def test_KMeansMachine():
# Test a KMeansMachine
means = np.array([[3, 70, 0], [4, 72, 0]], "float64")
test_val = np.array([3, 70, 1], "float64")
test_arr = np.array([[3, 70, 1], [5, 72, 0]], "float64")
for transform in (to_numpy, to_dask_array):
means, test_val, test_arr = transform(means, test_val, test_arr)
# Initializes a KMeansMachine
km = KMeansMachine(2)
km.centroids_ = means
# Distance and closest mean
np.testing.assert_equal(km.transform(test_val)[0], np.array([1]))
np.testing.assert_equal(km.transform(test_val)[1], np.array([6]))
index = km.predict(test_val)
assert index == 0
indices = km.predict(test_arr)
np.testing.assert_equal(indices, np.array([0, 1]))
# Check __eq__ and is_similar_to
km2 = KMeansMachine(2)
assert km != km2
assert not km.is_similar_to(km2)
km2 = copy.deepcopy(km)
assert km == km2
assert km.is_similar_to(km2)
km2.centroids_[0, 0] += 1
assert km != km2
assert not km.is_similar_to(km2)
def test_kmeans_a():
# Trains a KMeansMachine
# This files contains draws from two 1D Gaussian distributions:
# * 100 samples from N(-10,1)
# * 100 samples from N(10,1)
data = bob.io.base.load(datafile("samplesFrom2G_f64.hdf5", __name__, path="../data/"))
machine = KMeansMachine(2, 1)
trainer = KMeansTrainer()
# trainer.train(machine, data)
bob.learn.em.train(trainer, machine, data)
[variances, weights] = machine.get_variances_and_weights_for_each_cluster(data)
variances_b = numpy.ndarray(shape=(2, 1), dtype=numpy.float64)
weights_b = numpy.ndarray(shape=(2,), dtype=numpy.float64)
machine.__get_variances_and_weights_for_each_cluster_init__(variances_b, weights_b)
machine.__get_variances_and_weights_for_each_cluster_acc__(data, variances_b, weights_b)
machine.__get_variances_and_weights_for_each_cluster_fin__(variances_b, weights_b)
m1 = machine.get_mean(0)
m2 = machine.get_mean(1)
## Check means [-10,10] / variances [1,1] / weights [0.5,0.5]
if (m1 < m2):
means = numpy.array(([m1[0], m2[0]]), 'float64')
else:
means = numpy.array(([m2[0], m1[0]]), 'float64')
assert equals(means, numpy.array([-10., 10.]), 2e-1)
assert equals(variances, numpy.array([1., 1.]), 2e-1)
assert equals(weights, numpy.array([0.5, 0.5]), 1e-3)
assert equals(variances, variances_b, 1e-8)
assert equals(weights, weights_b, 1e-8)
def test_kmeans_a():
# Trains a KMeansMachine
# This files contains draws from two 1D Gaussian distributions:
# * 100 samples from N(-10,1)
# * 100 samples from N(10,1)
data = bob.io.base.load(datafile("samplesFrom2G_f64.hdf5", __name__, path="../data/"))
machine = KMeansMachine(2, 1)
trainer = KMeansTrainer()
#trainer.train(machine, data)
bob.learn.em.train(trainer,machine,data)
[variances, weights] = machine.get_variances_and_weights_for_each_cluster(data)
variances_b = numpy.ndarray(shape=(2,1), dtype=numpy.float64)
weights_b = numpy.ndarray(shape=(2,), dtype=numpy.float64)
