def test_height_linkage_tree():
# Check that the height of the results of linkage tree is sorted.
rng = np.random.RandomState(0)
mask = np.ones([10, 10], dtype=np.bool)
X = rng.randn(50, 100)
connectivity = grid_to_graph(*mask.shape)
for linkage_func in _TREE_BUILDERS.values():
children, n_nodes, n_leaves, parent = linkage_func(X.T, connectivity)
n_nodes = 2 * X.shape[1] - 1
assert len(children) + n_leaves == n_nodes
def test_n_components():
# Test n_components returned by linkage, average and ward tree
rng = np.random.RandomState(0)
X = rng.rand(5, 5)
# Connectivity matrix having five components.
connectivity = np.eye(5)
for linkage_func in _TREE_BUILDERS.values():
assert ignore_warnings(linkage_func)(X, connectivity)[1] == 5
def test_structured_linkage_tree():
# Check that we obtain the correct solution for structured linkage trees.
rng = np.random.RandomState(0)
mask = np.ones([10, 10], dtype=np.bool)
# Avoiding a mask with only 'True' entries
mask[4:7, 4:7] = 0
X = rng.randn(50, 100)
connectivity = grid_to_graph(*mask.shape)
for tree_builder in _TREE_BUILDERS.values():
children, n_components, n_leaves, parent = \
tree_builder(X.T, connectivity)
n_nodes = 2 * X.shape[1] - 1
assert len(children) + n_leaves == n_nodes
# Check that ward_tree raises a ValueError with a connectivity matrix
# of the wrong shape
with pytest.raises(ValueError):
tree_builder(X.T, np.ones((4, 4)))
# Check that fitting with no samples raises an error
with pytest.raises(ValueError):
tree_builder(X.T[:0], connectivity)
def test_unstructured_linkage_tree():
# Check that we obtain the correct solution for unstructured linkage trees.
rng = np.random.RandomState(0)
X = rng.randn(50, 100)
for this_X in (X, X[0]):
# With specified a number of clusters just for the sake of
# raising a warning and testing the warning code
with ignore_warnings():
children, n_nodes, n_leaves, parent = assert_warns(
UserWarning, ward_tree, this_X.T, n_clusters=10)
n_nodes = 2 * X.shape[1] - 1
assert len(children) + n_leaves == n_nodes
for tree_builder in _TREE_BUILDERS.values():
for this_X in (X, X[0]):
with ignore_warnings():
children, n_nodes, n_leaves, parent = assert_warns(
UserWarning, tree_builder, this_X.T, n_clusters=10)
n_nodes = 2 * X.shape[1] - 1
assert len(children) + n_leaves == n_nodes