def gracedb_sky_map(
coinc_file, psd_file, waveform, f_low, min_distance=None,
max_distance=None, prior_distance_power=None, nside=-1):
# LIGO-LW XML imports.
from . import ligolw
from glue.ligolw import table as ligolw_table
from glue.ligolw import utils as ligolw_utils
from glue.ligolw import lsctables
import lal.series
# Determine approximant, amplitude order, and phase order from command line arguments.
approximant, amplitude_order, phase_order = \
timing.get_approximant_and_orders_from_string(waveform)
# Read input file.
xmldoc, _ = ligolw_utils.load_fileobj(
coinc_file, contenthandler=ligolw.LSCTablesContentHandler)
# Locate the tables that we need.
coinc_inspiral_table = ligolw_table.get_table(xmldoc,
lsctables.CoincInspiralTable.tableName)
coinc_map_table = ligolw_table.get_table(xmldoc,
lsctables.CoincMapTable.tableName)
sngl_inspiral_table = ligolw_table.get_table(xmldoc,
lsctables.SnglInspiralTable.tableName)
# Locate the sngl_inspiral rows that we need.
coinc_inspiral = coinc_inspiral_table[0]
coinc_event_id = coinc_inspiral.coinc_event_id
event_ids = [coinc_map.event_id for coinc_map in coinc_map_table
if coinc_map.coinc_event_id == coinc_event_id]
sngl_inspirals = [(sngl_inspiral for sngl_inspiral in sngl_inspiral_table
if sngl_inspiral.event_id == event_id).next() for event_id in event_ids]
instruments = set(sngl_inspiral.ifo for sngl_inspiral in sngl_inspirals)
# Read PSDs.
if psd_file is None:
psds = None
else:
xmldoc, _ = ligolw_utils.load_fileobj(
psd_file, contenthandler=lal.series.PSDContentHandler)
psds = lal.series.read_psd_xmldoc(xmldoc)
# Rearrange PSDs into the same order as the sngl_inspirals.
psds = [psds[sngl_inspiral.ifo] for sngl_inspiral in sngl_inspirals]
# Interpolate PSDs.
psds = [timing.InterpolatedPSD(filter.abscissa(psd), psd.data.data)
for psd in psds]
# TOA+SNR sky localization
prob, epoch, elapsed_time = ligolw_sky_map(sngl_inspirals, approximant,
amplitude_order, phase_order, f_low,
min_distance, max_distance, prior_distance_power,
nside=nside, psds=psds)
return prob, epoch, elapsed_time, instruments
def gracedb_sky_map(
coinc_file, psd_file, waveform, f_low, min_distance=None,
max_distance=None, prior_distance_power=None,
method="toa_phoa_snr", nside=-1, chain_dump=None,
phase_convention='antifindchirp', f_high_truncate=1.0,
enable_snr_series=False):
# Read input file.
xmldoc, _ = ligolw_utils.load_fileobj(
coinc_file, contenthandler=ligolw.LSCTablesAndSeriesContentHandler)
# Locate the tables that we need.
coinc_inspiral_table = ligolw_table.get_table(xmldoc,
lsctables.CoincInspiralTable.tableName)
coinc_map_table = ligolw_table.get_table(xmldoc,
lsctables.CoincMapTable.tableName)
sngl_inspiral_table = ligolw_table.get_table(xmldoc,
lsctables.SnglInspiralTable.tableName)
# Locate the sngl_inspiral rows that we need.
coinc_inspiral = coinc_inspiral_table[0]
coinc_event_id = coinc_inspiral.coinc_event_id
event_ids = [coinc_map.event_id for coinc_map in coinc_map_table
if coinc_map.coinc_event_id == coinc_event_id]
sngl_inspirals = [next((sngl_inspiral for sngl_inspiral in sngl_inspiral_table
if sngl_inspiral.event_id == event_id)) for event_id in event_ids]
instruments = {sngl_inspiral.ifo for sngl_inspiral in sngl_inspirals}
# Try to load complex SNR time series.
snrs = ligolw.snr_series_by_sngl_inspiral_id_for_xmldoc(xmldoc)
try:
snrs = [snrs[sngl.event_id] for sngl in sngl_inspirals]
except KeyError:
snrs = None
# Read PSDs.
xmldoc, _ = ligolw_utils.load_fileobj(
psd_file, contenthandler=lal.series.PSDContentHandler)
psds = lal.series.read_psd_xmldoc(xmldoc, root_name=None)
# Rearrange PSDs into the same order as the sngl_inspirals.
psds = [psds[sngl_inspiral.ifo] for sngl_inspiral in sngl_inspirals]
# Interpolate PSDs.
psds = [timing.InterpolatedPSD(filter.abscissa(psd), psd.data.data,
f_high_truncate=f_high_truncate)
for psd in psds]
# Run sky localization
prob, epoch, elapsed_time = ligolw_sky_map(sngl_inspirals, waveform, f_low,
min_distance, max_distance, prior_distance_power, method=method,
nside=nside, psds=psds, phase_convention=phase_convention,
chain_dump=chain_dump, snr_series=snrs,
enable_snr_series=enable_snr_series)
return prob, epoch, elapsed_time, instruments
def gracedb_sky_map(
coinc_file, psd_file, waveform, f_low, min_distance=None,
max_distance=None, prior_distance_power=None,
method="toa_phoa_snr", nside=-1, chain_dump=None,
phase_convention='antifindchirp', f_high_truncate=1.0):
# LIGO-LW XML imports.
from . import ligolw
from glue.ligolw import table as ligolw_table
from glue.ligolw import utils as ligolw_utils
from glue.ligolw import lsctables
import lal.series
# Read input file.
xmldoc, _ = ligolw_utils.load_fileobj(
coinc_file, contenthandler=ligolw.LSCTablesContentHandler)
# Locate the tables that we need.
coinc_inspiral_table = ligolw_table.get_table(xmldoc,
lsctables.CoincInspiralTable.tableName)
coinc_map_table = ligolw_table.get_table(xmldoc,
lsctables.CoincMapTable.tableName)
sngl_inspiral_table = ligolw_table.get_table(xmldoc,
lsctables.SnglInspiralTable.tableName)
# Locate the sngl_inspiral rows that we need.
coinc_inspiral = coinc_inspiral_table[0]
coinc_event_id = coinc_inspiral.coinc_event_id
event_ids = [coinc_map.event_id for coinc_map in coinc_map_table
if coinc_map.coinc_event_id == coinc_event_id]
sngl_inspirals = [next((sngl_inspiral for sngl_inspiral in sngl_inspiral_table
if sngl_inspiral.event_id == event_id)) for event_id in event_ids]
instruments = set(sngl_inspiral.ifo for sngl_inspiral in sngl_inspirals)
# Read PSDs.
xmldoc, _ = ligolw_utils.load_fileobj(
psd_file, contenthandler=lal.series.PSDContentHandler)
psds = lal.series.read_psd_xmldoc(xmldoc)
# Rearrange PSDs into the same order as the sngl_inspirals.
psds = [psds[sngl_inspiral.ifo] for sngl_inspiral in sngl_inspirals]
# Interpolate PSDs.
psds = [timing.InterpolatedPSD(filter.abscissa(psd), psd.data.data,
f_high_truncate=f_high_truncate)
for psd in psds]
# Run sky localization
prob, epoch, elapsed_time = ligolw_sky_map(sngl_inspirals, waveform, f_low,
min_distance, max_distance, prior_distance_power, method=method,
nside=nside, psds=psds, phase_convention=phase_convention,
chain_dump=chain_dump)
return prob, epoch, elapsed_time, instruments
def get_segment_definer_comments(xml_file, include_version=True):
"""Returns a dict with the comment column as the value for each segment"""
from glue.ligolw.ligolw import LIGOLWContentHandler as h
lsctables.use_in(h)
# read segment definer table
xmldoc, _ = ligolw_utils.load_fileobj(xml_file,
gz=xml_file.name.endswith(".gz"),
contenthandler=h)
seg_def_table = table.get_table(xmldoc,
lsctables.SegmentDefTable.tableName)
# put comment column into a dict
comment_dict = {}
for seg_def in seg_def_table:
if include_version:
full_channel_name = ':'.join([str(seg_def.ifos),
str(seg_def.name),
str(seg_def.version)])
else:
full_channel_name = ':'.join([str(seg_def.ifos),
str(seg_def.name)])
comment_dict[full_channel_name] = seg_def.comment
return comment_dict
def fromsegmentxml(file, dict=False, id=None):
"""
Read a glue.segments.segmentlist from the file object file containing an
xml segment table.
Arguments:
file : file object
file object for segment xml file
Keyword Arguments:
dict : [ True | False ]
returns a glue.segments.segmentlistdict containing coalesced
glue.segments.segmentlists keyed by seg_def.name for each entry in the
contained segment_def_table. Default False
id : int
returns a glue.segments.segmentlist object containing only those
segments matching the given segment_def_id integer
"""
# load xmldocument and SegmentDefTable and SegmentTables
xmldoc, digest = utils.load_fileobj(file,
gz=file.name.endswith(".gz"),
contenthandler=lsctables.use_in(
ligolw.LIGOLWContentHandler))
seg_def_table = lsctables.SegmentDefTable.get_table(xmldoc)
seg_table = lsctables.SegmentTable.get_table(xmldoc)
if dict:
segs = segments.segmentlistdict()
else:
segs = segments.segmentlist()
seg_id = {}
for seg_def in seg_def_table:
seg_id[int(seg_def.segment_def_id)] = str(seg_def.name)
if dict:
segs[str(seg_def.name)] = segments.segmentlist()
for seg in seg_table:
if dict:
segs[seg_id[int(seg.segment_def_id)]]\
.append(segments.segment(seg.start_time, seg.end_time))
continue
if id and int(seg.segment_def_id) == id:
segs.append(segments.segment(seg.start_time, seg.end_time))
continue
segs.append(segments.segment(seg.start_time, seg.end_time))
if dict:
for seg_name in seg_id.values():
segs[seg_name] = segs[seg_name].coalesce()
else:
segs = segs.coalesce()
xmldoc.unlink()
return segs
def get_segment_definer_comments(xml_file, include_version=True):
"""Returns a dict with the comment column as the value for each segment"""
from glue.ligolw.ligolw import LIGOLWContentHandler as h
lsctables.use_in(h)
# read segment definer table
xmldoc, digest = ligolw_utils.load_fileobj(
xml_file, gz=xml_file.name.endswith(".gz"), contenthandler=h)
seg_def_table = table.get_table(xmldoc,
lsctables.SegmentDefTable.tableName)
# put comment column into a dict
comment_dict = {}
for seg_def in seg_def_table:
if include_version:
full_channel_name = ':'.join(
[str(seg_def.ifos),
str(seg_def.name),
str(seg_def.version)])
else:
full_channel_name = ':'.join(
[str(seg_def.ifos), str(seg_def.name)])
comment_dict[full_channel_name] = seg_def.comment
return comment_dict
def from_veto_definer_file(cls, fp, start=None, end=None, ifo=None):
"""Read a `DataQualityDict` from a LIGO_LW XML VetoDefinerTable.
