"""
Convenience classes for accessing hdf5 trigger files
"""
import h5py
import numpy as np
import logging
import inspect
import pickle
from itertools import chain
from io import BytesIO
from lal import LIGOTimeGPS, YRJUL_SI
from ligo.lw import ligolw
from ligo.lw import lsctables
from ligo.lw import utils as ligolw_utils
from ligo.lw.utils import process as ligolw_process
from pycbc import version as pycbc_version
from pycbc.io.ligolw import return_search_summary, return_empty_sngl
from pycbc import events, conversions, pnutils
from pycbc.events import ranking, veto
from pycbc.events import mean_if_greater_than_zero
from pycbc.pnutils import mass1_mass2_to_mchirp_eta
[docs]class HFile(h5py.File):
""" Low level extensions to the capabilities of reading an hdf5 File
"""
[docs] def select(self, fcn, *args, **kwds):
""" Return arrays from an hdf5 file that satisfy the given function
Parameters
----------
fcn : a function
A function that accepts the same number of argument as keys given
and returns a boolean array of the same length.
args : strings
A variable number of strings that are keys into the hdf5. These must
refer to arrays of equal length.
chunksize : {1e6, int}, optional
Number of elements to read and process at a time.
return_indices : bool, optional
If True, also return the indices of elements passing the function.
Returns
-------
values : np.ndarrays
A variable number of arrays depending on the number of keys into
the hdf5 file that are given. If return_indices is True, the first
element is an array of indices of elements passing the function.
>>> f = HFile(filename)
>>> snr = f.select(lambda snr: snr > 6, 'H1/snr')
"""
# get references to each array
refs = {}
data = {}
for arg in args:
refs[arg] = self[arg]
data[arg] = []
return_indices = kwds.get('return_indices', False)
indices = np.array([], dtype=np.uint64)
# To conserve memory read the array in chunks
chunksize = kwds.get('chunksize', int(1e6))
size = len(refs[arg])
i = 0
while i < size:
r = i + chunksize if i + chunksize < size else size
# Read each chunk's worth of data and find where it passes the function
partial = [refs[arg][i:r] for arg in args]
keep = fcn(*partial)
if return_indices:
indices = np.concatenate([indices, np.flatnonzero(keep) + i])
# Store only the results that pass the function
for arg, part in zip(args, partial):
data[arg].append(part[keep])
i += chunksize
# Combine the partial results into full arrays
if len(args) == 1:
res = np.concatenate(data[args[0]])
if return_indices:
return indices.astype(np.uint64), res
else:
return res
else:
res = tuple(np.concatenate(data[arg]) for arg in args)
if return_indices:
return (indices.astype(np.uint64),) + res
else:
return res
[docs]class DictArray(object):
""" Utility for organizing sets of arrays of equal length.
Manages a dictionary of arrays of equal length. This can also
be instantiated with a set of hdf5 files and the key values. The full
data is always in memory and all operations create new instances of the
DictArray.
"""
def __init__(self, data=None, files=None, groups=None):
""" Create a DictArray
Parameters
----------
data: dict, optional
Dictionary of equal length numpy arrays
files: list of filenames, optional
List of hdf5 file filenames. Incompatibile with the `data` option.
groups: list of strings
List of keys into each file. Required by the files option.
"""
# Check that input fits with how the DictArray is set up
if data and files:
raise RuntimeError('DictArray can only have data or files as '
'input, not both.')
if data is None and files is None:
raise RuntimeError('DictArray needs either data or files at'
'initialization. To set up an empty instance'
'use DictArray(data={})')
if files and not groups:
raise RuntimeError('If files are given then need groups.')
self.data = data
self.groups = groups
if files:
self.data = {}
for g in groups:
self.data[g] = []
for f in files:
d = HFile(f)
for g in groups:
if g in d:
self.data[g].append(d[g][:])
d.close()
for k in self.data:
if not len(self.data[k]) == 0:
self.data[k] = np.concatenate(self.data[k])
for k in self.data:
setattr(self, k, self.data[k])
def _return(self, data):
return self.__class__(data=data)
def __len__(self):
return len(self.data[tuple(self.data.keys())[0]])
def __add__(self, other):
if self.data == {}:
logging.debug('Adding data to a DictArray instance which'
' was initialized with an empty dict')
return self._return(data=other)
data = {}
for k in self.data:
try:
data[k] = np.concatenate([self.data[k], other.data[k]])
except KeyError:
logging.info('%s does not exist in other data' % k)
return self._return(data=data)
[docs] def select(self, idx):
""" Return a new DictArray containing only the indexed values
"""
data = {}
for k in self.data:
# Make sure each entry is an array (not a scalar)
data[k] = np.array(self.data[k][idx])
return self._return(data=data)
[docs] def remove(self, idx):
""" Return a new DictArray that does not contain the indexed values
"""
data = {}
for k in self.data:
data[k] = np.delete(self.data[k], np.array(idx, dtype=int))
return self._return(data=data)
[docs] def save(self, outname):
f = HFile(outname, "w")
for k in self.attrs:
f.attrs[k] = self.attrs[k]
for k in self.data:
f.create_dataset(k, data=self.data[k],
compression='gzip',
compression_opts=9,
shuffle=True)
f.close()
[docs]class StatmapData(DictArray):
def __init__(self, data=None, seg=None, attrs=None, files=None,
groups=('stat', 'time1', 'time2', 'trigger_id1',
'trigger_id2', 'template_id', 'decimation_factor',
'timeslide_id')):
super(StatmapData, self).__init__(data=data, files=files,
groups=groups)
if data:
self.seg=seg
self.attrs=attrs
elif files:
f = HFile(files[0], "r")
self.seg = f['segments']
self.attrs = f.attrs
def _return(self, data):
return self.__class__(data=data, attrs=self.attrs, seg=self.seg)
[docs] def cluster(self, window):
