add Reftime

Check the Fptime is good

1) Add Reftime
2) change code to fix raw amp =0 problem
3) add PedDefault needed for raw amp=0 problem

Add code to deal with raw amp = 0
Add code to read in default ped to use when raw amp = 0

Dave Mack introduced two new variables to the
calculation of beam current to described correction for
the nonlinearity above 60uA in BCM1 and BCM2
seen in the Fall 18, Spring 19 and Summer 19running.
See for example summer 2019
hallcweb.jlab.org/doc-private/ShowDocument?docid=1037
Fall 18/Spring 19
hallcweb.jlab.org/doc-private/ShowDocument?docid=1042

For a BCM scaler read the difference, Dcounts, from the
previous scaler and get the time difference, Dtime.
Original calculation is:
I = (Dcounts/Dtime-fBCMOffset)/BCM_Gain
Now add an non-linearity correction
I = I + fBCM_SatQuadratic*Max(I-fBCM_SatOffset,0.0)^2

Add parameters fBCM_SatOffset and fBCM_SatQuadratic
that can be optional read-in. If parameters are
not read-in the parameters are set to zero, so
there is no correction.

Add the non-linearity correction to all BCM current
calculations.

1.  If THcHelicity is told about the THcHelicityScaler object with
    the SetHelicityScaler method, it will use helicity scaler events
    to jump start generating the seed
2.  When beam off, helicity decoding can get lost if the helicity_freq
    parameter is not very close to the actual helicity reversal frequency
    (which seems to drift).  THcHelicity now calculates a recommended value
    of helicity_freq.

Add parameters to hold helicity scaler results:
  g%s_hscaler_plus[%d]
  g%s_hscaler_minus[%d]
  g%s_hscaler_sum[%d]
  g%s_hscaler_asy[%d]
  g%s_hscaler_asyerr[%d]
  g%s_hscaler_time (Time with defined helicity)
  g%s_hscaler_time_asy
  g%s_hscaler_triggers	(All triggers including where helicity not decoded)
  g%s_hscaler_triggers_plus
  g%s_hscaler_triggers_minus  (plus+minus is slightly less than triggers)
  g%s_hscaler_trigger_asy

%s is name assigned to THcHelicityScaler object
%d is scaler channel #.  0-31

  Now for 30 Hz, need to override in parameter file

  Fix case where fActualHelicity doesn't get defined (even as unknown)
  Report when helicity pattern from helcity scaler does not agree
    with pattern found from physics events

  Use qrt signal to identify quartets, find pattern if it doesn't.
  Fail over to HMS helicity signals if SHMS not found
  Add pcheck and cycle global vars (for fine tuning frequency)
  Start a helicity scaler class.  Just compares seeds for now.

THcTrigDet::Decode change the ADC/TDC window limits to be ">="
instead of ">".

THcTrigDet::ReadDatabase change default upper ADC/TDC window
limit to 100000 so that the DC are not cut by default setting.

1) THcDC
a) Add variable to tree called dc.InsideDipoleExit
which is a Bool_t flag that is kTRUE if golden track is inside the
dipole exit. Uses THcHallCSpectrometer::InsideDipoleExitWindow
in THcDC::SetFocalPlaneBestTrack to set variable.

2) THcHallCSpectrometer
a) Add method Bool_t InsideDipoleExitWindow which checks whether
the track is within the dipole exit window. Checks
prefix used for database to set flag
fUseSHMSDipoleExitWindow or fUseHMSDipoleExitWindow
to be true which is used in InsideDipoleExitWindow
to select either SHMSDipoleExitWindow or
HMSDipoleExitWindow method to be used as the test.
b) Hardcoded z distance from spectrometer focal plane to
dipole exit window.
c) Methods Bool_t SHMSDipoleExitWindow and
Bool_t HMSDipoleExitWindow return true/false if
the track was inside/outside the dipole exit window.
d) Added dipole exit window test to the BestTrackUsingPrune
method. Need to set parameter hprune_DipoleExit=1 or
pprune_DipoleExit=1 to use the test in the method.
By default it is turned off.

The LeftRight method determines the sign of the wire
distance for each hit in the spacepoint by looping
through all combinations of wire signs and fitting each
combination with a line  and selecting
the combination with the lowest chi-squared.
The fit to the line is known as the "stub" which
is an array of the x,dx/dz, y and dy/dz of the fit
and is associated each spacepoint. The stubs are
used later in LinkStubs method
to match spacepoints between two chambers to give a
possible tracks.

Previously the LeftRight method would only fit a
stub for a spacepoint with 4 hits in the chamber if the
parameter flag  HMSStyleChamber was true.
HMSStyleChamber refers to the 6 GeV HMS chambers
and we do not have them anymore.
But not fitting the spacepoint, the stub
was filled with zeros for x,dx/dz,y and dy/dz
and these spacepoints would never be matched with
other spacepoints to form a possible track.

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.