def _check_p_distance_vs_KDT(self, p):
bt = BallTree(self.X, leaf_size=10, metric='minkowski', p=p)
kdt = cKDTree(self.X, leafsize=10)
dist_bt, ind_bt = bt.query(self.X, k=5)
dist_kd, ind_kd = kdt.query(self.X, k=5, p=p)
assert_array_almost_equal(dist_bt, dist_kd)
def _check_p_distance_vs_KDT(self, p):
bt = BallTree(self.X, leaf_size=10, metric='minkowski', p=p)
kdt = cKDTree(self.X, leafsize=10)
dist_bt, ind_bt = bt.query(self.X, k=5)
dist_kd, ind_kd = kdt.query(self.X, k=5, p=p)
assert_array_almost_equal(dist_bt, dist_kd)
def _check_metrics_float(self, k, metric, kwargs):
bt = BallTree(self.X, metric=metric, **kwargs)
dist_bt, ind_bt = bt.query(self.X, k=k)
dm = DistanceMetric(metric=metric, **kwargs)
D = dm.pdist(self.X, squareform=True)
ind_dm = np.argsort(D, 1)[:, :k]
dist_dm = D[np.arange(self.X.shape[0])[:, None], ind_dm]
# we don't check the indices here because if there is a tie for
# nearest neighbor, then the test may fail. Distances will reflect
# whether the search was successful
assert_array_almost_equal(dist_bt, dist_dm)
def _check_metrics_bool(self, k, metric, kwargs):
bt = BallTree(self.Xbool, metric=metric, **kwargs)
dist_bt, ind_bt = bt.query(self.Ybool, k=k)
dm = DistanceMetric(metric=metric, **kwargs)
D = dm.cdist(self.Ybool, self.Xbool)
ind_dm = np.argsort(D, 1)[:, :k]
dist_dm = D[np.arange(self.Ybool.shape[0])[:, None], ind_dm]
# we don't check the indices here because there are very often
# ties for nearest neighbors, which cause the test to fail.
# Distances will be correct in either case.
assert_array_almost_equal(dist_bt, dist_dm)
def _check_metrics_float(self, k, metric, kwargs):
bt = BallTree(self.X, metric=metric, **kwargs)
dist_bt, ind_bt = bt.query(self.X, k=k)
dm = DistanceMetric(metric=metric, **kwargs)
D = dm.pdist(self.X, squareform=True)
ind_dm = np.argsort(D, 1)[:, :k]
dist_dm = D[np.arange(self.X.shape[0])[:, None], ind_dm]
# we don't check the indices here because if there is a tie for
# nearest neighbor, then the test may fail. Distances will reflect
# whether the search was successful
assert_array_almost_equal(dist_bt, dist_dm)
def _check_metrics_bool(self, k, metric, kwargs):
bt = BallTree(self.Xbool, metric=metric, **kwargs)
dist_bt, ind_bt = bt.query(self.Ybool, k=k)
dm = DistanceMetric(metric=metric, **kwargs)
D = dm.cdist(self.Ybool, self.Xbool)
ind_dm = np.argsort(D, 1)[:, :k]
dist_dm = D[np.arange(self.Ybool.shape[0])[:, None], ind_dm]
# we don't check the indices here because there are very often
# ties for nearest neighbors, which cause the test to fail.
# Distances will be correct in either case.
assert_array_almost_equal(dist_bt, dist_dm)
def test_query_radius_count(self):
# center the data
X = 2 * self.X - 1
dm = DistanceMetric()
D = dm.pdist(X, squareform=True)
r = np.mean(D)
bt = BallTree(X)
count1 = bt.query_radius(X, r, count_only=True)
count2 = (D <= r).sum(1)
assert_array_almost_equal(count1, count2)
def test_query_radius_count(self):
# center the data
X = 2 * self.X - 1
dm = DistanceMetric()
D = dm.pdist(X, squareform=True)
r = np.mean(D)
bt = BallTree(X)
count1 = bt.query_radius(X, r, count_only=True)
count2 = (D <= r).sum(1)
assert_array_almost_equal(count1, count2)
def test_query_radius_indices(self, n_queries=20):
# center the data
X = 2 * self.X - 1
dm = DistanceMetric()
D = dm.cdist(X[:n_queries], X)
r = np.mean(D)
bt = BallTree(X)
ind = bt.query_radius(X[:n_queries], r, return_distance=False)
ind2 = np.zeros(D.shape) + np.arange(D.shape[1])
ind = np.concatenate(map(np.sort, ind))
ind2 = ind2[D <= r]
assert_array_almost_equal(ind, ind2)
def test_query_radius_indices(self, n_queries=20):
# center the data
X = 2 * self.X - 1
dm = DistanceMetric()
D = dm.cdist(X[:n_queries], X)
r = np.mean(D)
bt = BallTree(X)
ind = bt.query_radius(X[:n_queries], r, return_distance=False)
ind2 = np.zeros(D.shape) + np.arange(D.shape[1])
ind = np.concatenate(map(np.sort, ind))
ind2 = ind2[D <= r]
assert_array_almost_equal(ind, ind2)
def test_query_radius_distance(self):
# center the data
X = 2 * self.X - 1
# choose a query point near the origin
query_pt = 0.01 * X[:1]
eps = 1E-15 # roundoff error can cause test to fail
bt = BallTree(X, leaf_size=5)
# compute reference distances
dm = DistanceMetric()
dist_true = dm.cdist(query_pt, X)[0]
dist_true.sort()
for r in np.linspace(dist_true[0], dist_true[-1], 10):
yield (self._check_query_radius_distance, X, bt, query_pt,
dist_true, r, eps)
def test_pickle(self):
bt1 = BallTree(self.X, leaf_size=1)
ind1, dist1 = bt1.query(self.X)
for protocol in (0, 1, 2):
yield (self._check_pickle, protocol, bt1, ind1, dist1)
def test_query_knn(self):
bt = BallTree(self.X)
kdt = cKDTree(self.X)
for k in (1, 2, 4, 8, 16):
for dualtree in [True, False]:
yield (self._check_query_knn, bt, kdt, k, dualtree)
def test_pickle(self):
bt1 = BallTree(self.X, leaf_size=1)
ind1, dist1 = bt1.query(self.X)
for protocol in (0, 1, 2):
yield (self._check_pickle, protocol, bt1, ind1, dist1)
