lalsuite 7.26.2.dev20251206__cp312-cp312-manylinux_2_28_x86_64.whl

lalsuite-7.26.2.dev20251206.data/scripts/lalapps_string_apply_vetoes

@@ -0,0 +1,171 @@
+#!python
+#
+# Copyright (C) 2010  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
+
+
+from optparse import OptionParser
+import sqlite3
+import sys
+
+
+from igwn_ligolw import dbtables
+from igwn_ligolw.utils import segments as ligolwsegments
+from lalburst import git_version
+
+
+__author__ = "Kipp Cannon <kipp.cannon@ligo.org>"
+__version__ = "git id %s" % git_version.id
+__date__ = git_version.date
+
+
+#
+# =============================================================================
+#
+#                                 Command Line
+#
+# =============================================================================
+#
+
+
+def parse_command_line():
+	parser = OptionParser(
+		version = "Name: %%prog\n%s" % git_version.verbose_msg,
+		usage = "%prog [options] [filename ...]",
+		description = "%prog constructs or clears and then populates the string_vetoed_sngl table providing a list of the sngl_burst event_ids of vetoed triggers.  This table is used by other post-processing tools like lalapps_string_meas_likelihood to determine which triggers have been vetoed and which haven't."
+	)
+	parser.add_option("-t", "--tmp-space", metavar = "path", help = "Path to a directory suitable for use as a work area while manipulating the database file.  The database file will be worked on in this directory, and then moved to the final location when complete.  This option is intended to improve performance when running in a networked environment, where there might be a local disk with higher bandwidth than is available to the filesystem on which the final output will reside.")
+	parser.add_option("-n", "--vetoes-name", metavar = "name", default = "vetoes", help = "Set the name of the segment lists to use as vetoes (default = \"vetoes\").")
+	parser.add_option("-v", "--verbose", action = "store_true", help = "Be verbose.")
+	options, filenames = parser.parse_args()
+
+	if not filenames:
+		raise ValueError("no input files!")
+
+	return options, filenames
+
+
+#
+# =============================================================================
+#
+#                                     Main
+#
+# =============================================================================
+#
+
+
+#
+# Command line.
+#
+
+
+options, filenames = parse_command_line()
+
+
+#
+# Iterate over files
+#
+
+
+def create_string_sngl_is_vetoed_function(connection, veto_segments_name = None):
+	"""
+	Creates a function named string_sngl_is_vetoed in the database at
+	connection.  The function accepts three parameters --- the
+	instrument name, and the integer and integer nanoseconds components
+	of a time --- and returns true if the instrument is vetoed at that
+	time or false otherwise.  veto_segments_name sets the name of the
+	segment lists used to define the vetoes.
+
+	If veto_segments_name is None then a no-op function is created that
+	always returns False.
+
+	Note:  this funtion requires igwn_ligolw.dbtables and
+	igwn_ligolw.utils.segments to be imported as dbtables and
+	ligolwsegments respectively.
+	"""
+	if veto_segments_name is None:
+		connection.create_function("string_sngl_is_vetoed", 3, lambda instrument, peak_time, peak_time_ns: False)
+		return
+	xmldoc = dbtables.get_xml(connection)
+	seglists = ligolwsegments.segmenttable_get_by_name(xmldoc, options.vetoes_name).coalesce()
+	xmldoc.unlink()
+	def is_vetoed(instrument, peak_time, peak_time_ns, seglists = seglists):
+		return instrument in seglists and dbtables.lsctables.LIGOTimeGPS(peak_time, peak_time_ns) in seglists[instrument]
+	connection.create_function("string_sngl_is_vetoed", 3, is_vetoed)
+
+
+for n, filename in enumerate(filenames):
+	#
+	# Open the database file.
+	#
+
+	if options.verbose:
+		print("%d/%d: %s" % (n + 1, len(filenames), filename), file=sys.stderr)
+
+	working_filename = dbtables.get_connection_filename(filename, tmp_path = options.tmp_space, verbose = options.verbose)
+	connection = sqlite3.connect(str(working_filename))
+
+	#
+	# Define the is_vetoed() SQL function.
