def make_psd_xmldoc(psddict):
Attributes = ligolw.sax.xmlreader.AttributesImpl
xmldoc = ligolw.Document()
root_name = u"psd"
lw = xmldoc.appendChild(ligolw.LIGO_LW(Attributes({u"Name": root_name})))
for instrument, psd in psddict.items():
xmlseries = _build_series(psd, (u"Frequency,Real", u"Frequency"), None,
'deltaF', 's^-1')
fs = lw.appendChild(xmlseries)
fs.appendChild(ligolw_param.from_pyvalue(u"instrument", instrument))
return xmldoc
def setUp(self):
self.detectors = [Detector(d) for d in ['H1', 'L1', 'V1']]
self.sample_rate = 4096.
self.earth_time = lal.REARTH_SI / lal.C_SI
# create a few random injections
self.injections = []
start_time = float(lal.GPSTimeNow())
taper_choices = ('TAPER_NONE', 'TAPER_START', 'TAPER_END', 'TAPER_STARTEND')
for i, taper in zip(xrange(20), itertools.cycle(taper_choices)):
inj = MyInjection()
inj.end_time = start_time + 40000 * i + \
numpy.random.normal(scale=3600)
random = numpy.random.uniform
inj.mass1 = random(low=1., high=20.)
inj.mass2 = random(low=1., high=20.)
inj.distance = random(low=0.9, high=1.1) * 1e6 * lal.PC_SI
inj.latitude = numpy.arccos(random(low=-1, high=1))
inj.longitude = random(low=0, high=2 * lal.PI)
inj.inclination = numpy.arccos(random(low=-1, high=1))
inj.polarization = random(low=0, high=2 * lal.PI)
inj.taper = taper
self.injections.append(inj)
# create LIGOLW document
xmldoc = ligolw.Document()
xmldoc.appendChild(ligolw.LIGO_LW())
# create sim inspiral table, link it to document and fill it
sim_table = lsctables.New(lsctables.SimInspiralTable)
xmldoc.childNodes[-1].appendChild(sim_table)
for i in xrange(len(self.injections)):
row = sim_table.RowType()
self.injections[i].fill_sim_inspiral_row(row)
row.process_id = 'process:process_id:0'
row.simulation_id = 'sim_inspiral:simulation_id:%d' % i
sim_table.append(row)
# write document to temp file
self.inj_file = tempfile.NamedTemporaryFile(suffix='.xml')
utils.write_fileobj(xmldoc, self.inj_file)
def _build_series(series, dim_names, comment, delta_name, delta_unit):
from pycbc_glue.ligolw import array as ligolw_array
Attributes = ligolw.sax.xmlreader.AttributesImpl
elem = ligolw.LIGO_LW(
Attributes({u"Name": unicode(series.__class__.__name__)}))
if comment is not None:
elem.appendChild(ligolw.Comment()).pcdata = comment
elem.appendChild(ligolw.Time.from_gps(series.epoch, u"epoch"))
elem.appendChild(ligolw_param.from_pyvalue(u"f0", series.f0, unit=u"s^-1"))
delta = getattr(series, delta_name)
if numpy.iscomplexobj(series.data.data):
data = numpy.row_stack((numpy.arange(len(series.data.data)) * delta,
series.data.data.real, series.data.data.imag))
else:
data = numpy.row_stack(
(numpy.arange(len(series.data.data)) * delta, series.data.data))
a = ligolw_array.from_array(series.name, data, dim_names=dim_names)
a.Unit = str(series.sampleUnits)
dim0 = a.getElementsByTagName(ligolw.Dim.tagName)[0]
dim0.Unit = delta_unit
dim0.Start = series.f0
dim0.Scale = delta
elem.appendChild(a)
return elem
def output_sngl_inspiral_table(outputFile,
tempBank,
metricParams,
ethincaParams,
programName="",
optDict=None,
outdoc=None,
**kwargs):
"""
Function that converts the information produced by the various pyCBC bank
generation codes into a valid LIGOLW xml file containing a sngl_inspiral
table and outputs to file.
