def get_segment_summary_times(scienceFile, segmentName):
"""
This function will find the times for which the segment_summary is set
for the flag given by segmentName.
Parameters
-----------
scienceFile : SegFile
The segment file that we want to use to determine this.
segmentName : string
The DQ flag to search for times in the segment_summary table.
Returns
---------
summSegList : glue.segments.segmentlist
The times that are covered in the segment summary table.
"""
# Parse the segmentName
segmentName = segmentName.split(':')
if not len(segmentName) in [2, 3]:
raise ValueError("Invalid channel name %s." % (segmentName))
ifo = segmentName[0]
channel = segmentName[1]
version = ''
if len(segmentName) == 3:
version = int(segmentName[2])
# Load the filename
xmldoc = utils.load_filename(
scienceFile.cache_entry.path,
gz=scienceFile.cache_entry.path.endswith("gz"),
contenthandler=ContentHandler)
# Get the segment_def_id for the segmentName
segmentDefTable = table.get_table(xmldoc, "segment_definer")
for entry in segmentDefTable:
if (entry.ifos == ifo) and (entry.name == channel):
if len(segmentName) == 2 or (entry.version == version):
segDefID = entry.segment_def_id
break
else:
raise ValueError("Cannot find channel %s in segment_definer table."\
%(segmentName))
# Get the segmentlist corresponding to this segmentName in segment_summary
segmentSummTable = table.get_table(xmldoc, "segment_summary")
summSegList = segments.segmentlist([])
for entry in segmentSummTable:
if entry.segment_def_id == segDefID:
segment = segments.segment(entry.start_time, entry.end_time)
summSegList.append(segment)
summSegList.coalesce()
return summSegList
def get_segment_summary_times(scienceFile, segmentName):
"""
This function will find the times for which the segment_summary is set
for the flag given by segmentName.
Parameters
-----------
scienceFile : SegFile
The segment file that we want to use to determine this.
segmentName : string
The DQ flag to search for times in the segment_summary table.
Returns
---------
summSegList : glue.segments.segmentlist
The times that are covered in the segment summary table.
"""
# Parse the segmentName
segmentName = segmentName.split(':')
if not len(segmentName) in [2,3]:
raise ValueError("Invalid channel name %s." %(segmentName))
ifo = segmentName[0]
channel = segmentName[1]
version = ''
if len(segmentName) == 3:
version = int(segmentName[2])
# Load the filename
xmldoc = utils.load_filename(scienceFile.cache_entry.path,
gz=scienceFile.cache_entry.path.endswith("gz"),
contenthandler=ContentHandler)
# Get the segment_def_id for the segmentName
segmentDefTable = table.get_table(xmldoc, "segment_definer")
for entry in segmentDefTable:
if (entry.ifos == ifo) and (entry.name == channel):
if len(segmentName) == 2 or (entry.version==version):
segDefID = entry.segment_def_id
break
else:
raise ValueError("Cannot find channel %s in segment_definer table."\
%(segmentName))
# Get the segmentlist corresponding to this segmentName in segment_summary
segmentSummTable = table.get_table(xmldoc, "segment_summary")
summSegList = segments.segmentlist([])
for entry in segmentSummTable:
if entry.segment_def_id == segDefID:
segment = segments.segment(entry.start_time, entry.end_time)
summSegList.append(segment)
summSegList.coalesce()
return summSegList
def select_segments_by_definer(segment_file, segment_name=None, ifo=None):
""" Return the list of segments that match the segment name
Parameters
----------
segment_file: str
path to segment xml file
segment_name: str
