diff --git a/bilby/__init__.py b/bilby/__init__.py
index eff33090a25b4c0147cce0166ac9b4ddbe433705..4b6ac0f52bfae1798ca6bf338f92294c0a96606b 100644
--- a/bilby/__init__.py
+++ b/bilby/__init__.py
@@ -4,7 +4,7 @@ Bilby
Bilby: a user-friendly Bayesian inference library.
-The aim of bilby is to provide user friendly interface to perform parameter
+The aim of bilby is to provide a user-friendly interface to perform parameter
estimation. It is primarily designed and built for inference of compact
binary coalescence events in interferometric data, but it can also be used for
more general problems.
diff --git a/bilby/core/prior/conditional.py b/bilby/core/prior/conditional.py
index cffbf2cec1270b6b657ffee9c53a4ee91a9f3fc7..c96c1a05da9b4e9aee7f2159b868c5e1fd1f7ded 100644
--- a/bilby/core/prior/conditional.py
+++ b/bilby/core/prior/conditional.py
@@ -129,7 +129,7 @@ def conditional_prior_factory(prior_class):
"""
if sorted(list(required_variables)) == sorted(self.required_variables):
- parameters = self.condition_func(self.reference_params, **required_variables)
+ parameters = self.condition_func(self.reference_params.copy(), **required_variables)
for key, value in parameters.items():
setattr(self, key, value)
elif len(required_variables) == 0:
diff --git a/bilby/core/prior/dict.py b/bilby/core/prior/dict.py
index a6be2ba737559309a0ae819571944740115172df..abb54e67b523390e81c7211d6435e2fe764ca565 100644
--- a/bilby/core/prior/dict.py
+++ b/bilby/core/prior/dict.py
@@ -16,7 +16,7 @@ from bilby.core.utils import logger, check_directory_exists_and_if_not_mkdir, Bi
class PriorDict(dict):
def __init__(self, dictionary=None, filename=None,
conversion_function=None):
- """ A set of priors
+ """ A dictionary of priors
Parameters
----------
diff --git a/bilby/core/prior/interpolated.py b/bilby/core/prior/interpolated.py
index 1f57fe22192c086cdf17d41578dc1e9213875575..7e5eb8f3e7b51097b0ab3d78229806daa44d6b17 100644
--- a/bilby/core/prior/interpolated.py
+++ b/bilby/core/prior/interpolated.py
@@ -44,6 +44,8 @@ class Interped(Prior):
"""
self.xx = xx
+ self.min_limit = min(xx)
+ self.max_limit = max(xx)
self._yy = yy
self.YY = None
self.probability_density = None
@@ -97,6 +99,8 @@ class Interped(Prior):
Updates the prior distribution if minimum is set to a different value.
+ Yields an error if value is set below instantiated x-array minimum.
+
Returns
-------
float: Minimum of the prior distribution
@@ -106,6 +110,8 @@ class Interped(Prior):
@minimum.setter
def minimum(self, minimum):
+ if minimum < self.min_limit:
+ raise ValueError('Minimum cannot be set below {}.'.format(round(self.min_limit, 2)))
self._minimum = minimum
if '_maximum' in self.__dict__ and self._maximum < np.inf:
self._update_instance()
@@ -116,6 +122,8 @@ class Interped(Prior):
Updates the prior distribution if maximum is set to a different value.
+ Yields an error if value is set above instantiated x-array maximum.
+
Returns
-------
float: Maximum of the prior distribution
@@ -125,6 +133,8 @@ class Interped(Prior):
@maximum.setter
def maximum(self, maximum):
+ if maximum > self.max_limit:
+ raise ValueError('Maximum cannot be set above {}.'.format(round(self.max_limit, 2)))
self._maximum = maximum
if '_minimum' in self.__dict__ and self._minimum < np.inf:
self._update_instance()
@@ -190,12 +200,12 @@ class FromFile(Interped):
"""
try:
- self.id = file_name
- xx, yy = np.genfromtxt(self.id).T
+ self.file_name = file_name
+ xx, yy = np.genfromtxt(self.file_name).T
super(FromFile, self).__init__(xx=xx, yy=yy, minimum=minimum,
maximum=maximum, name=name, latex_label=latex_label,
unit=unit, boundary=boundary)
except IOError:
- logger.warning("Can't load {}.".format(self.id))
+ logger.warning("Can't load {}.".format(self.file_name))
logger.warning("Format should be:")
logger.warning(r"x\tp(x)")
diff --git a/bilby/core/prior/joint.py b/bilby/core/prior/joint.py
index c9baa773f9d2b5789cf58261d544233a8bdd1b74..d2058d074414b14a90ebd2837c80e4287aa3cf35 100644
--- a/bilby/core/prior/joint.py
+++ b/bilby/core/prior/joint.py
