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 = lsctables.SimInspiralTable.get_table(doc)
except:
simInspiralTable = None
if simInspiralTriggers and simInspiralTable:
simInspiralTriggers.extend(simInspiralTable)
elif not simInspiralTriggers:
simInspiralTriggers = simInspiralTable
return simInspiralTriggers
def read_segfile_xml(segfile, verbose):
"""
Read segment file in ligolw xml type and return in glue.segments.segmentlist
format.
"""
from glue.ligolw import ligolw, utils, lsctables, table
lsctables.use_in(ligolw.LIGOLWContentHandler)
def ContentHandler(xmldoc):
return ligolw.LIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.StripTableName(attrs["Name"]) in ["segment"]))
utils.ContentHandler = ContentHandler
xmldoc = utils.load_url(segfile,
verbose=verbose,
gz=segfile.endswith(".gz"),
contenthandler=ligolw.LIGOLWContentHandler)
seg_list = segmentlist()
rows = table.get_table(xmldoc, lsctables.VetoDefTable.tableName)
for row in rows:
seg_list.append(segment(row.start_time, row.end_time))
xmldoc.unlink()
return seg_list
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 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 find_version_xml(segfile, seg, verbose):
"""
Find out the version of the flag for the given seg.
"""
from glue.ligolw import ligolw, utils, lsctables, table
lsctables.use_in(ligolw.LIGOLWContentHandler)
def ContentHandler(xmldoc):
return ligolw.LIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.StripTableName(attrs["Name"]) in ["segment_definer","segment_summary"]))
utils.ContentHandler = ContentHandler
xmldoc = utils.load_url(segfile,
verbose=verbose,
gz=segfile.endswith(".gz"),
contenthandler=ligolw.LIGOLWContentHandler)
for n, table_elem in enumerate(xmldoc.getElements(lambda e:\
(e.tagName == ligolw.Table.tagName))):
if n == 0:
definer = {}
for row in table_elem:
if row.name != "RESULT":
definer[str(
row.segment_def_id).split(":")[-1]] = row.version
if n == 1:
for row in table_elem:
if seg[0] >= row.start_time and seg[1] <= row.end_time:
if str(row.segment_def_id).split(
":")[-1] in definer.keys():
xmldoc.unlink()
return definer[str(row.segment_def_id).split(":")[-1]]
def find_version_xml(segfile,seg,verbose):
"""
Find out the version of the flag for the given seg.
"""
from glue.ligolw import ligolw,utils, lsctables, table
lsctables.use_in(ligolw.LIGOLWContentHandler)
def ContentHandler(xmldoc):
return ligolw.LIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.StripTableName(attrs["Name"]) in ["segment_definer","segment_summary"]))
utils.ContentHandler = ContentHandler
xmldoc = utils.load_url(segfile, verbose = verbose,gz = segfile.endswith(".gz"),contenthandler=ligolw.LIGOLWContentHandler)
for n, table_elem in enumerate(xmldoc.getElements(lambda e:\
(e.tagName == ligolw.Table.tagName))):
if n == 0:
definer = {}
for row in table_elem:
if row.name != "RESULT":
definer[str(row.segment_def_id).split(":")[-1]] = row.version
if n == 1:
for row in table_elem:
if seg[0] >= row.start_time and seg[1] <= row.end_time:
if str(row.segment_def_id).split(":")[-1] in definer.keys():
xmldoc.unlink()
return definer[str(row.segment_def_id).split(":")[-1]]
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 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 parse_veto_definer(veto_def_filename):
""" Parse a veto definer file from the filename and return a dictionary
indexed by ifo and veto definer category level.
Parameters
----------
veto_def_filename: str
The path to the veto definer file
Returns:
parsed_definition: dict
Returns a dictionary first indexed by ifo, then category level, and
finally a list of veto definitions.
"""
from glue.ligolw import table, lsctables, utils as ligolw_utils
from glue.ligolw.ligolw import LIGOLWContentHandler as h
lsctables.use_in(h)
indoc = ligolw_utils.load_filename(veto_def_filename, False,
contenthandler=h)
veto_table = table.get_table(indoc, 'veto_definer')
ifo = veto_table.getColumnByName('ifo')
name = veto_table.getColumnByName('name')
version = numpy.array(veto_table.getColumnByName('version'))
category = numpy.array(veto_table.getColumnByName('category'))
start = numpy.array(veto_table.getColumnByName('start_time'))
end = numpy.array(veto_table.getColumnByName('end_time'))
start_pad = numpy.array(veto_table.getColumnByName('start_pad'))
end_pad = numpy.array(veto_table.getColumnByName('end_pad'))
data = {}
for i in range(len(veto_table)):
if ifo[i] not in data:
data[ifo[i]] = {}
# The veto-definer categories are weird! Hardware injections are stored
# in "3" and numbers above that are bumped up by one (although not
# often used any more). So we remap 3 to H and anything above 3 to
# N-1. 2 and 1 correspond to 2 and 1 (YAY!)
if category[i] > 3:
curr_cat = "CAT_{}".format(category[i]-1)
elif category[i] == 3:
curr_cat = "CAT_H"
else:
curr_cat = "CAT_{}".format(category[i])
if curr_cat not in data[ifo[i]]:
data[ifo[i]][curr_cat] = []
veto_info = {'name': name[i],
'version': version[i],
'start': start[i],
'end': end[i],
'start_pad': start_pad[i],
'end_pad': end_pad[i],
}
data[ifo[i]][curr_cat].append(veto_info)
return data
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 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 loadSingleBurst( files, trigs_dict=None):
"""
loads snglburst tables (produced by Omicron) into trgdict object
files - is the list of file names
"""
if type(files) is str:
files = [files]
if trigs_dict is None:
trigs_dict = trigdict()
for file in files:
for row in table.get_table( ligolw_utils.load_filename(file, contenthandler=lsctables.use_in(ligolw.LIGOLWContentHandler)), lsctables.SnglBurstTable.tableName ):
channel = "%s-%s_%s"%(row.ifo, row.channel.replace("-","_"), row.search)
tcent = row.peak_time + 1e-9*row.peak_time_ns
tstart = row.start_time + 1e-9*row.start_time_ns
dur = row.duration
fpeak = row.peak_frequency
fcent = row.central_freq
bndwth = row.bandwidth
amp = row.amplitude
snr = row.snr
conf = row.confidence
chi2 = row.chisq
chi2_dof = row.chisq_dof
trigger = [tstart, dur, tcent, fpeak, fcent, bndwth, amp, snr, conf, chi2, chi2_dof]
if channel in trigs_dict.channels():
trigs_dict[channel].append( trigger ) ### SingleBurst trigger structure
else:
trigs_dict[channel] = [ trigger ]
return trigs_dict
def load_xml_file(filename):
"""Wrapper to ligolw's utils.load_filename"""
xml_doc = utils.load_filename(filename, gz=filename.endswith("gz"),
contenthandler=lsctables.use_in(
ligolw.LIGOLWContentHandler))
return xml_doc
def readCoincInspiralFromFiles(fileList, statistic=None):
"""
read in the Sngl and SimInspiralTables from a list of files
if Sngls are found, construct coincs, add injections (if any)
also return Sims (if any)
@param fileList: list of input files
@param statistic: instance of coincStatistic, to use in creating coincs
"""
if not fileList:
return coincInspiralTable(), None
if not (isinstance(statistic, coincStatistic)):
raise TypeError, "invalid statistic, must be coincStatistic"
sims = None
coincs = None
lsctables.use_in(ExtractCoincInspiralTableLIGOLWContentHandler)
for thisFile in fileList:
doc = utils.load_filename(
thisFile,
gz=(thisFile or "stdin").endswith(".gz"),
contenthandler=ExtractCoincInspiralTableLIGOLWContentHandler)
# extract the sim inspiral table
try:
simInspiralTable = lsctables.SimInspiralTable.get_table(doc)
if sims: sims.extend(simInspiralTable)
else: sims = simInspiralTable
except:
simInspiralTable = None
# extract the sngl inspiral table, construct coincs
try:
snglInspiralTable = lsctables.SnglInspiralTable.get_table(doc)
except:
snglInspiralTable = None
if snglInspiralTable:
coincFromFile = coincInspiralTable(snglInspiralTable, statistic)
if simInspiralTable:
coincFromFile.add_sim_inspirals(simInspiralTable)
if coincs: coincs.extend(coincFromFile)
else: coincs = coincFromFile
doc.unlink()
return coincs, sims
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 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 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 load_xml_table(file_name, table_name):
"""Load xml table from file."""
