def test_vq_large_nfeat(self):
X = np.random.rand(20, 20)
code_book = np.random.rand(3, 20)
codes0, dis0 = _vq.vq(X, code_book)
codes1, dis1 = py_vq(X, code_book)
assert_allclose(dis0, dis1, 1e-5)
assert_array_equal(codes0, codes1)
X = X.astype(np.float32)
code_book = code_book.astype(np.float32)
codes0, dis0 = _vq.vq(X, code_book)
codes1, dis1 = py_vq(X, code_book)
assert_allclose(dis0, dis1, 1e-5)
assert_array_equal(codes0, codes1)
def test_vq(self):
initc = np.concatenate(([[X[0]], [X[1]], [X[2]]]))
if TESTC:
label1, dist = _vq.vq(X, initc)
assert_array_equal(label1, LABEL1)
tlabel1, tdist = vq(X, initc)
else:
print("== not testing C imp of vq ==")
def test_vq_1d(self):
"""Test special rank 1 vq algo, python implementation."""
data = X[:, 0]
initc = data[:3]
a, b = _vq.vq(data, initc)
ta, tb = py_vq(data[:, np.newaxis], initc[:, np.newaxis])
assert_array_equal(a, ta)
assert_array_equal(b, tb)
def test_vq_large_features(self):
X = np.random.rand(10, 5) * 1000000
code_book = np.random.rand(2, 5) * 1000000
codes0, dis0 = _vq.vq(X, code_book)
codes1, dis1 = py_vq(X, code_book)
assert_allclose(dis0, dis1, 1e-5)
assert_array_equal(codes0, codes1)
def test_vq_1d(self):
"""Test special rank 1 vq algo, python implementation."""
data = X[:, 0]
initc = data[:3]
if TESTC:
a, b = _vq.vq(data, initc)
ta, tb = py_vq(data[:, np.newaxis], initc[:, np.newaxis])
assert_array_equal(a, ta)
assert_array_equal(b, tb)
else:
print("== not testing C imp of vq (rank 1) ==")
def test_vq(self):
initc = np.concatenate(([[X[0]], [X[1]], [X[2]]]))
label1, dist = _vq.vq(X, initc)
assert_array_equal(label1, LABEL1)
tlabel1, tdist = vq(X, initc)
def test_vq(self):
initc = np.concatenate(([[X[0]], [X[1]], [X[2]]]))
for tp in np.array, np.matrix:
label1, dist = _vq.vq(tp(X), tp(initc))
assert_array_equal(label1, LABEL1)
tlabel1, tdist = vq(tp(X), tp(initc))
def test_vq(self):
initc = np.concatenate(([[X[0]], [X[1]], [X[2]]]))
for tp in np.array, np.matrix:
label1, dist = _vq.vq(tp(X), tp(initc))
assert_array_equal(label1, LABEL1)
tlabel1, tdist = vq(tp(X), tp(initc))
def vq(obs, code_book, check_finite=True):
"""
Assign codes from a code book to observations.
Assigns a code from a code book to each observation. Each
observation vector in the 'M' by 'N' `obs` array is compared with the
centroids in the code book and assigned the code of the closest
centroid.
The features in `obs` should have unit variance, which can be
achieved by passing them through the whiten function. The code
book can be created with the k-means algorithm or a different
encoding algorithm.
Parameters
----------
obs : ndarray
Each row of the 'M' x 'N' array is an observation. The columns are
the "features" seen during each observation. The features must be
whitened first using the whiten function or something equivalent.
code_book : ndarray
The code book is usually generated using the k-means algorithm.
Each row of the array holds a different code, and the columns are
the features of the code.
>>> # f0 f1 f2 f3
>>> code_book = [
... [ 1., 2., 3., 4.], #c0
... [ 1., 2., 3., 4.], #c1
... [ 1., 2., 3., 4.]] #c2
check_finite : bool, optional
Whether to check that the input matrices contain only finite numbers.
Disabling may give a performance gain, but may result in problems
(crashes, non-termination) if the inputs do contain infinities or NaNs.
Default: True
Returns
-------
code : ndarray
A length M array holding the code book index for each observation.
dist : ndarray
The distortion (distance) between the observation and its nearest
code.
Examples
--------
>>> from numpy import array
>>> from scipy.cluster.vq import vq
>>> code_book = array([[1.,1.,1.],
... [2.,2.,2.]])
>>> features = array([[ 1.9,2.3,1.7],
... [ 1.5,2.5,2.2],
... [ 0.8,0.6,1.7]])
>>> vq(features,code_book)
(array([1, 1, 0],'i'), array([ 0.43588989, 0.73484692, 0.83066239]))
"""
obs = _asarray_validated(obs, check_finite=check_finite)
code_book = _asarray_validated(code_book, check_finite=check_finite)
ct = common_type(obs, code_book)
# avoid copying when dtype is the same
# should be replaced with c_obs = astype(ct, copy=False)
# when we get to numpy 1.7.0
if obs.dtype != ct:
c_obs = obs.astype(ct)
else:
c_obs = obs
if code_book.dtype != ct:
c_code_book = code_book.astype(ct)
else:
c_code_book = code_book
if ct in (single, double):
results = _vq.vq(c_obs, c_code_book)
else:
results = py_vq(obs, code_book)
return results
def test_vq(self):
initc = np.concatenate(([[X[0]], [X[1]], [X[2]]]))
label1, dist = _vq.vq(X, initc)
assert_array_equal(label1, LABEL1)
tlabel1, tdist = vq(X, initc)