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"""
Tests for the birch clustering algorithm.
"""
import numpy as np
import pytest
from sklearn.cluster import AgglomerativeClustering, Birch
from sklearn.cluster.tests.common import generate_clustered_data
from sklearn.datasets import make_blobs
from sklearn.exceptions import ConvergenceWarning
from sklearn.metrics import pairwise_distances_argmin, v_measure_score
from sklearn.utils._testing import assert_allclose, assert_array_equal
from sklearn.utils.fixes import CSR_CONTAINERS
def test_n_samples_leaves_roots(global_random_seed, global_dtype):
# Sanity check for the number of samples in leaves and roots
X, y = make_blobs(n_samples=10, random_state=global_random_seed)
X = X.astype(global_dtype, copy=False)
brc = Birch()
brc.fit(X)
n_samples_root = sum([sc.n_samples_ for sc in brc.root_.subclusters_])
n_samples_leaves = sum(
[sc.n_samples_ for leaf in brc._get_leaves() for sc in leaf.subclusters_]
)
assert n_samples_leaves == X.shape[0]
assert n_samples_root == X.shape[0]
def test_partial_fit(global_random_seed, global_dtype):
# Test that fit is equivalent to calling partial_fit multiple times
X, y = make_blobs(n_samples=100, random_state=global_random_seed)
X = X.astype(global_dtype, copy=False)
brc = Birch(n_clusters=3)
brc.fit(X)
brc_partial = Birch(n_clusters=None)
brc_partial.partial_fit(X[:50])
brc_partial.partial_fit(X[50:])
assert_allclose(brc_partial.subcluster_centers_, brc.subcluster_centers_)
# Test that same global labels are obtained after calling partial_fit
# with None
brc_partial.set_params(n_clusters=3)
brc_partial.partial_fit(None)
assert_array_equal(brc_partial.subcluster_labels_, brc.subcluster_labels_)
def test_birch_predict(global_random_seed, global_dtype):
# Test the predict method predicts the nearest centroid.
rng = np.random.RandomState(global_random_seed)
X = generate_clustered_data(n_clusters=3, n_features=3, n_samples_per_cluster=10)
X = X.astype(global_dtype, copy=False)
# n_samples * n_samples_per_cluster
shuffle_indices = np.arange(30)
rng.shuffle(shuffle_indices)
X_shuffle = X[shuffle_indices, :]
brc = Birch(n_clusters=4, threshold=1.0)
brc.fit(X_shuffle)
# Birch must preserve inputs' dtype
assert brc.subcluster_centers_.dtype == global_dtype
assert_array_equal(brc.labels_, brc.predict(X_shuffle))
centroids = brc.subcluster_centers_
nearest_centroid = brc.subcluster_labels_[
pairwise_distances_argmin(X_shuffle, centroids)
]
assert_allclose(v_measure_score(nearest_centroid, brc.labels_), 1.0)
def test_n_clusters(global_random_seed, global_dtype):
# Test that n_clusters param works properly
X, y = make_blobs(n_samples=100, centers=10, random_state=global_random_seed)
X = X.astype(global_dtype, copy=False)
brc1 = Birch(n_clusters=10)
brc1.fit(X)
assert len(brc1.subcluster_centers_) > 10
assert len(np.unique(brc1.labels_)) == 10
# Test that n_clusters = Agglomerative Clustering gives
# the same results.
gc = AgglomerativeClustering(n_clusters=10)
brc2 = Birch(n_clusters=gc)
brc2.fit(X)
assert_array_equal(brc1.subcluster_labels_, brc2.subcluster_labels_)
assert_array_equal(brc1.labels_, brc2.labels_)
# Test that a small number of clusters raises a warning.
brc4 = Birch(threshold=10000.0)
with pytest.warns(ConvergenceWarning):
brc4.fit(X)
@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_sparse_X(global_random_seed, global_dtype, csr_container):
# Test that sparse and dense data give same results
X, y = make_blobs(n_samples=100, centers=10, random_state=global_random_seed)
X = X.astype(global_dtype, copy=False)
brc = Birch(n_clusters=10)
brc.fit(X)
csr = csr_container(X)
brc_sparse = Birch(n_clusters=10)
brc_sparse.fit(csr)
# Birch must preserve inputs' dtype
assert brc_sparse.subcluster_centers_.dtype == global_dtype
assert_array_equal(brc.labels_, brc_sparse.labels_)
assert_allclose(brc.subcluster_centers_, brc_sparse.subcluster_centers_)
def test_partial_fit_second_call_error_checks():
# second partial fit calls will error when n_features is not consistent
# with the first call
X, y = make_blobs(n_samples=100)
brc = Birch(n_clusters=3)
brc.partial_fit(X, y)
msg = "X has 1 features, but Birch is expecting 2 features"
with pytest.raises(ValueError, match=msg):
brc.partial_fit(X[:, [0]], y)
def check_branching_factor(node, branching_factor):
subclusters = node.subclusters_
assert branching_factor >= len(subclusters)
for cluster in subclusters:
if cluster.child_:
check_branching_factor(cluster.child_, branching_factor)
def test_branching_factor(global_random_seed, global_dtype):
# Test that nodes have at max branching_factor number of subclusters
X, y = make_blobs(random_state=global_random_seed)
X = X.astype(global_dtype, copy=False)
