venv/lib/python3.10/site-packages/sklearn/cluster/tests/test_hdbscan.py

"""
Tests for HDBSCAN clustering algorithm
Based on the DBSCAN test code
"""
import numpy as np
import pytest
from scipy import stats
from scipy.spatial import distance

from sklearn.cluster import HDBSCAN
from sklearn.cluster._hdbscan._tree import (
    CONDENSED_dtype,
    _condense_tree,
    _do_labelling,
)
from sklearn.cluster._hdbscan.hdbscan import _OUTLIER_ENCODING
from sklearn.datasets import make_blobs
from sklearn.metrics import fowlkes_mallows_score
from sklearn.metrics.pairwise import _VALID_METRICS, euclidean_distances
from sklearn.neighbors import BallTree, KDTree
from sklearn.preprocessing import StandardScaler
from sklearn.utils import shuffle
from sklearn.utils._testing import assert_allclose, assert_array_equal
from sklearn.utils.fixes import CSC_CONTAINERS, CSR_CONTAINERS

X, y = make_blobs(n_samples=200, random_state=10)
X, y = shuffle(X, y, random_state=7)
X = StandardScaler().fit_transform(X)

ALGORITHMS = [
    "kd_tree",
    "ball_tree",
    "brute",
    "auto",
]

OUTLIER_SET = {-1} | {out["label"] for _, out in _OUTLIER_ENCODING.items()}


def check_label_quality(labels, threshold=0.99):
    n_clusters = len(set(labels) - OUTLIER_SET)
    assert n_clusters == 3
    assert fowlkes_mallows_score(labels, y) > threshold


@pytest.mark.parametrize("outlier_type", _OUTLIER_ENCODING)
def test_outlier_data(outlier_type):
    """
    Tests if np.inf and np.nan data are each treated as special outliers.
    """
    outlier = {
        "infinite": np.inf,
        "missing": np.nan,
    }[outlier_type]
    prob_check = {
        "infinite": lambda x, y: x == y,
        "missing": lambda x, y: np.isnan(x),
    }[outlier_type]
    label = _OUTLIER_ENCODING[outlier_type]["label"]
    prob = _OUTLIER_ENCODING[outlier_type]["prob"]

    X_outlier = X.copy()
    X_outlier[0] = [outlier, 1]
    X_outlier[5] = [outlier, outlier]
    model = HDBSCAN().fit(X_outlier)

    (missing_labels_idx,) = (model.labels_ == label).nonzero()
    assert_array_equal(missing_labels_idx, [0, 5])

    (missing_probs_idx,) = (prob_check(model.probabilities_, prob)).nonzero()
    assert_array_equal(missing_probs_idx, [0, 5])

    clean_indices = list(range(1, 5)) + list(range(6, 200))
    clean_model = HDBSCAN().fit(X_outlier[clean_indices])
    assert_array_equal(clean_model.labels_, model.labels_[clean_indices])


def test_hdbscan_distance_matrix():
    """
    Tests that HDBSCAN works with precomputed distance matrices, and throws the
    appropriate errors when needed.
    """
    D = euclidean_distances(X)
    D_original = D.copy()
    labels = HDBSCAN(metric="precomputed", copy=True).fit_predict(D)

    assert_allclose(D, D_original)
    check_label_quality(labels)

    msg = r"The precomputed distance matrix.*has shape"
    with pytest.raises(ValueError, match=msg):
        HDBSCAN(metric="precomputed", copy=True).fit_predict(X)

    msg = r"The precomputed distance matrix.*values"
    # Ensure the matrix is not symmetric
    D[0, 1] = 10
    D[1, 0] = 1
    with pytest.raises(ValueError, match=msg):
        HDBSCAN(metric="precomputed").fit_predict(D)


@pytest.mark.parametrize("sparse_constructor", [*CSR_CONTAINERS, *CSC_CONTAINERS])
def test_hdbscan_sparse_distance_matrix(sparse_constructor):
    """
    Tests that HDBSCAN works with sparse distance matrices.
    """
    D = distance.squareform(distance.pdist(X))
    D /= np.max(D)

    threshold = stats.scoreatpercentile(D.flatten(), 50)

