autogeneration of src/HallC_LinkDef.h - all using SCons

Eliminate print statement for tzero per wire in THcDriftChamberPlane:…

Fix mistake in THcScintillatorPlane::ProcessHits

Accidentally deleted line
btdcraw_pos = kTRUE;

in previouse commit

-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.

Merge branch 'shms_presh_develop' of https://github.com/Yero1990/hcana into Yero1990-shms_presh_develop

  Add "Good" variables to calorimeter class
     occupancies and multiplicities
     required to pass time and threshold cut
  Change some variables from arrays to vectors
  Modify how thresholds are calculated
  Remove obsolete variables: posadchits, negadchits
  Add flash adc debug flag
  Correctly delete pointers in destructor

  Add "Good" variables to calorimeter class
     occupancies and multiplicities
     required to pass time and threshold cut
  Change some variables from arrays to vectors
  Modify how thresholds are calculated
  Remove obsolete variables: posadchits, negadchits
  Add flash adc debug flag
  Correctly delete pointers in destructor

Make matched cluster variables of the array part of calorimeter private.

Initialize fY variable in the THcShowerHit::THcShowerHit default
constructor.

Correct typo in THcShowerArray::Clear, assign -1000 to fMatchClY.

Edit debug output in THcShowerArray::CoarseProcess and remove obsolete
comments THcShowerArray::MatchCluster.

Clear fSizeClustArray and fNblockHighEnergy quantitites in
THcShower::Clear, for just in case.

So files don't split.
Seems to be working, hcana has not crashed yet with file sizes
upto 2.6 GB.

Main purpose is to calculate the DC efficiency per wire
using the track information of the golden track.


THcDC.h
-----------
1) add method EfficiciencyPerWire
2) Add variables fWire_hit_did and fWire_hit_should

THcDC.cxx
------------
1) fWire_hit_did and fWire_hit_should are fixed length arrays
   the size of NPlanes that in set in method Init
2) Add variables wireHitDid and wireHitShould to the tree
3) In method SetFocalPlaneBestTrack add call to EfficiencyPerWire method
4) added EfficiencyPerWire method which loops over the hits
    and compares the wire number for the hit to the the track
    position at the plane (convert back to wire number).
    Then fills fWire_hit_did with the wire number if
    equal to the wire position of the hit equals the track.
    Also does loop over all planes and fills fWire_hit_should
    with the wire number of the track in each plane.

THcDriftChamberPlane.h and cxx
---------------------
1) Added method CalcWireFromPos

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

Podd commit text:

Add the eye offset.  Also add the ability to put vectors of variables
into a single (scalar) histogram, per the request of Hall C

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

Modified THcDriftChamberPlane.cxx and THcDriftChamberPlane.h

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

  New required Cerenkov and Aerogel parameters in hcana.def
  cuts and output.def updates
  remove now unsupported mirror efficiencies from report.template

Fix problem in THcAerogel::CoarseProcess with fNpeSum

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

Fix mistake in THcShowerArray and make the threshold a parameter

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.

Fix bug for corner case for gcc 4.4 and ROOT5

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

Modify THcHodoscope.cxx

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.