def test_method(self):
# Create mcmc
x0 = self.real_parameters * 1.1
mcmc = pints.PopulationMCMC(x0)
# PopulationMCMC uses adaptive covariance internally, so requires an
# initial phase
self.assertTrue(mcmc.needs_initial_phase())
self.assertTrue(mcmc.in_initial_phase())
# Test schedule
s = np.array([0, 0.1, 0.5])
mcmc.set_temperature_schedule(s)
self.assertTrue(np.all(s == mcmc.temperature_schedule()))
# Perform short run
chain = []
for i in range(100):
x = mcmc.ask()
fx = self.log_posterior(x)
sample = mcmc.tell(fx)
if i == 20:
self.assertTrue(mcmc.in_initial_phase())
mcmc.set_initial_phase(False)
self.assertFalse(mcmc.in_initial_phase())
if i >= 50:
chain.append(sample)
if np.all(sample == x):
self.assertEqual(mcmc.current_log_pdf(), fx)
chain = np.array(chain)
self.assertEqual(chain.shape[0], 50)
self.assertEqual(chain.shape[1], len(x0))
def test_errors(self):
mcmc = pints.PopulationMCMC(self.real_parameters)
self.assertRaises(ValueError, mcmc.set_temperature_schedule, 1)
self.assertRaises(ValueError, mcmc.set_temperature_schedule, [0])
self.assertRaises(ValueError, mcmc.set_temperature_schedule, [0.5])
mcmc.set_temperature_schedule([0, 0.5])
self.assertRaises(
ValueError, mcmc.set_temperature_schedule, [0.5, 0.5])
self.assertRaises(ValueError, mcmc.set_temperature_schedule, [0, -0.1])
self.assertRaises(ValueError, mcmc.set_temperature_schedule, [0, 1.1])
mcmc = pints.PopulationMCMC(self.real_parameters)
mcmc._initialise()
self.assertRaises(RuntimeError, mcmc._initialise)
self.assertRaises(
RuntimeError, mcmc.set_temperature_schedule, [0, 0.1])
mcmc = pints.PopulationMCMC(self.real_parameters)
self.assertRaises(RuntimeError, mcmc.tell, 1)
def test_hyperparameters(self):
mcmc = pints.PopulationMCMC(self.real_parameters)
self.assertEqual(mcmc.n_hyper_parameters(), 1)
# Test setting with an int
mcmc.set_temperature_schedule(7)
x = mcmc.temperature_schedule()
self.assertEqual(len(x), 7)
mcmc.set_temperature_schedule(8)
self.assertEqual(len(mcmc.temperature_schedule()), 8)
mcmc.set_hyper_parameters([7])
y = mcmc.temperature_schedule()
self.assertEqual(len(y), 7)
self.assertTrue(np.all(x == y))
# Test setting with a list
mcmc.set_temperature_schedule(x)
self.assertRaisesRegex(ValueError, 'First hyper-parameter',
mcmc.set_hyper_parameters, [x])