"""
# open file
if isinstance(fp, (str, unicode)):
fobj = open(fp, 'r')
else:
fobj = fp
xmldoc = ligolw_utils.load_fileobj(fobj)[0]
# read veto definers
veto_def_table = VetoDefTable.get_table(xmldoc)
out = cls()
for row in veto_def_table:
if ifo and row.ifo != ifo:
continue
if start and 0 < row.end_time < start:
continue
elif start:
row.start_time = max(row.start_time, start)
if end and row.start_time > end:
continue
elif end and not row.end_time:
row.end_time = end
elif end:
row.end_time = min(row.end_time, end)
flag = DataQualityFlag.from_veto_def(row)
if flag.name in out:
out[flag.name].valid.extend(flag.valid)
out[flag.name].valid.coalesce()
else:
out[flag.name] = flag
return out
def open_xmldoc(fobj, **kwargs):
"""Try and open an existing LIGO_LW-format file, or create a new Document
Parameters
----------
fobj : `str`, `file`
file path or open file object to read
**kwargs
other keyword arguments to pass to
:func:`~glue.ligolw.utils.load_filename`, or
:func:`~glue.ligolw.utils.load_fileobj` as appropriate
Returns
--------
xmldoc : :class:`~glue.ligolw.ligolw.Document`
either the `Document` as parsed from an existing file, or a new, empty
`Document`
"""
from glue.ligolw.lsctables import use_in
from glue.ligolw.ligolw import (Document, LIGOLWContentHandler)
from glue.ligolw.utils import load_filename, load_fileobj
try: # try and load existing file
if isinstance(fobj, string_types):
kwargs.setdefault('contenthandler', use_in(LIGOLWContentHandler))
return load_filename(fobj, **kwargs)
if isinstance(fobj, FILE_LIKE):
kwargs.setdefault('contenthandler', use_in(LIGOLWContentHandler))
return load_fileobj(fobj, **kwargs)[0]
except (OSError, IOError): # or just create a new Document
return Document()
def get_LVAdata_from_stdin(std_in, as_dict=False):
"""
this function takes an LVAlertTable from sys.stdin and it returns:
host: the machine the payload file was created on
full_path: the full path to (and including) the payload file
general_dir: the directory in gracedb that the output of your code should
be written to
uid: the gracedb unique id associated with the event in the LVAlertTable
"""
doc = utils.load_fileobj(std_in)[0]
lvatable = table.get_table(doc, LVAlertTable.tableName)
file = lvatable[0].file
uid = lvatable[0].uid
data_loc = lvatable[0].temp_data_loc
if as_dict:
return {
"file" : lvatable[0].file,
"uid" : lvatable[0].uid,
"data_loc" : lvatable[0].temp_data_loc,
"description" : lvatable[0].description,
"alert_type" : lvatable[0].alert_type,
}
return file, uid, data_loc
def open_xmldoc(fobj, **kwargs):
"""Try and open an existing LIGO_LW-format file, or create a new Document
Parameters
----------
fobj : `str`, `file`
file path or open file object to read
**kwargs
other keyword arguments to pass to
:func:`~glue.ligolw.utils.load_filename`, or
:func:`~glue.ligolw.utils.load_fileobj` as appropriate
Returns
--------
xmldoc : :class:`~glue.ligolw.ligolw.Document`
either the `Document` as parsed from an existing file, or a new, empty
`Document`
"""
from glue.ligolw.lsctables import use_in
from glue.ligolw.ligolw import (Document, LIGOLWContentHandler)
from glue.ligolw.utils import load_filename, load_fileobj
try: # try and load existing file
if isinstance(fobj, string_types):
kwargs.setdefault('contenthandler', use_in(LIGOLWContentHandler))
return load_filename(fobj, **kwargs)
if isinstance(fobj, FILE_LIKE):
kwargs.setdefault('contenthandler', use_in(LIGOLWContentHandler))
return load_fileobj(fobj, **kwargs)[0]
except (OSError, IOError): # or just create a new Document
return Document()
def from_xml(filename,
length,
delta_f,
low_freq_cutoff,
ifo_string=None,
root_name='psd'):
"""Read an ASCII file containing one-sided ASD or PSD data and generate
a frequency series with the corresponding PSD. The ASD or PSD data is
interpolated in order to match the desired resolution of the
generated frequency series.
Parameters
----------
filename : string
Path to a two-column ASCII file. The first column must contain
the frequency (positive frequencies only) and the second column
must contain the amplitude density OR power spectral density.
length : int
Length of the frequency series in samples.
delta_f : float
Frequency resolution of the frequency series in Herz.
low_freq_cutoff : float
Frequencies below this value are set to zero.
ifo_string : string
Use the PSD in the file's PSD dictionary with this ifo string.
If not given and only one PSD present in the file return that, if not
given and multiple (or zero) PSDs present an exception will be raised.
root_name : string (default='psd')
If given use this as the root name for the PSD XML file. If this means
nothing to you, then it is probably safe to ignore this option.
Returns
-------
psd : FrequencySeries
The generated frequency series.
"""
import lal.series
from glue.ligolw import utils as ligolw_utils
fp = open(filename, 'r')
ct_handler = lal.series.PSDContentHandler
fileobj, _ = ligolw_utils.load_fileobj(fp, contenthandler=ct_handler)
psd_dict = lal.series.read_psd_xmldoc(fileobj, root_name=root_name)
if ifo_string is not None:
psd_freq_series = psd_dict[ifo_string]
else:
if len(psd_dict.keys()) == 1:
psd_freq_series = psd_dict[tuple(psd_dict.keys())[0]]
else:
err_msg = "No ifo string given and input XML file contains not "
err_msg += "exactly one PSD. Specify which PSD you want to use."
raise ValueError(err_msg)
noise_data = psd_freq_series.data.data[:]
freq_data = numpy.arange(len(noise_data)) * psd_freq_series.deltaF
return from_numpy_arrays(freq_data, noise_data, length, delta_f,
low_freq_cutoff)
def fromsegmentxml(file, dict=False, id=None):
"""
Read a glue.segments.segmentlist from the file object file containing an
xml segment table.
Arguments:
file : file object
file object for segment xml file
Keyword Arguments:
dict : [ True | False ]
returns a glue.segments.segmentlistdict containing coalesced
glue.segments.segmentlists keyed by seg_def.name for each entry in the
contained segment_def_table. Default False
id : int
returns a glue.segments.segmentlist object containing only those
segments matching the given segment_def_id integer
"""
# load xmldocument and SegmentDefTable and SegmentTables
xmldoc, digest = utils.load_fileobj(file, gz=file.name.endswith(".gz"))
seg_def_table = table.get_table(xmldoc, lsctables.SegmentDefTable.tableName)
seg_table = table.get_table(xmldoc, lsctables.SegmentTable.tableName)
if dict:
segs = segments.segmentlistdict()
else:
segs = segments.segmentlist()
seg_id = {}
for seg_def in seg_def_table:
seg_id[int(seg_def.segment_def_id)] = str(seg_def.name)
if dict:
segs[str(seg_def.name)] = segments.segmentlist()
for seg in seg_table:
if dict:
segs[seg_id[int(seg.segment_def_id)]]\
.append(segments.segment(seg.start_time, seg.end_time))
continue
if id and int(seg.segment_def_id)==id:
segs.append(segments.segment(seg.start_time, seg.end_time))
continue
segs.append(segments.segment(seg.start_time, seg.end_time))
if dict:
for seg_name in seg_id.values():
segs[seg_name] = segs[seg_name].coalesce()
else:
segs = segs.coalesce()
xmldoc.unlink()
return segs
def test_pick_coinc():
coinc = pick_coinc()
xmldoc, _ = utils.load_fileobj(io.BytesIO(coinc),
contenthandler=ContentHandler)
coinc_inspiral_table = lsctables.CoincInspiralTable.get_table(xmldoc)
assert len(coinc_inspiral_table) == 1
coinc_inspiral, = coinc_inspiral_table
assert coinc_inspiral.get_end() <= mock_now()
def from_xml(filename, length, delta_f, low_freq_cutoff, ifo_string=None,
root_name='psd'):
"""Read an ASCII file containing one-sided ASD or PSD data and generate
a frequency series with the corresponding PSD. The ASD or PSD data is
interpolated in order to match the desired resolution of the
generated frequency series.
Parameters
----------
filename : string
Path to a two-column ASCII file. The first column must contain
the frequency (positive frequencies only) and the second column
must contain the amplitude density OR power spectral density.
length : int
Length of the frequency series in samples.
delta_f : float
Frequency resolution of the frequency series in Herz.
low_freq_cutoff : float
Frequencies below this value are set to zero.
ifo_string : string
Use the PSD in the file's PSD dictionary with this ifo string.
If not given and only one PSD present in the file return that, if not
given and multiple (or zero) PSDs present an exception will be raised.
root_name : string (default='psd')
If given use this as the root name for the PSD XML file. If this means
nothing to you, then it is probably safe to ignore this option.
Returns
-------
psd : FrequencySeries
The generated frequency series.
"""
import lal.series
from glue.ligolw import utils as ligolw_utils
fp = open(filename, 'r')
ct_handler = lal.series.PSDContentHandler
fileobj, _ = ligolw_utils.load_fileobj(fp, contenthandler=ct_handler)
psd_dict = lal.series.read_psd_xmldoc(fileobj, root_name=root_name)
if ifo_string is not None:
psd_freq_series = psd_dict[ifo_string]
else:
if len(psd_dict.keys()) == 1:
psd_freq_series = psd_dict[psd_dict.keys()[0]]
else:
err_msg = "No ifo string given and input XML file contains not "
err_msg += "exactly one PSD. Specify which PSD you want to use."
raise ValueError(err_msg)
noise_data = psd_freq_series.data.data[:]
freq_data = numpy.arange(len(noise_data)) * psd_freq_series.deltaF
return from_numpy_arrays(freq_data, noise_data, length, delta_f,
low_freq_cutoff)
def open_xmldoc(f, **kwargs):
"""Try and open an existing LIGO_LW-format file, or create a new Document
"""
from glue.ligolw.lsctables import use_in
from glue.ligolw.ligolw import Document
from glue.ligolw.utils import load_filename, load_fileobj
use_in(kwargs['contenthandler'])
try: # try and load existing file
if isinstance(f, string_types):
return load_filename(f, **kwargs)
if isinstance(f, FILE_LIKE):
return load_fileobj(f, **kwargs)[0]
except (OSError, IOError): # or just create a new Document
return Document()
def read_ligolw(filepath, table_name, columns=None):
from . import utils
# read table into GLUE LIGO_LW
if columns:
TableType = lsctables.TableByName[table_name]
_oldcols = TableType.loadcolumns
TableType.loadcolumns = columns
if isinstance(filepath, basestring):
xmldoc = ligolw_utils.load_filename(filepath)
else:
xmldoc,_ = ligolw_utils.load_fileobj(filepath)
out = ligolw_table.get_table(xmldoc, table_name)
if columns:
TableType.loadcolumns = _oldcols
return utils.to_table(out, columns=columns)
def _read_xml(f):
if f is None:
doc = filename = None
elif isinstance(f, Element):
doc = f
filename = ''
elif isinstance(f, six.string_types):
doc = load_filename(f, contenthandler=_ContentHandler)
filename = f
else:
doc, _ = load_fileobj(f, contenthandler=_ContentHandler)
try:
filename = f.name
except AttributeError:
filename = ''
return doc, filename
def _read_xml(f):
if f is None:
doc = filename = None
elif isinstance(f, Element):
doc = f
filename = ''
elif isinstance(f, six.string_types):
doc = load_filename(f, contenthandler=_ContentHandler)
filename = f
else:
doc, _ = load_fileobj(f, contenthandler=_ContentHandler)
try:
filename = f.name
except AttributeError:
filename = ''
return doc, filename
def read_ligolw_segments(file, flag=None):
"""Read segments for the given flag from the LIGO_LW XML file
"""
if isinstance(file, basestring):
f = open(file, 'r')
else:
f = file
xmldoc,_ = ligolw_utils.load_fileobj(f)
seg_def_table = ligolw_table.get_table(xmldoc,
lsctables.SegmentDefTable.tableName)
flags = []
dqflag = None
for row in seg_def_table:
name = ':'.join(["".join(row.get_ifos()), row.name])
if row.version:
name += ':%d' % row.version
if flag is None or name == flag:
dqflag = DataQualityFlag(name)
id_ = row.segment_def_id
break
if not dqflag:
raise ValueError("No segment definition found for flag='%s' in "
"file '%s'" % (flag, f.name))
dqflag.valid = SegmentList()
seg_sum_table = ligolw_table.get_table(xmldoc,
lsctables.SegmentSumTable.tableName)
for row in seg_sum_table:
if row.segment_def_id == id_:
try:
dqflag.valid.append(row.get())
except AttributeError:
dqflag.valid.append(Segment(row.start_time, row.end_time))
dqflag.active = SegmentList()
seg_table = ligolw_table.get_table(xmldoc, lsctables.SegmentTable.tableName)
for row in seg_table:
if row.segment_def_id == id_:
try:
dqflag.active.append(row.get())
except AttributeError:
dqflag.active.append(Segment(row.start_time, row.end_time))
if isinstance(file, basestring):
f.close()
return dqflag
def _read_xml(f, fallbackpath=None):
if f is None:
doc = filename = None
elif isinstance(f, Element):
doc = f
filename = ''
elif isinstance(f, str):
try:
doc = load_filename(f, contenthandler=ContentHandler)
except IOError as e:
if e.errno == errno.ENOENT and fallbackpath and \
not os.path.isabs(f):
f = os.path.join(fallbackpath, f)
doc = load_filename(f, contenthandler=ContentHandler)
else:
raise
filename = f
else:
doc, _ = load_fileobj(f, contenthandler=ContentHandler)
try:
filename = f.name
except AttributeError:
filename = ''
return doc, filename
for attr in 'spin1x spin1y spin2x spin2y'.split():
if getattr(sim_inspiral, attr):
raise NotImplementedError('sim_inspiral:{} column is nonzero,'
'but only aligned-spin templates are supported'.format(attr))
return super(TaylorF2RedSpinIntrinsicParams, cls).__new__(cls,
*(getattr(sim_inspiral, field) for field in cls._fields)
)
@property
def chi(self):
return lalsimulation.SimInspiralTaylorF2ReducedSpinComputeChi(
self.mass1, self.mass2, self.spin1z, self.spin2z)
# Read injection file.
xmldoc, _ = ligolw_utils.load_fileobj(
opts.input, contenthandler=ligolw_bayestar.LSCTablesContentHandler)
# Extract simulation table from injection file.
sim_inspiral_table = ligolw_table.get_table(xmldoc,
lsctables.SimInspiralTable.tableName)
# Get just the intrinsic parameters from the sim_inspiral table.
sim_inspiral_intrinsic_params = set(TaylorF2RedSpinIntrinsicParams(sim_inspiral)
for sim_inspiral in sim_inspiral_table)
if opts.low_frequency_cutoff is None:
# Get the low-frequency cutoffs from the sim_inspiral table.
f_lows = set(sim_inspiral.f_lower for sim_inspiral in sim_inspiral_table)
# There can be only one!
try:
def dump_flags(ifos=None, segment_url=None, match=None, unmatch=None,\
latest=False):
"""
Returns the list of all flags defined in the database.
