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/_sky_map.c

-/*
- * 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 with program; see the file COPYING. If not, write to the
- * Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
- * MA  02111-1307  USA
- */
-
-#include "config.h"
-#include <Python.h>
-/* Ignore warnings in Numpy API itself */
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wcast-qual"
-#include <numpy/arrayobject.h>
-#include <numpy/ufuncobject.h>
-#pragma GCC diagnostic pop
-#include <chealpix.h>
-#include <gsl/gsl_errno.h>
-#include <gsl/gsl_nan.h>
-#include <lal/bayestar_sky_map.h>
-#include <stddef.h>
-#include "six.h"
-
-
-static void capsule_free(PyObject *self)
-{
-    free(PyCapsule_GetPointer(self, NULL));
-}
-
-
-#define INPUT_LIST_OF_ARRAYS(NAME, NPYTYPE, DEPTH, CHECK) \
-{ \
-    const Py_ssize_t n = PySequence_Length(NAME##_obj); \
-    if (n < 0) \
-        goto fail; \
-    else if (n != nifos) { \
-        PyErr_SetString(PyExc_ValueError, #NAME \
-        " appears to be the wrong length for the number of detectors"); \
-        goto fail; \
-    } \
-    for (unsigned int iifo = 0; iifo < nifos; iifo ++) \
-    { \
-        PyObject *obj = PySequence_ITEM(NAME##_obj, iifo); \
-        if (!obj) goto fail; \
-        PyArrayObject *npy = (PyArrayObject *) \
-            PyArray_ContiguousFromAny(obj, NPYTYPE, DEPTH, DEPTH); \
-        Py_XDECREF(obj); \
-        if (!npy) goto fail; \
-        NAME##_npy[iifo] = npy; \
-        { CHECK } \
-        NAME[iifo] = PyArray_DATA(npy); \
-    } \
-}
-
-#define FREE_INPUT_LIST_OF_ARRAYS(NAME) \
-{ \
-    for (unsigned int iifo = 0; iifo < nifos; iifo ++) \
-        Py_XDECREF(NAME##_npy[iifo]); \
-}
-
-#define INPUT_VECTOR_NIFOS(CTYPE, NAME, NPYTYPE) \
-    NAME##_npy = (PyArrayObject *) \
-        PyArray_ContiguousFromAny(NAME##_obj, NPYTYPE, 1, 1); \
-    if (!NAME##_npy) goto fail; \
-    if (PyArray_DIM(NAME##_npy, 0) != nifos) \
-    { \
-        PyErr_SetString(PyExc_ValueError, #NAME \
-            " appears to be the wrong length for the number of detectors"); \
-        goto fail; \
-    } \
-    const CTYPE *NAME = PyArray_DATA(NAME##_npy);
-
-#define INPUT_VECTOR_DOUBLE_NIFOS(NAME) \
-    INPUT_VECTOR_NIFOS(double, NAME, NPY_DOUBLE)
-
-
-static PyArray_Descr *sky_map_descr;
-
-
-static PyArray_Descr *sky_map_create_descr(void)
-{
-    PyArray_Descr *dtype = NULL;
-    PyObject *dtype_dict = Py_BuildValue("{s(ssss)s(cccc)s(IIII)}",
-        "names", "UNIQ", "PROBDENSITY", "DISTMEAN", "DISTSTD",
-        "formats", NPY_ULONGLONGLTR, NPY_DOUBLELTR, NPY_DOUBLELTR, NPY_DOUBLELTR,
-        "offsets",
-        (unsigned int) offsetof(bayestar_pixel, uniq),
-        (unsigned int) offsetof(bayestar_pixel, value[0]),
-        (unsigned int) offsetof(bayestar_pixel, value[1]),
-        (unsigned int) offsetof(bayestar_pixel, value[2]));
-
-    if (dtype_dict)
-    {
-        PyArray_DescrConverter(dtype_dict, &dtype);
-        Py_DECREF(dtype_dict);
-    }
-
-    return dtype;
-}
-
-
-static PyObject *sky_map_toa_phoa_snr(
-    PyObject *NPY_UNUSED(module), PyObject *args, PyObject *kwargs)
-{
-    /* Input arguments */
-    double min_distance;
-    double max_distance;
-    int prior_distance_power;
-    int cosmology;
-    double gmst;
-    unsigned int nifos;
-    unsigned long nsamples = 0;
-    double sample_rate;
-    PyObject *epochs_obj;
-    PyObject *snrs_obj;
-    PyObject *responses_obj;
-    PyObject *locations_obj;
-    PyObject *horizons_obj;
-
-    /* Names of arguments */
-    static const char *keywords[] = {"min_distance", "max_distance",
-        "prior_distance_power", "cosmology", "gmst", "sample_rate", "epochs",
-        "snrs", "responses", "locations", "horizons", NULL};
-
