Guide for ANNIE Usage of STV-Analysis

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***Workflow***
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1. Enter the ANNIE ToolAnalysis container: './start_singularity.sh'
2. Set up the environment: 'source setup.sh'
3. Prepare input files (if necessary): 'root -l stvPrep.C'
4. Clean and compile: 'make clean' and 'make'
5. Univmake: './univmake files_to_process.txt tutorial_bin_config.txt output.root'
6. Systematic uncertainty: 'root -l tutorial_slice_plots.C'
7. XSec & Event Rate Plots: ./chi_square_cc0pi_christian

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***stvPrep***
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This script (stvPrep.C) prepares ANNIE MC PhaseIITree ntuples for univmake. It creates and adds flag branches used in tutorial_bin_config.txt from existing branches to the ntuple file. Also used to create correct flux_all and GENIE All branches.
To use:
1. 'hadd [target file] [source file 1] ...'
2. copy/move target file outside of /pnfs/
3. Edit target file path in stvPrep.C to match intended input
4. 'root -l stvPrep.C'

**Notes**:
-Input file path is hardcoded in stvPrep.C line 32
-Input file gets updated, no existing branches are rewritten
-Bug: DOES NOT RUN ON FILES LOCATED IN /pnfs/ (files MUST be moved outside of /pnfs/)
-DO NOT RUN DIRECTLY ON ANNIE MC PRODUCTION FILES (files get updated, make a copy first)
-Currently only works with MC files, not real data files. Will need updates in future
-Feel free to add extra flag/category branches! Please document any additions
-Does not check if additional branches already exist

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***DVShiftE***
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In place of detector systematics, ANNIE uses a generalized model based on through-going muons and michel electrons to smear reco observables to match the uncertainty of the detector.
-Find way to use multiple universes???
-UniverseMaker.hh lines 803-804 assign model and apply to reco observable.
-Official model does not yet exist, currently being worked on by Luis Mora-Lepin. Temporary model is gaussian function with mean of 0 and sigma of 1.5 added to observable.

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***Notable Differences between ANNIE & uBooNE***
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-TTree Name - SystematicsCalculator.hh line 854 & univmake.C line 28 & chi_square_cc0pi_christian.cpp line 364 - TTree name for ANNIE files is 'phaseIITriggerTree'
-POT Problem - SystematicsCalculator.hh line 861 - POT is hardcoded
  ANNIE MC ntuples do not include correct POT. POT is calculated externally for original GENIE files. The POT used for ANNIE MC ntuples is approximated based on the number of ntuple files to their corresponding GENIE files. A fix for this would be required in WCSim.
  Ensure POT on line 861 matches POT for all ANNIE MC files.
  POT for ANNIE numuMC, DV, and DVCV must be the same.
  The POT is ultimately an estimate. POT per event currently does not exist with ANNIE.
-Spline weight - UniverseMaker.hh lines 89, 102 - Spline Weight is non-existent and unnecessary for ANNIE so the weight was replaced with 1.
-univmake output - tutorial_slice_plots.C line 33 & chi_square_cc0pi_christian.cpp lines 179,666 - currently, univmake output is saved as 'output.root'
-ANNIE FV & flux - includes/AnnieGeometryTools.* - uses ANNIE FV and integrated flux window

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***Most up to date files***
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-BG file - (just a regular ntuple with only a single event, will need an actaul BG file in future)
/exp/annie/data/users/jminock/standard_tank_ntuples/PhaseIITree_bg2_ntuple.root
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_bg_ntuple.root

-MC files - File name, ~# of events, ~POT, been through stvPrep?
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_40k_stv_ntuple.root    40000  1.508e19 Y
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_400k_stv_ntuple.root   390000 1.493e20 Y
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_1mil_stv_ntuple_1.root 966999 3.706e20 Y
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_1mil_stv_ntuple_2.root 961997 3.694e20 Y
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_1mil_stv_ntuple_3.root 954998 3.649e20 Y
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_1mil_stv_ntuple_4.root 959996 3.676e20 Y
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_400k_BNB_ntuple.root  390000 1.493e20  Y
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_400k_DVCV_ntuple.root 390000 1.493e20  Y
/pnfs/annie/persistent/users/jminock/v1_3_3_stv_ntuples/PhaseIITree_400k_DV_ntuple.root   390000 1.493e20  Y

-fake data - Ntuples with only CV weight (use until we get real data working)
/pnfs/annie/persistent/users/jminock/fake-data-nuwro/stv_ntuples/ 39742  1.453e19 Y
/pnfs/annie/persistent/users/jminock/fake-data-nuwro/stv_ntuples/ 397478 1.431e20 Y
/pnfs/annie/persistent/users/jminock/fake-data-nuwro/stv_ntuples/ 992843 3.618e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_cv.root       444865 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_ccqel-up.root 474530 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_ccqel-dn.root 412453 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_ccres-up.root 465738 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_ccres-dn.root 420431 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_ccmec-up.root 449936 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_ccmec-dn.root 437033 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_flux-up.root  514323 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_flux-dn.root  373855 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_pmu-up.root   444577 1.7e20 Y
/exp/annie/data/users/mastbaum/cc0pi/fake_data/fake_data_pmu-dn.root   442997 1.7e20 Y

-stv output - Currently ran with corresponding MC as both MC and fake beam data - OUTDATED
/pnfs/annie/persistent/users/jminock/stv-output/stv-40k-output.root
/pnfs/annie/persistent/users/jminock/stv-output/stv-400k-output.root