xml_doc = utils.load_filename(
file_name,
gz=file_name.endswith("gz"),
contenthandler=glsctables.use_in(LIGOLWContentHandler))
return get_table(xml_doc, table_name)
def load_table(sim_file):
xml_doc = utils.load_filename(sim_file,
contenthandler=lsctables.use_in(
ligolw.LIGOLWContentHandler))
sim_inspiral_table = table.get_table(xml_doc,
lsctables.SimInspiralTable.tableName)
return sim_inspiral_table
def readCoincInspiralFromFiles(fileList,statistic=None):
"""
read in the Sngl and SimInspiralTables from a list of files
if Sngls are found, construct coincs, add injections (if any)
also return Sims (if any)
@param fileList: list of input files
@param statistic: instance of coincStatistic, to use in creating coincs
"""
if not fileList:
return coincInspiralTable(), None
if not (isinstance(statistic,coincStatistic)):
raise TypeError, "invalid statistic, must be coincStatistic"
sims = None
coincs = None
lsctables.use_in(ExtractCoincInspiralTableLIGOLWContentHandler)
for thisFile in fileList:
doc = utils.load_filename(thisFile, gz = (thisFile or "stdin").endswith(".gz"), contenthandler=ExtractCoincInspiralTableLIGOLWContentHandler)
# extract the sim inspiral table
try:
simInspiralTable = \
table.get_table(doc, lsctables.SimInspiralTable.tableName)
if sims: sims.extend(simInspiralTable)
else: sims = simInspiralTable
except: simInspiralTable = None
# extract the sngl inspiral table, construct coincs
try: snglInspiralTable = \
table.get_table(doc, lsctables.SnglInspiralTable.tableName)
except: snglInspiralTable = None
if snglInspiralTable:
coincFromFile = coincInspiralTable(snglInspiralTable,statistic)
if simInspiralTable:
coincFromFile.add_sim_inspirals(simInspiralTable)
if coincs: coincs.extend(coincFromFile)
else: coincs = coincFromFile
doc.unlink()
return coincs, sims
def build_content_handler(parent, filter_func):
"""Build a `~xml.sax.handler.ContentHandler` with a given filter
"""
from glue.ligolw.lsctables import use_in
class _ContentHandler(parent):
# pylint: disable=too-few-public-methods
def __init__(self, document):
super(_ContentHandler, self).__init__(document, filter_func)
return use_in(_ContentHandler)
def build_content_handler(parent, filter_func):
"""Build a `~xml.sax.handler.ContentHandler` with a given filter
"""
from glue.ligolw.lsctables import use_in
class _ContentHandler(parent):
# pylint: disable=too-few-public-methods
def __init__(self, document):
super(_ContentHandler, self).__init__(document, filter_func)
return use_in(_ContentHandler)
def read_multiinspiral_timeslides_from_files(file_list):
"""
Read time-slid multiInspiral tables from a list of files
"""
multis = None
time_slides = []
contenthandler = glsctables.use_in(LIGOLWContentHandler)
for this_file in file_list:
doc = utils.load_filename(this_file,
gz=this_file.endswith("gz"),
contenthandler=contenthandler)
# Extract the time slide table
time_slide_table = get_table(doc, lsctables.TimeSlideTable.tableName)
slide_mapping = {}
curr_slides = {}
for slide in time_slide_table:
curr_id = int(slide.time_slide_id)
if curr_id not in curr_slides:
curr_slides[curr_id] = {}
curr_slides[curr_id][slide.instrument] = slide.offset
elif slide.instrument not in curr_slides[curr_id]:
curr_slides[curr_id][slide.instrument] = slide.offset
for slide_id, offset_dict in curr_slides.items():
try:
# Is the slide already in the list and where?
offset_index = time_slides.index(offset_dict)
slide_mapping[slide_id] = offset_index
except ValueError:
# If not then add it
time_slides.append(offset_dict)
slide_mapping[slide_id] = len(time_slides) - 1
# Extract the multi inspiral table
try:
multi_inspiral_table = get_table(doc, 'multi_inspiral')
# Remap the time slide IDs
for multi in multi_inspiral_table:
new_id = slide_mapping[int(multi.time_slide_id)]
multi.time_slide_id = gilwdchar(
f"time_slide:time_slide_id:{new_id}")
if multis:
multis.extend(multi_inspiral_table)
else:
multis = multi_inspiral_table
except Exception as exc:
err_msg = "Unable to read a time-slid multiInspiral table "
err_msg += f"from {this_file}."
raise RuntimeError(err_msg) from exc
return multis, time_slides
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 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 read_segfile_xml(segfile,verbose):
"""
Read segment file in ligolw xml type and return in glue.segments.segmentlist
format.
"""
from glue.ligolw import ligolw,utils, lsctables, table
lsctables.use_in(ligolw.LIGOLWContentHandler)
def ContentHandler(xmldoc):
return ligolw.LIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.StripTableName(attrs["Name"]) in ["segment"]))
utils.ContentHandler = ContentHandler
xmldoc = utils.load_url(segfile, verbose = verbose,gz = segfile.endswith(".gz"),contenthandler=ligolw.LIGOLWContentHandler)
seg_list = segmentlist()
rows = table.get_table(xmldoc, lsctables.VetoDefTable.tableName)
for row in rows:
seg_list.append(segment(row.start_time, row.end_time))
xmldoc.unlink()
return seg_list
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 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 = lsctables.SimInspiralTable.get_table(doc)
except: simInspiralTable = None
if simInspiralTriggers and simInspiralTable:
simInspiralTriggers.extend(simInspiralTable)
elif not simInspiralTriggers:
simInspiralTriggers = simInspiralTable
return simInspiralTriggers
def ReadSnglInspiralFromFiles(fileList, verbose=False, filterFunc=None):
"""
Read the SnglInspiralTables from a list of files.
If filterFunc is not None, only keep triggers for which filterFunc
evaluates to True. Ex.: filterFunc=lambda sng: sng.snr >= 6.0
@param fileList: list of input files
@param verbose: print progress
"""
# NOTE: this function no longer carries out event ID mangling (AKA
# reassignment). Please adjust calling codes accordingly!
# This means that identical event IDs produced by lalapps_thinca in
# non-slide files having the same GPS start time will stay identical,
# affecting zerolag and injection runs made over the same data.
#
# In consequence, if the calling code is going to reconstruct coincs
# from the sngl event IDs, and if these include multiple injection
# runs, coinc finding should be done one file at a time - see the
# readCoincInspiralFromFiles function in CoincInspiralUtils.py
sngls = lsctables.New(lsctables.SnglInspiralTable, \
columns=lsctables.SnglInspiralTable.loadcolumns)
lsctables.use_in(ExtractSnglInspiralTableLIGOLWContentHandler)
for i, file in enumerate(fileList):
if verbose: print str(i + 1) + "/" + str(len(fileList)) + ": "
xmldoc = utils.load_filename(
file,
verbose=verbose,
contenthandler=ExtractSnglInspiralTableLIGOLWContentHandler)
try:
sngl_table = lsctables.SnglInspiralTable.get_table(xmldoc)
if filterFunc is not None:
iterutils.inplace_filter(filterFunc, sngl_table)
except ValueError: #some xml files have no sngl table, that's OK
sngl_table = None
if sngl_table: sngls.extend(sngl_table)
xmldoc.unlink() #free memory
return sngls
def ReadSnglInspiralFromFiles(fileList, verbose=False, filterFunc=None):
"""
Read the SnglInspiralTables from a list of files.
If filterFunc is not None, only keep triggers for which filterFunc
evaluates to True. Ex.: filterFunc=lambda sng: sng.snr >= 6.0
@param fileList: list of input files
@param verbose: print progress
"""
# NOTE: this function no longer carries out event ID mangling (AKA
# reassignment). Please adjust calling codes accordingly!
# This means that identical event IDs produced by lalapps_thinca in
# non-slide files having the same GPS start time will stay identical,
# affecting zerolag and injection runs made over the same data.
#
# In consequence, if the calling code is going to reconstruct coincs
# from the sngl event IDs, and if these include multiple injection
# runs, coinc finding should be done one file at a time - see the
# readCoincInspiralFromFiles function in CoincInspiralUtils.py
sngls = lsctables.New(lsctables.SnglInspiralTable, \
columns=lsctables.SnglInspiralTable.loadcolumns)
lsctables.use_in(ExtractSnglInspiralTableLIGOLWContentHandler)
for i,file in enumerate(fileList):
if verbose: print str(i+1)+"/"+str(len(fileList))+": "
xmldoc = utils.load_filename(file, verbose=verbose, contenthandler=ExtractSnglInspiralTableLIGOLWContentHandler)
try:
sngl_table = lsctables.SnglInspiralTable.get_table(xmldoc)
if filterFunc is not None:
iterutils.inplace_filter(filterFunc, sngl_table)
except ValueError: #some xml files have no sngl table, that's OK
sngl_table = None
if sngl_table: sngls.extend(sngl_table)
xmldoc.unlink() #free memory
return sngls
def read_ligolw(source,
contenthandler=None,
verbose=False,
non_lsc_tables_ok=True):
"""Read one or more LIGO_LW format files
Parameters
----------
source : `str`, `file`, `list`
one or more open files or file paths to read
contenthandler : `~xml.sax.handler.ContentHandler`, optional
content handler used to parse document
verbose : `bool`, optional
be verbose when reading files, default: `False`
non_lsc_tables_ok : `bool`, optional
if `False` error on unrecognised tables in documents, default: `True`
Returns
-------
xmldoc : :class:`~glue.ligolw.ligolw.Document`
the document object as parsed from the file(s)
"""
from glue.ligolw.ligolw import (Document, LIGOLWContentHandler)
from glue.ligolw import types
from glue.ligolw.lsctables import use_in
from glue.ligolw.utils.ligolw_add import ligolw_add
# mock ToPyType to link to numpy dtypes
topytype = types.ToPyType.copy()
for key in types.ToPyType:
if key in types.ToNumPyType:
types.ToPyType[key] = numpy.dtype(types.ToNumPyType[key]).type
# set default content handler
if contenthandler is None:
contenthandler = use_in(LIGOLWContentHandler)
# read one or more files into a single Document
try:
return ligolw_add(Document(),
file_list(source),
contenthandler=contenthandler,
verbose=verbose,
non_lsc_tables_ok=non_lsc_tables_ok)
finally: # replace ToPyType
types.ToPyType = topytype
def check_segment_availability(grb_name, grb_time, query_start, query_end,
offset, ifo, segmentName):
'''
Searches +/- offset from GRB time to download the latest segment lists then extracts times and puts them into a txt file.
