def test_region_est_ellipsoid(self):
"""
Tests that region_est_ellipsoid works.
"""
dist = MultivariateNormalDistribution(self.MEAN, self.COV)
# the model is irrelevant; we just want the updater to have some particles
# with the desired normal distribution.
u = SMCUpdater(MockModel(4), self.N_PARTICLES, dist)
# ask for a confidence level of 0.5
A, c = u.region_est_ellipsoid(level=0.5)
# center of ellipse should be the mean of the multinormal
assert_almost_equal(np.round(c), self.MEAN, 1)
# finally, the principal lengths of the ellipsoid
# should be the same as COV
_, QA, _ = np.linalg.svd(A)
_, QC, _ = np.linalg.svd(self.COV)
QA, QC = np.sqrt(QA), np.sqrt(QC)
assert_almost_equal(
QA / np.linalg.norm(QA),
QC / np.linalg.norm(QC),
1
)
def setUp(self):
super(TestSMCUpdater, self).setUp()
self.precession_model = SimplePrecessionModel()
self.num_precession_model = NumericalSimplePrecessionModel()
self.expparams = TestSMCUpdater.TEST_EXPPARAMS.reshape(-1, 1)
self.outcomes = self.precession_model.simulate_experiment(
TestSMCUpdater.MODELPARAMS,
TestSMCUpdater.TEST_EXPPARAMS,
repeat=1).reshape(-1, 1)
self.updater = SMCUpdater(self.precession_model,
TestSMCUpdater.N_PARTICLES,
TestSMCUpdater.PRIOR)
self.updater_bayes = SMCUpdaterBCRB(self.precession_model,
TestSMCUpdater.N_PARTICLES,
TestSMCUpdater.PRIOR,
adaptive=True)
self.num_updater = SMCUpdater(self.num_precession_model,
TestSMCUpdater.N_PARTICLES,
TestSMCUpdater.PRIOR)
self.num_updater_bayes = SMCUpdaterBCRB(self.num_precession_model,
TestSMCUpdater.N_PARTICLES,
TestSMCUpdater.PRIOR,
adaptive=True)
def perf_test(
model, n_particles, prior,
n_exp, heuristic_class,
true_model=None, true_prior=None
):
"""
Runs a trial of using SMC to estimate the parameters of a model, given a
number of particles, a prior distribution and an experiment design
heuristic.
:param qinfer.Model model: Model whose parameters are to
be estimated.
:param int n_particles: Number of SMC particles to use.
:param qinfer.Distribution prior: Prior to use in selecting
SMC particles.
:param int n_exp: Number of experimental data points to draw from the
model.
:param qinfer.Heuristic heuristic_class: Constructor function
for the experiment design heuristic to be used.
:param qinfer.Model true_model: Model to be used in
generating experimental data. If ``None``, assumed to be ``model``.
:param qinfer.Distribution true_prior: Prior to be used in
selecting the true model parameters. If ``None``, assumed to be
``prior``.
:rtype np.ndarray: See :ref:`perf_testing_struct` for more details on
the type returned by this function.
:return: A record array of performance metrics, indexed by the number
of experiments performed.
"""
if true_model is None:
true_model = model
if true_prior is None:
true_prior = prior
true_mps = true_prior.sample()
performance = np.zeros((n_exp,), dtype=PERFORMANCE_DTYPE)
updater = SMCUpdater(model, n_particles, prior)
heuristic = heuristic_class(updater)
for idx_exp in xrange(n_exp):
expparams = heuristic()
datum = true_model.simulate_experiment(true_mps, expparams)
with timing() as t:
updater.update(datum, expparams)
delta = updater.est_mean() - true_mps
performance[idx_exp]['elapsed_time'] = t.delta_t
performance[idx_exp]['loss'] = np.dot(model.Q, delta**2)
performance[idx_exp]['resample_count'] = updater.resample_count
return performance
def main():
m = SimpleMacroModel()
prior = UniformDistribution([[0, 1], [0, 1]])
u = SMCUpdater(m, 1000, prior)
modelparams = prior.sample()
expparams = np.array([(12.0,)], dtype=m.expparams_dtype)
datum = m.simulate_experiment(modelparams, expparams)
print datum
u.update(datum, expparams)
print u.est_mean()
print m.call_count
def setUp(self):
super(TestBayesRisk, self).setUp()
# Set up relevant models.
self.coin_model = CoinModel()
self.binomial_model = BinomialModel(self.coin_model)
# Set up updaters for these models using particle approximations
# of conjugate priors
self.updater_binomial = SMCUpdater(self.binomial_model,
TestBayesRisk.N_PARTICLES,
TestBayesRisk.PRIOR_BETA)
def setUp(self): super(TestSMCUpdater,self).setUp() self.precession_model = SimplePrecessionModel() self.num_precession_model = NumericalSimplePrecessionModel() self.expparams = TestSMCUpdater.TEST_EXPPARAMS.reshape(-1,1) self.outcomes = self.precession_model.simulate_experiment(TestSMCUpdater.MODELPARAMS, TestSMCUpdater.TEST_EXPPARAMS,repeat=1 ).reshape(-1,1) self.updater = SMCUpdater(self.precession_model, TestSMCUpdater.N_PARTICLES,TestSMCUpdater.PRIOR) self.updater_bayes = SMCUpdaterBCRB(self.precession_model, TestSMCUpdater.N_PARTICLES,TestSMCUpdater.PRIOR,adaptive=True) self.num_updater = SMCUpdater(self.num_precession_model, TestSMCUpdater.N_PARTICLES,TestSMCUpdater.PRIOR) self.num_updater_bayes = SMCUpdaterBCRB(self.num_precession_model, TestSMCUpdater.N_PARTICLES,TestSMCUpdater.PRIOR,adaptive=True)
def do_update(model, n_particles, prior, outcomes, expparams, return_all, resampler=None):
updater = SMCUpdater(model, n_particles, prior,
resampler=resampler
)
updater.batch_update(outcomes, expparams, resample_interval=1)
mean = updater.est_mean()
cov = updater.est_covariance_mtx()
if model.n_modelparams == 1:
mean = mean[0]
cov = cov[0, 0]
if not return_all:
return mean, cov
else:
return mean, cov, {
'updater': updater
}
def test_region_est_hull(self):
"""
Tests that test_region_est_hull works
"""
dist = MultivariateNormalDistribution(self.MEAN, self.COV)
# the model is irrelevant; we just want the updater to have some particles
# with the desired normal distribution.
u = SMCUpdater(MockModel(self.N_MPS), self.N_PARTICLES, dist)
faces, vertices = u.region_est_hull(level=0.95)
# In this multinormal case, the convex hull surface
# should be centered at MEAN
assert_almost_equal(np.round(np.mean(vertices, axis=0)),
np.round(self.MEAN))
# And a lower level should result in a smaller hull
# and therefore smaller sample variance
faces2, vertices2 = u.region_est_hull(level=0.2)
assert_array_less(np.var(vertices2, axis=0), np.var(vertices, axis=0))
def setUp(self):
super(TestInformationGain,self).setUp()