+	#
+
+	create_string_sngl_is_vetoed_function(connection, options.vetoes_name)
+
+	#
+	# (Re)build table.
+	#
+
+	cursor = connection.cursor()
+	cursor.execute("""
+DROP TABLE IF EXISTS string_vetoed_sngl;
+	""")
+	cursor.execute("""
+CREATE TABLE string_vetoed_sngl (event_id TEXT PRIMARY KEY)
+	""")
+	cursor.execute("""
+INSERT OR REPLACE INTO
+	string_vetoed_sngl
+SELECT
+	sngl_burst.event_id AS event_id
+FROM
+	sngl_burst
+WHERE
+	string_sngl_is_vetoed(sngl_burst.ifo, sngl_burst.peak_time, sngl_burst.peak_time_ns)
+	""")
+	cursor.close()
+
+	#
+	# Clean up.
+
+	connection.close()
+	dbtables.discard_connection_filename(filename, working_filename, verbose = options.verbose)
+
+
+#
+# Done.
+#

lalsuite-7.26.2.dev20251206.data/scripts/lalapps_string_calc_likelihood

@@ -0,0 +1,172 @@
+#!python
+#
+# Copyright (C) 2010  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
+
+
+from optparse import OptionParser
+import sqlite3
+import sys
+
+
+from igwn_ligolw import dbtables
+from lal.utils import CacheEntry
+from lalburst import git_version
+from lalburst import calc_likelihood
+from lalburst import SnglBurstUtils
+from lalburst import stringutils
+
+
+__author__ = "Kipp Cannon <kipp.cannon@ligo.org>"
+__version__ = "git id %s" % git_version.id
+__date__ = git_version.date
+
+
+#
+# =============================================================================
+#
+#                                 Command Line
+#
+# =============================================================================
+#
+
+
+def parse_command_line():
+	parser = OptionParser(
+		version = "Name: %%prog\n%s" % git_version.verbose_msg
+	)
+	parser.add_option("-c", "--input-cache", metavar = "filename", help = "Also process the files named in this LAL cache.  See lalapps_path2cache for information on how to produce a LAL cache file.")
+	parser.add_option("-l", "--likelihood-file", metavar = "filename", action = "append", help = "Set the name of the likelihood ratio data file to use.  Can be given more than once.")
+	parser.add_option("--likelihood-cache", metavar = "filename", help = "Also load the likelihood ratio data files listsed in this LAL cache.  See lalapps_path2cache for information on how to produce a LAL cache file.")
+	parser.add_option("-t", "--tmp-space", metavar = "path", help = "Path to a directory suitable for use as a work area while manipulating the database file.  The database file will be worked on in this directory, and then moved to the final location when complete.  This option is intended to improve performance when running in a networked environment, where there might be a local disk with higher bandwidth than is available to the filesystem on which the final output will reside.")
+	parser.add_option("--vetoes-name", metavar = "name", help = "Set the name of the segment lists to use as vetoes (default = do not apply vetoes).")
+	parser.add_option("-v", "--verbose", action = "store_true", help = "Be verbose.")
+	options, filenames = parser.parse_args()
+
+	options.likelihood_filenames = []
+	if options.likelihood_file is not None:
+		options.likelihood_filenames += options.likelihood_file
+	if options.likelihood_cache is not None:
+		options.likelihood_filenames += [CacheEntry(line).path for line in open(options.likelihood_cache)]
+	if not options.likelihood_filenames:
+		raise ValueError("no ranking statistic likelihood data files specified")
+
+	if options.input_cache:
+		filenames += [CacheEntry(line).path for line in open(options.input_cache)]
+	if not filenames:
+		raise ValueError("no candidate databases specified")
+
+	return options, filenames
+
+
+#
+# =============================================================================
+#
+#                                     Main
+#
+# =============================================================================
+#
+
+
+#
+# command line
+#
+
+
+options, filenames = parse_command_line()
+
+
+#
+# load likelihood data
+#
+
+
+coincparamsdistributions, likelihood_seglists = stringutils.load_likelihood_data(options.likelihood_filenames, verbose = options.verbose)
+if options.verbose:
+	print("computing event densities ...", file=sys.stderr)
+coincparamsdistributions.finish()
+
+
+#
+# iterate over files
+#
+
+
+for n, filename in enumerate(filenames):
+	#
+	# Open the database file.