'''
args = {
'grb_name': grb_name,
'query_start': query_start,
'query_end': query_end,
'ifo': ifo,
'segmentName': segmentName
}
cmd = "ligolw_segment_query --database --query-segments --include-segments '{segmentName}' --gps-start-time {query_start} --gps-end-time {query_end} > ./segments{ifo}_grb{grb_name}.xml".format(
**args)
print '>>', cmd
print
process = subprocess.Popen([cmd],
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
output, err = process.communicate()
# try to open the file
try:
doc = utils.load_filename(
"segments{ifo}_grb{grb_name}.xml".format(**args),
contenthandler=lsctables.use_in(ligolw.LIGOLWContentHandler))
except:
raise IOError, "Error reading file: segments{ifo}_grb{grb_name}.xml".format(
**args)
# extract the segment list from segment:table and store in a txt file
segs = table.get_table(doc, "segment")
seglist = segments.segmentlist(
segments.segment(s.start_time, s.end_time) for s in segs)
segmentsUtils.tosegwizard(file(
"{ifo}-science_grb{grb_name}.txt".format(**args), 'w'),
seglist,
header=True)
print ">> %s segments +/-%ds from %ds found:" % (ifo, offset, grb_time)
for s in segs:
print "Start:", s.start_time, "End:", s.end_time, "Duration:", s.end_time - s.start_time
print
return
def read_ligolw(source, contenthandler=None, verbose=False,
non_lsc_tables_ok=True):
"""Read one or more LIGO_LW format files
Parameters
----------
source : `str`, `file`, `list`
one or more open files or file paths to read
contenthandler : `~xml.sax.handler.ContentHandler`, optional
content handler used to parse document
verbose : `bool`, optional
be verbose when reading files, default: `False`
non_lsc_tables_ok : `bool`, optional
if `False` error on unrecognised tables in documents, default: `True`
Returns
-------
xmldoc : :class:`~glue.ligolw.ligolw.Document`
the document object as parsed from the file(s)
"""
from glue.ligolw.ligolw import (Document, LIGOLWContentHandler)
from glue.ligolw import types
from glue.ligolw.lsctables import use_in
from glue.ligolw.utils.ligolw_add import ligolw_add
# mock ToPyType to link to numpy dtypes
topytype = types.ToPyType.copy()
for key in types.ToPyType:
if key in types.ToNumPyType:
types.ToPyType[key] = numpy.dtype(types.ToNumPyType[key]).type
# set default content handler
if contenthandler is None:
contenthandler = use_in(LIGOLWContentHandler)
# read one or more files into a single Document
try:
return ligolw_add(Document(), file_list(source),
contenthandler=contenthandler, verbose=verbose,
non_lsc_tables_ok=non_lsc_tables_ok)
finally: # replace ToPyType
types.ToPyType = topytype
def ReadMultiInspiralFromFiles(fileList):
"""
Read the multiInspiral tables from a list of files
@param fileList: list of input files
"""
if not fileList:
return multiInspiralTable(), None
multis = None
for thisFile in fileList:
doc = utils.load_filename(thisFile,
gz=(thisFile or "stdin").endswith(".gz"), contenthandler = lsctables.use_in(ligolw.LIGOLWContentHandler))
# extract the multi inspiral table
try:
multiInspiralTable = lsctables.MultiInspiralTable.get_table(doc)
if multis: multis.extend(multiInspiralTable)
else: multis = multiInspiralTable
except: multiInspiralTable = None
return multis
def loadSingleBurst(files, trigs_dict=None):
"""
loads snglburst tables (produced by Omicron) into trgdict object
files - is the list of file names
"""
if type(files) is str:
files = [files]
if trigs_dict is None:
trigs_dict = trigdict()
for file in files:
for row in table.get_table(
ligolw_utils.load_filename(file,
contenthandler=lsctables.use_in(
ligolw.LIGOLWContentHandler)),
lsctables.SnglBurstTable.tableName):
channel = "%s-%s_%s" % (row.ifo, row.channel.replace(
"-", "_"), row.search)
tcent = row.peak_time + 1e-9 * row.peak_time_ns
tstart = row.start_time + 1e-9 * row.start_time_ns
dur = row.duration
fpeak = row.peak_frequency
fcent = row.central_freq
bndwth = row.bandwidth
amp = row.amplitude
snr = row.snr
conf = row.confidence
chi2 = row.chisq
chi2_dof = row.chisq_dof
trigger = [
tstart, dur, tcent, fpeak, fcent, bndwth, amp, snr, conf, chi2,
chi2_dof
]
if channel in trigs_dict.channels():
trigs_dict[channel].append(
trigger) ### SingleBurst trigger structure
else:
trigs_dict[channel] = [trigger]
return trigs_dict
from optparse import OptionParser from lal.utils import CacheEntry from glue.ligolw import ligolw from glue.ligolw import lsctables from glue.ligolw import utils from glue.ligolw.utils import process as ligolw_process from lalburst import git_version from lalburst import bucluster lsctables.use_in(ligolw.LIGOLWContentHandler) __author__ = "Kipp Cannon <*****@*****.**>" __version__ = "git id %s" % git_version.id __date__ = git_version.date # # ============================================================================= # # Command Line # # ============================================================================= #
"""
cache = lal.Cache()
for file in fileList:
AddFileToCache(file, cache)
return(cache)
class SummValueContentHandler(ligolw.PartialLIGOLWContentHandler):
"""
Content handler that only reads in the SummValue table
"""
def __init__(self, xmldoc):
ligolw.PartialLIGOLWContentHandler.__init__(self, xmldoc, lambda name, attrs: lsctables.IsTableProperties(lsctables.SummValueTable, name, attrs))
try:
lsctables.use_in(SummValueContentHandler)
except AttributeError:
# old glue did not allow .use_in().
# FIXME: remove when we can require the latest version of glue
pass
def initialise(opts, name, version = None):
"""
Create suffix and prefix that will be used to name the output files.
'version' is outdated and not used anymore.
@param opts : the user arguments (user_tag, gps_end_time and
gps_start_time are used).
@param name: name of the calling function/executable
@return prefix
def parse_veto_definer(veto_def_filename, ifos):
""" Parse a veto definer file from the filename and return a dictionary
indexed by ifo and veto definer category level.
Parameters
----------
veto_def_filename: str
The path to the veto definer file
ifos: str
The list of ifos for which we require information from the veto
definer file
Returns
--------
parsed_definition: dict
Returns a dictionary first indexed by ifo, then category level, and
finally a list of veto definitions.
"""
from glue.ligolw import table, lsctables, utils as ligolw_utils
from glue.ligolw.ligolw import LIGOLWContentHandler as h
lsctables.use_in(h)
data = {}
for ifo_name in ifos:
data[ifo_name] = {}
data[ifo_name]['CAT_H'] = []
for cat_num in range(1, 5):
data[ifo_name]['CAT_{}'.format(cat_num)] = []
indoc = ligolw_utils.load_filename(veto_def_filename, False,
contenthandler=h)
veto_table = table.get_table(indoc, 'veto_definer')
ifo = veto_table.getColumnByName('ifo')
name = veto_table.getColumnByName('name')
version = numpy.array(veto_table.getColumnByName('version'))
category = numpy.array(veto_table.getColumnByName('category'))
start = numpy.array(veto_table.getColumnByName('start_time'))
end = numpy.array(veto_table.getColumnByName('end_time'))
start_pad = numpy.array(veto_table.getColumnByName('start_pad'))
end_pad = numpy.array(veto_table.getColumnByName('end_pad'))
for i in range(len(veto_table)):
if ifo[i] not in data:
continue
# The veto-definer categories are weird! Hardware injections are stored
# in "3" and numbers above that are bumped up by one (although not
# often used any more). So we remap 3 to H and anything above 3 to
# N-1. 2 and 1 correspond to 2 and 1 (YAY!)
if category[i] > 3:
curr_cat = "CAT_{}".format(category[i]-1)
elif category[i] == 3:
curr_cat = "CAT_H"
else:
curr_cat = "CAT_{}".format(category[i])
veto_info = {'name': name[i],
'version': version[i],
'full_name': name[i]+':'+str(version[i]),
'start': start[i],
'end': end[i],
'start_pad': start_pad[i],
'end_pad': end_pad[i],
}
data[ifo[i]][curr_cat].append(veto_info)
return data
"""
import os, copy
import urlparse
import logging
from glue import segments, lal
from glue.ligolw import utils, table, lsctables, ligolw
from pycbc.workflow.core import OutSegFile, File, FileList, make_analysis_dir
from pycbc.frame import datafind_connection
class ContentHandler(ligolw.LIGOLWContentHandler):
pass
lsctables.use_in(ContentHandler)
def setup_datafind_workflow(workflow, scienceSegs, outputDir, segFilesList, tag=None):
"""
Setup datafind section of the workflow. This section is responsible for
generating, or setting up the workflow to generate, a list of files that
record the location of the frame files needed to perform the analysis.
