porting cosmic string ranking codes to gstlal-burst

gstlal-burst/python/string/string_extrinsics.py

+# Copyright (C) 2016,2017  Kipp Cannon
+# Copyright (C) 2011--2014  Kipp Cannon, Chad Hanna, Drew Keppel
+# Copyright (C) 2013  Jacob Peoples
+#
+# This program is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation; either version 2 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+
+#
+# =============================================================================
+#
+#                                   Preamble
+#
+# =============================================================================
+#
+
+
+import numpy
+
+from ligo.lw import ligolw
+from ligo.lw import array as ligolw_array
+from glue.text_progress_bar import ProgressBar
+from gstlal import stats as gstlalstats
+from lal import rate
+
+
+#
+# =============================================================================
+#
+#                               SNR, \chi^2 PDF
+#
+# =============================================================================
+#
+
+
+class NumeratorSNRCHIPDF(rate.BinnedLnPDF):
+	"""
+	Reports ln P(chi^2/rho^2 | rho, signal)
+	"""
+	# NOTE:  by happy coincidence numpy's broadcasting rules allow the
+	# inherited .at_centres() method to be used as-is
+	def __init__(self, *args, **kwargs):
+		super(rate.BinnedLnPDF, self).__init__(*args, **kwargs)
+		self.volume = self.bins[1].upper() - self.bins[1].lower()
+		# FIXME: instead of .shape and repeat() use .broadcast_to()
+		# when we can rely on numpy >= 1.8
+		#self.volume = numpy.broadcast_to(self.volume, self.bins.shape)
+		self.volume.shape = (1, len(self.volume))
+		self.volume = numpy.repeat(self.volume, len(self.bins[0]), 0)
+		self.norm = numpy.zeros((len(self.bins[0]), 1))
+
+	def __getitem__(self, coords):
+		return numpy.log(super(rate.BinnedLnPDF, self).__getitem__(coords)) - self.norm[self.bins(*coords)[0]]
+
+	def marginalize(self, *args, **kwargs):
+		raise NotImplementedError
+
+	def __iadd__(self, other):
+		# the total count is meaningless, it serves only to set the
+		# scale by which the density estimation kernel chooses its
+		# size, so we preserve the count across this operation.  if
+		# the two arguments have different counts, use the
+		# geometric mean unless one of the two is 0 in which case
+		# don't screw with the total count
+		self_count, other_count = self.array.sum(), other.array.sum()
+		super(rate.BinnedLnPDF, self).__iadd__(other)
+		if self_count and other_count:
+			self.array *= numpy.exp((numpy.log(self_count) + numpy.log(other_count)) / 2.) / self.array.sum()
+		self.norm = numpy.log(numpy.exp(self.norm) + numpy.exp(other.norm))
+		return self
+
+	def normalize(self):
+		# replace the vector with a new one so that we don't
+		# interfere with any copies that might have been made
+		with numpy.errstate(divide = "ignore"):
+			self.norm = numpy.log(self.array.sum(axis = 1))
+		self.norm.shape = (len(self.norm), 1)
+
+	@staticmethod
+	def add_signal_model(lnpdf, n, prefactors_range, df = 100, inv_snr_pow = 4., snr_min = 3.5, progressbar = None):
+		if df <= 0.:
+			raise ValueError("require df >= 0: %s" % repr(df))
+		pfs = numpy.linspace(prefactors_range[0], prefactors_range[1], 100)
+		if progressbar is not None:
+			progressbar.max = len(pfs)
+
+		# FIXME:  except for the low-SNR cut, the slicing is done
+		# to work around various overflow and loss-of-precision
+		# issues in the extreme parts of the domain of definition.
+		# it would be nice to identify the causes of these and
+		# either fix them or ignore them one-by-one with a comment
+		# explaining why it's OK to ignore the ones being ignored.
+		# for example, computing snrchi2 by exponentiating the sum
+		# of the logs of the terms might permit its evaluation
+		# everywhere on the domain.  can ncx2pdf() be made to work
+		# everywhere?
+		snrindices, rcossindices = lnpdf.bins[snr_min:1e10, 1e-10:1e10]
+		snr, dsnr = lnpdf.bins[0].centres()[snrindices], lnpdf.bins[0].upper()[snrindices] - lnpdf.bins[0].lower()[snrindices]
+		rcoss, drcoss = lnpdf.bins[1].centres()[rcossindices], lnpdf.bins[1].upper()[rcossindices] - lnpdf.bins[1].lower()[rcossindices]
+
+		snr2 = snr**2.