machine.__get_variances_and_weights_for_each_cluster_init__(variances_b, weights_b)
machine.__get_variances_and_weights_for_each_cluster_acc__(data, variances_b, weights_b)
machine.__get_variances_and_weights_for_each_cluster_fin__(variances_b, weights_b)
m1 = machine.get_mean(0)
m2 = machine.get_mean(1)
## Check means [-10,10] / variances [1,1] / weights [0.5,0.5]
if(m1<m2): means=numpy.array(([m1[0],m2[0]]), 'float64')
else: means=numpy.array(([m2[0],m1[0]]), 'float64')
assert equals(means, numpy.array([-10.,10.]), 2e-1)
assert equals(variances, numpy.array([1.,1.]), 2e-1)
assert equals(weights, numpy.array([0.5,0.5]), 1e-3)
assert equals(variances, variances_b, 1e-8)
assert equals(weights, weights_b, 1e-8)
def test_kmeans_machine():
# Test a KMeansMachine
means = numpy.array([[3, 70, 0], [4, 72, 0]], "float64")
# Initializes a KMeansMachine
kmeans_machine = KMeansMachine(2, 3)
kmeans_machine.means = means
kmeans_machine_after_pickle = pickle.loads(pickle.dumps(kmeans_machine))
assert numpy.allclose(kmeans_machine_after_pickle.means,
kmeans_machine.means, 10e-3)
def test_kmeans_noduplicate():
# Data/dimensions
dim_c = 2
dim_d = 3
seed = 0
data = numpy.array([[1, 2, 3], [1, 2, 3], [1, 2, 3], [4, 5, 6.]])
# Defines machine and trainer
machine = KMeansMachine(dim_c, dim_d)
trainer = KMeansTrainer()
rng = bob.core.random.mt19937(seed)
trainer.initialization_method = 'RANDOM_NO_DUPLICATE'
trainer.initialize(machine, data, rng)
# Makes sure that the two initial mean vectors selected are different
assert equals(machine.get_mean(0), machine.get_mean(1), 1e-8) == False
def test_trainer_execption():
from nose.tools import assert_raises
# Testing Inf
machine = KMeansMachine(2, 2)
data = numpy.array([[1.0, 2.0], [2, 3.], [1, 1.], [2, 5.], [numpy.inf, 1.0]])
trainer = KMeansTrainer()
assert_raises(ValueError, bob.learn.em.train, trainer, machine, data, 10)
# Testing Nan
machine = KMeansMachine(2, 2)
data = numpy.array([[1.0, 2.0], [2, 3.], [1, numpy.nan], [2, 5.], [2.0, 1.0]])
trainer = KMeansTrainer()
assert_raises(ValueError, bob.learn.em.train, trainer, machine, data, 10)
def test_kmeans_noduplicate(): # Data/dimensions dim_c = 2 dim_d = 3 seed = 0 data = numpy.array([[1,2,3],[1,2,3],[1,2,3],[4,5,6.]]) # Defines machine and trainer machine = KMeansMachine(dim_c, dim_d) trainer = KMeansTrainer() rng = bob.core.random.mt19937(seed) trainer.initialization_method = 'RANDOM_NO_DUPLICATE' trainer.initialize(machine, data, rng) # Makes sure that the two initial mean vectors selected are different assert equals(machine.get_mean(0), machine.get_mean(1), 1e-8) == False
def test_KMeansMachine_var_and_weight():
for transform in (to_numpy, to_dask_array):
kmeans = KMeansMachine(2)
kmeans.centroids_ = transform(np.array([[1.2, 1.3], [0.2, -0.3]]))
data = np.array([[1.0, 1], [1.2, 3], [0, 0], [0.3, 0.2], [0.2, 0]])