There could be multiple options here, the datafind jobs could be done at
run time or could be put into a dag. The subsequent jobs will know
what was done here from the OutFileList containing the datafind jobs
(and the Dagman nodes if appropriate.
For now the only implemented option is to generate the datafind files at
runtime. This module can also check if the frameFiles actually exist, check
whether the obtained segments line up with the original ones and update the
science segments to reflect missing data files.
def ReadMultiInspiralTimeSlidesFromFiles(fileList,
generate_output_tables=False):
"""
Read time-slid multiInspiral tables from a list of files
@param fileList: list of input files
"""
if not fileList:
return multiInspiralTable(), None
multis = None
timeSlides = []
segmentDict = {}
for thisFile in fileList:
doc = utils.load_filename(thisFile,
gz=(thisFile or "stdin").endswith(".gz"),
contenthandler=lsctables.use_in(
ligolw.LIGOLWContentHandler))
# Extract the time slide table
timeSlideTable = table.get_table(doc,
lsctables.TimeSlideTable.tableName)
slideMapping = {}
currSlides = {}
# NOTE: I think some of this is duplicated in the glue definition of the
# time slide table. Probably should move over to that
for slide in timeSlideTable:
currID = int(slide.time_slide_id)
if currID not in currSlides.keys():
currSlides[currID] = {}
currSlides[currID][slide.instrument] = slide.offset
elif slide.instrument not in currSlides[currID].keys():
currSlides[currID][slide.instrument] = slide.offset
for slideID, offsetDict in currSlides.items():
try:
# Is the slide already in the list and where?
offsetIndex = timeSlides.index(offsetDict)
slideMapping[slideID] = offsetIndex
except ValueError:
# If not then add it
timeSlides.append(offsetDict)
slideMapping[slideID] = len(timeSlides) - 1
# Get the mapping table
segmentMap = {}
timeSlideMapTable = table.get_table(
doc, lsctables.TimeSlideSegmentMapTable.tableName)
for entry in timeSlideMapTable:
segmentMap[int(entry.segment_def_id)] = int(entry.time_slide_id)
# Extract the segment table
segmentTable = table.get_table(doc, lsctables.SegmentTable.tableName)
for entry in segmentTable:
currSlidId = segmentMap[int(entry.segment_def_id)]
currSeg = entry.get()
if not segmentDict.has_key(slideMapping[currSlidId]):
segmentDict[slideMapping[currSlidId]] = segments.segmentlist()
segmentDict[slideMapping[currSlidId]].append(currSeg)
segmentDict[slideMapping[currSlidId]].coalesce()
# extract the multi inspiral table
try:
multiInspiralTable = table.get_table(
doc, lsctables.MultiInspiralTable.tableName)
# Remap the time slide IDs
for multi in multiInspiralTable:
newID = slideMapping[int(multi.time_slide_id)]
multi.time_slide_id = ilwd.ilwdchar(\
"time_slide:time_slide_id:%d" % (newID))
if multis: multis.extend(multiInspiralTable)
else: multis = multiInspiralTable
# except: multiInspiralTable = None
except:
raise
if not generate_output_tables:
return multis, timeSlides, segmentDict
else:
# Make a new time slide table
timeSlideTab = lsctables.New(lsctables.TimeSlideTable)
for slideID, offsetDict in enumerate(timeSlides):
for instrument in offsetDict.keys():
currTimeSlide = lsctables.TimeSlide()
currTimeSlide.instrument = instrument
currTimeSlide.offset = offsetDict[instrument]
currTimeSlide.time_slide_id = ilwd.ilwdchar(\
"time_slide:time_slide_id:%d" % (slideID))
currTimeSlide.process_id = ilwd.ilwdchar(\
"process:process_id:%d" % (0))
timeSlideTab.append(currTimeSlide)
# Make a new mapping table
timeSlideSegMapTab = lsctables.New(lsctables.TimeSlideSegmentMapTable)
for i in range(len(timeSlides)):
currMapEntry = lsctables.TimeSlideSegmentMap()
currMapEntry.time_slide_id = ilwd.ilwdchar(\
"time_slide:time_slide_id:%d" % (i))
currMapEntry.segment_def_id = ilwd.ilwdchar(\
"segment_def:segment_def_id:%d" % (i))
timeSlideSegMapTab.append(currMapEntry)
# Make a new segment table
newSegmentTable = lsctables.New(lsctables.SegmentTable)
segmentIDCount = 0
for i in range(len(timeSlides)):
currSegList = segmentDict[i]
for seg in currSegList:
currSegment = lsctables.Segment()
currSegment.segment_id = ilwd.ilwdchar(\
"segment:segment_id:%d" %(segmentIDCount))
segmentIDCount += 1
currSegment.segment_def_id = ilwd.ilwdchar(\
"segment_def:segment_def_id:%d" % (i))
currSegment.process_id = ilwd.ilwdchar(\
"process:process_id:%d" % (0))
currSegment.set(seg)
currSegment.creator_db = -1
currSegment.segment_def_cdb = -1
newSegmentTable.append(currSegment)
return multis,timeSlides,segmentDict,timeSlideTab,newSegmentTable,\
timeSlideSegMapTab
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()
#from sbank import git_version FIXME
from lalinspiral.sbank.bank import Bank
from lalinspiral.sbank.tau0tau3 import proposals
from lalinspiral.sbank.psds import noise_models, read_psd, get_PSD
from lalinspiral.sbank.waveforms import waveforms, SnglInspiralTable
import lal
import lalsimulation as lalsim
class ContentHandler(ligolw.LIGOLWContentHandler):
pass
lsctables.use_in(ContentHandler)
usage = """
lalapps_cbc_sbank: This program generates a template bank for compact
binary searches covering a given region of mass and spin parameter
space. The program supports the waveform approximants listed below and
is designed to be easily extensible to other waveform approximants as
they become available (see waveforms.py for details).
Supported template approximants:
\t%s
Example command lines:
** Generate a template bank of positively aligned-spin
def load_injections(fname):
from glue.ligolw import lsctables, utils, ligolw
lsctables.use_in(ligolw.LIGOLWContentHandler)
xmldoc = utils.load_filename(fname,
contenthandler=ligolw.LIGOLWContentHandler)
return lsctables.SimInspiralTable.get_table(xmldoc)
def ReadMultiInspiralTimeSlidesFromFiles(fileList,generate_output_tables=False):
"""
Read time-slid multiInspiral tables from a list of files
@param fileList: list of input files
"""
if not fileList:
return multiInspiralTable(), None
multis = None
timeSlides = []
segmentDict = {}
for thisFile in fileList:
doc = utils.load_filename(thisFile,
gz=(thisFile or "stdin").endswith(".gz"), contenthandler = lsctables.use_in(ligolw.LIGOLWContentHandler))
# Extract the time slide table
timeSlideTable = lsctables.TimeSlideTable.get_table(doc)
slideMapping = {}
currSlides = {}
# NOTE: I think some of this is duplicated in the glue definition of the
# time slide table. Probably should move over to that
for slide in timeSlideTable:
currID = int(slide.time_slide_id)
if currID not in currSlides.keys():
currSlides[currID] = {}
currSlides[currID][slide.instrument] = slide.offset
elif slide.instrument not in currSlides[currID].keys():
currSlides[currID][slide.instrument] = slide.offset
for slideID,offsetDict in currSlides.items():
try:
# Is the slide already in the list and where?
offsetIndex = timeSlides.index(offsetDict)
slideMapping[slideID] = offsetIndex
except ValueError:
# If not then add it
timeSlides.append(offsetDict)
slideMapping[slideID] = len(timeSlides) - 1
# Get the mapping table
segmentMap = {}
timeSlideMapTable = lsctables.TimeSlideSegmentMapTable.get_table(doc)
for entry in timeSlideMapTable:
segmentMap[int(entry.segment_def_id)] = int(entry.time_slide_id)
# Extract the segment table
segmentTable = lsctables.SegmentTable.get_table(doc)
for entry in segmentTable:
currSlidId = segmentMap[int(entry.segment_def_id)]
currSeg = entry.get()
if not segmentDict.has_key(slideMapping[currSlidId]):
segmentDict[slideMapping[currSlidId]] = segments.segmentlist()
segmentDict[slideMapping[currSlidId]].append(currSeg)
segmentDict[slideMapping[currSlidId]].coalesce()
# extract the multi inspiral table
try:
multiInspiralTable = lsctables.MultiInspiralTable.get_table(doc)
# Remap the time slide IDs
for multi in multiInspiralTable:
newID = slideMapping[int(multi.time_slide_id)]
multi.time_slide_id = ilwd.ilwdchar(\
"time_slide:time_slide_id:%d" % (newID))
if multis: multis.extend(multiInspiralTable)
else: multis = multiInspiralTable
# except: multiInspiralTable = None
except: raise
if not generate_output_tables:
return multis,timeSlides,segmentDict
else:
# Make a new time slide table
timeSlideTab = lsctables.New(lsctables.TimeSlideTable)
for slideID,offsetDict in enumerate(timeSlides):
for instrument in offsetDict.keys():
currTimeSlide = lsctables.TimeSlide()
currTimeSlide.instrument = instrument
currTimeSlide.offset = offsetDict[instrument]
currTimeSlide.time_slide_id = ilwd.ilwdchar(\
"time_slide:time_slide_id:%d" % (slideID))
currTimeSlide.process_id = ilwd.ilwdchar(\
"process:process_id:%d" % (0))
timeSlideTab.append(currTimeSlide)
# Make a new mapping table
timeSlideSegMapTab = lsctables.New(lsctables.TimeSlideSegmentMapTable)
for i in range(len(timeSlides)):
currMapEntry = lsctables.TimeSlideSegmentMap()
currMapEntry.time_slide_id = ilwd.ilwdchar(\
"time_slide:time_slide_id:%d" % (i))
currMapEntry.segment_def_id = ilwd.ilwdchar(\
"segment_def:segment_def_id:%d" % (i))
timeSlideSegMapTab.append(currMapEntry)
# Make a new segment table
newSegmentTable = lsctables.New(lsctables.SegmentTable)
segmentIDCount = 0
for i in range(len(timeSlides)):
currSegList = segmentDict[i]
for seg in currSegList:
currSegment = lsctables.Segment()
currSegment.segment_id = ilwd.ilwdchar(\
"segment:segment_id:%d" %(segmentIDCount))
segmentIDCount += 1
currSegment.segment_def_id = ilwd.ilwdchar(\
"segment_def:segment_def_id:%d" % (i))
currSegment.process_id = ilwd.ilwdchar(\
"process:process_id:%d" % (0))
currSegment.set(seg)
currSegment.creator_db = -1
currSegment.segment_def_cdb = -1
newSegmentTable.append(currSegment)
return multis,timeSlides,segmentDict,timeSlideTab,newSegmentTable,\
timeSlideSegMapTab
def startElement(self, name, attrs):
if attrs.has_key('Name') and table.Table.TableName(
attrs['Name']) == self.tabname:
self.tableElementName = name
# Got the right table, let's see if it's the right event
ligolw.LIGOLWContentHandler.startElement(self, name, attrs)
self.intable = True
elif self.intable: # We are in the correct table
ligolw.LIGOLWContentHandler.startElement(self, name, attrs)
def endElement(self, name):
if self.intable: ligolw.LIGOLWContentHandler.endElement(self, name)
if self.intable and name == self.tableElementName: self.intable = False
lsctables.use_in(LIGOLWContentHandlerExtractSimBurstTable)
posterior_name_to_sim_burst_extractor = {
'frequency': lambda sb: sb.frequency,
'duration': lambda sb: sb.duration,
'quality': lambda sb: sb.q,
'hrss': lambda sb: sb.hrss,
'psi': lambda sb: sb.psi,
'time': lambda sb: sb.time_geocent_gps + 1e-9 * sb.time_geocent_gps_ns,
'ra': lambda sb: sb.ra,
'dec': lambda sb: sb.dec,
'polar_angle': lambda sb: sb.pol_ellipse_angle,
'polar_eccentricity': lambda sb: sb.pol_ellipse_e,
'alpha': lambda sb: sb.pol_ellipse_angle
}
parser.add_option('--injXML', action='store', type='string', dest='injxml',
help='sim_inspiral XML file for injections')
parser.add_option('--outdir', action='store', type='string',
help='output directory')
parser.add_option('--postsamples', action='store', type='string',
default='posterior_samples.dat',
help='filename for posterior samples files')
parser.add_option('--par', action='append', default=[], type='string',
help='parameter names for the p-p plot')
parser.add_option('--skyPPfolder', action='store',dest='skypp',type='string',default=None,help='Path to folder containing png/pdf with 2D skyarea PP plots')
(options, args) = parser.parse_args()
injs = lsctables.SimInspiralTable.get_table(utils.load_filename(options.injxml,contenthandler=lsctables.use_in(ligolw.LIGOLWContentHandler)))
if options.par == []:
parameters = ['m1', 'm2', 'mc', 'eta', 'q', 'theta_jn', 'a1', 'a2', 'tilt1', 'tilt2', 'phi12', 'phi_jl', 'ra', 'dec', 'distance', 'time', 'phi_orb', 'psi']
else:
parameters = options.par
try:
os.mkdir(options.outdir)
except:
pass
pvalues = { }
posfiles=args
Ninj=0
for index,posfile in enumerate(posfiles):
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
}
#
# Remove everything between the dashed lines once we get rid of xml
# -----------------------------------------------------------------------------
#
from glue.ligolw import utils as ligolw_utils
from glue.ligolw import ligolw, table, lsctables
# dummy class needed for loading LIGOLW files
class LIGOLWContentHandler(ligolw.LIGOLWContentHandler):
pass
lsctables.use_in(LIGOLWContentHandler)
# Map parameter names used in pycbc to names used in the sim_inspiral
# table, if they are different
sim_inspiral_map = {
'ra': 'longitude',
'dec': 'latitude',
'approximant': 'waveform',
}
def set_sim_data(inj, field, data):
"""Sets data of a SimInspiral instance."""
try:
sim_field = sim_inspiral_map[field]
except KeyError:
from glue.ligolw import ligolw, lsctables, table, utils
import matplotlib
matplotlib.use('Agg')
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
import pycbc.pnutils
import pycbc.events
from pycbc.waveform import get_td_waveform, frequency_from_polarizations, amplitude_from_polarizations
import lal
logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
class DefaultContentHandler(ligolw.LIGOLWContentHandler):
pass
lsctables.use_in(DefaultContentHandler)
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('--coinc-file', type=str, required=True,
help='HDF file containing coincident CBC triggers')
parser.add_argument('--single-ifo-trigs', type=str, required=True,
help='HDF file containing single IFO CBC triggers')
parser.add_argument('--ifo', type=str, required=True,
help='IFO, L1 or H1')
parser.add_argument('--tmpltbank-file', type=str, required=True,
help='HDF file containing template information for CBC search')
parser.add_argument('--output-file', type=str, required=True,
help='Full path to output file')
parser.add_argument('--loudest-event-number', type=int, required=True, default=1,
help='Script will plot the Nth loudest coincident trigger')
parser.add_argument('--omicron-dir', type=str, required=True,
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
from pycbc.workflow.segment import fromsegmentxml
import pycbc.pnutils
import pycbc.events
from pycbc.waveform import get_td_waveform, frequency_from_polarizations, amplitude_from_polarizations
import lal
logging.basicConfig(format='%(asctime)s %(message)s', level=logging.INFO)
class DefaultContentHandler(ligolw.LIGOLWContentHandler):
pass
lsctables.use_in(DefaultContentHandler)
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('--coinc-file',
type=str,
required=True,
help='HDF file containing coincident CBC triggers')
parser.add_argument('--single-ifo-trigs',
type=str,
required=True,
help='HDF file containing single IFO CBC triggers')
parser.add_argument('--ifo', type=str, required=True, help='IFO, L1 or H1')
parser.add_argument(
'--tmpltbank-file',
type=str,
required=True,
help="")
( opts , args ) = parser.parse_args()
required_opts = ["name", "time", "padding_time", "config_file", "injection_config", "log_path"]
for opt in required_opts:
if getattr(opts, opt) is None:
raise ValueError("--%s is a required option" % opt)
if not opts.grb_file and (not opts.time or not opts.name):
raise ValueError("Either a valid GRB xml file must be specified or the GPS time and name of the GRB!")