""" Cluster the dict array, assuming it has the relevant Coinc colums,
time1, time2, stat, and timeslide_id
"""
# If no events, do nothing
if len(self.time1) == 0 or len(self.time2) == 0:
return self
from pycbc.events import cluster_coincs
interval = self.attrs['timeslide_interval']
cid = cluster_coincs(self.stat, self.time1, self.time2,
self.timeslide_id, interval, window)
return self.select(cid)
[docs] def save(self, outname):
super(StatmapData, self).save(outname)
with HFile(outname, "w") as f:
for key in self.seg.keys():
f['segments/%s/start' % key] = self.seg[key]['start'][:]
f['segments/%s/end' % key] = self.seg[key]['end'][:]
[docs]class MultiifoStatmapData(StatmapData):
def __init__(self, data=None, seg=None, attrs=None,
files=None, ifos=None):
groups = ['decimation_factor', 'stat', 'template_id', 'timeslide_id']
for ifo in ifos:
groups += ['%s/time' % ifo]
groups += ['%s/trigger_id' % ifo]
super(MultiifoStatmapData, self).__init__(data=data, files=files,
groups=groups, attrs=attrs,
seg=seg)
def _return(self, data):
ifolist = self.attrs['ifos'].split(' ')
return self.__class__(data=data, attrs=self.attrs, seg=self.seg,
ifos=ifolist)
[docs] def cluster(self, window):
""" Cluster the dict array, assuming it has the relevant Coinc colums,
time1, time2, stat, and timeslide_id
"""
# If no events, do nothing
pivot_ifo = self.attrs['pivot']
fixed_ifo = self.attrs['fixed']
if len(self.data['%s/time' % pivot_ifo]) == 0 or len(self.data['%s/time' % fixed_ifo]) == 0:
return self
from pycbc.events import cluster_coincs
interval = self.attrs['timeslide_interval']
cid = cluster_coincs(self.stat,
self.data['%s/time' % pivot_ifo],
self.data['%s/time' % fixed_ifo],
self.timeslide_id,
interval,
window)
return self.select(cid)
[docs]class FileData(object):
def __init__(self, fname, group=None, columnlist=None, filter_func=None):
"""
Parameters
----------
group : string
Name of group to be read from the file
columnlist : list of strings
Names of columns to be read; if None, use all existing columns
filter_func : string
String should evaluate to a Boolean expression using attributes
of the class instance derived from columns: ex. 'self.snr < 6.5'
"""
if not fname: raise RuntimeError("Didn't get a file!")
self.fname = fname
self.h5file = HFile(fname, "r")
if group is None:
if len(self.h5file.keys()) == 1:
group, = self.h5file.keys()
else:
raise RuntimeError("Didn't get a group!")
self.group_key = group
self.group = self.h5file[group]
self.columns = columnlist if columnlist is not None \
else list(self.group.keys())
self.filter_func = filter_func
self._mask = None
[docs] def close(self):
self.h5file.close()
@property
def mask(self):
"""
Create a mask implementing the requested filter on the datasets
Returns
-------
array of Boolean
True for dataset indices to be returned by the get_column method
"""
if self.filter_func is None:
raise RuntimeError("Can't get a mask without a filter function!")
else:
# only evaluate if no previous calculation was done
if self._mask is None:
# get required columns into the namespace as numpy arrays
for column in self.columns:
if column in self.filter_func:
setattr(self, column, self.group[column][:])
self._mask = eval(self.filter_func)
return self._mask
[docs] def get_column(self, col):
"""
Method designed to be analogous to legacy pylal.SnglInspiralUtils
functionality
Parameters
----------
col : string
Name of the dataset to be returned
Returns
-------
numpy array
Values from the dataset, filtered if requested
"""
# catch corner case with an empty file (group with no datasets)
if not len(self.group.keys()):
return np.array([])
vals = self.group[col]
if self.filter_func:
return vals[self.mask]
else:
return vals[:]
[docs]class DataFromFiles(object):
def __init__(self, filelist, group=None, columnlist=None, filter_func=None):
self.files = filelist
self.group = group
self.columns = columnlist
self.filter_func = filter_func
[docs] def get_column(self, col):
"""
Loop over files getting the requested dataset values from each
Parameters
----------
col : string
Name of the dataset to be returned
Returns
-------
numpy array
Values from the dataset, filtered if requested and
concatenated in order of file list
"""
logging.info('getting %s' % col)
vals = []
for f in self.files:
d = FileData(f, group=self.group, columnlist=self.columns,
filter_func=self.filter_func)
vals.append(d.get_column(col))
# Close each file since h5py has an upper limit on the number of
# open file objects (approx. 1000)
d.close()
logging.info('- got %i values' % sum(len(v) for v in vals))
return np.concatenate(vals)
[docs]class SingleDetTriggers(object):
"""
Provides easy access to the parameters of single-detector CBC triggers.
"""
# FIXME: Some of these are optional and should be kwargs.
def __init__(self, trig_file, bank_file, veto_file,
segment_name, filter_func, detector, premask=None):
logging.info('Loading triggers')
self.trigs_f = HFile(trig_file, 'r')
self.trigs = self.trigs_f[detector]
self.ifo = detector # convenience attributes
self.detector = detector
if bank_file:
logging.info('Loading bank')
self.bank = HFile(bank_file, 'r')
else:
logging.info('No bank file given')
# empty dict in place of non-existent hdf file
self.bank = {}
if premask is not None:
self.mask = premask
else:
self.mask = np.ones(len(self.trigs['end_time']), dtype=bool)
if veto_file:
logging.info('Applying veto segments')
# veto_mask is an array of indices into the trigger arrays
# giving the surviving triggers
logging.info('%i triggers before vetoes', self.mask.sum())
self.veto_mask, _ = events.veto.indices_outside_segments(
self.end_time, [veto_file],
ifo=detector, segment_name=segment_name)
idx = np.flatnonzero(self.mask)[self.veto_mask]
self.mask[:] = False
self.mask[idx] = True
logging.info('%i triggers remain after vetoes',
len(self.veto_mask))
