* 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

comp_histos.C does a chi-squared comparision between histograms
  in two root files. Need to create the subdirectory Output
  The execution is
  .x Macros/comp_histos.C("oldfile.root","newfile.root")

  Main purpose is for comparing histograms
  after changes to hcana. Histograms which are exactly the same
  have a chi-square = 0 .
  For histograms that fail the chi-square test, a list of
  names in placed in Output/hist_diff_NoMatch_output.txt
  and the histograms are plotted and the plots saved to
   Output/hist_diff_NoMatchoutput.pdf
  For histograms that pass the chi-square test, a list of
  names in placed in Output/hist_diff_Match_output.txt

Add gscalers.param to PARAM

gscalers.param will have the parameters for converting the BCM scalers into charge and current.

* added HODO EDTM to Maps and Param filrs for HMS/SHMS; Added block T.hms.* in epics_short.def in order to produce HMS Hodo EDTM leaf variable; Added Hodo EDTM to scaler.map

* undo changes in HMS hodo naming schemes for scalers map

* 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

* Updating repository with changes made at software workshop

* Added changes to PARAM & DBASE files to take appropriate HGC calibration constants for each run.

* Changed replay output to something more sensible

* Added new Analysis scripts to master

* Removing bloat from merge with branch Ryan

* Removing redundant files from master

* Added properly named, properly formatted calibration scripts to master

* Removed bloat with the README file

* Removed more bloat in data_files

* Updated calibration file

* Updated calibration script to include the NGC as well. Added calibration parameters to PARAM & DBASE in an identical method as the HGC.

* Updated calibraion scripts

* Removed tracking of .gitignore

* Added .gitignore...can't change branches otherwise

* Updated calibration script to include Eric's recommendation of cuting on TracksFired leaf.

* Updated investigation of the integrals of first few photoelectrons

* Updated display to show expected integral based on Poisson statistics

* Updated Calorimeter PARAM CALIB file after discussion with Varden

* Merged efficiencies from development branch to master

* Updated efficiency script to only display info if requested, and will now output the cuts on beta and timing

* Cleaned up efficiencies.C, now in more or less a final stage.
calibration still needs a little cleaning up, especially concerning the poisson/Guassian after processing which yielded little information.

* Updated calibration, much cleaner and sensible

* Added particle ID for tracksfired calibration strategy

* Changed the calibrated histograms to have identical limits/bins. Required merging some bins together from original data...should be okay.

* Updated files to include cut on delta p on all 3 Cherenkovs

* Cleaned up tracksfired calibration strategy

* Added quick README on instructions to run script

* Finialized the quick README.md

* Update README.md

* Update .gitignore

* Deleted unnecessary DBASE files

* Cleaned up Pull request

* Changed Cal Calib run488 file to remove old calib constants

* First hack at setting up coincidence replay

* Add coincidence trigger map

* Update merge list for example purposes

* Add coincidence map

* Create coincidence replay script

* Create separate DBASE directory for SHMS

* Create separate DBASE for SHMS

Fix plethora of issues in HMS replay scripts

* Do not delete onlineDict.h

Small correction to PARAM/SHMS/HODO/CALIB/ptofcalib.param

Set pdumptof = 1

Update PARAM files for hodo calibration

Create two files
htofcalib.param
ptofcalib.param

Each of these files sets the flag to dump the tof calibration
data to a file that is designated in the file.
The user has to add a line
gHcParms->Load("PARAM/HMS/HODO/htofcal.param");

or

gHcParms->Load("PARAM/SHMS/HODO/ptofcal.param");
to the replay script to get the  data files hodo calibration

Remove these parameters from the regular hodo calibration files.

* -Modified shms dc calib scripts in accord with the recent hallc replay restructure
-updated Drift Chamber Calib parameters for run 488 after making the changes to the calibration code

* removed tzero offsets from geom param file

* Ignor header file

* Fix typo in map file and get rid of debug statement

* Adapt shms scaler online GUI for new naming scheme

* Remove deprecated config files

Move scaler config files to own directory

* Fix scalers replay script so it does not seg fault

* Modify online GUI for HMS scalers to function with new naming scheme

* Auto-indent

* Move staggaling files to examples

* Add directory structure to online GUI

* Fix naming scheme and histo names to be consistant with the rest of the repo

* Same fix as previous commit but for HMS

* Modify production replay scripts to keep naming convention consistant with previous commits

* Apparently THaVhist cannot handle LaTeX alphabets

* Turn off tzero per wire param causing replay to crash and burn

* Uncomment event/trigger types.  Needs to be cleaned up later

* Remove deprecated detector directories

* Remove deprecated map files

* Exclude trigger histo with no real variable

* Include raster into stack map

* Uncomment lines which were causing a bajillion errors

Needs to be cleaned up at some point

* Remove deprecated parameter files

* Remove deprecated replay scripts

* Remove deprecated template file

Updated SHMS Pre/Shower gain constants for run 488

* -added primary kin to HMS single arm production replay script
-Minor fix in shms production replay script

* Minor addition in replay_production_hms.C

* -change primary kine names in hms/shms replay scripts

* -added elec_KIN/ dir. for electron kinematics DEF-files for HMS/SHMS
-include new def files in mergelist and update production def file

* Re-structure the PARAM files for HMS and added raster variables to thms.param

* restructure hallc_replay DBASE for HMS param files; add hodo/cer kpp_spring_2017 calibration directories and parameter files

* restructure HMS detector maps directory; add hms run 303 to standard.database

* -added Raster to HMS trigger map
-minor fix in commented raster names
-minor fix in name for HMS to SHMS in an shms map file

* -Include only one spectrometer in 'g.evtyp' variable for HMS/SHMS report file cuts (for the moment ...)

* -added new 'PRODUCTION' directory for HMS where all def files with 'good' variables are included
-copied python script/list from SHMS 'PRODUCTION' directory to HMS.
(This script combines individual detector def files into one)

* -added STACK directory in HMS Def-files dir, which includes only stack histograms (excludes EPICS variables)

* -added TEST_STANDS directory in HMS Def-Files to include raw and good
detector histograms

* -excluded hms Aerogel from def files (for now . . .)

* -updated HMS templates for scalers, stack and production

* Re-structure the PARAM files for HMS and added raster variables to thms.param

* restructure hallc_replay DBASE for HMS param files; add hodo/cer kpp_spring_2017 calibration directories and parameter files

* restructure HMS detector maps directory; add hms run 303 to standard.database

* -added Raster to HMS trigger map
-minor fix in commented raster names
-minor fix in name for HMS to SHMS in an shms map file

* -Include only one spectrometer in 'g.evtyp' variable for HMS/SHMS report file cuts (for the moment ...)

* -added new 'PRODUCTION' directory for HMS where all def files with 'good' variables are included
-copied python script/list from SHMS 'PRODUCTION' directory to HMS.
(This script combines individual detector def files into one)

* -added STACK directory in HMS Def-files dir, which includes only stack histograms (excludes EPICS variables)

* -added TEST_STANDS directory in HMS Def-Files to include raw and good
detector histograms

* -excluded hms Aerogel from def files (for now . . .)

* -updated HMS templates for scalers, stack and production

* -Restructurization of replay scripts in HMS

* Minor fixes in shms replay scripts

* -moved replay scripts to new directories