In method TrackCalc get the proper THcDCTrack array index
from the golden track by using method GetTrkNum
for use in the THcDC method
SetFocalPlaneBestTrack.

When creating the THaTrack array in THcDC::CoarseTrack
the array index between THaTrack and THcDCTrack arrays
 match. The THaTrack is also associated with the THcDCTrack
array index with the call SetTrkNum(index+1)

When selecting best track by lowest chi-squared the
THaTrack are sorted from lowest to highest chi-squared
The code made a mistake in the index used in
 SetFocalPlaneBestTrack. It used the array index of the
THaTrack which is now not in sync with the THcDCTrack.
Fixed problem by using the THaTrack method GetTrkNum
which gets the proper THcDCTrack array index.


This did NOT effect reconstructed target variables or
physics variables. It only effected the focal plane
varaiables that were selected as the "best" or "golden"
to be used for the tree for dc.x_fp , dc.xp_fp,
dc.y_fp , dc.yp_fp and for the residuals.

THcScintPlaneCluster is a new class to hold information
about scintillator plane clusters of paddle hits.
The clusters of paddles for each plane are formed in
THcHodoscope::TrackEffTest which is used in the tracking
efficiency.

Modify THcScintillatorPlane so that the cluster information
(number of clusters, size,pos, flag if cluster used)
is in the tree.

Modify THcHodoscope::TrackEffTest so position
difference  are taken for all clusters in X1 (or Y1)
with all clusters in X2 (Y2).

In THcDC.h change MAXTRACKS from 10 to 50. The maximum
number of tracks is set by parameter ntracks_max_fp

Previously the LinkStubs method would not create
a track if the total number of spacepoints in
the two chambers was larger than 10.

Now LinkStubs will create a vector of THcSpacePoints
of up to 100 spacepoints with no more than
50 spacepoints from chamber 1 and use that
to find possible tracks.

I

    Add variable fPruneSelect which is a flag for which prune
    test selected the good track.

    Put into tree as tr.PruneSelect
    PruneSelect = -1 if no track found
    PruneSelect = 0 if only one track found
    PruneSelect > 0 when more then one track found.

    Method BestTrackUsingPrune goes through the tests in order and
     if a track fails the test then it is flagged as bad and not
     tested in the subsequent tests.
     When only one track is left then fPruneSelect is set to the number of
     the test.


  fPruneSelect = 1  if xptar
  fPruneSelect = 2  if yptar
  fPruneSelect = 3  if ytar
  fPruneSelect = 4  if delta
  fPruneSelect = 5  if track beta
  fPruneSelect = 6  if track reduced degrees of freedom (NHits-4)
  fPruneSelect = 7  if Number of PMT
  fPruneSelect = 8  if track beta chi2
  fPruneSelect = 9  if track focal plane time
  fPruneSelect = 10 if track hit S2Y plane
  fPruneSelect = 11 if track hit S2X plane
  fPruneSelect = 12 if track chisq

    Add variable fTRIG1_RAW_CoinTime for raw cointime calculated by
    difference in SHMS trigger (TRIG1) in ROC1 minus
    SHMS trigger in ROC2.

    Add variable fTRIG4_RAW_CoinTime for raw cointime calculated by
    difference in HMS trigger (TRIG4) in ROC1 minus
    HMS trigger in ROC2.

    Add new variables using these raw time differences
    fTRIG1_epCoinTime
    fTRIG4_epCoinTime
    fTRIG1_eKCoinTime
    fTRIG4_eKCoinTime
    fTRIG1_ePiCoinTime
    fTRIG4_ePiCoinTime
    fTRIG1_ePosCoinTime
    fTRIG4_ePosCoinTime

  Previously the helicity code was not always setting the actual
  helicity.  It would then just use the helicity from the last event.
  This was almost always OK.  With this change, the helicity (T.helicity.hel)
  should be always defined.
  It is now sufficient to use just this variable when sorting events into
  plus and minus helicity.  The helicity value will be zero if the event
  occured during the settle period, or if the helicity decoder has not
  got enough data to have a seed.