Parameters
-----------
outputFile : string
Name of the file that the bank will be written to
tempBank : iterable
Each entry in the tempBank iterable should be a sequence of
[mass1,mass2,spin1z,spin2z] in that order.
metricParams : metricParameters instance
Structure holding all the options for construction of the metric
and the eigenvalues, eigenvectors and covariance matrix
needed to manipulate the space.
ethincaParams: {ethincaParameters instance, None}
Structure holding options relevant to the ethinca metric computation
including the upper frequency cutoff to be used for filtering.
NOTE: The computation is currently only valid for non-spinning systems
and uses the TaylorF2 approximant.
programName (key-word-argument) : string
Name of the executable that has been run
optDict (key-word argument) : dictionary
Dictionary of the command line arguments passed to the program
outdoc (key-word argument) : ligolw xml document
If given add template bank to this representation of a xml document and
write to disk. If not given create a new document.
kwargs : key-word arguments
All other key word arguments will be passed directly to
ligolw_process.register_to_xmldoc
"""
if optDict is None:
optDict = {}
if outdoc is None:
outdoc = ligolw.Document()
outdoc.appendChild(ligolw.LIGO_LW())
# get IFO to put in search summary table
ifos = []
if 'channel_name' in optDict.keys():
if optDict['channel_name'] is not None:
ifos = [optDict['channel_name'][0:2]]
proc_id = ligolw_process.register_to_xmldoc(outdoc,
programName,
optDict,
ifos=ifos,
**kwargs).process_id
sngl_inspiral_table = convert_to_sngl_inspiral_table(tempBank, proc_id)
# Calculate Gamma components if needed
if ethincaParams is not None:
if ethincaParams.doEthinca:
for sngl in sngl_inspiral_table:
# Set tau_0 and tau_3 values needed for the calculation of
# ethinca metric distances
(sngl.tau0, sngl.tau3) = pnutils.mass1_mass2_to_tau0_tau3(
sngl.mass1, sngl.mass2, metricParams.f0)
fMax_theor, GammaVals = calculate_ethinca_metric_comps(
metricParams,
ethincaParams,
sngl.mass1,
sngl.mass2,
spin1z=sngl.spin1z,
spin2z=sngl.spin2z,
full_ethinca=ethincaParams.full_ethinca)
# assign the upper frequency cutoff and Gamma0-5 values
sngl.f_final = fMax_theor
for i in xrange(len(GammaVals)):
setattr(sngl, "Gamma" + str(i), GammaVals[i])
# If Gamma metric components are not wanted, assign f_final from an
# upper frequency cutoff specified in ethincaParams
elif ethincaParams.cutoff is not None:
for sngl in sngl_inspiral_table:
sngl.f_final = pnutils.frequency_cutoff_from_name(
ethincaParams.cutoff, sngl.mass1, sngl.mass2, sngl.spin1z,
sngl.spin2z)
# set per-template low-frequency cutoff
if 'f_low_column' in optDict and 'f_low' in optDict and \
optDict['f_low_column'] is not None:
for sngl in sngl_inspiral_table:
setattr(sngl, optDict['f_low_column'], optDict['f_low'])
outdoc.childNodes[0].appendChild(sngl_inspiral_table)
# get times to put in search summary table
start_time = 0
end_time = 0
if 'gps_start_time' in optDict.keys() and 'gps_end_time' in optDict.keys():
start_time = optDict['gps_start_time']
end_time = optDict['gps_end_time']
# make search summary table
search_summary_table = lsctables.New(lsctables.SearchSummaryTable)
search_summary = return_search_summary(start_time, end_time,
len(sngl_inspiral_table), ifos,
**kwargs)
search_summary_table.append(search_summary)
outdoc.childNodes[0].appendChild(search_summary_table)
# write the xml doc to disk
proctable = table.get_table(outdoc, lsctables.ProcessTable.tableName)
ligolw_utils.write_filename(outdoc,
outputFile,
gz=outputFile.endswith('.gz'))
def __init__(self, ifos, coinc_results, **kwargs):
"""Initialize a ligolw xml representation of a zerolag trigger
for upload from pycbc live to gracedb.
Parameters
----------
ifos: list of strs
A list of the ifos pariticipating in this trigger
coinc_results: dict of values
A dictionary of values. The format is defined in
pycbc/events/coinc.py and matches the on disk representation
in the hdf file for this time.
