diff --git a/CHANGELOG.md b/CHANGELOG.md
index d341b2c68944679b63d46b035b51465c089347eb..9809cb44ad3fdf1a3b6df1c9c391a7e25084872f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,8 @@
- Renamed "prior" to "priors" in bilby.gw.likelihood.GravtitationalWaveTransient
for consistency with bilby.core. **WARNING**: This will break scripts which
use marginalization.
+- Added `outdir` kwarg for plotting methods in `bilby.core.result.Result`. This makes plotting
+into custom destinations easier.
- Fixed definition of matched_filter_snr, the interferometer method has become `ifo.inner_product`.
### Added
diff --git a/bilby/core/result.py b/bilby/core/result.py
index 26a456680f14f7892779dd228b4b1f936e7a94ff..0b96f48af7917d06aea568e4adafbd4da3812b7c 100644
--- a/bilby/core/result.py
+++ b/bilby/core/result.py
@@ -11,6 +11,7 @@ import corner
import scipy.stats
import matplotlib
import matplotlib.pyplot as plt
+from matplotlib import lines as mpllines
from . import utils
from .utils import (logger, infer_parameters_from_function,
@@ -119,9 +120,10 @@ class Result(object):
Version information for software used to generate the result. Note,
this information is generated when the result object is initialized
- Note:
- All sampling output parameters, e.g. the samples themselves are
- typically not given at initialisation, but set at a later stage.
+ Note
+ ---------
+ All sampling output parameters, e.g. the samples themselves are
+ typically not given at initialisation, but set at a later stage.
"""
@@ -151,6 +153,9 @@ class Result(object):
self.version = version
self.max_autocorrelation_time = max_autocorrelation_time
+ self.prior_values = None
+ self._kde = None
+
def __str__(self):
"""Print a summary """
if getattr(self, 'posterior', None) is not None:
@@ -285,7 +290,7 @@ class Result(object):
pass
return dictionary
- def save_to_file(self, overwrite=False):
+ def save_to_file(self, overwrite=False, outdir=None):
"""
Writes the Result to a deepdish h5 file
@@ -294,9 +299,12 @@ class Result(object):
overwrite: bool, optional
Whether or not to overwrite an existing result file.
default=False
+ outdir: str, optional
+ Path to the outdir. Default is the one stored in the result object.
"""
- file_name = result_file_name(self.outdir, self.label)
- utils.check_directory_exists_and_if_not_mkdir(self.outdir)
+ outdir = self._safe_outdir_creation(outdir, self.save_to_file)
+ file_name = result_file_name(outdir, self.label)
+
if os.path.isfile(file_name):
if overwrite:
logger.debug('Removing existing file {}'.format(file_name))
@@ -326,10 +334,10 @@ class Result(object):
logger.error("\n\n Saving the data has failed with the "
"following message:\n {} \n\n".format(e))
- def save_posterior_samples(self):
+ def save_posterior_samples(self, outdir=None):
"""Saves posterior samples to a file"""
- filename = '{}/{}_posterior_samples.txt'.format(self.outdir, self.label)
- utils.check_directory_exists_and_if_not_mkdir(self.outdir)
+ outdir = self._safe_outdir_creation(outdir, self.save_posterior_samples)
+ filename = '{}/{}_posterior_samples.txt'.format(outdir, self.label)
self.posterior.to_csv(filename, index=False, header=True)
def get_latex_labels_from_parameter_keys(self, keys):
@@ -389,7 +397,7 @@ class Result(object):
return self.posterior_volume / self.prior_volume(priors)
def get_one_dimensional_median_and_error_bar(self, key, fmt='.2f',
- quantiles=[0.16, 0.84]):
+ quantiles=(0.16, 0.84)):
""" Calculate the median and error bar for a given key
Parameters
@@ -398,8 +406,8 @@ class Result(object):
The parameter key for which to calculate the median and error bar
fmt: str, ('.2f')
A format string
- quantiles: list
- A length-2 list of the lower and upper-quantiles to calculate
+ quantiles: list, tuple
+ A length-2 tuple of the lower and upper-quantiles to calculate
the errors bars for.
Returns
@@ -428,8 +436,8 @@ class Result(object):
def plot_single_density(self, key, prior=None, cumulative=False,
title=None, truth=None, save=True,
file_base_name=None, bins=50, label_fontsize=16,
- title_fontsize=16, quantiles=[0.16, 0.84], dpi=300):
- """ Plot a 1D marginal density, either probablility or cumulative.
