Merge branch 'remove-bayestar-cruft' into 'master'

Remove old unmaintained versions of BAYESTAR-related files

See merge request !647

lalinference/.gitignore

@@ -57,11 +57,8 @@ python/lalinference/_bayespputils.so
 python/lalinference/_distance.so
 python/lalinference/_lalinference*
 python/lalinference/_moc.so
-python/lalinference/bayestar/_sky_map.so
-python/lalinference/bayestar/sky_map.so
 python/lalinference/git_version.py
 python/lalinference/lalinference.py
-python/lalinference_average_skymaps
 python/lalinference_burst_pp_pipe
 python/lalinference_coherence_test
 python/lalinference_compute_roq_weights

lalinference/configure.ac

@@ -20,7 +20,6 @@ AC_CONFIG_FILES([ \
   python/lalinference/bayestar/Makefile \
   python/lalinference/imrtgr/Makefile \
   python/lalinference/io/Makefile \
-  python/lalinference/io/events/Makefile \
   python/lalinference/plot/Makefile \
   python/lalinference/popprior/Makefile \
   python/lalinference/rapid_pe/Makefile \

lalinference/debian/python-lalinference.install

 usr/bin/cbcBayes*
 usr/bin/imrtgr_*
-usr/bin/lalinference_average_skymaps
 usr/bin/lalinference_burst_pp_pipe
 usr/bin/lalinference_coherence_test
 usr/bin/lalinference_compute_roq_weights

lalinference/lalinference.spec.in

@@ -182,7 +182,6 @@ rm -Rf ${RPM_BUILD_DIR}/%{name}-%{version}%{?nightly:-%{nightly}}
 %license COPYING
 %{_bindir}/cbcBayes*
 %{_bindir}/imrtgr_*
-%{_bindir}/lalinference_average_skymaps
 %{_bindir}/lalinference_burst_pp_pipe
 %{_bindir}/lalinference_coherence_test
 %{_bindir}/lalinference_compute_roq_weights

lalinference/python/Makefile.am

@@ -15,7 +15,6 @@ pybin_scripts = \
 	rapidpe_compute_intrinsic_grid \
 	rapidpe_calculate_overlap \
 	imrtgr_imr_consistency_test \
-	lalinference_average_skymaps \
 	lalinference_burst_pp_pipe \
 	lalinference_coherence_test \
 	lalinference_compute_roq_weights \

lalinference/python/lalinference/bayestar/Makefile.am

@@ -9,31 +9,8 @@ pymoduledir = $(pkgpythondir)/bayestar
 
 pymodule_PYTHON = \
 	__init__.py \
-	command.py \
-	decorator.py \
 	deprecation.py \
-	filter.py \
-	ligolw.py \
 	sky_map.py \
-	postprocess.py \
-	timing.py \
 	$(END_OF_LIST)
 
-if HAVE_CHEALPIX
-if SWIG_BUILD_PYTHON
-pymodule_LTLIBRARIES = _sky_map.la
-
-_sky_map_la_CPPFLAGS = $(AM_CPPFLAGS) $(SWIG_PYTHON_CPPFLAGS) -I$(top_srcdir)/src
-_sky_map_la_CFLAGS = $(AM_CFLAGS) $(SWIG_PYTHON_CFLAGS) -Wno-error
-_sky_map_la_LDFLAGS = $(top_builddir)/src/liblalinference.la -shared -module -avoid-version
-endif
-endif
-
-all-local: _sky_map.so
-
-_sky_map.so:
-	rm -f $@ && $(LN_S) .libs/$@
-
-CLEANFILES = _sky_map.so
-
 endif