"""
self.ifos = ifos
followup_ifos = kwargs.get('followup_ifos') or []
self.template_id = coinc_results['foreground/%s/template_id' %
self.ifos[0]]
# remember if this should be marked as HWINJ
self.is_hardware_injection = ('HWINJ' in coinc_results)
# Set up the bare structure of the xml document
outdoc = ligolw.Document()
outdoc.appendChild(ligolw.LIGO_LW())
proc_id = ligolw_process.register_to_xmldoc(
outdoc,
'pycbc', {},
ifos=ifos,
comment='',
version=pycbc_version.git_hash,
cvs_repository='pycbc/' + pycbc_version.git_branch,
cvs_entry_time=pycbc_version.date).process_id
# Set up coinc_definer table
coinc_def_table = lsctables.New(lsctables.CoincDefTable)
coinc_def_id = lsctables.CoincDefID(0)
coinc_def_row = lsctables.CoincDef()
coinc_def_row.search = "inspiral"
coinc_def_row.description = "sngl_inspiral<-->sngl_inspiral coincs"
coinc_def_row.coinc_def_id = coinc_def_id
coinc_def_row.search_coinc_type = 0
coinc_def_table.append(coinc_def_row)
outdoc.childNodes[0].appendChild(coinc_def_table)
# Set up coinc inspiral and coinc event tables
coinc_id = lsctables.CoincID(0)
coinc_event_table = lsctables.New(lsctables.CoincTable)
coinc_event_row = lsctables.Coinc()
coinc_event_row.coinc_def_id = coinc_def_id
coinc_event_row.nevents = len(ifos)
coinc_event_row.instruments = ','.join(ifos)
coinc_event_row.time_slide_id = lsctables.TimeSlideID(0)
coinc_event_row.process_id = proc_id
coinc_event_row.coinc_event_id = coinc_id
coinc_event_row.likelihood = 0.
coinc_event_table.append(coinc_event_row)
outdoc.childNodes[0].appendChild(coinc_event_table)
# compute SNR time series
subthreshold_sngl_time = numpy.mean(
[coinc_results['foreground/%s/end_time' % ifo] for ifo in ifos])
self.upload_snr_series = kwargs.get('upload_snr_series')
if self.upload_snr_series:
self.snr_series = {}
self.snr_series_psd = {}
htilde = kwargs['bank'][self.template_id]
for ifo in ifos + followup_ifos:
if ifo in ifos:
trig_time = coinc_results['foreground/%s/end_time' % ifo]
else:
trig_time = subthreshold_sngl_time
# NOTE we only check the state/DQ of followup IFOs here.
# IFOs producing the coincidence are assumed to also
# produce valid SNR series.
snr_series, snr_series_psd = compute_followup_snr_series(
kwargs['data_readers'][ifo],
htilde,
trig_time,
check_state=(ifo in followup_ifos))
if snr_series is not None:
self.snr_series[ifo] = snr_series
self.snr_series_psd[ifo] = snr_series_psd
# Set up sngls
sngl_inspiral_table = lsctables.New(lsctables.SnglInspiralTable)
coinc_event_map_table = lsctables.New(lsctables.CoincMapTable)
sngl_populated = None
for sngl_id, ifo in enumerate(ifos + followup_ifos):
if self.upload_snr_series and ifo not in self.snr_series:
# SNR series could not be computed, so skip this
continue
sngl = return_empty_sngl(nones=True)
sngl.event_id = lsctables.SnglInspiralID(sngl_id)
sngl.process_id = proc_id
sngl.ifo = ifo
names = [
n.split('/')[-1] for n in coinc_results
if 'foreground/%s' % ifo in n
]
for name in names:
val = coinc_results['foreground/%s/%s' % (ifo, name)]
if name == 'end_time':
sngl.set_end(lal.LIGOTimeGPS(val))
else:
try:
setattr(sngl, name, val)
except AttributeError:
pass
if sngl.mass1 and sngl.mass2:
sngl.mtotal, sngl.eta = pnutils.mass1_mass2_to_mtotal_eta(
sngl.mass1, sngl.mass2)
sngl.mchirp, _ = pnutils.mass1_mass2_to_mchirp_eta(