Keyword rguments:
ifo : [ str | list ]
list of ifos to query, or str for single ifo
segment_url : str
url of segment database, defaults to contents of S6_SEGMENT_SERVER
environment variable
match : [ str | regular pattern ]
regular expression to search against returned flag names, e.g, 'UPV'
unmatch : [ str | regular pattern ]
regular expression to negatively search against returned flag names
"""
if isinstance(ifos, str):
ifos = [ifos]
# get url
if not segment_url:
segment_url = os.getenv('S6_SEGMENT_SERVER')
# open connection to LDBD(W)Server
myClient = segmentdb_utils.setup_database(segment_url)
reply = StringIO(myClient.query(squery))
xmldoc, digest = utils.load_fileobj(reply)
seg_def_table = table.get_table(xmldoc, lsctables.SegmentDefTable.tableName)
# sort table by ifo, name and version
seg_def_table.sort(key=lambda flag: (flag.ifos[0], flag.name, \
flag.version), reverse=True)
flags = lsctables.New(type(seg_def_table))
for row in seg_def_table:
# test re match
if match and not re.search(match, row.name): continue
# test re unmatch
if unmatch and re.search(unmatch, row.name): continue
# only append latest versions of multiple flags
flatest=True
if latest:
# get all flags with same ifo and name
vflags = [f for f in flags if row.name==f.name and\
row.get_ifos()==f.get_ifos()]
# if later version in list, move on
for f in vflags:
if f.version>=row.version:
flatest=False
break
if not flatest:
continue
# append those flags matching ifos requirement
for ifo in ifos:
if ifo in row.get_ifos():
flags.append(row)
break
return flags
def fromsegmentxml(xml_file, return_dict=False, select_seg_def_id=None):
"""
Read a glue.segments.segmentlist from the file object file containing an
xml segment table.
Parameters
-----------
xml_file : file object
file object for segment xml file
return_dict : boolean, optional (default = False)
returns a glue.segments.segmentlistdict containing coalesced
glue.segments.segmentlists keyed by seg_def.name for each entry in the
contained segment_def_table.
select_seg_def_id : int, optional (default = None)
returns a glue.segments.segmentlist object containing only those
segments matching the given segment_def_id integer
Returns
--------
segs : glue.segments.segmentlist instance
The segment list contained in the file.
"""
# load xmldocument and SegmentDefTable and SegmentTables
xmldoc, digest = utils.load_fileobj(xml_file,
gz=xml_file.name.endswith(".gz"),
contenthandler=ContentHandler)
seg_def_table = table.get_table(xmldoc,
lsctables.SegmentDefTable.tableName)
seg_table = table.get_table(xmldoc, lsctables.SegmentTable.tableName)
if return_dict:
segs = segments.segmentlistdict()
else:
segs = segments.segmentlist()
seg_id = {}
for seg_def in seg_def_table:
# Here we want to encode ifo, channel name and version
full_channel_name = ':'.join([str(seg_def.ifos),
str(seg_def.name),
str(seg_def.version)])
seg_id[int(seg_def.segment_def_id)] = full_channel_name
if return_dict:
segs[full_channel_name] = segments.segmentlist()
for seg in seg_table:
seg_obj = segments.segment(
lal.LIGOTimeGPS(seg.start_time, seg.start_time_ns),
lal.LIGOTimeGPS(seg.end_time, seg.end_time_ns))
if return_dict:
segs[seg_id[int(seg.segment_def_id)]].append(seg_obj)
elif select_seg_def_id is not None:
if int(seg.segment_def_id) == select_seg_def_id:
segs.append(seg_obj)
else:
segs.append(seg_obj)
if return_dict:
for seg_name in seg_id.values():
segs[seg_name] = segs[seg_name].coalesce()
else:
segs = segs.coalesce()
xmldoc.unlink()
return segs
def setup_roq(cp):
"""
Generates cp objects with the different ROQs applied
"""
use_roq=False
if cp.has_option('paths','roq_b_matrix_directory') or cp.has_option('paths','computeroqweights'):
if not cp.has_option('analysis','roq'):
print("Warning: If you are attempting to enable ROQ by specifying roq_b_matrix_directory or computeroqweights,\n\
please use analysis.roq in your config file in future. Enabling ROQ.")
cp.set('analysis','roq',True)
if not cp.getboolean('analysis','roq'):
yield cp
raise StopIteration()
from numpy import genfromtxt, array
path=cp.get('paths','roq_b_matrix_directory')
if not os.path.isdir(path):
print("The ROQ directory %s does not seem to exist\n"%path)
sys.exit(1)
use_roq=True
roq_paths=os.listdir(path)
roq_params={}
roq_force_flow = None
if cp.has_option('lalinference','roq_force_flow'):
roq_force_flow = cp.getfloat('lalinference','roq_force_flow')
print("WARNING: Forcing the f_low to ", str(roq_force_flow), "Hz")
print("WARNING: Overwriting user choice of flow, srate, seglen, and (mc_min, mc_max and q-min) or (mass1_min, mass1_max, mass2_min, mass2_max)")
def key(item): # to order the ROQ bases
return float(item[1]['seglen'])
coinc_xml_obj = None
row=None
# Get file object of coinc.xml
if opts.gid is not None:
from ligo.gracedb.rest import GraceDb
gid=opts.gid
cwd=os.getcwd()
if cp.has_option('analysis', 'service-url'):
client = GraceDb(cp.get('analysis', 'service-url'))
else:
client = GraceDb()
coinc_xml_obj = ligolw_utils.load_fileobj(client.files(gid, "coinc.xml"), contenthandler = lsctables.use_in(ligolw.LIGOLWContentHandler))[0]
elif cp.has_option('input', 'coinc-xml'):
coinc_xml_obj = ligolw_utils.load_fileobj(open(cp.get('input', 'coinc-xml'), "rb"), contenthandler = lsctables.use_in(ligolw.LIGOLWContentHandler))[0]
# Get sim_inspiral from injection file
if cp.has_option('input','injection-file'):
print("Only 0-th event in the XML table will be considered while running with ROQ\n")
row = lsctables.SimInspiralTable.get_table(
ligolw_utils.load_filename(cp.get('input','injection-file'),contenthandler=lsctables.use_in(ligolw.LIGOLWContentHandler))
)[0]
roq_bounds = pipe_utils.Query_ROQ_Bounds_Type(path, roq_paths)
if roq_bounds == 'chirp_mass_q':
print('ROQ has bounds in chirp mass and mass-ratio')
mc_priors, trigger_mchirp = pipe_utils.get_roq_mchirp_priors(
path, roq_paths, roq_params, key, coinc_xml_obj=coinc_xml_obj, sim_inspiral=row
)
elif roq_bounds == 'component_mass':
print('ROQ has bounds in component masses')
# get component mass bounds, then compute the chirp mass that can be safely covered
# further below we pass along the component mass bounds to the sampler, not the tighter chirp-mass, q bounds
m1_priors, m2_priors, trigger_mchirp = pipe_utils.get_roq_component_mass_priors(
path, roq_paths, roq_params, key, coinc_xml_obj=coinc_xml_obj, sim_inspiral=row
)
mc_priors = {}
for (roq,m1_prior), (roq2,m2_prior) in zip(m1_priors.items(), m2_priors.items()):
mc_priors[roq] = sorted([pipe_utils.mchirp_from_components(m1_prior[1], m2_prior[0]), pipe_utils.mchirp_from_components(m1_prior[0], m2_prior[1])])
if cp.has_option('lalinference','trigger_mchirp'):
trigger_mchirp=float(cp.get('lalinference','trigger_mchirp'))
roq_mass_freq_scale_factor = pipe_utils.get_roq_mass_freq_scale_factor(mc_priors, trigger_mchirp, roq_force_flow)
if roq_mass_freq_scale_factor != 1.:
print('WARNING: Rescaling ROQ basis, please ensure it is allowed with the model used.')
# If the true chirp mass is unknown, add variations over the mass bins
if opts.gid is not None or (opts.injections is not None or cp.has_option('input','injection-file')) or cp.has_option('lalinference','trigger_mchirp') or cp.has_option('input', 'coinc-xml'):
for mc_prior in mc_priors:
mc_priors[mc_prior] = array(mc_priors[mc_prior])
# find mass bin containing the trigger
trigger_bin = None
for roq in roq_paths:
if mc_priors[roq][0]*roq_mass_freq_scale_factor <= trigger_mchirp <= mc_priors[roq][1]*roq_mass_freq_scale_factor:
trigger_bin = roq
print('Prior in Mchirp will be ['+str(mc_priors[roq][0]*roq_mass_freq_scale_factor)+','+str(mc_priors[roq][1]*roq_mass_freq_scale_factor)+'] to contain the trigger Mchirp '+str(trigger_mchirp))
break
roq_paths = [trigger_bin]
else:
for mc_prior in mc_priors:
mc_priors[mc_prior] = array(mc_priors[mc_prior])*roq_mass_freq_scale_factor
# write the master configparser
cur_basedir = cp.get('paths','basedir')
masterpath=os.path.join(cur_basedir,'config.ini')
with open(masterpath,'w') as cpfile:
cp.write(cpfile)
for roq in roq_paths:
this_cp = configparser.ConfigParser()
this_cp.optionxform = str
this_cp.read(masterpath)
basedir = this_cp.get('paths','basedir')
for dirs in 'basedir','daglogdir','webdir':
val = this_cp.get('paths',dirs)
newval = os.path.join(val,roq)
mkdirs(newval)
this_cp.set('paths',dirs,newval)
this_cp.set('paths','roq_b_matrix_directory',os.path.join(cp.get('paths','roq_b_matrix_directory'),roq))
flow=roq_params[roq]['flow'] / roq_mass_freq_scale_factor
srate=2.*roq_params[roq]['fhigh'] / roq_mass_freq_scale_factor
#if srate > 8192:
# srate = 8192
seglen=roq_params[roq]['seglen'] * roq_mass_freq_scale_factor
# params.dat uses the convention q>1 so our q_min is the inverse of their qmax
this_cp.set('engine','srate',str(srate))
this_cp.set('engine','seglen',str(seglen))
if this_cp.has_option('lalinference','flow'):
tmp=this_cp.get('lalinference','flow')
tmp=eval(tmp)
ifos=tmp.keys()
else:
tmp={}
ifos=eval(this_cp.get('analysis','ifos'))
for i in ifos:
tmp[i]=flow
this_cp.set('lalinference','flow',str(tmp))
if roq_bounds == 'chirp_mass_q':
mc_min=mc_priors[roq][0]*roq_mass_freq_scale_factor
mc_max=mc_priors[roq][1]*roq_mass_freq_scale_factor
# params.dat uses the convention q>1 so our q_min is the inverse of their qmax
q_min=1./float(roq_params[roq]['qmax'])
this_cp.set('engine','chirpmass-min',str(mc_min))
this_cp.set('engine','chirpmass-max',str(mc_max))
this_cp.set('engine','q-min',str(q_min))
this_cp.set('engine','comp-min', str(max(roq_params[roq]['compmin'] * roq_mass_freq_scale_factor, mc_min * pow(1+q_min, 1./5.) * pow(q_min, 2./5.))))
