def test_run_with_noise(random_state):
def func(x):
return (np.sin(x) + random_state.randn()).item(), 1.0
opt = Optimizer(dimensions=[(-2.0, 2.0)], n_initial_points=1)
opt.run(func, n_iter=2, n_samples=1, gp_burnin=0)
assert_almost_equal(opt.gp.alpha, np.ones(2))
def test_probability_of_improvement(random_state, input, expected):
opt = Optimizer(dimensions=[(-2.0, 2.0)],
n_initial_points=0,
random_state=random_state)
opt.tell([[-2.0], [-1.0], [0.0], [1.0], [2.0]], [2.0, 0.0, -2.0, 0.0, 2.0],
gp_burnin=10)
prob = opt.probability_of_optimality(
threshold=input["threshold"],
n_random_starts=20,
random_state=random_state,
normalized_scores=input["normalized_scores"],
)
np.testing.assert_almost_equal(prob, expected, decimal=2)
def test_initial_points():
opt = Optimizer(dimensions=[(-2.0, 2.0)], n_initial_points=5)
x = opt.ask()
opt.tell([x], [0.0])
assert opt._n_initial_points == opt.n_initial_points_ - 1
opt.tell([x], [0.0])
assert opt._n_initial_points == opt.n_initial_points_ - 2
opt.tell([[0.1], [0.2], [0.3]], [0.0, 0.1, 0.2], replace=True)
assert opt._n_initial_points == opt.n_initial_points_ - 3
def _make_optimizer(self, params_space):
"""Instantiate bask Optimizer class.
Parameters
----------
params_space : dict
Represents parameter search space. The keys are parameter
names (strings) and values are skopt.space.Dimension instances,
one of Real, Integer or Categorical.
Returns
-------
optimizer: Instance of the `Optimizer` class used for for search
in some parameter space.
"""
kwargs = self.optimizer_kwargs_.copy()
kwargs["dimensions"] = dimensions_aslist(params_space)
# Here we replace skopt's Optimizer:
optimizer = Optimizer(**kwargs)
for i in range(len(optimizer.space.dimensions)):
if optimizer.space.dimensions[i].name is not None:
continue
optimizer.space.dimensions[i].name = list(
sorted(params_space.keys()))[i]
return optimizer
def test_expected_optimality_gap(random_state, input, expected):
opt = Optimizer(dimensions=[(-2.0, 2.0)],
n_initial_points=0,
random_state=random_state)
opt.tell([[-2.0], [-1.0], [0.0], [1.0], [2.0]], [2.0, 0.0, -2.0, 0.0, 2.0],
gp_burnin=10)
gap = opt.expected_optimality_gap(
random_state=random_state,
n_probabilities=10,
n_space_samples=100,
n_gp_samples=100,
n_random_starts=10,
tol=0.1,
use_mean_gp=input["use_mean_gp"],
normalized_scores=input["normalized_scores"],
)
np.testing.assert_almost_equal(gap, expected, decimal=2)
def test_noise_vector():
opt = Optimizer(dimensions=[(-2.0, 2.0)], n_initial_points=5)
opt.tell(
[[-1.0], [0.0], [1.0], [0.5]],
[0.0, -1.0, 0.0, -1.0],
noise_vector=[1.0, 1.0, 1.0, 0.0],
)
x = opt.ask()
opt.tell([x], [0.0])
# Test, if the less noisy optimum (at 0.5) had a stronger impact on the mean process
# than the noisy optimum (at 0.0):
y_noisy, y = opt.gp.predict([[0.5], [0.625]])
assert y_noisy > y
# Check, if passing a single point works correctly:
x = opt.ask()
opt.tell(x, 0.0, noise_vector=0.5)
def test_multiple_asks():
# calling ask() multiple times without a tell() inbetween should
# be a "no op"
opt = Optimizer(dimensions=[(-2.0, 2.0)], n_initial_points=1)
opt.run(bench1, n_iter=3, gp_burnin=0, n_samples=1)
# tell() computes the next point ready for the next call to ask()
# hence there are three after three iterations
assert_equal(len(opt.Xi), 3)
opt.ask()
assert_equal(len(opt.Xi), 3)
assert_equal(opt.ask(), opt.ask())
def test_initial_points(init_strategy):
opt = Optimizer(dimensions=[(-2.0, 2.0)],
n_initial_points=3,
init_strategy=init_strategy)
x = opt.ask()
assert not isinstance(x[0], list)
opt.tell([x], [0.0])
assert opt._n_initial_points == opt.n_initial_points_ - 1
opt.tell([x], [0.0])
assert opt._n_initial_points == opt.n_initial_points_ - 2
assert opt.gp.chain_ is None
opt.tell([[0.1], [0.2], [0.3]], [0.0, 0.1, 0.2], replace=True)
assert opt._n_initial_points == opt.n_initial_points_ - 3
assert opt.gp.chain_ is not None
def test_optimum_intervals():
opt = Optimizer(dimensions=[(0.0, 1.0)],
random_state=0,
acq_func="mean",
n_points=100)
x = np.linspace(0, 1, num=20)[:, None]
y = np.cos(np.pi * 4 * x).flatten() + opt.rng.randn(20) * 0.1
opt.tell(x.tolist(), y.tolist(), gp_burnin=20, progress=False, n_samples=1)
intervals = opt.optimum_intervals(random_state=0, space_samples=100)
assert len(intervals) == 1
assert len(intervals[0]) >= 2
assert len(intervals[0][0]) == 2
intervals = opt.optimum_intervals(random_state=0,
space_samples=100,
multimodal=False)
assert len(intervals) == 1
assert len(intervals[0]) == 2
def local( # noqa: C901
tuning_config,
acq_function="mes",
acq_function_samples=1,
confidence=0.9,
data_path=None,
gp_burnin=5,
gp_samples=300,
gp_initial_burnin=100,
gp_initial_samples=300,
logfile="log.txt",
n_initial_points=30,
n_points=500,
plot_every=5,
plot_path="plots",
random_seed=0,
result_every=5,
resume=True,
verbose=False,
):
"""Run a local tune.