# Set up relevant models.
self.coin_model = CoinModel()
self.binomial_model = BinomialModel(self.coin_model)
# Set up updaters for these models using particle approximations
# of conjugate priors
self.updater_binomial = SMCUpdater(self.binomial_model,
TestInformationGain.N_PARTICLES,TestInformationGain.PRIOR_BETA)
def test_region_est_hull(self):
"""
Tests that test_region_est_hull works
"""
dist = MultivariateNormalDistribution(self.MEAN, self.COV)
# the model is irrelevant; we just want the updater to have some particles
# with the desired normal distribution.
u = SMCUpdater(MockModel(self.N_MPS), self.N_PARTICLES, dist)
faces, vertices = u.region_est_hull(level=0.95)
# In this multinormal case, the convex hull surface
# should be centered at MEAN
assert_almost_equal(
np.round(np.mean(vertices, axis=0)),
np.round(self.MEAN)
)
# And a lower level should result in a smaller hull
# and therefore smaller sample variance
faces2, vertices2 = u.region_est_hull(level=0.2)
assert_array_less(np.var(vertices2, axis=0), np.var(vertices, axis=0))
def setUp(self):
super(TestFisherInformation, self).setUp()
# Set up relevant models.
self.coin_model = CoinModel()
self.binomial_model = DifferentiableBinomialModel(self.coin_model)
# Set up updaters for these models using particle approximations
# of conjugate priors
self.updater_binomial = SMCUpdater(self.binomial_model,
TestFisherInformation.N_PARTICLES,
TestFisherInformation.PRIOR_BETA)
def test_est_credible_region(self):
"""
Tests that est_credible_region doesn't fail miserably
"""
dist = MultivariateNormalDistribution(self.MEAN, self.COV)
# the model is irrelevant; we just want the updater to have some particles
# with the desired normal distribution.
u = SMCUpdater(MockModel(self.N_MPS), self.N_PARTICLES, dist)
# first check that 0.95 confidence points consume 0.9 confidence points
points1 = u.est_credible_region(level=0.95)
points2 = u.est_credible_region(level=0.9)
assert_almost_equal(
np.sort(unique_rows(np.concatenate([points1, points2])), axis=0),
np.sort(points1, axis=0)
)
# do the same thing with different slice
points1 = u.est_credible_region(level=0.95, modelparam_slice=self.SLICE)
points2 = u.est_credible_region(level=0.9, modelparam_slice=self.SLICE)
assert_almost_equal(
np.sort(unique_rows(np.concatenate([points1, points2])), axis=0),
np.sort(points1, axis=0)
)
def main():
m = SimpleMacroModel()
prior = UniformDistribution([[0, 1], [0, 1]])
u = SMCUpdater(m, 1000, prior)
modelparams = prior.sample()
expparams = np.array([(12.0, )], dtype=m.expparams_dtype)
datum = m.simulate_experiment(modelparams, expparams)
print datum
u.update(datum, expparams)
print u.est_mean()
print m.call_count
class TestInformationGain(DerandomizedTestCase):
# Test the implementation of numerical information gain by comparing to
# numbers which were derived by doing analytic/numeric
# integrals of simple models (binomialm, poisson, and gaussian) in
# Mathematica. This test trusts that these calculations
# were done correctly.
ALPHA = 1
BETA = 3
PRIOR_BETA = BetaDistribution(alpha=ALPHA, beta=BETA)
N_PARTICLES = 10000
# Calculated in Mathematica, IG for the binomial model and the given expparams
NMEAS_EXPPARAMS = np.arange(1, 11, dtype=int)
BINOM_IG = np.array([
0.104002, 0.189223, 0.261496, 0.324283, 0.379815, 0.429613, 0.474764,
0.516069, 0.554138, 0.589446
])
def setUp(self):
super(TestInformationGain, self).setUp()
# Set up relevant models.
self.coin_model = CoinModel()
self.binomial_model = BinomialModel(self.coin_model)
# Set up updaters for these models using particle approximations
# of conjugate priors
self.updater_binomial = SMCUpdater(self.binomial_model,
TestInformationGain.N_PARTICLES,
TestInformationGain.PRIOR_BETA)
def test_finite_outcomes_ig(self):
# The binomial model has a finite number of outcomes. Test the
# ig calculation in this case.
expparams = self.NMEAS_EXPPARAMS.astype(
self.binomial_model.expparams_dtype)
# estimate the information gain
est_ig = self.updater_binomial.expected_information_gain(expparams)
# see if they roughly match
assert_almost_equal(est_ig, TestInformationGain.BINOM_IG, decimal=2)
class TestBayesRisk(DerandomizedTestCase):
# Test the implementation of numerical Bayes Risk by comparing to
# numbers which were derived by doing analytic/numeric
# integrals of simple models in Mathematica. This test trusts that
# these calculations were done correctly.
ALPHA = 1.
BETA = 3.
PRIOR_BETA = BetaDistribution(alpha=ALPHA, beta=BETA)
N_PARTICLES = 10000
NMEAS_EXPPARAMS = np.arange(1, 11, dtype=int)
def setUp(self):
super(TestBayesRisk, self).setUp()
# Set up relevant models.
self.coin_model = CoinModel()
self.binomial_model = BinomialModel(self.coin_model)
# Set up updaters for these models using particle approximations
# of conjugate priors
self.updater_binomial = SMCUpdater(self.binomial_model,
TestBayesRisk.N_PARTICLES,
TestBayesRisk.PRIOR_BETA)
def test_finite_outcomes_risk(self):
# The binomial model has a finite number of outcomes. Test the
# risk calculation in this case.
expparams = self.NMEAS_EXPPARAMS.astype(
self.binomial_model.expparams_dtype)
# estimate the risk
est_risk = self.updater_binomial.bayes_risk(expparams)
# compute exact risk
a, b = TestBayesRisk.ALPHA, TestBayesRisk.BETA
exact_risk = a * b / ((a + b) * (a + b + 1) *
(a + b + expparams['n_meas']))
# see if they roughly match
assert_almost_equal(est_risk, exact_risk, decimal=3)
class TestInformationGain(DerandomizedTestCase):
