Time difference variables now defined in output.def

Remove track related variables from the HMS Shower class, use ntuples
from the track (H.tr) block instead in the HMS calorimeter calibration
scripts.

- Remove a block of duplicated track related variables from the
THcShower class which have been added for calorimeter calibration
purposes.

- In hcal_calib directory, replace those variables with correspondent
variables from H.tr block in the calorimeter calibration class
(THcShowerCalib.h), in the cut (hcal_replay_cuts.def) and output
(output_hcal_replay.def) definitions.

      Compute time differences between planes
      Calculate beta and Chisquard for each track in the hodoscope.
      New variables: fBeta, fBetaChisq
      New histograms for time differences

Fixed the wrong raster channel assignment in raster_jun04.map. The X and Y channels needed to be switched.
In both map files, changed the plane assignments of all the raster channels to be 1 instead of 1,2,3,4. This then follows the ENGINE convention.

Added the raw raster ADC values to the histos and trees. Modified the ranges and binning of the
histogram definitions in output_bpw_.def accordingly.

This is a script created by Stephen Wood to convert engine type channel maps into hcana type mapfiles. Right now, this is only used when doing hcana and engine comparision for the raster.

In raster_jun04.map, reassigned the raster channels into a single plane instead of different planes.
This makes it easier for comparision with the engine.
Modified raster_test.C to analyze run 52947 in the cache directory.
Some minor clean up in the THcRaster.cxx class- removing comments and unused variables.

Read gpbeam in THcRaster::ReadDatabase
Add jan05.kinematics
Modified DBASE/raster_test.database to fill g_ctp_kinematics_filename
with DBASE/jan05.kinematics
Modified raster_test.C to load g_ctp_kinematics_filename

  12, 1, 1, 0 !ADC ROC#1 Sl#13 Ch#12 Fast Raster X-sync
  13, 2, 1, 1 !ADC ROC#1 Sl#13 Ch#13 Fast Raster X-signal
  14, 3, 1, 2 !ADC ROC#1 Sl#13 Ch#14 Fast Raster Y-sync
  15, 4, 1, 3 !ADC ROC#1 Sl#13 Ch#15 Fast Raster Y-signal
to
  12, 1, 1, 0 !ADC ROC#1 Sl#13 Ch#12 Fast Raster X-sync
  13, 1, 1, 1 !ADC ROC#1 Sl#13 Ch#13 Fast Raster X-signal
  14, 1, 1, 2 !ADC ROC#1 Sl#13 Ch#14 Fast Raster Y-sync
  15, 1, 1, 3 !ADC ROC#1 Sl#13 Ch#15 Fast Raster Y-signal
This works and it makes easier for the mapedit_rasterbcm.pl script to propagate these changes into ENGINE type map files.

  Files with the prefix raster_ are coppies of original *.database,
  and *.param files which now includes changes nessacery for
  decoding raster data. I created seperate files for these because I
  need to merge this code upstream before I can compare the raster
  decoding results with that of the analyzer. For e.g. the map files are
  different from the original map files. So Steve needs to create a perl
  script that can propgate these changes in the map files to the map
  file of the analyzer inorder for me to do the analyzer hcana
  comparision. Once the comparision is done and we are satisifies with
  the results, we will merge the changes with the original files and
  remove the files with the prefix raster_*.

  gbeam.param now included by general.param.  No need to load
  a separate parameter set to test raster/BPM code.

  examples/MAPS/raster_jun04.map adds new detector IDs for the raster
  and BPMs as follows:

Add the following IDs to the misc elements,
BEAM
 RASTER_ID= 18          ADC
 BPM_ID= 19             ADC

In the channel section did the following modification:
 sub , plane, counter, sig
  14, 1, 13, 1 !ADC ROC#1 Sl#15 Ch#14 Fast Raster X-sync
  15, 1, 14, 2 !ADC ROC#1 Sl#15 Ch#15 Fast Raster X-signal
  12, 1, 15, 3 !ADC ROC#1 Sl#15 Ch#12 Fast Raster Y-sync
  13, 1, 16, 4 !ADC ROC#1 Sl#15 Ch#13 Fast Raster Y-signal

  THcRasterRawHit class to helps with the decoding of the raster
     signals via THcHitList class.
  THcRasteredBeam class derives from THaApparatus to handle rastered beam.
  Modify Makefile and HallC_LinkDef.h to compile new classes

Added coding for read parameters from the hcana.param file.

In the hcana.param file added the four raster channels
graster_channels = "xsync xsig ysync ysig"

Created raster_test.C script to run the analyzer for raster code testing purpose. This was coppied from the hodotest.C

We have added a new parameter hcer_tot_pmts = 2 in hcana.param file.
It is equal to total number of PMTs in Cherenkov detector. With this
update, the THcCherenkov coarse process is complete. We have Raw adc,
pedestal subtracted adc, number of photo electrons and hits histograms
in the output root file for gas Cherenkov detector.

  Because git under Eclipse messes up soft links
  Use #include directive so desired file gets read

variables. Total photo electrons, total hits of adc 1, total hits of adc 2
and total hits. With this update we have transformed the FORTRAN code of
file /engine/HTRACKING/h_trans_cer.f to /hcana/ser/THcCherenkov.cxx

NOTE: The pedestal value in ENGINE is an integer but in hcana it is a
flaoting number. So it changes the pedestal substracted vlues of adc 1
and adc 2 and the number of photo electrons of adc 1 and 2 by very small
fraction. The difference of total photo electrons between ENGINE and hcana
is not more than 0.005.

  Parameters are retrieved in THcHallCSpectrometer::ReadDatabase
  Geometry information saved with
     SetCentralAngles and fPointOffset.SetXYX

  general.param - include SOS parameter for most devices
  hcana.param - add sos versions of previous hardwired parameters
  db_run.dat - put in an angle and mometum for SOS
  output.def - include sos detectors in root tree
  hodtest.C - Add SOS spectrometer and some of its detectors

  Remove link to engine
  Remove quick.csh script
  Undo changes to hodtest.C and hodtest_cuts.def

just for test purpose.

  Clone some DC tests from ENGINE test files to podd
  style cuts.  Make changes to source code to support these tests.
  Correct hits in plane line in example report file.

  If ThcAnalyzer::PrintReport sees a format descriptor with 'd' at
  the end, then the value is converted to the nearest int before formatting.

    Added variables using ENGINE names
       gen_run_number
       gen_run_starting_event
       gen_event_id_number

Inspired by ENGINE/CTP report generator
  Reports generated by
    THcAnalyzer::PrintReport(templatefilename,outputfilename)
    template is copied to output, {stuff} is replaced by the
       value of stuff.  Value can be formated with c formater, eg.
           {stuff:%.2f}
  ThcFormula added to allow more flexibility of variables.
    Can get number of times cuts pass or are called with:
       cutname.npassed (or cutname.scaler) and cutname.ncalled

Changed column and row numbering in THcShowerHit.h in order to get rid of
warning messages on unsigned and integer comaprisons when compiling;

Corrected a debug message in THcShower.cxx.