lalinference/python/lalinference/bayestar/decorator.py

-#
-# Copyright (C) 2013-2017  Leo Singer
-#
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the
-# Free Software Foundation; either version 2 of the License, or (at your
-# option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# You should have received a copy of the GNU General Public License along
-# with this program; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-#
-"""
-Collection of Python decorators.
-"""
-
-from functools import wraps
-from collections import Hashable
-from astropy.utils.misc import NumpyRNGContext
-
-__all__ = ('memoized', 'with_numpy_random_seed', 'as_dict')
-
-
-try:
-    from functools import lru_cache
-except ImportError:
-    # FIXME: Remove this when we drop support for Python < 3.2.
-    def memoized(func):
-        """Memoize a function or class by caching its return values for any
-        given arguments."""
-        cache = {}
-
-        @wraps(func)
-        def memo(*args, **kwargs):
-            # Create a key out of the arguments.
-            key = (args, frozenset(kwargs.items()))
-
-            if isinstance(args, Hashable):  # The key is immutable.
-                try:
-                    # Look up the return value for these arguments.
-                    ret = cache[key]
-                except KeyError:
-                    # Not found; invoke function and store return value.
-                    ret = cache[key] = func(*args, **kwargs)
-            else:  # The key is mutable. We can't cache it.
-                ret = func(*args, **kwargs)
-
-            # Done!
-            return ret
-
-        # Return wrapped function.
-        return memo
-else:
-    memoized = lru_cache(maxsize=None)
-
-
-def with_numpy_random_seed(func, seed=0):
-    """Decorate a function so that it is called with a pre-defined random seed.
-    The random seed is restored when the function returns."""
-
-    @wraps(func)
-    def wrapped_func(*args, **kwargs):
-        with NumpyRNGContext(seed):
-            ret = func(*args, **kwargs)
-        return ret
-
-    return wrapped_func
-
-
-def as_dict(func):
-    """Decorate a generator function to turn its output into a dict."""
-
-    @wraps(func)
-    def wrapped_func(*args, **kwargs):
-        return dict(func(*args, **kwargs))
-
-    return wrapped_func

lalinference/python/lalinference/bayestar/ligolw.py

-#
-# Copyright (C) 2013-2017  Leo Singer
-#
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the
-# Free Software Foundation; either version 2 of the License, or (at your
-# option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# You should have received a copy of the GNU General Public License along
-# with this program; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-#
-"""
-LIGO-LW convenience functions.
-"""
-
-# LIGO-LW XML imports.
-from glue.ligolw.utils import process as ligolw_process
-from glue.ligolw import ligolw
-from glue.ligolw import array as ligolw_array
-from glue.ligolw import param as ligolw_param
-from glue.ligolw import table as ligolw_table
-from glue.ligolw import lsctables
-from lalinspiral.inspinjfind import InspiralSCExactCoincDef
-
-
-def get_template_bank_f_low(xmldoc):
-    """Determine the low frequency cutoff from a template bank file,
-    whether the template bank was produced by lalapps_tmpltbank or
-    lalapps_cbc_sbank. bayestar_sim_to_tmpltbank does not have a command
-    line for the low-frequency cutoff; instead, it is recorded in a row
-    of the search_summvars table."""
-    try:
-        template_bank_f_low, = ligolw_process.get_process_params(
-            xmldoc, 'tmpltbank', '--low-frequency-cutoff')
-    except ValueError:
-        try:
-            template_bank_f_low, = ligolw_process.get_process_params(
-                xmldoc, 'lalapps_cbc_sbank', '--flow')
-        except ValueError:
-            try:
-                search_summvars_table = ligolw_table.get_table(
-                    xmldoc, lsctables.SearchSummVarsTable.tableName)
-                template_bank_f_low, = (
-                    search_summvars.value
-                    for search_summvars in search_summvars_table
-                    if search_summvars.name == 'low-frequency cutoff')
-            except ValueError:
-                raise ValueError("Could not determine low-frequency cutoff")
-    return template_bank_f_low
-
-
-def sim_coinc_and_sngl_inspirals_for_xmldoc(xmldoc):
-    """Retrieve (as a generator) all of the
-    (sim_inspiral, coinc_event, (sngl_inspiral, sngl_inspiral,
-    ... sngl_inspiral) tuples from found coincidences in a LIGO-LW XML
-    document."""
-
-    # Look up necessary tables.
-    coinc_table = ligolw_table.get_table(
-        xmldoc, lsctables.CoincTable.tableName)
-    coinc_def_table = ligolw_table.get_table(
-        xmldoc, lsctables.CoincDefTable.tableName)
-    coinc_map_table = ligolw_table.get_table(
-        xmldoc, lsctables.CoincMapTable.tableName)
-
-    # Look up coinc_def ids.
-    sim_coinc_def_id = coinc_def_table.get_coinc_def_id(
-        InspiralSCExactCoincDef.search,
-        InspiralSCExactCoincDef.search_coinc_type,
-        create_new=False)
-
-    def events_for_coinc_event_id(coinc_event_id):
-        for coinc_map in coinc_map_table:
-            if coinc_map.coinc_event_id == coinc_event_id:
-                for row in ligolw_table.get_table(
-                        xmldoc, coinc_map.table_name):
-                    column_name = coinc_map.event_id.column_name
-                    if getattr(row, column_name) == coinc_map.event_id:
-                        yield coinc_map.event_id, row
-
-    # Loop over all coinc_event <-> sim_inspiral coincs.
-    for sim_coinc in coinc_table:
-
-        # If this is not a coinc_event <-> sim_inspiral coinc, skip it.
-        if sim_coinc.coinc_def_id != sim_coinc_def_id:
-            continue
-
-        # Locate the sim_inspiral and coinc events.
-        sim_inspiral = None
-        coinc = None
-        for event_id, event in events_for_coinc_event_id(
-                sim_coinc.coinc_event_id):
-            if event_id.table_name == ligolw_table.Table.TableName(
-                    lsctables.SimInspiralTable.tableName):
-                if sim_inspiral is not None:
-                    raise RuntimeError(
-                        'Found more than one matching sim_inspiral entry')
-                sim_inspiral = event
-            elif event_id.table_name == ligolw_table.Table.TableName(
-                    lsctables.CoincTable.tableName):
-                if coinc is not None:
-                    raise RuntimeError(
-                        'Found more than one matching coinc entry')
-                coinc = event
-            else:
-                raise RuntimeError(
-                    "Did not expect coincidence to contain an event of "
-                    "type '{}'".format(event_id.table_name))
-
-        sngl_inspirals = tuple(
-            event for event_id, event in events_for_coinc_event_id(
-                coinc.coinc_event_id))
-
-        yield sim_inspiral, coinc, sngl_inspirals
-
-
-@lsctables.use_in
-class LSCTablesContentHandler(ligolw.LIGOLWContentHandler):
-    """Content handler for reading LIGO-LW XML files with LSC table schema."""
-
-
-@ligolw_array.use_in
-@ligolw_param.use_in
-@lsctables.use_in
-class LSCTablesAndSeriesContentHandler(ligolw.LIGOLWContentHandler):
-    """Content handler for reading LIGO-LW XML files with LSC table schema and
-    gridded arrays."""