data = transform(data)
variances, weights = kmeans.get_variances_and_weights_for_each_cluster(
data)
variances_result = np.array([[0.01, 1.0], [0.01555556, 0.00888889]])
weights_result = np.array([0.4, 0.6])
np.testing.assert_almost_equal(variances, variances_result, decimal=7)
np.testing.assert_equal(weights, weights_result)
def test_kmeans_plus_plus():
# Tests the K-Means++ initialization
dim_c = 5
dim_d = 7
n_samples = 150
data = numpy.random.randn(n_samples, dim_d)
seed = 0
# C++ implementation
machine = KMeansMachine(dim_c, dim_d)
trainer = KMeansTrainer()
trainer.rng = bob.core.random.mt19937(seed)
trainer.initialization_method = 'KMEANS_PLUS_PLUS'
trainer.initialize(machine, data)
# Python implementation
py_machine = KMeansMachine(dim_c, dim_d)
kmeans_plus_plus(py_machine, data, seed)
assert equals(machine.means, py_machine.means, 1e-8)
def test_kmeans_b():
# Trains a KMeansMachine
(arStd,std) = NormalizeStdArray(datafile("faithful.torch3.hdf5", __name__, path="../data/"))
machine = KMeansMachine(2, 2)
trainer = KMeansTrainer()
#trainer.seed = 1337
bob.learn.em.train(trainer,machine, arStd, convergence_threshold=0.001)
[variances, weights] = machine.get_variances_and_weights_for_each_cluster(arStd)
means = numpy.array(machine.means)
variances = numpy.array(variances)
multiplyVectorsByFactors(means, std)
multiplyVectorsByFactors(variances, std ** 2)
gmmWeights = bob.io.base.load(datafile('gmm.init_weights.hdf5', __name__, path="../data/"))
gmmMeans = bob.io.base.load(datafile('gmm.init_means.hdf5', __name__, path="../data/"))
gmmVariances = bob.io.base.load(datafile('gmm.init_variances.hdf5', __name__, path="../data/"))
if (means[0, 0] < means[1, 0]):
means = flipRows(means)
variances = flipRows(variances)
weights = flipRows(weights)
assert equals(means, gmmMeans, 1e-3)
assert equals(weights, gmmWeights, 1e-3)
assert equals(variances, gmmVariances, 1e-3)
# Check that there is no duplicate means during initialization
machine = KMeansMachine(2, 1)
trainer = KMeansTrainer()
trainer.initialization_method = 'RANDOM_NO_DUPLICATE'
data = numpy.array([[1.], [1.], [1.], [1.], [1.], [1.], [2.], [3.]])
bob.learn.em.train(trainer, machine, data)
assert (numpy.isnan(machine.means).any()) == False
def _voice_activity_detection(self,
energy_array: np.ndarray) -> np.ndarray:
"""Fits a 2 Gaussian GMM on the energy that splits between voice and silence."""
n_samples = len(energy_array)
# if energy does not change a lot, it may not be audio?
if np.std(energy_array) < 10e-5:
return np.zeros(shape=n_samples)
# Add an epsilon small Gaussian noise to avoid numerical issues (mainly due to artificial silence).
energy_array = (1e-6 * np.random.randn(n_samples)) + energy_array
# Normalize the energy array, make it an array of 1D samples
normalized_energy = utils.normalize_std_array(energy_array).reshape(
(-1, 1))