@@ -570,7 +570,15 @@ class MultivariateGaussianDist(BaseJointPriorDist):
if self.nmodes == 1:
mode = 0
else:
- mode = np.argwhere(self.cumweights - np.random.rand() > 0)[0][0]
+ if size == 1:
+ mode = np.argwhere(self.cumweights - np.random.rand() > 0)[0][0]
+ else:
+ # pick modes
+ mode = [
+ np.argwhere(self.cumweights - r > 0)[0][0]
+ for r in np.random.rand(size)
+ ]
+
samps = np.zeros((size, len(self)))
for i in range(size):
inbound = False
@@ -578,7 +586,10 @@ class MultivariateGaussianDist(BaseJointPriorDist):
# sample the multivariate Gaussian keys
vals = np.random.uniform(0, 1, len(self))
- samp = np.atleast_1d(self.rescale(vals, mode=mode))
+ if isinstance(mode, list):
+ samp = np.atleast_1d(self.rescale(vals, mode=mode[i]))
+ else:
+ samp = np.atleast_1d(self.rescale(vals, mode=mode))
samps[i, :] = samp
# check sample is in bounds (otherwise perform another draw)
diff --git a/bilby/core/sampler/pymultinest.py b/bilby/core/sampler/pymultinest.py
index 9421c8207c09dae938d4b37cf6b61a46c2853a42..eaa14ccef7ec2c570689e6d17f9f3e09f3cdfc07 100644
--- a/bilby/core/sampler/pymultinest.py
+++ b/bilby/core/sampler/pymultinest.py
@@ -271,6 +271,7 @@ class Pymultinest(NestedSampler):
current_time = time.time()
new_sampling_time = current_time - self.start_time
self.total_sampling_time += new_sampling_time
+ self.start_time = current_time
with open(self.time_file_path, 'w') as time_file:
time_file.write(str(self.total_sampling_time))
diff --git a/bilby/core/utils.py b/bilby/core/utils.py
index f007416b27e8a5923a379a9528b3c3c0c5188fd1..4e9ae263223595470c3cd227d2e339370b0306ad 100644
--- a/bilby/core/utils.py
+++ b/bilby/core/utils.py
@@ -6,7 +6,6 @@ import os
import shutil
from math import fmod
import argparse
-import traceback
import inspect
import functools
import types
@@ -16,11 +15,11 @@ from importlib import import_module
import json
import warnings
-from distutils.version import StrictVersion
import numpy as np
from scipy.interpolate import interp2d
from scipy.special import logsumexp
import pandas as pd
+import matplotlib.pyplot as plt
logger = logging.getLogger('bilby')
@@ -972,28 +971,6 @@ command_line_args, command_line_parser = set_up_command_line_arguments()
# Instantiate the default logging
setup_logger(print_version=False, log_level=command_line_args.log_level)
-if 'DISPLAY' in os.environ:
- logger.debug("DISPLAY={} environment found".format(os.environ['DISPLAY']))
- pass
-else:
- logger.debug('No $DISPLAY environment variable found, so importing \
- matplotlib.pyplot with non-interactive "Agg" backend.')
- import matplotlib
- import matplotlib.pyplot as plt
-
- non_gui_backends = matplotlib.rcsetup.non_interactive_bk
- for backend in non_gui_backends:
- try:
- logger.debug("Trying backend {}".format(backend))
- if StrictVersion(matplotlib.__version__) >= StrictVersion("3.1"):
- matplotlib.use(backend)
- else:
- matplotlib.use(backend, warn=False)
- plt.switch_backend(backend)
- break
- except Exception:
- print(traceback.format_exc())
-
class BilbyJsonEncoder(json.JSONEncoder):
@@ -1184,27 +1161,67 @@ def safe_file_dump(data, filename, module):
def latex_plot_format(func):
"""
- Wrap a plotting function to set rcParams so that text renders nicely with
- latex and Computer Modern Roman font.
+ Wrap the plotting function to set rcParams dependent on environment variables
+
+ The rcparams can be set directly from the env. variable `BILBY_STYLE` to
+ point to a matplotlib style file. Or, if `BILBY_STYLE=default` (any case) a
+ default setup is used, this is enabled by default. To not use any rcParams,
+ set `BILBY_STYLE=none`. Occasionally, issues arrise with the latex
+ `mathdefault` command. A fix is to define this command in the rcParams. An
+ env. variable `BILBY_MATHDEFAULT` can be used to turn this fix on/off.
+ Setting `BILBY_MATHDEFAULT=1` will enable the fix, all other choices
+ (including undefined) will disable it. Additionally, the BILBY_STYLE and
+ BILBY_MATHDEFAULT arguments can be passed into any
+ latex_plot_format-wrapped plotting function and will be set directly.
