def test_post_prior(tmpdir):
# Generate original chain
info: InputDict = {
"output": os.path.join(tmpdir, "gaussian"), "force": True,
"params": info_params, "sampler": info_sampler,
"likelihood": {"one": None}, "prior": {"gaussian": sampled_pdf}}
info_post: InputDict = {
"output": info["output"], "force": True,
"post": {"suffix": "foo", 'skip': 0.1,
"remove": {"prior": {"gaussian": None}},
"add": {"prior": {"target": target_pdf_prior}}}}
_, sampler = run(info)
if mpi.is_main_process():
mcsamples_in = loadMCSamples(info["output"], settings={'ignore_rows': 0.1})
target_mean, target_cov = mpi.share(_get_targets(mcsamples_in))
else:
target_mean, target_cov = mpi.share()
for mem in [False, True]:
post(info_post, sample=sampler.products()["sample"] if mem else None)
# Load with GetDist and compare
if mpi.is_main_process():
mcsamples = loadMCSamples(
info_post["output"] + _post_ + info_post["post"]["suffix"])
new_mean = mcsamples.mean(["a", "b"])
new_cov = mcsamples.getCovMat().matrix
mpi.share((new_mean, new_cov))
else:
new_mean, new_cov = mpi.share()
assert np.allclose(new_mean, target_mean)
assert np.allclose(new_cov, target_cov)
def check_convergence_and_learn_proposal(self):
"""
Checks the convergence of the sampling process, and, if requested,
learns a new covariance matrix for the proposal distribution from the covariance
of the last samples.
"""
# Compute Rminus1 of means
self.been_waiting = 0
if more_than_one_process():
# Compute and gather means and covs
use_first = int(self.n() / 2)
mean = self.collection.mean(first=use_first)
cov = self.collection.cov(first=use_first)
acceptance_rate = self.get_acceptance_rate(use_first)
Ns, means, covs, acceptance_rates = mpi.array_gather(
[self.n(), mean, cov, acceptance_rate])
else:
# Compute and gather means, covs and CL intervals of last m-1 chain fractions
m = 1 + self.Rminus1_single_split
cut = int(len(self.collection) / m)
try:
acceptance_rate = self.get_acceptance_rate(cut)
Ns = np.ones(m - 1) * cut
means = np.array([
self.collection.mean(first=i * cut, last=(i + 1) * cut - 1)
for i in range(1, m)
])
covs = np.array([
self.collection.cov(first=i * cut, last=(i + 1) * cut - 1)
for i in range(1, m)
])
except always_stop_exceptions:
raise
except Exception:
self.log.info(
"Not enough points in chain to check convergence. "
"Waiting for next checkpoint.")
return
acceptance_rates = None
if is_main_process():
self.progress.at[self.i_learn, "N"] = sum(Ns)
self.progress.at[self.i_learn, "timestamp"] = \
datetime.datetime.now().isoformat()
acceptance_rate = (np.average(acceptance_rates, weights=Ns)
if acceptance_rates is not None else
acceptance_rate)
self.log.info(
" - Acceptance rate: %.3f" +
(" = avg(%r)" % list(acceptance_rates)
if acceptance_rates is not None else ""), acceptance_rate)
self.progress.at[self.i_learn, "acceptance_rate"] = acceptance_rate
# "Within" or "W" term -- our "units" for assessing convergence
# and our prospective new covariance matrix
mean_of_covs = np.average(covs, weights=Ns, axis=0)
# "Between" or "B" term
# We don't weight with the number of samples in the chains here:
# shorter chains will likely be outliers, and we want to notice them
cov_of_means = np.atleast_2d(np.cov(means.T)) # , fweights=Ns)
# For numerical stability, we turn mean_of_covs into correlation matrix:
# rho = (diag(Sigma))^(-1/2) * Sigma * (diag(Sigma))^(-1/2)
# and apply the same transformation to the mean of covs (same eigenvals!)
d = np.sqrt(np.diag(cov_of_means))
corr_of_means = (cov_of_means / d).T / d
norm_mean_of_covs = (mean_of_covs / d).T / d
success_means = False
converged_means = False
# Cholesky of (normalized) mean of covs and eigvals of Linv*cov_of_means*L
try:
L = np.linalg.cholesky(norm_mean_of_covs)
except np.linalg.LinAlgError:
self.log.warning(
"Negative covariance eigenvectors. "
"This may mean that the covariance of the samples does not "
"contain enough information at this point. "
"Skipping learning a new covmat for now.")
else:
Linv = np.linalg.inv(L)
try:
eigvals = np.linalg.eigvalsh(
Linv.dot(corr_of_means).dot(Linv.T))
success_means = True
except np.linalg.LinAlgError:
self.log.warning("Could not compute eigenvalues. "
"Skipping learning a new covmat for now.")
