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import copy
import pytest
import torch
import torch.multiprocessing as mp
import torch_geometric
from torch_geometric.data import Data
from torch_geometric.data.storage import AttrType
from torch_geometric.testing import get_random_tensor_frame, withPackage
def test_data():
torch_geometric.set_debug(True)
x = torch.tensor([[1, 3, 5], [2, 4, 6]], dtype=torch.float).t()
edge_index = torch.tensor([[0, 0, 1, 1, 2], [1, 1, 0, 2, 1]])
data = Data(x=x, edge_index=edge_index).to(torch.device('cpu'))
data.validate(raise_on_error=True)
N = data.num_nodes
assert N == 3
assert data.node_attrs() == ['x']
assert data.edge_attrs() == ['edge_index']
assert data.x.tolist() == x.tolist()
assert data['x'].tolist() == x.tolist()
assert data.get('x').tolist() == x.tolist()
assert data.get('y', 2) == 2
assert data.get('y', None) is None
assert data.num_edge_types == 1
assert data.num_node_types == 1
assert next(data('x')) == ('x', x)
assert sorted(data.keys()) == ['edge_index', 'x']
assert len(data) == 2
assert 'x' in data and 'edge_index' in data and 'pos' not in data
data.apply_(lambda x: x.mul_(2), 'x')
assert torch.allclose(data.x, x)
data.requires_grad_('x')
assert data.x.requires_grad is True
D = data.to_dict()
assert len(D) == 2
assert 'x' in D and 'edge_index' in D
D = data.to_namedtuple()
assert len(D) == 2
assert D.x is not None and D.edge_index is not None
assert data.__cat_dim__('x', data.x) == 0
assert data.__cat_dim__('edge_index', data.edge_index) == -1
assert data.__inc__('x', data.x) == 0
assert data.__inc__('edge_index', data.edge_index) == data.num_nodes
assert not data.x.is_contiguous()
data.contiguous()
assert data.x.is_contiguous()
assert not data.is_coalesced()
data = data.coalesce()
assert data.is_coalesced()
clone = data.clone()
assert clone != data
assert len(clone) == len(data)
assert clone.x.data_ptr() != data.x.data_ptr()
assert clone.x.tolist() == data.x.tolist()
assert clone.edge_index.data_ptr() != data.edge_index.data_ptr()
assert clone.edge_index.tolist() == data.edge_index.tolist()
# Test `data.to_heterogeneous()`:
out = data.to_heterogeneous()
assert torch.allclose(data.x, out['0'].x)
assert torch.allclose(data.edge_index, out['0', '0'].edge_index)
data.edge_type = torch.tensor([0, 0, 1, 0])
out = data.to_heterogeneous()
assert torch.allclose(data.x, out['0'].x)
assert [store.num_edges for store in out.edge_stores] == [3, 1]
data.edge_type = None
data['x'] = x + 1
assert data.x.tolist() == (x + 1).tolist()
assert str(data) == 'Data(x=[3, 2], edge_index=[2, 4])'
dictionary = {'x': data.x, 'edge_index': data.edge_index}
data = Data.from_dict(dictionary)
assert sorted(data.keys()) == ['edge_index', 'x']
assert not data.has_isolated_nodes()
assert not data.has_self_loops()
assert data.is_undirected()
assert not data.is_directed()
assert data.num_nodes == 3
assert data.num_edges == 4
with pytest.warns(UserWarning, match='deprecated'):
assert data.num_faces is None
assert data.num_node_features == 2
assert data.num_features == 2
data.edge_attr = torch.randn(data.num_edges, 2)
assert data.num_edge_features == 2
data.edge_attr = None
data.x = None
with pytest.warns(UserWarning, match='Unable to accurately infer'):
assert data.num_nodes == 3
data.edge_index = None
with pytest.warns(UserWarning, match='Unable to accurately infer'):
assert data.num_nodes is None
assert data.num_edges == 0
data.num_nodes = 4
assert data.num_nodes == 4
data = Data(x=x, attribute=x)
assert len(data) == 2
assert data.x.tolist() == x.tolist()
assert data.attribute.tolist() == x.tolist()
face = torch.tensor([[0, 1], [1, 2], [2, 3]])
data = Data(num_nodes=4, face=face)
with pytest.warns(UserWarning, match='deprecated'):
assert data.num_faces == 2
assert data.num_nodes == 4
data = Data(title='test')
assert str(data) == "Data(title='test')"
assert data.num_node_features == 0
assert data.num_edge_features == 0
key = value = 'test_value'
data[key] = value
assert data[key] == value
del data[value]
del data[value] # Deleting unset attributes should work as well.