    D[D >= threshold] = 0.0
    D = sparse_constructor(D)
    D.eliminate_zeros()

    labels = HDBSCAN(metric="precomputed").fit_predict(D)
    check_label_quality(labels)


def test_hdbscan_feature_array():
    """
    Tests that HDBSCAN works with feature array, including an arbitrary
    goodness of fit check. Note that the check is a simple heuristic.
    """
    labels = HDBSCAN().fit_predict(X)

    # Check that clustering is arbitrarily good
    # This is a heuristic to guard against regression
    check_label_quality(labels)


@pytest.mark.parametrize("algo", ALGORITHMS)
@pytest.mark.parametrize("metric", _VALID_METRICS)
def test_hdbscan_algorithms(algo, metric):
    """
    Tests that HDBSCAN works with the expected combinations of algorithms and
    metrics, or raises the expected errors.
    """
    labels = HDBSCAN(algorithm=algo).fit_predict(X)
    check_label_quality(labels)

    # Validation for brute is handled by `pairwise_distances`
    if algo in ("brute", "auto"):
        return

    ALGOS_TREES = {
        "kd_tree": KDTree,
        "ball_tree": BallTree,
    }
    metric_params = {
        "mahalanobis": {"V": np.eye(X.shape[1])},
        "seuclidean": {"V": np.ones(X.shape[1])},
        "minkowski": {"p": 2},
        "wminkowski": {"p": 2, "w": np.ones(X.shape[1])},
    }.get(metric, None)

    hdb = HDBSCAN(
        algorithm=algo,
        metric=metric,
        metric_params=metric_params,
    )

    if metric not in ALGOS_TREES[algo].valid_metrics:
        with pytest.raises(ValueError):
            hdb.fit(X)
    elif metric == "wminkowski":
        with pytest.warns(FutureWarning):
            hdb.fit(X)
    else:
        hdb.fit(X)


def test_dbscan_clustering():
    """
    Tests that HDBSCAN can generate a sufficiently accurate dbscan clustering.
    This test is more of a sanity check than a rigorous evaluation.
    """
    clusterer = HDBSCAN().fit(X)
    labels = clusterer.dbscan_clustering(0.3)

    # We use a looser threshold due to dbscan producing a more constrained
    # clustering representation
    check_label_quality(labels, threshold=0.92)


@pytest.mark.parametrize("cut_distance", (0.1, 0.5, 1))
def test_dbscan_clustering_outlier_data(cut_distance):
    """
    Tests if np.inf and np.nan data are each treated as special outliers.
    """
    missing_label = _OUTLIER_ENCODING["missing"]["label"]
    infinite_label = _OUTLIER_ENCODING["infinite"]["label"]

    X_outlier = X.copy()
    X_outlier[0] = [np.inf, 1]
    X_outlier[2] = [1, np.nan]
    X_outlier[5] = [np.inf, np.nan]
    model = HDBSCAN().fit(X_outlier)
    labels = model.dbscan_clustering(cut_distance=cut_distance)

    missing_labels_idx = np.flatnonzero(labels == missing_label)
    assert_array_equal(missing_labels_idx, [2, 5])

    infinite_labels_idx = np.flatnonzero(labels == infinite_label)
    assert_array_equal(infinite_labels_idx, [0])

    clean_idx = list(set(range(200)) - set(missing_labels_idx + infinite_labels_idx))
    clean_model = HDBSCAN().fit(X_outlier[clean_idx])
    clean_labels = clean_model.dbscan_clustering(cut_distance=cut_distance)
    assert_array_equal(clean_labels, labels[clean_idx])


def test_hdbscan_best_balltree_metric():
    """
    Tests that HDBSCAN using `BallTree` works.
    """
    labels = HDBSCAN(
        metric="seuclidean", metric_params={"V": np.ones(X.shape[1])}
    ).fit_predict(X)
    check_label_quality(labels)


def test_hdbscan_no_clusters():
    """
    Tests that HDBSCAN correctly does not generate a valid cluster when the
    `min_cluster_size` is too large for the data.
    """
    labels = HDBSCAN(min_cluster_size=len(X) - 1).fit_predict(X)
    assert set(labels).issubset(OUTLIER_SET)


def test_hdbscan_min_cluster_size():
    """
    Test that the smallest non-noise cluster has at least `min_cluster_size`
    many points
    """
    for min_cluster_size in range(2, len(X), 1):
        labels = HDBSCAN(min_cluster_size=min_cluster_size).fit_predict(X)
        true_labels = [label for label in labels if label != -1]
        if len(true_labels) != 0:
            assert np.min(np.bincount(true_labels)) >= min_cluster_size


def test_hdbscan_callable_metric():
    """
    Tests that HDBSCAN works when passed a callable metric.
    """
    metric = distance.euclidean
    labels = HDBSCAN(metric=metric).fit_predict(X)
    check_label_quality(labels)


