From 0ac57e3db253414ea6625d583f8cc57e77df1b68 Mon Sep 17 00:00:00 2001
From: Colm Talbot <colm.talbot@ligo.org>
Date: Mon, 8 Oct 2018 02:01:46 -0500
Subject: [PATCH] update cpnest syntax
---
bilby/core/sampler/cpnest.py | 42 +++++++++++++++++++++++++-----------
sampler_requirements.txt | 2 +-
test/sampler_test.py | 12 ++++++-----
3 files changed, 37 insertions(+), 19 deletions(-)
diff --git a/bilby/core/sampler/cpnest.py b/bilby/core/sampler/cpnest.py
index 91cf7bc6..0fcdba59 100644
--- a/bilby/core/sampler/cpnest.py
+++ b/bilby/core/sampler/cpnest.py
@@ -1,7 +1,7 @@
from __future__ import absolute_import
import numpy as np
from pandas import DataFrame
-from ..utils import logger
+from ..utils import logger, check_directory_exists_and_if_not_mkdir
from .base_sampler import NestedSampler
@@ -15,27 +15,33 @@ class Cpnest(NestedSampler):
Keyword Arguments
-----------------
- npoints: int
+ nlive: int
The number of live points, note this can also equivalently be given as
- one of [nlive, nlives, n_live_points]
+ one of [npoints, nlives, n_live_points]
seed: int (1234)
Initialised random seed
- Nthreads: int, (1)
+ nthreads: int, (1)
Number of threads to use
maxmcmc: int (1000)
The maximum number of MCMC steps to take
- verbose: Bool
+ verbose: Bool (True)
If true, print information information about the convergence during
+ resume: Bool (False)
+ Whether or not to resume from a previous run
+ output: str
+ Where to write the CPNest, by default this is
+ {self.outdir}/cpnest_{self.label}/
"""
- default_kwargs = dict(verbose=1, Nthreads=1, Nlive=500, maxmcmc=1000,
- Poolsize=100, seed=None, balance_samplers=True)
+ default_kwargs = dict(verbose=1, nthreads=1, nlive=500, maxmcmc=1000,
+ seed=None, poolsize=100, nhamiltonian=0, resume=False,
+ output=None)
def _translate_kwargs(self, kwargs):
- if 'Nlive' not in kwargs:
+ if 'nlive' not in kwargs:
for equiv in self.npoints_equiv_kwargs:
if equiv in kwargs:
- kwargs['Nlive'] = kwargs.pop(equiv)
+ kwargs['nlive'] = kwargs.pop(equiv)
if 'seed' not in kwargs:
logger.warning('No seed provided, cpnest will use 1234.')
@@ -69,15 +75,25 @@ class Cpnest(NestedSampler):
bounds = [[self.priors[key].minimum, self.priors[key].maximum]
for key in self.search_parameter_keys]
model = Model(self.search_parameter_keys, bounds)
- out = CPNest(model, output=self.outdir, **self.kwargs)
+ out = CPNest(model, **self.kwargs)
out.run()
if self.plot:
out.plot()
- # Since the output is not just samples, but log_likelihood as well,
- # we turn this into a dataframe here. The index [0] here may be wrong
- self.result.posterior = DataFrame(out.posterior_samples[0])
+ self.result.posterior = DataFrame(out.posterior_samples)
self.result.log_evidence = out.NS.state.logZ
self.result.log_evidence_err = np.nan
return self.result
+
+ def _verify_kwargs_against_default_kwargs(self):
+ """
+ Set the directory where the output will be written.
+ """
+ if not self.kwargs['output']:
+ self.kwargs['output'] = \
+ '{}/cpnest_{}/'.format(self.outdir, self.label)
+ if self.kwargs['output'].endswith('/') is False:
+ self.kwargs['output'] = '{}/'.format(self.kwargs['output'])
+ check_directory_exists_and_if_not_mkdir(self.kwargs['output'])
+ NestedSampler._verify_kwargs_against_default_kwargs(self)
diff --git a/sampler_requirements.txt b/sampler_requirements.txt
index fbb2c32f..e81411d3 100644
--- a/sampler_requirements.txt
+++ b/sampler_requirements.txt
@@ -1,4 +1,4 @@
-cpnest
+cpnest>=0.9.4
dynesty
emcee
nestle
diff --git a/test/sampler_test.py b/test/sampler_test.py
index 56409d4a..963813f0 100644
--- a/test/sampler_test.py
+++ b/test/sampler_test.py
@@ -121,16 +121,18 @@ class TestCPNest(unittest.TestCase):
del self.sampler
def test_default_kwargs(self):
- expected = dict(verbose=1, Nthreads=1, Nlive=500, maxmcmc=1000,
- Poolsize=100, seed=None, balance_samplers=True)
+ expected = dict(verbose=1, nthreads=1, nlive=500, maxmcmc=1000,
+ seed=None, poolsize=100, nhamiltonian=0, resume=False,
+ output='outdir/cpnest_label/')
self.assertDictEqual(expected, self.sampler.kwargs)
def test_translate_kwargs(self):
- expected = dict(verbose=1, Nthreads=1, Nlive=250, maxmcmc=1000,
- Poolsize=100, seed=None, balance_samplers=True)
+ expected = dict(verbose=1, nthreads=1, nlive=250, maxmcmc=1000,
+ seed=None, poolsize=100, nhamiltonian=0, resume=False,
+ output='outdir/cpnest_label/')
for equiv in bilby.core.sampler.base_sampler.NestedSampler.npoints_equiv_kwargs:
new_kwargs = self.sampler.kwargs.copy()
- del new_kwargs['Nlive']
+ del new_kwargs['nlive']
new_kwargs[equiv] = 250
self.sampler.kwargs = new_kwargs
self.assertDictEqual(expected, self.sampler.kwargs)
--
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