def lal_ndebug():
"""Temporarily disable lal error messages, except for memory errors."""
mask = ~(lal.LALERRORBIT | lal.LALWARNINGBIT | lal.LALINFOBIT
| lal.LALTRACEBIT)
old_level = lal.GetDebugLevel()
lal.ClobberDebugLevel(old_level & mask)
try:
yield
finally:
lal.ClobberDebugLevel(old_level)
def main(args=None):
opts = parser().parse_args(args)
import logging
log = logging.getLogger('BAYESTAR')
# BAYESTAR imports.
from .. import omp
from ..io import fits, events
from ..bayestar import localize
# Other imports.
import os
from collections import OrderedDict
import numpy as np
import subprocess
import sys
# Squelch annoying and uninformative LAL log messages.
import lal
lal.ClobberDebugLevel(lal.LALNDEBUG)
log.info('Using %d OpenMP thread(s)', omp.num_threads)
# Read coinc file.
log.info(
'%s:reading input files', ','.join(file.name for file in opts.input))
event_source = events.open(*opts.input, sample=opts.pycbc_sample)
if opts.disable_detector:
event_source = events.detector_disabled.open(
event_source, opts.disable_detector)
mkpath(opts.output)
if opts.condor_submit:
if opts.seed is not None:
raise NotImplementedError(
'--seed does not yet work with --condor-submit')
if opts.coinc_event_id:
raise ValueError(
'must not set --coinc-event-id with --condor-submit')
with subprocess.Popen(['condor_submit'],
# FIXME: use text=True instead in Python >= 3.7
encoding=sys.stdin.encoding,
stdin=subprocess.PIPE) as proc:
f = proc.stdin
print('''
accounting_group = ligo.dev.o3.cbc.pe.bayestar
on_exit_remove = (ExitBySignal == False) && (ExitCode == 0)
on_exit_hold = (ExitBySignal == True) || (ExitCode != 0)
on_exit_hold_reason = (ExitBySignal == True \
? strcat("The job exited with signal ", ExitSignal) \
: strcat("The job exited with code ", ExitCode))
request_memory = 1000 MB
universe = vanilla
getenv = true
executable = /usr/bin/env
JobBatchName = BAYESTAR
environment = "OMP_NUM_THREADS=1"
''', file=f)
print('error =', os.path.join(opts.output, '$(cid).err'), file=f)
print('log =', os.path.join(opts.output, '$(cid).log'), file=f)
print('arguments = "',
*(arg for arg in sys.argv if arg != '--condor-submit'),
'--coinc-event-id $(cid)"', file=f)
print('queue cid in', *event_source, file=f)
sys.exit(proc.returncode)
if opts.coinc_event_id:
event_source = OrderedDict(
(key, event_source[key]) for key in opts.coinc_event_id)
count_sky_maps_failed = 0
# Loop over all sngl_inspiral <-> sngl_inspiral coincs.
for int_coinc_event_id, event in event_source.items():
coinc_event_id = 'coinc_event:coinc_event_id:{}'.format(
int_coinc_event_id)
# Loop over sky localization methods
log.info('%s:computing sky map', coinc_event_id)
if opts.chain_dump:
chain_dump = '%s.hdf5' % int_coinc_event_id
else:
chain_dump = None
try:
sky_map = localize(
event, opts.waveform, opts.f_low,
np.deg2rad(opts.min_inclination),
np.deg2rad(opts.max_inclination),
opts.min_distance,
opts.max_distance, opts.prior_distance_power,
opts.cosmology, mcmc=opts.mcmc, chain_dump=chain_dump,
enable_snr_series=opts.enable_snr_series,
f_high_truncate=opts.f_high_truncate)
sky_map.meta['objid'] = coinc_event_id
except (ArithmeticError, ValueError):
log.exception('%s:sky localization failed', coinc_event_id)
count_sky_maps_failed += 1
if not opts.keep_going:
raise
else:
log.info('%s:saving sky map', coinc_event_id)
filename = '%d.fits' % int_coinc_event_id
fits.write_sky_map(
os.path.join(opts.output, filename), sky_map, nest=True)
if count_sky_maps_failed > 0:
raise RuntimeError("{0} sky map{1} did not converge".format(
count_sky_maps_failed, 's' if count_sky_maps_failed > 1 else ''))
def main(args=None):
opts = parser().parse_args(args)
import logging
log = logging.getLogger('BAYESTAR')
# BAYESTAR imports.
from ..io import events, hdf5
from ..bayestar import condition, condition_prior, ez_emcee, log_post
# Other imports.
from astropy.table import Table
import numpy as np
import os
from collections import OrderedDict
import subprocess
import sys
# Squelch annoying and uniformative LAL log messages.
import lal
lal.ClobberDebugLevel(lal.LALNDEBUG)