The pTRIG1_TdcTime_ROC1, pTRIG4_TdcTime_ROC1
and pTRIG1_TdcTime_ROC2, pTRIG4_TdcTime_ROC2

should have been Double_t instead of Int_t
since the THcTrigDet.h function Get_CT_Trigtime
returns a Double_t which is the time convert to ns.

Do HMS pathlength correction using xptar and delta instead
of the focal plane quantities.

Fixed sign typo in fROC1_ePosCoinTime and fROC2_ePosCoinTime

Fix sign error in DeltaSHMSpathLength and DeltaHMSpathLength

Add tree variables
DeltaSHMSPathLength
DeltaHMSPathLength
had_coinCorr_Positron
elec_coinCorr

In THcScalerEvtHandler::AnalyzeBuffer there is a loop over
the scalers to keep track of scalers with a cut on the current.
There was a mistake in using scal_prev_read[nscal-1] instead of
dvars_prev_read[ivar] in the IF statement.

fGoodFlags holds event-by-event data, but was never cleared,
eventually growing to several hundred megabytes in a long analysis.
The effciency calculations in THcHodoEff that rely on the contents
of fGoodFlags have been most certainly garbage up to now.

I've replaced the event-by-event ClearEvent() method with the
standard virtual function Clear() and have added fGoodFlags.clear()
there.

Also, I've added assertions to the hodoscope code to check
the validity of some non-obvious array indices. Nothing triggers;
the index logic appears sound (despite its appearance ...)

This includes a particularly nasty leak in the shower code that caused
several hundred bytes to be lost _per event_.

Currently both CMake and SCons build not only libPodd, but also libHallA,
even though it is not required for hcana. hcana is linked only against
libPodd, however, so libHallA is simply a spurious byproduct.

Modify THcAerogel::CoarseProcess



For each PMT, fGoodPosAdcMult.at(npmt) was being set to the total number of positive PMTs with an
adc hit and fGoodNegAdcMult.at(npmt) was being set to the total number of negative PMTs with an
adc hit.

To be like the other dectectors make fGoodPosAdcMult.at(npmt)
and  GoodNegAdcMult.at(npmt) be the number of adc hits for that particular
PMT.

  For KaonLT, the kPulsePedestal values being returned for
  the helicity signal channels was 0 and 16380.  For SIDIS, the
  values for off and on are ~2000 and ~1400.  Made the default
  threshold 8000 instead of 1000.  Also added an optional parameter,
  "helicity_fadcthreshold" so that this threshold can be changed
  at run time.

Undoes delayed helicity reporting by learning seed of pseudo random
sequence used by injector helicity electronics.

This detector class should be added to the Trigger apparatus.
Delivers the global variables "hel" and "helrep".  "helrep" is the
reported delayed helicity and "hel" is the actual helicity.  + and -
helicity are reported as +1 and -1.  If the event is during a MPS
settling period, then the helicity variables are zero.  For the first
few seconds of a run, the "hel" variable will be zero as the pseudo
random sequence seed has not been determined.  (If the trigger class
is "T" and this detector is called "helicity", then these variables
will be T.helicity.hel and T.helicity.helrep.

By default, it is assumed that there is delayed reporting of 8 cycles
and that Quartets are used.  If delayed helicity reporting is not in
use, then set the parameter "helicity_delay" to zero.

  These signals are plus and minus signals, the MPS indicator, and
  the start of quartet indicator.  The time from the TI (with overflow
  detection) is also retrieved as this is needed when dealing with
  delayed helicity reporting.

  The helicity signals are in FADC250 channels.  The roc/slot/channel
  assignments for these signals are currently hardwired into the code.

Add the tree variable goodAdcMult which is the number of raw ADC pulses
  in an ADC channel per event for a given shower array block.

Fix problems in THcTrigDet.cxx

1) Read-in of the trigger reference time cuts was in ReadDatabase method
  when it should be in Init method. Moved to the Init method before
  call to InitHitList where the reference cuts are used.

