def test_logging(self):
""" Tests logging to screen and file. """
# No logging
with StreamCapture() as c:
sampler = pints.NestedRejectionSampler(self.log_likelihood,
self.log_prior)
sampler.set_posterior_samples(2)
sampler.set_iterations(10)
sampler.set_active_points_rate(10)
sampler.set_log_to_screen(False)
sampler.set_log_to_file(False)
samples, margin = sampler.run()
self.assertEqual(c.text(), '')
# Log to screen
with StreamCapture() as c:
sampler = pints.NestedRejectionSampler(self.log_likelihood,
self.log_prior)
sampler.set_posterior_samples(2)
sampler.set_iterations(20)
sampler.set_active_points_rate(10)
sampler.set_log_to_screen(True)
sampler.set_log_to_file(False)
samples, margin = sampler.run()
lines = c.text().splitlines()
self.assertEqual(lines[0], 'Running nested rejection sampling')
self.assertEqual(lines[1], 'Number of active points: 10')
self.assertEqual(lines[2], 'Total number of iterations: 20')
self.assertEqual(lines[3], 'Total number of posterior samples: 2')
self.assertEqual(lines[4], 'Iter. Eval. Time m:s')
pattern = re.compile('[0-9]+[ ]+[0-9]+[ ]+[0-9]{1}:[0-9]{2}.[0-9]{1}')
for line in lines[5:]:
self.assertTrue(pattern.match(line))
self.assertEqual(len(lines), 11)
# Log to file
with StreamCapture() as c:
with TemporaryDirectory() as d:
filename = d.path('test.txt')
sampler = pints.NestedRejectionSampler(self.log_likelihood,
self.log_prior)
sampler.set_posterior_samples(2)
sampler.set_iterations(10)
sampler.set_active_points_rate(10)
sampler.set_log_to_screen(False)
sampler.set_log_to_file(filename)
samples, margin = sampler.run()
with open(filename, 'r') as f:
lines = f.read().splitlines()
self.assertEqual(c.text(), '')
self.assertEqual(len(lines), 6)
self.assertEqual(lines[0], 'Iter. Eval. Time m:s')
pattern = re.compile('[0-9]+[ ]+[0-9]+[ ]+[0-9]{1}:[0-9]{2}.[0-9]{1}')
for line in lines[5:]:
self.assertTrue(pattern.match(line))
def test_ask(self):
# Tests ask.
sampler = pints.NestedRejectionSampler(self.log_prior)
pts = sampler.ask(1)
self.assertTrue(np.isfinite(self.log_likelihood(pts)))
# test multiple points being asked and tell'd
sampler = pints.NestedRejectionSampler(self.log_prior)
pts = sampler.ask(50)
self.assertEqual(len(pts), 50)
fx = [self.log_likelihood(pt) for pt in pts]
proposed = sampler.tell(fx)
self.assertTrue(len(proposed) > 1)
def test_getters_and_setters(self):
"""
Tests various get() and set() methods.
"""
sampler = pints.NestedRejectionSampler(self.log_likelihood,
self.log_prior)
# Iterations
x = sampler.iterations() + 1
self.assertNotEqual(sampler.iterations(), x)
sampler.set_iterations(x)
self.assertEqual(sampler.iterations(), x)
self.assertRaisesRegex(ValueError, 'negative', sampler.set_iterations,
-1)
# Active points rate
x = sampler.active_points_rate() + 1
self.assertNotEqual(sampler.active_points_rate(), x)
sampler.set_active_points_rate(x)
self.assertEqual(sampler.active_points_rate(), x)
self.assertRaisesRegex(ValueError, 'greater than 5',
sampler.set_active_points_rate, 5)
# Posterior samples
x = sampler.posterior_samples() + 1
self.assertNotEqual(sampler.posterior_samples(), x)
sampler.set_posterior_samples(x)
self.assertEqual(sampler.posterior_samples(), x)
self.assertRaisesRegex(ValueError, 'greater than zero',
sampler.set_posterior_samples, 0)
def test_hyper_params(self):
"""
Tests the hyper parameter interface is working.
"""
sampler = pints.NestedRejectionSampler(self.log_likelihood,
self.log_prior)
self.assertEqual(sampler.n_hyper_parameters(), 1)
sampler.set_hyper_parameters([6])
self.assertEqual(sampler.active_points_rate(), 6)
def test_quick_run(self):
""" Test a single run. """
sampler = pints.NestedRejectionSampler(self.log_likelihood,
self.log_prior)
sampler.set_posterior_samples(10)
sampler.set_iterations(50)
sampler.set_active_points_rate(50)
sampler.set_log_to_screen(False)
samples, margin = sampler.run()
# Check output: Note n returned samples = n posterior samples
self.assertEqual(samples.shape, (10, 2))
def test_getters_and_setters(self):
# Tests various get() and set() methods.
sampler = pints.NestedRejectionSampler(self.log_prior)
# Active points
x = sampler.n_active_points() + 1
self.assertNotEqual(sampler.n_active_points(), x)
sampler.set_n_active_points(x)
self.assertEqual(sampler.n_active_points(), x)
self.assertRaisesRegex(
ValueError, 'greater than 5', sampler.set_n_active_points, 5)
self.assertEqual(sampler.name(), 'Nested rejection sampler')
self.assertTrue(not sampler.needs_initial_phase())
def test_settings_check(self):
"""
Tests the settings check at the start of a run.
"""
sampler = pints.NestedRejectionSampler(self.log_likelihood,
self.log_prior)
sampler.set_posterior_samples(2)
sampler.set_iterations(10)
sampler.set_active_points_rate(10)
sampler.set_log_to_screen(False)
sampler.run()
sampler.set_posterior_samples(10)
self.assertRaisesRegex(ValueError, 'exceed 0.25', sampler.run)
def test_hyper_params(self):
# Tests the hyper parameter interface is working.
sampler = pints.NestedRejectionSampler(self.log_prior)
self.assertEqual(sampler.n_hyper_parameters(), 1)
sampler.set_hyper_parameters([220])