# FIXME this should use the hfile select interface to avoid
# memory and processing limitations.
if filter_func:
# get required columns into the namespace with dummy attribute
# names to avoid confusion with other class properties
logging.info('Setting up filter function')
for c in self.trigs.keys():
if c in filter_func:
setattr(self, '_'+c, self.trigs[c][:])
for c in self.bank.keys():
if c in filter_func:
# get template parameters corresponding to triggers
setattr(self, '_'+c,
np.array(self.bank[c])[self.trigs['template_id'][:]])
self.filter_mask = eval(filter_func.replace('self.', 'self._'))
# remove the dummy attributes
for c in chain(self.trigs.keys(), self.bank.keys()):
if c in filter_func: delattr(self, '_'+c)
self.mask = self.mask & self.filter_mask
logging.info('%i triggers remain after cut on %s',
sum(self.mask), filter_func)
def __getitem__(self, key):
# Is key in the TRIGGER_MERGE file?
try:
return self.get_column(key)
except KeyError:
pass
# Is key in the bank file?
try:
self.checkbank(key)
return self.bank[key][:][self.template_id]
except (RuntimeError, KeyError) as exc:
err_msg = "Cannot find {} in input files".format(key)
raise ValueError(err_msg) from exc
[docs] def checkbank(self, param):
if self.bank == {}:
return RuntimeError("Can't get %s values without a bank file"
% param)
[docs] def trig_dict(self):
"""Returns dict of the masked trigger valuse """
mtrigs = {}
for k in self.trigs:
if len(self.trigs[k]) == len(self.trigs['end_time']):
if self.mask is not None:
mtrigs[k] = self.trigs[k][self.mask]
else:
mtrigs[k] = self.trigs[k][:]
return mtrigs
[docs] @classmethod
def get_param_names(cls):
"""Returns a list of plottable CBC parameter variables"""
return [m[0] for m in inspect.getmembers(cls) \
if type(m[1]) == property]
[docs] def apply_mask(self, logic_mask):
"""Apply a boolean array to the set of triggers"""
if hasattr(self.mask, 'dtype') and (self.mask.dtype == 'bool'):
orig_indices = self.mask.nonzero()[0][logic_mask]
self.mask[:] = False
self.mask[orig_indices] = True
else:
self.mask = list(np.array(self.mask)[logic_mask])
[docs] def mask_to_n_loudest_clustered_events(self, rank_method,
n_loudest=10,
cluster_window=10):
"""Edits the mask property of the class to point to the N loudest
single detector events as ranked by ranking statistic. Events are
clustered so that no more than 1 event within +/- cluster-window will
be considered."""
# If this becomes memory intensive we can optimize
stat = rank_method.rank_stat_single((self.ifo, self.trig_dict()))
if len(stat) == 0:
# No triggers, so just return here
self.stat = np.array([])
return
times = self.end_time
index = stat.argsort()[::-1]
new_times = []
new_index = []
for curr_idx in index:
curr_time = times[curr_idx]
for time in new_times:
if abs(curr_time - time) < cluster_window:
break
else:
# Only get here if no other triggers within cluster window
new_index.append(curr_idx)
new_times.append(curr_time)
if len(new_index) >= n_loudest:
break
index = np.array(new_index)
index.sort()
self.stat = stat[index]
if hasattr(self.mask, 'dtype') and self.mask.dtype == 'bool':
orig_indices = np.flatnonzero(self.mask)[index]
self.mask = list(orig_indices)
elif isinstance(self.mask, list):
self.mask = list(np.array(self.mask)[index])
@property
def template_id(self):
return self.get_column('template_id').astype(int)
@property
def mass1(self):
self.checkbank('mass1')
return self.bank['mass1'][:][self.template_id]
@property
def mass2(self):
self.checkbank('mass2')
return self.bank['mass2'][:][self.template_id]
@property
def spin1z(self):
self.checkbank('spin1z')
return self.bank['spin1z'][:][self.template_id]
@property
def spin2z(self):
self.checkbank('spin2z')
return self.bank['spin2z'][:][self.template_id]
@property
def spin2x(self):
self.checkbank('spin2x')
return self.bank['spin2x'][:][self.template_id]
@property
def spin2y(self):
self.checkbank('spin2y')
return self.bank['spin2y'][:][self.template_id]
@property
def spin1x(self):
self.checkbank('spin1x')
return self.bank['spin1x'][:][self.template_id]
@property
def spin1y(self):
self.checkbank('spin1y')
return self.bank['spin1y'][:][self.template_id]
@property
def inclination(self):
self.checkbank('inclination')
return self.bank['inclination'][:][self.template_id]
@property
def f_lower(self):
self.checkbank('f_lower')
return self.bank['f_lower'][:][self.template_id]
@property
def approximant(self):
self.checkbank('approximant')
return self.bank['approximant'][:][self.template_id]
@property
def mtotal(self):
return self.mass1 + self.mass2
@property
def mchirp(self):
return conversions.mchirp_from_mass1_mass2(self.mass1, self.mass2)
@property
def eta(self):
return conversions.eta_from_mass1_mass2(self.mass1, self.mass2)
@property
def effective_spin(self):
# FIXME assumes aligned spins
return conversions.chi_eff(self.mass1, self.mass2,
self.spin1z, self.spin2z)