assert data.get(key) is None
assert data.get('title') == 'test'
torch_geometric.set_debug(False)
def test_data_attr_cache():
x = torch.randn(3, 16)
edge_index = torch.tensor([[0, 0, 1, 1, 2], [1, 1, 0, 2, 1]])
edge_attr = torch.randn(5, 4)
y = torch.tensor([0])
data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr, y=y)
assert data.is_node_attr('x')
assert 'x' in data._store._cached_attr[AttrType.NODE]
assert 'x' not in data._store._cached_attr[AttrType.EDGE]
assert 'x' not in data._store._cached_attr[AttrType.OTHER]
assert not data.is_node_attr('edge_index')
assert 'edge_index' not in data._store._cached_attr[AttrType.NODE]
assert 'edge_index' in data._store._cached_attr[AttrType.EDGE]
assert 'edge_index' not in data._store._cached_attr[AttrType.OTHER]
assert data.is_edge_attr('edge_attr')
assert 'edge_attr' not in data._store._cached_attr[AttrType.NODE]
assert 'edge_attr' in data._store._cached_attr[AttrType.EDGE]
assert 'edge_attr' not in data._store._cached_attr[AttrType.OTHER]
assert not data.is_edge_attr('y')
assert 'y' not in data._store._cached_attr[AttrType.NODE]
assert 'y' not in data._store._cached_attr[AttrType.EDGE]
assert 'y' in data._store._cached_attr[AttrType.OTHER]
def test_data_attr_cache_not_shared():
x = torch.rand((4, 4))
edge_index = torch.tensor([[0, 1, 2, 3, 0, 1], [0, 1, 2, 3, 0, 1]])
time = torch.arange(edge_index.size(1))
data = Data(x=x, edge_index=edge_index, time=time)
assert data.is_node_attr('x')
out = data.up_to(3.5)
# This is expected behavior due to the ambiguity of between node-level and
# edge-level tensors when they share the same number of nodes/edges.
assert out.is_node_attr('time')
assert not data.is_node_attr('time')
def test_to_heterogeneous_empty_edge_index():
data = Data(
x=torch.randn(5, 10),
edge_index=torch.empty(2, 0, dtype=torch.long),
)
hetero_data = data.to_heterogeneous()
assert hetero_data.node_types == ['0']
assert hetero_data.edge_types == []
assert len(hetero_data) == 1
assert torch.equal(hetero_data['0'].x, data.x)
hetero_data = data.to_heterogeneous(
node_type_names=['0'],
edge_type_names=[('0', 'to', '0')],
)
assert hetero_data.node_types == ['0']
assert hetero_data.edge_types == [('0', 'to', '0')]
assert len(hetero_data) == 2
assert torch.equal(hetero_data['0'].x, data.x)
assert torch.equal(hetero_data['0', 'to', '0'].edge_index, data.edge_index)
def test_data_subgraph():
x = torch.arange(5)
y = torch.tensor([0.])