sngl.mass1, sngl.mass2)
sngl_populated = sngl
if sngl.snr:
sngl.eff_distance = (sngl.sigmasq)**0.5 / sngl.snr
sngl_inspiral_table.append(sngl)
# Set up coinc_map entry
coinc_map_row = lsctables.CoincMap()
coinc_map_row.table_name = 'sngl_inspiral'
coinc_map_row.coinc_event_id = coinc_id
coinc_map_row.event_id = sngl.event_id
coinc_event_map_table.append(coinc_map_row)
if self.upload_snr_series and ifo in self.snr_series:
snr_series_to_xml(self.snr_series[ifo], outdoc, sngl.event_id)
# for subthreshold detectors, respect BAYESTAR's assumptions and checks
bayestar_check_fields = ('mass1 mass2 mtotal mchirp eta spin1x '
'spin1y spin1z spin2x spin2y spin2z').split()
for sngl in sngl_inspiral_table:
if sngl.ifo in followup_ifos:
for bcf in bayestar_check_fields:
setattr(sngl, bcf, getattr(sngl_populated, bcf))
sngl.set_end(lal.LIGOTimeGPS(subthreshold_sngl_time))
outdoc.childNodes[0].appendChild(coinc_event_map_table)
outdoc.childNodes[0].appendChild(sngl_inspiral_table)
# Set up the coinc inspiral table
coinc_inspiral_table = lsctables.New(lsctables.CoincInspiralTable)
coinc_inspiral_row = lsctables.CoincInspiral()
# This seems to be used as FAP, which should not be in gracedb
coinc_inspiral_row.false_alarm_rate = 0
coinc_inspiral_row.minimum_duration = 0.
coinc_inspiral_row.set_ifos(ifos)
coinc_inspiral_row.coinc_event_id = coinc_id
coinc_inspiral_row.mchirp = sngl_populated.mchirp
coinc_inspiral_row.mass = sngl_populated.mtotal
coinc_inspiral_row.end_time = sngl_populated.end_time
coinc_inspiral_row.end_time_ns = sngl_populated.end_time_ns
coinc_inspiral_row.snr = coinc_results['foreground/stat']
far = 1.0 / (lal.YRJUL_SI * coinc_results['foreground/ifar'])
coinc_inspiral_row.combined_far = far
coinc_inspiral_table.append(coinc_inspiral_row)
outdoc.childNodes[0].appendChild(coinc_inspiral_table)
self.outdoc = outdoc
self.time = sngl_populated.get_end()
def to_coinc_xml_object(self, file_name):
# FIXME: This function will only work with two ifos!!
outdoc = ligolw.Document()
outdoc.appendChild(ligolw.LIGO_LW())
ifos = [ifo for ifo in self.sngl_files.keys()]
proc_id = ligolw_process.register_to_xmldoc(
outdoc,
'pycbc', {},
ifos=ifos,
comment='',
version=pycbc_version.git_hash,
cvs_repository='pycbc/' + pycbc_version.git_branch,
cvs_entry_time=pycbc_version.date).process_id
search_summ_table = lsctables.New(lsctables.SearchSummaryTable)
coinc_h5file = self.coinc_file.h5file
start_time = coinc_h5file['segments']['coinc']['start'][:].min()
end_time = coinc_h5file['segments']['coinc']['end'][:].max()
num_trigs = len(self.sort_arr)
search_summary = return_search_summary(start_time, end_time, num_trigs,
ifos)
search_summ_table.append(search_summary)
outdoc.childNodes[0].appendChild(search_summ_table)
sngl_inspiral_table = lsctables.New(lsctables.SnglInspiralTable)
coinc_def_table = lsctables.New(lsctables.CoincDefTable)
coinc_event_table = lsctables.New(lsctables.CoincTable)
coinc_inspiral_table = lsctables.New(lsctables.CoincInspiralTable)
coinc_event_map_table = lsctables.New(lsctables.CoincMapTable)
time_slide_table = lsctables.New(lsctables.TimeSlideTable)
# Set up time_slide table
time_slide_id = lsctables.TimeSlideID(0)
for ifo in ifos:
time_slide_row = lsctables.TimeSlide()
time_slide_row.instrument = ifo