# Test the implementation of numerical information gain by comparing to
# numbers which were derived by doing analytic/numeric
# integrals of simple models (binomialm, poisson, and gaussian) in
# Mathematica. This test trusts that these calculations
# were done correctly.
ALPHA = 1
BETA = 3
PRIOR_BETA = BetaDistribution(alpha=ALPHA, beta=BETA)
N_PARTICLES = 10000
# Calculated in Mathematica, IG for the binomial model and the given expparams
NMEAS_EXPPARAMS = np.arange(1, 11, dtype=int)
BINOM_IG = np.array([0.104002,0.189223,0.261496,0.324283,0.379815,0.429613,0.474764,0.516069,0.554138,0.589446])
def setUp(self):
super(TestInformationGain,self).setUp()
# Set up relevant models.
self.coin_model = CoinModel()
self.binomial_model = BinomialModel(self.coin_model)
# Set up updaters for these models using particle approximations
# of conjugate priors
self.updater_binomial = SMCUpdater(self.binomial_model,
TestInformationGain.N_PARTICLES,TestInformationGain.PRIOR_BETA)
def test_finite_outcomes_ig(self):
# The binomial model has a finite number of outcomes. Test the
# ig calculation in this case.
expparams = self.NMEAS_EXPPARAMS.astype(self.binomial_model.expparams_dtype)
# estimate the information gain
est_ig = self.updater_binomial.expected_information_gain(expparams)
# see if they roughly match
assert_almost_equal(est_ig, TestInformationGain.BINOM_IG, decimal=2)
class TestBayesRisk(DerandomizedTestCase):
# Test the implementation of numerical Bayes Risk by comparing to
# numbers which were derived by doing analytic/numeric
# integrals of simple models in Mathematica. This test trusts that
# these calculations were done correctly.
ALPHA = 1.
BETA = 3.
PRIOR_BETA = BetaDistribution(alpha=ALPHA, beta=BETA)
N_PARTICLES = 10000
NMEAS_EXPPARAMS = np.arange(1, 11, dtype=int)
def setUp(self):
super(TestBayesRisk,self).setUp()
# Set up relevant models.
self.coin_model = CoinModel()
self.binomial_model = BinomialModel(self.coin_model)
# Set up updaters for these models using particle approximations
# of conjugate priors
self.updater_binomial = SMCUpdater(self.binomial_model,
TestBayesRisk.N_PARTICLES,TestBayesRisk.PRIOR_BETA)
def test_finite_outcomes_risk(self):
# The binomial model has a finite number of outcomes. Test the
# risk calculation in this case.
expparams = self.NMEAS_EXPPARAMS.astype(self.binomial_model.expparams_dtype)
# estimate the risk
est_risk = self.updater_binomial.bayes_risk(expparams)
# compute exact risk
a, b = TestBayesRisk.ALPHA, TestBayesRisk.BETA
exact_risk = a * b / ((a + b) * (a + b + 1) * (a + b + expparams['n_meas']))
# see if they roughly match
assert_almost_equal(est_risk, exact_risk, decimal=3)
def do_update(model, n_particles, prior, outcomes, expparams, return_all, resampler=None):
updater = SMCUpdater(model, n_particles, prior,
resampler=resampler
)
updater.batch_update(outcomes, expparams, resample_interval=1)
mean = updater.est_mean()
cov = updater.est_covariance_mtx()
if model.n_modelparams == 1:
mean = mean[0]
cov = cov[0, 0]
if not return_all:
return mean, cov
else:
return mean, cov, {
'updater': updater
}
def test_est_credible_region(self):
"""
Tests that est_credible_region doesn't fail miserably
"""
dist = MultivariateNormalDistribution(self.MEAN, self.COV)
# the model is irrelevant; we just want the updater to have some particles
# with the desired normal distribution.
u = SMCUpdater(MockModel(self.N_MPS), self.N_PARTICLES, dist)
# first check that 0.95 confidence points consume 0.9 confidence points
points1 = u.est_credible_region(level=0.95)
points2 = u.est_credible_region(level=0.9)
assert_almost_equal(
np.sort(unique_rows(np.concatenate([points1, points2])), axis=0),
np.sort(points1, axis=0))
# do the same thing with different slice
points1 = u.est_credible_region(level=0.95,
modelparam_slice=self.SLICE)
points2 = u.est_credible_region(level=0.9, modelparam_slice=self.SLICE)
assert_almost_equal(
np.sort(unique_rows(np.concatenate([points1, points2])), axis=0),
np.sort(points1, axis=0))
class TestSMCUpdater(DerandomizedTestCase):
# True model parameter for test
MODELPARAMS = np.array([
1,
])
TEST_EXPPARAMS = np.linspace(1., 10., 100, dtype=np.float)
PRIOR = UniformDistribution([[0, 2]])
N_PARTICLES = 10000
TEST_TARGET_COV = np.array([[0.01]])
def setUp(self):
super(TestSMCUpdater, self).setUp()
self.precession_model = SimplePrecessionModel()
self.num_precession_model = NumericalSimplePrecessionModel()
self.expparams = TestSMCUpdater.TEST_EXPPARAMS.reshape(-1, 1)
self.outcomes = self.precession_model.simulate_experiment(
TestSMCUpdater.MODELPARAMS,
TestSMCUpdater.TEST_EXPPARAMS,
repeat=1).reshape(-1, 1)
self.updater = SMCUpdater(self.precession_model,
TestSMCUpdater.N_PARTICLES,
TestSMCUpdater.PRIOR)
self.updater_bayes = SMCUpdaterBCRB(self.precession_model,
TestSMCUpdater.N_PARTICLES,
TestSMCUpdater.PRIOR,
adaptive=True)
self.num_updater = SMCUpdater(self.num_precession_model,
TestSMCUpdater.N_PARTICLES,
TestSMCUpdater.PRIOR)
self.num_updater_bayes = SMCUpdaterBCRB(self.num_precession_model,
TestSMCUpdater.N_PARTICLES,
TestSMCUpdater.PRIOR,
adaptive=True)
def test_smc_fitting(self):
"""
Checks that the fitters converge on true value on simple precession_model. Is a stochastic
test but I ran 100 times and there were no fails, with these parameters.
"""
self.updater.batch_update(self.outcomes, self.expparams)
self.updater_bayes.batch_update(self.outcomes, self.expparams)
self.num_updater.batch_update(self.outcomes, self.expparams)
self.num_updater_bayes.batch_update(self.outcomes, self.expparams)
#Assert that models have learned true model parameters from data
#test means
assert_almost_equal(self.updater.est_mean(),
TestSMCUpdater.MODELPARAMS, 2)
assert_almost_equal(self.updater_bayes.est_mean(),
TestSMCUpdater.MODELPARAMS, 2)
assert_almost_equal(self.num_updater.est_mean(),
TestSMCUpdater.MODELPARAMS, 2)
assert_almost_equal(self.num_updater_bayes.est_mean(),
TestSMCUpdater.MODELPARAMS, 2)
#Assert that covariances have been reduced below thresholds
#test covs
assert_array_less(self.updater.est_covariance_mtx(),
TestSMCUpdater.TEST_TARGET_COV)
assert_array_less(self.updater_bayes.est_covariance_mtx(),
TestSMCUpdater.TEST_TARGET_COV)
assert_array_less(self.num_updater.est_covariance_mtx(),
TestSMCUpdater.TEST_TARGET_COV)
assert_array_less(self.num_updater_bayes.est_covariance_mtx(),
TestSMCUpdater.TEST_TARGET_COV)
def test_bim(self):
"""
Checks that the fitters converge on true value on simple precession_model. Is a stochastic
test but I ran 100 times and there were no fails, with these parameters.