+
"""
@functools.wraps(func)
def wrapper_decorator(*args, **kwargs):
from matplotlib import rcParams
- _old_tex = rcParams["text.usetex"]
- _old_serif = rcParams["font.serif"]
- _old_family = rcParams["font.family"]
- if find_executable("latex"):
- rcParams["text.usetex"] = True
+
+ if "BILBY_STYLE" in kwargs:
+ bilby_style = kwargs.pop("BILBY_STYLE")
+ else:
+ bilby_style = os.environ.get("BILBY_STYLE", "default")
+
+ if "BILBY_MATHDEFAULT" in kwargs:
+ bilby_mathdefault = kwargs.pop("BILBY_MATHDEFAULT")
+ else:
+ bilby_mathdefault = int(os.environ.get("BILBY_MATHDEFAULT", "0"))
+
+ if bilby_mathdefault == 1:
+ logger.debug("Setting mathdefault in the rcParams")
rcParams['text.latex.preamble'] = r'\newcommand{\mathdefault}[1][]{}'
+
+ logger.debug("Using BILBY_STYLE={}".format(bilby_style))
+ if bilby_style.lower() == "none":
+ return func(*args, **kwargs)
+ elif os.path.isfile(bilby_style):
+ plt.style.use(bilby_style)
+ return func(*args, **kwargs)
+ elif bilby_style in plt.style.available:
+ plt.style.use(bilby_style)
+ return func(*args, **kwargs)
+ elif bilby_style.lower() == "default":
+ _old_tex = rcParams["text.usetex"]
+ _old_serif = rcParams["font.serif"]
+ _old_family = rcParams["font.family"]
+ if find_executable("latex"):
+ rcParams["text.usetex"] = True
+ else:
+ rcParams["text.usetex"] = False
+ rcParams["font.serif"] = "Computer Modern Roman"
+ rcParams["font.family"] = "serif"
+ rcParams["text.usetex"] = _old_tex
+ rcParams["font.serif"] = _old_serif
+ rcParams["font.family"] = _old_family
+ return func(*args, **kwargs)
else:
- rcParams["text.usetex"] = False
- rcParams["font.serif"] = "Computer Modern Roman"
- rcParams["font.family"] = "serif"
- value = func(*args, **kwargs)
- rcParams["text.usetex"] = _old_tex
- rcParams["font.serif"] = _old_serif
- rcParams["font.family"] = _old_family
- return value
+ logger.debug(
+ "Environment variable BILBY_STYLE={} not used"
+ .format(bilby_style)
+ )
+ return func(*args, **kwargs)
return wrapper_decorator
diff --git a/bilby/gw/conversion.py b/bilby/gw/conversion.py
index ca7f157ed656d0c8c528e733c8e082e8993f2c85..0b1f3aaccdb6d4f474c429758ed4691497a1c77e 100644
--- a/bilby/gw/conversion.py
+++ b/bilby/gw/conversion.py
@@ -1116,13 +1116,14 @@ def compute_snrs(sample, likelihood):
if isinstance(sample, dict):
signal_polarizations =\
likelihood.waveform_generator.frequency_domain_strain(sample)
+ likelihood.parameters.update(sample)
for ifo in likelihood.interferometers:
- signal = ifo.get_detector_response(signal_polarizations, sample)
+ per_detector_snr = likelihood.calculate_snrs(
+ signal_polarizations, ifo)
sample['{}_matched_filter_snr'.format(ifo.name)] =\
- ifo.matched_filter_snr(signal=signal)
+ per_detector_snr.complex_matched_filter_snr
sample['{}_optimal_snr'.format(ifo.name)] = \
- ifo.optimal_snr_squared(signal=signal) ** 0.5
-
+ per_detector_snr.optimal_snr_squared.real ** 0.5
else:
logger.info(
'Computing SNRs for every sample.')
diff --git a/bilby/gw/detector/strain_data.py b/bilby/gw/detector/strain_data.py
index ab7f5efd96efdc8761db072418632e62b1e19a59..6ba6db039ef244e5bb3295ba8796347af868a60f 100644
--- a/bilby/gw/detector/strain_data.py
+++ b/bilby/gw/detector/strain_data.py
@@ -408,6 +408,7 @@ class InterferometerStrainData(object):
self.time_array = array
elif domain == 'frequency':
self.frequency_array = array
+ self.start_time = start_time
return
elif sampling_frequency is None or duration is None:
raise ValueError(
diff --git a/bilby/gw/likelihood.py b/bilby/gw/likelihood.py
index 85f6677e97ae51be59ef5969a09109e310e0190c..f5817d5824d3de28c2bffcd464c2eeb6dde25cec 100644
--- a/bilby/gw/likelihood.py
+++ b/bilby/gw/likelihood.py
@@ -137,7 +137,7 @@ class GravitationalWaveTransient(Likelihood):
self.reference_ifo = None
if self.time_marginalization:
- self._check_prior_is_set(key='geocent_time')
+ self._check_marginalized_prior_is_set(key='geocent_time')
self._setup_time_marginalization()
priors['geocent_time'] = float(self.interferometers.start_time)
if self.jitter_time:
@@ -152,7 +152,7 @@ class GravitationalWaveTransient(Likelihood):
self.jitter_time = False
if self.phase_marginalization:
- self._check_prior_is_set(key='phase')
+ self._check_marginalized_prior_is_set(key='phase')
self._bessel_function_interped = None
self._setup_phase_marginalization()
priors['phase'] = float(0)
@@ -160,7 +160,7 @@ class GravitationalWaveTransient(Likelihood):
if self.distance_marginalization:
self._lookup_table_filename = None
- self._check_prior_is_set(key='luminosity_distance')
+ self._check_marginalized_prior_is_set(key='luminosity_distance')
self._distance_array = np.linspace(
self.priors['luminosity_distance'].minimum,
self.priors['luminosity_distance'].maximum, int(1e4))
@@ -234,7 +234,11 @@ class GravitationalWaveTransient(Likelihood):
complex_matched_filter_snr=complex_matched_filter_snr,
d_inner_h_squared_tc_array=d_inner_h_squared_tc_array)
- def _check_prior_is_set(self, key):
+ def _check_marginalized_prior_is_set(self, key):
+ if key in self.priors and self.priors[key].is_fixed:
+ raise ValueError(