# Note: self.max_iterations and self.convergence_threshold are used for both
# k-means and GMM training.
kmeans_trainer = KMeansMachine(
n_clusters=2,
convergence_threshold=self.convergence_threshold,
max_iter=self.max_iterations,
init_max_iter=self.max_iterations,
)
ubm_gmm = GMMMachine(
n_gaussians=2,
trainer="ml",
update_means=True,
update_variances=True,
update_weights=True,
convergence_threshold=self.convergence_threshold,
max_fitting_steps=self.max_iterations,
k_means_trainer=kmeans_trainer,
)
ubm_gmm.variance_thresholds = self.variance_threshold
ubm_gmm.fit(normalized_energy)
if np.isnan(ubm_gmm.means).any():
logger.warn("Annotation aborted: File contains NaN's")
return np.zeros(shape=n_samples, dtype=int)
# Classify
# Different behavior dep on which mean represents high energy (higher value)
labels = ubm_gmm.log_weighted_likelihood(normalized_energy)
if ubm_gmm.means.argmax() == 0: # High energy in means[0]
labels = labels.argmin(axis=0)
else: # High energy in means[1]
labels = labels.argmax(axis=0)
return labels
def test_kmeans_b():
# Trains a KMeansMachine
(arStd, std) = NormalizeStdArray(datafile("faithful.torch3.hdf5", __name__, path="../data/"))
machine = KMeansMachine(2, 2)
trainer = KMeansTrainer()
# trainer.seed = 1337
bob.learn.em.train(trainer, machine, arStd, convergence_threshold=0.001)
[variances, weights] = machine.get_variances_and_weights_for_each_cluster(arStd)
means = numpy.array(machine.means)
variances = numpy.array(variances)
multiplyVectorsByFactors(means, std)
multiplyVectorsByFactors(variances, std ** 2)
gmmWeights = bob.io.base.load(datafile('gmm.init_weights.hdf5', __name__, path="../data/"))
gmmMeans = bob.io.base.load(datafile('gmm.init_means.hdf5', __name__, path="../data/"))
gmmVariances = bob.io.base.load(datafile('gmm.init_variances.hdf5', __name__, path="../data/"))
if (means[0, 0] < means[1, 0]):
means = flipRows(means)
variances = flipRows(variances)
weights = flipRows(weights)
assert equals(means, gmmMeans, 1e-3)
assert equals(weights, gmmWeights, 1e-3)
assert equals(variances, gmmVariances, 1e-3)
# Check that there is no duplicate means during initialization
machine = KMeansMachine(2, 1)
trainer = KMeansTrainer()
trainer.initialization_method = 'RANDOM_NO_DUPLICATE'
data = numpy.array([[1.], [1.], [1.], [1.], [1.], [1.], [2.], [3.]])
bob.learn.em.train(trainer, machine, data)
assert (numpy.isnan(machine.means).any()) == False
def test_custom_trainer():
# Custom python trainer
ar = bob.io.base.load(
datafile("faithful.torch3_f64.hdf5", __name__, path="../data/"))
mytrainer = MyTrainer1()
machine = KMeansMachine(2, 2)
mytrainer.train(machine, ar)
for i in range(0, 2):
assert (ar[i + 1] == machine.means[i, :]).all()
def test_kmeans_fit_init_random():
np.random.seed(0)
data1 = np.random.normal(loc=1, size=(2000, 3))
data2 = np.random.normal(loc=-1, size=(2000, 3))
data = np.concatenate([data1, data2], axis=0)
for transform in (to_numpy, to_dask_array):
data = transform(data)
machine = KMeansMachine(2, init_method="random",
random_state=0).fit(data)
centroids = machine.centroids_[np.argsort(machine.centroids_[:, 0])]
expected = [
[-1.07329460, -1.06207104, -1.00714365],
[0.99529015, 0.99570570, 0.97580858],
]
np.testing.assert_almost_equal(centroids, expected, decimal=7)
def test_kmeans_fit_init_pp():
np.random.seed(0)
data1 = np.random.normal(loc=1, size=(2000, 3))
data2 = np.random.normal(loc=-1, size=(2000, 3))
data = np.concatenate([data1, data2], axis=0)
for transform in (to_numpy, to_dask_array):
data = transform(data)
machine = KMeansMachine(2, init_method="k-means++",
random_state=0).fit(data)
centroids = machine.centroids_[np.argsort(machine.centroids_[:, 0])]
expected = [
[-1.07173464, -1.06200356, -1.00724920],
[0.99479125, 0.99665564, 0.97689017],
]
np.testing.assert_almost_equal(centroids, expected, decimal=7)
def test_gmm_kmeans_plusplus_init():
n_gaussians = 3
machine = GMMMachine(
n_gaussians,
k_means_trainer=KMeansMachine(n_clusters=n_gaussians,
init_method="k-means++"),
)
data = np.array([[1.5, 1], [1, 1.5], [-1, 0.5], [-1.5, 0], [2, 2],
[2.5, 2.5]])
for transform in (to_numpy, to_dask_array):
data = transform(data)
machine = machine.fit(data)
expected_means = np.array([[2.25, 2.25], [-1.25, 0.25], [1.25, 1.25]])
expected_variances = np.array([[1 / 16, 1 / 16], [1 / 16, 1 / 16],
[1 / 16, 1 / 16]])
np.testing.assert_almost_equal(machine.means,
expected_means,
decimal=3)
np.testing.assert_almost_equal(machine.variances, expected_variances)
def fit(self, array, y=None, **kwargs):
"""Trains the UBM."""
