Modified Hodoscope and ScintillatorPlane  classes for new time calibration method.

Add AdcTimeWindowMin and Max for each pmt

Add tree variables GoodPosAdcMult and fGoodPosAdcHitUsed

Have variables fGoodPosAdcTdcDiffTime and fGoodNegAdcTdcDiffTime
which are the difference
between TDC time and ADC pulse time

Replace ADC pulse time cut with cut on difference
between TDC time and ADC pulse time to select
good ADC pulse.

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

    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

Include methods for FADC conversions and apply to non-raw data objects in THcRawAdcHit

Add raw pulse time data object to Cherenkov detector classes

Add raw pulse time data object to shower detector classes

Add raw pulse time data object to hodoscope detector class

  fpTimes, fScinTime, fScinSigma and fScinZpos are not used.
  These arrays were given fixed size of 53.
  This commit finishes issue #53

-Changed the name of a Good tdc variables
-Added all good adc and tdc variables
modified:   src/THcScintillatorPlane.cxx
modified:   src/THcScintillatorPlane.h

   Added to THcScintillatorPlane.h
   Initialize and clear in THcScintillatorPlane.cxx
Add raw multiplicities for ADCs and TDCs

-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.

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.

 - Added new leafs to the hodoscope tree.
 - Added new leafs to the aerogel tree.
 - Added new leafs to cerenkov tree.
 - Added new leafs to the shower tree.

Left all the old leafs in there. Will need a careful cleanup...

  Use xhodo_adc_mode to choose how to interpret data
    0 - Interpret as a standard ADC, subtracting pedestal found from ped events
    1 - Use integrated pulse from ADC.  Subtract the event by ev pedestal
    2 - Integrate the sample data, subtract ped found from ped events
    3 - Integrate the sample data, subtract dynamic pedestal
  xhodo_pedestal_scale is factor to multiply dynamic pedestal before
    subtracting.  For example, if uses 4 samples to get pedestal and
    is acquiring 86 samples, in mode 3, this should be 86/4
  xhodo_adc_diag_cut is a cut used to determine if diagnostic ADC
    stuff should be put in tree for each channel.  Need to set this so
    that hodoscope hitmaps get filled right.  Was 50 for Fastbus data.

  Default is to use new "invadc" parameters.  Use old style
  by setting Xtofusinginvadc=0

Lot's of changes to
 THcScintillator::ProcessHits
 THcHodoscope::EstimateFocalPlaneTimes
 THcHodoscope::FineProcess

  THcRawHodoHit gives reference time corrected TDC values
  THcScintillator plane adds a per plane offset to the raw tdc value
  First positive TDC value after adding offset is used

used to determine focal plane time for each hodoscope plane.
Add code to THcScintillatorPlane:DefineVariables to write out
focal plane time, number of paddles hit that passed minimal TDc cut
and number of paddle hit that were used in determining the focal plane time.
Add calls to THcScintillatorPlane.h to Set and Get the focal plane time
and number of paddle hits used to determine focal plane time for each hodoscope plane.

in THcScintillatorPlane

  in calculation of drift chamber start time

  Pulse height corrected times saved in THcHodoHit objects.
  PulseHeightCorrection method renamed to EstimateFocalPlaneTimes
    because the pulse height correction is now done in the
    ProcessHitsMethod.

   Don't repeat comparisons of tdc values
   with fScinTdcMin and fScinTdcMax because hits only get added to
   fHodoHits (and previously fPosTDCHits, fNegTDCHits, ...) if
   the times are within these ranges.
  In THcHodoscop, remove members of fTOFPInfo that are just used
   locally.

  Eliminate usage of GetParent() many times every event.

  Move hodo_slop retrieval to THcHodoscope
  Get fPosCenter array length from fNelem instead of fixing length at 16
  Remove now unneeded THcScintillatorPlane creation method

  For the most part this is making sure that the loop variable in
  a for loop is of the same type as the variable that it is compared
  against (Often a UInt_t).

This reverts commit e9ce1040.

Conflicts:
	src/THcHallCSpectrometer.cxx

  For the most part this is making sure that the loop variable in
  a for loop is of the same type as the variable that it is compared
  against (Often a UInt_t).