+ "Cannot use marginalized likelihood for {}: prior is fixed"
+ .format(key))
if key not in self.priors or not isinstance(
self.priors[key], Prior):
logger.warning(
diff --git a/bilby/gw/prior.py b/bilby/gw/prior.py
index e3523a36f8ed098113b08dbbf11c88518593707c..7d1b37da3bf3c0f35000fc699f6c48cd85aa772e 100644
--- a/bilby/gw/prior.py
+++ b/bilby/gw/prior.py
@@ -139,7 +139,10 @@ class Cosmological(Interped):
@minimum.setter
def minimum(self, minimum):
- self._set_limit(value=minimum, limit_dict=self._minimum)
+ if (self.name in self._minimum) and (minimum < self.minimum):
+ self._set_limit(value=minimum, limit_dict=self._minimum, recalculate_array=True)
+ else:
+ self._set_limit(value=minimum, limit_dict=self._minimum)
@property
def maximum(self):
@@ -147,11 +150,14 @@ class Cosmological(Interped):
@maximum.setter
def maximum(self, maximum):
- self._set_limit(value=maximum, limit_dict=self._maximum)
+ if (self.name in self._maximum) and (maximum > self.maximum):
+ self._set_limit(value=maximum, limit_dict=self._maximum, recalculate_array=True)
+ else:
+ self._set_limit(value=maximum, limit_dict=self._maximum)
- def _set_limit(self, value, limit_dict):
+ def _set_limit(self, value, limit_dict, recalculate_array=False):
"""
- Set either the limits for redshift luminosity and comoving distances
+ Set either of the limits for redshift, luminosity, and comoving distances
Parameters
----------
@@ -159,6 +165,8 @@ class Cosmological(Interped):
Limit value in current class' parameter
limit_dict: dict
The limit dictionary to modify in place
+ recalculate_array: boolean
+ Determines if the distance arrays are recalculated
"""
cosmology = get_cosmology(self.cosmology)
limit_dict[self.name] = value
@@ -185,6 +193,13 @@ class Cosmological(Interped):
limit_dict['luminosity_distance'] = (
cosmology.luminosity_distance(limit_dict['redshift']).value
)
+ if recalculate_array:
+ if self.name == 'redshift':
+ self.xx, self.yy = self._get_redshift_arrays()
+ elif self.name == 'comoving_distance':
+ self.xx, self.yy = self._get_comoving_distance_arrays()
+ elif self.name == 'luminosity_distance':
+ self.xx, self.yy = self._get_luminosity_distance_arrays()
try:
self._update_instance()
except (AttributeError, KeyError):
@@ -615,7 +630,9 @@ Prior._default_latex_labels = {
'lambda_1': '$\\Lambda_1$',
'lambda_2': '$\\Lambda_2$',
'lambda_tilde': '$\\tilde{\\Lambda}$',
- 'delta_lambda_tilde': '$\\delta\\tilde{\\Lambda}$'}
+ 'delta_lambda_tilde': '$\\delta\\tilde{\\Lambda}$',
+ 'chi_1': '$\\chi_1$',
+ 'chi_2': '$\\chi_2$'}
class CalibrationPriorDict(PriorDict):
diff --git a/docs/bilby-output.txt b/docs/bilby-output.txt
index 4426dd010d855b68cf3e79ff17870ba848242429..ed5cc8b64307977fcd53809e88123881bc667c5b 100644
--- a/docs/bilby-output.txt
+++ b/docs/bilby-output.txt
@@ -2,13 +2,11 @@
Bilby output
============
-In this document, we will describe what :code:`bilby` outputs, where it is stored,
-and how you can access it.
-
-When you call :code:`run_sampler`, there are two arguments :code:`outdir` and :code:`label` which
-are used in generating all the file names for saved data. In the rest of these
-documents, we'll assume the defaults where used (which are :code:`outdir` and
-:code:`label`).
+In this document, we will describe what :code:`bilby` outputs, where it is
+stored, and how you can access it. When you call :code:`run_sampler`, there
+are two arguments :code:`outdir` and :code:`label` which are used in generating
+all the file names for saved data. In the rest of these documents, we'll assume
+the defaults where used (which are :code:`outdir` and :code:`label`).
The result file
@@ -97,8 +95,8 @@ done via::
which will generate a file :code:`outdir/label_posterior.txt`.
-Visualising the results
---------------------
+Visualising the results
+-----------------------
Bilby also provides some useful built-in plotting tools. Some examples on how
to visualise results using these tools (and how to extend them) are shown in
one of the tutorials at `visualising_the_results.ipynb <https://git.ligo.org/lscsoft/bilby/-/blob/master/examples/tutorials/visualising_the_results.ipynb>`_.
diff --git a/docs/dynesty-guide.txt b/docs/dynesty-guide.txt
index fb74c7c7791b97a0370409ff010c7475f6baaa88..194326d7b32e0fb6a5a64d5d385512386b416666 100644
--- a/docs/dynesty-guide.txt
+++ b/docs/dynesty-guide.txt
@@ -49,34 +49,28 @@ until one of the stopping criteria are reached:
Bilby-specific implementation details
-------------------------------------
-In Bilby, we have re-implemented the :code:`sample="rwalk"` sample method. In
-dynesty, this method took an argument :code:`walks` which was the fixed number
-of walks to take each time a new point was proposed. In the bilby implementation,
-we still take an argument :code:`walks` which has the new meaning: the minimum
-number of walks to take (this ensures backward compatibility). Meanwhile, we
-add two new arguments
-1. :code:`maxmcmc`: the maximum number of walks to use. This naming is chosen for consistency with other codes. Default is 5000. If this limit is reached, a warning will be printed during sampling.