"""
bim_currents = []
num_bim_currents = []
bim_adaptives = []
num_bim_adaptives = []
#track bims throughout experiments
for i in range(self.outcomes.shape[0]):
self.updater_bayes.update(self.outcomes[i], self.expparams[i])
self.num_updater_bayes.update(self.outcomes[i], self.expparams[i])
bim_currents.append(self.updater_bayes.current_bim)
num_bim_currents.append(self.num_updater_bayes.current_bim)
bim_adaptives.append(self.updater_bayes.adaptive_bim)
num_bim_adaptives.append(self.num_updater_bayes.adaptive_bim)
bim_currents = np.array(bim_currents)
num_bim_currents = np.array(num_bim_currents)
bim_adaptives = np.array(bim_adaptives)
num_bim_adaptives = np.array(num_bim_adaptives)
#compare numerical and analytical bims
assert_almost_equal(bim_currents, num_bim_currents, 2)
assert_almost_equal(bim_adaptives, num_bim_adaptives, 2)
#verify that array copying of properties is working
assert not np.all(bim_currents == bim_currents[0, ...])
assert not np.all(num_bim_currents == num_bim_currents[0, ...])
assert not np.all(bim_adaptives == bim_adaptives[0, ...])
assert not np.all(num_bim_adaptives == num_bim_adaptives[0, ...])
#verify that BCRB is approximately reached
assert_almost_equal(self.updater_bayes.est_covariance_mtx(),
np.linalg.inv(self.updater_bayes.current_bim), 2)
assert_almost_equal(self.updater_bayes.est_covariance_mtx(),
np.linalg.inv(self.updater_bayes.adaptive_bim), 2)
assert_almost_equal(self.num_updater_bayes.est_covariance_mtx(),
np.linalg.inv(self.updater_bayes.current_bim), 2)
assert_almost_equal(self.num_updater_bayes.est_covariance_mtx(),
np.linalg.inv(self.updater_bayes.adaptive_bim), 2)
mps_buf.release()
eps_buf.release()
dest_buf.release()
# Now we concatenate over outcomes.
return FiniteOutcomeModel.pr0_to_likelihood_array(outcomes, pr0)
## SCRIPT ######################################################################
if __name__ == "__main__":
# NOTE: This is now redundant with the perf_testing module.
simple_model = SimplePrecessionModel()
for model in [AcceleratedPrecessionModel(), SimplePrecessionModel()]:
true = np.random.random(1)
updater = SMCUpdater(model, 100000, UniformDistribution([0, 1]))
tic = time.time()
for idx_exp in range(200):
if not (idx_exp % 20):
print(idx_exp)
expparams = np.array([(9 / 8)**idx_exp])
updater.update(simple_model.simulate_experiment(true, expparams),
expparams)
print(model, updater.est_mean(), true, time.time() - tic)
# Model and prior initialization.
prior = distributions.HilbertSchmidtUniform()
model = QubitStatePauliModel()
expparams = np.array(
[
([1, 0, 0], 1), # Records are indicated by tuples.
([0, 1, 0], 1),
([0, 0, 1], 1)
],
dtype=model.expparams_dtype)
# Make a dict of updater constructors. This will define what kinds
# of perfomance data we care about.
updater_ctors = dict()
if do_smc:
updater_ctors['SMC'] = lambda: SMCUpdater(model, n_particles, prior)
if do_ale:
ale_model = ale.ALEApproximateModel(model,
error_tol=err_tol,
est_hedge=hedge,
adapt_hedge=hedge)
updater_ctors['SMC_ALE'] = lambda: SMCUpdater(ale_model, n_particles,
prior)
# Make a dtype for holding performance data in a record array.
# Note that we could do this with out record arrays, but it's easy to
# use field names this way.
performance_dtype = [
('est_mean', 'f8'),
('est_cov_mat', 'f8'),
('true_err', 'f8'),
def _mk_updater(self, n_particles, **kwargs):
return SMCUpdater(self.model, n_particles, UniformDistribution([0, 1]), **kwargs)
from qinfer.distributions import UniformDistribution
from qinfer.smc import SMCUpdater
from qinfer.resamplers import LiuWestResampler
import numpy as np
import matplotlib.pyplot as plt
from qinfer.expdesign import ExperimentDesigner
import logging
log = logging.getLogger(__name__)
log.setLevel(logging.DEBUG)
model = T1Model()
prior = UniformDistribution(np.array([0, 10]))
N_particles = 1000000
updater = SMCUpdater(
model, N_particles, prior, resampler=LiuWestResampler(),
zero_weight_policy='reset'
)
designer = ExperimentDesigner(updater, opt_algo=1)
# Set the value of T1 to Learn, pick 1 value from prior
true_model = prior.sample()
# true_model=np.array([11.032], dtype=model.expparams_dtype)
performance_dtype = [
('expparams', 'float'),
('sim_outcome', 'float'),
('est_mean', 'float'),
]
# NMR EXPERIMENT Initialization*******************************
# going to normalize Mo max of 1.
# Copy the buffer back from the GPU and free memory there.
cl.enqueue_copy(self._queue, pr0, dest_buf)
mps_buf.release()
eps_buf.release()
dest_buf.release()
# Now we concatenate over outcomes.
return FiniteOutcomeModel.pr0_to_likelihood_array(outcomes, pr0)
## SCRIPT ######################################################################
if __name__ == "__main__":