-    /* Parse arguments */
-    /* FIXME: PyArg_ParseTupleAndKeywords should expect keywords to be const */
-    #pragma GCC diagnostic push
-    #pragma GCC diagnostic ignored "-Wincompatible-pointer-types"
-    if (!PyArg_ParseTupleAndKeywords(args, kwargs, "ddiiddOOOOO",
-        keywords, &min_distance, &max_distance, &prior_distance_power,
-        &cosmology, &gmst, &sample_rate, &epochs_obj, &snrs_obj,
-        &responses_obj, &locations_obj, &horizons_obj)) return NULL;
-    #pragma GCC diagnostic pop
-
-    /* Determine number of detectors */
-    {
-        Py_ssize_t n = PySequence_Length(epochs_obj);
-        if (n < 0) return NULL;
-        nifos = n;
-    }
-
-    /* Return value */
-    PyObject *out = NULL;
-    double log_bci, log_bsn;
-
-    /* Numpy array objects */
-    PyArrayObject *epochs_npy = NULL, *snrs_npy[nifos], *responses_npy[nifos],
-        *locations_npy[nifos], *horizons_npy = NULL;
-    memset(snrs_npy, 0, sizeof(snrs_npy));
-    memset(responses_npy, 0, sizeof(responses_npy));
-    memset(locations_npy, 0, sizeof(locations_npy));
-
-    /* Arrays of pointers for inputs with multiple dimensions */
-    const float complex *snrs[nifos];
-    const float (*responses[nifos])[3];
-    const double *locations[nifos];
-
-    /* Gather C-aligned arrays from Numpy types */
-    INPUT_VECTOR_DOUBLE_NIFOS(epochs)
-    INPUT_LIST_OF_ARRAYS(snrs, NPY_CFLOAT, 1,
-        npy_intp dim = PyArray_DIM(npy, 0);
-        if (iifo == 0)
-            nsamples = dim;
-        else if ((unsigned long)dim != nsamples)
-        {
-            PyErr_SetString(PyExc_ValueError,
-                "expected elements of snrs to be vectors of the same length");
-            goto fail;
-        }
-    )
-    INPUT_LIST_OF_ARRAYS(responses, NPY_FLOAT, 2,
-        if (PyArray_DIM(npy, 0) != 3 || PyArray_DIM(npy, 1) != 3)
-        {
-            PyErr_SetString(PyExc_ValueError,
-                "expected elements of responses to be 3x3 arrays");
-            goto fail;
-        }
-    )
-    INPUT_LIST_OF_ARRAYS(locations, NPY_DOUBLE, 1,
-        if (PyArray_DIM(npy, 0) != 3)
-        {
-            PyErr_SetString(PyExc_ValueError,
-                "expected elements of locations to be vectors of length 3");
-            goto fail;
-        }
-    )
-    INPUT_VECTOR_DOUBLE_NIFOS(horizons)
-
-    /* Call function */
-    gsl_error_handler_t *old_handler = gsl_set_error_handler_off();
-    size_t len;
-    bayestar_pixel *pixels;
-    Py_BEGIN_ALLOW_THREADS
-    pixels = bayestar_sky_map_toa_phoa_snr(&len, &log_bci, &log_bsn,
-        min_distance, max_distance, prior_distance_power, cosmology, gmst,
-        nifos, nsamples, sample_rate, epochs, snrs, responses, locations,
-        horizons);
-    Py_END_ALLOW_THREADS
-    gsl_set_error_handler(old_handler);
-
-    PyErr_CheckSignals();
-
-    if (!pixels)
-        goto fail;
-
-    /* Prepare output object */
-    PyObject *capsule = PyCapsule_New(pixels, NULL, capsule_free);
-    if (!capsule)
-        goto fail;
-
-    npy_intp dims[] = {len};
-    Py_INCREF(sky_map_descr);
-    out = PyArray_NewFromDescr(&PyArray_Type,
-        sky_map_descr, 1, dims, NULL, pixels, NPY_ARRAY_DEFAULT, NULL);
-    if (!out)
-    {
-        Py_DECREF(capsule);
-        goto fail;
-    }
-
-    if (PyArray_SetBaseObject((PyArrayObject *) out, capsule))
-    {
-        Py_DECREF(out);
-        out = NULL;
-        goto fail;
-    }
-
-fail: /* Cleanup */
-    Py_XDECREF(epochs_npy);
-    FREE_INPUT_LIST_OF_ARRAYS(snrs)
-    FREE_INPUT_LIST_OF_ARRAYS(responses)
-    FREE_INPUT_LIST_OF_ARRAYS(locations)
-    Py_XDECREF(horizons_npy);
-    if (out) {
-        out = Py_BuildValue("Ndd", out, log_bci, log_bsn);
-    }
-    return out;
-};
-
-
-static PyObject *log_likelihood_toa_phoa_snr(