# IMPROVEME: would like to have a way to access all get_freq and/or
# other pnutils.* names rather than hard-coding each one
# - eg make this part of a fancy interface to the bank file ?
@property
def f_seobnrv2_peak(self):
return pnutils.get_freq('fSEOBNRv2Peak', self.mass1, self.mass2,
self.spin1z, self.spin2z)
@property
def f_seobnrv4_peak(self):
return pnutils.get_freq('fSEOBNRv4Peak', self.mass1, self.mass2,
self.spin1z, self.spin2z)
@property
def end_time(self):
return self.get_column('end_time')
@property
def template_duration(self):
return self.get_column('template_duration')
@property
def snr(self):
return self.get_column('snr')
@property
def sgchisq(self):
return self.get_column('sg_chisq')
@property
def u_vals(self):
return self.get_column('u_vals')
@property
def rchisq(self):
return self.get_column('chisq') \
/ (self.get_column('chisq_dof') * 2 - 2)
@property
def psd_var_val(self):
return self.get_column('psd_var_val')
@property
def newsnr(self):
return ranking.newsnr(self.snr, self.rchisq)
@property
def newsnr_sgveto(self):
return ranking.newsnr_sgveto(self.snr, self.rchisq, self.sgchisq)
@property
def newsnr_sgveto_psdvar(self):
return ranking.newsnr_sgveto_psdvar(self.snr, self.rchisq,
self.sgchisq, self.psd_var_val)
@property
def newsnr_sgveto_psdvar_threshold(self):
return ranking.newsnr_sgveto_psdvar_threshold(self.snr, self.rchisq,
self.sgchisq, self.psd_var_val)
[docs] def get_ranking(self, rank_name, **kwargs):
return ranking.get_sngls_ranking_from_trigs(self, rank_name, **kwargs)
[docs] def get_column(self, cname):
# Fiducial value that seems to work, not extensively tuned.
MFRAC = 0.3
# If the mask accesses few enough elements then directly use it
# This can be slower than reading in all the elements if most of them
# will be read.
if self.mask is not None and (isinstance(self.mask, list) or \
(len(self.mask.nonzero()[0]) < (len(self.mask) * MFRAC))):
return self.trigs[cname][self.mask]
# We have a lot of elements to read so we resort to readin the entire
# array before masking.
elif self.mask is not None:
return self.trigs[cname][:][self.mask]
else:
return self.trigs[cname][:]
[docs]class ForegroundTriggers(object):
# Injection files are expected to only have 'exclusive' IFAR/FAP values,
# should use has_inc=False for these.
def __init__(self, coinc_file, bank_file, sngl_files=None, n_loudest=None,
group='foreground', has_inc=True):
self.coinc_file = FileData(coinc_file, group=group)
if 'ifos' in self.coinc_file.h5file.attrs:
self.ifos = self.coinc_file.h5file.attrs['ifos'].split(' ')
else:
raise ValueError("File doesn't have an 'ifos' attribute!",
coinc_file)
self.sngl_files = {}
if sngl_files is not None:
for sngl_file in sngl_files:
curr_dat = FileData(sngl_file)
curr_ifo = curr_dat.group_key
self.sngl_files[curr_ifo] = curr_dat
if not all([ifo in self.sngl_files.keys() for ifo in self.ifos]):
print("sngl_files: {}".format(sngl_files))
print("self.ifos: {}".format(self.ifos))
raise RuntimeError("IFOs in statmap file not all represented "
"by single-detector trigger files.")
if not sorted(self.sngl_files.keys()) == sorted(self.ifos):
logging.warning("WARNING: Single-detector trigger files "
"given for IFOs not in the statmap file")
self.bank_file = HFile(bank_file, "r")
self.n_loudest = n_loudest
self._inclusive = has_inc
self._sort_arr = None
self._template_id = None
self._trig_ids = None
self.get_active_segments()
@property
def sort_arr(self):
if self._sort_arr is None:
if self._inclusive:
try:
ifar = self.coinc_file.get_column('ifar')
except KeyError:
logging.warning("WARNING: Can't find inclusive IFAR!"
"Using exclusive IFAR instead ...")
ifar = self.coinc_file.get_column('ifar_exc')
self._inclusive = False
else:
ifar = self.coinc_file.get_column('ifar_exc')
sorting = ifar.argsort()[::-1]
if self.n_loudest:
sorting = sorting[:self.n_loudest]
self._sort_arr = sorting
return self._sort_arr
@property
def template_id(self):
if self._template_id is None:
template_id = self.get_coincfile_array('template_id')
self._template_id = template_id.astype(int)
return self._template_id
@property
def trig_id(self):
if self._trig_ids is not None:
return self._trig_ids
self._trig_ids = {}
for ifo in self.ifos:
self._trig_ids[ifo] = self.get_coincfile_array(ifo + '/trigger_id')
return self._trig_ids
[docs] def get_coincfile_array(self, variable):
return self.coinc_file.get_column(variable)[self.sort_arr]
[docs] def get_bankfile_array(self, variable):
try:
return self.bank_file[variable][:][self.template_id]
except IndexError:
if len(self.template_id) == 0:
return np.array([])
raise
[docs] def get_snglfile_array_dict(self, variable):
return_dict = {}
for ifo in self.ifos:
try:
tid = self.trig_id[ifo]
lgc = tid == -1
# Put in *some* value for the invalid points to avoid failure
# Make sure this doesn't change the cached internal array!
tid = np.copy(tid)
tid[lgc] = 0
# If small number of points don't read the full file
if len(tid) < 1000:
curr = []
hdf_dataset = self.sngl_files[ifo].group[variable]
for idx in tid:
curr.append(hdf_dataset[idx])
curr = np.array(curr)
else:
curr = self.sngl_files[ifo].get_column(variable)[tid]
except IndexError:
if len(self.trig_id[ifo]) == 0:
curr = np.array([])
lgc = curr == 0
else:
raise
return_dict[ifo] = (curr, np.logical_not(lgc))
return return_dict
[docs] def get_active_segments(self):
self.active_segments = {}
for ifo in self.ifos:
starts = self.sngl_files[ifo].get_column('search/start_time')
ends = self.sngl_files[ifo].get_column('search/end_time')
self.active_segments[ifo] = veto.start_end_to_segments(starts,
ends)
[docs] def get_end_time(self):
times_gen = (self.get_coincfile_array('{}/time'.format(ifo))
for ifo in self.ifos)
ref_times = np.array([mean_if_greater_than_zero(t)[0]
for t in zip(*times_gen)])
return ref_times
[docs] def get_ifos(self):
"""
Returns
-------
ifos_list
List of lists of ifo names involved in each foreground event.
