pycbc_generate_hwinj
#!/usr/bin/env python
# Copyright (C) 2015 Christopher M. Biwer
#
# 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 3 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.
import argparse
from glue.ligolw import ilwd
from glue.ligolw import ligolw
from glue.ligolw import lsctables
from glue.ligolw import utils
import logging
import numpy
import pycbc
import pycbc.version
from pycbc import DYN_RANGE_FAC
from pycbc import fft
from pycbc import pnutils
from pycbc import psd as _psd
from pycbc import strain as _strain
from pycbc.detector import Detector
from pycbc.inject import InjectionSet, legacy_approximant_name
from pycbc.filter import make_frequency_series
from pycbc.filter import sigmasq
from pycbc.types import Array, FrequencySeries, TimeSeries, zeros
from pycbc.types.optparse import MultiDetOptionAppendAction, convert_to_process_params_dict
from pycbc.waveform import FilterBank, get_td_waveform, td_approximants, taper_timeseries
import os
import sys
def _empty_row(obj):
"""Create an empty sim_inspiral or sngl_inspiral row where the columns have
default values of 0.0 for a float, 0 for an int, '' for a string. The ilwd
columns have a default where the index is 0.
"""
# check if sim_inspiral or sngl_inspiral
if obj == lsctables.SimInspiral:
row = lsctables.SimInspiral()
cols = lsctables.SimInspiralTable.validcolumns
else:
row = lsctables.SnglInspiral()
cols = lsctables.SnglInspiralTable.validcolumns
# populate columns with default values
for entry in cols.keys():
if cols[entry] in ['real_4','real_8']:
setattr(row,entry,0.)
elif cols[entry] == 'int_4s':
setattr(row,entry,0)
elif cols[entry] == 'lstring':
setattr(row,entry,'')
elif entry == 'process_id':
row.process_id = ilwd.ilwdchar("sim_inspiral:process_id:0")
elif entry == 'simulation_id':
row.simulation_id = ilwd.ilwdchar("sim_inspiral:simulation_id:0")
elif entry == 'event_id':
row.event_id = ilwd.ilwdchar("sngl_inspiral:event_id:0")
else:
raise ValueError("Column %s not recognized." %(entry) )
return row
def pad_timeseries_to_integer_length(timeseries, sample_rate):
''' This function zero pads a time series so that its length is an integer
multiple of the sampling rate.
Padding is adding symmetically to the start and end of the time series.
If the number of samples to pad is odd then the end zero padding will have
one more sample than the start zero padding.
'''
# calculate how many sample points needed to pad to get
# integer second time series
remainder = sample_rate - len(timeseries) % sample_rate
start_pad = int(remainder / 2)
end_pad = int(remainder - start_pad)
# make arrays of zeroes
start_array = numpy.zeros(start_pad)
end_array = numpy.zeros(end_pad)
# pad waveform with arrays of zeroes
initial_array = numpy.concatenate([start_array,timeseries,end_array])
return TimeSeries(initial_array, delta_t=timeseries.delta_t,
epoch=timeseries.start_time, dtype=timeseries.dtype)
# map order integer to a string that can be parsed by lalsimulation
pn_orders = {
'default' : -1,
'zeroPN' : 0,
'onePN' : 2,
'onePointFivePN' : 3,
'twoPN' : 4,
'twoPointFivePN' : 5,
'threePN' : 6,
'threePointFivePN' : 7,
'pseudoFourPN' : 8,
}
# command line usage
parser = argparse.ArgumentParser(
usage=__name__ + ' [--options]',
description="Generates a hardware injection waveform using "
"a time-domain waveform.")
# IFO network options
parser.add_argument('--network-snr', type=float, required=True,
help='The network SNR of the injection.')
# sky location options
parser.add_argument('--ra', type=float, required=True,
help='The right ascension of the injection in radians.')
parser.add_argument('--dec', type=float, required=True,
help='The declination of the injection in radians.')
parser.add_argument('--polarization', type=float, required=True,
help='The polarization of the injection in radians.')