lalinference/python/lalinference/bayestar/timing.py

-# -*- coding: utf-8
-#
-# Copyright (C) 2013-2015  Leo Singer
-#
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the
-# Free Software Foundation; either version 2 of the License, or (at your
-# option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# You should have received a copy of the GNU General Public License along
-# with this program; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-#
-from __future__ import division
-"""
-Functions for predicting timing accuracy of matched filters.
-"""
-
-
-import logging
-import numpy as np
-import lal
-import lalsimulation
-from scipy import interpolate
-from scipy import linalg
-
-from lalinference.bayestar.deprecation import warn
-warn('ligo.skymap.bayestar.filter')
-
-log = logging.getLogger('BAYESTAR')
-
-
-_noise_psd_funcs = {}
-
-
-class vectorize_swig_psd_func(object):
-    """Create a vectorized Numpy function from a SWIG-wrapped PSD function.
-    SWIG does not provide enough information for Numpy to determine the number
-    of input arguments, so we can't just use np.vectorize."""
-
-    def __init__(self, str):
-        self.__func = getattr(lalsimulation, str + 'Ptr')
-        self.__npyfunc = np.frompyfunc(getattr(lalsimulation, str), 1, 1)
-
-    def __call__(self, f):
-        fa = np.asarray(f)
-        df = np.diff(fa)
-        if fa.ndim == 1 and df.size > 1 and np.all(df[0] == df[1:]):
-            fa = np.concatenate((fa, [fa[-1] + df[0]]))
-            ret = lal.CreateREAL8FrequencySeries(
-                None, 0, fa[0], df[0], lal.DimensionlessUnit, fa.size)
-            lalsimulation.SimNoisePSD(ret, 0, self.__func)
-            ret = ret.data.data[:-1]
-        else:
-            ret = self.__npyfunc(f)
-        if not np.isscalar(ret):
-            ret = ret.astype(float)
-        return ret
-
-
-for _ifos, _func in (
-    (("H1", "H2", "L1", "I1"), 'SimNoisePSDaLIGOZeroDetHighPower'),
-    (("V1",), 'SimNoisePSDAdvVirgo'),
-    (("K1"), 'SimNoisePSDKAGRA')
-):
-    _func = vectorize_swig_psd_func(_func)
-    for _ifo in _ifos:
-        _noise_psd_funcs[_ifo] = _func
-
-
-def get_noise_psd_func(ifo):
-    """Find a function that describes the given interferometer's noise PSD."""
-    return _noise_psd_funcs[ifo]
-
-
-class InterpolatedPSD(interpolate.interp1d):
-    """Create a (linear in log-log) interpolating function for a discretely
-    sampled power spectrum S(f)."""
-
-    def __init__(self, f, S, f_high_truncate=1.0):
-        assert f_high_truncate <= 1.0
-        f = np.asarray(f)
-        S = np.asarray(S)
-
-        # Exclude DC if present
-        if f[0] == 0:
-            f = f[1:]
-            S = S[1:]
-        # FIXME: This is a hack to fix an issue with the detection pipeline's
-        # PSD conditioning. Remove this when the issue is fixed upstream.
-        if f_high_truncate < 1.0:
-            log.warn(
-                'Truncating PSD at %g of maximum frequency to suppress '
-                'rolloff artifacts. This option may be removed in the future.',
-                f_high_truncate)
-            keep = (f <= f_high_truncate * max(f))
-            f = f[keep]
-            S = S[keep]
-        super(InterpolatedPSD, self).__init__(
-            np.log(f), np.log(S),
-            kind='linear', bounds_error=False, fill_value=np.inf)
-        self._f_min = min(f)
-        self._f_max = max(f)
-
-    def __call__(self, f):
-        f_min = np.min(f)
-        f_max = np.max(f)
-        if f_min < self._f_min:
-            log.warn('Assuming PSD is infinite at %g Hz because PSD is only '
-                     'sampled down to %g Hz', f_min, self._f_min)
-        if f_max > self._f_max:
-            log.warn('Assuming PSD is infinite at %g Hz because PSD is only '
-                     'sampled up to %g Hz', f_max, self._f_max)