+ title_fontsize=16, quantiles=(0.16, 0.84), dpi=300):
+ """ Plot a 1D marginal density, either probability or cumulative.
Parameters
----------
@@ -458,8 +466,8 @@ class Result(object):
The number of histogram bins
label_fontsize, title_fontsize: int
The fontsizes for the labels and titles
- quantiles: list
- A length-2 list of the lower and upper-quantiles to calculate
+ quantiles: tuple
+ A length-2 tuple of the lower and upper-quantiles to calculate
the errors bars for.
dpi: int
Dots per inch resolution of the plot
@@ -493,7 +501,7 @@ class Result(object):
if isinstance(prior, Prior):
theta = np.linspace(ax.get_xlim()[0], ax.get_xlim()[1], 300)
- ax.plot(theta, Prior.prob(theta), color='C2')
+ ax.plot(theta, prior.prob(theta), color='C2')
if save:
fig.tight_layout()
@@ -508,7 +516,8 @@ class Result(object):
def plot_marginals(self, parameters=None, priors=None, titles=True,
file_base_name=None, bins=50, label_fontsize=16,
- title_fontsize=16, quantiles=[0.16, 0.84], dpi=300):
+ title_fontsize=16, quantiles=(0.16, 0.84), dpi=300,
+ outdir=None):
""" Plot 1D marginal distributions
Parameters
@@ -531,12 +540,14 @@ class Result(object):
bins: int
The number of histogram bins
label_fontsize, title_fontsize: int
- The fontsizes for the labels and titles
- quantiles: list
- A length-2 list of the lower and upper-quantiles to calculate
+ The font sizes for the labels and titles
+ quantiles: tuple
+ A length-2 tuple of the lower and upper-quantiles to calculate
the errors bars for.
dpi: int
Dots per inch resolution of the plot
+ outdir: str, optional
+ Path to the outdir. Default is the one store in the result object.
Returns
-------
@@ -558,7 +569,8 @@ class Result(object):
truths = self.injection_parameters
if file_base_name is None:
- file_base_name = '{}/{}_1d/'.format(self.outdir, self.label)
+ outdir = self._safe_outdir_creation(outdir, self.plot_marginals)
+ file_base_name = '{}/{}_1d/'.format(outdir, self.label)
check_directory_exists_and_if_not_mkdir(file_base_name)
if priors is True:
@@ -609,7 +621,8 @@ class Result(object):
**kwargs:
Other keyword arguments are passed to `corner.corner`. We set some
defaults to improve the basic look and feel, but these can all be
- overridden.
+ overridden. Also optional an 'outdir' argument which can be used
+ to override the outdir set by the absolute path of the result object.
Notes
-----
@@ -720,8 +733,8 @@ class Result(object):
if save:
if filename is None:
- utils.check_directory_exists_and_if_not_mkdir(self.outdir)
- filename = '{}/{}_corner.png'.format(self.outdir, self.label)
+ outdir = self._safe_outdir_creation(kwargs.get('outdir'), self.plot_corner)
+ filename = '{}/{}_corner.png'.format(outdir, self.label)
logger.debug('Saving corner plot to {}'.format(filename))
fig.savefig(filename, dpi=dpi)
plt.close(fig)
@@ -752,16 +765,16 @@ class Result(object):
ax.set_ylabel(self.parameter_labels[i])
fig.tight_layout()
- filename = '{}/{}_walkers.png'.format(self.outdir, self.label)
+ outdir = self._safe_outdir_creation(kwargs.get('outdir'), self.plot_walkers)
+ filename = '{}/{}_walkers.png'.format(outdir, self.label)
logger.debug('Saving walkers plot to {}'.format('filename'))
- utils.check_directory_exists_and_if_not_mkdir(self.outdir)
fig.savefig(filename)
plt.close(fig)
def plot_with_data(self, model, x, y, ndraws=1000, npoints=1000,
xlabel=None, ylabel=None, data_label='data',
data_fmt='o', draws_label=None, filename=None,
- maxl_label='max likelihood', dpi=300):
+ maxl_label='max likelihood', dpi=300, outdir=None):
""" Generate a figure showing the data and fits to the data
Parameters
@@ -787,6 +800,8 @@ class Result(object):
filename: str
If given, the filename to use. Otherwise, the filename is generated
from the outdir and label attributes.
