def gmm(data, k):
"""Cluster based on gaussian mixture models
Parameters
----------
data : dict
features structure
k : int
number of clusters
Returns
-------
cl : int array
cluster indicies
Notes
-----
This function requires scikits-learn
"""
try:
clf = mixture.GMM(n_states=k, cvtype='full')
except TypeError:
clf = mixture.GMM(n_components=k, cvtype='full')
clf.fit(data)
cl = clf.predict(data)
return cl
def classify_speech(energy):
""" Trains a two mixture GMM based on the energy component in each frame.
Usage: energy_segmentation = classify_speech(energy)
Inputs:
energy -- Numpy array of energy in each frame
Outputs:
energy_segmentation -- Numpy array of detected speech (1=speech, 0=silence)
"""
g = mixture.GMM(n_states=2)
g.fit(energy)
#Higher energy indicates speech, location in GMM mean
#vector can vary based on initial conditions
if g.means[0] > g.means[1]:
energy_tag = 0
silence_tag = 1
else:
energy_tag = 1
silence_tag = 0
speech_predict = g.predict(energy)
#Return 1 where speech detected, 0 otherwise
energy_segmentation = np.zeros(np.shape(energy), dtype=np.int)
energy_segmentation[speech_predict == energy_tag] = 1
energy_segmentation[speech_predict == silence_tag] = 0
return energy_segmentation
def test_train(self, params='wmc'):
g = mixture.GMM(self.n_states, self.cvtype)
g.weights = self.weights
g.means = self.means
g._covars = 20 * self.covars[self.cvtype]
# Create a training set by sampling from the predefined distribution.
train_obs = g.rvs(n_samples=100)
g.fit(train_obs, n_iter=0, init_params=params)
# Do one training iteration at a time so we can keep track of
# the log likelihood to make sure that it increases after each
# iteration.
trainll = []
for iter in xrange(5):
g.fit(train_obs,
n_iter=1,
params=params,
init_params='',
min_covar=1e-1)
trainll.append(g.score(train_obs).sum())
# Note that the log likelihood will sometimes decrease by a
# very small amount after it has more or less converged due to
# the addition of min_covar to the covariance (to prevent
# underflow). This is why the threshold is set to -0.5
# instead of 0.
self.assertTrue(np.all(np.diff(trainll) > -0.5))
def create_random_gmm(n_mix, n_features, cvtype):
from scikits.learn import mixture
g = mixture.GMM(n_mix, cvtype=cvtype)
g.means = np.random.randint(-20, 20, (n_mix, n_features))
mincv = 0.1
<<<<<<< REMOTE
def test_GMM_attributes():
n_states, n_features = 10, 4
cvtype = 'diag'
g = mixture.GMM(n_states, cvtype)
weights = np.random.rand(n_states)
weights = weights / weights.sum()
means = np.random.randint(-20, 20, (n_states, n_features))
assert g.n_states == n_states
assert g.cvtype == cvtype
g.weights = weights
assert_array_almost_equal(g.weights, weights)
assert_raises(ValueError, g.__setattr__, 'weights', 2 * weights)
assert_raises(ValueError, g.__setattr__, 'weights', [])
assert_raises(ValueError, g.__setattr__, 'weights',
np.zeros((n_states - 2, n_features)))
g.means = means
assert_array_almost_equal(g.means, means)
assert_raises(ValueError, g.__setattr__, 'means', [])
assert_raises(ValueError, g.__setattr__, 'means',
np.zeros((n_states - 2, n_features)))
covars = (0.1 + 2 * np.random.rand(n_states, n_features))**2
g._covars = covars
assert_array_almost_equal(g._covars, covars)
assert_raises(ValueError, g.__setattr__, 'covars', [])
assert_raises(ValueError, g.__setattr__, 'covars',
np.zeros((n_states - 2, n_features)))
assert_raises(ValueError, mixture.GMM, n_states=20, cvtype='badcvtype')
def test_rvs(self, n=100):
g = mixture.GMM(self.n_states, self.cvtype)
# Make sure the means are far apart so posteriors.argmax()
# picks the actual component used to generate the observations.
g.means = 20 * self.means
g._covars = np.maximum(self.covars[self.cvtype], 0.1)
g.weights = self.weights
samples = g.rvs(n)
self.assertEquals(samples.shape, (n, self.n_features))
def convert_type_db_gmm(u):
"""
Given compressed numpy arrays that specify a GMM from database
convert back to type scikits.learn.GMM
"""
world = mixture.GMM(n_states=np.size(u.ubm_means, 0))
world.means = u.ubm_means
vars_diag = np.zeros((np.size(u.ubm_vars, 0), np.size(u.ubm_vars, 1)),
dtype=np.float)
for i in range(np.size(vars_diag, 0)):
vars_diag[i, :] = np.diag(u.ubm_vars[i])
world.covars = vars_diag
world.weights = np.reshape(u.ubm_weights, (np.size(u.ubm_weights, 0), ))
return world
def test_eval(self):
g = mixture.GMM(self.n_states, self.cvtype)