Name of segment
ifo: str, optional
Returns
-------
seg: list of segments
"""
from pycbc_glue.ligolw.ligolw import LIGOLWContentHandler as h
lsctables.use_in(h)
indoc = ligolw_utils.load_filename(segment_file, False, contenthandler=h)
segment_table = table.get_table(indoc, 'segment')
seg_def_table = table.get_table(indoc, 'segment_definer')
def_ifos = seg_def_table.getColumnByName('ifos')
def_names = seg_def_table.getColumnByName('name')
def_ids = seg_def_table.getColumnByName('segment_def_id')
valid_id = []
for def_ifo, def_name, def_id in zip(def_ifos, def_names, def_ids):
if ifo and ifo != def_ifo:
continue
if segment_name and segment_name != def_name:
continue
valid_id += [def_id]
start = numpy.array(segment_table.getColumnByName('start_time'))
start_ns = numpy.array(segment_table.getColumnByName('start_time_ns'))
end = numpy.array(segment_table.getColumnByName('end_time'))
end_ns = numpy.array(segment_table.getColumnByName('end_time_ns'))
start, end = start + 1e-9 * start_ns, end + 1e-9 * end_ns
did = segment_table.getColumnByName('segment_def_id')
keep = numpy.array([d in valid_id for d in did])
if sum(keep) > 0:
return start_end_to_segments(start[keep], end[keep])
else:
return segmentlist([])
def select_segments_by_definer(segment_file, segment_name=None, ifo=None):
""" Return the list of segments that match the segment name
Parameters
----------
segment_file: str
path to segment xml file
segment_name: str
Name of segment
ifo: str, optional
Returns
-------
seg: list of segments
"""
from pycbc_glue.ligolw.ligolw import LIGOLWContentHandler as h; lsctables.use_in(h)
indoc = ligolw_utils.load_filename(segment_file, False, contenthandler=h)
segment_table = table.get_table(indoc, 'segment')
seg_def_table = table.get_table(indoc, 'segment_definer')
def_ifos = seg_def_table.getColumnByName('ifos')
def_names = seg_def_table.getColumnByName('name')
def_ids = seg_def_table.getColumnByName('segment_def_id')
valid_id = []
for def_ifo, def_name, def_id in zip(def_ifos, def_names, def_ids):
if ifo and ifo != def_ifo:
continue
if segment_name and segment_name != def_name:
continue
valid_id += [def_id]
start = numpy.array(segment_table.getColumnByName('start_time'))
start_ns = numpy.array(segment_table.getColumnByName('start_time_ns'))
end = numpy.array(segment_table.getColumnByName('end_time'))
end_ns = numpy.array(segment_table.getColumnByName('end_time_ns'))
start, end = start + 1e-9 * start_ns, end + 1e-9 * end_ns
did = segment_table.getColumnByName('segment_def_id')
keep = numpy.array([d in valid_id for d in did])
if sum(keep) > 0:
return start_end_to_segments(start[keep], end[keep])
else:
return segmentlist([])
def start_end_from_segments(segment_file):
"""
Return the start and end time arrays from a segment file.
Parameters
----------
segment_file: xml segment file
Returns
-------
start: numpy.ndarray
end: numpy.ndarray
"""
from pycbc_glue.ligolw.ligolw import LIGOLWContentHandler as h; lsctables.use_in(h)
indoc = ligolw_utils.load_filename(segment_file, False, contenthandler=h)
segment_table = table.get_table(indoc, lsctables.SegmentTable.tableName)
start = numpy.array(segment_table.getColumnByName('start_time'))
start_ns = numpy.array(segment_table.getColumnByName('start_time_ns'))
end = numpy.array(segment_table.getColumnByName('end_time'))
end_ns = numpy.array(segment_table.getColumnByName('end_time_ns'))
return start + start_ns * 1e-9, end + end_ns * 1e-9
def start_end_from_segments(segment_file):
"""
Return the start and end time arrays from a segment file.
Parameters
----------
segment_file: xml segment file
Returns
-------
start: numpy.ndarray
end: numpy.ndarray
"""
from pycbc_glue.ligolw.ligolw import LIGOLWContentHandler as h; lsctables.use_in(h)
indoc = ligolw_utils.load_filename(segment_file, False, contenthandler=h)
segment_table = table.get_table(indoc, lsctables.SegmentTable.tableName)
start = numpy.array(segment_table.getColumnByName('start_time'))
start_ns = numpy.array(segment_table.getColumnByName('start_time_ns'))
end = numpy.array(segment_table.getColumnByName('end_time'))
end_ns = numpy.array(segment_table.getColumnByName('end_time_ns'))
return start + start_ns * 1e-9, end + end_ns * 1e-9
def ReadSimInspiralFromFiles(fileList, verbose=False):
"""
Read the simInspiral tables from a list of files
@param fileList: list of input files
@param verbose: print ligolw_add progress
"""
simInspiralTriggers = None
lsctables.use_in(ExtractSimInspiralTableLIGOLWContentHandler)
for thisFile in fileList:
doc = utils.load_filename(thisFile, gz=(thisFile or "stdin").endswith(".gz"), verbose=verbose, contenthandler=ExtractSimInspiralTableLIGOLWContentHandler)
# extract the sim inspiral table
try: simInspiralTable = \
table.get_table(doc, lsctables.SimInspiralTable.tableName)
except: simInspiralTable = None
if simInspiralTriggers and simInspiralTable:
simInspiralTriggers.extend(simInspiralTable)
elif not simInspiralTriggers:
simInspiralTriggers = simInspiralTable
return simInspiralTriggers
def __init__(self, sim_file, **kwds):
self.indoc = ligolw_utils.load_filename(
sim_file, False, contenthandler=LIGOLWContentHandler)
self.table = table.get_table(self.indoc,
lsctables.SimInspiralTable.tableName)
self.extra_args = kwds
import pylab
from pycbc_glue.ligolw import table, utils, lsctables
from sys import argv
import numpy
pycbc_file = argv[1]
lal_file = argv[2]
pdoc = utils.load_filename(pycbc_file)
ldoc = utils.load_filename(lal_file)
ptrig = table.get_table(pdoc, lsctables.SnglInspiralTable.tableName)
ltrig = table.get_table(ldoc, lsctables.SnglInspiralTable.tableName)
t = table.get_table(pdoc, lsctables.FilterTable.tableName)
start = t[0].start_time
psnr = ptrig.get_column('snr')
pchi = ptrig.get_column('chisq')
pmc = ptrig.get_column('mchirp')
psig = ptrig.get_column('sigmasq')
pend_time = (ptrig.get_column('end_time') - start)+ 1e-9 * ptrig.get_column('end_time_ns')
lsnr = ltrig.get_column('snr')
lchi = ltrig.get_column('chisq')
lmc = ltrig.get_column('mchirp')
lsig = ltrig.get_column('sigmasq')
lend_time = (ltrig.get_column('end_time') - start) + 1e-9 * ltrig.get_column('end_time_ns')
def find_nearest(v1, v2):
i1 = []
def __init__(self, filename, approximant=None, parameters=None,
**kwds):
self.has_compressed_waveforms = False
ext = os.path.basename(filename)
if ext.endswith(('.xml', '.xml.gz', '.xmlgz')):
self.filehandler = None
self.indoc = ligolw_utils.load_filename(
filename, False, contenthandler=LIGOLWContentHandler)
self.table = table.get_table(
self.indoc, lsctables.SnglInspiralTable.tableName)
self.table = pycbc.io.WaveformArray.from_ligolw_table(self.table,
columns=parameters)
# inclination stored in xml alpha3 column
names = list(self.table.dtype.names)
names = tuple([n if n != 'alpha3' else 'inclination' for n in names])
# low frequency cutoff in xml alpha6 column
names = tuple([n if n!= 'alpha6' else 'f_lower' for n in names])
self.table.dtype.names = names
elif ext.endswith(('hdf', '.h5')):
self.indoc = None
f = h5py.File(filename, 'r')
self.filehandler = f
try:
fileparams = map(str, f.attrs['parameters'])
except KeyError:
# just assume all of the top-level groups are the parameters
fileparams = map(str, f.keys())
logging.info("WARNING: no parameters attribute found. "
"Assuming that %s " %(', '.join(fileparams)) +
"are the parameters.")
# use WaveformArray's syntax parser to figure out what fields
# need to be loaded
if parameters is None:
parameters = fileparams
common_fields = list(pycbc.io.WaveformArray(1,
names=parameters).fieldnames)
add_fields = list(set(parameters) &
(set(fileparams) - set(common_fields)))
# load
dtype = []
data = {}
for key in common_fields+add_fields:
data[str(key)] = f[key][:]
dtype.append((str(key), data[key].dtype))
num = f[fileparams[0]].size
self.table = pycbc.io.WaveformArray(num, dtype=dtype)
for key in data:
self.table[key] = data[key]
# add the compressed waveforms, if they exist
self.has_compressed_waveforms = 'compressed_waveforms' in f
else:
raise ValueError("Unsupported template bank file extension %s" %(
ext))
# if approximant is specified, override whatever was in the file
# (if anything was in the file)
if approximant is not None:
# get the approximant for each template
apprxs = self.parse_approximant(approximant)
if 'approximant' not in self.table.fieldnames:
self.table = self.table.add_fields(apprxs, 'approximant')
else:
self.table['approximant'] = apprxs
self.extra_args = kwds
self.ensure_hash()
# Grab all relevant Omicron trigger files
omicron_times = []
omicron_snr = []
omicron_freq = []
for era in eras:
# Generate list of all Omicron SnglBurst xml trigger files
file_list = glob.glob(args.omicron_dir +
'/%s/%s_Omicron/%s/%s-%s_Omicron-*.xml.gz' %
(args.ifo, args.omicron_channel, era, args.ifo,
args.omicron_channel.replace('-', '_')))
# Parse trigger files into SNR, time, and frequency for Omicron triggers
for file in file_list:
omicron_xml = utils.load_filename(file,
contenthandler=DefaultContentHandler)
snglburst_table = table.get_table(omicron_xml,
lsctables.SnglBurstTable.tableName)
for row in snglburst_table:
if (row.snr > args.omicron_snr_thresh
and omicron_start_time < row.peak_time < omicron_end_time):
omicron_times.append(row.peak_time +
row.peak_time_ns * 10**(-9))
omicron_snr.append(row.snr)
omicron_freq.append(row.peak_frequency)
# Generate inspiral waveform and calculate f(t) to plot on top of Omicron triggers
hp, hc = get_td_waveform(approximant='SEOBNRv2',
mass1=m1,
mass2=m2,
def __init__(self, sim_file, **kwds):
self.indoc = ligolw_utils.load_filename(
sim_file, False, contenthandler=LIGOLWContentHandler)
self.table = table.get_table(self.indoc, lsctables.SimInspiralTable.tableName)
self.extra_args = kwds
eras = [gps_era_start]
# Grab all relevant Omicron trigger files
omicron_times = []
omicron_snr = []
omicron_freq = []
for era in eras:
# Generate list of all Omicron SnglBurst xml trigger files
file_list = glob.glob(args.omicron_dir +
'/%s/%s_Omicron/%s/%s-%s_Omicron-*.xml.gz'
%(args.ifo,args.omicron_channel,era,args.ifo,args.omicron_channel.replace('-','_')))
# Parse trigger files into SNR, time, and frequency for Omicron triggers
for file in file_list:
omicron_xml = utils.load_filename(file, contenthandler=DefaultContentHandler)
snglburst_table = table.get_table(omicron_xml, lsctables.SnglBurstTable.tableName)
for row in snglburst_table:
if (row.snr > args.omicron_snr_thresh and
omicron_start_time < row.peak_time < omicron_end_time):
omicron_times.append(row.peak_time + row.peak_time_ns * 10**(-9))
omicron_snr.append(row.snr)
omicron_freq.append(row.peak_frequency)
# Generate inspiral waveform and calculate f(t) to plot on top of Omicron triggers
hp, hc = get_td_waveform(approximant='SEOBNRv2', mass1=m1, mass2=m2,