-        return np.where(
-            (f >= self._f_min) & (f <= self._f_max),
-            np.exp(super(InterpolatedPSD, self).__call__(np.log(f))), np.inf)
-
-
-class SignalModel(object):
-    """Class to speed up computation of signal/noise-weighted integrals and
-    Barankin and Cramér-Rao lower bounds on time and phase estimation.
-
-
-    Note that the autocorrelation series and the moments are related,
-    as shown below.
-
-    Create signal model:
-    >>> from . import filter
-    >>> sngl = lambda: None
-    >>> H = filter.sngl_inspiral_psd(
-    ...     'TaylorF2threePointFivePN', mass1=1.4, mass2=1.4)
-    >>> S = get_noise_psd_func('H1')
-    >>> W = filter.signal_psd_series(H, S)
-    >>> sm = SignalModel(W)
-
-    Compute one-sided autocorrelation function:
-    >>> out_duration = 0.1
-    >>> a, sample_rate = filter.autocorrelation(W, out_duration)
-
-    Restore negative time lags using symmetry:
-    >>> a = np.concatenate((a[:0:-1].conj(), a))
-
-    Compute the first 2 frequency moments by taking derivatives of the
-    autocorrelation sequence using centered finite differences.
-    The nth frequency moment should be given by (-1j)^n a^(n)(t).
-    >>> acor_moments = []
-    >>> for i in range(2):
-    ...     acor_moments.append(a[len(a) // 2])
-    ...     a = -0.5j * sample_rate * (a[2:] - a[:-2])
-    >>> assert np.all(np.isreal(acor_moments))
-    >>> acor_moments = np.real(acor_moments)
-
-    Compute the first 2 frequency moments using this class.
-    >>> quad_moments = [sm.get_sn_moment(i) for i in range(2)]
-
-    Compare them.
-    >>> for i, (am, qm) in enumerate(zip(acor_moments, quad_moments)):
-    ...     assert np.allclose(am, qm, rtol=0.05)
-    """
-
-    def __init__(self, h):
-        """Create a TaylorF2 signal model with the given masses, PSD function
-        S(f), PN amplitude order, and low-frequency cutoff."""
-
-        # Find indices of first and last nonzero samples.
-        nonzero = np.flatnonzero(h.data.data)
-        first_nonzero = nonzero[0]
-        last_nonzero = nonzero[-1]
-
-        # Frequency sample points
-        self.dw = 2 * np.pi * h.deltaF
-        f = h.f0 + h.deltaF * np.arange(first_nonzero, last_nonzero + 1)
-        self.w = 2 * np.pi * f
-
-        # Throw away leading and trailing zeros.
-        h = h.data.data[first_nonzero:last_nonzero + 1]
-
-        self.denom_integrand = 4 / (2 * np.pi) * h
-        self.den = np.trapz(self.denom_integrand, dx=self.dw)
-
-    def get_horizon_distance(self, snr_thresh=1):
-        return np.sqrt(self.den) / snr_thresh
-
-    def get_sn_average(self, func):
-        """Get the average of a function of angular frequency, weighted by the
-        signal to noise per unit angular frequency."""
-        num = np.trapz(func(self.w) * self.denom_integrand, dx=self.dw)
-        return num / self.den
-
-    def get_sn_moment(self, power):
-        """Get the average of angular frequency to the given power, weighted by
-        the signal to noise per unit frequency."""
-        return self.get_sn_average(lambda w: w**power)
-
-    def get_crb(self, snr):
-        """Get the Cramér-Rao bound, or inverse Fisher information matrix,
-        describing the phase and time estimation covariance."""
-        w1 = self.get_sn_moment(1)
-        w2 = self.get_sn_moment(2)
-        I = np.asarray(((1, -w1), (-w1, w2)))
-        return linalg.inv(I) / np.square(snr)
-
-    # FIXME: np.vectorize doesn't work on unbound instance methods. The
-    # excluded keyword, added in Numpy 1.7, could be used here to exclude the
-    # zeroth argument, self.
-    def __get_crb_toa_uncert(self, snr):
-        return np.sqrt(self.get_crb(snr)[1, 1])
-
-    def get_crb_toa_uncert(self, snr):
-        return np.frompyfunc(self.__get_crb_toa_uncert, 1, 1)(snr)

