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import copy
import logging
import math
from typing import Any, Dict, Optional, Tuple, Union
import numpy as np
import torch
from torch import Tensor
import torch_geometric.typing
from torch_geometric.data import (
Data,
FeatureStore,
GraphStore,
HeteroData,
TensorAttr,
remote_backend_utils,
)
from torch_geometric.data.storage import EdgeStorage, NodeStorage
from torch_geometric.typing import (
EdgeType,
FeatureTensorType,
InputEdges,
InputNodes,
NodeType,
OptTensor,
SparseTensor,
TensorFrame,
)
def index_select(
value: FeatureTensorType,
index: Tensor,
dim: int = 0,
) -> Tensor:
r"""Indexes the :obj:`value` tensor along dimension :obj:`dim` using the
entries in :obj:`index`.
Args:
value (torch.Tensor or np.ndarray): The input tensor.
index (torch.Tensor): The 1-D tensor containing the indices to index.
dim (int, optional): The dimension in which to index.
(default: :obj:`0`)
.. warning::
:obj:`index` is casted to a :obj:`torch.int64` tensor internally, as
`PyTorch currently only supports indexing
<https://github.com/pytorch/pytorch/issues/61819>`_ via
:obj:`torch.int64`.
"""
# PyTorch currently only supports indexing via `torch.int64`:
# https://github.com/pytorch/pytorch/issues/61819
index = index.to(torch.int64)
if isinstance(value, Tensor):
out: Optional[Tensor] = None
if torch.utils.data.get_worker_info() is not None:
# If we are in a background process, we write directly into a
# shared memory tensor to avoid an extra copy:
size = list(value.shape)
size[dim] = index.numel()
numel = math.prod(size)
if torch_geometric.typing.WITH_PT20:
storage = value.untyped_storage()._new_shared(
numel * value.element_size())
else:
storage = value.storage()._new_shared(numel)
out = value.new(storage).view(size)
return torch.index_select(value, dim, index, out=out)
if isinstance(value, TensorFrame):
assert dim == 0
return value[index]
elif isinstance(value, np.ndarray):
return torch.from_numpy(np.take(value, index, axis=dim))
raise ValueError(f"Encountered invalid feature tensor type "
f"(got '{type(value)}')")
def filter_node_store_(store: NodeStorage, out_store: NodeStorage,
index: Tensor):
# Filters a node storage object to only hold the nodes in `index`:
for key, value in store.items():
if key == 'num_nodes':
out_store.num_nodes = index.numel()
elif store.is_node_attr(key):
if isinstance(value, (Tensor, TensorFrame)):
index = index.to(value.device)
elif isinstance(value, np.ndarray):
index = index.cpu()
dim = store._parent().__cat_dim__(key, value, store)
out_store[key] = index_select(value, index, dim=dim)
def filter_edge_store_(store: EdgeStorage, out_store: EdgeStorage, row: Tensor,
col: Tensor, index: OptTensor, perm: OptTensor = None):
# Filters a edge storage object to only hold the edges in `index`,
# which represents the new graph as denoted by `(row, col)`:
for key, value in store.items():
if key == 'edge_index':
edge_index = torch.stack([row, col], dim=0).to(value.device)
# TODO Integrate `EdgeIndex` into `custom_store`.
# edge_index = EdgeIndex(
# torch.stack([row, col], dim=0).to(value.device),
# sparse_size=out_store.size(),
# sort_order='col',
# # TODO Support `is_undirected`.
# )
out_store.edge_index = edge_index
elif key == 'adj_t':