# waveform parameter options
parser.add_argument('--approximant', type=str, required=True,
choices=td_approximants(),
help='Approximant to use for generating waveform.')
parser.add_argument("--order", type=str, default='default',
choices = pn_orders.keys(),
help='The integer half-PN order at which to generate '
'the approximant.')
parser.add_argument('--mass1', type=float, required=True,
help='First mass of the binary in solar masses.')
parser.add_argument('--mass2', type=float, required=True,
help='Second mass of the binary in solar masses.')
parser.add_argument('--inclination', type=float, required=True,
help='Inclination of the binary in radians.')
parser.add_argument('--coa-phase', type=float, default=0.0,
help='Reference orbital phase parameter in radians. '
'Note, this is not the same as the constant '
'frequency-domain phase shift that is maximized '
'over in the standard matched-filter search and '
'which is also commonly called coa-phase.'
'Called phiRef in LALSimulation. '
'Called coa_phase in sim_inspiral tables.')
parser.add_argument('--taper', required=True,
choices=['TAPER_NONE', 'TAPER_START',
'TAPER_END', 'TAPER_STARTEND'],
help='Taper the wavform before FFT.')
parser.add_argument('--waveform-low-frequency-cutoff', type=float,
required=True,
help='Frequency to begin generating the waveform in Hz.')
# waveform spin parameter options
parser.add_argument('--spin1z', type=float, default=0.0,
help='(optional) Spin in z direction for mass1.')
parser.add_argument('--spin1y', type=float, default=0.0,
help='(optional) Spin in y direction for mass1.')
parser.add_argument('--spin1x', type=float, default=0.0,
help='(optional) Spin in x direction for mass1.')
parser.add_argument('--spin2z', type=float, default=0.0,
help='(optional) Spin in z direction for mass2.')
parser.add_argument('--spin2y', type=float, default=0.0,
help='(optional) Spin in y direction for mass2.')
parser.add_argument('--spin2x', type=float, default=0.0,
help='(optional) Spin in x direction for mass2.')
# tidal options
parser.add_argument('--lambda1', type=float, default=None,
help='(optional) Tidal lambda term for mass1.'
'WARNING: Giving this option will produce an XML '
'file containing a lambda1 column. This file will '
'not be readable by default methods.')
parser.add_argument('--lambda2', type=float, default=None,
help='(optional) Tidal lambda term for mass2. '
'WARNING: Giving this option will produce an XML '
'file containing a lambda2 column. This file will '
'not be readable by default methods.')
parser.add_argument('--dquad-mon1', type=float, default=None,
help='(optional) Tidal self-spin term for mass1, '
'for BHs this is 0 (its the deformation relative to '
'Kerr. '
'WARNING: Giving this option will produce an XML '
'file containing a dquad_mon1 column. This file will '
'not be readable by default methods.')
parser.add_argument('--dquad-mon2', type=float, default=None,
help='(optional) Tidal self-spin term for mass2, '
'for BHs this is 0 (its the deformation relative to '
'Kerr. '
'WARNING: Giving this option will produce an XML '
'file containing a dquad_mon2 column. This file will '
'not be readable by default methods.')
# Use this for NR injections
parser.add_argument('--numrel-data', type=str, default='',
help="Location of NR data file if using NR injections.")
# end time options
parser.add_argument('--geocentric-end-time', type=float, required=True,
help='The geocentric GPS end time of the injection.')
# data conditioning options
parser.add_argument('--low-frequency-cutoff', type=float, required=True,
help='Frequency to begin generating the PSD in Hz. This '
'is the start frequency of the SNR calculation.')
parser.add_argument('--high-frequency-cutoff', type=float,
help='(optional) Upper frequency to terminate the SNR '
'calculation. Default will be Nyquist frequency, '
'ie. int(sample_rate/2).')
# output options
parser.add_argument("--tag", type=str, default='hwinjcbc',
help="Prefix added to output filenames.")
parser.add_argument("--instruments", nargs="+", type=str, required=True,
help="List of instruments to analyze.")
# add option groups
fft.insert_fft_option_group(parser)
_strain.insert_strain_option_group_multi_ifo(parser)
_psd.insert_psd_option_group_multi_ifo(parser)
# parse command line
opts = parser.parse_args()
# verify options are sane if using strain options
if opts.psd_estimation:
_strain.verify_strain_options_multi_ifo(opts, parser, opts.instruments)
if not opts.psd_estimation and (opts.frame_files or opts.frame_type
or opts.frame_cache or opts.fake_strain):
raise KeyError("Must use --psd-estimation with frame options"
"(--frame-files, --frame-type, --frame-cache, "
"and --fake-strain).")