branching_factor = 9
# Purposefully set a low threshold to maximize the subclusters.
brc = Birch(n_clusters=None, branching_factor=branching_factor, threshold=0.01)
brc.fit(X)
check_branching_factor(brc.root_, branching_factor)
brc = Birch(n_clusters=3, branching_factor=branching_factor, threshold=0.01)
brc.fit(X)
check_branching_factor(brc.root_, branching_factor)
def check_threshold(birch_instance, threshold):
"""Use the leaf linked list for traversal"""
current_leaf = birch_instance.dummy_leaf_.next_leaf_
while current_leaf:
subclusters = current_leaf.subclusters_
for sc in subclusters:
assert threshold >= sc.radius
current_leaf = current_leaf.next_leaf_
def test_threshold(global_random_seed, global_dtype):
# Test that the leaf subclusters have a threshold lesser than radius
X, y = make_blobs(n_samples=80, centers=4, random_state=global_random_seed)
X = X.astype(global_dtype, copy=False)
brc = Birch(threshold=0.5, n_clusters=None)
brc.fit(X)
check_threshold(brc, 0.5)
brc = Birch(threshold=5.0, n_clusters=None)
brc.fit(X)
check_threshold(brc, 5.0)
def test_birch_n_clusters_long_int():
# Check that birch supports n_clusters with np.int64 dtype, for instance
# coming from np.arange. #16484
X, _ = make_blobs(random_state=0)
n_clusters = np.int64(5)
Birch(n_clusters=n_clusters).fit(X)
def test_feature_names_out():
"""Check `get_feature_names_out` for `Birch`."""
X, _ = make_blobs(n_samples=80, n_features=4, random_state=0)
brc = Birch(n_clusters=4)
brc.fit(X)
n_clusters = brc.subcluster_centers_.shape[0]
names_out = brc.get_feature_names_out()
assert_array_equal([f"birch{i}" for i in range(n_clusters)], names_out)
def test_transform_match_across_dtypes(global_random_seed):
X, _ = make_blobs(n_samples=80, n_features=4, random_state=global_random_seed)
brc = Birch(n_clusters=4, threshold=1.1)
Y_64 = brc.fit_transform(X)
Y_32 = brc.fit_transform(X.astype(np.float32))
assert_allclose(Y_64, Y_32, atol=1e-6)
def test_subcluster_dtype(global_dtype):
X = make_blobs(n_samples=80, n_features=4, random_state=0)[0].astype(
global_dtype, copy=False
)
brc = Birch(n_clusters=4)
assert brc.fit(X).subcluster_centers_.dtype == global_dtype
def test_both_subclusters_updated():
"""Check that both subclusters are updated when a node a split, even when there are
duplicated data points. Non-regression test for #23269.
"""
X = np.array(
[
[-2.6192791, -1.5053215],
[-2.9993038, -1.6863596],
[-2.3724914, -1.3438171],
[-2.336792, -1.3417323],
[-2.4089134, -1.3290224],
[-2.3724914, -1.3438171],
[-3.364009, -1.8846745],
[-2.3724914, -1.3438171],
[-2.617677, -1.5003285],
[-2.2960556, -1.3260119],
[-2.3724914, -1.3438171],
[-2.5459878, -1.4533926],
[-2.25979, -1.3003055],
[-2.4089134, -1.3290224],
[-2.3724914, -1.3438171],
[-2.4089134, -1.3290224],
[-2.5459878, -1.4533926],
[-2.3724914, -1.3438171],
[-2.9720619, -1.7058647],
[-2.336792, -1.3417323],
[-2.3724914, -1.3438171],
],
dtype=np.float32,
)
# no error
Birch(branching_factor=5, threshold=1e-5, n_clusters=None).fit(X)
# TODO(1.8): Remove
def test_birch_copy_deprecated():
X, _ = make_blobs(n_samples=80, n_features=4, random_state=0)
brc = Birch(n_clusters=4, copy=True)
with pytest.warns(FutureWarning, match="`copy` was deprecated"):
brc.fit(X)
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