def ExpandBank():
hep = HEPBankReducedSmooth
t = np.linspace(0, 350, 3500)
t1 = cp.Uniform(0, 150)
t2 = cp.Uniform(100, 260)
t1 = cp.Normal(70, 1)
t2 = cp.Normal(115, 1)
pdf = cp.J(t1, t2)
polynomials = cp.orth_ttr(order=2, dist=pdf) #No good for dependent
# polynomials = cp.orth_bert(N=2,dist=pdf)
# polynomials = cp.orth_gs(order=2,dist=pdf)
# polynomials = cp.orth_chol(order=2,dist=pdf)
if 1:
nodes, weights = cp.generate_quadrature(order=2,
domain=pdf,
rule="Gaussian")
# nodes, weights = cp.generate_quadrature(order=2, domain=pdf, rule="C")
# nodes, weights = cp.generate_quadrature(order=9, domain=pdf, rule="L")
print nodes.shape
samples = np.array([hep(t, *node) for node in nodes.T])
hepPCE = cp.fit_quadrature(polynomials, nodes, weights, samples)
else:
nodes = pdf.sample(10, 'S')
samples = np.array([hep(t, *node) for node in nodes.T])
hepPCE = cp.fit_regression(polynomials, nodes, samples, rule='T')
return hepPCE
def __init__(self):
#inzone perm [m^2]
var0 = RandVar('normal', [np.log(1e-13), 0.5])
#above zone perm [m^2]
var1 = RandVar('normal', [np.log(5e-14), 0.5])
#inzone phi [-]
var2 = RandVar('uniform', [0.1, 0.2])
#above zone phi [-]
var3 = RandVar('uniform', [0.05, 0.3])
#aquitard thickness [m]
var4 = RandVar('uniform', [10, 30])
#injection rate [Mt/yr]
var5 = RandVar('uniform', [0.5, 5])
self.varset = [var0, var1, var2, var3, var4, var5]
self.Nvar = len(self.varset)
self.jointDist = cp.J(
cp.Normal(mu=var0.param[0], sigma=var0.param[1]),
cp.Normal(mu=var1.param[0], sigma=var1.param[1]),
cp.Uniform(lo=var2.param[0], up=var2.param[1]),
cp.Uniform(lo=var3.param[0], up=var3.param[1]),
cp.Uniform(lo=var4.param[0], up=var4.param[1]),
cp.Uniform(lo=var5.param[0], up=var5.param[1]),
)
def test_resume():
vary = {'a': cp.Uniform(-5, 0), 'b': cp.Uniform(2, 10)}
sampler = QMCSampler(vary, 100, 390)
for _ in range(10):
sample = next(sampler)
with pytest.raises(StopIteration):
next(sampler)
def getUncertainty(parametric=True, initial=False, knowledge=False):
perturbations = {
'parametric': None,
'initial': None,
'knowledge': None,
}
if parametric:
# Define Uncertainty Joint PDF
CD = cp.Uniform(-0.10, 0.10) # CD
CL = cp.Uniform(-0.10, 0.10) # CL
rho0 = cp.Normal(0, 0.0333 * 1.5) # rho0
scaleHeight = cp.Uniform(-0.025, 0.01) # scaleheight
perturbations['parametric'] = cp.J(CD, CL, rho0, scaleHeight)
if knowledge:
pitch = cp.Normal(
0, np.radians(1. / 3.)