+ outdir: str, optional
+ Path to the outdir. Default is the one store in the result object.
"""
@@ -825,8 +840,8 @@ class Result(object):
ax.legend(numpoints=3)
fig.tight_layout()
if filename is None:
- utils.check_directory_exists_and_if_not_mkdir(self.outdir)
- filename = '{}/{}_plot_with_data'.format(self.outdir, self.label)
+ outdir = self._safe_outdir_creation(outdir, self.plot_with_data)
+ filename = '{}/{}_plot_with_data'.format(outdir, self.label)
fig.savefig(filename, dpi=dpi)
plt.close(fig)
@@ -944,20 +959,20 @@ class Result(object):
bool: True if attribute name matches with an attribute of other_object, False otherwise
"""
- A = getattr(self, name, False)
- B = getattr(other_object, name, False)
- logger.debug('Checking {} value: {}=={}'.format(name, A, B))
- if (A is not False) and (B is not False):
- typeA = type(A)
- typeB = type(B)
- if typeA == typeB:
- if typeA in [str, float, int, dict, list]:
+ a = getattr(self, name, False)
+ b = getattr(other_object, name, False)
+ logger.debug('Checking {} value: {}=={}'.format(name, a, b))
+ if (a is not False) and (b is not False):
+ type_a = type(a)
+ type_b = type(b)
+ if type_a == type_b:
+ if type_a in [str, float, int, dict, list]:
try:
- return A == B
+ return a == b
except ValueError:
return False
- elif typeA in [np.ndarray]:
- return np.all(A == B)
+ elif type_a in [np.ndarray]:
+ return np.all(a == b)
return False
@property
@@ -966,9 +981,9 @@ class Result(object):
Uses `scipy.stats.gaussian_kde` to generate the kernel density
"""
- try:
+ if self._kde:
return self._kde
- except AttributeError:
+ else:
self._kde = scipy.stats.gaussian_kde(
self.posterior[self.search_parameter_keys].values.T)
return self._kde
@@ -998,6 +1013,18 @@ class Result(object):
for s in sample]
return self.kde(ordered_sample)
+ def _safe_outdir_creation(self, outdir=None, caller_func=None):
+ if outdir is None:
+ outdir = self.outdir
+ try:
+ utils.check_directory_exists_and_if_not_mkdir(outdir)
+ except PermissionError:
+ raise FileMovedError("Can not write in the out directory.\n"
+ "Did you move the here file from another system?\n"
+ "Try calling " + caller_func.__name__ + " with the 'outdir' "
+ "keyword argument, e.g. " + caller_func.__name__ + "(outdir='.')")
+ return outdir
+
def plot_multiple(results, filename=None, labels=None, colours=None,
save=True, evidences=False, **kwargs):
@@ -1050,7 +1077,7 @@ def plot_multiple(results, filename=None, labels=None, colours=None,
hist_kwargs['color'] = c
fig = result.plot_corner(fig=fig, save=False, color=c, **kwargs)
default_filename += '_{}'.format(result.label)
- lines.append(matplotlib.lines.Line2D([0], [0], color=c))
+ lines.append(mpllines.Line2D([0], [0], color=c))
default_labels.append(result.label)
# Rescale the axes
@@ -1100,7 +1127,7 @@ def make_pp_plot(results, filename=None, save=True, **kwargs):
Returns
-------
fig:
- Matplotlib figure
+ matplotlib figure
"""
fig = plt.figure()
credible_levels = pd.DataFrame()
@@ -1122,3 +1149,11 @@ def make_pp_plot(results, filename=None, save=True, **kwargs):
filename = 'outdir/pp.png'
plt.savefig(filename)
return fig
+
+
+class ResultError(Exception):
+ """ Base exception for all Result related errors """
+
+
+class FileMovedError(ResultError):
+ """ Exceptions that occur when files have been moved """
diff --git a/test/result_test.py b/test/result_test.py
index 2308bceac466372aa4e58d5fb23d361f1a99093b..6dbc5a2342391a57a9286b9d304894ec32b8746d 100644
--- a/test/result_test.py
+++ b/test/result_test.py
@@ -25,9 +25,9 @@ class TestResult(unittest.TestCase):
injection_parameters=dict(x=0.5, y=0.5),
meta_data=dict(test='test'))
- N = 100
- posterior = pd.DataFrame(dict(x=np.random.normal(0, 1, N),
- y=np.random.normal(0, 1, N)))
+ n = 100