Ifos will be listed in the same order as self.ifos
"""
# Ian thinks this could be coded more simply and efficiently
# Note also that effectively the same thing is done as part of the
# to_coinc_hdf_object method
ifo_or_minus = []
for ifo in self.ifos:
ifo_trigs = np.where(self.get_coincfile_array(ifo + '/time') < 0,
'-', ifo)
ifo_or_minus.append(ifo_trigs)
ifos_list = [list(trig[trig != '-'])
for trig in iter(np.array(ifo_or_minus).T)]
return ifos_list
[docs] def to_coinc_xml_object(self, file_name):
outdoc = ligolw.Document()
outdoc.appendChild(ligolw.LIGO_LW())
ifos = list(self.sngl_files.keys())
proc_id = ligolw_process.register_to_xmldoc(outdoc, 'pycbc',
{}, instruments=ifos, comment='', version=pycbc_version.git_hash,
cvs_repository='pycbc/'+pycbc_version.git_branch,
cvs_entry_time=pycbc_version.date).process_id
search_summ_table = lsctables.New(lsctables.SearchSummaryTable)
coinc_h5file = self.coinc_file.h5file
try:
start_time = coinc_h5file['segments']['coinc']['start'][:].min()
end_time = coinc_h5file['segments']['coinc']['end'][:].max()
except KeyError:
start_times = []
end_times = []
for ifo_comb in coinc_h5file['segments']:
if ifo_comb == 'foreground_veto':
continue
seg_group = coinc_h5file['segments'][ifo_comb]
start_times.append(seg_group['start'][:].min())
end_times.append(seg_group['end'][:].max())
start_time = min(start_times)
end_time = max(end_times)
num_trigs = len(self.sort_arr)
search_summary = return_search_summary(start_time, end_time,
num_trigs, ifos)
search_summ_table.append(search_summary)
outdoc.childNodes[0].appendChild(search_summ_table)
sngl_inspiral_table = lsctables.New(lsctables.SnglInspiralTable)
coinc_def_table = lsctables.New(lsctables.CoincDefTable)
coinc_event_table = lsctables.New(lsctables.CoincTable)
coinc_inspiral_table = lsctables.New(lsctables.CoincInspiralTable)
coinc_event_map_table = lsctables.New(lsctables.CoincMapTable)
time_slide_table = lsctables.New(lsctables.TimeSlideTable)
# Set up time_slide table
time_slide_id = lsctables.TimeSlideID(0)
for ifo in ifos:
time_slide_row = lsctables.TimeSlide()
time_slide_row.instrument = ifo
time_slide_row.time_slide_id = time_slide_id
time_slide_row.offset = 0
time_slide_row.process_id = proc_id
time_slide_table.append(time_slide_row)
# Set up coinc_definer table
coinc_def_id = lsctables.CoincDefID(0)
coinc_def_row = lsctables.CoincDef()
coinc_def_row.search = "inspiral"
coinc_def_row.description = \
"sngl_inspiral<-->sngl_inspiral coincidences"
coinc_def_row.coinc_def_id = coinc_def_id
coinc_def_row.search_coinc_type = 0
coinc_def_table.append(coinc_def_row)
bank_col_names = ['mass1', 'mass2', 'spin1z', 'spin2z']
bank_col_vals = {}
for name in bank_col_names:
bank_col_vals[name] = self.get_bankfile_array(name)
coinc_event_names = ['ifar', 'time', 'fap', 'stat']
coinc_event_vals = {}
for name in coinc_event_names:
if name == 'time':
coinc_event_vals[name] = self.get_end_time()
else:
coinc_event_vals[name] = self.get_coincfile_array(name)
sngl_col_names = ['snr', 'chisq', 'chisq_dof', 'bank_chisq',
'bank_chisq_dof', 'cont_chisq', 'cont_chisq_dof',
'end_time', 'template_duration', 'coa_phase',
'sigmasq']
sngl_col_vals = {}
for name in sngl_col_names:
sngl_col_vals[name] = self.get_snglfile_array_dict(name)
sngl_event_count = 0
for idx in range(len(self.sort_arr)):
# Set up IDs and mapping values
coinc_id = lsctables.CoincID(idx)
# Set up sngls
sngl_mchirps = []
sngl_mtots = []
net_snrsq = 0
triggered_ifos = []
for ifo in ifos:
# If this ifo is not participating in this coincidence then
# ignore it and move on.
if not sngl_col_vals['snr'][ifo][1][idx]:
continue
triggered_ifos += [ifo]
event_id = lsctables.SnglInspiralID(sngl_event_count)
sngl_event_count += 1
sngl = return_empty_sngl()
sngl.event_id = event_id
sngl.ifo = ifo
net_snrsq += sngl_col_vals['snr'][ifo][0][idx]**2
for name in sngl_col_names:
val = sngl_col_vals[name][ifo][0][idx]
if name == 'end_time':
sngl.end = LIGOTimeGPS(val)
else:
setattr(sngl, name, val)
for name in bank_col_names:
val = bank_col_vals[name][idx]
setattr(sngl, name, val)
sngl.mtotal, sngl.eta = pnutils.mass1_mass2_to_mtotal_eta(
sngl.mass1, sngl.mass2)
sngl.mchirp, _ = pnutils.mass1_mass2_to_mchirp_eta(
sngl.mass1, sngl.mass2)
sngl.eff_distance = (sngl.sigmasq)**0.5 / sngl.snr
# If exact match is not used, get masses from single triggers
sngl_mchirps += [sngl.mchirp]
sngl_mtots += [sngl.mtotal]
sngl_inspiral_table.append(sngl)
# Set up coinc_map entry
coinc_map_row = lsctables.CoincMap()
coinc_map_row.table_name = 'sngl_inspiral'
coinc_map_row.coinc_event_id = coinc_id
coinc_map_row.event_id = event_id
coinc_event_map_table.append(coinc_map_row)
# Take the mean if exact match is not used
sngl_combined_mchirp = np.mean(sngl_mchirps)
sngl_combined_mtot = np.mean(sngl_mtots)
# Set up coinc inspiral and coinc event tables
coinc_event_row = lsctables.Coinc()
coinc_inspiral_row = lsctables.CoincInspiral()
coinc_event_row.coinc_def_id = coinc_def_id
coinc_event_row.nevents = len(triggered_ifos)
# NB, `coinc_event_row.instruments = triggered_ifos does not give a
# correct result with ligo.lw 1.7.1
coinc_event_row.instruments = ','.join(sorted(triggered_ifos))
coinc_inspiral_row.instruments = triggered_ifos
coinc_event_row.time_slide_id = time_slide_id
coinc_event_row.process_id = proc_id
coinc_event_row.coinc_event_id = coinc_id
coinc_inspiral_row.coinc_event_id = coinc_id
coinc_inspiral_row.mchirp = sngl_combined_mchirp
coinc_inspiral_row.mass = sngl_combined_mtot
coinc_inspiral_row.end = LIGOTimeGPS(coinc_event_vals['time'][idx])
coinc_inspiral_row.snr = net_snrsq**0.5
coinc_inspiral_row.false_alarm_rate = coinc_event_vals['fap'][idx]
coinc_inspiral_row.combined_far = 1./coinc_event_vals['ifar'][idx]
# Transform to Hz
coinc_inspiral_row.combined_far = \
coinc_inspiral_row.combined_far / YRJUL_SI
coinc_event_row.likelihood = coinc_event_vals['stat'][idx]
coinc_inspiral_row.minimum_duration = 0.
coinc_event_table.append(coinc_event_row)
coinc_inspiral_table.append(coinc_inspiral_row)
outdoc.childNodes[0].appendChild(coinc_def_table)
outdoc.childNodes[0].appendChild(coinc_event_table)
outdoc.childNodes[0].appendChild(coinc_event_map_table)
outdoc.childNodes[0].appendChild(time_slide_table)
outdoc.childNodes[0].appendChild(coinc_inspiral_table)
outdoc.childNodes[0].appendChild(sngl_inspiral_table)
ligolw_utils.write_filename(outdoc, file_name)
[docs] def to_coinc_hdf_object(self, file_name):
ofd = h5py.File(file_name,'w')
# Some fields are special cases
logging.info("Outputting search results")
time = self.get_end_time()
# time will be used later to determine active ifos
ofd['time'] = time
if self._inclusive:
ofd['ifar'] = self.get_coincfile_array('ifar')
ofd['p_value'] = self.get_coincfile_array('fap')
ofd['ifar_exclusive'] = self.get_coincfile_array('ifar_exc')
ofd['p_value_exclusive'] = self.get_coincfile_array('fap_exc')
# Coinc fields
for field in ['stat']:
ofd[field] = self.get_coincfile_array(field)
logging.info("Outputting template information")
# Bank fields
for field in ['mass1','mass2','spin1z','spin2z']:
ofd[field] = self.get_bankfile_array(field)
mass1 = self.get_bankfile_array('mass1')
mass2 = self.get_bankfile_array('mass2')
ofd['chirp_mass'], _ = mass1_mass2_to_mchirp_eta(mass1, mass2)
logging.info("Outputting single-trigger information")
logging.info("reduced chisquared")
chisq_vals_valid = self.get_snglfile_array_dict('chisq')
chisq_dof_vals_valid = self.get_snglfile_array_dict('chisq_dof')
for ifo in self.ifos:
chisq_vals = chisq_vals_valid[ifo][0]
chisq_valid = chisq_vals_valid[ifo][1]
chisq_dof_vals = chisq_dof_vals_valid[ifo][0]
rchisq = chisq_vals / (2. * chisq_dof_vals - 2.)
rchisq[np.logical_not(chisq_valid)] = -1.
ofd[ifo + '_chisq'] = rchisq
# Single-detector fields
for field in ['sg_chisq', 'end_time', 'sigmasq',
'psd_var_val']:
logging.info(field)
try:
vals_valid = self.get_snglfile_array_dict(field)
except KeyError:
logging.info(field + " is not present in the "
"single-detector files")
for ifo in self.ifos:
# Some of the values will not be valid for all IFOs,
# the `valid` parameter out of get_snglfile_array_dict
# tells us this, and we set the values to -1
vals = vals_valid[ifo][0]
valid = vals_valid[ifo][1]
vals[np.logical_not(valid)] = -1.
ofd[f'{ifo}_{field}'] = vals
snr_vals_valid = self.get_snglfile_array_dict('snr')
network_snr_sq = np.zeros_like(snr_vals_valid[self.ifos[0]][0])
for ifo in self.ifos:
vals = snr_vals_valid[ifo][0]
valid = snr_vals_valid[ifo][1]
vals[np.logical_not(valid)] = -1.