##############################################################################
# find available data
if opts.grb_file:
xmldoc = utils.load_filename(opts.grb_file, gz=opts.grb_file.endswith('.gz'), contenthandler = lsctables.use_in(ligolw.LIGOLWContentHandler))
ext_table = lsctables.ExtTriggersTable.get_table(xmldoc)
grb_time = ext_table[0].start_time
grb_name = os.path.basename(opts.grb_file)[3:-4]
grb_ra = ext_table[0].event_ra
grb_dec = ext_table[0].event_dec
else:
grb_name = opts.name[0]
grb_time = int(opts.time)
grb_ra = float(opts.ra)
grb_dec = float(opts.dec)
exttrig_config_file, grb_ifolist, onSourceSegment, offSourceSegment = exttrig_dataquery.exttrig_dataquery(grb_name, grb_time, grb_ra, grb_dec, opts.offset, opts.config_file, opts.extend, opts.useold, opts.make_plots, opts.make_xml)
##############################################################################
# create the config parser object and exttrig_dataquery ini file
from glue.ligolw import utils
import lalinference.cmap
from lalinference import fits
from lalinference import plot
import healpy as hp
import numpy as np
import os
import pickle
import sky_area.sky_area_clustering as sac
import matplotlib.pyplot as pp
class LIGOLWContentHandler(ligolw.LIGOLWContentHandler):
pass
lsctables.use_in(LIGOLWContentHandler)
def plot_skymap(output, skypost, pixresol=np.pi/180.0, nest=True,inj=None, fast=True):
nside = 1
while hp.nside2resol(nside) > pixresol:
nside *= 2
pix_post = skypost.as_healpix(nside, nest=nest, fast=fast)
fig = pp.figure(frameon=False)
ax = pp.subplot(111, projection='astro mollweide')
ax.cla()
ax.grid()
plot.healpix_heatmap(pix_post, nest=nest, vmin=0.0, vmax=np.max(pix_post), cmap=pp.get_cmap('cylon'))
if inj is not None:
def createInjectionFile(hipe_dir, cp, cpinj, injrun, injection_segment,
source_file, ipn_gps=None, usertag=None, verbose=False):
"""
Creates an master injection file containing all injections for this run.
Also reads the file and returns its contents
"""
cpinj = copy.deepcopy(cpinj)
# get the number of injections to be made
for opt in ['exttrig-inj-start','exttrig-inj-stop']:
value = int(cpinj.get(injrun,opt))
cpinj.remove_option(injrun,opt)
if 'start' in opt:
injStart = value
else:
injEnd = value
seed = hash_n_bits(hipe_dir, 31)
numberInjections = injEnd - injStart + 1 # e.g., 1 through 5000 inclusive
# get the jitter parameters
if cpinj.has_option(injrun, "jitter-skyloc"):
jitter_sigma_deg = cpinj.getfloat(injrun, "jitter-skyloc")
cpinj.remove_option(injrun, "jitter-skyloc")
else:
jitter_sigma_deg = None
# check if the specific Fermi systematic error needs to
# be added to the location jittering
if cpinj.has_option(injrun, "jitter-skyloc-fermi"):
jitter_skyloc_fermi = cpinj.getboolean(injrun, "jitter-skyloc-fermi")
cpinj.remove_option(injrun, "jitter-skyloc-fermi")
else:
jitter_skyloc_fermi = False
# check if we should align the total angular momentum
if cpinj.has_option(injrun, "align-total-spin"):
align_total_spin = cpinj.getboolean(injrun, "align-total-spin")
cpinj.remove_option(injrun, "align-total-spin")
else:
align_total_spin = False
# set all the arguments
argument = []
for (opt,value) in cpinj.items(injrun):
argument.append("--%s %s" % (opt, value) )
# add arguments on times and time-intervals
interval = abs(injection_segment)
injInterval = interval / numberInjections
argument.append(" --gps-start-time %d" % injection_segment[0] )
argument.append(" --gps-end-time %d" % injection_segment[1] )
argument.append(" --time-interval %f" % injInterval )
argument.append(" --time-step %f" % injInterval )
argument.append(" --seed %d" % seed )
argument.append(" --user-tag %s" % usertag)
# set output file as exttrig-file or IPN file with IPN GPS time
if ipn_gps:
argument.append(" --ipn-gps-time %d" % ipn_gps )
else:
argument.append(" --exttrig-file %s" % source_file )
# execute the command
executable = cp.get("condor", "inspinj")
arguments = " ".join(argument)
inspiralutils.make_external_call(executable + " " + arguments,
show_command=verbose)
# recreate the output filename
injFile = "HL-INJECTIONS_" + str(seed)
if usertag is not None:
injFile += "_" + usertag
injFile += "-%d-%d.xml" % (injection_segment[0], abs(injection_segment))
# move it into the GRB directory to avoid clutter
new_injFile = hipe_dir + "/" + injFile
os.rename(injFile, new_injFile)
# jitter the sky locations of the injections
if jitter_sigma_deg is not None:
# rename the original, then have ligolw_cbc_jitter_skyloc create a new one
os.rename(new_injFile, new_injFile + ".prejitter")
cmd = ["ligolw_cbc_jitter_skyloc"]
if jitter_skyloc_fermi:
cmd.append("--apply-fermi-error")
cmd.extend(["--jitter-sigma-deg",
str(jitter_sigma_deg), "--output-file", new_injFile,
new_injFile + ".prejitter"])
if verbose:
print(" ".join(cmd))
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = p.communicate()
if p.returncode != 0:
raise subprocess.CalledProcessError(p.returncode, "%s: %s" % (" ".join(cmd), err))
# rotate the binary so that total angular momentum has the current inclination
if align_total_spin:
# rename the original then have ligolw_cbc_align_total_spin create a new one
os.rename(new_injFile, new_injFile + ".prealign")
cmd = ["ligolw_cbc_align_total_spin", "--output-file", new_injFile,
new_injFile + ".prealign"]
if verbose:
print(" ".join(cmd))
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = p.communicate()
if p.returncode != 0:
raise subprocess.CalledProcessError(p.returncode, "%s: %s" % (" ".join(cmd), err))
# read in the file and the tables
doc = utils.load_filename(new_injFile, contenthandler = lsctables.use_in(ligolw.LIGOLWContentHandler))
sims = lsctables.SimInspiralTable.get_table(doc)
return sims, injInterval, numberInjections, new_injFile
print >> index_html_obj, "Target Channel: %s"%gwchannel
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
def check_segment_availability(grb_name, grb_time, query_start, query_end, offset, ifo, segmentName):
'''
Searches +/- offset from GRB time to download the latest segment lists then extracts times and puts them into a txt file.
'''
args = {'grb_name' : grb_name,
'query_start' : query_start,
'query_end' : query_end,
'ifo' : ifo,
'segmentName' : segmentName}
cmd = "ligolw_segment_query --database --query-segments --include-segments '{segmentName}' --gps-start-time {query_start} --gps-end-time {query_end} > ./segments{ifo}_grb{grb_name}.xml".format(**args)
print '>>',cmd
print
process = subprocess.Popen([cmd], shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
output,err = process.communicate()
# try to open the file
try:
doc = utils.load_filename("segments{ifo}_grb{grb_name}.xml".format(**args), contenthandler = lsctables.use_in(ligolw.LIGOLWContentHandler))
except:
raise IOError, "Error reading file: segments{ifo}_grb{grb_name}.xml".format(**args)
# extract the segment list from segment:table and store in a txt file
segs = table.get_table(doc, "segment")
seglist = segments.segmentlist(segments.segment(s.start_time, s.end_time) for s in segs)
segmentsUtils.tosegwizard(file("{ifo}-science_grb{grb_name}.txt".format(**args),'w'),seglist,header = True)
print ">> %s segments +/-%ds from %ds found:"%(ifo,offset,grb_time)
for s in segs:
print "Start:",s.start_time,"End:",s.end_time,"Duration:",s.end_time-s.start_time
print
return
def table_from_file(f,
tablename,
columns=None,
filt=None,
contenthandler=None,
nproc=1,
verbose=False):
"""Read a `~glue.ligolw.table.Table` from a LIGO_LW file.
Parameters
----------
f : `file`, `str`, `CacheEntry`, `list`, `Cache`
object representing one or more files. One of
- an open `file`
- a `str` pointing to a file path on disk
- a formatted `~lal.utils.CacheEntry` representing one file
- a `list` of `str` file paths
- a formatted `~glue.lal.Cache` representing many files
tablename : `str`
name of the table to read.
columns : `list`, optional
list of column name strings to read, default all.
filt : `function`, optional
function by which to `filter` events. The callable must accept as
input a row of the table event and return `True`/`False`.
contenthandler : `~glue.ligolw.ligolw.LIGOLWContentHandler`
SAX content handler for parsing LIGO_LW documents.