) # Initial attitude uncertainty in angle of attack, 1-deg 3-sigma
perturbations['knowledge'] = cp.J(pitch)
if initial:
V = cp.Uniform(-150, 150) # Entry velocity deviation
gamma = cp.Normal(0,
2.0 / 3.0) # Entry FPA deviation, +- 2 deg 3-sigma
perturbations['initial'] = cp.J(V, gamma)
return perturbations
def test_SVD_equivalence(self):
systemsize = 4
eigen_decayrate = 2.0
# Create Hadmard Quadratic object
QoI = examples.HadamardQuadratic(systemsize, eigen_decayrate)
# Create the joint distribution
jdist = cp.J(cp.Uniform(-1,1),
cp.Uniform(-1,1),
cp.Uniform(-1,1),
cp.Uniform(-1,1))
active_subspace_eigen = ActiveSubspace(QoI, n_dominant_dimensions=1,
n_monte_carlo_samples=10000,
use_svd=False, read_rv_samples=False,
write_rv_samples=True)
active_subspace_eigen.getDominantDirections(QoI, jdist)
active_subspace_svd = ActiveSubspace(QoI, n_dominant_dimensions=1,
n_monte_carlo_samples=10000,
use_svd=True, read_rv_samples=True,
write_rv_samples=False)
active_subspace_svd.getDominantDirections(QoI, jdist)
# Check the iso_eigenvals
np.testing.assert_almost_equal(active_subspace_eigen.iso_eigenvals, active_subspace_svd.iso_eigenvals)
# check the iso_eigenvecs
self.assertTrue(active_subspace_eigen.iso_eigenvecs.shape, active_subspace_svd.iso_eigenvecs.shape)
for i in range(active_subspace_eigen.iso_eigenvecs.shape[1]):
arr1 = active_subspace_eigen.iso_eigenvecs[:,i]
arr2 = active_subspace_svd.iso_eigenvecs[:,i]
if np.allclose(arr1, arr2) == False:
np.testing.assert_almost_equal(arr1, -arr2)
def test_ordered(self):
parameter_list = [["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_K", 36, cp.Normal(36, 1)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
uncertain_parameters = parameters.get_from_uncertain("name")
self.assertEqual(uncertain_parameters, ["gbar_Na", "gbar_K", "gbar_L"])
uncertain_parameters = parameters.get("name")
self.assertEqual(uncertain_parameters, ["gbar_Na", "gbar_K", "gbar_L"])
parameter_list = [["gbar_K", 36, cp.Normal(36, 1)],
["gbar_Na", 120,
cp.Uniform(110, 130)],
["gbar_L", 0.3, cp.Chi(1, 1, 0.3)]]
parameters = Parameters(parameter_list)
uncertain_parameters = parameters.get_from_uncertain("name")
self.assertEqual(uncertain_parameters, ["gbar_K", "gbar_Na", "gbar_L"])
uncertain_parameters = parameters.get("name")
self.assertEqual(uncertain_parameters, ["gbar_K", "gbar_Na", "gbar_L"])
uncertain_parameters = parameters.get("value")
self.assertEqual(uncertain_parameters, [36, 120, 0.3])
def data_vectors():
np.random.seed(10000000)
vary = {"x1": cp.Uniform(0.0, 1.0), "x2": cp.Uniform(0.0, 1.0)}
sampler = uq.sampling.MCSampler(vary, n_mc_samples=100)
data = {
('run_id', 0): [],
('x1', 0): [],
('x2', 0): [],
('g', 0): [],
('g', 1): [],
('g', 2): [],
('h', 0): [],
('h', 1): []
}
for run_id, sample in enumerate(sampler):
data[('run_id', 0)].append(run_id)
data[('x1', 0)].append(sample['x1'])
data[('x2', 0)].append(sample['x2'])
data[('g', 0)].append(sample['x1'])
data[('g', 1)].append(sample['x2'])
data[('g', 2)].append(sample['x1'] + sample['x2'])
data[('h', 0)].append(sample['x1'] * sample['x2'])
data[('h', 1)].append(sample['x1']**sample['x2'])