# NOTE: This is now redundant with the perf_testing module.
simple_model = SimplePrecessionModel()
for model in [AcceleratedPrecessionModel(), SimplePrecessionModel()]:
true = np.random.random(1)
updater = SMCUpdater(model, 100000, UniformDistribution([0, 1]))
tic = time.time()
for idx_exp in range(200):
if not (idx_exp % 20):
print(idx_exp)
expparams = np.array([(9 / 8) ** idx_exp])
updater.update(simple_model.simulate_experiment(true, expparams), expparams)
print(model, updater.est_mean(), true, time.time() - tic)
class TestSMCUpdater(DerandomizedTestCase): # True model parameter for test MODELPARAMS = np.array([1,]) TEST_EXPPARAMS = np.linspace(1.,10.,100,dtype=np.float) PRIOR = UniformDistribution([[0,2]]) N_PARTICLES = 10000 TEST_TARGET_COV = np.array([[0.01]]) def setUp(self): super(TestSMCUpdater,self).setUp() self.precession_model = SimplePrecessionModel() self.num_precession_model = NumericalSimplePrecessionModel() self.expparams = TestSMCUpdater.TEST_EXPPARAMS.reshape(-1,1) self.outcomes = self.precession_model.simulate_experiment(TestSMCUpdater.MODELPARAMS, TestSMCUpdater.TEST_EXPPARAMS,repeat=1 ).reshape(-1,1) self.updater = SMCUpdater(self.precession_model, TestSMCUpdater.N_PARTICLES,TestSMCUpdater.PRIOR) self.updater_bayes = SMCUpdaterBCRB(self.precession_model, TestSMCUpdater.N_PARTICLES,TestSMCUpdater.PRIOR,adaptive=True) self.num_updater = SMCUpdater(self.num_precession_model, TestSMCUpdater.N_PARTICLES,TestSMCUpdater.PRIOR) self.num_updater_bayes = SMCUpdaterBCRB(self.num_precession_model, TestSMCUpdater.N_PARTICLES,TestSMCUpdater.PRIOR,adaptive=True) def test_smc_fitting(self): """ Checks that the fitters converge on true value on simple precession_model. Is a stochastic test but I ran 100 times and there were no fails, with these parameters. """ self.updater.batch_update(self.outcomes,self.expparams) self.updater_bayes.batch_update(self.outcomes,self.expparams) self.num_updater.batch_update(self.outcomes,self.expparams) self.num_updater_bayes.batch_update(self.outcomes,self.expparams) #Assert that models have learned true model parameters from data #test means assert_almost_equal(self.updater.est_mean(),TestSMCUpdater.MODELPARAMS,2) assert_almost_equal(self.updater_bayes.est_mean(),TestSMCUpdater.MODELPARAMS,2) assert_almost_equal(self.num_updater.est_mean(),TestSMCUpdater.MODELPARAMS,2) assert_almost_equal(self.num_updater_bayes.est_mean(),TestSMCUpdater.MODELPARAMS,2) #Assert that covariances have been reduced below thresholds #test covs assert_array_less(self.updater.est_covariance_mtx(),TestSMCUpdater.TEST_TARGET_COV) assert_array_less(self.updater_bayes.est_covariance_mtx(),TestSMCUpdater.TEST_TARGET_COV) assert_array_less(self.num_updater.est_covariance_mtx(),TestSMCUpdater.TEST_TARGET_COV) assert_array_less(self.num_updater_bayes.est_covariance_mtx(),TestSMCUpdater.TEST_TARGET_COV) def test_bim(self): """ Checks that the fitters converge on true value on simple precession_model. Is a stochastic test but I ran 100 times and there were no fails, with these parameters. """ bim_currents = [] num_bim_currents = [] bim_adaptives = [] num_bim_adaptives = [] #track bims throughout experiments for i in range(self.outcomes.shape[0]): self.updater_bayes.update(self.outcomes[i],self.expparams[i]) self.num_updater_bayes.update(self.outcomes[i],self.expparams[i]) bim_currents.append(self.updater_bayes.current_bim) num_bim_currents.append(self.num_updater_bayes.current_bim) bim_adaptives.append(self.updater_bayes.adaptive_bim) num_bim_adaptives.append(self.num_updater_bayes.adaptive_bim) bim_currents = np.array(bim_currents) num_bim_currents = np.array(num_bim_currents) bim_adaptives = np.array(bim_adaptives) num_bim_adaptives = np.array(num_bim_adaptives) #compare numerical and analytical bims assert_almost_equal(bim_currents,num_bim_currents,2) assert_almost_equal(bim_adaptives,num_bim_adaptives,2) #verify that array copying of properties is working assert not np.all(bim_currents == bim_currents[0,...]) assert not np.all(num_bim_currents == num_bim_currents[0,...]) assert not np.all(bim_adaptives == bim_adaptives[0,...]) assert not np.all(num_bim_adaptives == num_bim_adaptives[0,...]) #verify that BCRB is approximately reached assert_almost_equal(self.updater_bayes.est_covariance_mtx(),np.linalg.inv(self.updater_bayes.current_bim),2) assert_almost_equal(self.updater_bayes.est_covariance_mtx(),np.linalg.inv(self.updater_bayes.adaptive_bim),2) assert_almost_equal(self.num_updater_bayes.est_covariance_mtx(),np.linalg.inv(self.updater_bayes.current_bim),2) assert_almost_equal(self.num_updater_bayes.est_covariance_mtx(),np.linalg.inv(self.updater_bayes.adaptive_bim),2)
def perf_test(
model, n_particles, prior, n_exp, heuristic_class,
true_model=None, true_prior=None, true_mps=None,
extra_updater_args=None
):
"""
Runs a trial of using SMC to estimate the parameters of a model, given a
number of particles, a prior distribution and an experiment design
heuristic.
:param qinfer.Model model: Model whose parameters are to
be estimated.
:param int n_particles: Number of SMC particles to use.
:param qinfer.Distribution prior: Prior to use in selecting
SMC particles.
:param int n_exp: Number of experimental data points to draw from the
model.
:param qinfer.Heuristic heuristic_class: Constructor function
for the experiment design heuristic to be used.
:param qinfer.Model true_model: Model to be used in
generating experimental data. If ``None``, assumed to be ``model``.
:param qinfer.Distribution true_prior: Prior to be used in
selecting the true model parameters. If ``None``, assumed to be
``prior``.
:param np.ndarray true_mps: The true model parameters. If ``None``,
it will be sampled from ``true_prior``. Note that the performance
record can only handle one outcome and therefore ONLY ONE TRUE MODEL.
An error will occur if ``true_mps.shape[0] > 1`` returns ``True``.
:param dict extra_updater_args: Extra keyword arguments for the updater,
such as resampling and zero-weight policies.
:rtype np.ndarray: See :ref:`perf_testing_struct` for more details on
the type returned by this function.
:return: A record array of performance metrics, indexed by the number
of experiments performed.
"""
if true_model is None:
true_model = model
if true_prior is None:
true_prior = prior
if true_mps is None:
true_mps = true_prior.sample()
if extra_updater_args is None:
extra_updater_args = {}
dtype, is_scalar_exp = actual_dtype(model)
performance = np.zeros((n_exp,), dtype=dtype)
updater = SMCUpdater(model, n_particles, prior, **extra_updater_args)
heuristic = heuristic_class(updater)
performance['true'] = true_mps
for idx_exp in xrange(n_exp):
expparams = heuristic()
datum = true_model.simulate_experiment(true_mps, expparams)
with timing() as t:
updater.update(datum, expparams)
est_mean = updater.est_mean()
delta = est_mean - true_mps
loss = np.dot(delta**2, model.Q)
performance[idx_exp]['elapsed_time'] = t.delta_t
performance[idx_exp]['loss'] = loss
performance[idx_exp]['resample_count'] = updater.resample_count
performance[idx_exp]['outcome'] = datum
performance[idx_exp]['est'] = est_mean
if is_scalar_exp:
performance[idx_exp]['experiment'] = expparams
else:
for param_name in [param[0] for param in model.expparams_dtype]:
performance[idx_exp][param_name] = expparams[param_name]
return performance
def sim_qubit_fid(n_meas, n_meas_rep, meas_dist, n_trials=100, n_particles=1000, n_rec=15):
r"""Calculates the average fidelity of the optimal estimator (approximated
by SMC) averaged over Haar random pure states and a random sample of
measurement outcomes. The estimator is calculated at a given number of
interim times throughout the tomographic process.
