"""Testing for Spectral Clustering methods"""
import re

import numpy as np
from scipy import sparse

import pytest

import pickle

from sklearn.utils import check_random_state
from sklearn.utils._testing import assert_array_equal
from sklearn.utils._testing import assert_warns_message

from sklearn.cluster import SpectralClustering, spectral_clustering
from sklearn.cluster._spectral import discretize
from sklearn.feature_extraction import img_to_graph
from sklearn.metrics import pairwise_distances
from sklearn.metrics import adjusted_rand_score
from sklearn.metrics.pairwise import kernel_metrics, rbf_kernel
from sklearn.neighbors import NearestNeighbors
from sklearn.datasets import make_blobs

try:
    from pyamg import smoothed_aggregation_solver  # noqa
    amg_loaded = True
except ImportError:
    amg_loaded = False


@pytest.mark.parametrize('eigen_solver', ('arpack', 'lobpcg'))
@pytest.mark.parametrize('assign_labels', ('kmeans', 'discretize'))
def test_spectral_clustering(eigen_solver, assign_labels):
    S = np.array([[1.0, 1.0, 1.0, 0.2, 0.0, 0.0, 0.0],
                  [1.0, 1.0, 1.0, 0.2, 0.0, 0.0, 0.0],
                  [1.0, 1.0, 1.0, 0.2, 0.0, 0.0, 0.0],
                  [0.2, 0.2, 0.2, 1.0, 1.0, 1.0, 1.0],
                  [0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0],
                  [0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0],
                  [0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0]])

    for mat in (S, sparse.csr_matrix(S)):
        model = SpectralClustering(random_state=0, n_clusters=2,
                                   affinity='precomputed',
                                   eigen_solver=eigen_solver,
                                   assign_labels=assign_labels
                                   ).fit(mat)
        labels = model.labels_
        if labels[0] == 0:
            labels = 1 - labels

        assert adjusted_rand_score(labels, [1, 1, 1, 0, 0, 0, 0]) == 1

        model_copy = pickle.loads(pickle.dumps(model))
        assert model_copy.n_clusters == model.n_clusters
        assert model_copy.eigen_solver == model.eigen_solver
        assert_array_equal(model_copy.labels_, model.labels_)


def test_spectral_unknown_mode():
    # Test that SpectralClustering fails with an unknown mode set.
    centers = np.array([
        [0., 0., 0.],
        [10., 10., 10.],
        [20., 20., 20.],
    ])
    X, true_labels = make_blobs(n_samples=100, centers=centers,
                                cluster_std=1., random_state=42)
    D = pairwise_distances(X)  # Distance matrix
    S = np.max(D) - D  # Similarity matrix
    S = sparse.coo_matrix(S)
    with pytest.raises(ValueError):
        spectral_clustering(S, n_clusters=2, random_state=0,
                            eigen_solver="<unknown>")


def test_spectral_unknown_assign_labels():
    # Test that SpectralClustering fails with an unknown assign_labels set.
    centers = np.array([
        [0., 0., 0.],
        [10., 10., 10.],
        [20., 20., 20.],
    ])
    X, true_labels = make_blobs(n_samples=100, centers=centers,
                                cluster_std=1., random_state=42)
    D = pairwise_distances(X)  # Distance matrix
    S = np.max(D) - D  # Similarity matrix
    S = sparse.coo_matrix(S)
    with pytest.raises(ValueError):
        spectral_clustering(S, n_clusters=2, random_state=0,
                            assign_labels="<unknown>")


def test_spectral_clustering_sparse():
    X, y = make_blobs(n_samples=20, random_state=0,
                      centers=[[1, 1], [-1, -1]], cluster_std=0.01)

    S = rbf_kernel(X, gamma=1)
    S = np.maximum(S - 1e-4, 0)
    S = sparse.coo_matrix(S)

    labels = SpectralClustering(random_state=0, n_clusters=2,
                                affinity='precomputed').fit(S).labels_
    assert adjusted_rand_score(y, labels) == 1


def test_precomputed_nearest_neighbors_filtering():
    # Test precomputed graph filtering when containing too many neighbors
    X, y = make_blobs(n_samples=200, random_state=0,
                      centers=[[1, 1], [-1, -1]], cluster_std=0.01)

    n_neighbors = 2
    results = []
    for additional_neighbors in [0, 10]:
        nn = NearestNeighbors(
            n_neighbors=n_neighbors + additional_neighbors).fit(X)
        graph = nn.kneighbors_graph(X, mode='connectivity')
        labels = SpectralClustering(random_state=0, n_clusters=2,
                                    affinity='precomputed_nearest_neighbors',
                                    n_neighbors=n_neighbors).fit(graph).labels_
        results.append(labels)

    assert_array_equal(results[0], results[1])


def test_affinities():
    # Note: in the following, random_state has been selected to have
    # a dataset that yields a stable eigen decomposition both when built
    # on OSX and Linux
    X, y = make_blobs(n_samples=20, random_state=0,
                      centers=[[1, 1], [-1, -1]], cluster_std=0.01)
    # nearest neighbors affinity
    sp = SpectralClustering(n_clusters=2, affinity='nearest_neighbors',
                            random_state=0)
    assert_warns_message(UserWarning, 'not fully connected', sp.fit, X)
    assert adjusted_rand_score(y, sp.labels_) == 1

    sp = SpectralClustering(n_clusters=2, gamma=2, random_state=0)
    labels = sp.fit(X).labels_
    assert adjusted_rand_score(y, labels) == 1