+	#
+
+	if options.verbose:
+		print("%d/%d: %s" % (n + 1, len(filenames), filename), file=sys.stderr)
+
+	working_filename = dbtables.get_connection_filename(filename, tmp_path = options.tmp_space, verbose = options.verbose)
+	connection = sqlite3.connect(str(working_filename))
+	if options.tmp_space is not None:
+		dbtables.set_temp_store_directory(connection, options.tmp_space, verbose = options.verbose)
+
+	#
+	# Summarize the database.
+	#
+
+	contents = SnglBurstUtils.CoincDatabase(connection, live_time_program = "StringSearch", search = "StringCusp", veto_segments_name = options.vetoes_name)
+	if options.verbose:
+		SnglBurstUtils.summarize_coinc_database(contents)
+	if not contents.seglists and options.verbose:
+		print("\twarning:  no segments found", file=sys.stderr)
+
+	#
+	# Build triangulators.  The timing uncertainty of +/- 8e-5 s was
+	# measured with lalapps_string_plot_binj and is essentially
+	# identical for H1, H2, L1, and V1.
+	#
+
+	triangulators = stringutils.triangulators(dict.fromkeys(contents.instruments, 8e-5))
+
+	#
+	# Run likelihood ratio calculation.
+	#
+
+	calc_likelihood.assign_likelihood_ratios(
+		connection = contents.connection,
+		coinc_def_id = contents.bb_definer_id,
+		offset_vectors = contents.time_slide_table.as_dict(),
+		vetoseglists = contents.vetoseglists,
+		events_func = lambda cursor, coinc_event_id: calc_likelihood.sngl_burst_events_func(cursor, coinc_event_id, contents.sngl_burst_table.row_from_cols),
+		veto_func = calc_likelihood.sngl_burst_veto_func,
+		ln_likelihood_ratio_func = coincparamsdistributions.ln_lr_from_triggers,
+		verbose = options.verbose
+	)
+
+	#
+	# Clean up.
+	#
+
+	contents.xmldoc.unlink()
+	connection.close()
+	dbtables.put_connection_filename(filename, working_filename, verbose = options.verbose)

lalsuite-7.26.2.dev20251206.data/scripts/lalapps_string_contour_plotter

@@ -0,0 +1,141 @@
+#!python
+#
+# Copyright (C) 2010  Andrew Mergl
+#
+# 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
+#
+# =============================================================================
+#
+
+#
+# This is a Python replacement for the contour_plotter.m MATLAB code
+#
+
+
+import math
+import matplotlib
+matplotlib.rcParams.update({
+	"font.size": 8.0,
+	"axes.titlesize": 10.0,
+	"axes.labelsize": 10.0,
+	"xtick.labelsize": 8.0,
+	"ytick.labelsize": 8.0,
+	"legend.fontsize": 8.0,
+	"figure.dpi": 300,
+	"savefig.dpi": 300,
+	"text.usetex": True
+})
+from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
+from matplotlib.figure import Figure
+
+import numpy
+from optparse import OptionParser
+
+from lalburst import git_version
+
+__author__ = "Andrew Mergl <>"
+__version__ = "git id %s" % git_version.id
+__date__ = git_version.date
+
+
+def parse_command_line():
+    parser = OptionParser(
+        version = "Name: %%prog\n%s" % git_version.verbose_msg
+    )
+    parser.add_option("-v", "--verbose", action = "store_true",
+                      help = "Be verbose.")
+    parser.add_option("-t", "--live-time", dest="livetime",
+                      type = "float",
+                      help = "The total amount of live time in the run")
+
+    options, filenames = parser.parse_args()
+    if options.livetime is None:
+        raise ValueError("No live time specified. Use -t or --live-time.")
+    if filenames is None:
+        raise ValueError("No data file specified.")
