* May 26, 2017 -- Long overdue push, some old Calibration Scripts but also the presently working analysis and Calibration scripts in Final Scripts directory.

* Updated Calibration with pulseAmp script.

* root file

* added Rootfiles

* Rewrote pulseAmp analysis, works much better now.
Included Degtiarenko's code to evaluate as a better alternative.
Started the write up for the actual calibration process

* Updated Analysis scripts, started deciphering Fortran code.

* test

* TEST

* test

* bla

* blah

* boring git stuff

* git stuff

* Made the master branch much more organized/presentable

* Finializing directory. Modified how calibration appears/output the calibration constants

* Updated the analysis and visualization scripts for NGC.

* Version of Calibration suitable for the Summer presentation.

* Removed debugging line

* commented out a cout line

* increased the total number of bins by two, since the bin width was reduced from 2ns to 1ns. This change produced better drift distances

* reduced drift time bin width to 1ns.

* reduced bin width to 1 ns/bin

* reduced bin width to 1 ns /bin

* Updated parameter files

COSY was run with Q2 set to 0.985*( ideal setting)
which better matches the focal plane distributions.
New optics reconstruction matrix.

* -added script that will output a parameter file with individual tzero values (NOT per ribbon cable as before)

* -included the execution of 'get_tzero_per_wire.param' in steering script.

* -added precicion to the t0 calculation. Although the calculation involved the ratios of two 'doubles', the t0 came out to be an integer. This imprecision was corrected.

* -add minor fix

* added minor fix to read in corrected t0 values

* minor fix

* most up-to-date shms DC param files

* -added the lines to read run number to the top of the script.

* -Modified SHMS DC DEF FILE to display drift times with binning scheme same as used in calib.
-Added the most up-to-date shms dc parameters obtained from the modified shms dc calib. script

* -set option to use per_wire tzero ON.

* -Added the fAdcTimeWindowMin/Max parameter values per plane for the hms/shms h(p)hodo.param file

* -added comments to SHMS/HMS hodo.param file

Modified DBASE/general.param
 #include "PARAM/SHMS/DC/pdc_tzero_per_wire.param"

Modified PARAM/SHMS/DC/pdc.param
  added parameter p_using_tzero_per_wire
  Set to 1 for tzero per wire

Add file PARAM/SHMS/DC/pdc_tzero_per_wire.param
  1) Has parameters for tzero offsets per wire
  2) The offsets were determined per connector
     and all wires in a connector have the same offset

Add file PARAM/SHMS/DC/pdriftmap_tzero_per_wire.param
   1) Drift map to use with p_using_tzero_per_wire=1
   2) Copy to pdriftmap.param

Add file PARAM/SHMS/DC/pdriftmap_plane.param
   1) Drift map to use with p_using_tzero_per_wire=0
   2) Copy to pdriftmap.param

Loaded f_adc_debug param file to the test stand replay script for NGC.
Added new 1D and 2D Histograms to the test stand NGC def files.

so far). This flag will add histograms that fall under the 'debug'
category from the source code.
-Loaded the fadc_debug parameter file to the test stand replay scripts (for
SHMS H.G.Cerenkov so far), to be used by experts ONLY.
-Added new 1D and 2D Histograms to the DEF files for SHMS H.G.Cerenkov so far.

hcal.param
   1) gains for run 303,
   2) hcal_AdcNegThreshold=0.
   3) hcal_AdcPosThreshold=0.

pcal.param
   1) gains for run 464
   2)pcal_AdcNegThreshold=0.
   3)pcal_AdcPosThreshold=0.
   4)pcal_arr_AdcThreshold=0.0

Modified DEF-files for new names for the Cherenkov and Aerogel

Add paramters for HMS aerogel

Add correct region paramters for Cherenkovs

Vardan calibrated the HMS (run 303) and SHMS (run 464) gain parameters
Add cuts on the ADC time
Updated the positions for SHMS preshower and fly's eye array
Have examples of histograms in hstackana_report.def and
  pstackana_report.def with cuts in hstackana_report_cuts.def and
  pstackana_report_cuts.def

Moved phgcer_tot_pmts and pngcer_tot_pmts = 4
   phgcer.param and pngcer.param
Did a first stab at  conversion for ADC chan to npe for both detectors
For Aerogel moved paero_num_pairs = 7 from pcana.param to paero.param

The calibration scripts work in a very specific way. First you have to change the
`wire_drift_times.h` to read the correct run. Then you have to change the
`pdc_plane_time_zero` in the parameter file to `1280`, since it is hardcoded.
Then you replay the run with these values and run the calibration. Then you
get the correct corrections to the time zero.

Fixed nested list in `CALIBRATION/hodo_calib/README.md` to markdown format.
Removed TODO tag from fixed parameter in `PARAM/SHMS/DC/pdc_tracking.param`.

Added README.md
Eliminate extraneous output files in tofcal.f
Set to use hfort.37 and pfort.37 as standard output files