+		snrchi2 = numpy.outer(snr2, rcoss) * df
+
+		arr = numpy.zeros_like(lnpdf.array)
+		for pf in pfs:
+			if progressbar is not None:
+				progressbar.increment()
+			arr[snrindices, rcossindices] += gstlalstats.ncx2pdf(snrchi2, df, numpy.array([pf * snr2]).T)
+
+		# convert to counts by multiplying by bin volume, and also
+		# multiply by an SNR powr law
+		arr[snrindices, rcossindices] *= numpy.outer(dsnr / snr**inv_snr_pow, drcoss)
+
+		# normalize to a total count of n
+		arr *= n / arr.sum()
+
+		# add to lnpdf
+		lnpdf.array += arr
+
+	def to_xml(self, *args, **kwargs):
+		elem = super(rate.BinnedLnPDF, self).to_xml(*args, **kwargs)
+		elem.appendChild(ligolw_array.Array.build("norm", self.norm))
+		return elem
+
+	@classmethod
+	def from_xml(cls, xml, name):
+		xml = cls.get_xml_root(xml, name)
+		self = super(rate.BinnedLnPDF, cls).from_xml(xml, name)
+		self.norm = ligolw_array.get_array(xml, "norm").array
+		return self

gstlal-burst/python/string/stringutils.py

+# Copyright (C) 2009--2018  Kipp Cannon
+#
+# This program is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation; either version 2 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+
+#
+# =============================================================================
+#
+#                                   Preamble
+#
+# =============================================================================
+#
+
+
+from __future__ import print_function
+
+
+try:
+	from fpconst import NegInf
+except ImportError:
+	NegInf = float("-inf")
+import itertools
+import math
+import numpy
+import scipy.stats
+import sys
+
+
+from ligo.lw import ligolw
+from ligo.lw import array as ligolw_array
+from ligo.lw import param as ligolw_param
+from ligo.lw import lsctables
+from ligo.lw import utils as ligolw_utils
+from ligo.lw.utils import process as ligolw_process
+import lal
+from lal import rate
+from ligo.segments import utils as segmentsUtils
+from lalburst import offsetvector
+from lalburst import snglcoinc
+
+from gstlal import string_lr_far
+
+
+__author__ = "Kipp Cannon <kipp.cannon@ligo.org>"
+from .git_version import date as __date__
+from .git_version import version as __version__
+
+
+#
+# =============================================================================
+#
+#                             Likelihood Machinery
+#
+# =============================================================================
+#
+
+
+#
+# Make a look-up table of time-of-arrival triangulators
+#
+
+
+def triangulators(timing_uncertainties):
+	"""
+	Return a dictionary of snglcoinc.TOATriangulator objects
+	initialized for a variety of instrument combinations.
+	timing_uncertainties is a dictionary of instrument->$\\Delta t$
+	pairs.  The return value is a dictionary of (instrument
+	tuple)->TOATrangulator mappings.  The instrument names in each
+	tuple are sorted in alphabetical order, and the triangulators are
+	constructed with the instruments in that order (the the
+	documentation for snglcoinc.TOATriangulator for more information).
+
+	Example:
+
+	>>> x = triangulators({"H1": 0.005, "L1": 0.005, "V1": 0.005})
+
+	constructs a dictionary of triangulators for every combination of
+	two or more instruments that can be constructed from those three.
+
+	The program lalapps_string_plot_binj can be used to measure the
+	timing uncertainties for the instruments in a search.
+	"""
+	allinstruments = sorted(timing_uncertainties.keys())
+
+	triangulators = {}
+	for n in range(2, len(allinstruments) + 1):
+		for instruments in itertools.combinations(allinstruments, n):
+			triangulators[instruments] = snglcoinc.TOATriangulator([lal.cached_detector_by_prefix[instrument].location for instrument in instruments], [timing_uncertainties[instrument] for instrument in instruments])
+
+	return triangulators
+
+
+#
+# A binning for instrument combinations
+#
+# FIXME:  we decided that the coherent and null stream naming convention
+# would look like
+#
+# H1H2:LSC-STRAIN_HPLUS, H1H2:LSC-STRAIN_HNULL
+#
+# and so on.  i.e., the +, x and null streams from a coherent network would
+# be different channels from a single instrument whose name would be the
+# mash-up of the names of the instruments in the network.  that is
+# inconsisntent with the "H1H2+", "H1H2-" shown here, so this needs to be
+# fixed but I don't know how.  maybe it'll go away before it needs to be
+# fixed.