-2. :code:`nact`: the number of auto-correlation times to use before accepting a point. Default is 5.
-
-The autocorrelation time calculation uses the `emcee
-<https://emcee.readthedocs.io/en/stable/>`_ autocorr methods. For a detailed
-discussion on the topics, see `this post by Dan Foreman-Mackey
-<https://dfm.io/posts/autocorr/>`_.
+In Bilby, we have re-implemented the :code:`sample="rwalk"` sample method (you
+can see exact details by looking at the function
+:code:`bilby.core.sampler.dynesty.sample_rwalk_bilby`. In dynesty, this method
+took an argument :code:`walks` which was the fixed number of walks to take each
+time a new point was proposed. In the bilby implementation, we still take an
+argument :code:`walks` which has the new meaning: the minimum number of walks
+to take (this ensures backward compatibility). Meanwhile, we add two new
+arguments
-You can revert to the original dynesty implementation by specifying
-:code:`sample="rwalk_dynesty"`.
+1. :code:`maxmcmc`: the maximum number of walks to use. This naming is chosen for consistency with other codes. Default is 5000. If this limit is reached, a warning will be printed during sampling.
-In addition, we also set several kwargs by default
+2. :code:`nact`: the number of auto-correlation times to use before accepting a point.
-1. :code:`nwalk` (alias of :code:`nlive`), the number of live poinst. This defaults to 1000.
-2. :code:`facc`: The target acceptance fraction for the 'rwalk'. In dynesty, this defaults 0.5, but in testing we found that a value of 0.2 produced better behaviour at boundaries.
+In general, poor convergance can be resolved by increasing :code:`nact`. For GW
+events, we find a value of 10 is typically okay. You can revert to the
+original dynesty implementation by specifying :code:`sample="rwalk_dynesty"`.
Understanding the output
------------------------
Before sampling begins, you will see a message like this
-
.. code-block:: console
10:42 bilby INFO : Single likelihood evaluation took 2.977e-03 s
diff --git a/docs/examples.txt b/docs/examples.txt
index bc5c9e9229dc8d5374cf1e805372fc485e0db8a0..e11954fb1fd597388f991ff89c91714eefe9b189 100644
--- a/docs/examples.txt
+++ b/docs/examples.txt
@@ -2,28 +2,26 @@
Examples
========
-1. `General inference examples <https://git.ligo.org/lscsoft/bilby/tree/master/examples/core_examples>`_
- - `A simple Gaussian likelihood <https://git.ligo.org/lscsoft/bilby/blob/master/examples/core_examples/gaussian_example.py>`_: a good example to see how to write your own likelihood.
- - `Linear regression for unknown noise <https://git.ligo.org/lscsoft/bilby/blob/master/examples/core_examples/linear_regression_unknown_noise.py>`_: fitting to general time-domain data.
+1. `General inference examples <https://git.ligo.org/lscsoft/bilby/tree/master/examples/core_examples>`_:
+ * `A simple Gaussian likelihood <https://git.ligo.org/lscsoft/bilby/blob/master/examples/core_examples/gaussian_example.py>`_: a good example to see how to write your own likelihood.
+ * `Linear regression for unknown noise <https://git.ligo.org/lscsoft/bilby/blob/master/examples/core_examples/linear_regression_unknown_noise.py>`_: fitting to general time-domain data.
-2. `Examples of injecting and recovering
- data <https://git.ligo.org/lscsoft/bilby/tree/master/examples/gw_examples/injection_examples>`__
- - `4-parameter CBC tutorial <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/fast_tutorial.py>`__
- - `15-parameter CBC tutorial <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/standard_15d_cbc_tutorial.py>`__
- - `Create your own source model <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/create_your_own_source_model.py>`__
- - `Create your own time-domain source model <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/create_your_own_time_domain_source_model.py>`__
- - `How to specify the prior <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/how_to_specify_the_prior.py>`__
- - `Using a partially marginalized likelihood <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/marginalized_likelihood.py>`__
- - `Injecting and recovering a neutron-star equation of state <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/bns_eos_example.py>`__
+2. `Examples of injecting and recovering data <https://git.ligo.org/lscsoft/bilby/tree/master/examples/gw_examples/injection_examples>`__:
+ * `4-parameter CBC tutorial <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/fast_tutorial.py>`__
+ * `15-parameter CBC tutorial <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/standard_15d_cbc_tutorial.py>`__
+ * `Create your own source model <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/create_your_own_source_model.py>`__
+ * `Create your own time-domain source model <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/create_your_own_time_domain_source_model.py>`__
+ * `How to specify the prior <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/how_to_specify_the_prior.py>`__
+ * `Using a partially marginalized likelihood <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/marginalized_likelihood.py>`__
+ * `Injecting and recovering a neutron-star equation of state <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/injection_examples/bns_eos_example.py>`__
-3. `Examples using open
- data <https://git.ligo.org/lscsoft/bilby/tree/master/examples/gw_examples/data_examples>`__