:param n_meas: The number of copies of the system given in each
tomographic run
:type n_meas: Integer
:param n_meas_rep: The number of measurement outcomes to average the
fidelity over for each copy of the system in a
tomographic run
:type n_meas_rep: Integer
:param meas_dist: Object defining the distribution from which to draw
measurement directions
:type meas_dist: Object possessing `sample(n)` function that returns a
numpy.array((2, n)) of unit vectors in
:math:`\mathbb{C}^2`
:param n_trials: The number of tomographic runs (aka samples from the
pure state prior) the fidelity is averaged over
:type n_trials: Integer
:param n_particles: Number of SMC particles to use
:type n_particles: Integer
:param n_rec: Number of places to record average fidelity (on a log
scale)
:type n_rec: Integer
:returns: An array with the calculated average fidelities at the
specified times for all tomographic runs
:return type: numpy.array((n_trials, n_rec))
"""
n_qubits = 1 # This function isn't guaranteed to generalize by changing
# this value, but it is included here to aid readability and
# aid any future generalization efforts
dim = 2 * n_qubits
# Record data on a logarithmic scale
rec_idxs = np.unique(np.round(np.logspace(0, np.log10(n_meas), n_rec)))
n_rec = rec_idxs.shape[0]
# Allocate result array
fidelities = np.empty((n_trials, n_rec))
# Instantiate model and state prior
model = HaarTestModel(n_qubits=n_qubits)
prior = HaarDistribution(n_qubits=n_qubits)
# Sample all the measurement directions used at once (since some samplers
# might be more efficient doing things this way)
raw_meas_dirs = meas_dist.sample(n_trials * n_meas)
# Reshape the measurement directions to be a n_trials x n_meas array of unit
# vectors in C^2
meas_dirs = np.reshape(raw_meas_dirs.T, (n_trials, n_meas, 2))
for trial_idx in xrange(n_trials):
# Pick a random true state and instantiate the Bayes updater
true_state = prior.sample()
true_vec = model.param2vec(true_state)
updater = SMCUpdater(model, n_particles, prior, resampler=LiuWestResampler(a=0.95, h=None))
rec_idx = 0
for meas_idx in xrange(n_meas):
meas_dir = meas_dirs[trial_idx, meas_idx]
# Set the experimental parameters for the measurement
expparams = np.array([(meas_dir, n_meas_rep)], dtype=model.expparams_dtype)
# Simulate data and update
data = model.simulate_experiment(true_state, expparams)
updater.update(data, expparams)
if meas_idx + 1 in rec_idxs:
# Generate the estimated state -> average then maximal
# eigenvector
weights = updater.particle_weights
locs = updater.particle_locations
avg_state = 1j * np.zeros([dim, dim])
for idx_locs in xrange(n_particles):
psi = model.param2vec(locs[idx_locs][np.newaxis])
avg_state += weights[idx_locs] * np.outer(psi, psi.conj())
eigs = la.eig(avg_state)
max_eig = eigs[1][:, np.argmax(eigs[0])]
fidelities[trial_idx, rec_idx] = model.fidelity(true_vec, max_eig)
rec_idx += 1
# Give progress updates
print(100 * ((trial_idx + 1) / n_trials))
return fidelities
import numpy as np
import matplotlib.pyplot as plt
import time
import Lorentzian_fit as LF
from qinfer.expdesign import ExperimentDesigner
import os
import logging
log = logging.getLogger(__name__)
log.setLevel(logging.DEBUG)
model = T1Model()
prior = UniformDistribution([0, 100])
N_particles=100000
updater = SMCUpdater(model, N_particles, prior, resampler=LiuWestResampler(0.98),zero_weight_policy='reset')
designer=ExperimentDesigner(updater,opt_algo=1)
#Set the value of T1 to Learn, pick 1 value from prior
#true_model=prior.sample()
true_model=np.array([6.8], dtype=model.expparams_dtype)
performance_dtype = [
('expparams', 'float'),
('sim_outcome', 'float'),
('est_mean', 'float'),
('covariance', 'float'),
]
#NMR EXPERIMENT Initialization*******************************
def perf_test(
model, n_particles, prior, n_exp, heuristic_class,
true_model=None, true_prior=None, true_mps=None,
extra_updater_args=None
):
"""
Runs a trial of using SMC to estimate the parameters of a model, given a
number of particles, a prior distribution and an experiment design
heuristic.
:param qinfer.Model model: Model whose parameters are to
be estimated.
:param int n_particles: Number of SMC particles to use.
:param qinfer.Distribution prior: Prior to use in selecting
SMC particles.
:param int n_exp: Number of experimental data points to draw from the
model.
:param qinfer.Heuristic heuristic_class: Constructor function
for the experiment design heuristic to be used.
:param qinfer.Model true_model: Model to be used in
generating experimental data. If ``None``, assumed to be ``model``.
Note that if the true and estimation models have different numbers
of parameters, the loss will be calculated by aligning the
respective model vectors "at the right," analogously to the
convention used by NumPy broadcasting.
:param qinfer.Distribution true_prior: Prior to be used in
selecting the true model parameters. If ``None``, assumed to be
``prior``.
:param numpy.ndarray true_mps: The true model parameters. If ``None``,
it will be sampled from ``true_prior``. Note that as this function
runs exactly one trial, only one model parameter vector may be passed.
In particular, this requires that ``len(true_mps.shape) == 1``.
:param dict extra_updater_args: Extra keyword arguments for the updater,
such as resampling and zero-weight policies.
:rtype np.ndarray: See :ref:`perf_testing_struct` for more details on
the type returned by this function.
:return: A record array of performance metrics, indexed by the number
of experiments performed.