ofd[ifo + '_snr'] = vals
network_snr_sq[valid] += vals[valid] ** 2.0
ofd['network_snr'] = np.sqrt(network_snr_sq)
logging.info("Triggered detectors")
# Create a n_ifos by n_events matrix, with the ifo letter if the
# event contains a trigger from the ifo, empty string if not
triggered_matrix = [[ifo[0] if v else ''
for v in snr_vals_valid[ifo][1]]
for ifo in self.ifos]
# Combine the ifo letters to make a single string per event
triggered_detectors = [''.join(triggered).encode('ascii')
for triggered in zip(*triggered_matrix)]
ofd.create_dataset('trig', data=triggered_detectors,
dtype='<S3')
logging.info("active detectors")
# Create a n_ifos by n_events matrix, with the ifo letter if the
# ifo was active at the event time, empty string if not
active_matrix = [[ifo[0] if t in self.active_segments[ifo]
else '' for t in time]
for ifo in self.ifos]
# Combine the ifo letters to make a single string per event
active_detectors = [''.join(active_at_time).encode('ascii')
for active_at_time in zip(*active_matrix)]
ofd.create_dataset('obs', data=active_detectors,
dtype='<S3')
ofd.close()
[docs]class ReadByTemplate(object):
# Default assignment to {} is OK for a variable used only in __init__
def __init__(self, filename, bank=None, segment_name=None, veto_files=None,
gating_veto_windows={}):
self.filename = filename
self.file = h5py.File(filename, 'r')
self.ifo = tuple(self.file.keys())[0]
self.valid = None
self.bank = h5py.File(bank, 'r') if bank else {}
# Determine the segments which define the boundaries of valid times
# to use triggers
key = '%s/search/' % self.ifo
s, e = self.file[key + 'start_time'][:], self.file[key + 'end_time'][:]
self.segs = veto.start_end_to_segments(s, e).coalesce()
if segment_name is None:
segment_name = []
if veto_files is None:
veto_files = []
for vfile, name in zip(veto_files, segment_name):
veto_segs = veto.select_segments_by_definer(vfile, ifo=self.ifo,
segment_name=name)
self.segs = (self.segs - veto_segs).coalesce()
if self.ifo in gating_veto_windows:
gating_veto = gating_veto_windows[self.ifo].split(',')
gveto_before = float(gating_veto[0])
gveto_after = float(gating_veto[1])
if gveto_before > 0 or gveto_after < 0:
raise ValueError("Gating veto window values must be negative "
"before gates and positive after gates.")
if not (gveto_before == 0 and gveto_after == 0):
autogate_times = np.unique(
self.file[self.ifo + '/gating/auto/time'][:])
if self.ifo + '/gating/file' in self.file:
detgate_times = self.file[self.ifo + '/gating/file/time'][:]
else:
detgate_times = []
gate_times = np.concatenate((autogate_times, detgate_times))
gating_veto_segs = veto.start_end_to_segments(
gate_times + gveto_before,
gate_times + gveto_after
).coalesce()
self.segs = (self.segs - gating_veto_segs).coalesce()
self.valid = veto.segments_to_start_end(self.segs)
[docs] def get_data(self, col, num):
"""Get a column of data for template with id 'num'.
Parameters
----------
col: str
Name of column to read
num: int
The template id to read triggers for
Returns
-------
data: numpy.ndarray
The requested column of data
"""
ref = self.file['%s/%s_template' % (self.ifo, col)][num]
return self.file['%s/%s' % (self.ifo, col)][ref]
[docs] def set_template(self, num):
"""Set the active template to read from.
Parameters
----------
num: int
The template id to read triggers for.
Returns
-------
trigger_id: numpy.ndarray
The indices of this templates triggers.
"""
self.template_num = num
times = self.get_data('end_time', num)
# Determine which of these template's triggers are kept after
# applying vetoes
if self.valid:
self.keep = veto.indices_within_times(times, self.valid[0],
self.valid[1])
# logging.info('applying vetoes')
else:
self.keep = np.arange(0, len(times))
if self.bank != {}:
self.param = {}
if 'parameters' in self.bank.attrs:
for col in self.bank.attrs['parameters']:
self.param[col] = self.bank[col][self.template_num]
else:
for col in self.bank:
self.param[col] = self.bank[col][self.template_num]
# Calculate the trigger id by adding the relative offset in self.keep
# to the absolute beginning index of this templates triggers stored
# in 'template_boundaries'
trigger_id = self.keep + \
self.file['%s/template_boundaries' % self.ifo][num]
return trigger_id
def __getitem__(self, col):
""" Return the column of data for current active template after
applying vetoes
Parameters
----------
col: str
Name of column to read
Returns
-------
data: numpy.ndarray
The requested column of data
"""
if self.template_num is None:
raise ValueError('You must call set_template to first pick the '
'template to read data from')
data = self.get_data(col, self.template_num)
data = data[self.keep] if self.valid else data
return data
chisq_choices = ['traditional', 'cont', 'bank', 'max_cont_trad', 'sg',
'max_bank_cont', 'max_bank_trad', 'max_bank_cont_trad']
[docs]def get_chisq_from_file_choice(hdfile, chisq_choice):
f = hdfile
if chisq_choice in ['traditional','max_cont_trad', 'max_bank_trad',
'max_bank_cont_trad']:
trad_chisq = f['chisq'][:]
# We now need to handle the case where chisq is not actually calculated
# 0 is used as a sentinel value
trad_chisq_dof = f['chisq_dof'][:]
trad_chisq /= (trad_chisq_dof * 2 - 2)
if chisq_choice in ['cont', 'max_cont_trad', 'max_bank_cont',
'max_bank_cont_trad']:
cont_chisq = f['cont_chisq'][:]
cont_chisq_dof = f['cont_chisq_dof'][:]
cont_chisq /= cont_chisq_dof
if chisq_choice in ['bank', 'max_bank_cont', 'max_bank_trad',
'max_bank_cont_trad']:
bank_chisq = f['bank_chisq'][:]
bank_chisq_dof = f['bank_chisq_dof'][:]
bank_chisq /= bank_chisq_dof
if chisq_choice == 'sg':
chisq = f['sg_chisq'][:]
elif chisq_choice == 'traditional':
chisq = trad_chisq
elif chisq_choice == 'cont':
chisq = cont_chisq
elif chisq_choice == 'bank':
chisq = bank_chisq
elif chisq_choice == 'max_cont_trad':
chisq = np.maximum(trad_chisq, cont_chisq)
