def test_multivariate_sim_and_obs_mcmc_thetacon(self):
"""
Tests mcmc for multivariate sim and obs model with theta constraint function
"""
print(
'Testing multivariate sim and obs SepiaMCMC w theta constraint...',
flush=True)
data = self.multi_sim_and_obs_data
def fcon(x):
return (x[:, 0] + x[:, 1]) < 0.8
theta_init = np.array([[0.2, 0.3, 0.5]])
model = SepiaModel(data, theta_init=theta_init, theta_fcon=fcon)
model.tune_step_sizes(50, 10)
model.do_mcmc(100)
samples = model.get_samples()
self.assertTrue(
np.all(samples['theta'][:, 0] + samples['theta'][:, 1] < 0.8))
def test_univariate_sim_and_obs_saveload(self):
"""
Tests save/load for univariate sim and obs model
"""
print('Testing univariate sim and obs save/load...', flush=True)
data = self.univ_sim_and_obs_data
model = SepiaModel(data)
model.tune_step_sizes(50, 10)
model.do_mcmc(100)
model.save_model_info(overwrite=True)
new_model = SepiaModel(data)
new_model.restore_model_info()
# check num stuff
self.assertEqual(model.num.logLik, new_model.num.logLik)
self.assertTrue(np.allclose(model.num.uw, new_model.num.uw))
self.assertTrue(np.allclose(model.num.SigWl, new_model.num.SigWl))
# check param stuff
for p1, p2 in zip(model.params, new_model.params):
self.assertTrue(p1.name == p2.name)
self.assertTrue(np.allclose(p1.fixed, p2.fixed))
self.assertTrue(np.allclose(p1.val, p2.val))
self.assertTrue(np.allclose(np.array(p1.mcmc.draws), np.array(p2.mcmc.draws)))
if p1.name != 'logPost':
self.assertTrue(np.allclose(p1.mcmc.stepParam, p2.mcmc.stepParam))
self.assertTrue(p1.mcmc.stepType == p2.mcmc.stepType)
self.assertTrue(np.allclose(np.array(p1.prior.bounds), np.array(p2.prior.bounds)))
self.assertTrue(np.allclose(np.array(p1.prior.params), np.array(p2.prior.params)))
self.assertTrue(p1.prior.dist == p2.prior.dist)
new_model.do_mcmc(10)
data = SepiaData(t_sim=design,
y_sim=y_sim,
y_ind_sim=y_ind,
y_obs=y_obs,
y_ind_obs=y_ind)
data.standardize_y()
data.transform_xt()
data.create_K_basis(n_features - 1)
print(data)
# Setup model
# We have a known observation error
Sigy = np.diag(
np.squeeze(
(0.01 * np.ones(n_features) * y_obs) / data.sim_data.orig_y_sd**2))
model = SepiaModel(data, Sigy)
# Modify priors to match Matlab
model.params.lamWs.prior.bounds[1] = np.inf
model.params.lamWs.prior.params = [np.ones((1, 11)), np.zeros((1, 11))]
# Do mcmc
model.tune_step_sizes(100, 25)
model.do_mcmc(10000)
samples_dict = model.get_samples()
with open('data/sepia_mcmc_samples1-5000.pkl', 'wb') as f:
pickle.dump(samples_dict, f)
with open('data/sepia_model.pkl', 'wb') as f:
pickle.dump(model, f)
D_dense = np.zeros(shape=(h_dense.shape[0], pv))
for j in range(pv):
D_obs[:, j] = norm.pdf(h_field, D_grid[j], D_width)
D_sim[:, j] = norm.pdf(h_sim, D_grid[j], D_width)
D_dense[:, j] = norm.pdf(h_dense, D_grid[j], D_width)
data.create_D_basis(D_obs=D_obs.T, D_sim=D_sim)
#
# Data setup completed
#
nmcmc = 5000
#
# Standard mcmc reference model setup and sampling
#
model_ref = SepiaModel(data)
model_ref.tune_step_sizes(50, 20, verbose=False)
# burn in the model. This is qualitative, and needs to be assessed on trace plots
# This model is actually OK, but do 10 samples for 'burn-in'
model_ref.do_mcmc(10, prog=False)
# and discard those samples
model_ref.clear_samples()
tref = time() # timing start
model_ref.do_mcmc(nmcmc)
print('Single-process mcmc took %f s' % (time() - tref), flush=True)
#
# Perform the same operation with parallel mcmc chains
#
model = SepiaModel(data) # new model instance
model.tune_step_sizes(50, 20, verbose=False) # optimize step sizes
model.do_mcmc(10, prog=False) # The same burn-in process
#%%
model = SepiaModel(data)
#%%
cachefile_name='multivariate_example_with_prediction.pkl'
import os.path
import pickle
use_save_file=False
if use_save_file and os.path.isfile(cachefile_name):
model=pickle.load(open(cachefile_name, "rb" ))
else:
model.tune_step_sizes(50, 20)
model.do_mcmc(1000)
if use_save_file:
pickle.dump(model, open( cachefile_name, "w+b" ))
#%%
# Extract MCMC samples into dictionary with parameter names
samples_dict = {p.name: p.mcmc_to_array() for p in model.params.mcmcList}
for i, k in enumerate(samples_dict.keys()):
param_shape = samples_dict[k].shape[1]
if param_shape >= 5:
ncol = 5
nrow = int(np.ceil(param_shape / ncol))
else: