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import warnings
import sys
from copy import deepcopy
from threading import Lock
import numpy as np
from numpy.testing import (
assert_array_equal, assert_equal, assert_, suppress_warnings
)
import pytest
from pytest import raises as assert_raises
from scipy.cluster.vq import (kmeans, kmeans2, py_vq, vq, whiten,
ClusterError, _krandinit)
from scipy.cluster import _vq
from scipy.conftest import array_api_compatible
from scipy.sparse._sputils import matrix
from scipy._lib import array_api_extra as xpx
from scipy._lib._array_api import (
SCIPY_ARRAY_API, array_namespace, xp_copy, xp_assert_close, xp_assert_equal
)
pytestmark = [array_api_compatible, pytest.mark.usefixtures("skip_xp_backends")]
skip_xp_backends = pytest.mark.skip_xp_backends
TESTDATA_2D = np.array([
-2.2, 1.17, -1.63, 1.69, -2.04, 4.38, -3.09, 0.95, -1.7, 4.79, -1.68, 0.68,
-2.26, 3.34, -2.29, 2.55, -1.72, -0.72, -1.99, 2.34, -2.75, 3.43, -2.45,
2.41, -4.26, 3.65, -1.57, 1.87, -1.96, 4.03, -3.01, 3.86, -2.53, 1.28,
-4.0, 3.95, -1.62, 1.25, -3.42, 3.17, -1.17, 0.12, -3.03, -0.27, -2.07,
-0.55, -1.17, 1.34, -2.82, 3.08, -2.44, 0.24, -1.71, 2.48, -5.23, 4.29,
-2.08, 3.69, -1.89, 3.62, -2.09, 0.26, -0.92, 1.07, -2.25, 0.88, -2.25,
2.02, -4.31, 3.86, -2.03, 3.42, -2.76, 0.3, -2.48, -0.29, -3.42, 3.21,
-2.3, 1.73, -2.84, 0.69, -1.81, 2.48, -5.24, 4.52, -2.8, 1.31, -1.67,
-2.34, -1.18, 2.17, -2.17, 2.82, -1.85, 2.25, -2.45, 1.86, -6.79, 3.94,
-2.33, 1.89, -1.55, 2.08, -1.36, 0.93, -2.51, 2.74, -2.39, 3.92, -3.33,
2.99, -2.06, -0.9, -2.83, 3.35, -2.59, 3.05, -2.36, 1.85, -1.69, 1.8,
-1.39, 0.66, -2.06, 0.38, -1.47, 0.44, -4.68, 3.77, -5.58, 3.44, -2.29,
2.24, -1.04, -0.38, -1.85, 4.23, -2.88, 0.73, -2.59, 1.39, -1.34, 1.75,
-1.95, 1.3, -2.45, 3.09, -1.99, 3.41, -5.55, 5.21, -1.73, 2.52, -2.17,
0.85, -2.06, 0.49, -2.54, 2.07, -2.03, 1.3, -3.23, 3.09, -1.55, 1.44,
-0.81, 1.1, -2.99, 2.92, -1.59, 2.18, -2.45, -0.73, -3.12, -1.3, -2.83,
0.2, -2.77, 3.24, -1.98, 1.6, -4.59, 3.39, -4.85, 3.75, -2.25, 1.71, -3.28,
3.38, -1.74, 0.88, -2.41, 1.92, -2.24, 1.19, -2.48, 1.06, -1.68, -0.62,
-1.3, 0.39, -1.78, 2.35, -3.54, 2.44, -1.32, 0.66, -2.38, 2.76, -2.35,
3.95, -1.86, 4.32, -2.01, -1.23, -1.79, 2.76, -2.13, -0.13, -5.25, 3.84,
-2.24, 1.59, -4.85, 2.96, -2.41, 0.01, -0.43, 0.13, -3.92, 2.91, -1.75,
-0.53, -1.69, 1.69, -1.09, 0.15, -2.11, 2.17, -1.53, 1.22, -2.1, -0.86,
-2.56, 2.28, -3.02, 3.33, -1.12, 3.86, -2.18, -1.19, -3.03, 0.79, -0.83,
0.97, -3.19, 1.45, -1.34, 1.28, -2.52, 4.22, -4.53, 3.22, -1.97, 1.75,
-2.36, 3.19, -0.83, 1.53, -1.59, 1.86, -2.17, 2.3, -1.63, 2.71, -2.03,
3.75, -2.57, -0.6, -1.47, 1.33, -1.95, 0.7, -1.65, 1.27, -1.42, 1.09, -3.0,
3.87, -2.51, 3.06, -2.6, 0.74, -1.08, -0.03, -2.44, 1.31, -2.65, 2.99,
-1.84, 1.65, -4.76, 3.75, -2.07, 3.98, -2.4, 2.67, -2.21, 1.49, -1.21,
1.22, -5.29, 2.38, -2.85, 2.28, -5.6, 3.78, -2.7, 0.8, -1.81, 3.5, -3.75,