+#
+
+
+class InstrumentBins(rate.HashableBins):
+	"""
+	Example:
+
+	>>> x = InstrumentBins()
+	>>> x[frozenset(("H1", "L1"))]
+	55
+	>>> x.centres()[55]
+	frozenset(['H1', 'L1'])
+	"""
+
+	names = ("E0", "E1", "E2", "E3", "G1", "H1", "H2", "H1H2+", "H1H2-", "L1", "V1")
+
+	def __init__(self, names):
+		super(InstrumentBins, self).__init__(frozenset(combo) for n in range(len(names) + 1) for combo in itertools.combinations(names, n))
+
+	# FIXME:  hack to allow instrument binnings to be included as a
+	# dimension in multi-dimensional PDFs by defining a volume for
+	# them.  investigate more sensible ways to do this.  maybe NDBins
+	# and BinnedDensity should understand the difference between
+	# functional and parametric co-ordinates.
+	def lower(self):
+		return numpy.arange(0, len(self), dtype = "double")
+	def upper(self):
+		return numpy.arange(1, len(self) + 1, dtype = "double")
+
+	xml_bins_name = u"instrumentbins"
+
+# NOTE:  side effect of importing this module:
+rate.NDBins.xml_bins_name_mapping.update({
+	InstrumentBins.xml_bins_name: InstrumentBins,
+	InstrumentBins: InstrumentBins.xml_bins_name
+})
+
+
+#
+# for ranking statistic
+#
+
+def kwarggeniter(d, min_instruments):
+	d = tuple(sorted(d.items()))
+	return map(dict, itertools.chain(*(itertools.combinations(d, i) for i in range(min_instruments, len(d) + 1))))
+
+def kwarggen(snrs, chi2s_over_snr2s, min_instruments):
+	for snrs, chi2s_over_snr2s in zip(
+		kwarggeniter(snrs, min_instruments),
+		kwarggeniter(chi2s_over_snr2s, min_instruments)
+	):
+		yield {
+			"snrs": snrs,
+			"chi2s_over_snr2s": chi2s_over_snr2s,
+		}
+
+
+#
+# Parameter distributions
+#
+
+
+class StringCoincParamsDistributions(snglcoinc.LnLikelihoodRatioMixin):
+	ligo_lw_name_suffix = u"stringcusp_coincparamsdistributions"
+
+	@ligolw_array.use_in
+	@ligolw_param.use_in
+	@lsctables.use_in
+	class LIGOLWContentHandler(ligolw.LIGOLWContentHandler):
+		pass
+
+	def __init__(self, instruments, snr_threshold, min_instruments=2):
+		self.triangulators = triangulators(dict.fromkeys(instruments, 8e-5))
+		self.numerator = string_lr_far.LnSignalDensity(instruments = instruments, min_instruments = min_instruments, snr_threshold = snr_threshold)
+		self.denominator = string_lr_far.LnNoiseDensity(instruments = instruments, min_instruments = min_instruments, snr_threshold = snr_threshold)
+		self.candidates = string_lr_far.LnLRDensity(instruments = instruments, min_instruments = min_instruments, snr_threshold = snr_threshold)
+
+	@property
+	def min_instruments(self):
+		return self.denominator.min_instruments
+	
+	def __call__(self, **kwargs):
+		"""
+		Evaluate the ranking statistic.
+		"""
+		# Full lnL ranking stat, defined to be the largest lnL from
+		# all allowed subsets of trigges. Maximizes over 2+ IFO combos.
