode, fAdcTimeWindowMin and fAdcTimeWindowMax
2) Add method CoarseProcessHits
3) In ProcessHits fill fPosThresh and fNegThresh with a fix
    value of 250 integrated channels above pedestal.
     Need to make this a parameter.

THcShowerPlane.h and cxx
1)Gets fADCMode, fAdcTimeWindowMin and fAdcTimeWindowMax from THcShower
2) Add method CoarseProcessHits
3) In ProcessHits fill fPosThresh and fNegThresh with a fix
    value of 250 integrated channels above pedestal.
     Need to make this a parameter.

Add method
GetF250_PeakPedestalRatio() {return fPeakPedestalRatio;};

so that a detector class can calculate the pedestal that was used
in determining the pedestal subtracted FADC Pulse Integral.

This is useful if the detector class wants to set a threshold
above the pedestal.

The change was made so that NonTrackingDetector could have information
on the "best" track in their FineProcess method.

In THcHallCSpectrometer::FindVertices the "best" track will be selected
and the Track object will its SetIndex method to set the index to 0 for
the best track. The other track will have index=1 or greater.

In the NonTrackingDetector FineProcess, the track that is selected to
be the "best" can be found by looping through the tracks checking
track index using Track.GetIndex() for find the track with Index=0.

In  the NonTrackingDetector's CoarseProcess they need to set quantities
for the Track object needed for selection of "best" track for the
"prune" and "usingscin" track selection methods.

1) In THcHallCSpectrometer:
  a) Moved selection methods of "best" track from TrackCalc to FindVertices.
  b) Removed setting of Golden Track in the selection methods.
  c) Add setting of Track Index=0 for "best" track in each selection method.
  d) Modified TrackCalc method to loop through Track object and find
     the track with Index=0 and set the Golden Track equal to this Track.

2) In THcHodoscope.cxx
  a) Moved all calculations in FineProcess into CoarseProcess
  b) CoarseProcess calculates the scintillator Beta for each Track
     and does Track->SetBeta.
  c) In determination "zcor" for corrected hits times
      use fBetaNominal instead fBetap from track. Still use Track
      to get distance.
  c) Eliminate fBetap variable which was using the Track momentum
  d) Add variable fBeta which is just from scintillator times.
  e) In FineProcess fill fBeta with the the beta associated
     with the "best" track determined by selecting Track with index=0

In HcTrigDet::Init moved InitHitList after gHcDetectorMap->FillMap so that the refindex can be filled for the trigger TDC modules
In ReadDatabase add parameters fTdcOffset and fTdcChanperNS
In Decode set fTdcTime[cnt] = rawTdcHit.GetTime()*fTdcChanperNS-fTdcOffset
Ths makes the time into a positive number wiht units of ns
Need to add the parameter to either thms.param or tshms.param or
it will use defaults of 0.1 and 300.
Need to eventually get the fTdcChanperNS from event 125.

	In THcAerogel.cxx, mean pedestals are calculated if
	fMinPeds>0. Set fMinPeds to default zero in
	THcAerogel::InitializePedestals. Reinitialize it with
	paero_min_peds parameter in paero.param file.

Add variables fX_fp_best,fY_fp_best,fXp_fp_best,fYp_fp_best to THcDC.h
Modified THcDC::CoarseTrack so that the variables are filled with the
quantities from the track with the smallest chi-squared.
Modified THcDC::TrackFit so that the fResidual per plane is filled with
for the track with the lowest chi-squared.
Modified THcDC::DefineVariables so that access the variables as
dc.x_fp,dc.y_fp,dc.xp_fp and dc.yp_fp

Add array fADC_hit that is a flag if there is a hit in the ADC
fADC_hit is set in Decode method
The FADC has a threshold on accepting ADC hit
Modified CoarseProcess method to eliminate old FASTBUS bias in the analysis

Temporarily set THcHodoscope.cxx so that only the first three planes are used to calculate the focal
plane time and beta.
In THcHodoscope , Modified format for writing out the dump file used in hodo calibration.
Add cosmicflag to THcScintillatorPLane so the corrected time is done right for cosmics.
Modified hc_hodo_calib/tofcal.f so that it uses detector 10 as the reference
and that it writes out better defualts for parameters in there are not enough events for a PMT.

THcHodoHit.h add methods to set and get the ADC peak amp and time
THcScintillatorPlane::ProcessHits changed to set the ADC peak amp and time in the Hodohit
DefineVariable added variables to tree

Moved the writing out of the "0" to the fDumpOut for hodo calibrations
to immediatiately after the TOF with track info calculations.
Before it had been after then lines

  if ( !fChern || !fShower ) {
    return 0;
  }

so if Cerenkov and shower were not used in replay the code would not get
to write out the "0" which is used to denote the end of an event data for
the calibration script.

PSE125 holds information about setting of F250 modules. Now this
information is used to set `fNPedestalSamples` and `fNPeakSamples`
parameters of `THcRawAdcHit`.

This is done through `THcHitList`, since it has information about
which crate and module each channel is in. Currently, the information
is set for each event, because of the hitlist and analyzer design.

I added the neccessary support for these changes to all raw hit
classes.

  Provides methods get NSA, NSB, and NPED for each crate

Corrected warning message for missing refchan to correctly display reference channel.
Modified warningg message for missing refindex to include information about reference channel.

	Cycle over array of pedestal subtracted fADC signals fA_p in
	the same order as it was filled.

fScinHitPaddle is a std::vector<std::vector<Double_t>>. It was
cleared and rebuilt for each event with the same structure,
instead of just zeroing out all the values.

Now it is created in only one place, and than zeroed instead of
cleared.

Changed data type in fScinHitPaddle from Double_t to Int_t. Should
be changed to bool, but then all logic should be changed.

There was a weird bug in the code, that only triggered for some runs.
It turns out, in the `THcHodoscope::FineProcess` the hits in each plane
were created only for number of paddles in first plane. SHMS, however,
has 13 paddles in first plane and 14 and 21 paddles in last two planes.

The problem is fixed now, but part of that code should be rewritten for
efficiency.

With the new raw and good varibles added to the tree, these variables are not needed in the tree.

Applied changes in several files to reflect this.
Minor fix in `THcRawHodoHit`.

When calculating the residuals, consider all track candidates instead of only the first track.  Moreover, eliminate the instances when there was no hit in a plane then the residual was returned as zero.