time_slide_row.time_slide_id = time_slide_id
time_slide_row.offset = 0
time_slide_row.process_id = proc_id
time_slide_table.append(time_slide_row)
# Set up coinc_definer table
coinc_def_id = lsctables.CoincDefID(0)
coinc_def_row = lsctables.CoincDef()
coinc_def_row.search = "inspiral"
coinc_def_row.description = "sngl_inspiral<-->sngl_inspiral coincidences"
coinc_def_row.coinc_def_id = coinc_def_id
coinc_def_row.search_coinc_type = 0
coinc_def_table.append(coinc_def_row)
bank_col_names = ['mass1', 'mass2', 'spin1z', 'spin2z']
bank_col_vals = {}
for name in bank_col_names:
bank_col_vals[name] = self.get_bankfile_array(name)
coinc_event_names = ['ifar', 'time1', 'fap', 'stat']
coinc_event_vals = {}
for name in coinc_event_names:
coinc_event_vals[name] = self.get_coincfile_array(name)
sngl_col_names = [
'snr', 'chisq', 'chisq_dof', 'bank_chisq', 'bank_chisq_dof',
'cont_chisq', 'cont_chisq_dof', 'end_time', 'template_duration',
'coa_phase', 'sigmasq'
]
sngl_col_vals = {}
for name in sngl_col_names:
sngl_col_vals[name] = self.get_snglfile_array_dict(name)
for idx in xrange(len(self.sort_arr)):
# Set up IDs and mapping values
coinc_id = lsctables.CoincID(idx)
# Set up sngls
# FIXME: As two-ifo is hardcoded loop over all ifos
sngl_combined_mchirp = 0
sngl_combined_mtot = 0
for ifo in ifos:
sngl_id = self.trig_id[ifo][idx]
event_id = lsctables.SnglInspiralID(sngl_id)
sngl = return_empty_sngl()
sngl.event_id = event_id
sngl.ifo = ifo
for name in sngl_col_names:
val = sngl_col_vals[name][ifo][idx]
if name == 'end_time':
sngl.set_end(LIGOTimeGPS(val))
else:
setattr(sngl, name, val)
for name in bank_col_names:
val = bank_col_vals[name][idx]
setattr(sngl, name, val)
sngl.mtotal, sngl.eta = pnutils.mass1_mass2_to_mtotal_eta(
sngl.mass1, sngl.mass2)
sngl.mchirp, _ = pnutils.mass1_mass2_to_mchirp_eta(
sngl.mass1, sngl.mass2)
sngl.eff_distance = (sngl.sigmasq)**0.5 / sngl.snr
sngl_combined_mchirp += sngl.mchirp
sngl_combined_mtot += sngl.mtotal
sngl_inspiral_table.append(sngl)
# Set up coinc_map entry
coinc_map_row = lsctables.CoincMap()
coinc_map_row.table_name = 'sngl_inspiral'
coinc_map_row.coinc_event_id = coinc_id
coinc_map_row.event_id = event_id
coinc_event_map_table.append(coinc_map_row)
sngl_combined_mchirp = sngl_combined_mchirp / len(ifos)
sngl_combined_mtot = sngl_combined_mtot / len(ifos)
# Set up coinc inspiral and coinc event tables
coinc_event_row = lsctables.Coinc()
coinc_inspiral_row = lsctables.CoincInspiral()
coinc_event_row.coinc_def_id = coinc_def_id
coinc_event_row.nevents = len(ifos)
coinc_event_row.instruments = ','.join(ifos)
coinc_inspiral_row.set_ifos(ifos)
coinc_event_row.time_slide_id = time_slide_id
coinc_event_row.process_id = proc_id
coinc_event_row.coinc_event_id = coinc_id
coinc_inspiral_row.coinc_event_id = coinc_id
coinc_inspiral_row.mchirp = sngl_combined_mchirp
coinc_inspiral_row.mass = sngl_combined_mtot
coinc_inspiral_row.set_end(\
LIGOTimeGPS(coinc_event_vals['time1'][idx]))
coinc_inspiral_row.snr = coinc_event_vals['stat'][idx]
coinc_inspiral_row.false_alarm_rate = coinc_event_vals['fap'][idx]
coinc_inspiral_row.combined_far = 1. / coinc_event_vals['ifar'][idx]
# Transform to Hz
coinc_inspiral_row.combined_far = \
coinc_inspiral_row.combined_far / YRJUL_SI
coinc_event_row.likelihood = 0.
coinc_inspiral_row.minimum_duration = 0.