- - `Analysing the first Binary Black hole detection, GW150914 <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/data_examples/GW150914.py>`__
+3. `Examples using open data <https://git.ligo.org/lscsoft/bilby/tree/master/examples/gw_examples/data_examples>`__:
+ * `Analysing the first Binary Black hole detection, GW150914 <https://git.ligo.org/lscsoft/bilby/blob/master/examples/gw_examples/data_examples/GW150914.py>`__
-4. `Notebook-style tutorials <https://git.ligo.org/lscsoft/bilby/tree/master/examples/tutorials>`__
+4. `Notebook-style tutorials <https://git.ligo.org/lscsoft/bilby/tree/master/examples/tutorials>`__:
- - `Comparing different samplers <https://git.ligo.org/lscsoft/bilby/blob/master/examples/tutorials/compare_samplers.ipynb>`__
- - `Visualising the output <https://git.ligo.org/lscsoft/bilby/blob/master/examples/tutorials/visualising_the_results.ipynb>`__
+ * `Comparing different samplers <https://git.ligo.org/lscsoft/bilby/blob/master/examples/tutorials/compare_samplers.ipynb>`__
+ * `Visualising the output <https://git.ligo.org/lscsoft/bilby/blob/master/examples/tutorials/visualising_the_results.ipynb>`__
diff --git a/docs/faq.txt b/docs/faq.txt
new file mode 100644
index 0000000000000000000000000000000000000000..55063c8f1411d343565fadb33cb1bdc022093c1d
--- /dev/null
+++ b/docs/faq.txt
@@ -0,0 +1,19 @@
+=========================
+Frequency Asked Questions
+=========================
+
+Plotting questions
+------------------
+
+I'm running into latex errors when :code:`bilby` tries to create plots, what should I do?
+
+Matplotlib can be a little finicky. We wrap plotting commands in a function
+which can set up the rcParams and we use environment variables to allow
+configuration of this. See the docstring of this function for the allowed
+configuration options
+
+
+.. autofunction:: bilby.core.utils.latex_plot_format
+
+
+
diff --git a/docs/gw_prior.txt b/docs/gw_prior.txt
index 1167ec7edf9aa407575b4a37e5e60796095e6874..03c360a52f3beb913feddbad3a6fd323a5e07b9d 100644
--- a/docs/gw_prior.txt
+++ b/docs/gw_prior.txt
@@ -1,32 +1,132 @@
.. gw_prior:
===================================
-Transient Graviatiaonal wave priors
+Transient Gravitational wave priors
===================================
+We provide two base prior dictionaries for binary black hole (BBH) and binary
+neutron star (BNS) systems. These are :code:`bilby.gw.prior.BBHPriorDict` and
+:code:`bilby.gw.prior.BNSPriorDict` respectively. For BBHs this generates all
+the BBH mass parameters so constraints can be placed on any mass parameters.
+For BNSs it also generates the tidal deformability parameters.
+
+You can load in the default priors by running, e.g.
+
+.. code:: python
+
+ >>> prior = bilby.gw.prior.BBHPriorDict()
+
+This prior has a complete set of parameters for a BBH system. You can modify
+this, for example to set a different prior range for the chirp mass
+
+.. code:: python
+
+ >>> prior["chirp_mass"] = bilby.core.prior.Uniform(30, 31, "chirp_mass")
+
+.. note::
+ If you are using a tidal waveform, you need to specify a frequency domain
+ source model which includes tidal effects, e.g.
+
+ .. code:: python
+
+ frequency_domain_source_model=lal_binary_neutron_star
+
+
+Prior files
+===========
+
+As an alternative to specifying the prior in a python script, we also provide
+the ability to use a prior file. For example, given a file :code:`bbh.prior`
+which contains:
+
+.. literalinclude:: /../bilby/gw/prior_files/precessing_spins_bbh.prior
+
+You can load this with
+
+.. code:: python
+
+ prior = bilby.gw.prior.BBHPriorDict("bbh.prior")
+
+Here we see several examples of different types of priors. For those available
+in the :code:`bilby.core.prior` module, you can specify these without a prefix,
+but for other (including any exisiting in your own modules) you need to specify
+the module path.
+
+Aligned spins waveform with tides off
+-------------------------------------
+
+.. literalinclude:: /../bilby/gw/prior_files/aligned_spins_bbh.prior
+
+Aligned spins waveform with tides on
+------------------------------------
+
+.. literalinclude:: /../bilby/gw/prior_files/aligned_spins_bns.prior
+
+Precessing spins waveform with tides off
+----------------------------------------
+
+.. literalinclude:: /../bilby/gw/prior_files/precessing_spins_bbh.prior
+
+Precessing spins waveform with tides on
+---------------------------------------
+
+.. literalinclude:: /../bilby/gw/prior_files/precessing_spins_bns.prior
+
+
+Modifying the prior
+-------------------
+
+Taking the example priors above, you can copy and modify them to suite your
+needs. For example, to fix a parameter to a given value
+
+.. code:: python
+
+ parameter_name = <value>
+
+while to constrain the prior to a certain range , you can use:
+
+.. code:: python
+
+ parameter_name = Constraint(name='parameter_name', minimum=<value>, maximum=<value>)
+
+
+Priors using a Jupyter notebook
+===============================
+
+Bilby saves as output the prior volume sampled. You might also find useful to
+produce priors directly from a Jupyter notebook. You can have a look at one of
+the Bilby tutorials to check how you define and plot priors in a Jupyter notebook:
+`making_priors.ipynb <https://git.ligo.org/lscsoft/bilby/-/blob/master/examples/tutorials/making_priors.ipynb>`_.