this_cp.set('engine','comp-max', str(mc_max * pow(1+q_min, 1./5.) * pow(q_min, -3./5.)))
elif roq_bounds == 'component_mass':
m1_min = m1_priors[roq][0]
m1_max = m1_priors[roq][1]
m2_min = m2_priors[roq][0]
m2_max = m2_priors[roq][1]
this_cp.set('engine','mass1-min',str(m1_min))
this_cp.set('engine','mass1-max',str(m1_max))
this_cp.set('engine','mass2-min',str(m2_min))
this_cp.set('engine','mass2-max',str(m2_max))
yield this_cp
raise StopIteration()
def main(args=None):
from glue.ligolw import lsctables
from glue.ligolw.utils import process as ligolw_process
from glue.ligolw import utils as ligolw_utils
from glue.ligolw import ligolw
import lal.series
from scipy import stats
p = parser()
args = p.parse_args(args)
xmldoc = ligolw.Document()
xmlroot = xmldoc.appendChild(ligolw.LIGO_LW())
process = register_to_xmldoc(xmldoc, p, args)
cosmo = cosmology.default_cosmology.get_cosmology_from_string(
args.cosmology)
ns_mass_min = 1.0
ns_mass_max = 2.0
bh_mass_min = 5.0
bh_mass_max = 50.0
ns_astro_spin_min = -0.05
ns_astro_spin_max = +0.05
ns_astro_mass_dist = stats.norm(1.33, 0.09)
ns_astro_spin_dist = stats.uniform(ns_astro_spin_min,
ns_astro_spin_max - ns_astro_spin_min)
ns_broad_spin_min = -0.4
ns_broad_spin_max = +0.4
ns_broad_mass_dist = stats.uniform(ns_mass_min, ns_mass_max - ns_mass_min)
ns_broad_spin_dist = stats.uniform(ns_broad_spin_min,
ns_broad_spin_max - ns_broad_spin_min)
bh_astro_spin_min = -0.99
bh_astro_spin_max = +0.99
bh_astro_mass_dist = stats.pareto(b=1.3)
bh_astro_spin_dist = stats.uniform(bh_astro_spin_min,
bh_astro_spin_max - bh_astro_spin_min)
bh_broad_spin_min = -0.99
bh_broad_spin_max = +0.99
bh_broad_mass_dist = stats.reciprocal(bh_mass_min, bh_mass_max)
bh_broad_spin_dist = stats.uniform(bh_broad_spin_min,
bh_broad_spin_max - bh_broad_spin_min)
if args.distribution.startswith('bns_'):
m1_min = m2_min = ns_mass_min
m1_max = m2_max = ns_mass_max
if args.distribution.endswith('_astro'):
x1_min = x2_min = ns_astro_spin_min
x1_max = x2_max = ns_astro_spin_max
m1_dist = m2_dist = ns_astro_mass_dist
x1_dist = x2_dist = ns_astro_spin_dist
elif args.distribution.endswith('_broad'):
x1_min = x2_min = ns_broad_spin_min
x1_max = x2_max = ns_broad_spin_max
m1_dist = m2_dist = ns_broad_mass_dist
x1_dist = x2_dist = ns_broad_spin_dist
else: # pragma: no cover
assert_not_reached()
elif args.distribution.startswith('nsbh_'):
m1_min = bh_mass_min
m1_max = bh_mass_max
m2_min = ns_mass_min
m2_max = ns_mass_max
if args.distribution.endswith('_astro'):
x1_min = bh_astro_spin_min
x1_max = bh_astro_spin_max
x2_min = ns_astro_spin_min
x2_max = ns_astro_spin_max
m1_dist = bh_astro_mass_dist
m2_dist = ns_astro_mass_dist
x1_dist = bh_astro_spin_dist
x2_dist = ns_astro_spin_dist
elif args.distribution.endswith('_broad'):
x1_min = bh_broad_spin_min
x1_max = bh_broad_spin_max
x2_min = ns_broad_spin_min
x2_max = ns_broad_spin_max
m1_dist = bh_broad_mass_dist
m2_dist = ns_broad_mass_dist
x1_dist = bh_broad_spin_dist
x2_dist = ns_broad_spin_dist
else: # pragma: no cover
assert_not_reached()
elif args.distribution.startswith('bbh_'):
m1_min = m2_min = bh_mass_min
m1_max = m2_max = bh_mass_max
if args.distribution.endswith('_astro'):
x1_min = x2_min = bh_astro_spin_min
x1_max = x2_max = bh_astro_spin_max
m1_dist = m2_dist = bh_astro_mass_dist
x1_dist = x2_dist = bh_astro_spin_dist
elif args.distribution.endswith('_broad'):
x1_min = x2_min = bh_broad_spin_min
x1_max = x2_max = bh_broad_spin_max
m1_dist = m2_dist = bh_broad_mass_dist
x1_dist = x2_dist = bh_broad_spin_dist
else: # pragma: no cover
assert_not_reached()
else: # pragma: no cover
assert_not_reached()
dists = (m1_dist, m2_dist, x1_dist, x2_dist)
# Read PSDs
psds = list(
lal.series.read_psd_xmldoc(
ligolw_utils.load_fileobj(
args.reference_psd,
contenthandler=lal.series.PSDContentHandler)[0]).values())
# Construct mass1, mass2, spin1z, spin2z grid.
m1 = np.geomspace(m1_min, m1_max, 10)
m2 = np.geomspace(m2_min, m2_max, 10)
x1 = np.linspace(x1_min, x1_max, 10)
x2 = np.linspace(x2_min, x2_max, 10)
params = m1, m2, x1, x2
# Calculate the maximum distance on the grid.
max_z = get_max_z(cosmo,
psds,
args.waveform,
args.f_low,
args.min_snr,
m1,
m2,
x1,
x2,
jobs=args.jobs)
max_distance = sensitive_distance(cosmo, max_z).to_value(units.Mpc)
# Find piecewise constant approximate upper bound on distance.
max_distance = cell_max(max_distance)
# Calculate V * T in each grid cell
cdfs = [dist.cdf(param) for param, dist in zip(params, dists)]
cdf_los = [cdf[:-1] for cdf in cdfs]
cdfs = [np.diff(cdf) for cdf in cdfs]
probs = np.prod(np.meshgrid(*cdfs, indexing='ij'), axis=0)
probs /= probs.sum()
probs *= 4 / 3 * np.pi * max_distance**3
volume = probs.sum()
probs /= volume
probs = probs.ravel()
volumetric_rate = args.nsamples / volume * units.year**-1 * units.Mpc**-3
# Draw random grid cells
dist = stats.rv_discrete(values=(np.arange(len(probs)), probs))
indices = np.unravel_index(dist.rvs(size=args.nsamples),
max_distance.shape)
# Draw random intrinsic params from each cell
cols = {}
cols['mass1'], cols['mass2'], cols['spin1z'], cols['spin2z'] = [
dist.ppf(stats.uniform(cdf_lo[i], cdf[i]).rvs(size=args.nsamples))
for i, dist, cdf_lo, cdf in zip(indices, dists, cdf_los, cdfs)
]
# Draw random extrinsic parameters
cols['distance'] = stats.powerlaw(
a=3, scale=max_distance[indices]).rvs(size=args.nsamples)
cols['longitude'] = stats.uniform(0, 2 * np.pi).rvs(size=args.nsamples)
cols['latitude'] = np.arcsin(stats.uniform(-1, 2).rvs(size=args.nsamples))
cols['inclination'] = np.arccos(
stats.uniform(-1, 2).rvs(size=args.nsamples))
cols['polarization'] = stats.uniform(0, 2 * np.pi).rvs(size=args.nsamples)
cols['coa_phase'] = stats.uniform(-np.pi,
2 * np.pi).rvs(size=args.nsamples)
cols['time_geocent'] = stats.uniform(1e9, units.year.to(
units.second)).rvs(size=args.nsamples)
# Convert from sensitive distance to redshift and comoving distance.
# FIXME: Replace this brute-force lookup table with a solver.
z = np.linspace(0, max_z.max(), 10000)
ds = sensitive_distance(cosmo, z).to_value(units.Mpc)
dc = cosmo.comoving_distance(z).to_value(units.Mpc)
z_for_ds = interp1d(ds, z, kind='cubic', assume_sorted=True)
dc_for_ds = interp1d(ds, dc, kind='cubic', assume_sorted=True)
zp1 = 1 + z_for_ds(cols['distance'])
cols['distance'] = dc_for_ds(cols['distance'])
# Apply redshift factor to convert from comoving distance and source frame
# masses to luminosity distance and observer frame masses.
for key in ['distance', 'mass1', 'mass2']:
cols[key] *= zp1
# Populate sim_inspiral table
sims = xmlroot.appendChild(lsctables.New(lsctables.SimInspiralTable))
for row in zip(*cols.values()):
sims.appendRow(**dict(dict.fromkeys(sims.validcolumns, None),
process_id=process.process_id,
simulation_id=sims.get_next_id(),
waveform=args.waveform,
f_lower=args.f_low,
**dict(zip(cols.keys(), row))))
# Record process end time.
process.comment = str(volumetric_rate)
ligolw_process.set_process_end_time(process)
# Write output file.
write_fileobj(xmldoc, args.output)
def main(args=None):
p = parser()
opts = p.parse_args(args)
# LIGO-LW XML imports.
from glue.ligolw import ligolw
from glue.ligolw.param import Param
from glue.ligolw.utils import process as ligolw_process
from glue.ligolw.utils.search_summary import append_search_summary
from glue.ligolw import utils as ligolw_utils
from glue.ligolw.lsctables import (New, CoincDefTable, CoincID,
CoincInspiralTable, CoincMapTable,
CoincTable, ProcessParamsTable,
ProcessTable, SimInspiralTable,
SnglInspiralTable, TimeSlideTable)
# glue, LAL and pylal imports.
from ligo import segments
import glue.lal
import lal.series
import lalsimulation
from lalinspiral.inspinjfind import InspiralSCExactCoincDef
from lalinspiral.thinca import InspiralCoincDef
from tqdm import tqdm
# FIXME: disable progress bar monitor thread.
#
# I was getting error messages that look like this:
#
# Traceback (most recent call last):
# File "/tqdm/_tqdm.py", line 885, in __del__
# self.close()
# File "/tqdm/_tqdm.py", line 1090, in close
# self._decr_instances(self)
# File "/tqdm/_tqdm.py", line 454, in _decr_instances
# cls.monitor.exit()
# File "/tqdm/_monitor.py", line 52, in exit
# self.join()
# File "/usr/lib64/python3.6/threading.py", line 1053, in join
# raise RuntimeError("cannot join current thread")
# RuntimeError: cannot join current thread
#
# I don't know what causes this... maybe a race condition in tqdm's cleanup
# code. Anyway, this should disable the tqdm monitor thread entirely.
tqdm.monitor_interval = 0
# BAYESTAR imports.
from ..io.events.ligolw import ContentHandler
from ..bayestar import filter
# Read PSDs.
xmldoc, _ = ligolw_utils.load_fileobj(
opts.reference_psd, contenthandler=lal.series.PSDContentHandler)
psds = lal.series.read_psd_xmldoc(xmldoc, root_name=None)
psds = {
key: filter.InterpolatedPSD(filter.abscissa(psd), psd.data.data)
for key, psd in psds.items() if psd is not None
}
psds = [psds[ifo] for ifo in opts.detector]
# Extract simulation table from injection file.
inj_xmldoc, _ = ligolw_utils.load_fileobj(opts.input,
contenthandler=ContentHandler)
orig_sim_inspiral_table = SimInspiralTable.get_table(inj_xmldoc)
# Prune injections that are outside distance limits.
orig_sim_inspiral_table[:] = [
row for row in orig_sim_inspiral_table
if opts.min_distance <= row.distance <= opts.max_distance
]
# Open output file.
xmldoc = ligolw.Document()
xmlroot = xmldoc.appendChild(ligolw.LIGO_LW())
# Create tables. Process and ProcessParams tables are copied from the
# injection file.
coinc_def_table = xmlroot.appendChild(New(CoincDefTable))
coinc_inspiral_table = xmlroot.appendChild(New(CoincInspiralTable))
coinc_map_table = xmlroot.appendChild(New(CoincMapTable))
coinc_table = xmlroot.appendChild(New(CoincTable))
xmlroot.appendChild(ProcessParamsTable.get_table(inj_xmldoc))
xmlroot.appendChild(ProcessTable.get_table(inj_xmldoc))
sim_inspiral_table = xmlroot.appendChild(New(SimInspiralTable))
sngl_inspiral_table = xmlroot.appendChild(New(SnglInspiralTable))
time_slide_table = xmlroot.appendChild(New(TimeSlideTable))