coinc_event_table.append(coinc_event_row)
coinc_inspiral_table.append(coinc_inspiral_row)
outdoc.childNodes[0].appendChild(coinc_def_table)
outdoc.childNodes[0].appendChild(coinc_event_table)
outdoc.childNodes[0].appendChild(coinc_event_map_table)
outdoc.childNodes[0].appendChild(time_slide_table)
outdoc.childNodes[0].appendChild(coinc_inspiral_table)
outdoc.childNodes[0].appendChild(sngl_inspiral_table)
ligolw_utils.write_filename(outdoc, file_name)
def make_exttrig_file(cp, ifos, sci_seg, out_dir):
'''
Make an ExtTrig xml file containing information on the external trigger
Parameters
----------
cp : pycbc.workflow.configuration.WorkflowConfigParser object
The parsed configuration options of a pycbc.workflow.core.Workflow.
ifos : str
String containing the analysis interferometer IDs.
sci_seg : glue.segments.segment
The science segment for the analysis run.
out_dir : str
The output directory, destination for xml file.
Returns
-------
xml_file : pycbc.workflow.File object
The xml file with external trigger information.
'''
# Initialise objects
xmldoc = ligolw.Document()
xmldoc.appendChild(ligolw.LIGO_LW())
tbl = lsctables.New(lsctables.ExtTriggersTable)
cols = tbl.validcolumns
xmldoc.childNodes[-1].appendChild(tbl)
row = tbl.appendRow()
# Add known attributes for this GRB
setattr(row, "event_ra", float(cp.get("workflow", "ra")))
setattr(row, "event_dec", float(cp.get("workflow", "dec")))
setattr(row, "start_time", int(cp.get("workflow", "trigger-time")))
setattr(row, "event_number_grb", str(cp.get("workflow", "trigger-name")))
# Fill in all empty rows
for entry in cols.keys():
if not hasattr(row, entry):
if cols[entry] in ['real_4','real_8']:
setattr(row,entry,0.)
elif cols[entry] == 'int_4s':
setattr(row,entry,0)
elif cols[entry] == 'lstring':
setattr(row,entry,'')
elif entry == 'process_id':
row.process_id = ilwd.ilwdchar("external_trigger:process_id:0")
elif entry == 'event_id':
row.event_id = ilwd.ilwdchar("external_trigger:event_id:0")
else:
print("Column %s not recognized" %(entry), file=sys.stderr)
raise ValueError
# Save file
xml_file_name = "triggerGRB%s.xml" % str(cp.get("workflow",
"trigger-name"))
xml_file_path = os.path.join(out_dir, xml_file_name)
utils.write_filename(xmldoc, xml_file_path)
xml_file_url = urlparse.urljoin("file:", urllib.pathname2url(xml_file_path))
xml_file = File(ifos, xml_file_name, sci_seg, file_url=xml_file_url)
xml_file.PFN(xml_file_url, site="local")
return xml_file
print "RUNNING DATAFIND"
datafinds, scienceSegs = _workflow.setup_datafind_workflow(
workflow, scienceSegs, dfDir, segsList)
# This is needed to know what times will be analysed by daily ahope
# Template bank stuff
banks = _workflow.setup_tmpltbank_workflow(workflow, scienceSegs, datafinds,
dfDir)
# Do matched-filtering
insps = _workflow.setup_matchedfltr_workflow(workflow, scienceSegs, datafinds,
banks, dfDir)
# Now construct the summary XML file
outdoc = ligolw.Document()
outdoc.appendChild(ligolw.LIGO_LW())
# FIXME: PROGRAM NAME and dictionary of opts should be variables defined up above
proc_id = ligolw_process.register_to_xmldoc(outdoc, 'dayhopetest',
vars(args)).process_id
for ifo in workflow.ifos:
# Lets get the segment lists we need
segIfoFiles = segsList.find_output_with_ifo(ifo)
# SCIENCE
sciSegFile = segIfoFiles.find_output_with_tag('SCIENCE')
assert (len(sciSegFile) == 1)
sciSegFile = sciSegFile[0]
sciSegs = sciSegFile.segmentList
# SCIENCE_OK
sciokSegFile = segIfoFiles.find_output_with_tag('SCIENCE_OK')
assert (len(sciokSegFile) == 1)
sciokSegFile = sciokSegFile[0]