    X = check_random_state(10).rand(10, 5) * 10

    kernels_available = kernel_metrics()
    for kern in kernels_available:
        # Additive chi^2 gives a negative similarity matrix which
        # doesn't make sense for spectral clustering
        if kern != 'additive_chi2':
            sp = SpectralClustering(n_clusters=2, affinity=kern,
                                    random_state=0)
            labels = sp.fit(X).labels_
            assert (X.shape[0],) == labels.shape

    sp = SpectralClustering(n_clusters=2, affinity=lambda x, y: 1,
                            random_state=0)
    labels = sp.fit(X).labels_
    assert (X.shape[0],) == labels.shape

    def histogram(x, y, **kwargs):
        # Histogram kernel implemented as a callable.
        assert kwargs == {}    # no kernel_params that we didn't ask for
        return np.minimum(x, y).sum()

    sp = SpectralClustering(n_clusters=2, affinity=histogram, random_state=0)
    labels = sp.fit(X).labels_
    assert (X.shape[0],) == labels.shape

    # raise error on unknown affinity
    sp = SpectralClustering(n_clusters=2, affinity='<unknown>')
    with pytest.raises(ValueError):
        sp.fit(X)


@pytest.mark.parametrize('n_samples', [50, 100, 150, 500])
def test_discretize(n_samples):
    # Test the discretize using a noise assignment matrix
    random_state = np.random.RandomState(seed=8)
    for n_class in range(2, 10):
        # random class labels
        y_true = random_state.randint(0, n_class + 1, n_samples)
        y_true = np.array(y_true, float)
        # noise class assignment matrix
        y_indicator = sparse.coo_matrix((np.ones(n_samples),
                                         (np.arange(n_samples),
                                          y_true)),
                                        shape=(n_samples,
                                               n_class + 1))
        y_true_noisy = (y_indicator.toarray()
                        + 0.1 * random_state.randn(n_samples,
                                                   n_class + 1))
        y_pred = discretize(y_true_noisy, random_state=random_state)
        assert adjusted_rand_score(y_true, y_pred) > 0.8


# TODO: Remove when pyamg does replaces sp.rand call with np.random.rand
# https://github.com/scikit-learn/scikit-learn/issues/15913
@pytest.mark.filterwarnings(
    "ignore:scipy.rand is deprecated:DeprecationWarning:pyamg.*")
# TODO: Remove when pyamg removes the use of np.float
@pytest.mark.filterwarnings(
    "ignore:`np.float` is a deprecated alias:DeprecationWarning:pyamg.*")
def test_spectral_clustering_with_arpack_amg_solvers():
    # Test that spectral_clustering is the same for arpack and amg solver
    # Based on toy example from plot_segmentation_toy.py

    # a small two coin image
    x, y = np.indices((40, 40))

    center1, center2 = (14, 12), (20, 25)
    radius1, radius2 = 8, 7

    circle1 = (x - center1[0]) ** 2 + (y - center1[1]) ** 2 < radius1 ** 2
    circle2 = (x - center2[0]) ** 2 + (y - center2[1]) ** 2 < radius2 ** 2

    circles = circle1 | circle2
    mask = circles.copy()
    img = circles.astype(float)

    graph = img_to_graph(img, mask=mask)
    graph.data = np.exp(-graph.data / graph.data.std())

    labels_arpack = spectral_clustering(
        graph, n_clusters=2, eigen_solver='arpack', random_state=0)

    assert len(np.unique(labels_arpack)) == 2

    if amg_loaded:
        labels_amg = spectral_clustering(
            graph, n_clusters=2, eigen_solver='amg', random_state=0)
        assert adjusted_rand_score(labels_arpack, labels_amg) == 1
    else:
        with pytest.raises(ValueError):
            spectral_clustering(graph, n_clusters=2, eigen_solver='amg',
                                random_state=0)


def test_n_components():
    # Test that after adding n_components, result is different and
    # n_components = n_clusters by default
    X, y = make_blobs(n_samples=20, random_state=0,
                      centers=[[1, 1], [-1, -1]], cluster_std=0.01)
    sp = SpectralClustering(n_clusters=2, random_state=0)
    labels = sp.fit(X).labels_
    # set n_components = n_cluster and test if result is the same
    labels_same_ncomp = SpectralClustering(n_clusters=2, n_components=2,
                                           random_state=0).fit(X).labels_
    # test that n_components=n_clusters by default
    assert_array_equal(labels, labels_same_ncomp)

    # test that n_components affect result
    # n_clusters=8 by default, and set n_components=2
    labels_diff_ncomp = SpectralClustering(n_components=2,
                                           random_state=0).fit(X).labels_
    assert not np.array_equal(labels, labels_diff_ncomp)


@pytest.mark.parametrize('assign_labels', ('kmeans', 'discretize'))
def test_verbose(assign_labels, capsys):
    # Check verbose mode of KMeans for better coverage.
    X, y = make_blobs(n_samples=20, random_state=0,
                      centers=[[1, 1], [-1, -1]], cluster_std=0.01)

    SpectralClustering(n_clusters=2, random_state=42, verbose=1).fit(X)

    captured = capsys.readouterr()

    assert re.search(r"Computing label assignment using", captured.out)

    if assign_labels == "kmeans":
        assert re.search(r"Initialization complete", captured.out)
        assert re.search(r"Iteration [0-9]+, inertia", captured.out)


# TODO: Remove in 1.1
@pytest.mark.parametrize("affinity", ["precomputed",
                                      "precomputed_nearest_neighbors"])
def test_pairwise_is_deprecated(affinity):
    sp = SpectralClustering(affinity=affinity)
    msg = r"Attribute _pairwise was deprecated in version 0\.24"
    with pytest.warns(FutureWarning, match=msg):
        sp._pairwise