elif chisq_choice == 'max_bank_cont':
chisq = np.maximum(bank_chisq, cont_chisq)
elif chisq_choice == 'max_bank_trad':
chisq = np.maximum(bank_chisq, trad_chisq)
elif chisq_choice == 'max_bank_cont_trad':
chisq = np.maximum(np.maximum(bank_chisq, cont_chisq), trad_chisq)
else:
err_msg = "Do not recognize --chisq-choice %s" % chisq_choice
raise ValueError(err_msg)
return chisq
[docs]def save_dict_to_hdf5(dic, filename):
"""
Parameters
----------
dic:
python dictionary to be converted to hdf5 format
filename:
desired name of hdf5 file
"""
with h5py.File(filename, 'w') as h5file:
recursively_save_dict_contents_to_group(h5file, '/', dic)
[docs]def recursively_save_dict_contents_to_group(h5file, path, dic):
"""
Parameters
----------
h5file:
h5py file to be written to
path:
path within h5py file to saved dictionary
dic:
python dictionary to be converted to hdf5 format
"""
for key, item in dic.items():
if isinstance(item, (np.ndarray, np.int64, np.float64, str, int, float,
bytes, tuple, list)):
h5file[path + str(key)] = item
elif isinstance(item, dict):
recursively_save_dict_contents_to_group(h5file, path + key + '/', item)
else:
raise ValueError('Cannot save %s type' % type(item))
[docs]def load_hdf5_to_dict(h5file, path):
"""
Parameters
----------
h5file:
h5py file to be loaded as a dictionary
path:
path within h5py file to load: '/' for the whole h5py file
Returns
-------
dic:
dictionary with hdf5 file group content
"""
dic = {}
for key, item in h5file[path].items():
if isinstance(item, h5py.Dataset):
dic[key] = item[()]
elif isinstance(item, h5py.Group):
dic[key] = load_hdf5_to_dict(h5file, path + key + '/')
else:
raise ValueError('Cannot load %s type' % type(item))
return dic
[docs]def combine_and_copy(f, files, group):
""" Combine the same column from multiple files and save to a third"""
# ensure that the files input is stable for iteration order
assert isinstance(files, (list, tuple))
f[group] = np.concatenate([fi[group][:] if group in fi else \
np.array([], dtype=np.uint32) for fi in files])
[docs]def name_all_datasets(files):
assert isinstance(files, (list, tuple))
datasets = []
for fi in files:
datasets += get_all_subkeys(fi, '/')
return set(datasets)
[docs]def get_all_subkeys(grp, key):
subkey_list = []
subkey_start = key
if key == '':
grpk = grp
else:
grpk = grp[key]
for sk in grpk.keys():
path = subkey_start + '/' + sk
if isinstance(grp[path], h5py.Dataset):
subkey_list.append(path.lstrip('/'))
else:
subkey_list += get_all_subkeys(grp, path)
# returns an empty list if there is no dataset or subgroup within the group
return subkey_list
#
# =============================================================================
#
# Checkpointing utilities
#
# =============================================================================
#
[docs]def dump_state(state, fp, path=None, dsetname='state',
protocol=pickle.HIGHEST_PROTOCOL):
"""Dumps the given state to an hdf5 file handler.
The state is stored as a raw binary array to ``{path}/{dsetname}`` in the
given hdf5 file handler. If a dataset with the same name and path is
already in the file, the dataset will be resized and overwritten with the
new state data.
Parameters
----------
state : any picklable object
The sampler state to dump to file. Can be the object returned by
any of the samplers' `.state` attribute (a dictionary of dictionaries),
or any picklable object.
fp : h5py.File
An open hdf5 file handler. Must have write capability enabled.
path : str, optional
The path (group name) to store the state dataset to. Default (None)
will result in the array being stored to the top level.
dsetname : str, optional
The name of the dataset to store the binary array to. Default is
``state``.
protocol : int, optional
The protocol version to use for pickling. See the :py:mod:`pickle`
module for more details.
"""
memfp = BytesIO()
pickle.dump(state, memfp, protocol=protocol)
dump_pickle_to_hdf(memfp, fp, path=path, dsetname=dsetname)
[docs]def dump_pickle_to_hdf(memfp, fp, path=None, dsetname='state'):
"""Dumps pickled data to an hdf5 file object.
Parameters
----------
memfp : file object
Bytes stream of pickled data.
fp : h5py.File
An open hdf5 file handler. Must have write capability enabled.
path : str, optional
The path (group name) to store the state dataset to. Default (None)
will result in the array being stored to the top level.
dsetname : str, optional
The name of the dataset to store the binary array to. Default is
``state``.
"""
memfp.seek(0)
bdata = np.frombuffer(memfp.read(), dtype='S1')
if path is not None:
dsetname = path + '/' + dsetname
if dsetname not in fp:
fp.create_dataset(dsetname, shape=bdata.shape, maxshape=(None,),
dtype=bdata.dtype)
elif bdata.size != fp[dsetname].shape[0]:
fp[dsetname].resize((bdata.size,))
fp[dsetname][:] = bdata
[docs]def load_state(fp, path=None, dsetname='state'):
"""Loads a sampler state from the given hdf5 file object.
The sampler state is expected to be stored as a raw bytes array which can
be loaded by pickle.
Parameters
----------
fp : h5py.File
An open hdf5 file handler.
path : str, optional
The path (group name) that the state data is stored to. Default (None)
is to read from the top level.
dsetname : str, optional
The name of the dataset that the state data is stored to. Default is
``state``.
"""
if path is not None:
fp = fp[path]
bdata = fp[dsetname][()].tobytes()
return pickle.load(BytesIO(bdata))
__all__ = ('HFile', 'DictArray', 'StatmapData', 'MultiifoStatmapData',
'FileData', 'DataFromFiles', 'SingleDetTriggers',
'ForegroundTriggers', 'ReadByTemplate', 'chisq_choices',
'get_chisq_from_file_choice', 'save_dict_to_hdf5',
'recursively_save_dict_contents_to_group', 'load_hdf5_to_dict',
'combine_and_copy', 'name_all_datasets', 'get_all_subkeys',
'dump_state', 'dump_pickle_to_hdf', 'load_state')