instructions_sample1.inst

#Instruction File Sample
#
#Note that many of the pipeline related configuration options can specified on
#stage-by-stage basis as well. The local (stage) option will have precedence
#over the global options. Not including an option in an instructions block
#implicitly result in the default operation for option to be performed. This
#applies for the VEGAS cuts and configuration options as well. Be careful, as
#the default operations/values may differ from what is desirable.
#
#Analysis/Configuration Keys and pipeline-specific options are case sensitive at the moment. 
#Configuration/Cuts options must be specfied using convention expected by VEGAS  
#Leading and trailing whitespace will stripped before parsing, and identation is not
#required.

#These are the global configuration options for the script
GLOBALCONFIG{

	WORKINGDIR=/home/vhep/ssscott/tmp #Top level directory for this analysis
	RAWDATADIR=/veritas_data/raw

	#Runlist group tag associations. The tag is arbitrary alphanumeric specifier of your
	#choice. Omitting the group specifier for a single runlist analysis should be
	#work, but has not yet been tested.
	RUNLIST:GRP1=./sample_runlist1_1.rl
	RUNLIST:GRP2=./sample_runlist1_2.rl

	#The following DB Options are also accessible by stage 2
	DBHOSTNAME=romulus.ucsc.edu
	DBUSERNAME=readonly

	USECONDOR=True #Must use condor for now
}:

#Below are instructions blocks for the VEGAS analysis. Note that the pipeline
#should insensitive the ordering of the blocks. It should work out the correct
#execution order on its own. The VEGAS stage instructions can include any
#option found in the cuts and configuration files. Together, these should be the same as
#the options that can specified on the command line. 

#The following are the VIVA specific options that can be used in VIVA VASTAGE blocks. These
#are all optional and can be omitted entirely if desired.
#USEEXISTINGOUTPUT=True|False
#
#Manually specify the input directory/directories. Multiple directories are separated a colon.
#INPUTDIR=/my/manual/input/directory
#
#OUTPUTDIR=/my/manual/output/directory
#CLEANUP=all|output|output_bad|logs|logs_bad

#Parallel Stage1 analyses
VASTAGE1:GRP1{
	#You can use existing data in the output directory!
	USEEXISTINGOUTPUT=True
}

VASTAGE1:GRP2{
	USEEXISTINGOUTPUT=True
}


#Parallel Stage2 analyses
#Each analysis needs to wait only on the stages it depends upon
VASTAGE2:GRP1{
	USEEXISTINGOUTPUT=True
}

VASTAGE2:GRP2{
	USEEXISTINGOUTPUT=True
}

#Combined Stage 4 analysis. This will need to wait for both the above stage2
#analyses to complete. In practice, this is the opposite of what you might
#normally do (combined analysis for stages 1 & 2, separate analyses for later
#stages)
VASTAGE4:GRP1{

	USEEXISTINGOUTPUT=True

	LTM_LookupTableFile="/veritas_data/lookup_tables/v250/lt_Oct2012_ua_ATM21_7samples_vegasv250rc5_allOffsets_LZA_noise150fix.root"
	DistanceUpper=0/1.43
	SizeLower=0/400
	NTubesMin=0/5

}

VASTAGE4:GRP2{

	USEEXISTINGOUTPUT=True

	LTM_LookupTableFile="/veritas_data/lookup_tables/v250/lt_Oct2012_ua_ATM21_7samples_vegasv250rc5_allOffsets_LZA_noise150fix.root"
	DistanceUpper=0/1.43
	SizeLower=0/400
	NTubesMin=0/5

}

VASTAGE5:GRP1{

	USEEXISTINGOUTPUT=True

	#Specify whether stage5 should use time cuts from the database.
	#When this is set to true, DB time cuts will be used in addition to any
	#user-specified time cuts in the runlist. All time cuts used are logged
	#in a text file in the output directory for this stage.
	USEDBTIMECUTS=True
	
	MeanScaledWidthLower=0.05
	MeanScaledWidthUpper=1.1
	MeanScaledLengthLower=0.05
	MeanScaledLengthUpper=1.3
	MaxHeightLower=7
	Method="VAStereoEventSelection"

}

VASTAGE5:GRP2{

	USEEXISTINGOUTPUT=True
	USEDBTIMECUTS=True
	MeanScaledWidthLower=0.05
	MeanScaledWidthUpper=1.1
	MeanScaledLengthLower=0.05
	MeanScaledLengthUpper=1.4
	Method="VAStereoEventSelection"

}

#For stage 6, the specially formatted runlist will written automatically. 
VASTAGE6:GRP1:GRP2{

	USEEXISTINGOUTPUT=False

	#Enable/Disable the vaStage6 cross-check between the configuration-specifed 
	#theta^2 cut and that used in the generation of the effective area file(s).
	OverrideEACheck=False

	#These should set the defaults within the stage 6 configuration and be applied
	#to each run group in the case where a group-level configuration is not
	#specified
	S6A_RingSize=0.17
	RBM_SearchWindowSqCut=0.03
	S6A_ExcludeSource=1
	S6A_SourceExclusionRadius=0.4
	S6A_TestPositionRA=83.6333
	S6A_TestPositionDEC=22.0145

	#Example spectral analysis options. See the vaStage6 configuration file for
	#additional options.
	#S6A_Spectrum=1
        #EA_UseReconstructedEnergy=1
	#EA_RealSpectralIndex=-4.7
        #SP_UL=1
        #SP_EnergyBinning=1
	#SP_NumberOfBins=5
	#SP_MinEnergy=-0.96
	#SP_MaxEnergy=-1.0

	#Note that is should also be possible to specify config options on group by
	#group basis in the following way:
	#S6A_RingSize:GRP1=0.17
	#RBM_SearchWindowSqCut:GRP1=0.03
	#S6A_RingSize:GRP2=0.17
	#RBM_SearchWindowSqCut:GRP2=0.03
	#
	#This is especially useful if multiple effective area files are needed.
	#Effective areas can be assigned to each group separately in the following way.
	#Note that EA:GRP=EAFILEPATH is a VIVA specific option
	#Check the stage6 runlist in the output directory to ensure that these assignments
	#have been done correctly.
	#
	#EA:GRP1=/veritas_data/effective_areas/ea_Oct2012_ua_ATM21_vegasv250rc5_7sam_050off_s400t2_std_MSW1p1_MSL1p3_MH7_ThetaSq0p03_LZA_fixed150.root
	#EA:GRP2=/veritas_data/effective_areas/ea_Oct2012_ua_ATM21_vegasv250rc5_7sam_050off_s400t2_std_MSW1p1_MSL1p3_MH7_ThetaSq0p03_LZA_fixed150.root
	#
	#BDT cuts files can be specified in a similar way to EAs:
	#
	#BDTCUTSFILE:GRP1=/veritas_data/BDT/cuts/ua_ATM21/Hillas_M3D_BDT_ua_ATM21_soft_DETECTION.cut
	#BDTCUTSFILE:GRP2=/veritas_data/BDT/cuts/ua_ATM22/Hillas_M3D_BDT_ua_ATM22_soft_DETECTION.cut

}