+ posterior = pd.DataFrame(dict(x=np.random.normal(0, 1, n),
+ y=np.random.normal(0, 1, n)))
result.posterior = posterior
result.log_evidence = 10
result.log_evidence_err = 11
@@ -66,7 +66,7 @@ class TestResult(unittest.TestCase):
injection_parameters=dict(x=0.5, y=0.5),
meta_data=dict(test='test'))
with self.assertRaises(ValueError):
- result.priors
+ _ = result.priors
self.assertEqual(result.parameter_labels, result.search_parameter_keys)
self.assertEqual(result.parameter_labels_with_unit, result.search_parameter_keys)
@@ -102,14 +102,14 @@ class TestResult(unittest.TestCase):
def test_unset_posterior(self):
self.result.posterior = None
with self.assertRaises(ValueError):
- self.result.posterior
+ _ = self.result.posterior
def test_save_and_load(self):
self.result.save_to_file()
loaded_result = bilby.core.result.read_in_result(
outdir=self.result.outdir, label=self.result.label)
- self.assertTrue(
- all(self.result.posterior == loaded_result.posterior))
+ self.assertTrue(pd.DataFrame.equals
+ (self.result.posterior, loaded_result.posterior))
self.assertTrue(self.result.fixed_parameter_keys == loaded_result.fixed_parameter_keys)
self.assertTrue(self.result.search_parameter_keys == loaded_result.search_parameter_keys)
self.assertEqual(self.result.meta_data, loaded_result.meta_data)
@@ -146,31 +146,28 @@ class TestResult(unittest.TestCase):
filename = '{}/{}_posterior_samples.txt'.format(self.result.outdir, self.result.label)
self.assertTrue(os.path.isfile(filename))
df = pd.read_csv(filename)
- self.assertTrue(all(self.result.posterior == df))
+ self.assertTrue(np.allclose(self.result.posterior.values, df.values))
def test_samples_to_posterior(self):
self.result.posterior = None
x = [1, 2, 3]
y = [4, 6, 8]
- log_likelihood = [6, 7, 8]
+ log_likelihood = np.array([6, 7, 8])
self.result.samples = np.array([x, y]).T
self.result.log_likelihood_evaluations = log_likelihood
self.result.samples_to_posterior(priors=self.result.priors)
self.assertTrue(all(self.result.posterior['x'] == x))
self.assertTrue(all(self.result.posterior['y'] == y))
- self.assertTrue(
- all(self.result.posterior['log_likelihood'] == log_likelihood))
- self.assertTrue(
- all(self.result.posterior['c'] == self.result.priors['c'].peak))
- self.assertTrue(
- all(self.result.posterior['d'] == self.result.priors['d'].peak))
+ self.assertTrue(np.array_equal(self.result.posterior.log_likelihood.values, log_likelihood))
+ self.assertTrue(all(self.result.posterior.c.values == self.result.priors['c'].peak))
+ self.assertTrue(all(self.result.posterior.d.values == self.result.priors['d'].peak))
def test_calculate_prior_values(self):
self.result.calculate_prior_values(priors=self.result.priors)
self.assertEqual(len(self.result.posterior), len(self.result.prior_values))
def test_plot_multiple(self):
- filename='multiple.png'.format(self.result.outdir)
+ filename = 'multiple.png'.format(self.result.outdir)
bilby.core.result.plot_multiple([self.result, self.result],
filename=filename)
self.assertTrue(os.path.isfile(filename))
@@ -188,8 +185,8 @@ class TestResult(unittest.TestCase):
x = np.linspace(0, 1, 10)
y = np.linspace(0, 1, 10)
- def model(x):
- return x
+ def model(xx):
+ return xx
self.result.plot_with_data(model, x, y, ndraws=10)
self.assertTrue(
os.path.isfile('{}/{}_plot_with_data.png'.format(
@@ -260,9 +257,8 @@ class TestResult(unittest.TestCase):
sample = [dict(x=0, y=0.1), dict(x=0.8, y=0)]
self.assertTrue(
isinstance(self.result.posterior_probability(sample), np.ndarray))
- self.assertTrue(
- all(self.result.posterior_probability(sample)
- == self.result.kde([[0, 0.1], [0.8, 0]])))
+ self.assertTrue(np.array_equal(self.result.posterior_probability(sample),
+ self.result.kde([[0, 0.1], [0.8, 0]])))
if __name__ == '__main__':