# Write process metadata to output file.
process = register_to_xmldoc(xmldoc,
p,
opts,
ifos=opts.detector,
comment="Simulated coincidences")
# Add search summary to output file.
all_time = segments.segment(
[glue.lal.LIGOTimeGPS(0),
glue.lal.LIGOTimeGPS(2e9)])
append_search_summary(xmldoc, process, inseg=all_time, outseg=all_time)
# Create a time slide entry. Needed for coinc_event rows.
time_slide_id = time_slide_table.get_time_slide_id(
{ifo: 0
for ifo in opts.detector}, create_new=process)
# Populate CoincDef table.
inspiral_coinc_def = copy.copy(InspiralCoincDef)
inspiral_coinc_def.coinc_def_id = coinc_def_table.get_next_id()
coinc_def_table.append(inspiral_coinc_def)
found_coinc_def = copy.copy(InspiralSCExactCoincDef)
found_coinc_def.coinc_def_id = coinc_def_table.get_next_id()
coinc_def_table.append(found_coinc_def)
# Precompute values that are common to all simulations.
detectors = [
lalsimulation.DetectorPrefixToLALDetector(ifo) for ifo in opts.detector
]
responses = [det.response for det in detectors]
locations = [det.location for det in detectors]
if opts.jobs == 1:
pool_map = map
else:
from .. import omp
from multiprocessing import Pool
omp.num_threads = 1 # disable OpenMP parallelism
pool_map = Pool(opts.jobs).imap
func = functools.partial(simulate,
psds=psds,
responses=responses,
locations=locations,
measurement_error=opts.measurement_error,
f_low=opts.f_low,
waveform=opts.waveform)
# Make sure that each thread gets a different random number state.
# We start by drawing a random integer s in the main thread, and
# then the i'th subprocess will seed itself with the integer i + s.
#
# The seed must be an unsigned 32-bit integer, so if there are n
# threads, then s must be drawn from the interval [0, 2**32 - n).
#
# Note that *we* are thread 0, so there are a total of
# n=1+len(sim_inspiral_table) threads.
seed = np.random.randint(0, 2**32 - len(sim_inspiral_table) - 1)
np.random.seed(seed)
count_coincs = 0
with tqdm(total=len(orig_sim_inspiral_table)) as progress:
for sim_inspiral, simulation in zip(
orig_sim_inspiral_table,
pool_map(
func,
zip(
np.arange(len(orig_sim_inspiral_table)) + seed + 1,
orig_sim_inspiral_table))):
progress.update()
sngl_inspirals = []
used_snr_series = []
net_snr = 0.0
count_triggers = 0
# Loop over individual detectors and create SnglInspiral entries.
for ifo, (horizon, abs_snr, arg_snr, toa, series) \
in zip(opts.detector, simulation):
if np.random.uniform() > opts.duty_cycle:
continue
elif abs_snr >= opts.snr_threshold:
# If SNR < threshold, then the injection is not found.
# Skip it.
count_triggers += 1
net_snr += np.square(abs_snr)
elif not opts.keep_subthreshold:
continue
# Create SnglInspiral entry.
used_snr_series.append(series)
sngl_inspirals.append(
sngl_inspiral_table.RowType(**dict(
dict.fromkeys(sngl_inspiral_table.validcolumns, None),
process_id=process.process_id,
ifo=ifo,
mass1=sim_inspiral.mass1,
mass2=sim_inspiral.mass2,
spin1x=sim_inspiral.spin1x,
spin1y=sim_inspiral.spin1y,
spin1z=sim_inspiral.spin1z,
spin2x=sim_inspiral.spin2x,
spin2y=sim_inspiral.spin2y,
spin2z=sim_inspiral.spin2z,
end=toa,
snr=abs_snr,
coa_phase=arg_snr,
eff_distance=horizon / abs_snr)))
net_snr = np.sqrt(net_snr)
# If too few triggers were found, then skip this event.
if count_triggers < opts.min_triggers:
continue
# If network SNR < threshold, then the injection is not found.
# Skip it.
if net_snr < opts.net_snr_threshold:
continue
# Add Coinc table entry.
coinc = coinc_table.appendRow(
coinc_event_id=coinc_table.get_next_id(),
process_id=process.process_id,
coinc_def_id=inspiral_coinc_def.coinc_def_id,
time_slide_id=time_slide_id,
insts=opts.detector,
nevents=len(opts.detector),
likelihood=None)
# Add CoincInspiral table entry.
coinc_inspiral_table.appendRow(
coinc_event_id=coinc.coinc_event_id,
instruments=[
sngl_inspiral.ifo for sngl_inspiral in sngl_inspirals
],
end=lal.LIGOTimeGPS(1e-9 * np.mean([
sngl_inspiral.end.ns() for sngl_inspiral in sngl_inspirals
if sngl_inspiral.end is not None
])),
mass=sim_inspiral.mass1 + sim_inspiral.mass2,
mchirp=sim_inspiral.mchirp,
combined_far=0.0, # Not provided
false_alarm_rate=0.0, # Not provided
minimum_duration=None, # Not provided
snr=net_snr)
# Record all sngl_inspiral records and associate them with coincs.
for sngl_inspiral, series in zip(sngl_inspirals, used_snr_series):
# Give this sngl_inspiral record an id and add it to the table.
sngl_inspiral.event_id = sngl_inspiral_table.get_next_id()
sngl_inspiral_table.append(sngl_inspiral)
if opts.enable_snr_series:
elem = lal.series.build_COMPLEX8TimeSeries(series)
elem.appendChild(
Param.from_pyvalue(u'event_id',
sngl_inspiral.event_id))
xmlroot.appendChild(elem)
# Add CoincMap entry.
coinc_map_table.appendRow(
coinc_event_id=coinc.coinc_event_id,
table_name=sngl_inspiral_table.tableName,
event_id=sngl_inspiral.event_id)
# Record injection
if not opts.preserve_ids:
sim_inspiral.simulation_id = sim_inspiral_table.get_next_id()
sim_inspiral_table.append(sim_inspiral)
count_coincs += 1
progress.set_postfix(saved=count_coincs)
# Record coincidence associating injections with events.
for i, sim_inspiral in enumerate(sim_inspiral_table):
coinc = coinc_table.appendRow(
coinc_event_id=coinc_table.get_next_id(),
process_id=process.process_id,
coinc_def_id=found_coinc_def.coinc_def_id,
time_slide_id=time_slide_id,
instruments=None,
nevents=None,
likelihood=None)
coinc_map_table.appendRow(coinc_event_id=coinc.coinc_event_id,
table_name=sim_inspiral_table.tableName,
event_id=sim_inspiral.simulation_id)
coinc_map_table.appendRow(coinc_event_id=coinc.coinc_event_id,
table_name=coinc_table.tableName,
event_id=CoincID(i))
# Record process end time.
ligolw_process.set_process_end_time(process)
# Write output file.
write_fileobj(xmldoc, opts.output)
# BAYESTAR imports.
from lalinference.bayestar.decorator import memoized
from lalinference.io import fits
from lalinference.bayestar import ligolw as ligolw_bayestar
from lalinference.bayestar import filter
from lalinference.bayestar import timing
from lalinference.bayestar.sky_map import ligolw_sky_map, rasterize
# Other imports.
import numpy as np
# Read coinc file.
log.info('%s:reading input XML file', opts.input.name)
xmldoc, _ = ligolw_utils.load_fileobj(
opts.input,
contenthandler=ligolw_bayestar.LSCTablesAndSeriesContentHandler)
if opts.psd_files: # read pycbc psds here
import lal
from glue.segments import segment, segmentlist
import h5py
# FIXME: This should be imported from pycbc.
DYN_RANGE_FAC = 5.9029581035870565e+20
class psd_segment(segment):
def __new__(cls, psd, *args):
return segment.__new__(cls, *args)
def __init__(self, psd, *args):
def setup_roq(cp):
"""
Generates cp objects with the different ROQs applied
"""
use_roq = False
if cp.has_option('paths', 'roq_b_matrix_directory') or cp.has_option(
'paths', 'computeroqweights'):
if not cp.has_option('analysis', 'roq'):
print(
"Warning: If you are attempting to enable ROQ by specifying roq_b_matrix_directory or computeroqweights,\n\
please use analysis.roq in your config file in future. Enabling ROQ."
)
cp.set('analysis', 'roq', True)
if not cp.getboolean('analysis', 'roq'):
yield cp
raise StopIteration()
from numpy import genfromtxt, array
path = cp.get('paths', 'roq_b_matrix_directory')
if not os.path.isdir(path):
print("The ROQ directory %s does not seem to exist\n" % path)
sys.exit(1)
use_roq = True
roq_paths = os.listdir(path)
roq_params = {}
roq_force_flow = None
if cp.has_option('lalinference', 'roq_force_flow'):
roq_force_flow = cp.getfloat('lalinference', 'roq_force_flow')
print("WARNING: Forcing the f_low to ", str(roq_force_flow), "Hz")
print(
"WARNING: Overwriting user choice of flow, srate, seglen, and (mc_min, mc_max and q-min) or (mass1_min, mass1_max, mass2_min, mass2_max)"
)
def key(item): # to order the ROQ bases
return float(item[1]['seglen'])
coinc_xml_obj = None
row = None
# Get file object of coinc.xml
if opts.gid is not None:
from ligo.gracedb.rest import GraceDb
gid = opts.gid
cwd = os.getcwd()
if cp.has_option('analysis', 'service-url'):
client = GraceDb(cp.get('analysis', 'service-url'))
else:
client = GraceDb()
coinc_xml_obj = ligolw_utils.load_fileobj(
client.files(gid, "coinc.xml"),
contenthandler=lsctables.use_in(ligolw.LIGOLWContentHandler))[0]
elif cp.has_option('input', 'coinc-xml'):
coinc_xml_obj = ligolw_utils.load_fileobj(
open(cp.get('input', 'coinc-xml'), "rb"),
contenthandler=lsctables.use_in(ligolw.LIGOLWContentHandler))[0]
# Get sim_inspiral from injection file
if cp.has_option('input', 'injection-file'):
print(
"Only 0-th event in the XML table will be considered while running with ROQ\n"
)
row = lsctables.SimInspiralTable.get_table(
ligolw_utils.load_filename(cp.get('input', 'injection-file'),
contenthandler=lsctables.use_in(
ligolw.LIGOLWContentHandler)))[0]
roq_bounds = pipe_utils.Query_ROQ_Bounds_Type(path, roq_paths)
if roq_bounds == 'chirp_mass_q':
print('ROQ has bounds in chirp mass and mass-ratio')
mc_priors, trigger_mchirp = pipe_utils.get_roq_mchirp_priors(
path,
roq_paths,
roq_params,
key,
coinc_xml_obj=coinc_xml_obj,
sim_inspiral=row)
elif roq_bounds == 'component_mass':
print('ROQ has bounds in component masses')
# get component mass bounds, then compute the chirp mass that can be safely covered
# further below we pass along the component mass bounds to the sampler, not the tighter chirp-mass, q bounds
m1_priors, m2_priors, trigger_mchirp = pipe_utils.get_roq_component_mass_priors(
path,
roq_paths,
roq_params,
key,
coinc_xml_obj=coinc_xml_obj,
sim_inspiral=row)
mc_priors = {}
for (roq, m1_prior), (roq2, m2_prior) in zip(m1_priors.items(),
m2_priors.items()):
mc_priors[roq] = sorted([
pipe_utils.mchirp_from_components(m1_prior[1], m2_prior[0]),
pipe_utils.mchirp_from_components(m1_prior[0], m2_prior[1])
])
if cp.has_option('lalinference', 'trigger_mchirp'):
trigger_mchirp = float(cp.get('lalinference', 'trigger_mchirp'))
roq_mass_freq_scale_factor = pipe_utils.get_roq_mass_freq_scale_factor(
mc_priors, trigger_mchirp, roq_force_flow)
if roq_mass_freq_scale_factor != 1.:
print(
'WARNING: Rescaling ROQ basis, please ensure it is allowed with the model used.'