edge_index = torch.tensor([[0, 1, 1, 2, 2, 3, 3, 4],
[1, 0, 2, 1, 3, 2, 4, 3]])
edge_weight = torch.arange(edge_index.size(1))
data = Data(x=x, y=y, edge_index=edge_index, edge_weight=edge_weight,
num_nodes=5)
out = data.subgraph(torch.tensor([1, 2, 3]))
assert len(out) == 5
assert torch.equal(out.x, torch.arange(1, 4))
assert torch.equal(out.y, data.y)
assert out.edge_index.tolist() == [[0, 1, 1, 2], [1, 0, 2, 1]]
assert torch.equal(out.edge_weight, edge_weight[torch.arange(2, 6)])
assert out.num_nodes == 3
# Test unordered selection:
out = data.subgraph(torch.tensor([3, 1, 2]))
assert len(out) == 5
assert torch.equal(out.x, torch.tensor([3, 1, 2]))
assert torch.equal(out.y, data.y)
assert out.edge_index.tolist() == [[1, 2, 2, 0], [2, 1, 0, 2]]
assert torch.equal(out.edge_weight, edge_weight[torch.arange(2, 6)])
assert out.num_nodes == 3
out = data.subgraph(torch.tensor([False, False, False, True, True]))
assert len(out) == 5
assert torch.equal(out.x, torch.arange(3, 5))
assert torch.equal(out.y, data.y)
assert out.edge_index.tolist() == [[0, 1], [1, 0]]
assert torch.equal(out.edge_weight, edge_weight[torch.arange(6, 8)])
assert out.num_nodes == 2
out = data.edge_subgraph(torch.tensor([1, 2, 3]))
assert len(out) == 5
assert out.num_nodes == data.num_nodes
assert torch.equal(out.x, data.x)
assert torch.equal(out.y, data.y)
assert out.edge_index.tolist() == [[1, 1, 2], [0, 2, 1]]
assert torch.equal(out.edge_weight, edge_weight[torch.tensor([1, 2, 3])])
out = data.edge_subgraph(
torch.tensor([False, True, True, True, False, False, False, False]))
assert len(out) == 5
assert out.num_nodes == data.num_nodes
assert torch.equal(out.x, data.x)
assert torch.equal(out.y, data.y)
assert out.edge_index.tolist() == [[1, 1, 2], [0, 2, 1]]
assert torch.equal(out.edge_weight, edge_weight[torch.tensor([1, 2, 3])])
def test_data_subgraph_with_list_field():
x = torch.arange(5)
y = list(range(5))
edge_index = torch.tensor([[0, 1, 1, 2, 2, 3, 3, 4],
[1, 0, 2, 1, 3, 2, 4, 3]])
data = Data(x=x, y=y, edge_index=edge_index)
out = data.subgraph(torch.tensor([1, 2, 3]))
assert len(out) == 3
assert out.x.tolist() == out.y == [1, 2, 3]
out = data.subgraph(torch.tensor([False, True, True, True, False]))
assert len(out) == 3
assert out.x.tolist() == out.y == [1, 2, 3]
def test_data_empty_subgraph():
data = Data(x=torch.arange(5), y=torch.tensor(0.0))
out = data.subgraph(torch.tensor([1, 2, 3]))
assert 'edge_index' not in out
assert torch.equal(out.x, torch.arange(1, 4))
assert torch.equal(out.y, data.y)
assert out.num_nodes == 3
def test_copy_data():
data = Data(x=torch.randn(20, 5))
out = copy.copy(data)
assert id(data) != id(out)
assert id(data._store) != id(out._store)
assert len(data.stores) == len(out.stores)
for store1, store2 in zip(data.stores, out.stores):
assert id(store1) != id(store2)
assert id(data) == id(store1._parent())
assert id(out) == id(store2._parent())
assert data.x.data_ptr() == out.x.data_ptr()
out = copy.deepcopy(data)
assert id(data) != id(out)
assert id(data._store) != id(out._store)
assert len(data.stores) == len(out.stores)
for store1, store2 in zip(data.stores, out.stores):
assert id(store1) != id(store2)
assert id(data) == id(store1._parent())
assert id(out) == id(store2._parent())
assert data.x.data_ptr() != out.x.data_ptr()
assert data.x.tolist() == out.x.tolist()
def test_data_sort():
x = torch.randn(4, 16)
edge_index = torch.tensor([[0, 0, 0, 2, 1, 3], [1, 2, 3, 0, 0, 0]])
edge_attr = torch.randn(6, 8)
