def vn_ldas_gap_check(vn_xml_file,vn_flag,ldas_gap_xml_file):
# read in summary intervals of vn_flag
vndoc = ligolw_utils.load_url(vn_xml_file, gz = (vn_xml_file or "stdin").endswith(".gz"))
vn_sums=segmentdb_utils.find_segments(vndoc,"%s" % vn_flag,use_segment_table=False)
# read in segment and summary intervals of LDAS allowed gaps
ldasdoc = ligolw_utils.load_url(ldas_gap_xml_file, gz = (ldas_gap_xml_file or "stdin").endswith(".gz"))
ldas_gaps=segmentdb_utils.find_segments(ldasdoc,'H1:RESULT:1')
ldas_sums=segmentdb_utils.find_segments(ldasdoc,'H1:DCH-MISSING_LDAS_C02_L2:1',use_segment_table=False)
if len(ldas_sums) == 0:
message = "no LDAS info was found within the specified time in the database!"
print(message)
return
# if valid Vn file and ldas files both found, do further testings:
if len(vn_sums) > 1 :
vn_sum_gaps=segmentlist([segment(vn_sums[0][0],vn_sums[-1][1])]) - vn_sums
if vn_sum_gaps == ldas_gaps:
message = ""
else:
message = "test failed. Found unexpected gaps in LDAS frames: %s \n" % vn_sum_gaps - ldas_gaps
print(message)
return
else:
if (len(vn_sums & ldas_gaps) == 0):
message = ""
else:
message = "test failed. Found overlap between %s summary intervals and LDAS allowed gaps: \n" % (vn_flag, vn_sums - ldas_gaps)
print(message)
return
print(message)
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
from glue.ligolw import table
from glue.ligolw import utils
def ContentHandler(xmldoc):
return ligolw.PartialLIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.StripTableName(attrs["Name"]) in ["segment"]))
try:
table.use_in(ligolw.PartialLIGOLWContentHandler)
except AttributeError:
# old glue did not allow .use_in().
# FIXME: remove when we can require the latest version of glue
pass
xmldoc = utils.load_url(segfile, verbose = verbose,gz = segfile.endswith(".gz"), contenthandler = ContentHandler)
seg_list = segmentlist()
for table_elem in xmldoc.getElements(lambda e:\
(e.tagName == ligolw.Table.tagName)):
for row in table_elem:
seg_list.append(segment(row.start_time, row.end_time))
xmldoc.unlink()
return seg_list
def find_version_xml(segfile,seg,verbose):
"""
Find out the version of the flag for the given seg.
"""
from glue.ligolw import ligolw
from glue.ligolw import table
from glue.ligolw import utils
def ContentHandler(xmldoc):
return ligolw.PartialLIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.StripTableName(attrs["Name"]) in ["segment_definer","segment_summary"]))
try:
table.use_in(ligolw.PartialLIGOLWContentHandler)
except AttributeError:
# old glue did not allow .use_in().
# FIXME: remove when we can require the latest version of glue
pass
xmldoc = utils.load_url(segfile, verbose = verbose,gz = segfile.endswith(".gz"), contenthandler = ContentHandler)
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
from glue.ligolw import table
from glue.ligolw import utils
def ContentHandler(xmldoc):
return ligolw.PartialLIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.Table.TableName(attrs["Name"]) in ["segment_definer","segment_summary"]))
try:
table.use_in(ligolw.PartialLIGOLWContentHandler)
except AttributeError:
# old glue did not allow .use_in().
# FIXME: remove when we can require the latest version of glue
pass
xmldoc = utils.load_url(segfile, verbose = verbose,gz = segfile.endswith(".gz"), contenthandler = ContentHandler)
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 read_segfile_xml(segfile,verbose):
"""
Read segment file in ligolw xml type and return in glue.segments.segmentlist
format.