Goldent track is moved to THcHallCSpectrometer::TrackCalc()
  if  fSelUsingScin == 0 then golden track is calculated just
  like podd. i.e. it is the first track with minimum chi2/ndf
  with sorting ON

  if fSelUsingScin == 1 then golden track is calculetd just like
  engine/HTRACKING/h_select_best_track_using_scin.h. This method
  gives the best track with minimum value of chi2/ndf but with
  additional cuts on the tracks. These cuts are on dedx, beta
  and on energy.

  This commit also corrects and modifies the beta code written
  in the THcHodoscope::FineProcess

  At this point we have godlend track and in additoion to
  previous vlues the following values are set to a track:
  Energy, beta, chi2 of beta and dedx[track][first hit].

NOTE: For some tracks we have large differences in value of chi
      square between ENGINE and hcana and this is already
      discussed in the last group meeting. Following emails are
      exchanged regarding this difference of chisquare.

email to Mark:

Hi Mark,
I tried to trace the origin of difference of the chi square value between
ENGINE and hcana. Please see the attached file, it has long table which I
cannot present in this email. Or you can see the file at the following
link, thanks.

https://userweb.jlab.org/~zahmed/chi2diff.txt

Ahmed

Mark's reply:
Ahmed,
        Thanks. I agree with what you see, but there is also another reason
for the difference. For the space point in ch2 the engine and hcana
choose different left/right combinations. That is why you see the large
jump in the summed chi2 from planes 9 and 10. The two codes pick
different left/right because there is a cut on the difference between the
measured stub xp and an expected xp = sp->GetX()/875  and one code has a combination
slightly below the cut value and the other slightly above. I do not see a way
to make the codes agree more exactly since the stub fitting involves a matrix
inversion.

                Cheers,
                       Mark

This commmit is only for Beta. THcHodoscope is modified and few
bugs are fixed. I will not make pull request for this commit.
Pull request will be made after the completion of Golden track
in THcHallCSpectrometer.

Conversion of h_tof.f to THcHodoscope::CoarseProcess method.

 Quick summary of third version at  branch zafar1:

 New functions in THcScintillatorPlane.h
 ---------------------------------------
    TClonesArray* GetPosADC() { return fPosADCHits;}; // Ahmed
    TClonesArray* GetNegADC() { return fNegADCHits;}; // Ahmed
    TClonesArray* GetPosTDC() { return fPosTDCHits;}; // Ahmed
    TClonesArray* GetNegTDC() { return fNegTDCHits;}; // Ahmed

 New data members in THcHodoscope.h
 ----------------------------------
    TClonesArray* scinPosADC; // Ahmed
    TClonesArray* scinNegADC; // Ahmed
    TClonesArray* scinPosTDC; // Ahmed
    TClonesArray* scinNegTDC; // Ahmed

 Action in THcHodoscope::CoarseProcess
 -------------------------------------
 scinPosADC = fPlanes[ip]-GetPosADC();
 hitPaddle  = (THcSignalHit*)scinPosADC->At(ihit))->GetPaddleNumber()-1;

The arrays are  frPosTDCHits, frNegTDCHits,frPosADCHits and frNegADCHits
There are filled in THcScintillatorPlane:ProcessHits
2) Also modified THcScintillatorPlane::ProcessHits explicitly set variable
padnum=hit->fCounter and index=padnum-1 so the the TClone arrays for
scintillator variable set padnum=1,16 while the index=0-15
Want pdnum=1-16 because it is used in a hitogram fo counts versus
paddle number
3) Because of change to filling PaddleNumber in ProcessHits had
to modify THcScintillatorPlane::PulseHeightCorrection so the
index variable "j" is set to etPaddleNumber()-1 .

GN: finished debugging the hodoscope start time calculation. Results match 1-to-1 the corresponding "engine" result.

Calculating pulse height correction for the hodoscope.
Calculating focal plane times for each scintillator plane - (in THcScintillatorPlane)
Calculating hodoscope start time (average of fp times) - (in THcHodoscope)

hodoscope start time.