# Stack all the samples in a 2D array of features
if isinstance(array, da.Array):
array = array.persist()
# if input is a list (or SampleBatch) of 2 dimensional arrays, stack them
if array[0].ndim == 2:
array = np.vstack(array)
logger.debug(
f"Creating UBM machine with {self.number_of_gaussians} gaussians and {len(array)} samples"
)
self.ubm = GMMMachine(
n_gaussians=self.number_of_gaussians,
trainer="ml",
max_fitting_steps=self.ubm_training_iterations,
convergence_threshold=self.training_threshold,
update_means=self.update_means,
update_variances=self.update_variances,
update_weights=self.update_weights,
mean_var_update_threshold=self.variance_threshold,
k_means_trainer=KMeansMachine(
self.number_of_gaussians,
convergence_threshold=self.training_threshold,
max_iter=self.kmeans_training_iterations,
init_method="k-means||",
init_max_iter=self.kmeans_init_iterations,
random_state=self.init_seed,
oversampling_factor=self.kmeans_oversampling_factor,
),
)
# Train the GMM
logger.info("Training UBM GMM")
self.ubm.fit(array)
return self
def test_KMeansMachine():
# Test a KMeansMachine
means = numpy.array([[3, 70, 0], [4, 72, 0]], 'float64')
mean = numpy.array([3,70,1], 'float64')
# Initializes a KMeansMachine
km = KMeansMachine(2,3)
km.means = means
assert km.shape == (2,3)
# Sets and gets
assert (km.means == means).all()
assert (km.get_mean(0) == means[0,:]).all()
assert (km.get_mean(1) == means[1,:]).all()
km.set_mean(0, mean)
assert (km.get_mean(0) == mean).all()
# Distance and closest mean
eps = 1e-10
assert equals( km.get_distance_from_mean(mean, 0), 0, eps)
assert equals( km.get_distance_from_mean(mean, 1), 6, eps)
(index, dist) = km.get_closest_mean(mean)
assert index == 0
assert equals( dist, 0, eps)
assert equals( km.get_min_distance(mean), 0, eps)
# Loads and saves
filename = str(tempfile.mkstemp(".hdf5")[1])
km.save(bob.io.base.HDF5File(filename, 'w'))
km_loaded = KMeansMachine(bob.io.base.HDF5File(filename))
assert km == km_loaded
# Resize
km.resize(4,5)
assert km.shape == (4,5)
# Copy constructor and comparison operators
km.resize(2,3)
km2 = KMeansMachine(km)
assert km2 == km
assert (km2 != km) is False
assert km2.is_similar_to(km)
means2 = numpy.array([[3, 70, 0], [4, 72, 2]], 'float64')
km2.means = means2
assert (km2 == km) is False
assert km2 != km
assert (km2.is_similar_to(km)) is False
# Clean-up
os.unlink(filename)
import matplotlib.pyplot as plt
from sklearn.datasets import load_iris
from bob.learn.em import KMeansMachine
iris_data = load_iris()
data = iris_data.data
setosa = data[iris_data.target == 0]
versicolor = data[iris_data.target == 1]
virginica = data[iris_data.target == 2]
# Training KMeans
# 3 clusters with a feature dimensionality of 2
machine = KMeansMachine(n_clusters=3, init_method="k-means++").fit(data)
predictions = machine.predict(data)
# Plotting
figure, ax = plt.subplots()
plt.scatter(setosa[:, 0], setosa[:, 1], c="darkcyan", label="setosa")
plt.scatter(versicolor[:, 0],