4.17, -1.29, 2.99, -5.92, 3.43, -1.83, 1.23, -1.24, -1.04, -2.56, 2.37,
-3.26, 0.39, -4.63, 2.51, -4.52, 3.04, -1.7, 0.36, -1.41, 0.04, -2.1, 1.0,
-1.87, 3.78, -4.32, 3.59, -2.24, 1.38, -1.99, -0.22, -1.87, 1.95, -0.84,
2.17, -5.38, 3.56, -1.27, 2.9, -1.79, 3.31, -5.47, 3.85, -1.44, 3.69,
-2.02, 0.37, -1.29, 0.33, -2.34, 2.56, -1.74, -1.27, -1.97, 1.22, -2.51,
-0.16, -1.64, -0.96, -2.99, 1.4, -1.53, 3.31, -2.24, 0.45, -2.46, 1.71,
-2.88, 1.56, -1.63, 1.46, -1.41, 0.68, -1.96, 2.76, -1.61,
2.11]).reshape((200, 2))
# Global data
X = np.array([[3.0, 3], [4, 3], [4, 2],
[9, 2], [5, 1], [6, 2], [9, 4],
[5, 2], [5, 4], [7, 4], [6, 5]])
CODET1 = np.array([[3.0000, 3.0000],
[6.2000, 4.0000],
[5.8000, 1.8000]])
CODET2 = np.array([[11.0/3, 8.0/3],
[6.7500, 4.2500],
[6.2500, 1.7500]])
LABEL1 = np.array([0, 1, 2, 2, 2, 2, 1, 2, 1, 1, 1])
class TestWhiten:
def test_whiten(self, xp):
desired = xp.asarray([[5.08738849, 2.97091878],
[3.19909255, 0.69660580],
[4.51041982, 0.02640918],
[4.38567074, 0.95120889],
[2.32191480, 1.63195503]])
obs = xp.asarray([[0.98744510, 0.82766775],
[0.62093317, 0.19406729],
[0.87545741, 0.00735733],
[0.85124403, 0.26499712],
[0.45067590, 0.45464607]])
xp_assert_close(whiten(obs), desired, rtol=1e-5)
@pytest.fixture
def whiten_lock(self):
return Lock()
@skip_xp_backends('jax.numpy',
reason='jax arrays do not support item assignment')
def test_whiten_zero_std(self, xp, whiten_lock):
desired = xp.asarray([[0., 1.0, 2.86666544],
[0., 1.0, 1.32460034],
[0., 1.0, 3.74382172]])
obs = xp.asarray([[0., 1., 0.74109533],
[0., 1., 0.34243798],
[0., 1., 0.96785929]])
with whiten_lock:
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
xp_assert_close(whiten(obs), desired, rtol=1e-5)
assert_equal(len(w), 1)
assert_(issubclass(w[-1].category, RuntimeWarning))
def test_whiten_not_finite(self, xp):
for bad_value in xp.nan, xp.inf, -xp.inf:
obs = xp.asarray([[0.98744510, bad_value],
[0.62093317, 0.19406729],
[0.87545741, 0.00735733],
[0.85124403, 0.26499712],
[0.45067590, 0.45464607]])
assert_raises(ValueError, whiten, obs)
@pytest.mark.skipif(SCIPY_ARRAY_API,
reason='`np.matrix` unsupported in array API mode')
def test_whiten_not_finite_matrix(self, xp):
for bad_value in np.nan, np.inf, -np.inf:
obs = matrix([[0.98744510, bad_value],
[0.62093317, 0.19406729],
[0.87545741, 0.00735733],
[0.85124403, 0.26499712],
[0.45067590, 0.45464607]])
assert_raises(ValueError, whiten, obs)
class TestVq:
@skip_xp_backends(cpu_only=True)
def test_py_vq(self, xp):
initc = np.concatenate([[X[0]], [X[1]], [X[2]]])
# label1.dtype varies between int32 and int64 over platforms
label1 = py_vq(xp.asarray(X), xp.asarray(initc))[0]
xp_assert_equal(label1, xp.asarray(LABEL1, dtype=xp.int64),
check_dtype=False)
@pytest.mark.skipif(SCIPY_ARRAY_API,
reason='`np.matrix` unsupported in array API mode')
def test_py_vq_matrix(self, xp):
initc = np.concatenate([[X[0]], [X[1]], [X[2]]])