lalinference/python/lalinference/io/Makefile.am

@@ -3,8 +3,6 @@ MOSTLYCLEANFILES =
 EXTRA_DIST =
 include $(top_srcdir)/gnuscripts/lalsuite_python.am
 
-SUBDIRS = events
-
 if HAVE_PYTHON
 
 pymoduledir = $(pkgpythondir)/io

lalinference/python/lalinference/io/events/Makefile.am

-BUILT_SOURCES =
-MOSTLYCLEANFILES =
-EXTRA_DIST =
-include $(top_srcdir)/gnuscripts/lalsuite_python.am
-
-if HAVE_PYTHON
-
-pymoduledir = $(pkgpythondir)/io/events
-
-pymodule_PYTHON = \
-	__init__.py \
-	base.py \
-	detector_disabled.py \
-	ligolw.py \
-	gracedb.py \
-	hdf.py \
-	magic.py \
-	sqlite.py
-
-endif

lalinference/python/lalinference/io/events/__init__.py

-# Copyright (C) 2017-2018  Leo Singer
-#
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the
-# Free Software Foundation; either version 2 of the License, or (at your
-# option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# You should have received a copy of the GNU General Public License along
-# with this program; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-#
-from __future__ import absolute_import
-import os
-import pkgutil
-import six
-
-__all__ = ()
-
-# Import all symbols from all submodules of this module.
-for _, module, _ in pkgutil.iter_modules([os.path.dirname(__file__)]):
-    six.exec_('from . import {0};'
-              '__all__ += getattr({0}, "__all__", ());'
-              'from .{0} import *'.format(module))
-    del module
-
-# Clean up
-del os, pkgutil, six
-
-from lalinference.bayestar.deprecation import warn
-warn('ligo.skymap.io.events')

lalinference/python/lalinference/io/events/base.py

-# Copyright (C) 2017  Leo Singer
-#
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the
-# Free Software Foundation; either version 2 of the License, or (at your
-# option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# You should have received a copy of the GNU General Public License along
-# with this program; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-#
-"""
-Base classes for reading events from search pipelines.
-"""
-
-from abc import ABCMeta, abstractproperty
-from collections import Mapping
-import six
-
-__all__ = ('EventSource', 'Event', 'SingleEvent')
-
-
-def _fmt(obj, keys):
-    kvs = ', '.join('{}={!r}'.format(key, getattr(obj, key)) for key in keys)
-    return '<{}({})>'.format(obj.__class__.__name__, kvs)
-
-
-class EventSource(Mapping):
-    """Abstraction of a source of coincident events."""
-
-    def __str__(self):
-        try:
-            length = len(self)
-        except NotImplementedError:
-            contents = '...'
-        else:
-            contents = '...{} items...'.format(length)
-        return '<{}({{{}}})>'.format(self.__class__.__name__, contents)
-
-    def __repr__(self):
-        try:
-            len(self)
-        except NotImplementedError:
-            contents = '...'
-        else:
-            contents = ', '.join('{}: {!r}'.format(key, value)
-                                 for key, value in self.items())
-        return '{}({{{}}})'.format(self.__class__.__name__, contents)
-
-
-class Event(six.with_metaclass(ABCMeta)):
-    """Abstraction of a coincident trigger."""
-
-    @abstractproperty
-    def singles(self):
-        """Tuple of single-detector triggers."""
-        raise NotImplementedError
-
-    @abstractproperty
-    def template_args(self):
-        """Dictionary of template parameters."""
-        raise NotImplementedError
-