# setup log
logging_level = logging.DEBUG
logging.basicConfig(format='%(asctime)s : %(message)s', level=logging_level)
# check that sample rates are the same
for ifo in opts.instruments:
if opts.sample_rate[ifo] != opts.sample_rate[opts.instruments[0]]:
logging.warn('Sample rates must be equal for all IFOs.')
sys.exit()
sample_rate = opts.sample_rate[opts.instruments[0]]
# set upper frequency cutoff if not given
if opts.high_frequency_cutoff:
f_high = opts.high_frequency_cutoff
else:
f_high = int(sample_rate / 2)
# check that frame types are not lists
if opts.frame_type:
for key,value in opts.frame_type.items():
if type(opts.frame_type[key]) == list:
opts.frame_type[key] = value[0]
# set an initial distance to generate waveform
distance = 40.0
# set network SNR to 0.0
network_snr = 0.0
# create output XML file
logging.info('Creating XML file')
outdoc = ligolw.Document()
outdoc.appendChild(ligolw.LIGO_LW())
# put opts into a dict for the process table
opts_dict = convert_to_process_params_dict(opts)
# create process table
proc_id = utils.process.register_to_xmldoc(
outdoc, sys.argv[0], opts_dict,
comment="", ifos=[''.join(opts.instruments)],
version=pycbc.version.git_hash,
cvs_repository='pycbc/'+pycbc.version.git_branch,
cvs_entry_time=pycbc.version.date).process_id
# create sim_inspiral row for injection
# and populate non-IFO-specific columns in XML output file
# If using tidal terms some hacking is currently needed. Hopefully this can
# be resolved in the future by using HDF injection files!
if opts.lambda1 is not None:
lsctables.SimInspiralTable.validcolumns['lambda1'] = 'real_4'
if opts.lambda2 is not None:
lsctables.SimInspiralTable.validcolumns['lambda2'] = 'real_4'
if opts.dquad_mon1 is not None:
lsctables.SimInspiralTable.validcolumns['dquad_mon1'] = 'real_4'
if opts.dquad_mon2 is not None:
lsctables.SimInspiralTable.validcolumns['dquad_mon2'] = 'real_4'
# You'd think that would it to redefine the table columns, but wait, it gets
# worse!
class SimInspiralNew(lsctables.SimInspiral):
__slots__ = lsctables.SimInspiralTable.validcolumns.keys()
lsctables.SimInspiral = SimInspiralNew
lsctables.SimInspiralTable.RowType = SimInspiralNew
# create sim_inspiral table
sim_table = lsctables.New(lsctables.SimInspiralTable,
columns=lsctables.SimInspiralTable.validcolumns)
outdoc.childNodes[0].appendChild(sim_table)
sim = _empty_row(lsctables.SimInspiral)
sim.f_lower = opts.waveform_low_frequency_cutoff
sim.geocent_end_time = int(opts.geocentric_end_time)
sim.geocent_end_time_ns = int(opts.geocentric_end_time % 1 * 1e9)
sim.inclination = opts.inclination
sim.coa_phase = opts.coa_phase
sim.latitude = opts.dec
sim.longitude = opts.ra
sim.mass1 = opts.mass1
sim.mass2 = opts.mass2
sim.mchirp, sim.eta = pnutils.mass1_mass2_to_mchirp_eta(sim.mass1, sim.mass2)
sim.spin1z = opts.spin1z
sim.spin1y = opts.spin1y
sim.spin1x = opts.spin1x
sim.spin2z = opts.spin2z
sim.spin2y = opts.spin2y
sim.spin2x = opts.spin2x
if opts.lambda1 is not None:
sim.lambda1 = opts.lambda1
if opts.lambda2 is not None:
sim.lambda2 = opts.lambda2
if opts.dquad_mon1 is not None:
sim.dquad_mon1 = opts.dquad_mon1
if opts.dquad_mon2 is not None:
sim.dquad_mon2 = opts.dquad_mon2
sim.polarization = opts.polarization
sim.taper = opts.taper
sim.distance = distance
sim.numrel_data = opts.numrel_data
# construct waveform string that can be parsed by lalsimulation
waveform_string = opts.approximant