# Make sure the means are far apart so posteriors.argmax()
# picks the actual component used to generate the observations.
g.means = 20 * self.means
g._covars = self.covars[self.cvtype]
g.weights = self.weights
gaussidx = np.repeat(range(self.n_states), 5)
nobs = len(gaussidx)
obs = np.random.randn(nobs, self.n_features) + g.means[gaussidx]
ll, posteriors = g.eval(obs)
self.assertEqual(len(ll), nobs)
self.assertEqual(posteriors.shape, (nobs, self.n_states))
assert_array_almost_equal(posteriors.sum(axis=1), np.ones(nobs))
assert_array_equal(posteriors.argmax(axis=1), gaussidx)
def create_random_gmm(n_mix, n_features, cvtype):
from scikits.learn import mixture
g = mixture.GMM(n_mix, cvtype=cvtype)
g.means = np.random.randint(-20, 20, (n_mix, n_features))
mincv = 0.1
g.covars = {
'spherical': (mincv + mincv * np.random.rand(n_mix))**2,
'tied':
_generate_random_spd_matrix(n_features) + mincv * np.eye(n_features),
'diag': (mincv + mincv * np.random.rand(n_mix, n_features))**2,
'full':
np.array([
_generate_random_spd_matrix(n_features) +
mincv * np.eye(n_features) for x in xrange(n_mix)
])
}[cvtype]
g.weights = hmm.normalize(np.random.rand(n_mix))
return g
def map_adapt_speaker(obs, world, r_m=16.0, r_w=16.0):
# Catch fatal errors
assert isinstance(world, type(mixture.GMM()))
assert np.size(obs, 1) == np.size(world.means, 1)
assert np.size(obs, 0) > 1
#Cast if passed in int type
r_m = float(r_m)
r_w = float(r_w)
#Posterior probabilities
# for X = {x_1, ..., x_T}
# P(i|x_t) = w_i * p_i(x_t) / sum_j=1_M(w_j * P_j(x_t))
posterior = world.predict_proba(obs)
#print np.shape(posterior)
n_i = np.sum(posterior, 0)
#print np.shape(n_i)
E_i = np.zeros((world.n_states, np.size(obs, 1)), dtype=np.float)
for i in range(world.n_states):
#print np.shape(posterior[:,i]), np.shape(obs), np.shape(n_i[i])
post_i = np.reshape(posterior[:, i], (np.size(obs, 0), 1))
#print np.shape(post_i)
E_i[i, :] = np.sum(post_i * obs, 0) / n_i[i]
a_i_mean = np.reshape(n_i / (n_i + r_m), (world.n_states, 1))
a_i_weight = n_i / (n_i + r_w)
T = float(np.size(obs, 0))
w_hat = a_i_weight * n_i / T + (1.0 - a_i_weight) * world.weights
w_hat = w_hat / np.sum(w_hat)
#print np.shape(E_i), np.shape(world.means), np.shape(a_i_mean)
u_hat = a_i_mean * E_i + (1.0 - a_i_mean) * world.means
return w_hat, u_hat
def train_gmm(obs, world=None, params={'num_mixtures': 1024}):
""" Trains a GMM using N mixtures from given observations.
Usage: world = train_gmm(obs, world, params)
Inputs:
obs -- MxN Numpy array of observations (M observations to be clustered in N-dimensional space)
world -- Previous world model to use for initialization (if not supplied, will initialize automagically)
params -- {'num_mixtures': X} Use X mixtures in model, defaults to 1024
Outputs:
world -- GMM class output (contains means, weights, covars)
"""
if log(params['num_mixtures'],2) % 1:
logging.warn('Number of mixtures not power of 2. Will run slow.')
if not world:
world = mixture.GMM(n_states=params['num_mixtures'])
world.fit(obs)
else:
world.fit(obs, init_params='')
return world
features = shapeAnalysis(mask)
features += colorAnalysis(hsv, mask)
#features += featurePoints(greyscaleImg, mask)
print "features : ", features
nbFeatures = len(features)
n, m = 100, 2
# generate random sample, two components
np.random.seed(0)
C = np.random.randn(n, nbFeatures)
X = np.r_[np.dot(np.random.randn(nbFeatures, n), C),
np.random.randn(n, nbFeatures) + C]
clf = mixture.GMM(n_states=10, cvtype='tied')
clf.fit(X)
print clf.decode(X)
splot = pl.subplot(111, aspect='equal')
color_iter = itertools.cycle(['r', 'g', 'b', 'c'])
Y_ = clf.predict(X)
for i, (mean, covar, color) in enumerate(zip(clf.means, clf.covars,
color_iter)):
v, w = np.linalg.eigh(covar)
u = w[0] / np.linalg.norm(w[0])
pl.scatter(X[Y_ == i, 0], X[Y_ == i, 1], .8, color=color)
angle = np.arctan(u[1] / u[0])
angle = 180 * angle / np.pi # convert to degrees
import numpy as np
from scikits.learn import mixture
import itertools
import pylab as pl
import matplotlib as mpl
n, m = 300, 2
# generate random sample, two components
np.random.seed(0)
C = np.array([[0., -0.7], [3.5, .7]])
X = np.r_[np.dot(np.random.randn(n, 2), C),
np.random.randn(n, 2) + np.array([3, 3])]
clf = mixture.GMM(n_states=2, cvtype='full')
clf.fit(X)
splot = pl.subplot(111, aspect='equal')
color_iter = itertools.cycle(['r', 'g', 'b', 'c'])
Y_ = clf.predict(X)
for i, (mean, covar, color) in enumerate(zip(clf.means, clf.covars,
color_iter)):
v, w = np.linalg.eigh(covar)
u = w[0] / np.linalg.norm(w[0])
pl.scatter(X[Y_ == i, 0], X[Y_ == i, 1], .8, color=color)
angle = np.arctan(u[1] / u[0])
angle = 180 * angle / np.pi # convert to degrees
ell = mpl.patches.Ellipse(mean, v[0], v[1], 180 + angle, color=color)