lalinference_coherence_test.py

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##python
'''
This program simply computes the bayes factor between the coherent and incoherent models
given as input the B files for the run.
'''
 
from __future__ import print_function
 
from optparse import OptionParser
import sys
import os
import matplotlib
matplotlib.use("Agg")
from pylab import loadtxt
from math import log,exp
 
usage='''%prog [options] coherent_B.txt incoherent1_B.txt incoherent2_B.txt ... incoherentN_B.txt
%prog takes a list of arguments which specify FIRST the coherent B.txt file, followed by all the
B.txt files from the individual runs on each IFO. The coherent file must be specified first.
 
The code will then perform either the test of coherent vs incoherent signal models, i.e.
B_{CI} = Z_co / Z_1 * Z_2 * Z_3
 
or a test of coherent vs incoherent
B_{CIN} = Z_co / (Z_1 * Z_2 * Z_3 + N_{123})
 
or the test of coherent vs ( incoherent signal or noise ) models, i.e.
B_{CIN} = Z_co / Z_{inc OR noise}
with Z_{inc OR noise} = sum over all permutations of the signal and noise hypotheses in each detector
e.g. for 2 detectors:
Z_{inc OR noise} =
see also https://dcc.ligo.org/LIGO-T1600068
 
Output will be written to stdout, and to a text file specified by the --outfile option.
 
'''
 
parser=OptionParser(usage)
parser.add_option("-c","--coherent-incoherent",action="store_true",dest="ci",help="Perform coherence test of Coherent signal vs incoherent signal",default=False )
parser.add_option("-n","--coherent-incoherent-noise", dest="cin", action="store_true",  help="Perform coherence test of coherent signal vs incoherent signal or noise", default=False )
parser.add_option("-b","--new-coherent-incoherent-noise", dest="cin_or_n", action="store_true",  help="Perform coherence test of coherent signal vs incoherent signal or noise using the most inclusive hypothesis", default=False )
parser.add_option("-o","--outfile",default=None, help="Optional output file name", metavar="OUTFILE.txt",type="string",action="store")
 
(opts,args)=parser.parse_args()
 
def get_metadata_hdf5(filename,key):
    import h5py
    with h5py.File(filename,'r') as hdf:
        g=hdf['lalinference']
        if(len(g.keys()))>1:
            print('Error: multiple runs %s found in input file %s'%g.keys(),filename)
            sys.exit(1)
        # Descend into run group
        g=g[list(g.keys())[0]]
        return g.attrs[key]
 
# Sanity check input arguments
if len(args)==0:
        print('No input files specified')
        sys.exit(1)
 
if( sum([opts.ci,opts.cin,opts.cin_or_n])!=1):
        print('Please specify one of -c, -n or -b. See help for details.')
        sys.exit(1)
 
cofile=args[0]
incofiles=args[1:]
 
if len(incofiles)<2:
        print('Cannot perform coherence test on less than 2 IFOs')
        sys.exit(0)
 
if len(incofiles)==0:
        print('Error: You must specify incoherent input files')
        sys.exit(1)
 
def logadd(a,b):
    if(a>b): (a,b)=(b,a)
    return (b+log(1+exp(a-b)))
 
def get_metadata_old(Bfile,key):
    print('Looking for '+Bfile)
    if os.access(Bfile,os.R_OK):
        outstat = loadtxt(Bfile)
        if key=='log_evidence':
            return outstat[1]
        if key=='log_noise_evidence':
            return outstat[2]
        if key=='log_bayes_factor':
            return outstat[0]
        print('Unknown key %s'%(key))
        return None
    else:
        return None
 
def get_metadata(filename,key):
    if '.h5' in filename or '.hdf' in filename:
        return get_metadata_hdf5(filename,key)
    else:
        return get_metadata_old(filename,key)
 
Zco = get_metadata(cofile,'log_evidence')
Zinco=0
Z_single_noise = [ get_metadata(inco,'log_noise_evidence') for inco in incofiles]
Z_single_signal = [ get_metadata(inco,'log_evidence') for inco in incofiles]
 
# we compute now the evidence for the hypothesis "incoherent signal OR noise" as the
# sum over all posible permutations over mutually exclusive sub propositions
 
from itertools import combinations
try:
    from scipy.special import logsumexp
except ImportError:  # scipy < 0.19.0
    from scipy.misc import logsumexp
 
def not_seen(t, seen=set()):
    return False if t[0] in seen or t[1] in seen else seen.update(t) or True
 
Z_incoherentORnoise = logsumexp([sum(p) for p in list(filter(lambda t, seen=set(): False if t[0] in seen or t[1] in seen else seen.update(t) or True, combinations(Z_single_signal+Z_single_noise, len(Z_single_signal))))])
 
for inco in incofiles:
        Zinco+=get_metadata(inco,'log_evidence')
Znoise = get_metadata(cofile,'log_noise_evidence')
 
if(opts.outfile is not None):
        out=open(opts.outfile,'w')
 
if(opts.ci):
    B=Zco-Zinco
if (opts.cin):
    B=Zco-logadd(Zinco,Znoise)
if(opts.cin_or_n):
    B=Zco-Z_incoherentORnoise
 
print('%.3f'%(B))
 
if(opts.outfile is not None ):
        print('%.3f'%(B), file=out)
        out.close()