@pytest.mark.parametrize("tree", ["kd_tree", "ball_tree"])
def test_hdbscan_precomputed_non_brute(tree):
    """
    Tests that HDBSCAN correctly raises an error when passing precomputed data
    while requesting a tree-based algorithm.
    """
    hdb = HDBSCAN(metric="precomputed", algorithm=tree)
    msg = "precomputed is not a valid metric for"
    with pytest.raises(ValueError, match=msg):
        hdb.fit(X)


@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_hdbscan_sparse(csr_container):
    """
    Tests that HDBSCAN works correctly when passing sparse feature data.
    Evaluates correctness by comparing against the same data passed as a dense
    array.
    """

    dense_labels = HDBSCAN().fit(X).labels_
    check_label_quality(dense_labels)

    _X_sparse = csr_container(X)
    X_sparse = _X_sparse.copy()
    sparse_labels = HDBSCAN().fit(X_sparse).labels_
    assert_array_equal(dense_labels, sparse_labels)

    # Compare that the sparse and dense non-precomputed routines return the same labels
    # where the 0th observation contains the outlier.
    for outlier_val, outlier_type in ((np.inf, "infinite"), (np.nan, "missing")):
        X_dense = X.copy()
        X_dense[0, 0] = outlier_val
        dense_labels = HDBSCAN().fit(X_dense).labels_
        check_label_quality(dense_labels)
        assert dense_labels[0] == _OUTLIER_ENCODING[outlier_type]["label"]

        X_sparse = _X_sparse.copy()
        X_sparse[0, 0] = outlier_val
        sparse_labels = HDBSCAN().fit(X_sparse).labels_
        assert_array_equal(dense_labels, sparse_labels)

    msg = "Sparse data matrices only support algorithm `brute`."
    with pytest.raises(ValueError, match=msg):
        HDBSCAN(metric="euclidean", algorithm="ball_tree").fit(X_sparse)


@pytest.mark.parametrize("algorithm", ALGORITHMS)
def test_hdbscan_centers(algorithm):
    """
    Tests that HDBSCAN centers are calculated and stored properly, and are
    accurate to the data.
    """
    centers = [(0.0, 0.0), (3.0, 3.0)]
    H, _ = make_blobs(n_samples=2000, random_state=0, centers=centers, cluster_std=0.5)
    hdb = HDBSCAN(store_centers="both").fit(H)

    for center, centroid, medoid in zip(centers, hdb.centroids_, hdb.medoids_):
        assert_allclose(center, centroid, rtol=1, atol=0.05)
        assert_allclose(center, medoid, rtol=1, atol=0.05)

    # Ensure that nothing is done for noise
    hdb = HDBSCAN(
        algorithm=algorithm, store_centers="both", min_cluster_size=X.shape[0]
    ).fit(X)
    assert hdb.centroids_.shape[0] == 0
    assert hdb.medoids_.shape[0] == 0


def test_hdbscan_allow_single_cluster_with_epsilon():
    """
    Tests that HDBSCAN single-cluster selection with epsilon works correctly.
    """
    rng = np.random.RandomState(0)
    no_structure = rng.rand(150, 2)
    # without epsilon we should see many noise points as children of root.
    labels = HDBSCAN(
        min_cluster_size=5,
        cluster_selection_epsilon=0.0,
        cluster_selection_method="eom",
        allow_single_cluster=True,
    ).fit_predict(no_structure)
    unique_labels, counts = np.unique(labels, return_counts=True)
    assert len(unique_labels) == 2