else:
Rminus1 = max(np.abs(eigvals))
self.progress.at[self.i_learn, "Rminus1"] = Rminus1
# For real square matrices, a possible def of the cond number is:
condition_number = Rminus1 / min(np.abs(eigvals))
self.log.debug(" - Condition number = %g",
condition_number)
self.log.debug(" - Eigenvalues = %r", eigvals)
self.log.info(
" - Convergence of means: R-1 = %f after %d accepted steps"
% (Rminus1, sum(Ns)) +
(" = sum(%r)" %
list(Ns) if more_than_one_process() else ""))
# Have we converged in means?
# (criterion must be fulfilled twice in a row)
converged_means = max(
Rminus1, self.Rminus1_last) < self.Rminus1_stop
else:
mean_of_covs = None
success_means = None
converged_means = False
Rminus1 = None
success_means, converged_means = mpi.share(
(success_means, converged_means))
# Check the convergence of the bounds of the confidence intervals
# Same as R-1, but with the rms deviation from the mean bound
# in units of the mean standard deviation of the chains
if converged_means:
if more_than_one_process():
mcsamples = self.collection.sampled_to_getdist_mcsamples(
first=use_first)
try:
bound = np.array([[
mcsamples.confidence(i,
limfrac=self.Rminus1_cl_level /
2.,
upper=which)
for i in range(self.model.prior.d())
] for which in [False, True]]).T
success_bounds = True
except:
bound = None
success_bounds = False
bounds = np.array(mpi.gather(bound))
else:
try:
mcsamples_list = [
self.collection.sampled_to_getdist_mcsamples(
first=i * cut, last=(i + 1) * cut - 1)
for i in range(1, m)
]
except always_stop_exceptions:
raise
except:
self.log.info(
"Not enough points in chain to check c.l. convergence. "
"Waiting for next checkpoint.")
return
try:
bounds = [
np.array([[
mcs.confidence(i,
limfrac=self.Rminus1_cl_level / 2.,
upper=which)
for i in range(self.model.prior.d())
] for which in [False, True]]).T
for mcs in mcsamples_list
]
success_bounds = True
except:
bounds = None
success_bounds = False
if is_main_process():
if success_bounds:
Rminus1_cl = (np.std(bounds, axis=0).T /
np.sqrt(np.diag(mean_of_covs)))
self.log.debug(" - normalized std's of bounds = %r",
Rminus1_cl)
Rminus1_cl = np.max(Rminus1_cl)
self.progress.at[self.i_learn, "Rminus1_cl"] = Rminus1_cl
self.log.info(
" - Convergence of bounds: R-1 = %f after %d " %
(Rminus1_cl,
(sum(Ns) if more_than_one_process() else self.n())) +
"accepted steps" +
(" = sum(%r)" %
list(Ns) if more_than_one_process() else ""))
if Rminus1_cl < self.Rminus1_cl_stop:
self.converged = True
self.log.info("The run has converged!")
self._Ns = Ns
else:
self.log.info(
"Computation of the bounds was not possible. "
"Waiting until the next converge check.")
# Broadcast and save the convergence status and the last R-1 of means
if success_means:
self.Rminus1_last, self.converged = mpi.share((
Rminus1, self.converged) if is_main_process() else None)
# Do we want to learn a better proposal pdf?
if self.learn_proposal and not self.converged:
good_Rminus1 = (self.learn_proposal_Rminus1_max >
self.Rminus1_last >
self.learn_proposal_Rminus1_min)
if not good_Rminus1:
self.mpi_info(
"Convergence less than requested for updates: "
"waiting until the next convergence check.")
return
mean_of_covs = mpi.share(mean_of_covs)
try:
self.proposer.set_covariance(mean_of_covs)
self.mpi_info(
" - Updated covariance matrix of proposal pdf.")
self.mpi_debug("%r", mean_of_covs)
except:
self.mpi_debug(
"Updating covariance matrix failed unexpectedly. "
"waiting until next covmat learning attempt.")
# Save checkpoint info
self.write_checkpoint()
def test_post_likelihood():
"""
Swaps likelihood "gaussian" for "target".
It also tests aggregated chi2's by removing and adding a likelihood to an existing
type.
"""
# Generate original chain
orig_interval = OutputOptions.output_inteveral_s
try:
OutputOptions.output_inteveral_s = 0
info_params_local = deepcopy(info_params)
info_params_local["dummy"] = 0
dummy_loglike_add = 0.1
dummy_loglike_remove = 0.01
info = {
"output": None,
"force": True,
"params": info_params_local,
"sampler": info_sampler,
"likelihood": {
"gaussian": {
"external": sampled_pdf,
"type": "A"
},
"dummy": {
"external": lambda dummy: 1,
"type": "BB"
},
"dummy_remove": {
"external": lambda dummy: dummy_loglike_add,
"type": "BB"
}
}
}
info_out, sampler = run(info)
samples_in = mpi.gather(sampler.products()["sample"])
if mpi.is_main_process():
mcsamples_in = MCSamplesFromCobaya(info_out, samples_in)
else:
mcsamples_in = None
info_out.update({
"post": {
"suffix": "foo",
"remove": {
"likelihood": {
"gaussian": None,
"dummy_remove": None
}
},
"add": {
"likelihood": {
"target": {
"external": target_pdf,
"type": "A",
"output_params": ["cprime"]
},
"dummy_add": {
"external": lambda dummy: dummy_loglike_remove,
"type": "BB"
}
}
}
}
})
info_post_out, products_post = post(info_out,
sampler.products()["sample"])
samples = mpi.gather(products_post["sample"])
# Load with GetDist and compare
if mcsamples_in:
target_mean, target_cov = mpi.share(_get_targets(mcsamples_in))
mcsamples = MCSamplesFromCobaya(info_post_out,
samples,
name_tag="sample")
new_mean = mcsamples.mean(["a", "b"])
new_cov = mcsamples.getCovMat().matrix
mpi.share((new_mean, new_cov))
else:
target_mean, target_cov = mpi.share()
new_mean, new_cov = mpi.share()
assert np.allclose(new_mean, target_mean)
assert np.allclose(new_cov, target_cov)
assert allclose(products_post["sample"]["chi2__A"],
products_post["sample"]["chi2__target"])
assert allclose(
products_post["sample"]["chi2__BB"],
products_post["sample"]["chi2__dummy"] +
products_post["sample"]["chi2__dummy_add"])
finally:
OutputOptions.output_inteveral_s = orig_interval
def body_of_test(dim, tmpdir=None, random_state=None):
mindim = 4
assert dim > mindim, "Needs dimension>%d for the test." % mindim
if mpi.is_main_process():
random_state = np.random.default_rng(random_state)
i_s = list(range(dim))
random_state.shuffle(i_s)
initial_random_covmat = random_cov(dim * [[0, 1]],
random_state=random_state)
mpi.share((i_s, initial_random_covmat))
else:
i_s, initial_random_covmat = mpi.share()
n_altered = int(dim / 4)
i_proposal = i_s[:n_altered]
i_ref = i_s[n_altered:2 * n_altered]
i_prior = i_s[2 * n_altered:3 * n_altered]
removed = list(chain(*(i_proposal, i_ref, i_prior)))
i_covmat = [i for i in range(dim) if i not in removed]
for i in removed:
diag = initial_random_covmat[i, i]
initial_random_covmat[:, i] = 0
initial_random_covmat[i, :] = 0
initial_random_covmat[i, i] = diag
# Prepare info, including refs, priors and reduced covmat
prefix = "a_"
if mpi.is_main_process():
input_order = list(range(dim))
random_state.shuffle(input_order)
else:
input_order = None
input_order = mpi.share(input_order)
info: InputDict = {"likelihood": {"one": None}, "params": {}}
for i in input_order:
p = prefix + str(i)
info["params"][p] = {
"prior": {
"dist": "norm",
"loc": 0,
"scale": 1000
}
}
sigma = np.sqrt(initial_random_covmat[i, i])
if i in i_proposal:
info["params"][p]["proposal"] = sigma
elif i in i_ref:
info["params"][prefix + str(i)]["ref"] = {
"dist": "norm",
"scale": sigma
}
elif i in i_prior:
info["params"][prefix + str(i)]["prior"]["scale"] = sigma
reduced_covmat = initial_random_covmat[np.ix_(i_covmat, i_covmat)]
reduced_covmat_params = [prefix + str(i) for i in i_covmat]
info["sampler"] = {"mcmc": {}}
if tmpdir:
filename = os.path.join(str(tmpdir), "mycovmat.dat")
header = " ".join(reduced_covmat_params)
np.savetxt(filename, reduced_covmat, header=header)
info["sampler"]["mcmc"]["covmat"] = str(filename)
else:
info["sampler"]["mcmc"]["covmat_params"] = reduced_covmat_params
info["sampler"]["mcmc"]["covmat"] = reduced_covmat
to_compare = initial_random_covmat[np.ix_(input_order, input_order)]
def callback(sampler):
assert np.allclose(to_compare, sampler.proposer.get_covariance())
info["sampler"]["mcmc"].update({
"callback_function": callback,
"callback_every": 1,
"max_samples": 1,
"burn_in": 0
})
run(info)
def body_of_test(info_logpdf, kind, tmpdir, derived=False, manual=False):
rand = mpi.share(random())
prefix = os.path.join(tmpdir, "%d" % round(1e8 * rand)) + os.sep
if mpi.is_main_process():
if os.path.exists(prefix):
shutil.rmtree(prefix)
# build updated info
info = {
"output": prefix,
"params": {
"x": {
"prior": {
"min": 0,
"max": 1
},
"proposal": 0.05
},
"y": {
"prior": {
"min": -1,
"max": 1
},
"proposal": 0.05
}
},
"sampler": {
"mcmc": {
"max_samples": (10 if not manual else 5000),
"learn_proposal": False
}
}
}
if derived:
info["params"].update({
"r": {
"min": 0,
"max": 1
},
"theta": {
"min": -0.5,
"max": 0.5
}
})
# Complete according to kind
if kind == "prior":
info.update({"prior": info_logpdf, "likelihood": {"one": None}})
elif kind == "likelihood":
info.update({"likelihood": info_logpdf})
else:
raise ValueError("Kind of test not known.")