Parameters defined in the `tuning_config` file always take precedence.
"""
json_dict = json.load(tuning_config)
settings, commands, fixed_params, param_ranges = load_tuning_config(json_dict)
log_level = logging.DEBUG if verbose else logging.INFO
log_format = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
root_logger = logging.getLogger()
root_logger.setLevel(log_level)
file_logger = logging.FileHandler(settings.get("logfile", logfile))
file_logger.setFormatter(log_format)
root_logger.addHandler(file_logger)
console_logger = logging.StreamHandler(sys.stdout)
console_logger.setFormatter(log_format)
root_logger.addHandler(console_logger)
logging.debug(f"Got the following tuning settings:\n{json_dict}")
# 1. Create seed sequence
ss = np.random.SeedSequence(settings.get("random_seed", random_seed))
# 2. Create kernel
# 3. Create optimizer
random_state = np.random.RandomState(np.random.MT19937(ss.spawn(1)[0]))
opt = Optimizer(
dimensions=list(param_ranges.values()),
n_points=settings.get("n_points", n_points),
n_initial_points=settings.get("n_initial_points", n_initial_points),
# gp_kernel=kernel, # TODO: Let user pass in different kernels
gp_kwargs=dict(normalize_y=True),
# gp_priors=priors, # TODO: Let user pass in priors
acq_func=settings.get("acq_function", acq_function),
acq_func_kwargs=dict(alpha="inf", n_thompson=20),
random_state=random_state,
)
X = []
y = []
noise = []
iteration = 0
# 3.1 Resume from existing data:
if data_path is None:
data_path = "data.npz"
if resume:
path = pathlib.Path(data_path)
if path.exists():
with np.load(path) as importa:
X = importa["arr_0"].tolist()
y = importa["arr_1"].tolist()
noise = importa["arr_2"].tolist()
if len(X[0]) != opt.space.n_dims:
logging.error(
"The number of parameters are not matching the number of "
"dimensions. Rename the existing data file or ensure that the "
"parameter ranges are correct."
)
sys.exit(1)
reduction_needed, X_reduced, y_reduced, noise_reduced = reduce_ranges(
X, y, noise, opt.space
)
if reduction_needed:
backup_path = path.parent / (
path.stem + f"_backup_{int(time.time())}" + path.suffix
)
logging.warning(
f"The parameter ranges are smaller than the existing data. "
f"Some points will have to be discarded. "
f"The original {len(X)} data points will be saved to "
f"{backup_path}"
)
np.savez_compressed(
backup_path, np.array(X), np.array(y), np.array(noise)
)
X = X_reduced
y = y_reduced
noise = noise_reduced
iteration = len(X)
logging.info(
f"Importing {iteration} existing datapoints. This could take a while..."
)
opt.tell(
X,
y,
noise_vector=noise,
gp_burnin=settings.get("gp_initial_burnin", gp_initial_burnin),
gp_samples=settings.get("gp_initial_samples", gp_initial_samples),
n_samples=settings.get("n_samples", 1),
progress=True,
)
logging.info("Importing finished.")