    # Arbitrary heuristic. Would prefer something more precise.
    assert counts[unique_labels == -1] > 30

    # for this random seed an epsilon of 0.18 will produce exactly 2 noise
    # points at that cut in single linkage.
    labels = HDBSCAN(
        min_cluster_size=5,
        cluster_selection_epsilon=0.18,
        cluster_selection_method="eom",
        allow_single_cluster=True,
        algorithm="kd_tree",
    ).fit_predict(no_structure)
    unique_labels, counts = np.unique(labels, return_counts=True)
    assert len(unique_labels) == 2
    assert counts[unique_labels == -1] == 2


def test_hdbscan_better_than_dbscan():
    """
    Validate that HDBSCAN can properly cluster this difficult synthetic
    dataset. Note that DBSCAN fails on this (see HDBSCAN plotting
    example)
    """
    centers = [[-0.85, -0.85], [-0.85, 0.85], [3, 3], [3, -3]]
    X, y = make_blobs(
        n_samples=750,
        centers=centers,
        cluster_std=[0.2, 0.35, 1.35, 1.35],
        random_state=0,
    )
    labels = HDBSCAN().fit(X).labels_

    n_clusters = len(set(labels)) - int(-1 in labels)
    assert n_clusters == 4
    fowlkes_mallows_score(labels, y) > 0.99


@pytest.mark.parametrize(
    "kwargs, X",
    [
        ({"metric": "precomputed"}, np.array([[1, np.inf], [np.inf, 1]])),
        ({"metric": "precomputed"}, [[1, 2], [2, 1]]),
        ({}, [[1, 2], [3, 4]]),
    ],
)
def test_hdbscan_usable_inputs(X, kwargs):
    """
    Tests that HDBSCAN works correctly for array-likes and precomputed inputs
    with non-finite points.
    """
    HDBSCAN(min_samples=1, **kwargs).fit(X)


@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_hdbscan_sparse_distances_too_few_nonzero(csr_container):
    """
    Tests that HDBSCAN raises the correct error when there are too few
    non-zero distances.
    """
    X = csr_container(np.zeros((10, 10)))

    msg = "There exists points with fewer than"
    with pytest.raises(ValueError, match=msg):
        HDBSCAN(metric="precomputed").fit(X)


@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
def test_hdbscan_sparse_distances_disconnected_graph(csr_container):
    """
    Tests that HDBSCAN raises the correct error when the distance matrix
    has multiple connected components.
    """
    # Create symmetric sparse matrix with 2 connected components
    X = np.zeros((20, 20))
    X[:5, :5] = 1
    X[5:, 15:] = 1
    X = X + X.T
    X = csr_container(X)
    msg = "HDBSCAN cannot be perfomed on a disconnected graph"
    with pytest.raises(ValueError, match=msg):
        HDBSCAN(metric="precomputed").fit(X)


def test_hdbscan_tree_invalid_metric():
    """
    Tests that HDBSCAN correctly raises an error for invalid metric choices.
    """
    metric_callable = lambda x: x
    msg = (
        ".* is not a valid metric for a .*-based algorithm\\. Please select a different"
        " metric\\."
    )

    # Callables are not supported for either
    with pytest.raises(ValueError, match=msg):
        HDBSCAN(algorithm="kd_tree", metric=metric_callable).fit(X)
    with pytest.raises(ValueError, match=msg):
        HDBSCAN(algorithm="ball_tree", metric=metric_callable).fit(X)

    # The set of valid metrics for KDTree at the time of writing this test is a
    # strict subset of those supported in BallTree
    metrics_not_kd = list(set(BallTree.valid_metrics) - set(KDTree.valid_metrics))
    if len(metrics_not_kd) > 0:
        with pytest.raises(ValueError, match=msg):
            HDBSCAN(algorithm="kd_tree", metric=metrics_not_kd[0]).fit(X)


def test_hdbscan_too_many_min_samples():
    """
    Tests that HDBSCAN correctly raises an error when setting `min_samples`
    larger than the number of samples.
    """
    hdb = HDBSCAN(min_samples=len(X) + 1)
    msg = r"min_samples (.*) must be at most"
    with pytest.raises(ValueError, match=msg):
        hdb.fit(X)


def test_hdbscan_precomputed_dense_nan():
    """
    Tests that HDBSCAN correctly raises an error when providing precomputed
    distances with `np.nan` values.
    """
    X_nan = X.copy()
    X_nan[0, 0] = np.nan
    msg = "np.nan values found in precomputed-dense"
    hdb = HDBSCAN(metric="precomputed")
    with pytest.raises(ValueError, match=msg):
        hdb.fit(X_nan)