data = Data(x=x, edge_index=edge_index, edge_attr=edge_attr)
assert not data.is_sorted(sort_by_row=True)
assert not data.is_sorted(sort_by_row=False)
out = data.sort(sort_by_row=True)
assert out.is_sorted(sort_by_row=True)
assert not out.is_sorted(sort_by_row=False)
assert torch.equal(out.x, data.x)
assert out.edge_index.tolist() == [[0, 0, 0, 1, 2, 3], [1, 2, 3, 0, 0, 0]]
assert torch.equal(
out.edge_attr,
data.edge_attr[torch.tensor([0, 1, 2, 4, 3, 5])],
)
out = data.sort(sort_by_row=False)
assert not out.is_sorted(sort_by_row=True)
assert out.is_sorted(sort_by_row=False)
assert torch.equal(out.x, data.x)
assert out.edge_index.tolist() == [[1, 2, 3, 0, 0, 0], [0, 0, 0, 1, 2, 3]]
assert torch.equal(
out.edge_attr,
data.edge_attr[torch.tensor([4, 3, 5, 0, 1, 2])],
)
def test_debug_data():
torch_geometric.set_debug(True)
Data()
Data(edge_index=torch.zeros((2, 0), dtype=torch.long), num_nodes=10)
Data(face=torch.zeros((3, 0), dtype=torch.long), num_nodes=10)
Data(edge_index=torch.tensor([[0, 1], [1, 0]]), edge_attr=torch.randn(2))
Data(x=torch.torch.randn(5, 3), num_nodes=5)
Data(pos=torch.torch.randn(5, 3), num_nodes=5)
Data(norm=torch.torch.randn(5, 3), num_nodes=5)
torch_geometric.set_debug(False)
def run(rank, data_list):
for data in data_list:
assert data.x.is_shared()
data.x.add_(1)
def test_data_share_memory():
data_list = [Data(x=torch.zeros(8)) for _ in range(10)]
for data in data_list:
assert not data.x.is_shared()
assert torch.all(data.x == 0.0)
mp.spawn(run, args=(data_list, ), nprocs=4, join=True)
for data in data_list:
assert data.x.is_shared()
assert torch.all(data.x > 0.0)
def test_data_setter_properties():
class MyData(Data):
def __init__(self):
super().__init__()
self.my_attr1 = 1
self.my_attr2 = 2
@property
def my_attr1(self):
return self._my_attr1
@my_attr1.setter
def my_attr1(self, value):
self._my_attr1 = value
data = MyData()
assert data.my_attr2 == 2
assert 'my_attr1' not in data._store
assert data.my_attr1 == 1
data.my_attr1 = 2
assert 'my_attr1' not in data._store
assert data.my_attr1 == 2
def test_data_update():
data = Data(x=torch.arange(0, 5), y=torch.arange(5, 10))
other = Data(z=torch.arange(10, 15), x=torch.arange(15, 20))
data.update(other)
assert len(data) == 3
assert torch.equal(data.x, torch.arange(15, 20))
assert torch.equal(data.y, torch.arange(5, 10))
assert torch.equal(data.z, torch.arange(10, 15))
# Feature Store ###############################################################
def test_basic_feature_store():
data = Data()
x = torch.randn(20, 20)
data.not_a_tensor_attr = 10 # don't include, not a tensor attr
data.bad_attr = torch.randn(10, 20) # don't include, bad cat_dim
# Put tensor:
assert data.put_tensor(copy.deepcopy(x), attr_name='x', index=None)
assert torch.equal(data.x, x)
# Put (modify) tensor slice:
x[15:] = 0
data.put_tensor(0, attr_name='x', index=slice(15, None, None))
# Get tensor:
out = data.get_tensor(attr_name='x', index=None)
assert torch.equal(x, out)
# Get tensor size:
assert data.get_tensor_size(attr_name='x') == (20, 20)
# Get tensor attrs:
tensor_attrs = data.get_all_tensor_attrs()
assert len(tensor_attrs) == 1
assert tensor_attrs[0].attr_name == 'x'
# Remove tensor:
assert 'x' in data.__dict__['_store']
data.remove_tensor(attr_name='x', index=None)
assert 'x' not in data.__dict__['_store']
# Graph Store #################################################################
@withPackage('torch_sparse')
def test_basic_graph_store():
r"""Test the core graph store API."""