# NOTE: We expect `(row, col)` to be sorted by `col` (CSC layout).
row = row.to(value.device())
col = col.to(value.device())
edge_attr = value.storage.value()
if edge_attr is not None:
if index is not None:
index = index.to(edge_attr.device)
edge_attr = index_select(edge_attr, index, dim=0)
else:
edge_attr = None
sparse_sizes = out_store.size()[::-1]
# TODO Currently, we set `is_sorted=False`, see:
# https://github.com/pyg-team/pytorch_geometric/issues/4346
out_store.adj_t = SparseTensor(row=col, col=row, value=edge_attr,
sparse_sizes=sparse_sizes,
is_sorted=False, trust_data=True)
elif store.is_edge_attr(key):
if index is None:
out_store[key] = None
continue
dim = store._parent().__cat_dim__(key, value, store)
if isinstance(value, (Tensor, TensorFrame)):
index = index.to(value.device)
elif isinstance(value, np.ndarray):
index = index.cpu()
if perm is None:
out_store[key] = index_select(value, index, dim=dim)
else:
if isinstance(value, (Tensor, TensorFrame)):
perm = perm.to(value.device)
elif isinstance(value, np.ndarray):
perm = perm.cpu()
out_store[key] = index_select(
value,
perm[index.to(torch.int64)],
dim=dim,
)
def filter_data(data: Data, node: Tensor, row: Tensor, col: Tensor,
edge: OptTensor, perm: OptTensor = None) -> Data:
# Filters a data object to only hold nodes in `node` and edges in `edge`:
out = copy.copy(data)
filter_node_store_(data._store, out._store, node)
filter_edge_store_(data._store, out._store, row, col, edge, perm)
return out
def filter_hetero_data(
data: HeteroData,
node_dict: Dict[NodeType, Tensor],
row_dict: Dict[EdgeType, Tensor],
col_dict: Dict[EdgeType, Tensor],
edge_dict: Dict[EdgeType, OptTensor],
perm_dict: Optional[Dict[EdgeType, OptTensor]] = None,
) -> HeteroData:
# Filters a heterogeneous data object to only hold nodes in `node` and
# edges in `edge` for each node and edge type, respectively:
out = copy.copy(data)
for node_type in out.node_types:
# Handle the case of disconneted graph sampling:
if node_type not in node_dict:
node_dict[node_type] = torch.empty(0, dtype=torch.long)
filter_node_store_(data[node_type], out[node_type],
node_dict[node_type])
for edge_type in out.edge_types:
# Handle the case of disconneted graph sampling:
if edge_type not in row_dict:
row_dict[edge_type] = torch.empty(0, dtype=torch.long)
if edge_type not in col_dict:
col_dict[edge_type] = torch.empty(0, dtype=torch.long)
if edge_type not in edge_dict:
edge_dict[edge_type] = torch.empty(0, dtype=torch.long)
filter_edge_store_(
data[edge_type],
out[edge_type],
row_dict[edge_type],
col_dict[edge_type],
edge_dict[edge_type],
perm_dict.get(edge_type, None) if perm_dict else None,
)
return out
def filter_custom_store(
feature_store: FeatureStore,
graph_store: GraphStore,
node: Tensor,
row: Tensor,
col: Tensor,
edge: OptTensor,
custom_cls: Optional[Data] = None,
) -> Data:
r"""Constructs a :class:`~torch_geometric.data.Data` object from a feature
store and graph store instance.
"""
# Construct a new `Data` object:
data = custom_cls() if custom_cls is not None else Data()
data.edge_index = torch.stack([row, col], dim=0)
# Filter node storage:
required_attrs = []
for attr in feature_store.get_all_tensor_attrs():
attr.index = node # TODO Support edge features.
required_attrs.append(attr)
data.num_nodes = attr.index.size(0)
# NOTE Here, we utilize `feature_store.multi_get` to give the feature store
# full control over optimizing how it returns features (since the call is
# synchronous, this amounts to giving the feature store control over all
# iteration).
tensors = feature_store.multi_get_tensor(required_attrs)
for i, attr in enumerate(required_attrs):
data[attr.attr_name] = tensors[i]
return data
def filter_custom_hetero_store(
feature_store: FeatureStore,
graph_store: GraphStore,
node_dict: Dict[str, Tensor],
row_dict: Dict[str, Tensor],
col_dict: Dict[str, Tensor],
edge_dict: Dict[str, OptTensor],
custom_cls: Optional[HeteroData] = None,
) -> HeteroData:
r"""Constructs a :class:`~torch_geometric.data.HeteroData` object from a
feature store and graph store instance.
"""
# Construct a new `HeteroData` object:
data = custom_cls() if custom_cls is not None else HeteroData()
# Filter edge storage:
# TODO support edge attributes
for attr in graph_store.get_all_edge_attrs():
key = attr.edge_type
if key in row_dict and key in col_dict:
edge_index = torch.stack([row_dict[key], col_dict[key]], dim=0)
data[attr.edge_type].edge_index = edge_index
# Filter node storage:
required_attrs = []
for attr in feature_store.get_all_tensor_attrs():
if attr.group_name in node_dict:
attr.index = node_dict[attr.group_name]
required_attrs.append(attr)
data[attr.group_name].num_nodes = attr.index.size(0)
