Generalized calibration to first determine appropriate timing cuts (hence new "preprocess" files), removing the need of arbitrary hard-coded timing values.

Modify hcana.param and hmsflags.param to use the
  latest matrix fit.

Modify pcana.param and shmsflags.param to use the
  latest matrix fit.

* Include helicity scalers to scaler maps

* Update trigger detector maps

* Update parameter files with helicity channels

* added HMS ME and readme

* add y center offset found from optics

* hmsflags to be used with optimized hms ME

* mod readme

* set wire t0 = card t0 in card mode (fixes anomaly in parameter file) :: set good event definition as ndata==1 && cal_energy>0.1 && cer_npe>1.0

* minor fix in wire t0 tzero determination from card tzero

* added t0_card_err criteria to determine whether to set t0 per card to zero because of low statistics. (Some edge cards also have low statistics when the calibration has PID cuts )

* Added GetCardT0_alternative() method, which determines the T0 of the per-card drift time if certain criteria are met, such as the number of entries per card. This method was developed to correctly account for the T0 for edge cards with low statistics. Although this is rare to find, there were ocassions in which entries for edge cards were low adter applying PID cuts.

* moved 'old_scripts' directory to UTIL_ED

* Added optional num_evts argument to take '-1' as an option to loop over all events in the TTree.

* updated good_event definition: X.cal.etot>0.1&&X.cer_npeSum>1.0&&(5/6 PLANE HITS)

* added percent variable to determine fit region for HMS/SHMS independently

* add t0_err_threshold as criteria for accepting good wire drift time fits

* Started to implement Per Card DC Calibration: 1)Added per-card methods in header file, 2)Added varible plane_cars[NPLANES] to store max number of disc. cards in a plane

* added per-card histogram definitions

* added GetCard() method

* Added option to calibrated by card ... Currently working on EventLoop() method

* Implement GetCard() method within EventLoop() method :: Add option to fill uncorrected plane and card drift times while in 'card' mode during the calibration

* added GetTwentyPercent_Card() method

* added FitCardDriftTime() method

* re-arranged methods

* added card histograms to WriteToFile() method

* added mode string to setup directory methood

* Working version of DC Calib using 'card' optional argument

* Finished implementing per card DC Calibration

* remove optional flag dc_1hit, since ndata==1 cut was made a requirement for good track

* remove useless method printInitVar() :: remove useless variable dir_log_name

* remove pintInit() method from main_calib.C :: rename offset to tdc_offset

* Added SetTdcOffset() method to initialize the tdc offsets values independently of the event loop, and save some lines of coding

* incorporated ApplyTZeroCorrection() Method into the EventLoop() Method, with an oprional parameter. This way, there will be a single event loop in the entire code

* removed un-necessary ndata_wirenum variable. Removed pid_hadron optional flag, removed h(p)EL_CLEAN tdcTime cut since it is too restrictive, and cerenkov/calorimeter cuts can be used instead

* added chamber1/2 hit counters to require at least 5/6 planes hit per event per chamber as critereon for good event

* Added option to EventLoop() method to fill Uncorrected times

* Fix typo in HMS production cuts

* Corrected EDTM cuts and adjusted HMS TDC reference time cut to improve hodoscope efficiencies

* Fix bug for BCM cut currents in template files

* Add new BCM gains and offsets

* Update kinematics files

* Updated the kinematics files to be up-to-date. Note that the files had not been updated through the last two shifts (now fixed).

* updated kinematics files

* kinematics file from night shift

* Updated kinematics file, corrected mistake in HMS momentum that snuck in during OWL

* Kinematics files up to run 1799/2713 (HMS/SHMS)

* Include focal plane quantites in the tree

* Update kinematics files

* Updated kinematics files

* Update kinematics files

* Update submodules

Added setup_Directory() method to main_calib.C :: Added README for DC Calibration :: changed directory named from shms_dc_calib to dc_calib (#424)

* added HMS/SHMS DC Calib README :: changed directory name from shms_dc_calib to dc_calib

* added setup_Directpry() method in main_calib.C

* added optional flag to require single hit per event per plane for calibration :: re-define cuts for pid_hadron/pid_elec flags

* changed calorimeter leaf from X.cal.etotnorm to X.cal.etot

* added capability to created HMS/SHMS DC Calib Log directories to store the calibration information produced by the calibration script

* clean-up of SHMS DC Calibration Dir

* Added functionality to loop over Max number of entries, if user enters entries exceeding this maximum :: Add calorimeter etot_norm cut for beackground cleanup

* DC Calib: added option to only perform ONLY EL-CLEAN trigger cut, which reduces the background events in the chambers

* added the requirement for each event to a ONLY 1 hit, by requiring ndata==1. This way, background produced from multiple hits can be reduced.

* 1). Set 'hdrift1stbin' parameter by +1 ns offset, to improve the drift distances. 2). Added variable 't_zero_final' which includes the tdc offsets (from HMS ONLY), as opposed to only including the tzero value. This is used in the LookUpTable method() 3). Remove 0.5 ns offset from the min/max time, which puts integer drift time values at the edge of a given bin 4). Reduced total number of bins in which the drift time integration is done from 274 ns to 189 ns, since it was determined (from a conversation with Mark Jones), that drift times beyond this value had no contribution to the drift distance.

added optional pid_hadron cut in DC calibration :: changed 'good drift time fit' criteria to also consider fit slope of >0.2, based on previous observations of bad fits (#420)

2. Added capability for HMS/SHMS to calibrate using PID cuts on cerenkon/el clean trigger

Updated to match updated HCANA

Updated hcana code to have adcTimeWindowMin and Max
  for each Cerenkvo PMT so need to modify the
  adcTimeWindowMin and Max parameters to be an array.
  Keep them at -1000 and 1000 ns .

This adcTimeWindow is used to select which hit in the
 multihit ADC channel is pick as the "good" hit to
 us the later analysis.

Add branch=master to UTIL_ED

1) Applied weighted averages to edge wires
2) Added TDC offset correction to some of the 16-groups for HMS DC
3) Started Integration range at -20 ns for LookUp Table