2) Modified the selection of the good TDC hit for filling the TdcTimeRaw
and TdcTime. Previosly used the TdcTime but not picks the TDC hit with the TdcTimeRaw that is within
the time min and max windows that can be set by parameters. Default windows are min=0 and max=10000.
If two hits in the time window then selects last hit within window.
If not hits within time window then TdcTimeRaw=0 and TdcTime=0.
The TdcMultiplicity is always filled.

1) Read-in of the trigger reference time cuts was in ReadDatabase method
  when it should be in Init method. Moved to the Init method before
  call to InitHitList where the reference cuts are used.

2) Modified the selection of the good TDC hit for filling the TdcTimeRaw
and TdcTime. Previosly used the TdcTime but not picks the TDC hit with the TdcTimeRaw that is within
the time min and max windows that can be set by parameters. Default windows are min=0 and max=10000.
If two hits in the time window then selects last hit within window.
If not hits within time window then TdcTimeRaw=0 and TdcTime=0.
The TdcMultiplicity is always filled.

1) THcTrigDet
   a) Modify code to use string vector fTrigNames to identify which of the trigger
     trigger detector TDC signals to use for coincidence timing. This
      replaces the hard-coded names. The integer array fTrigId[4] keeps
     track of the array ID in the overall fTDcNames vector that goes
      with the fTrigNames[4]
   b) The fTrigNames must be in order of SHMS ROC1, HMS ROC1, SHMS ROC2
     and HMS ROC2.
   c) Default names are "pTRIG1_ROC1","pTRIG4_ROC1","pTRIG1_ROC2","pTRIG4_ROC2"
      The parameter is t_coin_trigNames
      For example:
      t_coin_trigNames="pTRIG1_ROC1 pTRIG4_ROC1 pTRIG1_ROC2 pTRIG4_ROC2"
      This parameter is read-in and the split into a string vector fTrigNames.
   d) In HcTrigDet::ReadDatabase , all members of fTrigID array are set
to -1 then a loop over all Tdc in the trigger detector looks for match between
fTdcNames amd fTrigNames to set fTrigId. If match not found the fTrigId = -1.
   e) In THcTrigDet.h made new method Get_CT_TrigTime(Int_t ii) to be used
in in THcCoinTime to get the 4 trigger times: SHMS ROC1 (ii=0), HMS ROC1 (ii=1),
SHMS ROC2 (ii=2) and HMS ROC2 (ii=3).  If fTrigId[ii]=0 then it returns 0
otherwise returns fTdcTime[fTrigID[ii]].

2) THcCoinTime
  a) Previously used the raw trigger times and had a hard-coded 0.1 ns/channel
conversion. Now use the trigger times which already are in ns using the
ns/channel conversion set in the TrigDet.
  b) Now use the new TrgiDet method Get_CT_TrigTime(ii) to get the
trigger times for SHMS ROC1, HMS ROC1, SHMS ROC2 and HMS ROC2.

Added TClonesArray* fRawHits which an array of THcDCHit object for all
hits in the drift chamber. This is filled during Process method.

Added tree variable raw.wirenum whihc is array of wire numbers for all hits in the drift chamber.

* updated mispointing calculations

* added TMath::Abs() for HMS angles, since it has a '-' sign in the kin. file

Don't confuse index of scalers with slot number

See https://github.com/JeffersonLab/analyzer/commit/cd7c26b5b1161115a0e35a4824148b78a189e986

NOTE:
This changes the format of the "variable" lines in the db map file that
defines the scaler layout.

The number after the variable directive is now the slot number instead of
the index of which scaler module (starting from zero) is being used.
Updated DBASE/db_PScalevt.dat and DBASE/db_HScalevt.dat files which have
been generated by an updated MAPS/SCALERS/make_scaler_db.py.  This change is
made so that the "variable" line format is the same as used in
THaScalerEvtHandler.cxx.

  Determine readout side in THcDriftChamberPlane at initialization time.