versicolor[:, 1],
c="goldenrod",
label="versicolor")
plt.scatter(virginica[:, 0], virginica[:, 1], c="dimgrey", label="virginica")
plt.scatter(
machine.centroids_[:, 0],
machine.centroids_[:, 1],
c="blue",
marker="x",
def test_KMeansMachine():
# Test a KMeansMachine
means = numpy.array([[3, 70, 0], [4, 72, 0]], 'float64')
mean = numpy.array([3, 70, 1], 'float64')
# Initializes a KMeansMachine
km = KMeansMachine(2, 3)
km.means = means
assert km.shape == (2, 3)
# Sets and gets
assert (km.means == means).all()
assert (km.get_mean(0) == means[0, :]).all()
assert (km.get_mean(1) == means[1, :]).all()
km.set_mean(0, mean)
assert (km.get_mean(0) == mean).all()
# Distance and closest mean
eps = 1e-10
assert equals(km.get_distance_from_mean(mean, 0), 0, eps)
assert equals(km.get_distance_from_mean(mean, 1), 6, eps)
(index, dist) = km.get_closest_mean(mean)
assert index == 0
assert equals(dist, 0, eps)
assert equals(km.get_min_distance(mean), 0, eps)
# Loads and saves
filename = str(tempfile.mkstemp(".hdf5")[1])
km.save(bob.io.base.HDF5File(filename, 'w'))
km_loaded = KMeansMachine(bob.io.base.HDF5File(filename))
assert km == km_loaded
# Resize
km.resize(4, 5)
assert km.shape == (4, 5)
# Copy constructor and comparison operators
km.resize(2, 3)
km2 = KMeansMachine(km)
assert km2 == km
assert (km2 != km) is False
assert km2.is_similar_to(km)
means2 = numpy.array([[3, 70, 0], [4, 72, 2]], 'float64')
km2.means = means2
assert (km2 == km) is False
assert km2 != km
assert (km2.is_similar_to(km)) is False
# Clean-up
os.unlink(filename)
This pipeline is composed of the following steps:
- annotator: Energy_2Gauss (VAD on 2 Gaussians)
- extractor: Cepstral (MFCC, 60 features)
- algorithm: GMM (trained in the pipeline as a Transformer, and used as BioAlgorithm
for enrollment and scoring)
"""
# Number of Gaussians for the UBM (used by kmeans and GMM)
n_gaussians = 256
# Kmeans machine used for GMM initialization
kmeans_trainer = KMeansMachine(
n_clusters=n_gaussians,
max_iter=25,
convergence_threshold=0.0,
init_max_iter=5,
oversampling_factor=64,
)
# Algorithm used for enrollment and scoring, trained first as a Transformer.
bioalgorithm = GMM(
n_gaussians=n_gaussians,
max_fitting_steps=25,
enroll_iterations=1,
convergence_threshold=
0.0, # Maximum number of iterations as stopping criterion
k_means_trainer=kmeans_trainer,
random_state=2,
)
from bob.bio.spear.extractor import Cepstral
from bob.bio.spear.transformer import ReferenceIdEncoder
from bob.learn.em import KMeansMachine
from bob.pipelines import wrap
SEED = 0
ubm = GMM(
n_gaussians=256,
max_fitting_steps=2,
convergence_threshold=
1e-3, # Maximum number of iterations as stopping criterion
k_means_trainer=KMeansMachine(
n_clusters=256,
max_iter=2,
random_state=SEED,
init_max_iter=5,
oversampling_factor=64,
),
return_stats_in_transform=True,
)
bioalgorithm = ISV(
# ISV parameters
r_U=50,
random_state=SEED,
em_iterations=2,
enroll_iterations=1,
# GMM parameters
ubm=ubm,
)