Update HMS/SHMS calibration constants to have units of pC instead of channesl to match updated HCANA

* Calibration script now uses normalized energy for particle ID and can update calibration constants directly. Both scripts use PROOF-lite by default. Added a run_cal script for ease of use. README now reflects updated scripts.

* Calibration/running script cleanup

* fixed stash print

* as designed hms dc param

* new hms dc param to be used

added 12 GeV HMS DC initial parameters, but it still needs to be updated after survey is done (#237)

* Overwrite scaler chan name with Empty if description is "Empty".

* Update scaler.map
  More complete implementation of user pages
  Correct the SHMS S2Y mapping

* Add optional title to overlay2.C macro

* SHMS test stand update

* Fix SHMS calorimeter onlineGUI config

* Make make_scaler_db.py have unix format rather than DOS format

* Generate special lines for Charge, Current and Time in scaler configs

* Accomadate extra "page" column in scaler.map
  in make_scaler_db.py conversion script

* Add extra "page" column to scaler.map for new xscaler
  (And remove underscore in SHMS HODO EDTM description)

removed SHMS DC Parameters being loaded for specific runs, since now we have a common SHMS DC parameter file for all KPP runs

deleted obselete SHMS DC Param file, since I did the calibration for Run 484, and the parameters produced relatively flat drift distances independetn of Run 484 or 488 from KPP

Calibration script now uses normalized energy for particle ID and can update calibration constants directly. Both scripts use PROOF-lite by default. Added a run_cal script for ease of use. README now reflects updated scripts. (#224)

* re-organized the onlineGUI sub-directories

* update the README to match directory structure

add re-structured SHMS DC Calibration in terms of classes and methods. This is a version of the SHMS DC Calibration code that seems to work. Along with the parameter files produce by it. (#228)

* added files used for shms dc alignment

* moved some dc alignment files around

* removed script in production

* updated shms geo param

* updated plots for shms dc monitoring

* Include trigger apparatus reference time into param list

* Inlcude trigger apparatus reference times into trigger maps

* Update HMS maps accordingly

* Update SHMS maps accordingly

Needs https://github.com/JeffersonLab/hcana_gem installed and built
  in ../hcana_gem and thishcana_gem.sh or thishcana_gem.csh to have been
  sourced.

* added files used for shms dc alignment

* moved some dc alignment files around

* removed script in production

* Add SHMS FADC reference time signal

* Modify report files and templates to better quantify the deadtimes

* Push initial changes for Steve

* Include failed state of HMS scalers replay script

* Include proper(?) method for obtaining event 129 scaler reads

* Ensure that trigger apparatus cut file has similar flow to stack and production to avoid confusion

* Remove reference time which serves as a reference time for the trigger apparatus

* Update maps corresponding to previous commit

* Ignore # files

* Update test stand cuts file to match production and stack

* Update test stand cuts file to match production and stack on HMS side

* Update cuts files to handle new event type stucture corresponding to mulitple triggers

* Make cuts only HMS specific

* Do the same for the SHMS and correct the template files

* Correct template files

* Add pedestal event because of historical reasons (needs to be fixed)

* Do the same for the SHMS

* Add SHMS FADC reference time signal

* Modify report files and templates to better quantify the deadtimes

* Push initial changes for Steve

* Include failed state of HMS scalers replay script

* Include proper(?) method for obtaining event 129 scaler reads

* Ensure that trigger apparatus cut file has similar flow to stack and production to avoid confusion

* Remove reference time which serves as a reference time for the trigger apparatus

* Update maps corresponding to previous commit

* Ignore # files

* Update test stand cuts file to match production and stack

* Update test stand cuts file to match production and stack on HMS side

* Add vim lint to .gitignore

* Update replay scripts to search in a list of paths

- NOTE: This requires the podd submodule be updated to include
  modifcations to the THaRun constructor that can search a pathList.

- The default './raw' and './cache' pathnames that are searched here
  should generally be symlinks to the relevant local path on the Hall C
  cluster, and the /cache/mss/hallc/.../raw/ path, respectively. For
  example:
    cd hallc_replay
    ln -s /net/cdaq/cdaql3data/coda/data/raw raw
    ln -s /cache/mss/hallc/spring17/raw      cache

- FWIW: The batch filtering of the replay scripts was done with
  this perl script:
    cd SCRIPTS/
    find . -name '*.C' -exec ./filter.pl {} \;
  --- filter.pl ---
  #!/usr/bin/perl

  use File::Slurp;

  my $file = read_file($ARGV[0]);

  $file =~ s/\Qchar RunFileName[100];\E\W*\Qsprintf(RunFileName, RunFileNamePattern, RunNumber);\E\W*\QTHaRun* run = new THaRun(RunFileName);\E/THaRun* run = new THaRun( pathList, Form(RunFileNamePattern, RunNumber) );/s;

  $file =~ s/\Qconst char* RunFileNamePattern = "\E.*?\/(.*?\.dat)";/const char* RunFileNamePattern = "$1";\n  vector<TString> pathList;\n    pathList.push_back(".");\n    pathList.push_back(".\/raw");\n    pathList.push_back(".\/cache");\n/s;

  write_file("$ARGV[0]", $file);
  ---

* Include consolidated SHMS TI trigger inputs into HMS trigger maps

* Include SHMS TI trigger inputs into HMS test stand maps

* Include consolidated HMS TI trigger inputs into SHMS trigger maps

* Include HMS TI trigger inputs into SHMS test stand maps

* Point HMS DC test stand to 6 GeV chamber histos

* Update scaler map and database to include mixed HMS and SHMS triggers

* Add ignore stuff

* Include TI trigger inputs into scalers

* Add TI trigger inputs to param files

* Add TI trigger inputs to trigger maps

* Add HMS trigger apparatus variables to trigger test stand

* Remove raster from trigger apparatus map

Update HMS maps to include new TI trigger inputs

* Remove fast raster from trigger apparatus map

* Add TI trigger inputs to SHMS maps

* Add efficiency calculations for the layers of the calorimeters.

* Add efficiency calculation for the Array part of calorimeter.

* Update phgcer_calib.param

@vardant These calibration numbers should be included in hallc_replay/PARAM/SHMS/HGCER/CALIB/KPP_Spring_2017/.  For reference the gain constants for run 464 were phgcer_adc_to_npe = 1/111., 1/118., 1/122., 1/125.

* Update pcal_geom.param

Fix some typos

* Incorporate fast raster DEFfiles into appropriate infrastructure

* Tweak DEFfiles to match previous pull request