Returns
-------
table : `~glue.ligolw.table.Table`
`Table` of data with given columns filled
"""
from glue.ligolw.ligolw import Document
from glue.ligolw import (table, lsctables)
from glue.ligolw.utils.ligolw_add import ligolw_add
# find table class
tableclass = lsctables.TableByName[table.Table.TableName(tablename)]
# get content handler
if contenthandler is None:
contenthandler = get_partial_contenthandler(tableclass)
# allow cache multiprocessing
if nproc != 1:
return tableclass.read(f,
columns=columns,
contenthandler=contenthandler,
nproc=nproc,
format='cache')
lsctables.use_in(contenthandler)
# set columns to read
if columns is not None:
_oldcols = tableclass.loadcolumns
tableclass.loadcolumns = columns
# generate Document and populate
files = file_list(f)
xmldoc = Document()
ligolw_add(xmldoc,
files,
non_lsc_tables_ok=True,
contenthandler=contenthandler,
verbose=verbose)
# extract table
out = tableclass.get_table(xmldoc)
if verbose:
gprint('%d rows found in %s table' % (len(out), out.tableName))
# filter output
if filt:
if verbose:
gprint('filtering rows ...', end=' ')
try:
out_ = out.copy()
except AttributeError:
out_ = table.new_from_template(out)
out_.extend(filter(filt, out))
out = out_
if verbose:
gprint('%d rows remaining\n' % len(out))
# reset loadcolumns and return
if columns is not None:
tableclass.loadcolumns = _oldcols
return out
def exttrig_dataquery(grb_name, grb_time, grb_ra, grb_dec, offset, config_file, extend=False, useold=False, make_plots=False, make_xml=False):
'''
Finds science time of all available IFOs.
'''
##############################################################################
# get segment duration and minimum amount of science time
##############################################################################
# read the configuration file
cp = ConfigParser.ConfigParser()
cp.read(config_file)
# define hardcoded variables
basic_ifolist = ifolist = ['H1','H2','L1','V1']
catlist = [1,2,3]
sensitivity_dict = {"H1": 1, "L1": 2, "H2": 3, "V1": 4, "G1": 5}
# get segment length from configuration file
pad_data = int(cp.get('data','pad-data'))
if cp.has_option('data','segment-duration'):
blockDuration = segmentDuration = psdDuration = int(cp.get('data','segment-duration'))
elif cp.has_option('data','segment-length'):
blockDuration = segmentDuration = psdDuration = int(cp.get('data','segment-length')) /int(cp.get('data','sample-rate'))
else:
raise ValueError, "EXIT: Cannot find segment-duration in [data] section of configuration file!"
# get sample rate
if cp.has_option('data','sample-rate'):
sampleRate = int(cp.get('data', 'sample-rate'))
print ">> Sample rate has been set to: %d"%sampleRate
print
else:
print ">> ERROR: Need to specify sample-rate in [data] section of configuration file in order to calculate inputs for downstream processes."
sys.exit()
# if not extend option then need to get block duration
if not extend:
if cp.has_option('data','block-duration'):
blockDuration = int(cp.get('data','block-duration'))
elif cp.has_option('data','segment-length'):
s_length = int(cp.get('data', 'segment-length'))
s_num = int(cp.get('data', 'number-of-segments'))
s_rate = int(cp.get('data', 'sample-rate'))
s_overlap = int(cp.get('inspiral', 'segment-overlap'))
# calculate blockDuration
blockDuration = ( s_length * s_num - ( s_num - 1 ) * s_overlap ) / s_rate
else:
raise ValueError, "EXIT: Cannot find block-duration in [data] section of configuration file! Either set block-duration or use --extend option."
# calculate the minimum amount of science time need and how the length of quanta to be added on both ends of the analysis time
minscilength = blockDuration + 2 * pad_data
quanta = segmentDuration / 2
# if extend beyond minscilength; add segments of quanta length to each end of segment
print ">> Minimum science segment length is: %ss"%minscilength
print
if extend:
print ">> Will extend minimum science segment by quanta of: %ss"%quanta
print
##############################################################################
# get list of segments for each IFO and put in science txt file
##############################################################################
if not useold:
# external call to ligolw_segment_query
query_start = int(grb_time - offset)
query_end = int(grb_time + offset)
for ifo in ifolist:
if cp.has_option('segments','%s-segments'%ifo.lower()):
segmentName = cp.get('segments','%s-segments'%ifo.lower())
check_segment_availability(grb_name, grb_time, query_start, query_end, offset, ifo, segmentName)
##############################################################################
# get veto files
##############################################################################
if not useold:
# get and read veto definer file
veto_file_url = cp.get('exttrig','cvs_veto_definer')
veto_file_path,headers = urllib.urlretrieve(veto_file_url,os.path.basename(veto_file_url))
# do ligolw_segments_from_cats
deltat = 500
args = {'start_time' : int(grb_time - offset - deltat),
'end_time' : int(grb_time + offset + deltat),
'veto_file_path' : veto_file_path}
cmd = "ligolw_segments_from_cats --database --veto-file={veto_file_path} --separate-categories --gps-start-time {start_time} --gps-end-time {end_time} --output-dir=. --individual-results".format(**args)
print '>>',cmd
print
process = subprocess.Popen([cmd], shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
output,err = process.communicate()
# Rename the veto files for easier handling
veto_files = glob.glob('./*VETOTIME_CAT*{start_time}*xml'.format(**args))
for filename in veto_files:
p = filename.split('-')
newname = "%s-%s_grb%s.xml"%(p[0], p[1], grb_name)
shutil.move(filename, newname)
##############################################################################
# look in txt files and find segment with onsource and minscilength
##############################################################################
# create segment that is +/- offset of GRB time
onsource = [grb_time - int(cp.get('exttrig','onsource_left')),\
grb_time + int(cp.get('exttrig','onsource_right'))]
onSourceSegment = segments.segment(onsource[0], onsource[1])
# get segments in science txt files; see if segments length at least minscilength
# if no then discard them; if yes then put in segdict[ifo] and ifo in ifolist
basic_segdict = segdict = segments.segmentlistdict()
for ifo in ifolist:
# check configuration file
if not cp.has_option('segments','%s-segments' % ifo.lower()):
continue
# find segment with onsource and check it is at least minscilength
ifo_segfile = '%s-science_grb%s.txt' %(ifo, grb_name)
if os.path.exists(ifo_segfile):
tmplist = segmentsUtils.fromsegwizard(open(ifo_segfile))
try:
s = tmplist.find(onSourceSegment)
except ValueError:
# if onsource not in segments then move on to next IFO
continue
if abs(tmplist[s]) >= minscilength:
segdict[ifo] = segments.segmentlist([tmplist[s]])
basic_segdict[ifo] = segments.segmentlist([s for s in tmplist])
ifolist = segdict.keys()
if len(ifolist) < 2:
print "EXIT: Less than 2 interferometers have available data!"
sys.exit()
##############################################################################
# apply vetoes
##############################################################################
# apply
print ">> Vetoes that overlap with science segments:"
for ifo in ifolist:
# flag; True if IFO not vetoed
cat_flag = True
for cat in catlist:
# create list and check for overlaps
xmlsegfile = "./%s-VETOTIME_CAT%s_grb%s.xml" %(ifo, cat, grb_name)
if os.path.exists(xmlsegfile) and cat_flag:
testseg = segments.segment([segdict[ifo][0][0],segdict[ifo][0][1]])
list_overlaps = []
# load the content of the veto-file
xmldoc = utils.load_filename(xmlsegfile, gz = False, contenthandler = lsctables.use_in(ligolw.LIGOLWContentHandler))
segs = lsctables.SegmentTable.get_table(xmldoc)
segdefs = lsctables.SegmentDefTable.get_table(xmldoc)
# create a mapping between the segments and their definitions
defdict = {}
for segdef in segdefs:
defdict[segdef.segment_def_id] = segdef.name
# find veto segments that intersect science segment of IFO with onsource
for seg in segs:
s = segments.segment(seg.start_time, seg.end_time)
if testseg.intersects(s):
id = seg.segment_def_id
list_overlaps.append([defdict[id], seg.start_time, seg.end_time])
# cut veto CAT1 segments out of science segment; CAT1,2,3 veto IFO if in onsource will veto IFO
for name, segstart, segend in list_overlaps:
print "CAT%s IFO %s, Start: %d End: %d because %s"%(cat, ifo, segstart, segend, name)
s = segments.segment(segstart, segend)
if onSourceSegment.intersects(s):
segdict.pop(ifo, None)
cat_flag = False
break
if cat == 1:
vetoes = segments.segmentlist(segments.segment(s[1], s[2]) for s in list_overlaps)
segdict[ifo] -= vetoes
# get list of IFOs
ifolist = segdict.keys()
print
if len(ifolist) < 2:
print "EXIT: After vetoes, less than 2 interferometers have available data!"