df = pd.DataFrame(data)
return sampler, df
def testCuba():
from cubature import cubature as cuba
CD = cp.Uniform(-0.10, 0.10) # CD
CL = cp.Uniform(-0.10, 0.10) # CL
rho0 = cp.Normal(0, 0.0333) # rho0
scaleHeight = cp.Uniform(-0.05, 0.05) # scaleheight
pdf = cp.J(CD, CL, rho0, scaleHeight)
def PDF(x, *args, **kwargs):
return pdf.pdf(np.array(x).T)
x0 = np.array([-0.10, -0.10, -0.5, -0.05])
xf = np.array([0.10, 0.10, 0.5, 0.05])
P, err = cuba(PDF,
ndim=4,
fdim=1,
xmin=x0,
xmax=xf,
vectorized=True,
adaptive='p')
print "Multi-dimensional integral of the PDF over its support = {}".format(
P[0])
print "Total error in integration = {}".format(err[0])
def halton_sequence(w, h, n):
distribution = chaospy.J(chaospy.Uniform(0, w), chaospy.Uniform(0, h))
samples = distribution.sample(n, rule="halton")
x_samples = samples[0] + np.random.uniform(0, 1, n)
y_samples = samples[1] + np.random.uniform(0, 1, n)
return np.clip(x_samples, 0, w), np.clip(y_samples, 0, h)
def test_lhc():
vary = {'a': cp.Uniform(-5, 3), 'b': cp.Uniform(2, 10)}
sampler = uq.sampling.quasirandom.LHCSampler(vary, max_num=10)
for sample in sampler:
assert (sample['a'] >= -5.0)
assert (sample['a'] <= 3.0)
assert (sample['b'] >= 2.0)
assert (sample['b'] <= 10.0)
def test_constant_expected():
"""Test if polynomial constant behave as expected."""
distribution = chaospy.J(chaospy.Uniform(-1.2, 1.2),
chaospy.Uniform(-2.0, 2.0))
const = chaospy.polynomial(7.)
assert chaospy.E(const, distribution[0]) == const
assert chaospy.E(const, distribution) == const
assert chaospy.Var(const, distribution) == 0.
def test_restart_dict():
vary = {'a': cp.Uniform(-5, 0), 'b': cp.Uniform(2, 10)}
sampler = QMCSampler(vary, 100)
for _ in range(10):
next(sampler)
restart = sampler.get_restart_dict()
assert(restart['vary'] == Vary(vary).serialize())
assert(restart['count'] == 10)
assert(restart['n_mc_samples'] == 100)
def test_halton():
vary = {'a': cp.Uniform(-5, 3), 'b': cp.Uniform(2, 10)}
sampler = uq.sampling.quasirandom.HaltonSampler(vary, max_num=10)
for sample in sampler:
assert (sample['a'] >= -5.0)
assert (sample['a'] <= 3.0)
assert (sample['b'] >= 2.0)
assert (sample['b'] <= 10.0)
assert (sampler.n_samples() == 10)
def test_l_n_exception():
vary = {
"gravity": cp.Uniform(9.8, 1.0),
"mass": cp.Uniform(2.0, 10.0),
}
with pytest.raises(RuntimeError):
sampler = uq.sampling.SCSampler(vary=vary,
polynomial_order=1,
sparse=True)
def setup_cannonsim_app():
params = {
"angle": {
"type": "float",
"min": 0.0,
"max": 6.28,
"default": 0.79},
"air_resistance": {
"type": "float",
"min": 0.0,
"max": 1.0,
"default": 0.2},
"height": {
"type": "float",
"min": 0.0,
"max": 1000.0,
"default": 1.0},
"time_step": {
"type": "float",
"min": 0.0001,
"max": 1.0,
"default": 0.01},
"gravity": {
"type": "float",
"min": 0.0,
"max": 1000.0,
"default": 9.8},
"mass": {
"type": "float",
"min": 0.0001,
"max": 1000.0,
"default": 1.0},
"velocity": {
"type": "float",
"min": 0.0,
"max": 1000.0,
"default": 10.0}}
encoder = uq.encoders.GenericEncoder(
template_fname='tests/cannonsim/test_input/cannonsim.template',
delimiter='#',
target_filename='in.cannon')