if not pn_orders[opts.order] == -1:
waveform_string += opts.order
sim.waveform = waveform_string
name, phase_order = legacy_approximant_name(sim.waveform)
# create sngl_inspiral table
sngl_table = lsctables.New(lsctables.SnglInspiralTable,
columns=lsctables.SnglInspiralTable.validcolumns)
outdoc.childNodes[0].appendChild(sngl_table)
# create sngl_inspiral row for injection
# and populate non-IFO-specific columns in XML output file
sngl = _empty_row(lsctables.SnglInspiral)
sngl.mass1 = opts.mass1
sngl.mass2 = opts.mass2
sngl.mchirp, sngl.eta = pnutils.mass1_mass2_to_mchirp_eta(sngl.mass1,
sngl.mass2)
sngl.mtotal = sngl.mass1 + sngl.mass2
sngl.spin1z = opts.spin1z
sngl.spin1y = opts.spin1y
sngl.spin1x = opts.spin1x
sngl.spin2z = opts.spin2z
sngl.spin2y = opts.spin2y
sngl.spin2x = opts.spin2x
# generate waveform
logging.info('Generating waveform at %.3fMpc beginning at %.3fHz for '
'SNR calculation', sim.distance, opts.waveform_low_frequency_cutoff)
h_plus, h_cross = get_td_waveform(sim, approximant=name,
phase_order=phase_order,
f_lower=opts.waveform_low_frequency_cutoff,
delta_t=1.0 / sample_rate)
# zero pad polarizations to get integer second time series
h_plus = pad_timeseries_to_integer_length(h_plus, sample_rate)
h_cross = pad_timeseries_to_integer_length(h_cross, sample_rate)
# get strain time series
# strain is used to estimate a PSD so if user supplies PSD
# then genreate a zeroNoise TimeSeries to get length, delta_f, etc.
if not opts.psd_estimation:
opts.fake_strain = "zeroNoise"
strain_dict = _strain.from_cli_multi_ifos(opts, opts.instruments,
dyn_range_fac=DYN_RANGE_FAC)
# organize options for multi-IFO PSD
# if not generating strain then set those related options to None
stilde_dict = {}
length_dict = {}
delta_f_dict = {}
low_frequency_cutoff_dict = {}
for ifo in opts.instruments:
stilde_dict[ifo] = strain_dict[ifo].to_frequencyseries()
length_dict[ifo] = len(stilde_dict[ifo])
delta_f_dict[ifo] = stilde_dict[ifo].delta_f
low_frequency_cutoff_dict[ifo] = opts.low_frequency_cutoff
# get PSD
logging.info('Generating PSDs')
psd_dict = _psd.from_cli_multi_ifos(
opts, length_dict, delta_f_dict,
low_frequency_cutoff_dict, opts.instruments,
strain_dict=strain_dict,
dyn_range_factor=DYN_RANGE_FAC,
precision="double")
# loop over IFOs to calculate sigma
for ifo in opts.instruments:
# get Detector instance for IFO
det = Detector(ifo)
# get time delay to detector from center of the Earth
time_delay = det.time_delay_from_earth_center(sim.longitude, sim.latitude,
sim.geocent_end_time)
end_time = sim.geocent_end_time + time_delay
# get antenna pattern
f_plus, f_cross = det.antenna_pattern(sim.longitude, sim.latitude,
sim.polarization,
sim.geocent_end_time)
# calculate strain
logging.info('Calculating strain for %s', ifo)
strain = f_plus * h_plus + f_cross * h_cross
# taper waveform
logging.info('Tapering strain for %s', ifo)
strain = taper_timeseries(strain, tapermethod=sim.taper)
# FFT strain
logging.info('FFT strain for %s', ifo)
strain_tilde = make_frequency_series(strain)
# interpolate PSD to waveform delta_f
if psd_dict[ifo].delta_f != strain_tilde.delta_f:
logging.info('Interpolating PSD for %s from %fHz to %fHz',
ifo, psd_dict[ifo].delta_f, strain_tilde.delta_f)
psd_dict[ifo] = _psd.interpolate(
psd_dict[ifo], strain_tilde.delta_f)
# calculate sigma-squared SNR
logging.info('Calculating sigma for %s', ifo)
sigma_squared = sigmasq(
