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Commit 858eb446 authored by Leo Pound Singer's avatar Leo Pound Singer
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Port bayestar_samples_ppplot, rename to ligo-skymap-plot-pp-samples

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CHANGES.rst
View file @ 858eb446
......@@ -17,6 +17,10 @@ Changelog
- Add the ``ligo-skymap-flatten`` tool to convert multi-resolution HEALPix
files to flat, fixed-resolution, implicitly indexed HEALPix files.
- Bring back ``bayestar_samples_ppplot`` from LALInference as
``ligo-skymap-plot-pp-samples``, a tool for making P-P plots to compare a sky
map with posterior samples.
0.0.17 (2018-10-24)
===================
......
ligo/skymap/tool/bayestar_samples_ppplot.py deleted 100644 → 0
View file @ c05e966b
#
# 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 3 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, see <http://www.gnu.org/licenses/>.
#
"""
Create a P-P plot to compare a posterior sample chain with a sky map.
"""
# Command line interface.
from argparse import FileType
from lalinference.bayestar import command
parser = command.ArgumentParser(parents=[command.figure_parser])
parser.add_argument(
'skymap', metavar='SKYMAP.fits[.gz]', type=FileType('rb'),
help='FITS sky map file')
parser.add_argument(
'samples', metavar='SAMPLES.hdf5', type=FileType('rb'),
help='HDF5 posterior sample chain file')
parser.add_argument(
'-m', '--max-points', type=int,
help='Maximum number of posterior sample points [default: all of them]')
parser.add_argument(
'-p', '--contour', default=[], nargs='+', type=float,
metavar='PERCENT',
help='Report the areas and volumes within the smallest contours '
'containing this much probability.')
args = parser.parse_args()
# Late imports.
import re
from astropy.table import Table
from astropy.utils.misc import NumpyRNGContext
from matplotlib import pyplot as plt
import numpy as np
from lalinference import io
import lalinference.plot
from lalinference.bayestar.postprocess import find_injection_moc
from scipy.interpolate import interp1d
# Read input.
skymap = io.read_sky_map(args.skymap.name, moc=True)
chain = io.read_samples(args.samples.name)
# If required, downselect to a smaller number of posterior samples.
if args.max_points is not None:
chain = Table(np.random.permutation(chain)[:args.max_points])
# Calculate P-P plot.
contours = np.asarray(args.contour)
result = find_injection_moc(skymap, chain['ra'], chain['dec'], chain['dist'],
contours=1e-2 * contours)
def fmt(x, sigfigs, force_scientific=False):
"""Round and format a number in scientific notation."""
places = sigfigs - int(np.floor(np.log10(x)))
x_rounded = np.around(x, places)
if places <= 0 and not force_scientific:
return '{:d}'.format(int(x_rounded))
else:
s = ('{:.' + str(sigfigs) + 'e}').format(x_rounded)
return re.sub(r'^(.*)e\+?(-?)0*(\d+)$', r'$\1 \\times 10^{\2\3}$', s)
# Make Matplotlib figure.
fig = plt.figure(figsize=(6, 6))
ax = fig.add_subplot(111, projection='pp_plot')
ax.add_diagonal()
ax.add_series(result.searched_prob, label='R.A., Dec.')
searched_area_func = interp1d(np.linspace(0, 1, len(chain)),
np.sort(result.searched_area),
bounds_error=False)
if 'DISTMU' in skymap.colnames:
ax.add_series(result.searched_prob_dist, label='Distance')
ax.add_series(result.searched_prob_vol, label='Volume')
searched_vol_func = interp1d(np.linspace(0, 1, len(chain)),
np.sort(result.searched_vol),
bounds_error=False)
for p, area, vol in zip(
args.contour, result.contour_areas, result.contour_vols):
text = '{:g}%\n{} deg$^2$'.format(p, fmt(area, 2))
if 'DISTMU' in skymap.colnames:
text += '\n{} Mpc$^3$'.format(fmt(vol, 2, force_scientific=True))
ax.annotate(
text, (1e-2 * p, 1e-2 * p), (0, -150),
xycoords='data', textcoords='offset points',
horizontalalignment='right', backgroundcolor='white',
arrowprops=dict(connectionstyle='bar,angle=0,fraction=0',
arrowstyle='-|>', linewidth=2, color='black'))
area = searched_area_func(1e-2 * p)
text = '{:g}%\n{} deg$^2$'.format(p, fmt(area, 2))
if 'DISTMU' in skymap.colnames:
vol = searched_vol_func(1e-2 * p)
text += '\n{} Mpc$^3$'.format(fmt(vol, 2, force_scientific=True))
ax.annotate(
text, (1e-2 * p, 1e-2 * p), (-75, 0),
xycoords='data', textcoords='offset points',
horizontalalignment='right', verticalalignment='center',
backgroundcolor='white',
arrowprops=dict(connectionstyle='bar,angle=0,fraction=0',
arrowstyle='-|>', linewidth=2, color='black'))
ax.set_xlabel('searched probability')
ax.set_ylabel('cumulative fraction of posterior samples')
ax.set_title(args.skymap.name)
ax.legend()
ax.grid()
# Show or save output.
args.output()
ligo/skymap/tool/ligo_skymap_plot_pp_samples.py 0 → 100644
View file @ 858eb446
#
# Copyright (C) 2017-2018 Leo Singer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
"""
Create a P-P plot to compare a posterior sample chain with a sky map.