decoder = uq.decoders.SimpleCSV(
target_filename='output.csv', output_columns=[
'Dist', 'lastvx', 'lastvy'], header=0)
collater = uq.collate.AggregateSamples(average=False)
vary = {
"gravity": cp.Uniform(9.8, 1.0),
"mass": cp.Uniform(2.0, 10.0),
}
cannon_sampler = uq.sampling.RandomSampler(vary=vary, max_num=5)
cannon_action = uq.actions.ExecuteLocal("tests/cannonsim/bin/cannonsim in.cannon output.csv")
cannon_stats = uq.analysis.BasicStats(qoi_cols=['Dist', 'lastvx', 'lastvy'])
return params, encoder, decoder, collater, cannon_sampler, cannon_action, cannon_stats
def test_sampling():
vary = {'a': cp.Uniform(-5, 0), 'b': cp.Uniform(2, 10)}
sampler = MCSampler(vary, 100)
assert (sampler.n_samples() == 400)
for _ in range(sampler.n_samples()):
sample = next(sampler)
assert (sample['a'] >= -5 and sample['a'] <= 0)
assert (sample['b'] >= 2 and sample['b'] <= 10)
with pytest.raises(StopIteration):
next(sampler)
def test_2():
"""Return test 2."""
p_gc_legendre_two = partial(quadrature_gauss_legendre_two, a=0, b=1)
approaches = []
approaches += [monte_carlo_naive_two_dimensions, monte_carlo_quasi_two_dimensions]
approaches += [p_gc_legendre_two]
distribution = cp.J(cp.Uniform(0, 1), cp.Uniform(0, 1))
for approach in approaches:
np.testing.assert_almost_equal(approach(distribution.pdf), 1.0)
def test_init_object_dist(self):
parameter_list = [Parameter("gbar_Na", 120, cp.Uniform(110, 130)),
Parameter("gbar_K", 36),
Parameter("gbar_L", 10.3)]
parameters = Parameters(parameter_list, distribution=cp.Uniform(110, 130))
self.assertIsInstance(parameters, Parameters)
self.assertIsInstance(parameters["gbar_Na"], Parameter)
self.assertIsInstance(parameters["gbar_K"], Parameter)
self.assertIsInstance(parameters["gbar_L"], Parameter)
self.assertIsInstance(parameters.distribution, cp.Dist)
def test_on_exponential(self):
systemsize = 2
QoI = examples.Exp_07xp03y(systemsize)
jdist = cp.J(cp.Uniform(-1,1),
cp.Uniform(-1,1))
active_subspace = ActiveSubspace(QoI, n_dominant_dimensions=1, n_monte_carlo_samples=10000)
active_subspace.getDominantDirections(QoI, jdist)
expected_W1 = QoI.a / np.linalg.norm(QoI.a)
np.testing.assert_almost_equal(active_subspace.dominant_dir[:,0], expected_W1)
def test_get_active_sampler(tmp_path):
camp = uq.Campaign(name='test', work_dir=tmp_path)
vary = {
"angle": cp.Uniform(0.0, 1.0),
"height": cp.Uniform(2.0, 10.0),
"velocity": cp.Normal(10.0, 1.0),
"mass": cp.Uniform(1.0, 5.0)
}
sampler = uq.sampling.RandomSampler(vary=vary)
camp.set_sampler(sampler)
assert camp.get_active_sampler() == sampler
def settings(tmpdir):
params = {
"temp_init": {
"type": "float",
"min": 0.0,
"max": 100.0,
"default": 95.0
},
"kappa": {
"type": "float",
"min": 0.0,
"max": 0.1,
"default": 0.025
},
"t_env": {
"type": "float",
"min": 0.0,
"max": 40.0,
"default": 15.0
},
"out_file": {
"type": "string",
"default": "output.csv"
}
}
output_filename = params["out_file"]["default"]
output_columns = ["te"]
encoder = uq.encoders.GenericEncoder(
template_fname='tests/cooling/cooling.template',
delimiter='$',
target_filename='cooling_in.json')
decoder = uq.decoders.SimpleCSV(target_filename=output_filename,