+		return max(super(StringCoincParamsDistribution, self).__call__(**kwargs) for kwargs in kwarggen(min_instruments = self.min_instruments, **kwargs))
+
+	def __iadd__(self, other):
+		if type(self) != type(other):
+			raise TypeError(other)
+		if set(self.triangulators.keys()) != set(other.triangulators.keys()):
+			raise ValueError("incompatible instruments")
+		self.numerator += other.numerator
+		self.denominator += other.denominator
+		self.candidates += other.candidates
+		return self
+
+	def copy(self):
+		new = type(self)([])
+		new.triangulators = self.triangulators	# share reference
+		new.numerator = self.numerator.copy()
+		new.denominator = self.denominator.copy()
+		new.candidates = self.candidates.copy()
+		return new
+
+	def coinc_params(self, events, offsetvector):
+		params = {}
+
+		#
+		# check for coincs that have been vetoed entirely
+		#
+
+		if len(events) < 2:
+			return params
+
+		#
+		# Initialize the parameter dictionary, sort the events by
+		# instrument name (the multi-instrument parameters are defined for
+		# the instruments in this order and the triangulators are
+		# constructed this way too), and retrieve the sorted instrument
+		# names
+		#
+
+		events = tuple(sorted(events, key = lambda event: event.ifo))
+		instruments = tuple(event.ifo for event in events)
+
+		return dict(
+			snrs = dict((event.ifo, event.snr) for event in events),
+			chi2s_over_snr2s = dict((event.ifo, event.chisq / event.chisq_dof / event.snr**2.) for event in events),
+		)
+
+	def ln_lr_from_triggers(self, events, offsetvector):
+		return self(**self.coinc_params(events, offsetvector))
+
+	def finish(self):
+		self.numerator.finish()
+		self.denominator.finish()
+		self.candidates.finish()
+		return self
+
+	@classmethod
+	def get_xml_root(cls, xml, name):
+		name = u"%s:%s" % (name, cls.ligo_lw_name_suffix)
+		xml = [elem for elem in xml.getElementsByTagName(ligolw.LIGO_LW.tagName) if elem.hasAttribute(u"Name") and elem.Name == name]
+		if len(xml) != 1:
+			raise ValueError("XML tree must contain exactly one %s element named %s" % (ligolw.LIGO_LW.tagName, name))
+		return xml[0]
+
+	@classmethod
+	def from_xml(cls, xml, name):
+		xml = cls.get_xml_root(xml, name)
+		self = cls([])
+		self.numerator = string_lr_far.LnSignalDensity.from_xml(xml, "numerator")
+		self.denominator = string_lr_far.LnNoiseDensity.from_xml(xml, "denominator")
+		self.candidates = string_lr_far.LnLRDensity.from_xml(xml, "candidates")
+		instruments = self.candidates.instruments
+		self.triangulators = triangulators(dict.fromkeys(instruments, 8e-5))
+		return self
+
+	def to_xml(self, name):
+		xml = ligolw.LIGO_LW({u"Name": u"%s:%s" % (name, self.ligo_lw_name_suffix)})
+		xml.appendChild(self.numerator.to_xml("numerator"))
+		xml.appendChild(self.denominator.to_xml("denominator"))
+		xml.appendChild(self.candidates.to_xml("candidates"))
+		return xml
+
+
+#
+# I/O
+#
+
+
+def load_likelihood_data(filenames, verbose = False):
+	coinc_params = None
+	seglists = None
+	for n, filename in enumerate(filenames, 1):
+		if verbose:
+			print("%d/%d:" % (n, len(filenames)), end=' ', file=sys.stderr)
+		xmldoc = ligolw_utils.load_filename(filename, verbose = verbose, contenthandler = StringCoincParamsDistributions.LIGOLWContentHandler)
+		this_coinc_params = StringCoincParamsDistributions.from_xml(xmldoc, u"string_cusp_likelihood")
+		this_seglists = lsctables.SearchSummaryTable.get_table(xmldoc).get_out_segmentlistdict(lsctables.ProcessTable.get_table(xmldoc).get_ids_by_program(u"lalapps_string_meas_likelihood")).coalesce()
+		xmldoc.unlink()
+		if coinc_params is None:
+			coinc_params = this_coinc_params
+		else:
+			coinc_params += this_coinc_params
+		if seglists is None:
+			seglists = this_seglists
+		else:
+			seglists |= this_seglists
+	return coinc_params, seglists
+
+
+#
+# =============================================================================
+#
+#                                   Livetime
+#
+# =============================================================================
+#
+
+
+def time_slides_livetime(seglists, time_slides, min_instruments, verbose = False, clip = None):
+	"""
+	seglists is a segmentlistdict of times when each of a set of
+	instruments were on, time_slides is a sequence of
+	instrument-->offset dictionaries, each vector of offsets in the
+	sequence is applied to the segmentlists and the total time during
+	which at least min_instruments were on is summed and returned.  If
+	clip is not None, after each offset vector is applied to seglists
+	the result is intersected with clip before computing the livetime.
+	If verbose is True then progress reports are printed to stderr.