DYN_RANGE_FAC * strain_tilde,
psd=psd_dict[ifo],
low_frequency_cutoff=opts.low_frequency_cutoff,
high_frequency_cutoff=f_high)
logging.info('Sigma integrated from %.3f to %.3fHz for %s is %.3f',
opts.low_frequency_cutoff, f_high, ifo,
numpy.sqrt(sigma_squared))
# populate IFO end time columns
setattr(sim, ifo[0].lower()+'_end_time', int(end_time))
setattr(sim, ifo[0].lower()+'_end_time_ns', int(end_time % 1 * 1e9))
# populate IFO distance columns
eff_distance = det.effective_distance(sim.distance,
sim.longitude, sim.latitude,
sim.polarization,
sim.geocent_end_time,
sim.inclination)
setattr(sim, 'eff_dist_'+ifo[0].lower(), eff_distance)
# populate IFO end time columns
sngl.end_time = int(end_time)
sngl.end_time_ns = int(end_time % 1 * 1e9)
# include sigma in network SNR calculation
network_snr += sigma_squared
# distance scaling factor to get target snr
network_snr = numpy.sqrt(network_snr)
scale = network_snr / opts.network_snr
sim.distance = scale*sim.distance
for ifo in opts.instruments:
attrname='eff_dist_'+ifo[0].lower()
effdist=getattr(sim,attrname)
setattr(sim,attrname,effdist*scale)
# generate waveform
logging.info('Generating waveform at %.3fMpc beginning at %.3fHz for '
'SNR calculation', sim.distance, opts.waveform_low_frequency_cutoff)
h_plus, h_cross = get_td_waveform(sim, approximant=name,
phase_order=phase_order,
f_lower=opts.waveform_low_frequency_cutoff,
delta_t=1.0 / sample_rate)
# zero pad polarizations to get integer second time series
h_plus = pad_timeseries_to_integer_length(h_plus, sample_rate)
h_cross = pad_timeseries_to_integer_length(h_cross, sample_rate)
# figure out length of time series to inject waveform into
logging.info('Calculating number of sample points in output file')
h_plus, _ = get_td_waveform(sim, approximant=name, phase_order=phase_order,
delta_t=1.0/sample_rate)
pad_seconds = 5
template_duration_seconds = int( len(h_plus) / sample_rate ) + 1
start_time = int(sim.geocent_end_time) - template_duration_seconds - pad_seconds
end_time = int(sim.geocent_end_time) + 1 + pad_seconds
num_samples = (end_time - start_time) * sample_rate
# append rows to XML tables
sim_table.append(sim)
sngl_table.append(sngl)
# construct filenames prefix
prefix = opts.tag + '_' + str(start_time)
# save XML output file if it does not exist
logging.info('Writing XML file')
xml_filename = prefix + '.xml.gz'
if os.path.exists(xml_filename):
logging.warn('Filename %s already exists and will not be overwritten',
xml_filename)
sys.exit()
else:
utils.write_filename(outdoc, xml_filename, gz=xml_filename.endswith('gz'))
# loop over IFOs for writing waveforms to file
for ifo in opts.instruments:
# create a time series of zeroes to inject waveform into
initial_array = numpy.zeros(num_samples, dtype=strain.dtype)
output = TimeSeries(initial_array, delta_t=1.0 / sample_rate,
epoch=start_time, dtype=strain.dtype)
# inject waveform
logging.info('Injecting %s waveform into timeseries of zeroes', ifo)
injections = InjectionSet(xml_filename)
injections.apply(output, ifo)
# set output filename
txt_filename = prefix + '_' + ifo + '.txt'
# check if filename exists
if os.path.exists(txt_filename):
logging.warn('Filename %s already exists and will not be overwritten',
txt_filename)
sys.exit()
# save waveform as single-column ASCII for awgstream to use
logging.info('Writing strain for %s', ifo)
numpy.savetxt(txt_filename, output)
# finish
logging.info('Done')