"""
if true_model is None:
true_model = model
if true_prior is None:
true_prior = prior
if true_mps is None:
true_mps = true_prior.sample()
if extra_updater_args is None:
extra_updater_args = {}
n_min_modelparams = min(model.n_modelparams, true_model.n_modelparams)
dtype, is_scalar_exp = actual_dtype(model, true_model)
performance = np.zeros((n_exp,), dtype=dtype)
updater = SMCUpdater(model, n_particles, prior, **extra_updater_args)
heuristic = heuristic_class(updater)
for idx_exp in range(n_exp):
# Set inside the loop to handle the case where the
# true model is time-dependent as well as the estimation model.
performance[idx_exp]['true'] = true_mps
expparams = heuristic()
datum = true_model.simulate_experiment(true_mps, expparams)
with timing() as t:
updater.update(datum, expparams)
# Update the true model.
true_mps = true_model.update_timestep(
promote_dims_left(true_mps, 2), expparams
)[:, :, 0]
est_mean = updater.est_mean()
delta = np.subtract(*shorten_right(est_mean, true_mps))
loss = np.dot(delta**2, model.Q[-n_min_modelparams:])
performance[idx_exp]['elapsed_time'] = t.delta_t
performance[idx_exp]['loss'] = loss
performance[idx_exp]['resample_count'] = updater.resample_count
performance[idx_exp]['outcome'] = datum
performance[idx_exp]['est'] = est_mean
if is_scalar_exp:
performance[idx_exp]['experiment'] = expparams
else:
for param_name in [param[0] for param in model.expparams_dtype]:
performance[idx_exp][param_name] = expparams[param_name]
return performance
def fid_smc(n_meas, K, n_qubits=1, n_trials=100, n_particles=1000, n_rec=15):
"""
Evaluates the average fidelity incurred by using sequential Monte Carlo
(SMC) to estimate pure states.
:param n_meas: The number of copies of the system given in each
tomographic run
:type n_meas: Integer
:param K: Number of single-shot measurements
:type K: Integer
:param n_trials: Number of times to run the SMC estimation procedure.
:type n_trials: Integer
:param n_particles: Number of SMC particles to use.
:type n_particles: Integer
:param n_rec: Number of place to record data (on a log scale)
:type n_rec: Integer
:returns: Dictionary of various fidelities and timings
:return type: Dictionary
"""
dim = int(2 ** n_qubits)
# Record data on a logarithmic scale
rec_idx = np.unique(np.round(np.logspace(0, np.log10(n_meas), n_rec)))
n_rec = rec_idx.shape[0]
# Allocate arrays to hold results.
fidelity_mub = np.empty((n_trials, n_rec))
fidelity_opt = np.empty((n_trials, n_rec))
fidelity_WM = np.empty((n_trials, n_rec))
fidelity_DST = np.empty((n_trials, n_rec))
# Instantiate models and distributions
model = HaarTestModel(n_qubits=n_qubits)
prior = HaarDistribution(n_qubits=n_qubits)
measMUB = MUBDistribution()
measWM = WeakMeasDistribution(eps=0.05)
measDST = DSTDistribution(0.1)
timing = np.empty((n_trials,))
# Make and show a progress bar.
"""
prog = ProgressBar()
prog.show()
"""
for idx_trial in xrange(n_trials):
# Pick a random true state and instantiate the Bayes updater
true_state = prior.sample()
true_vec = model.param2vec(true_state)
updater_opt = SMCUpdater(model, n_particles, prior, resampler=LiuWestResampler(a=0.95, h=None))
updater_mub = SMCUpdater(model, n_particles, prior, resampler=LiuWestResampler(a=0.95, h=None))
updater_WM = SMCUpdater(model, n_particles, prior, resampler=LiuWestResampler(a=0.95, h=None))
updater_DST = SMCUpdater(model, n_particles, prior, resampler=LiuWestResampler(a=0.95, h=None))
# Record the start time.
tic = time.time()
idx_rec = 0
for idx_meas in xrange(n_meas):
# Choose a random measurement direction
foo = prior.sample()
meas_opt = model.param2vec(foo)
meas_mub = measMUB.sample()
meas_WM = measWM.sample()[:, 0]
meas_DST = measDST.sample()[:, 0]
expparams_opt = np.array([(meas_opt, K)], dtype=model.expparams_dtype)
expparams_mub = np.array([(meas_mub, K)], dtype=model.expparams_dtype)
expparams_WM = np.array([(meas_WM, K)], dtype=model.expparams_dtype)
expparams_DST = np.array([(meas_DST, K)], dtype=model.expparams_dtype)
# Simulate data and update
data_opt = model.simulate_experiment(true_state, expparams_opt)
updater_opt.update(data_opt, expparams_opt)
data_mub = model.simulate_experiment(true_state, expparams_mub)
updater_mub.update(data_mub, expparams_mub)
data_WM = model.simulate_experiment(true_state, expparams_WM)
updater_WM.update(data_WM, expparams_WM)
data_DST = model.simulate_experiment(true_state, expparams_DST)
updater_DST.update(data_DST, expparams_DST)
if idx_meas + 1 in rec_idx:
# Generate the estimated state -> average then maximal eigenvector
weights = updater_opt.particle_weights
locs = updater_opt.particle_locations
ave_state = 1j * np.zeros([dim, dim])
for idx_locs in xrange(n_particles):
psi = model.param2vec(locs[idx_locs][np.newaxis])
ave_state += weights[idx_locs] * np.outer(psi, psi.conj())
eigs = la.eig(ave_state)
max_eig = eigs[1][:, np.argmax(eigs[0])]
fidelity_opt[idx_trial, idx_rec] = model.fidelity(true_vec, max_eig)
# MUB
weights = updater_mub.particle_weights
locs = updater_mub.particle_locations
ave_state = 1j * np.zeros([dim, dim])
for idx_locs in xrange(n_particles):
psi = model.param2vec(locs[idx_locs][np.newaxis])
ave_state += weights[idx_locs] * np.outer(psi, psi.conj())
eigs = la.eig(ave_state)
max_eig = eigs[1][:, np.argmax(eigs[0])]
fidelity_mub[idx_trial, idx_rec] = model.fidelity(true_vec, max_eig)
# Weak Measurement
weights = updater_WM.particle_weights
locs = updater_WM.particle_locations
ave_state = 1j * np.zeros([dim, dim])
for idx_locs in xrange(n_particles):
psi = model.param2vec(locs[idx_locs][np.newaxis])
ave_state += weights[idx_locs] * np.outer(psi, psi.conj())
eigs = la.eig(ave_state)
max_eig = eigs[1][:, np.argmax(eigs[0])]
fidelity_WM[idx_trial, idx_rec] = model.fidelity(true_vec, max_eig)
# DST Measurement
weights = updater_DST.particle_weights
locs = updater_DST.particle_locations
ave_state = 1j * np.zeros([dim, dim])
for idx_locs in xrange(n_particles):
psi = model.param2vec(locs[idx_locs][np.newaxis])
ave_state += weights[idx_locs] * np.outer(psi, psi.conj())
eigs = la.eig(ave_state)
max_eig = eigs[1][:, np.argmax(eigs[0])]
fidelity_DST[idx_trial, idx_rec] = model.fidelity(true_vec, max_eig)
idx_rec += 1
# Record how long it took us.
timing[idx_trial] = time.time() - tic
print(100 * ((idx_trial + 1) / n_trials))
# prog.value = 100 * ((idx_trial + 1) / n_trials)
return {
"fidelity_opt": fidelity_opt,
"fidelity_mub": fidelity_mub,
"fidelity_WM": fidelity_WM,
"fidelity_DST": fidelity_DST,
"timing": timing,
}
def test_in_credible_region(self):
"""
Tests that in_credible_region works.