+
+Notes on GW-specific priors
+===========================
+
A Cosmological GW prior, :code:`Cosmological`:
+----------------------------------------------
.. autoclass:: bilby.gw.prior.Cosmological
:members:
Uniform in Comoving Volume GW Prior (inherited from Cosmological) :code:`UniformComovingVolume`:
+------------------------------------------------------------------------------------------------
.. autoclass:: bilby.gw.prior.UniformComovingVolume
:members:
Uniform in Source Frame GW Prior :code:`UniformSourceFrame`:
+------------------------------------------------------------
.. autoclass:: bilby.gw.prior.UniformSourceFrame
:members:
Aligned Spine GW Prior :code:`AlignedSpin`:
+-------------------------------------------
.. autoclass:: bilby.gw.prior.AlignedSpin
:members:
HealPixMap JointPriorDist (See JointPriors in bilby.core.prior.joint) :code:`HealPixMapPriorDist`:
+--------------------------------------------------------------------------------------------------
.. autoclass:: bilby.gw.prior.HealPixMapPriorDist
:members:
-
-
diff --git a/docs/index.txt b/docs/index.txt
index dbc2948a90c7449c39691454bb359bb297f0da22..4f4074a62eb4a9f34e41e44923a182cc56c285f4 100644
--- a/docs/index.txt
+++ b/docs/index.txt
@@ -27,5 +27,6 @@ Welcome to bilby's documentation!
writing-documentation
hyperparameters
containers
+ faq
diff --git a/docs/installation.txt b/docs/installation.txt
index 96dc0f90d1d8cc0ae7a09e0be727b21f28402ecf..7a6a88f7daebd16e28d6dc1420e5eca98f26107e 100644
--- a/docs/installation.txt
+++ b/docs/installation.txt
@@ -93,7 +93,7 @@ The `requirements.txt
<https://git.ligo.org/lscsoft/bilby/blob/master/requirements.txt>`_ is a
minimal set of requirements for using :code:`bilby`. Additionally, we provide:
-1. `optional_requirements.txt
+1. The file `optional_requirements.txt
<https://git.ligo.org/lscsoft/bilby/blob/master/optional_requirements.txt>`_
which you should install if you plan to use :code:`bilby` for
gravitational-wave data analysis.
diff --git a/docs/prior.txt b/docs/prior.txt
index 8e5f2944d1d315edc23cd5af2cd38394dcb828a6..f55aafe76324d984a2e013402477184a96d5170c 100644
--- a/docs/prior.txt
+++ b/docs/prior.txt
@@ -30,22 +30,9 @@ simple example that sets a uniform prior for :code:`a`, and a fixed value for
Notice, that the :code:`latex_label` is optional, but if given will be used
when generating plots. Latex label strings containing escape characters like :code:`\t`
should either be preceded by :code:`r'` or include an extra backslash. As an example,
-either :code:`r'$\theta$'` or :code:`'$\\theta$'` is permissable. For a list of
-recognized escape sequences, see the `python docs <https://docs.python.org/2.0/ref/strings.html>`_.
+either :code:`r'$\theta$'` or :code:`'$\\theta$'` is permissable. For a list of
+recognized escape sequences, see the `python docs <https://docs.python.org/2.0/ref/strings.html>`_.
---------------
-Default priors
---------------
-
-If any model parameter required by the :ref:`likelihood` are not defined in the
-`priors` dictionary passed to :ref:`run_sampler <run_sampler>` then the code
-will try to use a default prior. By default, these are setup for a binary black
-hole and defined in a file like this
-
-.. literalinclude:: /../bilby/gw/prior_files/binary_black_holes.prior
-
-You can define your own default prior and pass a string pointing to that file
-to :ref:`run_sampler <run_sampler>`.
--------------------------
@@ -92,7 +79,7 @@ Multivariate Gaussian prior
We provide a prior class for correlated parameters in the form of a
`multivariate Gaussian distribution <https://en.wikipedia.org/wiki/Multivariate_normal_distribution>`_.
-To set the prior you first must define the distribution using the
+To set the prior you first must define the distribution using the
:class:`bilby.core.prior.MultivariateGaussianDist` class. This requires the names of the
correlated variables, their means, and either the covariance matrix or the correlation
matrix and standard deviations, e.g.:
@@ -209,72 +196,4 @@ Sample from this distribution and plot the samples.
------
-Gravitational wave priors
-=========================
-
-We provide default conversion functions for the BBH and BNS PriorDicts.
-
-For BBHs this generates all the BBH mass parameters so constraints can be placed on any mass parameters.
-
-For BNSs it also generates the tidal deformability parameters.
-
------------------
-Prior Examples
------------------
-
-Here we show some examples of prior files for different waveform families.