+    return options, filenames
+
+
+def cosmo_contour(x, y, avg, min, max, p, neventsUL, filename):
+    fig = Figure()
+    FigureCanvas(fig)
+    fig.set_size_inches(4.5, 4.5 / ((1 + math.sqrt(5)) / 2))
+    axes = fig.add_axes((.12, .15, .98 - .12, .90 - .15))
+    axes.loglog()
+    #axes.contourf(x, y, numpy.log(avg/p), 100, cmap = cm.bone)
+    #axes.contourf(x, y, numpy.log(min/p), 100, cmap = cm.bone)
+    #axes.contourf(x, y, numpy.log(max/p), 100, cmap = cm.bone)
+    axes.contour(x, y, avg/p, [neventsUL], linestyles='solid', colors='r')
+    axes.contour(x, y, min/p, [neventsUL], linestyles='dashed', colors='r')
+    axes.contour(x, y, max/p, [neventsUL], linestyles='dashed', colors='r')
+    axes.set_xlim([x.min(),x.max()])
+    axes.set_ylim([y.min(),y.max()])
+    axes.set_title(r"$P = %g$" % p)
+    axes.set_xlabel(r"$G\mu$")
+    axes.set_ylabel(r"$\epsilon$")
+    fig.savefig(filename)
+
+#main
+
+options, filenames = parse_command_line()
+
+#read cs_gamma file output
+#the columns should be p,index,epsilon,Gmu,gammaAverage,gammaMin,gammaMax
+p, n, eps, gmu, avg, min, max = [], [], [], [], [], [], []
+for line in open(filenames[0], 'r'):
+    line = line.strip()
+    if line[0] in "%#":
+        continue
+    for arr, val in zip((p, n, eps, gmu, avg, min, max), line.split()):
+        arr.append(float(val))
+
+epsindex = dict((b, a) for a, b in enumerate(sorted(set(eps))))
+gmuindex = dict((b, a) for a, b in enumerate(sorted(set(gmu))))
+
+# check for rounding errors producing a wrong count of x and y values
+assert len(epsindex) * len(gmuindex) == len(gmu)
+# program only works if all values in the data file are for the same p and that p is 1
+assert set(p) == set([1])
+
+avgarr = numpy.zeros([len(epsindex), len(gmuindex)], dtype = "double")
+minarr = numpy.zeros([len(epsindex), len(gmuindex)], dtype = "double")
+maxarr = numpy.zeros([len(epsindex), len(gmuindex)], dtype = "double")
+
+for e, g, val in zip(eps, gmu, avg):
+	avgarr[epsindex[e], gmuindex[g]] = val
+for e, g, val in zip(eps, gmu, min):
+	minarr[epsindex[e], gmuindex[g]] = val
+for e, g, val in zip(eps, gmu, max):
+	maxarr[epsindex[e], gmuindex[g]] = val
+
+avgarr *= options.livetime
+minarr *= options.livetime
+maxarr *= options.livetime
+
+numberofeventsUL = -numpy.log(1-0.90)
+
+x = numpy.array(sorted(gmuindex.keys()))
+y = numpy.array(sorted(epsindex.keys()))
+
+cosmo_contour(x, y, avgarr, minarr, maxarr, 1.000, numberofeventsUL, "gmu-eps-p1e+0")
+cosmo_contour(x, y, avgarr, minarr, maxarr, 0.100, numberofeventsUL, "gmu-eps-p1e-1")
+cosmo_contour(x, y, avgarr, minarr, maxarr, 0.010, numberofeventsUL, "gmu-eps-p1e-2")
+cosmo_contour(x, y, avgarr, minarr, maxarr, 0.001, numberofeventsUL, "gmu-eps-p1e-3")

lalsuite-7.26.2.dev20251206.data/scripts/lalapps_string_contour_plotter_largeloops

@@ -0,0 +1,133 @@
+#!python
+#
+# Copyright (C) 2018 Daichi Tsuna
+#
+# 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
+#
+# =============================================================================
+#
+
+#
+# This is a Python replacement for the contour_plotter.m MATLAB code
+# Specific for the "large loop" case, where constraints are drawn on the Gmu-p plane.