# If there is an ext function that is not a string, don't write output!
stringy = {k: v for k, v in info_logpdf.items() if isinstance(v, str)}
if stringy != info_logpdf:
info.pop("output")
# Run
updated_info, sampler = run(info)
products = sampler.products()
# Test values
logprior_base = -np.log((info["params"]["x"]["prior"]["max"] -
info["params"]["x"]["prior"]["min"]) *
(info["params"]["y"]["prior"]["max"] -
info["params"]["y"]["prior"]["min"]))
logps = {
name: logpdf(
**{
arg: products["sample"][arg].values
for arg in getfullargspec(logpdf)[0]
})
for name, logpdf in {
"half_ring": half_ring_func,
"gaussian_y": gaussian_func
}.items()
}
# Test #1: values of logpdfs
if kind == "prior":
columns_priors = [
c for c in products["sample"].data.columns
if c.startswith("minuslogprior")
]
assert np.allclose(
products["sample"][columns_priors[0]].values,
np.sum(products["sample"][columns_priors[1:]].values, axis=-1)), (
"The single prior values do not add up to the total one.")
assert np.allclose(
logprior_base + sum(logps[p] for p in info_logpdf),
-products["sample"]["minuslogprior"].values), (
"The value of the total prior is not reproduced correctly.")
assert np.isclose(
sampler.model.logprior({
'x': products["sample"]["x"][0],
'y': products["sample"]["y"][0]
}), -products["sample"]["minuslogprior"][0]
), ("The value of the total prior is not reproduced from mode.logprior."
)
elif kind == "likelihood":
for lik in info["likelihood"]:
assert np.allclose(
-2 * logps[lik], products["sample"][get_chi2_name(lik)].values
), ("The value of the likelihood '%s' is not reproduced correctly."
% lik)
assert np.allclose(
logprior_base + sum(logps[p] for p in info_logpdf),
-products["sample"]["minuslogpost"].values), (
"The value of the posterior is not reproduced correctly.")
# Test derived parameters, if present -- for now just for "r"
if derived:
derived_values = {
param:
func(**{arg: products["sample"][arg].values
for arg in ["x", "y"]})
for param, func in derived_funcs.items()
}
assert all(
np.allclose(v, products["sample"][p].values)
for p, v in derived_values.items()
), ("The value of the derived parameters is not reproduced correctly.")
# Test updated info -- scripted
if kind == "prior":
assert info["prior"] == updated_info["prior"], (
"The prior information has not been updated correctly.")
elif kind == "likelihood":
# Transform the likelihood info to the "external" convention and add defaults
info_likelihood = deepcopy(info["likelihood"])
for lik, value in list(info_likelihood.items()):
if not hasattr(value, "get"):
info_likelihood[lik] = {"external": value}
info_likelihood[lik].update({
k: v
for k, v in Likelihood.get_defaults().items()
if k not in info_likelihood[lik]
})
for k in ["input_params", "output_params"]:
info_likelihood[lik].pop(k, None)
updated_info["likelihood"][lik].pop(k)
assert info_likelihood == updated_info["likelihood"], (
"The likelihood information has not been updated correctly\n %r vs %r"
% (info_likelihood, updated_info["likelihood"]))
# Test updated info -- yaml
# For now, only if ALL external pdfs are given as strings,
# since the YAML load fails otherwise
if stringy == info_logpdf:
updated_output_file = os.path.join(prefix,
FileSuffix.updated + ".yaml")
with open(updated_output_file) as updated:
updated_yaml = yaml_load("".join(updated.readlines()))
for k, v in stringy.items():
to_test = updated_yaml[kind][k]
if kind == "likelihood":
to_test = to_test["external"]
assert to_test == info_logpdf[k], (
"The updated external pdf info has not been written correctly."
)
