- Each detector should override ManualInitTree(TTree*)
- This method should be used to add branches to the tree
- These branches should be data members of the detector.

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_.

- Mixins defined in Logger.h
- Mixin used in base classes (THcDC is currently a good example)

Added a few more spdlog loggers

Added logging to many.

- Added logging to hodoscope, aerogel hitlist and detectormap
- Working on scandalizer features.

Added logging.

Added more logging.

added more logging.

More logging.

- Added logging to hodoscope, aerogel hitlist and detectormap
- Working on scandalizer features.

- Mixins defined in Logger.h
- Mixin used in base classes (THcDC is currently a good example)

Modify code in CoarseProcess to add (subtract) time due to hit
location in paddle for positive (negative) PMT for new hodoscope
beta parameters.

Add tree variables TimeHist_Sigma, TimeHist_Peak and TimeHist_Hits
for the peak,sigma and number of hits of the histogram
 of PMT times used in EstimateFocalPlaneTime

  Add doxygen groups "Apparatuses" and "Decoders"
  Make sure every class is in a group
  Make sure most classes have a \brief description
  Improve comments for some classes including THcHallCSpectrometer
     and hodoscope classes
  Change some Doxyfile defaults.  Include sources files.

  Set hodoscopes to standard ADC mode for example hodtest.C script
  badcraw_pos and badcraw_neg always true if not Dynamic pedestal mode
  Don't crash in hodoscope if there is no Cherenkov.

Modified Hodoscope and ScintillatorPlane  classes for new time calibration method.

In Setup : Set name of histogram to include initial of spectrometer
   that it belongs. Each event in EstimateFocalPLaneTime the histogram
   is fill with the scintillator times so that a cut can be placed
   to throw out bad scintillator times relative to the mean of
   all scintillator times.

Elminiate "void" in THcHodoscope::EstimateFocalPlaneTime( void )

Modify so default starttime is -1000.

Modify so if no hits in scintillator then EstimateFocalPlane is not called.

fFPTimeAll is the average focal plane time from all
  scintillator times. In EstimatedFocalPlaneTime fFPTimeAll is set to
  starttime which is the average FP time without using the DC track.

If there are tracks, then a focal plane time is calculated
for each track using the track information to improve the focal
plane time calculation and save for each track. Previously
 fFPTimeAll was being filled for each track, so in effect
fFPTimeAll was being filled with the FP time of the last track.
ALso there was no check that nFPTimeSum was not zero when
calculating average FP time, so one could get NaN values for
fFPTimeAll

To fix the problem , added  and modified line

Double_t fptime=-1000;
if (nFPTimeSum>0) fptime = FPTimeSum/nFPTimeSum;

And moved setting fFPTimeAll to THcHodoscope::FineProcess
Now fFPTimeAll is set the the average focal plane time of
the golden track.

Add AdcTimeWindowMin and Max for each pmt

Add tree variables GoodPosAdcMult and fGoodPosAdcHitUsed

Moved the old track efficiency tests to OriginalTrackEffTest method and
this is presently commented out. Eventually can be eliminated.

The old track efficiency assumed that both planes had matching
  paddlle spacing which is not true for SHMS.

Added new method TrackEffTest which calculates the number of clusters
  in each plane and the position for the cluster for scintillator
  paddle that had good times in both ends. Selects events with
  one cluster with size of 1 or 2 in either 4 of 4 planes
  or 3 of 4 planes. Also checks that the events are inside
  a given range of scintillator paddles.

  So that the counts can be reported in report files.

   First hit above this cut is taken as the reference time.
   Cuts are per detector and read as an optional parameter in
   each detector class.  TDCs and Flash ADC times have separate cuts.