spin1x=0, spin1y=0, spin1z=s1z,
spin2x=0, spin2y=0, spin2z=s2z,
delta_t=(1./32768.), f_lower=30)
import pylab
from pycbc_glue.ligolw import table, utils, lsctables
from sys import argv
import numpy
pycbc_file = argv[1]
lal_file = argv[2]
pdoc = utils.load_filename(pycbc_file)
ldoc = utils.load_filename(lal_file)
ptrig = table.get_table(pdoc, lsctables.SnglInspiralTable.tableName)
ltrig = table.get_table(ldoc, lsctables.SnglInspiralTable.tableName)
t = table.get_table(pdoc, lsctables.FilterTable.tableName)
start = t[0].start_time
psnr = ptrig.get_column('snr')
pchi = ptrig.get_column('chisq')
pmc = ptrig.get_column('mchirp')
psig = ptrig.get_column('sigmasq')
pend_time = (ptrig.get_column('end_time') -
start) + 1e-9 * ptrig.get_column('end_time_ns')
lsnr = ltrig.get_column('snr')
lchi = ltrig.get_column('chisq')
lmc = ltrig.get_column('mchirp')
lsig = ltrig.get_column('sigmasq')
lend_time = (ltrig.get_column('end_time') -
start) + 1e-9 * ltrig.get_column('end_time_ns')
def __init__(self, filename, approximant=None, parameters=None, **kwds):
self.has_compressed_waveforms = False
ext = os.path.basename(filename)
if ext.endswith(('.xml', '.xml.gz', '.xmlgz')):
self.filehandler = None
self.indoc = ligolw_utils.load_filename(
filename, False, contenthandler=LIGOLWContentHandler)
self.table = table.get_table(self.indoc,
lsctables.SnglInspiralTable.tableName)
self.table = pycbc.io.WaveformArray.from_ligolw_table(
self.table, columns=parameters)
# inclination stored in xml alpha3 column
names = list(self.table.dtype.names)
names = tuple(
[n if n != 'alpha3' else 'inclination' for n in names])
# low frequency cutoff in xml alpha6 column
names = tuple([n if n != 'alpha6' else 'f_lower' for n in names])
self.table.dtype.names = names
elif ext.endswith(('hdf', '.h5')):
self.indoc = None
f = h5py.File(filename, 'r')
self.filehandler = f
try:
fileparams = map(str, f.attrs['parameters'])
except KeyError:
# just assume all of the top-level groups are the parameters
fileparams = map(str, f.keys())
logging.info("WARNING: no parameters attribute found. "
"Assuming that %s " % (', '.join(fileparams)) +
"are the parameters.")
# use WaveformArray's syntax parser to figure out what fields
# need to be loaded
if parameters is None:
parameters = fileparams
common_fields = list(
pycbc.io.WaveformArray(1, names=parameters).fieldnames)
add_fields = list(
set(parameters) & (set(fileparams) - set(common_fields)))
# load
dtype = []
data = {}
for key in common_fields + add_fields:
data[str(key)] = f[key][:]
dtype.append((str(key), data[key].dtype))
num = f[fileparams[0]].size
self.table = pycbc.io.WaveformArray(num, dtype=dtype)
for key in data:
self.table[key] = data[key]
# add the compressed waveforms, if they exist
self.has_compressed_waveforms = 'compressed_waveforms' in f
else:
raise ValueError("Unsupported template bank file extension %s" %
(ext))
# if approximant is specified, override whatever was in the file
# (if anything was in the file)
if approximant is not None:
# get the approximant for each template
apprxs = self.parse_approximant(approximant)
if 'approximant' not in self.table.fieldnames:
self.table = self.table.add_fields(apprxs, 'approximant')
else:
self.table['approximant'] = apprxs
self.extra_args = kwds
self.ensure_hash()
