def test_plot_multiple_2d_gaussian_slices(self):
from pyapprox.visualization import plot_multiple_2d_gaussian_slices
mean = np.array([0, 1, -1])
covariance = np.diag(np.array([1, 0.5, 0.025]))
texfilename = 'slices.tex'
plot_multiple_2d_gaussian_slices(
mean[:10], np.diag(covariance)[:10], texfilename,
reference_gaussian_data=(0., 1.), show=False)
import glob
import os
filenames = glob.glob(texfilename[:-4]+'*')
for filename in filenames:
os.remove(filename)
def posterior_covariance_helper(prior,
rank,
comparison_tol,
test_sampling=False,
plot=False):
"""
Test that the Laplace posterior approximation can be obtained using
the action of the sqrt prior covariance computed using a PDE solve
Parameters
----------
prior : MultivariateGaussian object
The model which must be able to compute the action of the sqrt of the
prior covariance (and its tranpose) on a set of vectors
rank : integer
The rank of the linear model used to generate the observations
comparision_tol :
tolerances for each of the internal comparisons. This allows different
accuracy for PDE based operators
"""
# Define prior sqrt covariance and covariance operators
L_op = prior.sqrt_covariance_operator
# Extract prior information required for computing exact posterior
# mean and covariance
num_vars = prior.num_vars()
prior_mean = np.zeros((num_vars), float)
L = L_op(np.eye(num_vars), False)
L_T = L_op(np.eye(num_vars), True)
assert_ndarray_allclose(L.T,
L_T,
rtol=comparison_tol,
atol=0,
msg='Comparing prior sqrt and transpose')
prior_covariance = np.dot(L, L_T)
prior_pointwise_variance = prior.pointwise_variance()
assert_ndarray_allclose(np.diag(prior_covariance),
prior_pointwise_variance,
rtol=1e-14,
atol=0,
msg='Comparing prior pointwise variance')
misfit_model, noise_covariance_inv, obs = setup_quadratic_misfit_problem(
prior, rank, noise_sigma2=1)
# Get analytical mean and covariance
prior_hessian = np.linalg.inv(prior_covariance)
exact_laplace_mean, exact_laplace_covariance = \
laplace_posterior_approximation_for_linear_models(
misfit_model.Amatrix, prior.mean, prior_hessian,
noise_covariance_inv, obs)
# Define prior conditioned misfit operator
sample = np.zeros(num_vars)
misfit_hessian_operator = MisfitHessianVecOperator(misfit_model,
sample,
fd_eps=None)
LHL_op = PriorConditionedHessianMatVecOperator(L_op,
misfit_hessian_operator)
# For testing purposes build entire L*H*L matrix using operator
# and compare to result based upon explicit matrix mutiplication
LHL_op = LHL_op.apply(np.eye(num_vars), transpose=False)
H = misfit_model.hessian(sample)
assert np.allclose(
H,
np.dot(np.dot(misfit_model.Amatrix.T, noise_covariance_inv),
misfit_model.Amatrix))
LHL_mat = np.dot(L_T, np.dot(H, L))
assert_ndarray_allclose(
LHL_mat,
LHL_op,
rtol=comparison_tol,
msg='Comparing prior matrix and operator based LHL')
# Test singular values obtained by randomized svd using operator
# are the same as those obtained using singular decomposition
Utrue, Strue, Vtrue = np.linalg.svd(LHL_mat)
Utrue, Vtrue = adjust_sign_svd(Utrue, Vtrue)
standard_svd_opts = {'num_singular_values': rank, 'num_extra_samples': 10}
svd_opts = {'single_pass': True, 'standard_opts': standard_svd_opts}
L_post_op = get_laplace_covariance_sqrt_operator(L_op,
misfit_hessian_operator,
svd_opts,
weights=None,
min_singular_value=0.0)
#print np.max((Strue[:rank]-L_post_op.e_r)/Strue[0])
max_error = np.max(Strue[:rank] - L_post_op.e_r)
assert max_error / Strue[0] < comparison_tol, max_error / Strue[0]
assert_ndarray_allclose(Vtrue.T[:, :rank],
L_post_op.V_r,
rtol=1e-6,
msg='Comparing eigenvectors')
L_post_op.V_r = Vtrue.T[:, :rank]
# Test posterior sqrt covariance operator transpose is the same as
# explicit matrix transpose of matrix obtained by prior sqrt
# covariance operator
L_post = L_post_op.apply(np.eye(num_vars), transpose=False)
L_post_T = L_post_op.apply(np.eye(num_vars), transpose=True)
assert_ndarray_allclose(L_post.T,
L_post_T,
rtol=comparison_tol,
msg='Comparing posterior sqrt and transpose')
# Test posterior covariance operator produced matrix is the same
# as the exact posterior covariance obtained using analytical formula
if rank == num_vars:
# this test only makes sense if entire set of directions is found
# if low rank approx is used then this will ofcourse induce errors
post_covariance = np.dot(L_post, L_post_T)
assert_ndarray_allclose(
exact_laplace_covariance,
post_covariance,
rtol=comparison_tol,
atol=0.,
msg='Comparing matrix and operator based posterior covariance')
# Test pointwise covariance of posterior
post_pointwise_variance, prior_pointwise_variance=\
get_pointwise_laplace_variance_using_prior_variance(
prior, L_post_op, prior_pointwise_variance)
assert_ndarray_allclose(np.diag(exact_laplace_covariance),
post_pointwise_variance,
rtol=comparison_tol,
atol=0.,
msg='Comparing pointwise variance')
if not test_sampling:
return
num_samples = int(2e5)
posterior_samples = sample_from_laplace_posterior(exact_laplace_mean,
L_post_op,
num_vars,
num_samples,
weights=None)
assert_ndarray_allclose(exact_laplace_covariance,
np.cov(posterior_samples),
atol=1e-2 * exact_laplace_covariance.max(),
rtol=0.,
msg='Comparing posterior samples covariance')
assert_ndarray_allclose(exact_laplace_mean.squeeze(),
np.mean(posterior_samples, axis=1),
atol=2e-2,
rtol=0.,
msg='Comparing posterior samples mean')
if plot:
# plot marginals of posterior using orginal ordering
from pyapprox.visualization import plot_multiple_2d_gaussian_slices
texfilename = 'slices.tex'
plot_multiple_2d_gaussian_slices(
exact_laplace_mean[:10],
np.diag(exact_laplace_covariance)[:10],
texfilename,
reference_gaussian_data=(0., 1.),
show=False)
# plot marginals of posterior in rotated coordinates
# from most to least important.
# The following is not feasiable in practice as we cannot compute
# entire covariance matrix in full space. But we have
# C_r = V_r*L*V_r*D*V_r.T*L.T*V_r.T
# is we compute matrix products from right to left we only have to
# compute at most (d x r) matrices. And if only want first 20 say
# variances then can apply C_r to vectors e_i i=1,...,20
# then we need at most (dx20 matrices)
texfilename = 'rotated-slices.tex'
V_r = L_post_op.V_r
plot_multiple_2d_gaussian_slices(
np.dot(V_r.T, exact_laplace_mean[:10]),
np.diag(np.dot(V_r.T, np.dot(exact_laplace_covariance, V_r)))[:10],
texfilename,
reference_gaussian_data=(0., 1.),
show=True)