+	"""
+	livetime = 0.0
+	seglists = seglists.copy()	# don't modify original
+	N = len(time_slides)
+	if verbose:
+		print("computing the live time for %d time slides:" % N, file=sys.stderr)
+	for n, time_slide in enumerate(time_slides):
+		if verbose:
+			print("\t%.1f%%\r" % (100.0 * n / N), end=' ', file=sys.stderr)
+		seglists.offsets.update(time_slide)
+		if clip is None:
+			livetime += float(abs(segmentsUtils.vote(seglists.values(), min_instruments)))
+		else:
+			livetime += float(abs(segmentsUtils.vote((seglists & clip).values(), min_instruments)))
+	if verbose:
+		print("\t100.0%", file=sys.stderr)
+	return livetime
+
+
+def time_slides_livetime_for_instrument_combo(seglists, time_slides, instruments, verbose = False, clip = None):
+	"""
+	like time_slides_livetime() except computes the time for which
+	exactly the instruments given by the sequence instruments were on
+	(and nothing else).
+	"""
+	livetime = 0.0
+	# segments for instruments that must be on
+	onseglists = seglists.copy(keys = instruments)
+	# segments for instruments that must be off
+	offseglists = seglists.copy(keys = set(seglists) - set(instruments))
+	N = len(time_slides)
+	if verbose:
+		print("computing the live time for %s in %d time slides:" % (", ".join(instruments), N), file=sys.stderr)
+	for n, time_slide in enumerate(time_slides):
+		if verbose:
+			print("\t%.1f%%\r" % (100.0 * n / N), end=' ', file=sys.stderr)
+		onseglists.offsets.update(time_slide)
+		offseglists.offsets.update(time_slide)
+		if clip is None:
+			livetime += float(abs(onseglists.intersection(onseglists.keys()) - offseglists.union(offseglists.keys())))
+		else:
+			livetime += float(abs((onseglists & clip).intersection(onseglists.keys()) - offseglists.union(offseglists.keys())))
+	if verbose:
+		print("\t100.0%", file=sys.stderr)
+	return livetime
+
+
+#
+# =============================================================================
+#
+#                              Database Utilities
+#
+# =============================================================================
+#
+
+
+def create_recovered_ln_likelihood_ratio_table(connection, coinc_def_id):
+	"""
+	Create a temporary table named "recovered_ln_likelihood_ratio"
+	containing two columns:  "simulation_id", the simulation_id of an
+	injection, and "ln_likelihood_ratio", the highest log likelihood
+	ratio at which that injection was recovered by a coincidence of
+	type coinc_def_id.
+	"""
+	cursor = connection.cursor()
+	cursor.execute("""
+CREATE TEMPORARY TABLE recovered_ln_likelihood_ratio (simulation_id TEXT PRIMARY KEY, ln_likelihood_ratio REAL)
+	""")
+	cursor.execute("""
+INSERT OR REPLACE INTO
+	recovered_ln_likelihood_ratio
+SELECT
+	sim_burst.simulation_id AS simulation_id,
+	MAX(coinc_event.likelihood) AS ln_likelihood_ratio
+FROM
+	sim_burst
+	JOIN coinc_event_map AS a ON (
+		a.table_name == "sim_burst"
+		AND a.event_id == sim_burst.simulation_id
+	)
+	JOIN coinc_event_map AS b ON (
+		b.coinc_event_id == a.coinc_event_id
+	)
+	JOIN coinc_event ON (
+		b.table_name == "coinc_event"
+		AND b.event_id == coinc_event.coinc_event_id
+	)
+WHERE
+	coinc_event.coinc_def_id == ?
+GROUP BY
+	sim_burst.simulation_id
+	""", (coinc_def_id,))
+	cursor.close()
+
+
+def create_sim_burst_best_string_sngl_map(connection, coinc_def_id):
+	"""
+	Construct a sim_burst --> best matching coinc_event mapping.
+	"""
+	connection.cursor().execute("""
+CREATE TEMPORARY TABLE
+	sim_burst_best_string_sngl_map
+AS
+	SELECT
+		sim_burst.simulation_id AS simulation_id,
+		(
+			SELECT
+				sngl_burst.event_id
+			FROM
+				coinc_event_map AS a
+				JOIN coinc_event_map AS b ON (
+					b.coinc_event_id == a.coinc_event_id
+				)
+				JOIN coinc_event ON (
+					coinc_event.coinc_event_id == a.coinc_event_id
+				)
+				JOIN sngl_burst ON (
+					b.table_name == 'sngl_burst'
+					AND b.event_id == sngl_burst.event_id