-To constrain a certain parameter to a fixed value, you just need:
-
-.. code:: python
-
- parameter_name = <value>
-
-------
-
-To constrain the prior to a certain range , you can use:
-
-.. code:: python
-
- parameter_name = Constraint(name='parameter_name', minimum=<value>, maximum=<value>)
-
-------
-
-Note that to activate the tidal effect you need to specify in your configuration
-file:
-
-.. code:: python
-
- frequency_domain_source_model=lal_binary_neutron_star
-
-------
-
-
-Aligned spins waveform with tides off
-==============
-
-.. literalinclude:: /../bilby/gw/prior_files/aligned_spins_waveform_tides_off.prior
-
-Aligned spins waveform with tides on
-==============
-
-.. literalinclude:: /../bilby/gw/prior_files/aligned_spins_waveform_tides_on.prior
-
-Precessing spins waveform with tides off
-==============
-
-.. literalinclude:: /../bilby/gw/prior_files/precessing_spins_waveform_tides_off.prior
-
-Precessing spins waveform with tides on
-==============
-
-.. literalinclude:: /../bilby/gw/prior_files/precessing_spins_waveform_tides_on.prior
-
-
------------------
-Priors using a Jupyter notebook
------------------
-Bilby saves as output the prior volume sampled. You might also find useful to
-produce priors directly from a Jupyter notebook. You can have a look at one of
-the Bilby tutorials to check how you define and plot priors in a Jupyter notebook:
-`making_priors.ipynb <https://git.ligo.org/lscsoft/bilby/-/blob/master/examples/tutorials/making_priors.ipynb>`_.
diff --git a/test/gw_prior_test.py b/test/gw_prior_test.py
index 7e864bd65d08193d2a51a32ecfb6918c1e72545e..8ac622575285f074af85a8101658d28302d8a71f 100644
--- a/test/gw_prior_test.py
+++ b/test/gw_prior_test.py
@@ -458,6 +458,14 @@ class TestUniformComovingVolumePrior(unittest.TestCase):
)
self.assertEqual(prior.maximum, 10000)
+ def test_increase_maximum(self):
+ prior = bilby.gw.prior.UniformComovingVolume(
+ minimum=10, maximum=10000, name="luminosity_distance"
+ )
+ prior.maximum = 20000
+ prior_sample = prior.sample(5000)
+ self.assertGreater(np.mean(prior_sample), 10000)
+
def test_zero_minimum_works(self):
prior = bilby.gw.prior.UniformComovingVolume(
minimum=0, maximum=10000, name="luminosity_distance"
diff --git a/test/test.mplstyle b/test/test.mplstyle
new file mode 100644
index 0000000000000000000000000000000000000000..a7048566e81a70081f84f2af8e08ccd6fce1538d
--- /dev/null
+++ b/test/test.mplstyle
@@ -0,0 +1 @@
+figure.figsize: 3.4, 2.5
diff --git a/test/utils_test.py b/test/utils_test.py
index 557c5ad4e63be17a898992267a3b0282abf78a33..d587457722328806e2ba03a331e667b7a910e798 100644
--- a/test/utils_test.py
+++ b/test/utils_test.py
@@ -1,9 +1,11 @@
from __future__ import absolute_import, division
-
import unittest
+import os
+
import numpy as np
from astropy import constants
import lal
+import matplotlib.pyplot as plt
import bilby
from bilby.core import utils
@@ -253,5 +255,63 @@ class TestReflect(unittest.TestCase):
self.assertTrue(np.testing.assert_allclose(utils.reflect(xprime), x) is None)
+class TestLatexPlotFormat(unittest.TestCase):
+ def setUp(self):
+ self.x = np.linspace(0, 1)
+ self.y = np.sin(self.x)
+ self.filename = "test_plot.png"
+
+ def tearDown(self):
+ if os.path.isfile(self.filename):
+ os.remove(self.filename)
+
+ def test_default(self):
+ @bilby.core.utils.latex_plot_format
+ def plot():
+ fig, ax = plt.subplots()
+ ax.plot(self.x, self.y)
+ fig.savefig(self.filename)
+ plot()
+ self.assertTrue(os.path.isfile(self.filename))
+
+ def test_mathedefault_one(self):
+ @bilby.core.utils.latex_plot_format
+ def plot():
+ fig, ax = plt.subplots()
+ ax.plot(self.x, self.y)
+ fig.savefig(self.filename)
+ plot(BILBY_MATHDEFAULT=1)
+ self.assertTrue(os.path.isfile(self.filename))
+
+ def test_mathedefault_zero(self):
+ @bilby.core.utils.latex_plot_format
+ def plot():
+ fig, ax = plt.subplots()
+ ax.plot(self.x, self.y)
+ fig.savefig(self.filename)
+ plot(BILBY_MATHDEFAULT=0)
+ self.assertTrue(os.path.isfile(self.filename))
+
+ def test_matplotlib_style(self):
+ @bilby.core.utils.latex_plot_format
+ def plot():
+ fig, ax = plt.subplots()
+ ax.plot(self.x, self.y)
+ fig.savefig(self.filename)
+
+ plot(BILBY_STYLE="fivethirtyeight")
+ self.assertTrue(os.path.isfile(self.filename))
+
+ def test_user_style(self):
+ @bilby.core.utils.latex_plot_format
+ def plot():
+ fig, ax = plt.subplots()
+ ax.plot(self.x, self.y)
+ fig.savefig(self.filename)
+
+ plot(BILBY_STYLE="test/test.mplstyle")
+ self.assertTrue(os.path.isfile(self.filename))
+
+
if __name__ == "__main__":
unittest.main()