# Read coinc file.
log.info('%s:reading input files',
','.join(file.name for file in opts.input))
event_source = events.open(*opts.input, sample=opts.pycbc_sample)
mkpath(opts.output)
if opts.condor_submit:
if opts.seed is not None:
raise NotImplementedError(
'--seed does not yet work with --condor-submit')
if opts.coinc_event_id:
raise ValueError(
'must not set --coinc-event-id with --condor-submit')
with subprocess.Popen(
['condor_submit'],
# FIXME: use text=True instead in Python >= 3.7
encoding=sys.stdin.encoding,
stdin=subprocess.PIPE) as proc:
f = proc.stdin
print('''
accounting_group = ligo.dev.o3.cbc.pe.bayestar
on_exit_remove = (ExitBySignal == False) && (ExitCode == 0)
on_exit_hold = (ExitBySignal == True) || (ExitCode != 0)
on_exit_hold_reason = (ExitBySignal == True \
? strcat("The job exited with signal ", ExitSignal) \
: strcat("The job exited with code ", ExitCode))
request_memory = 1000 MB
universe = vanilla
getenv = true
executable = /usr/bin/env
JobBatchName = BAYESTAR
environment = "OMP_NUM_THREADS=1"
''',
file=f)
print('error =', os.path.join(opts.output, '$(cid).err'), file=f)
print('log =', os.path.join(opts.output, '$(cid).log'), file=f)
print('arguments = "',
*(arg for arg in sys.argv if arg != '--condor-submit'),
'--coinc-event-id $(cid)"',
file=f)
print('queue cid in', *event_source, file=f)
sys.exit(proc.returncode)
if opts.coinc_event_id:
event_source = OrderedDict(
(key, event_source[key]) for key in opts.coinc_event_id)
# Loop over all sngl_inspiral <-> sngl_inspiral coincs.
for int_coinc_event_id, event in event_source.items():
coinc_event_id = 'coinc_event:coinc_event_id:{}'.format(
int_coinc_event_id)
log.info('%s:preparing', coinc_event_id)
epoch, sample_rate, epochs, snrs, responses, locations, horizons = \
condition(event, waveform=opts.waveform, f_low=opts.f_low,
enable_snr_series=opts.enable_snr_series,
f_high_truncate=opts.f_high_truncate)
min_distance, max_distance, prior_distance_power, cosmology = \
condition_prior(horizons, opts.min_distance, opts.max_distance,
opts.prior_distance_power, opts.cosmology)
gmst = lal.GreenwichMeanSiderealTime(epoch)
max_abs_t = 2 * snrs.data.shape[1] / sample_rate
xmin = [0, -1, min_distance, -1, 0, 0]
xmax = [2 * np.pi, 1, max_distance, 1, 2 * np.pi, 2 * max_abs_t]
names = 'ra dec distance inclination twopsi time'.split()
transformed_names = 'ra sin_dec distance u twopsi time'.split()
forward_transforms = [
identity, np.sin, identity, np.cos, identity, identity
]
reverse_transforms = [
identity, np.arcsin, identity, np.arccos, identity, identity
]
kwargs = dict(min_distance=min_distance,
max_distance=max_distance,
prior_distance_power=prior_distance_power,
cosmology=cosmology,
gmst=gmst,
sample_rate=sample_rate,
epochs=epochs,
snrs=snrs,
responses=responses,
locations=locations,
horizons=horizons)
# Fix parameters
for i, key in reversed(list(enumerate(['ra', 'dec', 'distance']))):
value = getattr(opts, key)
if value is None:
continue
if key in ['ra', 'dec']:
# FIXME: figure out a more elegant way to address different
# units in command line arguments and posterior samples
value = np.deg2rad(value)
kwargs[transformed_names[i]] = forward_transforms[i](value)
del (xmin[i], xmax[i], names[i], transformed_names[i],
forward_transforms[i], reverse_transforms[i])
log.info('%s:sampling', coinc_event_id)
# Run MCMC
chain = ez_emcee(log_post, xmin, xmax, kwargs=kwargs, vectorize=True)
# Transform back from sin_dec to dec and cos_inclination to inclination
for i, func in enumerate(reverse_transforms):
chain[:, i] = func(chain[:, i])
# Create Astropy table
chain = Table(rows=chain, names=names)
log.info('%s:saving posterior samples', coinc_event_id)
hdf5.write_samples(chain,
os.path.join(opts.output,
'{}.hdf5'.format(int_coinc_event_id)),
path='/bayestar/posterior_samples',
overwrite=True)
import logging
log = logging.getLogger('BAYESTAR')