output_columns=output_columns)
vary = {"kappa": cp.Uniform(0.025, 0.075), "t_env": cp.Uniform(15, 25)}
cooling_sampler = uq.sampling.PCESampler(vary=vary, polynomial_order=3)
cooling_stats = uq.analysis.PCEAnalysis(sampler=cooling_sampler,
qoi_cols=output_columns)
settings = {
'params': params,
'encoder': encoder,
'decoder': decoder,
'cooling_sampler': cooling_sampler,
'cooling_stats': cooling_stats
}
return settings
def get_joint_uniform_distribution(dim, lower=0, upper=1):
if dim == 1:
return cp.Uniform(lower, upper)
elif dim == 2:
return cp.J(cp.Uniform(lower, upper), cp.Uniform(lower, upper))
elif dim == 3:
return cp.J(cp.Uniform(lower, upper), cp.Uniform(lower, upper),
cp.Uniform(lower, upper))
elif dim == 4:
return cp.J(cp.Uniform(lower, upper), cp.Uniform(lower, upper),
cp.Uniform(lower, upper), cp.Uniform(lower, upper))
else:
print("Wrong input dimension")
return None
def run_sc_samples(work_dir):
# Set up a fresh campaign called "sc"
my_campaign = uq.Campaign(name='ocean', work_dir=work_dir)
# Define parameter space
params = {
"decay_time_nu": {
"type": "float",
"min": 0.0,
"max": 1000.0,
"default": 5.0},
"decay_time_mu": {
"type": "float",
"min": 0.0,
"max": 1000.0,
"default": 90.0},
"out_file": {
"type": "string",
"default": "output.csv"}}
output_filename = params["out_file"]["default"]
output_columns = ["E_mean", "Z_mean", "E_std", "Z_std"]
# Create an encoder, decoder and collation element for PCE test app
encoder = uq.encoders.GenericEncoder(
template_fname= HOME + '/sc/ocean.template',
delimiter='$',
target_filename='ocean_in.json')
decoder = uq.decoders.SimpleCSV(target_filename=output_filename,
output_columns=output_columns,
header=0)
collater = uq.collate.AggregateSamples(average=False)
# Add the SC app (automatically set as current app)
my_campaign.add_app(name="sc",
params=params,
encoder=encoder,
decoder=decoder,
collater=collater)
# Create the sampler
vary = {
"decay_time_nu": cp.Uniform(1.0, 5.0),
"decay_time_mu": cp.Uniform(85.0, 95.0)
}
my_sampler = uq.sampling.SCSampler(vary=vary, polynomial_order=6)
# Associate the sampler with the campaign
my_campaign.set_sampler(my_sampler)
def test_gp(tmp_path):
campaign = uq.Campaign(name='test', work_dir=tmp_path)
params = {
"temp_init": {
"type": "float",
"min": 0.0,
"max": 100.0,
"default": 95.0
},
"kappa": {
"type": "float",
"min": 0.0,
"max": 0.1,
"default": 0.025
},
"t_env": {
"type": "float",
"min": 0.0,
"max": 40.0,
"default": 15.0
},
"out_file": {
"type": "string",
"default": "output.csv"
}
}
output_filename = params["out_file"]["default"]
output_columns = ["te"]
# Create an encoder and decoder for PCE test app
encoder = uq.encoders.GenericEncoder(
template_fname='tests/cooling/cooling.template',
delimiter='$',
target_filename='cooling_in.json')
decoder = uq.decoders.SimpleCSV(target_filename=output_filename,
output_columns=output_columns)
execute = ExecuteLocal("{} cooling_in.json".format(
os.path.abspath("tests/cooling/cooling_model.py")))
actions = Actions(CreateRunDirectory('/tmp'), Encode(encoder), execute,
Decode(decoder))
vary = {"kappa": cp.Uniform(0.025, 0.075), "t_env": cp.Uniform(15, 25)}