-    PyObject *NPY_UNUSED(module), PyObject *args, PyObject *kwargs)
-{
-    /* Input arguments */
-    double ra;
-    double sin_dec;
-    double distance;
-    double u;
-    double twopsi;
-    double t;
-    double gmst;
-    unsigned int nifos;
-    unsigned long nsamples = 0;
-    double sample_rate;
-    PyObject *epochs_obj;
-    PyObject *snrs_obj;
-    PyObject *responses_obj;
-    PyObject *locations_obj;
-    PyObject *horizons_obj;
-
-    /* Names of arguments */
-    static const char *keywords[] = {"params", "gmst", "sample_rate", "epochs",
-        "snrs", "responses", "locations", "horizons", NULL};
-
-    /* Parse arguments */
-    /* FIXME: PyArg_ParseTupleAndKeywords should expect keywords to be const */
-    #pragma GCC diagnostic push
-    #pragma GCC diagnostic ignored "-Wincompatible-pointer-types"
-    if (!PyArg_ParseTupleAndKeywords(args, kwargs, "(dddddd)ddOOOOO",
-        keywords, &ra, &sin_dec, &distance, &u, &twopsi, &t, &gmst,
-        &sample_rate, &epochs_obj, &snrs_obj, &responses_obj, &locations_obj,
-        &horizons_obj)) return NULL;
-    #pragma GCC diagnostic pop
-
-    /* Determine number of detectors */
-    {
-        Py_ssize_t n = PySequence_Length(epochs_obj);
-        if (n < 0) return NULL;
-        nifos = n;
-    }
-
-    /* Return value */
-    PyObject *out = NULL;
-
-    /* Numpy array objects */
-    PyArrayObject *epochs_npy = NULL, *snrs_npy[nifos], *responses_npy[nifos],
-        *locations_npy[nifos], *horizons_npy = NULL;
-    memset(snrs_npy, 0, sizeof(snrs_npy));
-    memset(responses_npy, 0, sizeof(responses_npy));
-    memset(locations_npy, 0, sizeof(locations_npy));
-
-    /* Arrays of pointers for inputs with multiple dimensions */
-    const float complex *snrs[nifos];
-    const float (*responses[nifos])[3];
-    const double *locations[nifos];
-
-    /* Gather C-aligned arrays from Numpy types */
-    INPUT_VECTOR_DOUBLE_NIFOS(epochs)
-    INPUT_LIST_OF_ARRAYS(snrs, NPY_CFLOAT, 1,
-        npy_intp dim = PyArray_DIM(npy, 0);
-        if (iifo == 0)
-            nsamples = dim;
-        else if ((unsigned long)dim != nsamples)
-        {
-            PyErr_SetString(PyExc_ValueError,
-                "expected elements of snrs to be vectors of the same length");
-            goto fail;
-        }
-    )
-    INPUT_LIST_OF_ARRAYS(responses, NPY_FLOAT, 2,
-        if (PyArray_DIM(npy, 0) != 3 || PyArray_DIM(npy, 1) != 3)
-        {
-            PyErr_SetString(PyExc_ValueError,
-                "expected elements of responses to be 3x3 arrays");
-            goto fail;
-        }
-    )
-    INPUT_LIST_OF_ARRAYS(locations, NPY_DOUBLE, 1,
-        if (PyArray_DIM(npy, 0) != 3)
-        {
-            PyErr_SetString(PyExc_ValueError,
-                "expected elements of locations to be vectors of length 3");
-            goto fail;
-        }
-    )
-    INPUT_VECTOR_DOUBLE_NIFOS(horizons)
-
-    /* Call function */
-    gsl_error_handler_t *old_handler = gsl_set_error_handler_off();
-    const double ret = bayestar_log_likelihood_toa_phoa_snr(ra, sin_dec,
-        distance, u, twopsi, t, gmst, nifos, nsamples, sample_rate, epochs,
-        snrs, responses, locations, horizons);
-    gsl_set_error_handler(old_handler);
-
-    /* Prepare output object */
-    out = PyFloat_FromDouble(ret);
-
-fail: /* Cleanup */
-    Py_XDECREF(epochs_npy);
-    FREE_INPUT_LIST_OF_ARRAYS(snrs)
-    FREE_INPUT_LIST_OF_ARRAYS(responses)
-    FREE_INPUT_LIST_OF_ARRAYS(locations)
-    Py_XDECREF(horizons_npy);
-    return out;
-};
-
-
-static void signal_amplitude_model_loop(
-    char **args, npy_intp *dimensions, npy_intp *steps, void *NPY_UNUSED(data))
-{
-    const npy_intp n = dimensions[0];
-
-    for (npy_intp i = 0; i < n; i ++)
-    {