# BAYESTAR imports.
from lalinference.io import fits, events
from lalinference.bayestar.sky_map import localize
# Other imports.
import os
from collections import OrderedDict
import sys
import six
# Squelch annoying and uniformative LAL log messages.
import lal
lal.ClobberDebugLevel(lal.LALNDEBUG)
# Read coinc file.
log.info('%s:reading input files', ','.join(file.name for file in opts.input))
event_source = events.open(*opts.input, sample=opts.pycbc_sample)
command.mkpath(opts.output)
if opts.condor_submit:
if opts.coinc_event_id:
raise ValueError('must not set --coinc-event-id with --condor-submit')
cmd = [
'condor_submit', 'accounting_group=ligo.dev.o3.cbc.pe.bayestar',
'on_exit_remove = (ExitBySignal == False) && (ExitCode == 0)',
'on_exit_hold = (ExitBySignal == True) || (ExitCode != 0)',
'on_exit_hold_reason = (ExitBySignal == True ? strcat("The job exited with signal ", ExitSignal) : strcat("The job exited with signal ", ExitCode))',
def main(args=None):
opts = parser().parse_args(args)
import logging
import os
import re
import sys
import tempfile
import urllib.parse
from ..bayestar import localize, rasterize
from ..io import fits
from ..io import events
from .. import omp
from ..util.file import rename
import ligo.gracedb.logging
import ligo.gracedb.rest
import numpy as np
# Squelch annoying and uniformative LAL log messages.
import lal
lal.ClobberDebugLevel(lal.LALNDEBUG)
log = logging.getLogger('BAYESTAR')
log.info('Using %d OpenMP thread(s)', omp.num_threads)
# If no GraceDB IDs were specified on the command line, then read them
# from stdin line-by-line.
graceids = opts.graceid if opts.graceid else iterlines(sys.stdin)
# Fire up a GraceDb client
# FIXME: Mimic the behavior of the GraceDb command line client, where the
# environment variable GRACEDB_SERVICE_URL overrides the default service
# URL. It would be nice to get this behavior into the gracedb package
# itself.
gracedb = ligo.gracedb.rest.GraceDb(
os.environ.get('GRACEDB_SERVICE_URL',
ligo.gracedb.rest.DEFAULT_SERVICE_URL))
# Determine the base URL for event pages.
scheme, netloc, *_ = urllib.parse.urlparse(gracedb._service_url)
base_url = urllib.parse.urlunparse((scheme, netloc, 'events', '', '', ''))
if opts.chain_dump:
chain_dump = re.sub(r'.fits(.gz)?$', r'.hdf5', opts.output)
else:
chain_dump = None
tags = ("sky_loc", )
if not opts.no_tag:
tags += ("lvem", )
event_source = events.gracedb.open(graceids, gracedb)
if opts.disable_detector:
event_source = events.detector_disabled.open(event_source,
opts.disable_detector)
for graceid in event_source.keys():
try:
event = event_source[graceid]
except: # noqa: E722
log.exception('failed to read event %s from GraceDB', graceid)
continue
# Send log messages to GraceDb too
if not opts.dry_run:
handler = ligo.gracedb.logging.GraceDbLogHandler(gracedb, graceid)
handler.setLevel(logging.INFO)
logging.root.addHandler(handler)
# A little bit of Cylon humor
log.info('by your command...')
try:
# perform sky localization
log.info("starting sky localization")
sky_map = localize(event,
opts.waveform,
opts.f_low,
np.deg2rad(opts.min_inclination),
np.deg2rad(opts.max_inclination),
opts.min_distance,
opts.max_distance,
opts.prior_distance_power,
opts.cosmology,
mcmc=opts.mcmc,
chain_dump=chain_dump,
enable_snr_series=opts.enable_snr_series,
f_high_truncate=opts.f_high_truncate)
if not opts.enable_multiresolution:
sky_map = rasterize(sky_map)
sky_map.meta['objid'] = str(graceid)
sky_map.meta['url'] = '{}/{}'.format(base_url, graceid)
log.info("sky localization complete")
# upload FITS file
with tempfile.TemporaryDirectory() as fitsdir:
fitspath = os.path.join(fitsdir, opts.output)
fits.write_sky_map(fitspath, sky_map, nest=True)
log.debug('wrote FITS file: %s', opts.output)
if opts.dry_run:
rename(fitspath, os.path.join('.', opts.output))
else:
gracedb.writeLog(graceid,
"BAYESTAR rapid sky localization ready",
filename=fitspath,
tagname=tags)
log.debug('uploaded FITS file')
except KeyboardInterrupt:
# Produce log message and then exit if we receive SIGINT (ctrl-C).
log.exception("sky localization failed")
raise
except: # noqa: E722
# Produce log message for any otherwise uncaught exception.
# Unless we are in dry-run mode, keep going.
log.exception("sky localization failed")
if opts.dry_run:
# Then re-raise the exception if we are in dry-run mode
raise
if not opts.dry_run:
# Remove old log handler
logging.root.removeHandler(handler)
del handler