def test_generator_flow_no_targets():
generator = PaddedGraphGenerator(graphs=graphs)
seq = generator.flow(graphs=[0, 1, 2], batch_size=2)
assert isinstance(seq, PaddedGraphSequence)
assert len(seq) == 2 # two batches
# The first batch should be size 2 and the second batch size 1
values_0, targets_0 = seq[0]
assert len(values_0) == 3
assert values_0[0].shape[0] == 2
assert values_0[1].shape[0] == 2
assert values_0[2].shape[0] == 2
assert targets_0 is None
values_1, targets_1 = seq[1]
assert len(values_1) == 3
assert values_1[0].shape[0] == 1
assert values_1[1].shape[0] == 1
assert values_1[2].shape[0] == 1
assert targets_1 is None
def test_generator_flow_shuffle():
generator = PaddedGraphGenerator(graphs=graphs)
num_epochs_to_check = 5
def get_batches(seq):
return [seq[i][0] for i in range(len(seq))]
def batches_all_equal(batches, other_batches):
checks = [
inp.shape == other_inp.shape and np.allclose(inp, other_inp)
for batch, other_batch in zip(batches, other_batches)
for inp, other_inp in zip(batch, other_batch)
]
return all(checks)
def get_next_epoch_batches(seq):
seq.on_epoch_end()
return get_batches(seq)
# shuffle = False
seq = generator.flow(graphs=[0, 1, 2], batch_size=2, shuffle=False)
batches = get_batches(seq)
for _ in range(num_epochs_to_check):
assert batches_all_equal(batches, get_next_epoch_batches(seq))
# shuffle = True, fixed seed
seq = generator.flow(graphs=[0, 1, 2], batch_size=2, shuffle=True, seed=0)
batches = get_batches(seq)
at_least_one_different = False
for _ in range(num_epochs_to_check):
if not batches_all_equal(batches, get_next_epoch_batches(seq)):
at_least_one_different = True
assert at_least_one_different
def test_generator_flow_StellarGraphs():
generator = PaddedGraphGenerator(graphs=graphs)
graph_ilocs = [1, 2, 0]
seq_1 = generator.flow(graph_ilocs)
seq_2 = generator.flow([graphs[1], graphs[2], graphs[0]])
assert all(g1 == g2 for g1, g2 in zip(seq_1.graphs, seq_2.graphs))
def test_generator_flow_with_targets():
generator = PaddedGraphGenerator(graphs=graphs)
seq = generator.flow(graphs=[1, 2], targets=np.array([0, 1]), batch_size=1)
assert isinstance(seq, PaddedGraphSequence)
for batch in seq:
assert batch[0][0].shape[0] == 1
assert batch[0][1].shape[0] == 1
assert batch[0][2].shape[0] == 1
assert batch[1].shape[0] == 1
def test_generator_flow_invalid_batch_size():
with pytest.raises(
ValueError,
match="expected batch_size.*strictly positive integer, found -1"):
PaddedGraphGenerator(graphs=graphs).flow(graphs=[0], batch_size=-1)
with pytest.raises(TypeError,
match="expected batch_size.*integer type, found float"):
PaddedGraphGenerator(graphs=graphs).flow(graphs=[0], batch_size=2.0)
with pytest.raises(
ValueError,
match="expected batch_size.*strictly positive integer, found 0"):
PaddedGraphGenerator(graphs=graphs).flow(graphs=[0], batch_size=0)
def test_generator_flow_StellarGraphs():
generator = PaddedGraphGenerator(graphs=graphs)
graph_ilocs = [1, 2, 0]
seq_1 = generator.flow(graph_ilocs)
seq_2 = generator.flow([graphs[1], graphs[2], graphs[0]])
assert len(seq_1) == len(seq_2) == 3
for (values_1, targets_1), (values_2, targets_2) in zip(seq_1, seq_2):
assert len(values_1) == len(values_2) == 3
assert targets_1 is targets_2 is None
for arr_1, arr_2 in zip(values_1, values_2):
np.testing.assert_array_equal(arr_1, arr_2)
def test_generator_flow_check_padding():
generator = PaddedGraphGenerator(graphs=graphs)
seq = generator.flow(graphs=[0, 2], batch_size=2)
assert isinstance(seq, PaddedGraphSequence)