sys.exit()
##############################################################################
# determine segment to be analyzed
##############################################################################
# sort from most sensitive to least sensitive
def sensitivity_cmp(ifo1, ifo2):
return cmp(sensitivity_dict[ifo1], sensitivity_dict[ifo2])
ifolist.sort(sensitivity_cmp)
# compares IFOs and finds the segment to analyze
# now try getting off-source segments
# start trying with all IFOs
# work our way through subsets; beginning with most sensitive combinations
test_combos = itertools.chain(*itertools.imap(lambda n: iterutils.choices(ifolist, n), xrange(len(ifolist), 1, -1)))
off_source_segment = None
the_ifo_combo = []
for ifo_combo in test_combos:
# find conincident science time of IFOs
trial_seglist = segdict.intersection(ifo_combo)
if abs(trial_seglist) < minscilength:
print "EXIT: IFOs do not overlap enough for minscilength",abs(trial_seglist)
sys.exit()
else:
pass
# find segment with grb_time inside
try:
super_seg = trial_seglist[trial_seglist.find(onSourceSegment)].contract(pad_data)
except ValueError:
print "EXIT: ValueError with super_seg"
sys.exit()
if onSourceSegment not in super_seg:
print "EXIT: onsource not in super_seg"
sys.exit()
# find int division of onsource time intervals before and after grb
tplus = (super_seg[1] - onSourceSegment[1])
tminus = (onSourceSegment[0] - super_seg[0])
# get minimum number of onsource time intervals in offsource
tmin = ( minscilength - 2*pad_data - abs(onSourceSegment) )
# cut to get minscilength
if tplus + tminus > tmin:
half_max = tmin // 2
if tplus < half_max:
print ">> Left sticks out so cut it."
remainder = tmin - tplus
tminus = min(remainder, tminus)
elif tminus < half_max:
print ">> Right sticks out so cut it."
remainder = tmin - tminus
tplus = min(remainder, tplus)
else:
print ">> Both sides stick out so cut as symmetrically as possible."
tminus = half_max
tplus = tmin - half_max # odd trial sticks out on right
if tplus + tminus < tmin:
offsource = None
temp_segment = segments.segment((onSourceSegment[0] - tminus - pad_data, onSourceSegment[1] + tplus + pad_data))
if temp_segment is not None:
offsource = temp_segment
ifolist = list(ifo_combo)
if extend:
# extend as many adjacent 128 second blocks as possible
begin_time = offsource[0] - quanta * (abs(super_seg[0]-offsource[0])//quanta)
end_time = offsource[1] + quanta * (abs(super_seg[1]-offsource[1])//quanta)
offsource = segments.segment((begin_time,end_time))
break
print
# check length at least minscilength
if abs(offsource) < minscilength:
print abs(offsource),minscilength
print "EXIT: Calculated offsource segment but less than minscilength!"
sys.exit()
# check if no detectors can be used then exit
if len(ifolist) < 2:
print "EXIT: Calculated offsource segment but less than two IFOs!"
sys.exit()
# check edge case
if abs(offsource[0]-onsource[0]) < pad_data or abs(offsource[1]-onsource[1]) < pad_data:
print "WARNING: GRB time close to edge of offsource. Its within the padding time."
# concatenate "H1L1V1", etc.
ifolist.sort()
ifotag = "".join(ifolist)
print ">> Offsource segment for %s GRB is:"%ifotag
print "Start:",offsource[0],"End:",offsource[1],"Duration:",offsource[1]-offsource[0],"Left:",grb_time-offsource[0],"Right:",offsource[1]-grb_time
print
##############################################################################
# output
##############################################################################
# write analyse txt files
for ifo in basic_ifolist:
if ifo in ifolist:
analysisFP = open('%s-analyse_grb%s.txt' %(ifo,grb_name),'w')
analysisFP.write('# seg\t start \t stop \t duration\n')
analysisFP.write('0\t %d\t %d\t %d\n' %(offsource[0],offsource[1],offsource[1]-offsource[0]))
else:
analysisFP = open('%s-analyse_grb%s.txt' %(ifo,grb_name),'w')
analysisFP.write('# seg\t start \t stop \t duration\n')
# calculate blockDuration
blockDuration = int(abs(offsource[0]-offsource[1])) - 2 * pad_data
# calculate psdDuration
# gets largest power of two such that blockDuration/psdDuration = psdRatio
# could have done a binary & operator that is faster but this is more user-friendly I believe
min_psdDuration = int(cp.get('exttrig', 'min-psd-length'))
psdRatio = int(cp.get('exttrig', 'psd-ratio'))
psdDuration = 2**int(numpy.log2(blockDuration/psdRatio))
if psdDuration < min_psdDuration:
print "EXIT: PSD segment duration is too short. It is %ds but needs to be at least %ds in length."%(psdDuration,min_psdDuration)
sys.exit()
# some downstream processes (e.g. lalapps_tmpltbank) cannot handle these inputs
if cp.has_option('data', 'segment-duration'):
cp.remove_option('data', 'segment-duration')
cp.remove_option('data', 'block-duration')
# some downstream processes (e.g. lalapps_tmpltbank) requires these options to run
print ">> Using sample rate of %d to calculate inputs for downstream processes."%sampleRate
print
segmentLength = segmentDuration*sampleRate
segmentCount = blockDuration/(segmentDuration/2) - 1 # subtract 1 because one segment length is overlapped
segmentOverlap = segmentLength/2
cp.set('data', 'segment-length', segmentLength)
cp.set('data', 'number-of-segments', segmentCount)
cp.set('inspiral', 'segment-overlap', segmentOverlap)
# set values for [coh_PTF_inspral] section in configuration file
cp.set('coh_PTF_inspiral', 'block-duration', blockDuration)
cp.set('coh_PTF_inspiral', 'segment-duration', segmentDuration)
cp.set('coh_PTF_inspiral', 'psd-segment-duration', psdDuration)
cp.set('coh_PTF_inspiral', 'pad-data', pad_data)
f = open('grb%s.ini'%grb_name,'w')
cp.write(f)
f.close()
print ">> The [data] section of the configuration file has been edited with the following values:"
print "sample-rate=",sampleRate
print "segment-length=",segmentLength
print "number-of-segments=",segmentCount
print "segment-overlap=",segmentOverlap
print
print ">> The [coh_PTF_inspiral] section of the configuration file has been edited with the following values:"
print "block-duration =",blockDuration
print "segment-duration =",segmentDuration
print "psd-segment-duration =",psdDuration
print "pad-data =",pad_data
print
# plot segments
offSourceSegment = segments.segment(offsource[0], offsource[1])
plot_window = segments.segment(grb_time-offset, grb_time+offset)
plot_segments(basic_segdict, onSourceSegment, offSourceSegment, grb_time, plot_window, "segment_plot_%s.png"%grb_name, grb_name)
# make xml file
if make_xml:
# create a new xml document with an ExtTriggers Table
xmldoc = ligolw.Document()
xmldoc.appendChild(ligolw.LIGO_LW())
tbl = lsctables.New(lsctables.ExtTriggersTable)
xmldoc.childNodes[-1].appendChild(tbl)
# set the values we need
row = lsctables.ExtTriggersTable()
row.process_id = None
row.det_alts = None
row.det_band = None
row.det_fluence = None
row.det_fluence_int = None
row.det_name = None
row.det_peak = None
row.det_peak_int = None
row.det_snr = ''
row.email_time = 0
row.event_dec = float(grb_dec)
row.event_dec_err = 0.0
row.event_epoch = ''
row.event_err_type = ''
row.event_ra = float(grb_ra)
row.event_ra_err = 0.0
row.start_time = grb_time
row.start_time_ns = 0
row.event_type = ''
row.event_z = 0.0
row.event_z_err = 0.0
row.notice_comments = ''
row.notice_id = ''
row.notice_sequence = ''
row.notice_time = 0
row.notice_type = ''
row.notice_url = ''
row.obs_fov_dec = 0.0
row.obs_fov_dec_width = 0.0
row.obs_fov_ra = 0.0
row.obs_fov_ra_width = 0.0
row.obs_loc_ele = 0.0
row.obs_loc_lat = 0.0
row.obs_loc_long = 0.0
row.ligo_fave_lho = 0.0
row.ligo_fave_llo = 0.0
row.ligo_delay = 0.0
row.event_number_gcn = 9999
row.event_number_grb = grb_name
row.event_status = 0
# insert into the table and write file
tbl.extend([row])
filename = 'grb%s.xml' % grb_name
utils.write_filename(xmldoc, filename)
# plot all vetoes
if make_plots:
vetodict = segments.segmentlistdict()
for cat in catlist:
for ifo in ifolist:
vetofile = "%s-VETOTIME_CAT%s_grb%s.xml" % (ifo, cat, grb_name)
xmldoc = utils.load_filename(vetofile, gz = False, contenthandler = lsctables.use_in(ligolw.LIGOLWContentHandler))
segs = lsctables.SegmentTable.get_table(xmldoc)
segdefs = lsctables.SegmentDefTable.get_table(xmldoc)
vetodict[ifo] = segments.segmentlist(segments.segment(s.start_time, s.end_time) for s in segs)
if vetodict:
plot_segments(vetodict, onSourceSegment, offSourceSegment, grb_time, plot_window, "veto_plot_CAT%s_%s.png"%(cat,grb_name), "%s CAT%s"%(grb_name, cat))
# return
return 'grb%s.ini'%grb_name, ifolist, onSourceSegment, offSourceSegment