# label1.dtype varies between int32 and int64 over platforms
label1 = py_vq(matrix(X), matrix(initc))[0]
assert_array_equal(label1, LABEL1)
@skip_xp_backends(np_only=True, reason='`_vq` only supports NumPy backend')
def test_vq(self, xp):
initc = np.concatenate([[X[0]], [X[1]], [X[2]]])
label1, _ = _vq.vq(xp.asarray(X), xp.asarray(initc))
assert_array_equal(label1, LABEL1)
_, _ = vq(xp.asarray(X), xp.asarray(initc))
@pytest.mark.skipif(SCIPY_ARRAY_API,
reason='`np.matrix` unsupported in array API mode')
def test_vq_matrix(self, xp):
initc = np.concatenate([[X[0]], [X[1]], [X[2]]])
label1, _ = _vq.vq(matrix(X), matrix(initc))
assert_array_equal(label1, LABEL1)
_, _ = vq(matrix(X), matrix(initc))
@skip_xp_backends(cpu_only=True)
def test_vq_1d(self, xp):
# Test special rank 1 vq algo, python implementation.
data = X[:, 0]
initc = data[:3]
a, b = _vq.vq(data, initc)
data = xp.asarray(data)
initc = xp.asarray(initc)
ta, tb = py_vq(data[:, np.newaxis], initc[:, np.newaxis])
# ta.dtype varies between int32 and int64 over platforms
xp_assert_equal(ta, xp.asarray(a, dtype=xp.int64), check_dtype=False)
xp_assert_equal(tb, xp.asarray(b))
@skip_xp_backends(np_only=True, reason='`_vq` only supports NumPy backend')
def test__vq_sametype(self, xp):
a = xp.asarray([1.0, 2.0], dtype=xp.float64)
b = a.astype(xp.float32)
assert_raises(TypeError, _vq.vq, a, b)
@skip_xp_backends(np_only=True, reason='`_vq` only supports NumPy backend')
def test__vq_invalid_type(self, xp):
a = xp.asarray([1, 2], dtype=int)
assert_raises(TypeError, _vq.vq, a, a)
@skip_xp_backends(cpu_only=True)
def test_vq_large_nfeat(self, xp):
X = np.random.rand(20, 20)
code_book = np.random.rand(3, 20)
codes0, dis0 = _vq.vq(X, code_book)
codes1, dis1 = py_vq(
xp.asarray(X), xp.asarray(code_book)
)
xp_assert_close(dis1, xp.asarray(dis0), rtol=1e-5)
# codes1.dtype varies between int32 and int64 over platforms
xp_assert_equal(codes1, xp.asarray(codes0, dtype=xp.int64), check_dtype=False)
X = X.astype(np.float32)
code_book = code_book.astype(np.float32)
codes0, dis0 = _vq.vq(X, code_book)
codes1, dis1 = py_vq(
xp.asarray(X), xp.asarray(code_book)
)
xp_assert_close(dis1, xp.asarray(dis0, dtype=xp.float64), rtol=1e-5)
# codes1.dtype varies between int32 and int64 over platforms
xp_assert_equal(codes1, xp.asarray(codes0, dtype=xp.int64), check_dtype=False)
@skip_xp_backends(cpu_only=True)
def test_vq_large_features(self, xp):
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(
xp.asarray(X), xp.asarray(code_book)
)
xp_assert_close(dis1, xp.asarray(dis0), rtol=1e-5)
# codes1.dtype varies between int32 and int64 over platforms
xp_assert_equal(codes1, xp.asarray(codes0, dtype=xp.int64), check_dtype=False)
# Whole class skipped on GPU for now;
# once pdist/cdist are hooked up for CuPy, more tests will work
@skip_xp_backends(cpu_only=True)
class TestKMean:
def test_large_features(self, xp):