"""
dist = MultivariateNormalDistribution(self.MEAN, self.COV)
# the model is irrelevant; we just want the updater to have some particles
# with the desired normal distribution.
u = SMCUpdater(MockModel(4), self.N_PARTICLES, dist)
# some points to test with
test_points = np.random.multivariate_normal(self.MEAN, self.COV, self.N_PARTICLES)
# method='pce'
results = [
u.in_credible_region(test_points, level=0.9, method='pce'),
u.in_credible_region(test_points, level=0.84, method='pce'),
u.in_credible_region(test_points, level=0.5, method='pce'),
]
assert_almost_equal(
np.array([np.mean(x.astype('float')) for x in results]),
np.array([0.9, 0.84, 0.5]),
3
)
# method='hpd-hull'
results1 = [
u.in_credible_region(test_points, level=0.9, method='hpd-hull'),
u.in_credible_region(test_points, level=0.84, method='hpd-hull'),
u.in_credible_region(test_points, level=0.5, method='hpd-hull'),
]
assert_array_less(
np.array([0.9, 0.84, 0.5]),
np.array([np.mean(x.astype('float')) for x in results1])
)
# method='hpd-mvee'
results2 = [
u.in_credible_region(test_points, level=0.9, method='hpd-mvee'),
u.in_credible_region(test_points, level=0.84, method='hpd-mvee'),
u.in_credible_region(test_points, level=0.5, method='hpd-mvee'),
]
assert_array_less(
np.array([0.9, 0.84, 0.5]),
np.array([np.mean(x.astype('float')) for x in results2])
)
# the mvee should be bigger than the convex hull.
# this passes iff all points in the ellipses are
# also in the hulls.
assert_array_less(
np.hstack([x.astype('float') for x in results1]),
np.hstack([x.astype('float') for x in results2]) + 0.5
)
# check for no failures with slices.
u.in_credible_region(test_points[:100,self.SLICE], level=0.9, method='pce', modelparam_slice=self.SLICE)
u.in_credible_region(test_points[:100,self.SLICE], level=0.9, method='hpd-hull', modelparam_slice=self.SLICE)
u.in_credible_region(test_points[:100,self.SLICE], level=0.9, method='hpd-mvee', modelparam_slice=self.SLICE)
# check for no failures with single inputs
assert(u.in_credible_region(test_points[0,:], level=0.9, method='pce').size == 1)
assert(u.in_credible_region(test_points[0,:], level=0.9, method='hpd-hull').size == 1)
assert(u.in_credible_region(test_points[0,:], level=0.9, method='hpd-mvee').size == 1)
def perf_test(model,
n_particles,
prior,
n_exp,
heuristic_class,
true_model=None,
true_prior=None,
true_mps=None,
extra_updater_args=None):
"""
Runs a trial of using SMC to estimate the parameters of a model, given a
number of particles, a prior distribution and an experiment design
heuristic.
:param qinfer.Model model: Model whose parameters are to
be estimated.
:param int n_particles: Number of SMC particles to use.
:param qinfer.Distribution prior: Prior to use in selecting
SMC particles.
:param int n_exp: Number of experimental data points to draw from the
model.
:param qinfer.Heuristic heuristic_class: Constructor function
for the experiment design heuristic to be used.
:param qinfer.Model true_model: Model to be used in
generating experimental data. If ``None``, assumed to be ``model``.
Note that if the true and estimation models have different numbers
of parameters, the loss will be calculated by aligning the
respective model vectors "at the right," analogously to the
convention used by NumPy broadcasting.
:param qinfer.Distribution true_prior: Prior to be used in
selecting the true model parameters. If ``None``, assumed to be
``prior``.
:param numpy.ndarray true_mps: The true model parameters. If ``None``,
it will be sampled from ``true_prior``. Note that as this function
runs exactly one trial, only one model parameter vector may be passed.
In particular, this requires that ``len(true_mps.shape) == 1``.
:param dict extra_updater_args: Extra keyword arguments for the updater,
such as resampling and zero-weight policies.
:rtype np.ndarray: See :ref:`perf_testing_struct` for more details on
the type returned by this function.
:return: A record array of performance metrics, indexed by the number
of experiments performed.
"""
if true_model is None:
true_model = model
if true_prior is None:
true_prior = prior
if true_mps is None:
true_mps = true_prior.sample()
if extra_updater_args is None:
extra_updater_args = {}
n_min_modelparams = min(model.n_modelparams, true_model.n_modelparams)
dtype, is_scalar_exp = actual_dtype(model, true_model)
performance = np.zeros((n_exp, ), dtype=dtype)
updater = SMCUpdater(model, n_particles, prior, **extra_updater_args)
heuristic = heuristic_class(updater)
for idx_exp in range(n_exp):
# Set inside the loop to handle the case where the
# true model is time-dependent as well as the estimation model.
performance[idx_exp]['true'] = true_mps
expparams = heuristic()
datum = true_model.simulate_experiment(true_mps, expparams)
with timing() as t:
updater.update(datum, expparams)
# Update the true model.
true_mps = true_model.update_timestep(promote_dims_left(true_mps, 2),
expparams)[:, :, 0]
est_mean = updater.est_mean()
delta = np.subtract(*shorten_right(est_mean, true_mps))
loss = np.dot(delta**2, model.Q[-n_min_modelparams:])
performance[idx_exp]['elapsed_time'] = t.delta_t
performance[idx_exp]['loss'] = loss
performance[idx_exp]['resample_count'] = updater.resample_count
performance[idx_exp]['outcome'] = datum
performance[idx_exp]['est'] = est_mean
if is_scalar_exp:
performance[idx_exp]['experiment'] = expparams
else:
for param_name in [param[0] for param in model.expparams_dtype]:
performance[idx_exp][param_name] = expparams[param_name]
return performance
#imports and intializations
from __future__ import division
from t1_model import T1Model
from qinfer.distributions import UniformDistribution
#from qinfer.distributions import NormalDistribution
from qinfer.smc import SMCUpdater
from qinfer.resamplers import LiuWestResampler
import numpy as np
import matplotlib.pyplot as plt
model = T1Model()
prior = UniformDistribution([0, 1])
N_particles=10000
updater = SMCUpdater(model, N_particles, prior, resampler=LiuWestResampler(0.98),zero_weight_policy='reset')
#Set the value of T1 to Learn, pick 1 value from prior
true_model=prior.sample()
performance_dtype = [
('expparams', 'float'),
('sim_outcome', 'float'),
('est_mean', 'float'),
]
trials=10
data = np.zeros((trials, 1), dtype=performance_dtype)
for idx_trials in xrange(trials):
