From 3cc57b54ea49af4841084d2b21bebc1170f84ed8 Mon Sep 17 00:00:00 2001
From: Gregory Ashton <gregory.ashton@ligo.org>
Date: Fri, 6 Sep 2019 23:14:02 +1000
Subject: [PATCH] Pass the periodic list through to dynesty
- Ensures the periodic argument is passed through to the dynesty making
the points wander outside the allowed range
- Fix tests
---
bilby/core/sampler/dynesty.py | 5 +++++
test/sampler_test.py | 24 +++++++++++++++++++-----
2 files changed, 24 insertions(+), 5 deletions(-)
diff --git a/bilby/core/sampler/dynesty.py b/bilby/core/sampler/dynesty.py
index 79f21fda0..5c81f45ee 100644
--- a/bilby/core/sampler/dynesty.py
+++ b/bilby/core/sampler/dynesty.py
@@ -208,6 +208,11 @@ class Dynesty(NestedSampler):
logger.debug("Setting reflective boundary for {}".format(key))
self._reflective.append(ii)
+ # The periodic kwargs passed into dynesty allows the parameters to
+ # wander out of the bounds, this includes both periodic and reflective.
+ # these are then handled in the prior_transform
+ self.kwargs["periodic"] = sorted(self._periodic + self._reflective)
+
def run_sampler(self):
import dynesty
if self.kwargs['live_points'] is None:
diff --git a/test/sampler_test.py b/test/sampler_test.py
index 9fc906017..5835f5a15 100644
--- a/test/sampler_test.py
+++ b/test/sampler_test.py
@@ -132,8 +132,8 @@ class TestDynesty(unittest.TestCase):
def setUp(self):
self.likelihood = MagicMock()
self.priors = bilby.core.prior.PriorDict()
- self.priors['a'] = bilby.core.prior.Prior(boundary='periodic')
- self.priors['b'] = bilby.core.prior.Prior(boundary='reflective')
+ self.priors['a'] = bilby.core.prior.Prior()
+ self.priors['b'] = bilby.core.prior.Prior()
self.sampler = bilby.core.sampler.Dynesty(self.likelihood, self.priors,
outdir='outdir', label='label',
use_ratio=False, plot=False,
@@ -155,15 +155,15 @@ class TestDynesty(unittest.TestCase):
logl_max=np.inf, add_live=True, print_progress=True, save_bounds=False,
walks=20, update_interval=600, print_func='func')
self.sampler.kwargs['print_func'] = 'func' # set this manually as this is not testable otherwise
- self.assertListEqual([0, 1], self.sampler.kwargs['periodic']) # Check this separately
- self.sampler.kwargs['periodic'] = None # The dict comparison can't handle lists
+ self.assertEqual([], self.sampler.kwargs['periodic']) # Check this separately
+ self.sampler.kwargs['periodic'] = expected['periodic'] # The dict comparison can't handle lists
for key in self.sampler.kwargs.keys():
print("key={}, expected={}, actual={}"
.format(key, expected[key], self.sampler.kwargs[key]))
self.assertDictEqual(expected, self.sampler.kwargs)
def test_translate_kwargs(self):
- expected = dict(bound='multi', sample='rwalk', periodic=[0, 1], verbose=True,
+ expected = dict(bound='multi', sample='rwalk', periodic=[], verbose=True,
check_point_delta_t=600, nlive=1000, first_update=None,
npdim=None, rstate=None, queue_size=None, pool=None,
use_pool=None, live_points=None, logl_args=None, logl_kwargs=None,
@@ -181,6 +181,20 @@ class TestDynesty(unittest.TestCase):
self.sampler.kwargs['print_func'] = 'func' # set this manually as this is not testable otherwise
self.assertDictEqual(expected, self.sampler.kwargs)
+ def test_prior_boundary(self):
+ self.priors['a'] = bilby.core.prior.Prior(boundary='periodic')
+ self.priors['b'] = bilby.core.prior.Prior(boundary='reflective')
+ self.priors['c'] = bilby.core.prior.Prior(boundary=None)
+ self.priors['d'] = bilby.core.prior.Prior(boundary='reflective')
+ self.priors['e'] = bilby.core.prior.Prior(boundary='periodic')
+ self.sampler = bilby.core.sampler.Dynesty(self.likelihood, self.priors,
+ outdir='outdir', label='label',
+ use_ratio=False, plot=False,
+ skip_import_verification=True)
+ self.assertEqual([0, 1, 3, 4], self.sampler.kwargs["periodic"])
+ self.assertEqual([0, 4], self.sampler._periodic)
+ self.assertEqual([1, 3], self.sampler._reflective)
+
class TestEmcee(unittest.TestCase):
--
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