-        /* FIXME: args must be void ** to avoid alignment warnings */
-        #pragma GCC diagnostic push
-        #pragma GCC diagnostic ignored "-Wcast-align"
-        *(double complex *) &args[4][i * steps[4]] =
-            bayestar_signal_amplitude_model(
-            *(double complex *) &args[0][i * steps[0]],
-            *(double complex *) &args[1][i * steps[1]],
-            *(double *)         &args[2][i * steps[2]],
-            *(double *)         &args[3][i * steps[3]]);
-        #pragma GCC diagnostic pop
-    }
-}
-
-
-static PyObject *test(
-    PyObject *NPY_UNUSED(module), PyObject *NPY_UNUSED(arg))
-{
-    int ret;
-    gsl_error_handler_t *old_handler = gsl_set_error_handler_off();
-    Py_BEGIN_ALLOW_THREADS
-    ret = bayestar_test();
-    Py_END_ALLOW_THREADS
-    gsl_set_error_handler(old_handler);
-    return PyLong_FromLong(ret);
-}
-
-
-static PyMethodDef methods[] = {
-    {"toa_phoa_snr", (PyCFunction)sky_map_toa_phoa_snr,
-        METH_VARARGS | METH_KEYWORDS, "fill me in"},
-    {"log_likelihood_toa_phoa_snr", (PyCFunction)log_likelihood_toa_phoa_snr,
-        METH_VARARGS | METH_KEYWORDS, "fill me in"},
-    {"test", (PyCFunction)test,
-        METH_NOARGS, "fill me in"},
-    {NULL, NULL, 0, NULL}
-};
-
-
-static PyModuleDef moduledef = {
-    PyModuleDef_HEAD_INIT,
-    "_sky_map", NULL, -1, methods,
-    NULL, NULL, NULL, NULL
-};
-
-
-static const PyUFuncGenericFunction
-    signal_amplitude_model_loops[] = {signal_amplitude_model_loop};
-
-static const char signal_amplitude_model_ufunc_types[] = {
-    NPY_CDOUBLE, NPY_CDOUBLE, NPY_DOUBLE, NPY_DOUBLE, NPY_CDOUBLE};
-
-static void *const no_ufunc_data[] = {NULL};
-
-
-PyMODINIT_FUNC PyInit__sky_map(void); /* Silence -Wmissing-prototypes */
-PyMODINIT_FUNC PyInit__sky_map(void)
-{
-    PyObject *module = NULL;
-
-    gsl_set_error_handler_off();
-    import_array();
-    import_umath();
-
-    sky_map_descr = sky_map_create_descr();
-    if (!sky_map_descr)
-        goto done;
-
-    module = PyModule_Create(&moduledef);
-    if (!module)
-        goto done;
-
-    /* Ignore warnings in Numpy API */
-    #pragma GCC diagnostic push
-    #ifdef __clang__
-    #pragma GCC diagnostic ignored "-Wincompatible-pointer-types-discards-qualifiers"
-    #else
-    #pragma GCC diagnostic ignored "-Wdiscarded-qualifiers"
-    #endif
-
-    PyModule_AddObject(
-        module, "signal_amplitude_model", PyUFunc_FromFuncAndData(
-            signal_amplitude_model_loops, no_ufunc_data,
-            signal_amplitude_model_ufunc_types, 1, 4, 1, PyUFunc_None,
-            "signal_amplitude_model", NULL, 0));
-
-    #pragma GCC diagnostic pop
-
-done:
-    return module;
-}
-
-
-SIX_COMPAT_MODULE(_sky_map)

lalinference/python/lalinference/bayestar/command.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.
-#
-"""
-Functions that support the command line interface.
-"""
-
-from __future__ import print_function
-import argparse
-from distutils.dir_util import mkpath
-from distutils.errors import DistutilsFileError
-import glob
-import inspect
-import itertools
-import logging
-import os
-import sys
-import tempfile
-import matplotlib
-from matplotlib import cm
-from ..plot import cmap
-from ..util import sqlite
-
-
-# Set no-op Matplotlib backend to defer importing anything that requires a GUI
-# until we have determined that it is necessary based on the command line
-# arguments.
-if 'matplotlib.pyplot' in sys.modules:
-    from matplotlib import pyplot as plt
-    plt.switch_backend('Template')
-else:
-    matplotlib.use('Template', warn=False, force=True)
-
-
-# FIXME: Remove this after all Matplotlib monkeypatches are obsolete.
-import matplotlib
-import distutils.version
-mpl_version = distutils.version.LooseVersion(matplotlib.__version__)