Implement a second method of selecting best reference time.
  If InitHitList is passed a possitive reference time cut,
    use the first reference time above that cut.  If none of the
    hits pass the cut, then no reference time is set
  If InitHitList is passed a negative cut, the cut is taken to be
    the absolute value of the cut, but a reference time is garuanteed
    to be set as long as there is at least one reference time hit.
    If none of the reference time hits pass the cut, then the last
    hit is taken to be the reference time.  (Should be the largest.)

Allow reference time cuts for all the spectrometer detector classes
  Hodoscopes, drift chambers, Aerogels, Gas Cherenkovs, Calorimeters

  Add End method to each detector that calls MissReport which
  prints the number of events with missing TDC and ADC reference times.

Add TH1f histogram hTime to replace timehist array

Eliminate cut on fStartTimeCenter in selecting good
  focal plane times.

  Each detector object will check the global variable X.present each
  event.  If X.present is false, it indicates that the parent
  spectrometer object determineted that this spectrometer is not in
  this event, and therefor reference times are not expected.  If
  X.present is false, then the reference time warning messages will
  be suppressed.

Add ability to cut on number of PE in Cherenkov when dumping events
  for TOF calibration

Add parameter fTOFCalib_cer_lo

Add ability to cut on track beta when dumping events
  for TOF calibration

Add parameter fTOFCalib_beta_lo and fTOFCalib_beta_hi

Parameters are optional. Default set to kBig or -kBig

THere was already a possible cut on Shower energy/momentum

  This is because it is offsetting PulseTime which is double and to
  be consistent with the other detectors.

Moved writing of the TOF calibration dump file to FineProcess
Added cut on shower energy/momenutum
Add parameters fTOFCalib_shtrk_lo and fTOFCalib_shtrk_hi .

Add parameter fNumPlanesBetaCalc which allows one to set how many
planes to use in beta calculations. Useful for SHMS.
fNumPlanesBetaCalc defaults to 4 if not set.

    THcHodoscope.cxx
    1. Remove from the use of "temp_planes" for SHMS which
         used only 3 planes for beta and determination of start time.

    2. With change of Integral ADC to pC, change TMath::Sqrt(TMath::Max(20.0,adc_pos))
      to Math::Sqrt(TMath::Max(20.0*.020,adc_pos)) to convert 20 channels to pC

    3. Set fGoodFlags[itrack][ip][iphit].onTrack = kTRUE; when fTOFPInfo[ih].onTrack
       Was always FALSE before.

    4. Modify FineProcess
       a. Add calculation of the track X and Y track position at each plane.
       b. Calculate the difference between the track position and position
          measured by hodoscope center. If multiple paddles hit then take
          average of the paddles.

    THcScintillatorPlane.h and cxx

    1. add variables fHitDistance,fTrackXPosition and fTrackYPosition
    2. add methods GetHitDistance(),GetTrackXPosition(),GetTrackYPosition()
    3. add methods SetHitDistance,SetTrackXPosition,SetTrackYPosition
    4. add variables to tree DiffDisTrack,TrackXPos and TrackYPos
    5. set GoodPosAdcPulseTime to frPosAdcPulseTime
    6. set fGoodNegAdcPulseTime to frNegAdcPulseTime
    7. in HodoHit set PosADCtime and NegADCtime to PulseTime

-Added fAdcTimeWindow Min/Max to THcHodoscope.cxx (.h)
-Added fAdcTimeWindow Min/Max to THcScintillatorPlane.cxx (.h)
-Initialized loop over number of hits inside the FillDynamic_Pedestal() method
-added some variables in the THcScintillatorPlane.cxx Dynamic Pedestal Method
-Added loop over adc_pos and adc_neg hits, and required the hits to fall
within fAdcTimeWindow Min/Max
-Added the requirement of at least a valid (adc && tdc) on either end of a bar
-re-defined boolean operator for adc_pos/adc_neg to be True if  they passed the errorflag and timeCUT requirements in the fADC_Dynamic Pedestal method.
-- deleted adc_pos/neg initial definitions, and set their initial values to -999.

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.