"""
from glue.ligolw import ligolw
from glue.ligolw import table
from glue.ligolw import utils
def ContentHandler(xmldoc):
return ligolw.PartialLIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.Table.TableName(attrs["Name"]) in ["segment"]))
try:
table.use_in(ligolw.PartialLIGOLWContentHandler)
except AttributeError:
# old glue did not allow .use_in().
# FIXME: remove when we can require the latest version of glue
pass
xmldoc = utils.load_url(segfile, verbose = verbose,gz = segfile.endswith(".gz"), contenthandler = ContentHandler)
seg_list = segmentlist()
for table_elem in xmldoc.getElements(lambda e:\
(e.tagName == ligolw.Table.tagName)):
for row in table_elem:
seg_list.append(segment(row.start_time, row.end_time))
xmldoc.unlink()
return seg_list
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 read_segfile_xml(segfile, verbose):
"""
Read segment file in ligolw xml type and return in glue.segments.segmentlist
format.
"""
from glue.ligolw import ligolw
from glue.ligolw import table
from glue.ligolw import utils
def ContentHandler(xmldoc):
return ligolw.PartialLIGOLWContentHandler(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"))
seg_list = segmentlist()
for table_elem in xmldoc.getElements(lambda e:\
(e.tagName == ligolw.Table.tagName)):
for row in table_elem:
seg_list.append(segment(row.start_time, row.end_time))
xmldoc.unlink()
return seg_list
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 vn_ldas_gap_check(vn_xml_file, vn_flag, ldas_gap_xml_file):
# read in summary intervals of vn_flag
vndoc = ligolw_utils.load_url(vn_xml_file,
gz=(vn_xml_file or "stdin").endswith(".gz"))
vn_sums = segmentdb_utils.find_segments(vndoc,
"%s" % vn_flag,
use_segment_table=False)
# read in segment and summary intervals of LDAS allowed gaps
ldasdoc = ligolw_utils.load_url(ldas_gap_xml_file,
gz=(ldas_gap_xml_file
or "stdin").endswith(".gz"))
ldas_gaps = segmentdb_utils.find_segments(ldasdoc, 'H1:RESULT:1')
ldas_sums = segmentdb_utils.find_segments(ldasdoc,
'H1:DCH-MISSING_LDAS_C02_L2:1',
use_segment_table=False)
if len(ldas_sums) == 0:
message = "no LDAS info was found within the specified time in the database!"
print(message)
return
# if valid Vn file and ldas files both found, do further testings:
if len(vn_sums) > 1:
vn_sum_gaps = segmentlist([segment(vn_sums[0][0], vn_sums[-1][1])
]) - vn_sums
if vn_sum_gaps == ldas_gaps:
message = ""
else:
message = "test failed. Found unexpected gaps in LDAS frames: %s \n" % vn_sum_gaps - ldas_gaps
print(message)
return
else:
if (len(vn_sums & ldas_gaps) == 0):
message = ""
else:
message = "test failed. Found overlap between %s summary intervals and LDAS allowed gaps: \n" % (
vn_flag, vn_sums - ldas_gaps)
print(message)
return
print(message)
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_trigs_xml(GWcursor, trigger_file, segs, min_thresh, tracker, verbose):
"""
Read trigger data from xml file that has ligolw xml format.
Many lines in this function are adapted from ligolw_print by Kipp Cannon
and modified to suit the need.
"""
from glue.ligolw import ligolw
from glue.ligolw import table
from glue.ligolw import lsctables
from glue.ligolw import utils
# speed hacks
# replace Glue's pure Python LIGOTimeGPS class with pyLAL's C version
from pylal.xlal.datatypes.ligotimegps import LIGOTimeGPS
lsctables.LIGOTimeGPS = LIGOTimeGPS
# Enable column interning to save memory
table.RowBuilder = table.InterningRowBuilder
# for now, hardcode the table/column names
# FIXME: assuming there is only one of those tables in the file
tables = ['sngl_burst', 'sngl_inspiral', 'sngl_ringdown']
columns = ['end_time', 'end_time_ns', 'snr']
# don't parse other tables so as to improve parsing speed and reduce memory
# requirements.
def ContentHandler(xmldoc):
return ligolw.PartialLIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.StripTableName(attrs["Name"]) in tables))
try:
lsctables.use_in(ligolw.PartialLIGOLWContentHandler)
except AttributeError:
# old glue did not allow .use_in().
# FIXME: remove when we can require the latest version of glue
pass
# FIXME: find a way to load only columns necessary
# something like lsctables.SnglInspiral.loadcolumns = columns?
xmldoc = utils.load_url(trigger_file, verbose = verbose,\
gz = trigger_file.endswith(".gz"),
contenthandler = ContentHandler)
table.InterningRowBuilder.strings.clear()
for table_elem in xmldoc.getElements(lambda e:\
(e.tagName == ligolw.Table.tagName)):
# trigger specific time retrieval functions
if table_elem.tableName[:-6] in ('sngl_inspiral'):
get_time = lambda row: row.get_end()
elif table_elem.tableName[:-6] in ('sngl_burst'):
get_time = lambda row: row.get_peak()
elif table_elem.tableName[:-6] in ('sngl_ringdown'):
get_time = lambda row: row.get_start()
else:
print >> sys.stderr, "Error: This should not be happening. Please contact to the author with the error trace."
sys.exit(1)
for row in table_elem:
t = get_time(row)
if t in segs:
if row.snr > min_thresh:
# insert into the database
# micro second for GPS time is accurate enough
GWcursor.execute("insert into GWtrigs values (?, ?)",
("%.3f" % t, "%.2f" % row.snr))
tracker['counter'] += 1
else:
# some triggers are outside of segments
tracker['outside'] = True
xmldoc.unlink()
return GWcursor
def get_trigs_xml(GWcursor,trigger_file,segs,min_thresh,tracker,verbose):
"""
Read trigger data from xml file that has ligolw xml format.
Many lines in this function are adapted from ligolw_print by Kipp Cannon
and modified to suit the need.
"""
from glue.ligolw import ligolw
from glue.ligolw import table
from glue.ligolw import lsctables
from glue.ligolw import utils
# speed hacks
# replace Glue's pure Python LIGOTimeGPS class with pyLAL's C version
from pylal.xlal.datatypes.ligotimegps import LIGOTimeGPS
lsctables.LIGOTimeGPS = LIGOTimeGPS
# Enable column interning to save memory
table.RowBuilder = table.InterningRowBuilder
# for now, hardcode the table/column names
# FIXME: assuming there is only one of those tables in the file
tables = ['sngl_burst','sngl_inspiral','sngl_ringdown']
columns = ['end_time','end_time_ns','snr']
# don't parse other tables so as to improve parsing speed and reduce memory
# requirements.
def ContentHandler(xmldoc):
return ligolw.PartialLIGOLWContentHandler(xmldoc, lambda name, attrs:\
(name == ligolw.Table.tagName) and\
(table.Table.TableName(attrs["Name"]) in tables))
try:
lsctables.use_in(ligolw.PartialLIGOLWContentHandler)
except AttributeError:
# old glue did not allow .use_in().
# FIXME: remove when we can require the latest version of glue
pass
# FIXME: find a way to load only columns necessary
# something like lsctables.SnglInspiral.loadcolumns = columns?
xmldoc = utils.load_url(trigger_file, verbose = verbose,\
gz = trigger_file.endswith(".gz"),
contenthandler = ContentHandler)
table.InterningRowBuilder.strings.clear()
for table_elem in xmldoc.getElements(lambda e:\
(e.tagName == ligolw.Table.tagName)):
# trigger specific time retrieval functions
if table_elem.tableName[:-6] in ('sngl_inspiral'):
get_time = lambda row: row.get_end()
elif table_elem.tableName[:-6] in ('sngl_burst'):
get_time = lambda row: row.get_peak()
elif table_elem.tableName[:-6] in ('sngl_ringdown'):
get_time = lambda row: row.get_start()
else:
print >> sys.stderr, "Error: This should not be happening. Please contact to the author with the error trace."
sys.exit(1)
for row in table_elem:
t = get_time(row)
if t in segs:
if row.snr > min_thresh:
# insert into the database
# micro second for GPS time is accurate enough
GWcursor.execute("insert into GWtrigs values (?, ?)",("%.3f"%t, "%.2f"%row.snr))
tracker['counter'] += 1
else:
# some triggers are outside of segments
tracker['outside'] = True
xmldoc.unlink()
return GWcursor