"""
import re
import numpy as np
from . import figure_parser, ArgumentParser, FileType
def fmt(x, sigfigs, force_scientific=False):
"""Round and format a number in scientific notation."""
places = sigfigs - int(np.floor(np.log10(x)))
x_rounded = np.around(x, places)
if places <= 0 and not force_scientific:
return '{:d}'.format(int(x_rounded))
else:
s = ('{:.' + str(sigfigs) + 'e}').format(x_rounded)
return re.sub(r'^(.*)e\+?(-?)0*(\d+)$', r'$\1 \\times 10^{\2\3}$', s)
def parser():
parser = ArgumentParser(parents=[figure_parser])
parser.add_argument(
'skymap', metavar='SKYMAP.fits[.gz]', type=FileType('rb'),
help='FITS sky map file')
parser.add_argument(
'samples', metavar='SAMPLES.hdf5', type=FileType('rb'),
help='HDF5 posterior sample chain file')
parser.add_argument(
'-m', '--max-points', type=int,
help='Maximum number of posterior sample points '
'[default: all of them]')
parser.add_argument(
'-p', '--contour', default=[], nargs='+', type=float,
metavar='PERCENT',
help='Report the areas and volumes within the smallest contours '
'containing this much probability.')
return parser
def main(args=None):
args = parser().parse_args(args)
# Late imports.
from astropy.table import Table
from matplotlib import pyplot as plt
from scipy.interpolate import interp1d
from .. import io
from .. import plot as _ # noqa: F401
from ..postprocess import find_injection_moc
# Read input.
skymap = io.read_sky_map(args.skymap.name, moc=True)
chain = io.read_samples(args.samples.name)
# If required, downselect to a smaller number of posterior samples.
if args.max_points is not None:
chain = Table(np.random.permutation(chain)[:args.max_points])
# Calculate P-P plot.
contours = np.asarray(args.contour)
result = find_injection_moc(skymap,
chain['ra'], chain['dec'], chain['dist'],
contours=1e-2 * contours)
# Make Matplotlib figure.
fig = plt.figure(figsize=(6, 6))
ax = fig.add_subplot(111, projection='pp_plot')
ax.add_diagonal()
ax.add_series(result.searched_prob, label='R.A., Dec.')
searched_area_func = interp1d(np.linspace(0, 1, len(chain)),
np.sort(result.searched_area),
bounds_error=False)
if 'DISTMU' in skymap.colnames:
ax.add_series(result.searched_prob_dist, label='Distance')
ax.add_series(result.searched_prob_vol, label='Volume')
searched_vol_func = interp1d(np.linspace(0, 1, len(chain)),
np.sort(result.searched_vol),
bounds_error=False)
for p, area, vol in zip(
args.contour, result.contour_areas, result.contour_vols):
text = '{:g}%\n{} deg$^2$'.format(p, fmt(area, 2))
if 'DISTMU' in skymap.colnames:
text += '\n{} Mpc$^3$'.format(fmt(vol, 2, force_scientific=True))
ax.annotate(
text, (1e-2 * p, 1e-2 * p), (0, -150),
xycoords='data', textcoords='offset points',
horizontalalignment='right', backgroundcolor='white',
arrowprops=dict(connectionstyle='bar,angle=0,fraction=0',
arrowstyle='-|>', linewidth=2, color='black'))
area = searched_area_func(1e-2 * p)
text = '{:g}%\n{} deg$^2$'.format(p, fmt(area, 2))
if 'DISTMU' in skymap.colnames:
vol = searched_vol_func(1e-2 * p)
text += '\n{} Mpc$^3$'.format(fmt(vol, 2, force_scientific=True))
ax.annotate(
text, (1e-2 * p, 1e-2 * p), (-75, 0),
xycoords='data', textcoords='offset points',
horizontalalignment='right', verticalalignment='center',
backgroundcolor='white',
arrowprops=dict(connectionstyle='bar,angle=0,fraction=0',
arrowstyle='-|>', linewidth=2, color='black'))
ax.set_xlabel('searched probability')
ax.set_ylabel('cumulative fraction of posterior samples')
ax.set_title(args.skymap.name)
ax.legend()
ax.grid()
# Show or save output.
args.output()
setup.cfg
View file @ 858eb446
......@@ -78,6 +78,7 @@ ligo-skymap-flatten = ligo.skymap.tool.ligo_skymap_flatten:main
ligo-skymap-from-samples = ligo.skymap.tool.ligo_skymap_from_samples:main
ligo-skymap-plot = ligo.skymap.tool.ligo_skymap_plot:main
ligo-skymap-plot-airmass = ligo.skymap.tool.ligo_skymap_plot_airmass:main
ligo-skymap-plot-pp-samples = ligo.skymap.tool.ligo_skymap_plot_pp_samples:main
ligo-skymap-plot-stats = ligo.skymap.tool.ligo_skymap_plot_stats:main
ligo-skymap-plot-volume = ligo.skymap.tool.ligo_skymap_plot_volume:main
ligo-skymap-stats = ligo.skymap.tool.ligo_skymap_stats:main
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