@pytest.mark.parametrize("allow_single_cluster", [True, False])
@pytest.mark.parametrize("epsilon", [0, 0.1])
def test_labelling_distinct(global_random_seed, allow_single_cluster, epsilon):
    """
    Tests that the `_do_labelling` helper function correctly assigns labels.
    """
    n_samples = 48
    X, y = make_blobs(
        n_samples,
        random_state=global_random_seed,
        # Ensure the clusters are distinct with no overlap
        centers=[
            [0, 0],
            [10, 0],
            [0, 10],
        ],
    )

    est = HDBSCAN().fit(X)
    condensed_tree = _condense_tree(
        est._single_linkage_tree_, min_cluster_size=est.min_cluster_size
    )
    clusters = {n_samples + 2, n_samples + 3, n_samples + 4}
    cluster_label_map = {n_samples + 2: 0, n_samples + 3: 1, n_samples + 4: 2}
    labels = _do_labelling(
        condensed_tree=condensed_tree,
        clusters=clusters,
        cluster_label_map=cluster_label_map,
        allow_single_cluster=allow_single_cluster,
        cluster_selection_epsilon=epsilon,
    )

    first_with_label = {_y: np.where(y == _y)[0][0] for _y in list(set(y))}
    y_to_labels = {_y: labels[first_with_label[_y]] for _y in list(set(y))}
    aligned_target = np.vectorize(y_to_labels.get)(y)
    assert_array_equal(labels, aligned_target)


def test_labelling_thresholding():
    """
    Tests that the `_do_labelling` helper function correctly thresholds the
    incoming lambda values given various `cluster_selection_epsilon` values.
    """
    n_samples = 5
    MAX_LAMBDA = 1.5
    condensed_tree = np.array(
        [
            (5, 2, MAX_LAMBDA, 1),
            (5, 1, 0.1, 1),
            (5, 0, MAX_LAMBDA, 1),
            (5, 3, 0.2, 1),
            (5, 4, 0.3, 1),
        ],
        dtype=CONDENSED_dtype,
    )
    labels = _do_labelling(
        condensed_tree=condensed_tree,
        clusters={n_samples},
        cluster_label_map={n_samples: 0, n_samples + 1: 1},
        allow_single_cluster=True,
        cluster_selection_epsilon=1,
    )
    num_noise = condensed_tree["value"] < 1
    assert sum(num_noise) == sum(labels == -1)

    labels = _do_labelling(
        condensed_tree=condensed_tree,
        clusters={n_samples},
        cluster_label_map={n_samples: 0, n_samples + 1: 1},
        allow_single_cluster=True,
        cluster_selection_epsilon=0,
    )
    # The threshold should be calculated per-sample based on the largest
    # lambda of any simbling node. In this case, all points are siblings
    # and the largest value is exactly MAX_LAMBDA.
    num_noise = condensed_tree["value"] < MAX_LAMBDA
    assert sum(num_noise) == sum(labels == -1)


# TODO(1.6): Remove
def test_hdbscan_warning_on_deprecated_algorithm_name():
    # Test that warning message is shown when algorithm='kdtree'
    msg = (
        "`algorithm='kdtree'`has been deprecated in 1.4 and will be renamed"
        " to'kd_tree'`in 1.6. To keep the past behaviour, set `algorithm='kd_tree'`."
    )
    with pytest.warns(FutureWarning, match=msg):
        HDBSCAN(algorithm="kdtree").fit(X)

    # Test that warning message is shown when algorithm='balltree'
    msg = (
        "`algorithm='balltree'`has been deprecated in 1.4 and will be renamed"
        " to'ball_tree'`in 1.6. To keep the past behaviour, set"
        " `algorithm='ball_tree'`."
    )
    with pytest.warns(FutureWarning, match=msg):
        HDBSCAN(algorithm="balltree").fit(X)


@pytest.mark.parametrize("store_centers", ["centroid", "medoid"])
def test_hdbscan_error_precomputed_and_store_centers(store_centers):
    """Check that we raise an error if the centers are requested together with
    a precomputed input matrix.

    Non-regression test for:
    https://github.com/scikit-learn/scikit-learn/issues/27893
    """
    rng = np.random.RandomState(0)
    X = rng.random((100, 2))
    X_dist = euclidean_distances(X)
    err_msg = "Cannot store centers when using a precomputed distance matrix."
    with pytest.raises(ValueError, match=err_msg):
        HDBSCAN(metric="precomputed", store_centers=store_centers).fit(X_dist)