+#
+
+
+import matplotlib
+matplotlib.rcParams.update({
+	"font.size": 8.0,
+	"axes.titlesize": 10.0,
+	"axes.labelsize": 10.0,
+	"xtick.labelsize": 8.0,
+	"ytick.labelsize": 8.0,
+	"legend.fontsize": 8.0,
+	"figure.dpi": 300,
+	"savefig.dpi": 300,
+	"text.usetex": True
+})
+from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
+from matplotlib.figure import Figure
+
+import numpy
+from optparse import OptionParser
+
+from lalburst import git_version
+
+__author__ = "Daichi Tsuna <>"
+__version__ = "git id %s" % git_version.id
+__date__ = git_version.date
+
+
+def parse_command_line():
+    parser = OptionParser(
+        version = "Name: %%prog\n%s" % git_version.verbose_msg
+    )
+    parser.add_option("-v", "--verbose", action = "store_true",
+                      help = "Be verbose.")
+    parser.add_option("-t", "--live-time", dest="livetime",
+                      type = "float",
+                      help = "The total amount of live time in the run")
+
+    options, filenames = parser.parse_args()
+    if options.livetime is None:
+        raise ValueError("No live time specified. Use -t or --live-time.")
+    if filenames is None:
+        raise ValueError("No data file specified.")
+    return options, filenames
+
+
+def cosmo_contour(x, y, avg, min, max, neventsUL, filename):
+    fig = Figure()
+    FigureCanvas(fig)
+    fig.set_size_inches(4.5, 4.5)
+    axes = fig.add_axes((.12, .15, .98 - .12, .90 - .15))
+    axes.loglog()
+    axes.contour(x, y, avg, [neventsUL], linestyles='solid', colors='r')
+    axes.contour(x, y, min, [neventsUL], linestyles='dashed', colors='r')
+    axes.contour(x, y, max, [neventsUL], linestyles='dashed', colors='r')
+    axes.set_xlim([x.min(),x.max()])
+    axes.set_ylim([y.min(),y.max()])
+    axes.set_title(r"95\% upper limit")
+    axes.set_xlabel(r"$G\mu$")
+    axes.set_ylabel(r"$p$")
+    fig.savefig(filename)
+
+#main
+
+options, filenames = parse_command_line()
+
+#read cs_gamma file output
+#the columns should be p,Gmu,gammaAverage,gammaMin,gammaMax
+prob, gmu, avg, min, max = [], [], [], [], []
+for line in open(filenames[0], 'r'):
+    line = line.strip()
+    if line[0] in "%#":
+        continue
+    for arr, val in zip((prob, gmu, avg, min, max), line.split()):
+        arr.append(float(val))
+
+gmuindex = dict((b, a) for a, b in enumerate(sorted(set(gmu))))
+pindex = dict((b, a) for a, b in enumerate(sorted(set(prob))))
+
+# check for rounding errors producing a wrong count of x and y values
+assert len(pindex) * len(gmuindex) == len(gmu)
+
+avgarr = numpy.zeros([len(pindex), len(gmuindex)], dtype = "double")
+minarr = numpy.zeros([len(pindex), len(gmuindex)], dtype = "double")
+maxarr = numpy.zeros([len(pindex), len(gmuindex)], dtype = "double")
+
+for p, g, val in zip(prob, gmu, avg):
+	avgarr[pindex[p], gmuindex[g]] = val
+for p, g, val in zip(prob, gmu, min):
+	minarr[pindex[p], gmuindex[g]] = val
+for p, g, val in zip(prob, gmu, max):
+	maxarr[pindex[p], gmuindex[g]] = val
+
+avgarr *= options.livetime
+minarr *= options.livetime
+maxarr *= options.livetime
+
+numberofeventsUL = -numpy.log(1-0.95)
+
+x = numpy.array(sorted(gmuindex.keys()))
+y = numpy.array(sorted(pindex.keys()))
+
+cosmo_contour(x, y, avgarr, minarr, maxarr, numberofeventsUL, "constraint")