)
# If the true chirp mass is unknown, add variations over the mass bins
if opts.gid is not None or (opts.injections is not None or cp.has_option(
'input', 'injection-file')) or cp.has_option(
'lalinference', 'trigger_mchirp') or cp.has_option(
'input', 'coinc-xml'):
for mc_prior in mc_priors:
mc_priors[mc_prior] = array(mc_priors[mc_prior])
# find mass bin containing the trigger
trigger_bin = None
for roq in roq_paths:
if mc_priors[roq][
0] * roq_mass_freq_scale_factor <= trigger_mchirp <= mc_priors[
roq][1] * roq_mass_freq_scale_factor:
trigger_bin = roq
print('Prior in Mchirp will be [' +
str(mc_priors[roq][0] * roq_mass_freq_scale_factor) +
',' +
str(mc_priors[roq][1] * roq_mass_freq_scale_factor) +
'] to contain the trigger Mchirp ' + str(trigger_mchirp))
break
roq_paths = [trigger_bin]
else:
for mc_prior in mc_priors:
mc_priors[mc_prior] = array(
mc_priors[mc_prior]) * roq_mass_freq_scale_factor
# write the master configparser
cur_basedir = cp.get('paths', 'basedir')
masterpath = os.path.join(cur_basedir, 'config.ini')
with open(masterpath, 'w') as cpfile:
cp.write(cpfile)
for roq in roq_paths:
this_cp = configparser.ConfigParser()
this_cp.optionxform = str
this_cp.read(masterpath)
basedir = this_cp.get('paths', 'basedir')
for dirs in 'basedir', 'daglogdir', 'webdir':
val = this_cp.get('paths', dirs)
newval = os.path.join(val, roq)
mkdirs(newval)
this_cp.set('paths', dirs, newval)
this_cp.set(
'paths', 'roq_b_matrix_directory',
os.path.join(cp.get('paths', 'roq_b_matrix_directory'), roq))
flow = roq_params[roq]['flow'] / roq_mass_freq_scale_factor
srate = 2. * roq_params[roq]['fhigh'] / roq_mass_freq_scale_factor
#if srate > 8192:
# srate = 8192
seglen = roq_params[roq]['seglen'] * roq_mass_freq_scale_factor
# params.dat uses the convention q>1 so our q_min is the inverse of their qmax
this_cp.set('engine', 'srate', str(srate))
this_cp.set('engine', 'seglen', str(seglen))
if this_cp.has_option('lalinference', 'flow'):
tmp = this_cp.get('lalinference', 'flow')
tmp = eval(tmp)
ifos = tmp.keys()
else:
tmp = {}
ifos = eval(this_cp.get('analysis', 'ifos'))
for i in ifos:
tmp[i] = flow
this_cp.set('lalinference', 'flow', str(tmp))
if roq_bounds == 'chirp_mass_q':
mc_min = mc_priors[roq][0] * roq_mass_freq_scale_factor
mc_max = mc_priors[roq][1] * roq_mass_freq_scale_factor
# params.dat uses the convention q>1 so our q_min is the inverse of their qmax
q_min = 1. / float(roq_params[roq]['qmax'])
this_cp.set('engine', 'chirpmass-min', str(mc_min))
this_cp.set('engine', 'chirpmass-max', str(mc_max))
this_cp.set('engine', 'q-min', str(q_min))
this_cp.set(
'engine', 'comp-min',
str(
max(
roq_params[roq]['compmin'] *
roq_mass_freq_scale_factor,
mc_min * pow(1 + q_min, 1. / 5.) *
pow(q_min, 2. / 5.))))
this_cp.set(
'engine', 'comp-max',
str(mc_max * pow(1 + q_min, 1. / 5.) * pow(q_min, -3. / 5.)))
elif roq_bounds == 'component_mass':
m1_min = m1_priors[roq][0]
m1_max = m1_priors[roq][1]
m2_min = m2_priors[roq][0]
m2_max = m2_priors[roq][1]
this_cp.set('engine', 'mass1-min', str(m1_min))
this_cp.set('engine', 'mass1-max', str(m1_max))
this_cp.set('engine', 'mass2-min', str(m2_min))
this_cp.set('engine', 'mass2-max', str(m2_max))
yield this_cp
raise StopIteration()
def gracedb_sky_map(coinc_file,
psd_file,
waveform,
f_low,
min_distance=None,
max_distance=None,
prior_distance_power=None,
method="toa_phoa_snr",
nside=-1,
chain_dump=None,
f_high_truncate=1.0,
enable_snr_series=False):
# Read input file.
log.debug('reading coinc file')
xmldoc, _ = ligolw_utils.load_fileobj(
coinc_file, contenthandler=ligolw.LSCTablesAndSeriesContentHandler)
# Locate the tables that we need.
coinc_inspiral_table = ligolw_table.get_table(
xmldoc, lsctables.CoincInspiralTable.tableName)
coinc_map_table = ligolw_table.get_table(xmldoc,
lsctables.CoincMapTable.tableName)
sngl_inspiral_table = ligolw_table.get_table(
xmldoc, lsctables.SnglInspiralTable.tableName)
# Attempt to determine phase convention from process table.
try:
process_table = ligolw_table.get_table(
xmldoc, lsctables.ProcessTable.tableName)
process, = process_table
process_name = process.program.lower()
except ValueError:
process_name = ''
if 'pycbc' in process_name:
phase_convention = 'findchirp'
else:
phase_convention = 'antifindchirp'
# Locate the sngl_inspiral rows that we need.
coinc_inspiral = coinc_inspiral_table[0]
coinc_event_id = coinc_inspiral.coinc_event_id
event_ids = [
coinc_map.event_id for coinc_map in coinc_map_table
if coinc_map.coinc_event_id == coinc_event_id
]
sngl_inspirals = [
next((sngl_inspiral for sngl_inspiral in sngl_inspiral_table
if sngl_inspiral.event_id == event_id)) for event_id in event_ids
]
# Try to load complex SNR time series.
snrs = ligolw.snr_series_by_sngl_inspiral_id_for_xmldoc(xmldoc)
try:
snrs = [snrs[sngl.event_id] for sngl in sngl_inspirals]
except KeyError:
snrs = None
# Read PSDs.
log.debug('reading PSDs time series')
xmldoc, _ = ligolw_utils.load_fileobj(
psd_file, contenthandler=lal.series.PSDContentHandler)
psds = lal.series.read_psd_xmldoc(xmldoc, root_name=None)
# Rearrange PSDs into the same order as the sngl_inspirals.
psds = [psds[sngl_inspiral.ifo] for sngl_inspiral in sngl_inspirals]
# Interpolate PSDs.
log.debug('constructing PSD interpolants')
psds = [
timing.InterpolatedPSD(filter.abscissa(psd),
psd.data.data,
f_high_truncate=f_high_truncate) for psd in psds
]
# Run sky localization
return ligolw_sky_map(sngl_inspirals,
waveform,
f_low,
min_distance,
max_distance,
prior_distance_power,
method=method,
nside=nside,
psds=psds,
phase_convention=phase_convention,
chain_dump=chain_dump,
snr_series=snrs,
enable_snr_series=enable_snr_series)
def gracedb_sky_map(coinc_file,
psd_file,
waveform,
f_low,
min_distance=None,
max_distance=None,
prior=None,
reference_frequency=None,
nside=-1):
# LIGO-LW XML imports.
from glue.ligolw import table as ligolw_table
from glue.ligolw import utils as ligolw_utils
from glue.ligolw import lsctables
# Determine approximant, amplitude order, and phase order from command line arguments.
approximant, amplitude_order, phase_order = timing.get_approximant_and_orders_from_string(
waveform)
# Read input file.
xmldoc, _ = ligolw_utils.load_fileobj(coinc_file)
# Locate the tables that we need.
coinc_inspiral_table = ligolw_table.get_table(
xmldoc, lsctables.CoincInspiralTable.tableName)
coinc_map_table = ligolw_table.get_table(xmldoc,
lsctables.CoincMapTable.tableName)
sngl_inspiral_table = ligolw_table.get_table(
xmldoc, lsctables.SnglInspiralTable.tableName)
# Locate the sngl_inspiral rows that we need.
coinc_inspiral = coinc_inspiral_table[0]
coinc_event_id = coinc_inspiral.coinc_event_id
event_ids = [
coinc_map.event_id for coinc_map in coinc_map_table
if coinc_map.coinc_event_id == coinc_event_id
]
sngl_inspirals = [(sngl_inspiral for sngl_inspiral in sngl_inspiral_table
if sngl_inspiral.event_id == event_id).next()
for event_id in event_ids]
# Read PSDs.
if psd_file is None:
psds = None
else:
xmldoc, _ = ligolw_utils.load_fileobj(psd_file)
psds = read_psd_xmldoc(xmldoc)
# Rearrange PSDs into the same order as the sngl_inspirals.
psds = [psds[sngl_inspiral.ifo] for sngl_inspiral in sngl_inspirals]
# Interpolate PSDs.
psds = [
timing.InterpolatedPSD(filter.abscissa(psd), psd.data.data)
for psd in psds
]
# TOA+SNR sky localization
return ligolw_sky_map(sngl_inspirals,
approximant,
amplitude_order,
phase_order,
f_low,
min_distance,
max_distance,
prior,
reference_frequency=reference_frequency,
nside=nside,
psds=psds)
def fromsegmentxml(xml_file, return_dict=False, select_seg_def_id=None):
""" Read a glue.segments.segmentlist from the file object file
containing an xml segment table.
Parameters
-----------
xml_file : file object
file object for segment xml file
return_dict : boolean, optional (default = False)
returns a glue.segments.segmentlistdict containing coalesced
glue.segments.segmentlists keyed by seg_def.name for each entry in the
contained segment_def_table.
select_seg_def_id : int, optional (default = None)
returns a glue.segments.segmentlist object containing only those
segments matching the given segment_def_id integer
Returns
--------
segs : glue.segments.segmentlist instance
The segment list contained in the file.
"""
# load XML with SegmentDefTable and SegmentTable
xmldoc, digest = utils.load_fileobj(xml_file,
gz=xml_file.name.endswith(".gz"),
contenthandler=ContentHandler)
seg_def_table = table.get_table(xmldoc,
lsctables.SegmentDefTable.tableName)
seg_table = table.get_table(xmldoc, lsctables.SegmentTable.tableName)
if return_dict:
segs = segments.segmentlistdict()
else:
segs = segments.segmentlist()
seg_id = {}
for seg_def in seg_def_table:
# encode ifo, channel name and version
full_channel_name = ':'.join(
[str(seg_def.ifos),
str(seg_def.name),
str(seg_def.version)])
seg_id[int(seg_def.segment_def_id)] = full_channel_name
if return_dict:
segs[full_channel_name] = segments.segmentlist()
for seg in seg_table:
seg_obj = segments.segment(
lal.LIGOTimeGPS(seg.start_time, seg.start_time_ns),
lal.LIGOTimeGPS(seg.end_time, seg.end_time_ns))
if return_dict:
segs[seg_id[int(seg.segment_def_id)]].append(seg_obj)
elif select_seg_def_id is not None:
if int(seg.segment_def_id) == select_seg_def_id:
segs.append(seg_obj)
else:
segs.append(seg_obj)
if return_dict:
for seg_name in seg_id.values():
segs[seg_name] = segs[seg_name].coalesce()
else:
segs = segs.coalesce()
xmldoc.unlink()
return segs
def main():
usage ="""%%prog [options] GROUP TYPE EVENTFILE
where GROUP is one of %(groups)s
TYPE is one of %(types)s
EVENTFILE is file containing event data. '-' indicates stdin.
%%prog [options] replace GRACEID EVENTFILE
where GROUP is one of %(groups)s
TYPE is one of %(types)s
EVENTFILE is file containing event data. '-' indicates stdin.
%%prog [options] ping
Test server connection
%%prog [options] upload GRACEID FILE [COMMENT]
where GRACEID is the id of an existing candidate event in GraCEDb
FILE is the name of the file to upload. '-' indicates stdin.
COMMENT is an optional annotation to enter into the log
Upload FILE to the private data area for a candidate event. To apply
a tag, use the --tag-name option (and --tag-display-name if desired.)
%%prog [options] download GRACEID FILE [DESTINATION]
where GRACEID is the id of an existing candidate event in GraCEDb
FILE is the name of the file previosuly uploaded.
DESTINATION is the download destination. '-' indicates stdout.
default is same file name as FILE
Download FILE from private data area of a candidate event
%%prog [options] log GRACEID COMMENT
where GRACEID is the id of an existing candidate event in GraCEDb
COMMENT is text that will be entered into the event's log
Enter a comment into the log for a candidate event. To apply a tag,
use the --tag-name option (and --tag-display-name if desired).