# Generate a data set with large values, and run kmeans on it to
# (regression for 1077).
d = 300
n = 100
m1 = np.random.randn(d)
m2 = np.random.randn(d)
x = 10000 * np.random.randn(n, d) - 20000 * m1
y = 10000 * np.random.randn(n, d) + 20000 * m2
data = np.empty((x.shape[0] + y.shape[0], d), np.float64)
data[:x.shape[0]] = x
data[x.shape[0]:] = y
# use `seed` to ensure backwards compatibility after SPEC7
kmeans(xp.asarray(data), 2, seed=1)
def test_kmeans_simple(self, xp):
rng = np.random.default_rng(54321)
initc = np.concatenate([[X[0]], [X[1]], [X[2]]])
code1 = kmeans(xp.asarray(X), xp.asarray(initc), iter=1, rng=rng)[0]
xp_assert_close(code1, xp.asarray(CODET2))
@pytest.mark.skipif(SCIPY_ARRAY_API,
reason='`np.matrix` unsupported in array API mode')
def test_kmeans_simple_matrix(self, xp):
rng = np.random.default_rng(54321)
initc = np.concatenate([[X[0]], [X[1]], [X[2]]])
code1 = kmeans(matrix(X), matrix(initc), iter=1, rng=rng)[0]
xp_assert_close(code1, CODET2)
def test_kmeans_lost_cluster(self, xp):
# This will cause kmeans to have a cluster with no points.
data = xp.asarray(TESTDATA_2D)
initk = xp.asarray([[-1.8127404, -0.67128041],
[2.04621601, 0.07401111],
[-2.31149087, -0.05160469]])
kmeans(data, initk)
with suppress_warnings() as sup:
sup.filter(UserWarning,
"One of the clusters is empty. Re-run kmeans with a "
"different initialization")
kmeans2(data, initk, missing='warn')
assert_raises(ClusterError, kmeans2, data, initk, missing='raise')
def test_kmeans2_simple(self, xp):
rng = np.random.default_rng(12345678)
initc = xp.asarray(np.concatenate([[X[0]], [X[1]], [X[2]]]))
arrays = [xp.asarray] if SCIPY_ARRAY_API else [np.asarray, matrix]
for tp in arrays:
code1 = kmeans2(tp(X), tp(initc), iter=1, rng=rng)[0]
code2 = kmeans2(tp(X), tp(initc), iter=2, rng=rng)[0]
xp_assert_close(code1, xp.asarray(CODET1))
xp_assert_close(code2, xp.asarray(CODET2))
@pytest.mark.skipif(SCIPY_ARRAY_API,
reason='`np.matrix` unsupported in array API mode')
def test_kmeans2_simple_matrix(self, xp):
rng = np.random.default_rng(12345678)
initc = xp.asarray(np.concatenate([[X[0]], [X[1]], [X[2]]]))
code1 = kmeans2(matrix(X), matrix(initc), iter=1, rng=rng)[0]
code2 = kmeans2(matrix(X), matrix(initc), iter=2, rng=rng)[0]
xp_assert_close(code1, CODET1)
xp_assert_close(code2, CODET2)
def test_kmeans2_rank1(self, xp):
data = xp.asarray(TESTDATA_2D)
data1 = data[:, 0]
initc = data1[:3]
code = xp_copy(initc, xp=xp)
# use `seed` to ensure backwards compatibility after SPEC7
kmeans2(data1, code, iter=1, seed=1)[0]
kmeans2(data1, code, iter=2)[0]
def test_kmeans2_rank1_2(self, xp):
data = xp.asarray(TESTDATA_2D)
data1 = data[:, 0]
kmeans2(data1, 2, iter=1)
def test_kmeans2_high_dim(self, xp):
# test kmeans2 when the number of dimensions exceeds the number
# of input points
data = xp.asarray(TESTDATA_2D)
data = xp.reshape(data, (20, 20))[:10, :]
kmeans2(data, 2)
@skip_xp_backends('jax.numpy',
reason='jax arrays do not support item assignment')
def test_kmeans2_init(self, xp):
rng = np.random.default_rng(12345678)
data = xp.asarray(TESTDATA_2D)
k = 3
kmeans2(data, k, minit='points', rng=rng)
kmeans2(data[:, 1], k, minit='points', rng=rng) # special case (1-D)
kmeans2(data, k, minit='++', rng=rng)
kmeans2(data[:, 1], k, minit='++', rng=rng) # special case (1-D)
# minit='random' can give warnings, filter those
with suppress_warnings() as sup:
sup.filter(message="One of the clusters is empty. Re-run.")
