Python dist_metrics.DistanceMetric类代码示例

def test_input_data_size():
    # Regression test for #6288
    # Previoulsly, a metric requiring a particular input dimension would fail
    def custom_metric(x, y):
        assert x.shape[0] == 3
        return np.sum((x - y) ** 2)

    rng = check_random_state(0)
    X = rng.rand(10, 3)

    pyfunc = DistanceMetric.get_metric("pyfunc", func=dist_func, p=2)
    eucl = DistanceMetric.get_metric("euclidean")
    assert_array_almost_equal(pyfunc.pairwise(X), eucl.pairwise(X))

def test_pyfunc_metric():
    def dist_func(x1, x2, p):
        return np.sum((x1 - x2) ** p) ** (1. / p)

    X = np.random.random((10, 3))

    euclidean = DistanceMetric.get_metric("euclidean")
    pyfunc = DistanceMetric.get_metric("pyfunc", func=dist_func, p=2)

    D1 = euclidean.pairwise(X)
    D2 = pyfunc.pairwise(X)

    assert_allclose(D1, D2)

def check_pdist_bool(metric, D_true):
    dm = DistanceMetric.get_metric(metric)
    D12 = dm.pairwise(X1_bool)
    # Based on https://github.com/scipy/scipy/pull/7373
    # When comparing two all-zero vectors, scipy>=1.2.0 jaccard metric
    # was changed to return 0, instead of nan.
    if metric == 'jaccard' and LooseVersion(scipy_version) < '1.2.0':
        D_true[np.isnan(D_true)] = 0
    assert_array_almost_equal(D12, D_true)

def test_pyfunc_metric():
    X = np.random.random((10, 3))

    euclidean = DistanceMetric.get_metric("euclidean")
    pyfunc = DistanceMetric.get_metric("pyfunc", func=dist_func, p=2)

    # Check if both callable metric and predefined metric initialized
    # DistanceMetric object is picklable
    euclidean_pkl = pickle.loads(pickle.dumps(euclidean))
    pyfunc_pkl = pickle.loads(pickle.dumps(pyfunc))

    D1 = euclidean.pairwise(X)
    D2 = pyfunc.pairwise(X)

    D1_pkl = euclidean_pkl.pairwise(X)
    D2_pkl = pyfunc_pkl.pairwise(X)

    assert_array_almost_equal(D1, D2)
    assert_array_almost_equal(D1_pkl, D2_pkl)

def test_kd_tree_two_point(dualtree):
    n_samples, n_features = (100, 3)
    rng = check_random_state(0)
    X = rng.random_sample((n_samples, n_features))
    Y = rng.random_sample((n_samples, n_features))
    r = np.linspace(0, 1, 10)
    kdt = KDTree(X, leaf_size=10)

    D = DistanceMetric.get_metric("euclidean").pairwise(Y, X)
    counts_true = [(D <= ri).sum() for ri in r]

    counts = kdt.two_point_correlation(Y, r=r, dualtree=dualtree)
    assert_array_almost_equal(counts, counts_true)

def test_ball_tree_two_point(n_samples=100, n_features=3):
    np.random.seed(0)
    X = np.random.random((n_samples, n_features))
    Y = np.random.random((n_samples, n_features))
    r = np.linspace(0, 1, 10)
    bt = BallTree(X, leaf_size=10)

    D = DistanceMetric.get_metric("euclidean").pairwise(Y, X)
    counts_true = [(D <= ri).sum() for ri in r]

    def check_two_point(r, dualtree):
        counts = bt.two_point_correlation(Y, r=r, dualtree=dualtree)
        assert_array_almost_equal(counts, counts_true)

    for dualtree in (True, False):
        yield check_two_point, r, dualtree

def test_haversine_metric():
    def haversine_slow(x1, x2):
        return 2 * np.arcsin(np.sqrt(np.sin(0.5 * (x1[0] - x2[0])) ** 2
                                     + np.cos(x1[0]) * np.cos(x2[0]) *
                                     np.sin(0.5 * (x1[1] - x2[1])) ** 2))

    X = np.random.random((10, 2))

    haversine = DistanceMetric.get_metric("haversine")

    D1 = haversine.pairwise(X)
    D2 = np.zeros_like(D1)
    for i, x1 in enumerate(X):
        for j, x2 in enumerate(X):
            D2[i, j] = haversine_slow(x1, x2)

    assert_array_almost_equal(D1, D2)
    assert_array_almost_equal(haversine.dist_to_rdist(D1),
                              np.sin(0.5 * D2) ** 2)

def check_pdist(metric, kwargs, D_true):
    dm = DistanceMetric.get_metric(metric, **kwargs)
    D12 = dm.pairwise(X1)
    assert_array_almost_equal(D12, D_true)

def check_cdist_bool(metric, D_true):
    dm = DistanceMetric.get_metric(metric)
    D12 = dm.pairwise(X1_bool, X2_bool)
    assert_array_almost_equal(D12, D_true)

 def check_pdist(self, metric, kwargs, D_true):
     if metric == 'canberra' and cmp_version(scipy.__version__, '0.9') <= 0:
         raise SkipTest("Canberra distance incorrect in scipy < 0.9")
     dm = DistanceMetric.get_metric(metric, **kwargs)
     D12 = dm.pairwise(self.X1)
     assert_allclose(D12, D_true)

def test_pickle_bool_metrics(metric):
    dm = DistanceMetric.get_metric(metric)
    D1 = dm.pairwise(X1_bool)
    dm2 = pickle.loads(pickle.dumps(dm))
    D2 = dm2.pairwise(X1_bool)
    assert_array_almost_equal(D1, D2)

 def check_cdist(self, metric, kwargs, D_true):
     dm = DistanceMetric.get_metric(metric, **kwargs)
     D12 = dm.pairwise(self.X1, self.X2)
     assert_array_almost_equal(D12, D_true)

 def check_pickle_bool(self, metric):
     dm = DistanceMetric.get_metric(metric)
     D1 = dm.pairwise(self.X1_bool)
     dm2 = pickle.loads(pickle.dumps(dm))
     D2 = dm2.pairwise(self.X1_bool)
     assert_array_almost_equal(D1, D2)

 def check_cdist(self, metric, kwargs, D_true):
     if metric == "canberra" and cmp_version(scipy.__version__, "0.9") <= 0:
         raise SkipTest("Canberra distance incorrect in scipy < 0.9")
     dm = DistanceMetric.get_metric(metric, **kwargs)
     D12 = dm.pairwise(self.X1, self.X2)
     assert_array_almost_equal(D12, D_true)

 def check_pdist_bool(self, metric, D_true):
     dm = DistanceMetric.get_metric(metric)
     D12 = dm.pairwise(self.X1_bool)
     assert_allclose(D12, D_true)