%%prog [options] label GRACEID LABEL
Label event with GRACEDID with LABEL. LABEL must already exist.
%%prog [options] tag GRACEID LOG_N TAG_NAME [DISP_NAME]
where GRACEID is the id of an existing candidate event in GraCEDb
LOG_N is the number of the log message.
TAG_NAME is the name of the tag
DISP_NAME is the tag display name (ignored for existing tags)
Tag an existing log message. Alternatively, the tag name and
display name can be passed in with the --tag-name and
--tag-display-name options.
%%prog [options] delete_tag GRACEID LOG_N TAG_NAME
Remove a tag from a log message. Alternatively, the tag name
can be passed in with the --tag-name option.
%%prog [options] search SEARCH PARAMS
Search paramaters are a list of requirements to be satisfied. They
may be GPS times, GPS time ranges, graceids and ranges, group(s),
analysis type(s), labels, etc. Note that text is case insensitive
Example: %%prog search G0100..G0200 mbta LUMIN_GO
Environment Variables:
GRACEDB_SERVICE_URL (can be overridden by --service-url)
HTTP_PROXY (can be overridden by --proxy)
X509_USER_PROXY
X509_USER_CERT
X509_USER_KEY
Credentials are looked for in this order:
(1) $(X509_USER_CERT) / $(X509_USER_KEY)
(2) $(X509_USER_PROXY)
(3) Default location of grid proxy ( /tmp/x509up_u$(UID) )
(4) $(HOME)/.globus/usercert.pem / $(HOME)/.globus/userkey.pem
Note that comments can only be 200 characters long.
Longer strings will be truncated.""" % {
'groups' : 'CBC, Burst, Stochastic, Coherent, Test, External',
'types' : ", ".join(validTypes),
}
from optparse import OptionParser
op = OptionParser(usage=usage)
op.add_option("-p", "--proxy", dest="proxy",
help="HTTP Proxy", metavar="PROXY[:PORT]")
op.add_option("-s", "--service-url", dest="service",
help="GraCEDb Service URL", metavar="URL")
op.add_option("-f", "--filename", dest="filename",
help="If data is read from stdin, use this as the filename.", metavar="NAME")
op.add_option("-a", "--alert", dest="alert",
help="Send an LV alert (deprecated; alerts sent by default)",
action="store_true", default=None
)
op.add_option("-c", "--columns", dest="columns",
help="Comma separated list of event attributes to include in results (only meaningful in search)",
default=DEFAULT_COLUMNS
)
op.add_option("-l", "--ligolw", dest="ligolw",
help="Download ligolw file of combined search results (not meaningful outside of search). NOTE: Produces an ERROR if any of the events returned by the search do not have coinc.xml files.",
action="store_true", default=False
)
op.add_option("-t", "--tag-name", dest="tagName",
help="tag name in database (only used for log, upload, tag, and delete_tag)",
default=None
)
op.add_option("-d", "--tag-display-name", dest="tagDispName",
help="tag display name (ignored for existing tags)",
default=None
)
options, args = op.parse_args()
try:
from glue.ligolw import ligolw
from glue.ligolw import lsctables
from glue.ligolw import utils
from glue.ligolw.utils import ligolw_add
except:
if options.ligolw:
error("ligolw modules not found")
exit(1)
else:
pass
proxy = options.proxy or os.environ.get('HTTP_PROXY', None)
service = options.service or \
os.environ.get('GRACEDB_SERVICE_URL', None) or \
DEFAULT_SERVICE_URL
if options.alert is not None:
warning("alert option is deprecated. Alerts are now sent by default.")
proxyport = None
if proxy and proxy.find(':') > 0:
try:
proxy, proxyport = proxy.split(':')
proxyport = int(proxyport)
except:
op.error("Malformed proxy: '%s'" % proxy)
if proxyport:
client = Client(service,
proxy_host=proxy,
proxy_port=proxyport)
else:
client = Client(service, proxy_host=proxy)
if len(args) < 1:
op.error("not enough arguments")
elif args[0] == 'ping':
response = client.ping()
if response.status==200:
output("%s: 200 OK" % service)
exit(0)
elif args[0] == 'upload':
if len(args) < 3:
op.error("not enough arguments for upload")
graceid = args[1]
filename = args[2]
comment = " ".join(args[3:])
tagName = options.tagName
tagDispName = options.tagDispName
response = client.writeLog(graceid, comment, filename, None,
tagName, tagDispName)
elif args[0] == 'download':
if len(args) not in [2,3,4]:
op.error("not enough arguments for download")
graceid = args[1]
if len(args) == 2:
# get/print listing.
response = client.files(graceid)
if response and response.status == 200:
for fname in json.loads(response.read()):
print(fname)
exit(0)
print(response.reason)
exit(1)
filename = args[2]
if len(args) == 4:
outfile = args[3]
else:
outfile = os.path.basename(filename)
response = client.download(graceid, filename, outfile)
if response:
# no response means file saved. any other response is an error message.
print response
exit(1)
exit(0)
elif args[0] == 'log':
if len(args) < 3:
op.error("not enough arguments for log")
graceid = args[1]
message = " ".join(args[2:])
response = client.writeLog(graceid, message, options.tagName, options.tagDispName)
elif args[0] == 'tag':
if options.tagName:
if len(args) != 2:
op.error("wrong number of arguments for tag")
tagName = options.tagName
tagDispName = options.tagDispName
else:
if len(args) not in [4,5]:
op.error("wrong number of arguments for tag")
tagName = args[3]
tagDispName = None
if len(args)==5:
tagDispName = args[4]
graceid = args[1]
logN = args[2]
response = client.createTag(graceid, logN, tagName, tagDispName)
elif args[0] == 'delete_tag':
error("len args = %s" % len(args))
error("args = %s" % args)
if options.tagName:
if len(args) != 2:
op.error("wrong number of arguments for delete_tag")
tagName = options.tagName
else:
if len(args) != 4:
op.error("wrong number of arguments for delete_tag")
tagName = args[3]
graceid = args[1]
logN = args[2]
response = client.deleteTag(graceid, logN, tagName)
elif args[0] == 'label':
if len(args) != 3:
op.error("wrong number of arguments for label")
graceid = args[1]
label = args[2]
response = client.writeLabel(graceid, label)
elif args[0] == 'search':
query = " ".join(args[1:])
columns = options.columns
columns = columns.replace('DEFAULTS',DEFAULT_COLUMNS)
columns = columns.split(',')
count = None # XXX Let's just get rid of this?
orderby = None # XXX Should we implement this?
events = client.events(query, orderby, count, columns)
if options.ligolw:
xmldoc = ligolw.Document()
for e in events:
graceid = e['graceid']
try:
r = client.files(graceid, "coinc.xml")
utils.load_fileobj(r, xmldoc = xmldoc)
except:
error("Missing coinc.xml for %s. Cannot build ligolw output." % graceid)
exit(1)
ligolw_add.reassign_ids(xmldoc)
ligolw_add.merge_ligolws(xmldoc)
ligolw_add.merge_compatible_tables(xmldoc)
xmldoc.write()
else:
accessFun = {
"labels" : lambda e: \
",".join(e['labels'].keys()),
"dataurl" : lambda e: e['links']['files'],
}
header = "#" + "\t".join(columns)
output(header)
for e in events:
row = [ accessFun.get(column, lambda e: defaultAccess(e,column))(e) for column in columns ]
row = "\t".join(row)
output(row)
return 0
elif args[0] == 'replace':
if len(args) != 3:
op.error("wrong number of args for replace")
graceid = args[1]
filename = args[2]
response = client.replaceEvent(graceid, filename)
elif len(args) == 3:
# Create a new event.
group = args[0]
type = args[1]
filename = args[2]
# Check that the group and type are known to the API.
# NB: the dictionary returned by the API has keys and values
# reversed w.r.t. the typeCodeMap above.
foundType = False
for key, value in client.analysis_types.items():
if type==str(value):
type = key
foundType = True
if not foundType:
error("Type must be one of: ", ", ".join(client.analysis_types.values()))
sys.exit(1)
foundGroup = True if (unicode(group) in client.groups) else False
if not foundGroup:
error("Group must be one of: ", ", ".join(client.groups))
sys.exit(1)
response = client.createEvent(group, type, filename)
if not response:
error("There was a problem. Did you do grid-proxy-init -rfc?")
sys.exit(1)
# XXX Must output graceid for consistency with earlier client.
# Therefore, must deal with response here rather than at the end.
exitCode = 0
status = response.status
if status >= 400:
exitCode=1
try:
rv = response.read()
except:
rv = response
try:
rv = json.loads(rv)
except:
pass
if 'graceid' in rv.keys():
output(rv['graceid'])
elif 'error' in rv.keys():
exitCode=1
error(rv['error'])
return exitCode
else:
op.error("")
sys.exit(1)
# Output the response.
exitCode = 0
try:
rv = response.read()
status = response.status
except:
rv = response
try:
responseBody = json.loads(rv)
except:
responseBody = rv
if status >= 400:
exitCode=1
if isinstance(responseBody, str):
output("%d: %s" % (status, responseBody))
else:
output("Server returned %d" % status)
if ('error' in responseBody) and response['error']:
error(response['error'])
exitCode = 1
if ('warning' in responseBody) and response['warning']:
warning(response['warning'])
if ('output' in responseBody) and response['output']:
output(response['output'])
return exitCode
def frominjectionfile(file, type, ifo=None, start=None, end=None):
"""
Read generic injection file object file containing injections of the given
type string. Returns an 'Sim' lsctable of the corresponding type.