# NOTE Here, we utilize `feature_store.multi_get` to give the feature store
# full control over optimizing how it returns features (since the call is
# synchronous, this amounts to giving the feature store control over all
# iteration).
tensors = feature_store.multi_get_tensor(required_attrs)
for i, attr in enumerate(required_attrs):
data[attr.group_name][attr.attr_name] = tensors[i]
return data
# Input Utilities #############################################################
def get_input_nodes(
data: Union[Data, HeteroData, Tuple[FeatureStore, GraphStore]],
input_nodes: Union[InputNodes, TensorAttr],
input_id: Optional[Tensor] = None,
) -> Tuple[Optional[str], Tensor, Optional[Tensor]]:
def to_index(nodes, input_id) -> Tuple[Tensor, Optional[Tensor]]:
if isinstance(nodes, Tensor) and nodes.dtype == torch.bool:
nodes = nodes.nonzero(as_tuple=False).view(-1)
if input_id is not None:
assert input_id.numel() == nodes.numel()
else:
input_id = nodes
return nodes, input_id
if not isinstance(nodes, Tensor):
nodes = torch.tensor(nodes, dtype=torch.long)
if input_id is not None:
assert input_id.numel() == nodes.numel()
return nodes, input_id
if isinstance(data, Data):
if input_nodes is None:
return None, torch.arange(data.num_nodes), None
return None, *to_index(input_nodes, input_id)
elif isinstance(data, HeteroData):
assert input_nodes is not None
if isinstance(input_nodes, str):
return input_nodes, torch.arange(data[input_nodes].num_nodes), None
assert isinstance(input_nodes, (list, tuple))
assert len(input_nodes) == 2
assert isinstance(input_nodes[0], str)
node_type, input_nodes = input_nodes
if input_nodes is None:
return node_type, torch.arange(data[node_type].num_nodes), None
return node_type, *to_index(input_nodes, input_id)
else: # Tuple[FeatureStore, GraphStore]
feature_store, graph_store = data
assert input_nodes is not None
if isinstance(input_nodes, Tensor):
return None, *to_index(input_nodes, input_id)
if isinstance(input_nodes, str):
num_nodes = remote_backend_utils.num_nodes( #
feature_store, graph_store, input_nodes)
return input_nodes, torch.arange(num_nodes), None
if isinstance(input_nodes, (list, tuple)):
assert len(input_nodes) == 2
assert isinstance(input_nodes[0], str)
node_type, input_nodes = input_nodes
if input_nodes is None:
num_nodes = remote_backend_utils.num_nodes( #
feature_store, graph_store, input_nodes)
return node_type, torch.arange(num_nodes), None
return node_type, *to_index(input_nodes, input_id)
def get_edge_label_index(
data: Union[Data, HeteroData, Tuple[FeatureStore, GraphStore]],
edge_label_index: InputEdges,
) -> Tuple[Optional[str], Tensor]:
edge_type = None
if isinstance(data, Data):
if edge_label_index is None:
return None, data.edge_index
return None, edge_label_index
assert edge_label_index is not None
assert isinstance(edge_label_index, (list, tuple))
if isinstance(data, HeteroData):
if isinstance(edge_label_index[0], str):
edge_type = edge_label_index
edge_type = data._to_canonical(*edge_type)
assert edge_type in data.edge_types
return edge_type, data[edge_type].edge_index
assert len(edge_label_index) == 2
edge_type, edge_label_index = edge_label_index
edge_type = data._to_canonical(*edge_type)
if edge_label_index is None:
return edge_type, data[edge_type].edge_index
return edge_type, edge_label_index
else: # Tuple[FeatureStore, GraphStore]
_, graph_store = data
# Need the edge index in COO for LinkNeighborLoader:
def _get_edge_index(edge_type):
row_dict, col_dict, _ = graph_store.coo([edge_type])
row = list(row_dict.values())[0]
col = list(col_dict.values())[0]
return torch.stack((row, col), dim=0)
if isinstance(edge_label_index[0], str):
edge_type = edge_label_index
return edge_type, _get_edge_index(edge_type)
assert len(edge_label_index) == 2
edge_type, edge_label_index = edge_label_index
if edge_label_index is None:
return edge_type, _get_edge_index(edge_type)
return edge_type, edge_label_index
def infer_filter_per_worker(data: Any) -> bool:
out = True
if isinstance(data, (Data, HeteroData)) and data.is_cuda:
out = False
logging.debug(f"Inferred 'filter_per_worker={out}' option for feature "
f"fetching routines of the data loader")
return out
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