sampler = uq.sampling.quasirandom.LHCSampler(vary=vary)
campaign.add_app(name='test_app', params=params, actions=actions)
campaign.set_app('test_app')
campaign.set_sampler(sampler)
campaign.execute(nsamples=100).collate()
df = campaign.get_collation_result()
analysis = uq.analysis.gp_analyse.GaussianProcessSurrogate(
['kappa', 't_env'], ['te'])
result = analysis.analyse(df)
def data():
# fix random seed to make this test deterministic
np.random.seed(10000000)
# Create the sampler
vary = {"x1": cp.Uniform(0.0, 1.0), "x2": cp.Uniform(0.0, 1.0)}
sampler = uq.sampling.SCSampler(vary)
data = {('run_id', 0): [], ('x1', 0): [], ('x2', 0): [], ('f', 0): []}
for run_id, sample in enumerate(sampler):
data[('run_id', 0)].append(run_id)
data[('x1', 0)].append(sample['x1'])
data[('x2', 0)].append(sample['x2'])
data[('f', 0)].append(sobol_g_func([sample['x1'], sample['x2']], d=2))
df = pd.DataFrame(data)
return sampler, df
def setup_params_dist(icestupa, params):
params_range = []
for param in params:
y_lim = get_parameter_metadata(param)['ylim']
if param in ['r_F', 'D_F']:
param_range = cp.Uniform(
getattr(icestupa, param) * y_lim[0],
getattr(icestupa, param) * y_lim[1])
else:
param_range = cp.Uniform(y_lim[0], y_lim[1])
params_range.append(param_range)
print("\t%s : %s\n" % (param, param_range))
tuned_params = {params[i]: params_range[i] for i in range(len(params))}
return tuned_params
def test_dependent_density():
"""Assert that manually create dependency structure holds."""
distribution1 = chaospy.Exponential(1)
distribution2 = chaospy.Uniform(lower=0, upper=distribution1)
distribution = chaospy.J(distribution1, distribution2)
assert distribution.pdf([0.5, 0.6]) == 0
assert distribution.pdf([0.5, 0.4]) > 0
def distribution(parameter):
if parameter == 0:
raise ValueError(
"Creating a percentage distribution around 0 does not work")
return cp.Uniform(parameter - abs(interval / 2. * parameter),
parameter + abs(interval / 2. * parameter))
def test_str_uncertain(self):
self.parameter = Parameter("gbar_Na", 120, cp.Uniform(110, 130))
result = str(self.parameter)
self.assertEqual(result, "gbar_Na: 120 - Uncertain")
def test_sc(tmpdir, campaign):
params = {
"Pe": {
"type": "float",
"min": "1.0",
"max": "2000.0",
"default": "100.0"
},
"f": {
"type": "float",
"min": "0.0",
"max": "10.0",
"default": "1.0"
},
"out_file": {
"type": "string",
"default": "output.csv"
}
}
output_filename = params["out_file"]["default"]
output_columns = ["u"]
encoder = uq.encoders.GenericEncoder(
template_fname=f'tests/sc/sc.template',
delimiter='$',
target_filename='sc_in.json')
decoder = uq.decoders.SimpleCSV(target_filename=output_filename,
output_columns=output_columns,
header=0)
collater = uq.collate.AggregateSamples(average=False)
vary = {"Pe": cp.Uniform(100.0, 200.0), "f": cp.Normal(1.0, 0.1)}
sampler = uq.sampling.SCSampler(vary=vary, polynomial_order=1)
actions = uq.actions.ExecuteLocal(f"tests/sc/sc_model.py sc_in.json")
stats = uq.analysis.SCAnalysis(sampler=sampler, qoi_cols=output_columns)
campaign(tmpdir, 'sc', 'sc', params, encoder, decoder, sampler, collater,
actions, stats, vary, 0, 1)