Arguments:
file : file object
type : [ "inspiral" | "burst" | "ringdown" ]
Keyword arguments:
ifo : [ "G1" | "H1" | "H2" | "L1" | "V1" ]
"""
# read type
type = type.lower()
# read injection xml
xml = re.compile('(xml$|xml.gz$)')
if re.search(xml,file.name):
xmldoc,digest = utils.load_fileobj(file)
injtable = table.get_table(xmldoc,'sim_%s:table' % (type))
# read injection txt
else:
cchar = re.compile('[#%<!()_\[\]{}:;\'\"]+')
#== construct new Sim{Burst,Inspiral,Ringdown}Table
injtable = lsctables.New(lsctables.__dict__['Sim%sTable' % (type.title())])
if type=='inspiral':
columns = ['geocent_end_time.geocent_end_time_ns',\
'h_end_time.h_end_time_ns',\
'l_end_time.l_end_time_ns',\
'v_end_time.v_end_time_ns',\
'distance']
for line in file.readlines():
if re.match(cchar,line):
continue
# set up siminspiral object
inj = lsctables.SimInspiral()
# split data
sep = re.compile('[\s,=]+')
data = sep.split(line)
# set attributes
inj.geocent_end_time = int(data[0].split('.')[0])
inj.geocent_end_time_ns = int(data[0].split('.')[1])
inj.h_end_time = int(data[1].split('.')[0])
inj.h_end_time_ns = int(data[1].split('.')[1])
inj.l_end_time = int(data[2].split('.')[0])
inj.l_end_time_ns = int(data[2].split('.')[1])
inj.v_end_time = int(data[3].split('.')[0])
inj.v_end_time_ns = int(data[3].split('.')[1])
inj.distance = float(data[4])
injtable.append(inj)
if type=='burst':
if file.readlines()[0].startswith('filestart'):
# if given parsed burst file
file.seek(0)
snrcol = { 'G1':23, 'H1':19, 'L1':21, 'V1':25 }
for line in file.readlines():
inj = lsctables.SimBurst()
# split data
sep = re.compile('[\s,=]+')
data = sep.split(line)
# set attributes
# gps time
if 'burstgps' in data:
idx = data.index('burstgps')+1
geocent = LIGOTimeGPS(data[idx])
inj.time_geocent_gps = geocent.seconds
inj.time_geocent_gps_ns = geocent.nanoseconds
else:
continue
#inj.waveform = data[4]
#inj.waveform_number = int(data[5])
# frequency
if 'freq' in data:
idx = data.index('freq')+1
inj.frequency = float(data[idx])
else:
continue
# SNR a.k.a. amplitude
if ifo and 'snr%s' % ifo in data:
idx = data.index('snr%s' % ifo)+1
inj.amplitude = float(data[idx])
elif 'rmsSNR' in data:
idx = data.index('rmsSNR')+1
inj.amplitude = float(data[idx])
else:
continue
if 'phi' in data:
idx = data.index('phi' )+1
inj.ra = float(data[idx])*24/(2*math.pi)
if 'theta' in data:
idx = data.index('theta' )+1
inj.ra = 90-(float(data[idx])*180/math.pi)
if ifo and 'hrss%s' % ifo in data:
idx = data.index('hrss%s' % ifo)+1
inj.hrss = float(data[idx])
elif 'hrss' in data:
idx = data.index('hrss')+1
inj.hrss = float(data[idx])
# extra columns to be added when I know how
#inj.q = 0
#inj.q = float(data[11])
#h_delay = LIGOTimeGPS(data[41])
#inj.h_peak_time = inj.time_geocent_gps+h_delay.seconds
#inj.h_peak_time_ns = inj.time_geocent_gps_ns+h_delay.nanoseconds
#l_delay = LIGOTimeGPS(data[43])
#inj.l_peak_time = inj.time_geocent_gps+l_delay.seconds
#inj.l_peak_time_ns = inj.time_geocent_gps_ns+l_delay.nanoseconds
#v_delay = LIGOTimeGPS(data[43])
#inj.v_peak_time = inj.time_geocent_gps+v_delay.seconds
#inj.v_peak_time_ns = inj.time_geocent_gps_ns+v_delay.nanoseconds
injtable.append(inj)
else:
# if given parsed burst file
file.seek(0)
for line in file.readlines():
inj = lsctables.SimBurst()
# split data
sep = re.compile('[\s,]+')
data = sep.split(line)
# set attributes
geocent = LIGOTimeGPS(data[0])
inj.time_geocent_gps = geocent.seconds
inj.time_geocent_gps_ns = geocent.nanoseconds
injtable.append(inj)
injections = table.new_from_template(injtable)
if not start: start = 0
if not end: end = 9999999999
span = segments.segmentlist([ segments.segment(start, end) ])
get_time = dqTriggerUtils.def_get_time(injections.tableName)
injections.extend(inj for inj in injtable if get_time(inj) in span)
return injections
def get_coinc_xmldoc(gracedb_client, graceid, filename="coinc.xml"):
return ligolw_utils.load_fileobj(get_filename(gracedb_client,
graceid,
filename=filename),
contenthandler=LIGOLWContentHandler)[0]
### load settings for accessing dmt segment files
dq_name = config.get('get_science_segments', 'include')
segdb_url = config.get('get_science_segments', 'segdb')
if opts.verbose:
print 'querrying science segments'
### this returns a string
seg_xml_file = idq.segment_query(config,
opts.start,
opts.end,
url=segdb_url)
### write seg_xml_file to disk
lsctables.use_in(ligolw.LIGOLWContentHandler)
xmldoc = ligolw_utils.load_fileobj(
seg_xml_file, contenthandler=ligolw.LIGOLWContentHandler)[0]
### science segments xml filename
seg_file = idq.segxml(gdbdir, "%s_%s" % (filetag, dq_name), opts.start,
opts.end - opts.start)
if opts.verbose:
print ' writing science segments to file : ' + seg_file
ligolw_utils.write_filename(xmldoc, seg_file, gz=seg_file.endswith(".gz"))
(scisegs, coveredseg) = idq.extract_dq_segments(
seg_file, dq_name) ### read in segments from xml file
if opts.verbose:
print 'finding idq segments'
idqsegs = idq.get_idq_segments(realtimedir,
opts.start,
out_xmldoc.appendChild(ligolw.LIGO_LW())
# Write process metadata to output file.
process = command.register_to_xmldoc(
out_xmldoc, parser, opts, ifos=opts.detector, comment="Little hope!")
# Add search summary to output file.
all_time = segments.segment([glue.lal.LIGOTimeGPS(0), glue.lal.LIGOTimeGPS(2e9)])
search_summary_table = lsctables.New(lsctables.SearchSummaryTable)
out_xmldoc.childNodes[0].appendChild(search_summary_table)
summary = ligolw_search_summary.append_search_summary(out_xmldoc, process,
inseg=all_time, outseg=all_time)
# Read template bank file.
progress.update(-1, 'reading ' + opts.template_bank.name)
xmldoc, _ = ligolw_utils.load_fileobj(
opts.template_bank, contenthandler=ligolw_bayestar.LSCTablesContentHandler)
# Determine the low frequency cutoff from the template bank file.
template_bank_f_low = ligolw_bayestar.get_template_bank_f_low(xmldoc)
template_bank = ligolw_table.get_table(xmldoc,
lsctables.SnglInspiralTable.tableName)
# Read injection file.
progress.update(-1, 'reading ' + opts.input.name)
xmldoc, _ = ligolw_utils.load_fileobj(
opts.input, contenthandler=ligolw_bayestar.LSCTablesContentHandler)
# Extract simulation table from injection file.
sim_inspiral_table = ligolw_table.get_table(xmldoc,
lsctables.SimInspiralTable.tableName)
subparser.add_argument('ifo1', choices=available_ifos)
subparser.add_argument('ifo2', choices=available_ifos)
subparser = add_parser(conj)
subparser.add_argument('ifos', choices=available_ifos, nargs='+')
subparser = add_parser(amplify)
subparser.add_argument('ifos', choices=available_ifos, nargs='+')
subparser.add_argument('gain', type=float)
args = parser.parse_args()
kwargs = dict(args.__dict__)
func = locals()[kwargs.pop('func')]
infile = kwargs.pop('input')
outfile = kwargs.pop('output')
# Read input file.
xmldoc, _ = load_fileobj(
infile, contenthandler=LSCTablesAndSeriesContentHandler)
# Process it.
process = command.register_to_xmldoc(xmldoc, parser, args)
func(xmldoc, **kwargs)
set_process_end_time(process)
# Write output file.
with SignalsTrap():
write_fileobj(
xmldoc, outfile, gz=(os.path.splitext(outfile.name)[-1] == '.gz'))
index_html_obj.close()
#=============================================
# sciseg query
#=============================================
if opts.ignore_science_segments:
logger.info("ignoring science segments")
scisegs = [[gpsstart, gpsstart+stride]]
else:
logger.info("generating science segments")
try:
seg_xml_file = idq.segment_query(config, gpsstart, gpsstart+stride, url=config.get("get_science_segments","segdb"))
lsctables.use_in(ligolw.LIGOLWContentHandler)
xmldoc = utils.load_fileobj(seg_xml_file, contenthandler=ligolw.LIGOLWContentHandler)[0]
seg_file = "%s/science_segements-%d-%d.xml.gz"%(this_sumdir, int(gpsstart), int(stride))
logger.info("writting science segments to file : %s"%seg_file)
utils.write_filename(xmldoc, seg_file, gz=seg_file.endswith(".gz"))
(scisegs, coveredseg) = idq.extract_dq_segments(seg_file, config.get('get_science_segments', 'include'))
except Exception as e:
traceback.print_exc()
logger.info("ERROR: segment generation failed. Skipping this summary period.")
gpsstart += stride
continue
#=============================================
comment="Simulated coincidences")
# Add search summary to output file.
all_time = segments.segment(
[glue.lal.LIGOTimeGPS(0),
glue.lal.LIGOTimeGPS(2e9)])
search_summary_table = lsctables.New(lsctables.SearchSummaryTable)
out_xmldoc.childNodes[0].appendChild(search_summary_table)
summary = ligolw_search_summary.append_search_summary(out_xmldoc,
process,
inseg=all_time,
outseg=all_time)
# Read PSDs.
progress.update(-1, 'reading ' + opts.reference_psd.name)
xmldoc, _ = ligolw_utils.load_fileobj(
opts.reference_psd, contenthandler=lal.series.PSDContentHandler)
psds = lal.series.read_psd_xmldoc(xmldoc, root_name=None)
psds = {
key: timing.InterpolatedPSD(filter.abscissa(psd), psd.data.data)
for key, psd in psds.items() if psd is not None
}
# Read injection file.
progress.update(-1, 'reading ' + opts.input.name)
xmldoc, _ = ligolw_utils.load_fileobj(
opts.input, contenthandler=ligolw_bayestar.LSCTablesContentHandler)
# Extract simulation table from injection file.
sim_inspiral_table = ligolw_table.get_table(
xmldoc, lsctables.SimInspiralTable.tableName)
def gracedb_sky_map(coinc_file,
psd_file,
waveform,
f_low,
min_distance=None,
max_distance=None,
prior_distance_power=None,
method="toa_phoa_snr",
nside=-1,
chain_dump=None,
phase_convention='antifindchirp',
f_high_truncate=1.0,
enable_snr_series=False):
# Read input file.
xmldoc, _ = ligolw_utils.load_fileobj(
coinc_file, contenthandler=ligolw.LSCTablesAndSeriesContentHandler)
# Locate the tables that we need.
coinc_inspiral_table = ligolw_table.get_table(
xmldoc, lsctables.CoincInspiralTable.tableName)
coinc_map_table = ligolw_table.get_table(xmldoc,
lsctables.CoincMapTable.tableName)
sngl_inspiral_table = ligolw_table.get_table(
xmldoc, lsctables.SnglInspiralTable.tableName)
# Locate the sngl_inspiral rows that we need.
coinc_inspiral = coinc_inspiral_table[0]
coinc_event_id = coinc_inspiral.coinc_event_id
event_ids = [
coinc_map.event_id for coinc_map in coinc_map_table
if coinc_map.coinc_event_id == coinc_event_id
]
sngl_inspirals = [
next((sngl_inspiral for sngl_inspiral in sngl_inspiral_table
if sngl_inspiral.event_id == event_id)) for event_id in event_ids
]
instruments = {sngl_inspiral.ifo for sngl_inspiral in sngl_inspirals}
# Try to load complex SNR time series.
snrs = ligolw.snr_series_by_sngl_inspiral_id_for_xmldoc(xmldoc)
try:
snrs = [snrs[sngl.event_id] for sngl in sngl_inspirals]
except KeyError:
snrs = None
# Read PSDs.
xmldoc, _ = ligolw_utils.load_fileobj(
psd_file, contenthandler=lal.series.PSDContentHandler)
psds = lal.series.read_psd_xmldoc(xmldoc, root_name=None)
# Rearrange PSDs into the same order as the sngl_inspirals.
psds = [psds[sngl_inspiral.ifo] for sngl_inspiral in sngl_inspirals]
# Interpolate PSDs.
psds = [
timing.InterpolatedPSD(filter.abscissa(psd),
psd.data.data,
f_high_truncate=f_high_truncate) for psd in psds
]
# Run sky localization
prob, epoch, elapsed_time = ligolw_sky_map(
sngl_inspirals,
waveform,
f_low,
min_distance,
max_distance,
prior_distance_power,
method=method,
nside=nside,
psds=psds,
phase_convention=phase_convention,
chain_dump=chain_dump,
snr_series=snrs,
enable_snr_series=enable_snr_series)
return prob, epoch, elapsed_time, instruments
def dump_flags(ifos=None, segment_url=None, match=None, unmatch=None,\
latest=False):
"""
Returns the list of all flags defined in the database.
Keyword rguments:
ifo : [ str | list ]
list of ifos to query, or str for single ifo
segment_url : str
url of segment database, defaults to contents of S6_SEGMENT_SERVER
environment variable
match : [ str | regular pattern ]
regular expression to search against returned flag names, e.g, 'UPV'
unmatch : [ str | regular pattern ]
regular expression to negatively search against returned flag names
"""
if isinstance(ifos, str):
ifos = [ifos]
# get url
if not segment_url:
segment_url = os.getenv('S6_SEGMENT_SERVER')
# open connection to LDBD(W)Server
myClient = segmentdb_utils.setup_database(segment_url)
reply = StringIO(myClient.query(squery))
xmldoc, digest = utils.load_fileobj(reply)
seg_def_table = lsctables.SegmentDefTable.get_table(xmldoc)
# sort table by ifo, name and version
seg_def_table.sort(key=lambda flag: (flag.ifos[0], flag.name, \
flag.version), reverse=True)
flags = lsctables.New(type(seg_def_table))
for row in seg_def_table:
# test re match
if match and not re.search(match, row.name): continue
# test re unmatch
if unmatch and re.search(unmatch, row.name): continue
# only append latest versions of multiple flags
flatest = True
if latest:
# get all flags with same ifo and name
vflags = [f for f in flags if row.name==f.name and\
row.get_ifos()==f.get_ifos()]
# if later version in list, move on
for f in vflags:
if f.version >= row.version:
flatest = False
break
if not flatest:
continue
# append those flags matching ifos requirement
for ifo in ifos:
if ifo in row.get_ifos():
flags.append(row)
break
return flags