assert len(seq) == 1
# The largest graph has 6 nodes vs 3 for the smallest one.
# Check that the data matrices have the correct size 6
batch = seq[0]
assert batch[0][0].shape == (2, 6, 4)
assert batch[0][1].shape == (2, 6)
assert batch[0][2].shape == (2, 6, 6)
for mask in batch[0][1]:
assert np.sum(mask) == 6 or np.sum(mask) == 3
def test_generator_init_hin():
graphs_mixed = [
example_graph_random(feature_size=2, n_nodes=6),
example_hin_1(is_directed=False),
]
with pytest.raises(
ValueError,
match="graphs: node generator requires graphs with single node type.*found.*2",
):
generator = PaddedGraphGenerator(graphs=graphs_mixed)
def test_generator_empty():
graphs = [
example_graph_random(feature_size=2, n_nodes=4),
example_graph_random(feature_size=2, node_types=0, edge_types=0),
]
with pytest.raises(
ValueError,
match=
"graphs: expected every graph to be non-empty, found graph with no nodes",
):
generator = PaddedGraphGenerator(graphs=graphs)
generator = PaddedGraphGenerator(graphs=graphs[:1])
with pytest.raises(
ValueError,
match=
"graphs: expected every graph to be non-empty, found graph with no nodes",
):
seq = generator.flow(graphs)
def test_generator_hin():
graphs_mixed = [
example_graph_random(feature_size=2, n_nodes=6),
example_hin_1(is_directed=False),
]
with pytest.raises(
ValueError,
match=
"graphs: expected only graphs with a single node type.*found.*'A', 'B'",
):
generator = PaddedGraphGenerator(graphs=graphs_mixed)
generator = PaddedGraphGenerator(graphs=graphs_mixed[:1])
with pytest.raises(
ValueError,
match=
"graphs: expected only graphs with a single node type.*found.*'A', 'B'",
):
seq = generator.flow(graphs_mixed)
def test_generator_adj_normalisation(symmetric_normalization):
graph = example_graph(feature_size=4)
generator = PaddedGraphGenerator(graphs=[graph])
seq = generator.flow(graphs=[0],
symmetric_normalization=symmetric_normalization)
adj_norm_seq = seq.normalized_adjs[0].todense()
adj = np.array(graph.to_adjacency_matrix().todense())
np.fill_diagonal(adj, 1)
if symmetric_normalization:
inv_deg = np.diag(np.sqrt(1.0 / adj.sum(axis=1)))
adj_norm = inv_deg.dot(adj).dot(inv_deg)
else:
inv_deg = np.diag(1.0 / adj.sum(axis=1))
adj_norm = inv_deg.dot(adj)
assert np.allclose(adj_norm_seq, adj_norm)
def test_generator_different_feature_numbers():
graphs_diff_num_features = [
example_graph_random(feature_size=2, n_nodes=6),
example_graph_random(feature_size=4, n_nodes=5),
]
with pytest.raises(
ValueError,
match=
"graphs: expected node features for all graph to have same dimensions,.*2.*4",
):
generator = PaddedGraphGenerator(graphs=graphs_diff_num_features)
generator = PaddedGraphGenerator(graphs=graphs_diff_num_features[:1])
with pytest.raises(
ValueError,
match=
"graphs: expected node features for all graph to have same dimensions,.*2.*4",
):
seq = generator.flow(graphs_diff_num_features)
def test_generator_init_nx_graph():
graphs_nx = [
example_graph_random(feature_size=4, n_nodes=3, is_directed=False),
example_graph_random(feature_size=4, n_nodes=2,
is_directed=False).to_networkx(),
]
with pytest.raises(
TypeError,
match="graphs: expected.*StellarGraph.*found MultiGraph."):
generator = PaddedGraphGenerator(graphs=graphs_nx)
def test_generator_flow_no_targets():
generator = PaddedGraphGenerator(graphs=graphs)
seq = generator.flow(graph_ilocs=[0, 1, 2], batch_size=2)
assert isinstance(seq, PaddedGraphSequence)
assert len(seq) == 2 # two batches
# The first batch should be size 2 and the second batch size 1
batch_0 = seq[0]
assert batch_0[0][0].shape[0] == 2
assert batch_0[0][1].shape[0] == 2
assert batch_0[0][2].shape[0] == 2
assert batch_0[1] is None
batch_1 = seq[1]
assert batch_1[0][0].shape[0] == 1
assert batch_1[0][1].shape[0] == 1
assert batch_1[0][2].shape[0] == 1
assert batch_1[1] is None
def test_generator_pairs(use_targets, use_ilocs):
generator = PaddedGraphGenerator(graphs=graphs)
targets = [12, 34, 56] if use_targets else None
ilocs = [(1, 0), (0, 2), (2, 1)]
input = ilocs if use_ilocs else [[graphs[x] for x in pair]
for pair in ilocs]
seq = generator.flow(input, targets=targets, batch_size=2)
assert len(seq) == 2
values_0, targets_0 = seq[0]
assert len(values_0) == 6
assert values_0[0].shape == (2, 6, 4)
assert values_0[3].shape == (2, 6, 4)
np.testing.assert_array_equal(values_0[1], [_mask(5, 6), _mask(6, 6)])
np.testing.assert_array_equal(values_0[4], [_mask(6, 6), _mask(3, 6)])
assert values_0[2].shape == (2, 6, 6)
assert values_0[5].shape == (2, 6, 6)
if use_targets:
np.testing.assert_array_equal(targets_0, [12, 34])
else:
assert targets_0 is None
values_1, targets_1 = seq[1]
assert len(values_1) == 6
assert values_1[0].shape == (1, 5, 4)
assert values_1[3].shape == (1, 5, 4)
np.testing.assert_array_equal(values_1[1], [_mask(3, 5)])
np.testing.assert_array_equal(values_1[4], [_mask(5, 5)])
assert values_1[2].shape == (1, 5, 5)
assert values_1[5].shape == (1, 5, 5)
if use_targets:
np.testing.assert_array_equal(targets_1, [56])
else:
assert targets_1 is None
def test_generator_flow_invalid_shape():
generator = PaddedGraphGenerator(graphs=graphs)
with pytest.raises(ValueError,
match=r"graphs: expected a shape .* found shape \(\)"):
generator.flow(0)
with pytest.raises(
ValueError,
match=r"graphs: expected a shape .* found shape \(2, 3, 4\)"):
generator.flow(np.ones((2, 3, 4)))
def test_generator_flow_incorrect_targets():
generator = PaddedGraphGenerator(graphs=graphs)
with pytest.raises(
ValueError, match="expected targets to be the same length as node_ids,.*1 vs 2"
):
generator.flow(graph_ilocs=[0, 1], targets=np.array([0]))
with pytest.raises(
TypeError, match="targets: expected an iterable or None object, found int"
):
generator.flow(graph_ilocs=[0, 1], targets=1)
def test_generator_init():
generator = PaddedGraphGenerator(graphs=graphs)
assert len(generator.graphs) == len(graphs)
