def mcmc_emcee(self, n_walkers, n_run, n_burn, mean_start, sigma_start):
"""
returns the mcmc analysis of the parameter space
"""
sampler = emcee.EnsembleSampler(n_walkers, self.cosmoParam.numParam, self.chain.likelihood)
p0 = emcee.utils.sample_ball(mean_start, sigma_start, n_walkers)
new_pos, _, _, _ = sampler.run_mcmc(p0, n_burn)
sampler.reset()
store = InMemoryStorageUtil()
for pos, prob, _, _ in sampler.sample(new_pos, iterations=n_run):
store.persistSamplingValues(pos, prob, None)
return store.samples
class TestCosmoHammerSampler(object):
storageUtil = None
samples = np.array([[1, 2, 3], [4, 5, 6]])
prob = np.array([1, 1])
def setup(self):
self.storageUtil = InMemoryStorageUtil()
def test_no_data(self):
assert self.storageUtil.samplesBurnin == None
assert self.storageUtil.probBurnin == None
def test_persistBurninValues(self):
self.storageUtil.persistBurninValues(self.samples, self.prob, [])
assert self.storageUtil.samplesBurnin is not None
assert self.storageUtil.probBurnin is not None
assert self.storageUtil.samplesBurnin.shape == (2, 3)
assert self.storageUtil.probBurnin.shape == (2, )
self.storageUtil.persistBurninValues(self.samples, self.prob, [])
assert self.storageUtil.samplesBurnin is not None
assert self.storageUtil.probBurnin is not None
assert self.storageUtil.samplesBurnin.shape == (4, 3)
assert self.storageUtil.probBurnin.shape == (4, )
def test_persistSamplingValues(self):
self.storageUtil.persistSamplingValues(self.samples, self.prob, [])
assert self.storageUtil.samples is not None
assert self.storageUtil.prob is not None
assert self.storageUtil.samples.shape == (2, 3)
assert self.storageUtil.prob.shape == (2, )
self.storageUtil.persistSamplingValues(self.samples, self.prob, [])
assert self.storageUtil.samples is not None
assert self.storageUtil.prob is not None
assert self.storageUtil.samples.shape == (4, 3)
assert self.storageUtil.prob.shape == (4, )
class TestCosmoHammerSampler(object):
storageUtil = None
samples = np.array([[1, 2, 3], [4, 5, 6]])
prob = np.array([1, 1])
def setup(self):
self.storageUtil = InMemoryStorageUtil()
def test_no_data(self):
assert self.storageUtil.samplesBurnin == None
assert self.storageUtil.probBurnin == None
def test_persistBurninValues(self):
self.storageUtil.persistBurninValues(self.samples, self.prob, [])
assert self.storageUtil.samplesBurnin is not None
assert self.storageUtil.probBurnin is not None
assert self.storageUtil.samplesBurnin.shape == (2, 3)
assert self.storageUtil.probBurnin.shape == (2,)
self.storageUtil.persistBurninValues(self.samples, self.prob, [])
assert self.storageUtil.samplesBurnin is not None
assert self.storageUtil.probBurnin is not None
assert self.storageUtil.samplesBurnin.shape == (4, 3)
assert self.storageUtil.probBurnin.shape == (4,)
def test_persistSamplingValues(self):
self.storageUtil.persistSamplingValues(self.samples, self.prob, [])
assert self.storageUtil.samples is not None
assert self.storageUtil.prob is not None
assert self.storageUtil.samples.shape == (2, 3)
assert self.storageUtil.prob.shape == (2,)
self.storageUtil.persistSamplingValues(self.samples, self.prob, [])
assert self.storageUtil.samples is not None
assert self.storageUtil.prob is not None
assert self.storageUtil.samples.shape == (4, 3)
assert self.storageUtil.prob.shape == (4,)