# 4. Main optimization loop:
while True:
logging.info("Starting iteration {}".format(iteration))
result_every_n = settings.get("result_every", result_every)
if (
result_every_n > 0
and iteration % result_every_n == 0
and opt.gp.chain_ is not None
):
result_object = create_result(Xi=X, yi=y, space=opt.space, models=[opt.gp])
try:
best_point, best_value = expected_ucb(result_object, alpha=0.0)
best_point_dict = dict(zip(param_ranges.keys(), best_point))
logging.info(f"Current optimum:\n{best_point_dict}")
logging.info(f"Estimated value: {best_value}")
confidence_val = settings.get("confidence", confidence)
confidence_out = confidence_intervals(
optimizer=opt,
param_names=list(param_ranges.keys()),
hdi_prob=confidence_val,
opt_samples=1000,
multimodal=False,
)
logging.info(
f"{confidence_val*100}% confidence intervals:\n{confidence_out}"
)
except ValueError:
logging.info(
"Computing current optimum was not successful. "
"This can happen in rare cases and running the "
"tuner again usually works."
)
plot_every_n = settings.get("plot_every", plot_every)
if (
plot_every_n > 0
and iteration % plot_every_n == 0
and opt.gp.chain_ is not None
):
logging.getLogger("matplotlib.font_manager").disabled = True
if opt.space.n_dims == 1:
logging.warning(
"Plotting for only 1 parameter is not supported yet."
)
else:
logging.debug("Starting to compute the next plot.")
result_object = create_result(
Xi=X, yi=y, space=opt.space, models=[opt.gp]
)
plt.style.use("dark_background")
fig, ax = plt.subplots(
nrows=opt.space.n_dims,
ncols=opt.space.n_dims,
figsize=(3 * opt.space.n_dims, 3 * opt.space.n_dims),
)
fig.patch.set_facecolor("#36393f")
for i in range(opt.space.n_dims):
for j in range(opt.space.n_dims):
ax[i, j].set_facecolor("#36393f")
timestr = time.strftime("%Y%m%d-%H%M%S")
plot_objective(
result_object, dimensions=list(param_ranges.keys()), fig=fig, ax=ax
)
plotpath = pathlib.Path(settings.get("plot_path", plot_path))
plotpath.mkdir(parents=True, exist_ok=True)
full_plotpath = plotpath / f"{timestr}-{iteration}.png"
plt.savefig(
full_plotpath,
pad_inches=0.1,
dpi=300,
bbox_inches="tight",
facecolor="#36393f",
)
logging.info(f"Saving a plot to {full_plotpath}.")
plt.close(fig)
point = opt.ask()
point_dict = dict(zip(param_ranges.keys(), point))
logging.info("Testing {}".format(point_dict))
engine_json = prepare_engines_json(commands=commands, fixed_params=fixed_params)
logging.debug(f"engines.json is prepared:\n{engine_json}")
write_engines_json(engine_json, point_dict)
logging.info("Start experiment")
now = datetime.now()
out_exp, out_exp_err = run_match(**settings)
later = datetime.now()
difference = (later - now).total_seconds()
logging.info(f"Experiment finished ({difference}s elapsed).")
logging.debug(f"Raw result:\n{out_exp}\n{out_exp_err}")
score, error = parse_experiment_result(out_exp, **settings)
logging.info("Got score: {} +- {}".format(score, error))
logging.info("Updating model")
while True:
try:
now = datetime.now()
# We fetch kwargs manually here to avoid collisions:
n_samples = settings.get("acq_function_samples", acq_function_samples)
gp_burnin = settings.get("gp_burnin", gp_burnin)
gp_samples = settings.get("gp_samples", gp_samples)
if opt.gp.chain_ is None:
gp_burnin = settings.get("gp_initial_burnin", gp_initial_burnin)
gp_samples = settings.get("gp_initial_samples", gp_initial_samples)
opt.tell(
point,
score,
n_samples=n_samples,
gp_samples=gp_samples,
gp_burnin=gp_burnin,
)
else:
opt.tell(
point,
score,
n_samples=n_samples,
gp_samples=gp_samples,
gp_burnin=gp_burnin,
)
later = datetime.now()
difference = (later - now).total_seconds()
logging.info(f"GP sampling finished ({difference}s)")
logging.debug(f"GP kernel: {opt.gp.kernel_}")
except ValueError:
logging.warning(
"Error encountered during fitting. Trying to sample chain a bit. "
"If this problem persists, restart the tuner to reinitialize."
)
opt.gp.sample(n_burnin=5, priors=opt.gp_priors)
else:
break
X.append(point)
y.append(score)
noise.append(error)
iteration = len(X)
with AtomicWriter(data_path, mode="wb", overwrite=True).open() as f:
np.savez_compressed(f, np.array(X), np.array(y), np.array(noise))
def test_error_on_invalid_priors():
opt = Optimizer(dimensions=[(-2.0, 2.0)], gp_priors=[], n_initial_points=0)
with pytest.raises(ValueError):
opt.tell([(0.0, )], 0.0)
def test_no_error_on_unknown_kwargs():
Optimizer(dimensions=[(-2.0, 2.0)],
n_initial_points=5,
unknown_argument=42)