data = Data()
def assert_equal_tensor_tuple(expected, actual):
assert len(expected) == len(actual)
for i in range(len(expected)):
assert torch.equal(expected[i], actual[i])
# We put all three tensor types: COO, CSR, and CSC, and we get them back
# to confirm that `GraphStore` works as intended.
coo = (torch.tensor([0, 1]), torch.tensor([1, 2]))
csr = (torch.tensor([0, 1, 2, 2]), torch.tensor([1, 2]))
csc = (torch.tensor([0, 1]), torch.tensor([0, 0, 1, 2]))
# Put:
data.put_edge_index(coo, layout='coo', size=(3, 3))
data.put_edge_index(csr, layout='csr')
data.put_edge_index(csc, layout='csc')
# Get:
assert_equal_tensor_tuple(coo, data.get_edge_index('coo'))
assert_equal_tensor_tuple(csr, data.get_edge_index('csr'))
assert_equal_tensor_tuple(csc, data.get_edge_index('csc'))
# Get attrs:
edge_attrs = data.get_all_edge_attrs()
assert len(edge_attrs) == 3
# Remove:
coo, csr, csc = edge_attrs
data.remove_edge_index(coo)
data.remove_edge_index(csr)
data.remove_edge_index(csc)
assert len(data.get_all_edge_attrs()) == 0
def test_data_generate_ids():
x = torch.randn(3, 8)
edge_index = torch.tensor([[0, 0, 1, 1, 2], [1, 1, 0, 2, 1]])
data = Data(x=x, edge_index=edge_index)
assert len(data) == 2
data.generate_ids()
assert len(data) == 4
assert data.n_id.tolist() == [0, 1, 2]
assert data.e_id.tolist() == [0, 1, 2, 3, 4]
@withPackage('torch_frame')
def test_data_with_tensor_frame():
tf = get_random_tensor_frame(num_rows=10)
data = Data(tf=tf, edge_index=torch.randint(0, 10, size=(2, 20)))
# Test basic attributes:
assert data.is_node_attr('tf')
assert data.num_nodes == tf.num_rows
assert data.num_edges == 20
assert data.num_node_features == tf.num_cols
# Test subgraph:
index = torch.tensor([1, 2, 3])
sub_data = data.subgraph(index)
assert sub_data.num_nodes == 3
for key, value in sub_data.tf.feat_dict.items():
assert torch.allclose(value, tf.feat_dict[key][index])
mask = torch.tensor(
[False, True, True, True, False, False, False, False, False, False])
data_sub = data.subgraph(mask)
assert data_sub.num_nodes == 3
for key, value in sub_data.tf.feat_dict.items():
assert torch.allclose(value, tf.feat_dict[key][mask])
@pytest.mark.parametrize('num_nodes', [4])
@pytest.mark.parametrize('num_edges', [8])
def test_data_time_handling(num_nodes, num_edges):
data = Data(
x=torch.randn(num_nodes, 12),
edge_index=torch.randint(0, num_nodes, (2, num_edges)),
edge_attr=torch.rand((num_edges, 16)),
time=torch.arange(num_edges),
num_nodes=num_nodes,
)
assert data.is_edge_attr('time')
assert not data.is_node_attr('time')
assert data.is_sorted_by_time()
out = data.up_to(5)
assert out.num_edges == 6
assert torch.allclose(out.x, data.x)
assert torch.equal(out.edge_index, data.edge_index[:, :6])
assert torch.allclose(out.edge_attr, data.edge_attr[:6])
assert torch.equal(out.time, data.time[:6])
out = data.snapshot(2, 5)
assert out.num_edges == 4
assert torch.allclose(out.x, data.x)
assert torch.equal(out.edge_index, data.edge_index[:, 2:6])
assert torch.allclose(out.edge_attr, data.edge_attr[2:6, :])
assert torch.equal(out.time, data.time[2:6])
out = data.sort_by_time()
assert data.is_sorted_by_time()
out = data.concat(data)
assert out.num_nodes == 8
assert not out.is_sorted_by_time()
assert torch.allclose(out.x, torch.cat([data.x, data.x], dim=0))
assert torch.equal(
out.edge_index,
torch.cat([data.edge_index, data.edge_index], dim=1),
)
assert torch.allclose(
out.edge_attr,
torch.cat([data.edge_attr, data.edge_attr], dim=0),
)
assert torch.allclose(out.time, torch.cat([data.time, data.time], dim=0))
out = out.sort_by_time()
assert torch.equal(out.time, data.time.repeat_interleave(2))
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