kmeans2(data, k, minit='random', rng=rng)
kmeans2(data[:, 1], k, minit='random', rng=rng) # special case (1-D)
@pytest.fixture
def krand_lock(self):
return Lock()
@pytest.mark.skipif(sys.platform == 'win32',
reason='Fails with MemoryError in Wine.')
def test_krandinit(self, xp, krand_lock):
data = xp.asarray(TESTDATA_2D)
datas = [xp.reshape(data, (200, 2)),
xp.reshape(data, (20, 20))[:10, :]]
k = int(1e6)
xp_test = array_namespace(data)
with krand_lock:
for data in datas:
rng = np.random.default_rng(1234)
init = _krandinit(data, k, rng, xp_test)
orig_cov = xpx.cov(data.T, xp=xp_test)
init_cov = xpx.cov(init.T, xp=xp_test)
xp_assert_close(orig_cov, init_cov, atol=1.1e-2)
def test_kmeans2_empty(self, xp):
# Regression test for gh-1032.
assert_raises(ValueError, kmeans2, xp.asarray([]), 2)
def test_kmeans_0k(self, xp):
# Regression test for gh-1073: fail when k arg is 0.
assert_raises(ValueError, kmeans, xp.asarray(X), 0)
assert_raises(ValueError, kmeans2, xp.asarray(X), 0)
assert_raises(ValueError, kmeans2, xp.asarray(X), xp.asarray([]))
def test_kmeans_large_thres(self, xp):
# Regression test for gh-1774
x = xp.asarray([1, 2, 3, 4, 10], dtype=xp.float64)
res = kmeans(x, 1, thresh=1e16)
xp_assert_close(res[0], xp.asarray([4.], dtype=xp.float64))
xp_assert_close(res[1], xp.asarray(2.3999999999999999, dtype=xp.float64)[()])
@skip_xp_backends('jax.numpy',
reason='jax arrays do not support item assignment')
def test_kmeans2_kpp_low_dim(self, xp):
# Regression test for gh-11462
rng = np.random.default_rng(2358792345678234568)
prev_res = xp.asarray([[-1.95266667, 0.898],
[-3.153375, 3.3945]], dtype=xp.float64)
res, _ = kmeans2(xp.asarray(TESTDATA_2D), 2, minit='++', rng=rng)
xp_assert_close(res, prev_res)
@pytest.mark.thread_unsafe
@skip_xp_backends('jax.numpy',
reason='jax arrays do not support item assignment')
def test_kmeans2_kpp_high_dim(self, xp):
# Regression test for gh-11462
rng = np.random.default_rng(23587923456834568)
n_dim = 100
size = 10
centers = np.vstack([5 * np.ones(n_dim),
-5 * np.ones(n_dim)])
data = np.vstack([
rng.multivariate_normal(centers[0], np.eye(n_dim), size=size),
rng.multivariate_normal(centers[1], np.eye(n_dim), size=size)
])
data = xp.asarray(data)
res, _ = kmeans2(data, 2, minit='++', rng=rng)
xp_assert_equal(xp.sign(res), xp.sign(xp.asarray(centers)))
def test_kmeans_diff_convergence(self, xp):
# Regression test for gh-8727
obs = xp.asarray([-3, -1, 0, 1, 1, 8], dtype=xp.float64)
res = kmeans(obs, xp.asarray([-3., 0.99]))
xp_assert_close(res[0], xp.asarray([-0.4, 8.], dtype=xp.float64))
xp_assert_close(res[1], xp.asarray(1.0666666666666667, dtype=xp.float64)[()])
@skip_xp_backends('jax.numpy',
reason='jax arrays do not support item assignment')
def test_kmeans_and_kmeans2_random_seed(self, xp):
seed_list = [
1234, np.random.RandomState(1234), np.random.default_rng(1234)
]
for seed in seed_list:
seed1 = deepcopy(seed)
seed2 = deepcopy(seed)
data = xp.asarray(TESTDATA_2D)
# test for kmeans
res1, _ = kmeans(data, 2, seed=seed1)
res2, _ = kmeans(data, 2, seed=seed2)
xp_assert_close(res1, res2) # should be same results
# test for kmeans2
for minit in ["random", "points", "++"]:
res1, _ = kmeans2(data, 2, minit=minit, seed=seed1)
res2, _ = kmeans2(data, 2, minit=minit, seed=seed2)
xp_assert_close(res1, res2) # should be same results
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