import copy
import re
import warnings
from collections import defaultdict, namedtuple
from collections.abc import Mapping
from itertools import chain
from typing import Any, Dict, List, NamedTuple, Optional, Tuple, Union
import torch
from torch import Tensor
from typing_extensions import Self
from torch_geometric.data import EdgeAttr, FeatureStore, GraphStore, TensorAttr
from torch_geometric.data.data import BaseData, Data, size_repr, warn_or_raise
from torch_geometric.data.graph_store import EdgeLayout
from torch_geometric.data.storage import BaseStorage, EdgeStorage, NodeStorage
from torch_geometric.typing import (
DEFAULT_REL,
EdgeTensorType,
EdgeType,
FeatureTensorType,
NodeOrEdgeType,
NodeType,
QueryType,
SparseTensor,
TensorFrame,
torch_frame,
)
from torch_geometric.utils import (
bipartite_subgraph,
contains_isolated_nodes,
is_sparse,
is_undirected,
mask_select,
)
NodeOrEdgeStorage = Union[NodeStorage, EdgeStorage]
[docs]class HeteroData(BaseData, FeatureStore, GraphStore):
r"""A data object describing a heterogeneous graph, holding multiple node
and/or edge types in disjunct storage objects.
Storage objects can hold either node-level, link-level or graph-level
attributes.
In general, :class:`~torch_geometric.data.HeteroData` tries to mimic the
behavior of a regular **nested** :python:`Python` dictionary.
In addition, it provides useful functionality for analyzing graph
structures, and provides basic PyTorch tensor functionalities.
.. code-block::
from torch_geometric.data import HeteroData
data = HeteroData()
# Create two node types "paper" and "author" holding a feature matrix:
data['paper'].x = torch.randn(num_papers, num_paper_features)
data['author'].x = torch.randn(num_authors, num_authors_features)
# Create an edge type "(author, writes, paper)" and building the
# graph connectivity:
data['author', 'writes', 'paper'].edge_index = ... # [2, num_edges]
data['paper'].num_nodes
>>> 23
data['author', 'writes', 'paper'].num_edges
>>> 52
# PyTorch tensor functionality:
data = data.pin_memory()
data = data.to('cuda:0', non_blocking=True)
Note that there exists multiple ways to create a heterogeneous graph data,
*e.g.*:
* To initialize a node of type :obj:`"paper"` holding a node feature
matrix :obj:`x_paper` named :obj:`x`:
.. code-block:: python
from torch_geometric.data import HeteroData
# (1) Assign attributes after initialization,
data = HeteroData()
data['paper'].x = x_paper
# or (2) pass them as keyword arguments during initialization,
data = HeteroData(paper={ 'x': x_paper })
# or (3) pass them as dictionaries during initialization,
data = HeteroData({'paper': { 'x': x_paper }})
* To initialize an edge from source node type :obj:`"author"` to
destination node type :obj:`"paper"` with relation type :obj:`"writes"`
holding a graph connectivity matrix :obj:`edge_index_author_paper` named
:obj:`edge_index`:
.. code-block:: python
# (1) Assign attributes after initialization,
data = HeteroData()
data['author', 'writes', 'paper'].edge_index = edge_index_author_paper
# or (2) pass them as keyword arguments during initialization,
data = HeteroData(author__writes__paper={
'edge_index': edge_index_author_paper
})
# or (3) pass them as dictionaries during initialization,
data = HeteroData({
('author', 'writes', 'paper'):
{ 'edge_index': edge_index_author_paper }
})
"""
def __init__(self, _mapping: Optional[Dict[str, Any]] = None, **kwargs):
super().__init__()
self.__dict__['_global_store'] = BaseStorage(_parent=self)
self.__dict__['_node_store_dict'] = {}
self.__dict__['_edge_store_dict'] = {}
for key, value in chain((_mapping or {}).items(), kwargs.items()):
if '__' in key and isinstance(value, Mapping):
key = tuple(key.split('__'))
if isinstance(value, Mapping):
self[key].update(value)
else:
setattr(self, key, value)
[docs] @classmethod
def from_dict(cls, mapping: Dict[str, Any]) -> Self:
r"""Creates a :class:`~torch_geometric.data.HeteroData` object from a
dictionary.
"""
out = cls()
for key, value in mapping.items():
if key == '_global_store':
out.__dict__['_global_store'] = BaseStorage(
_parent=out, **value)
elif isinstance(key, str):
out._node_store_dict[key] = NodeStorage(
_parent=out, _key=key, **value)
else:
out._edge_store_dict[key] = EdgeStorage(
_parent=out, _key=key, **value)
return out
def __getattr__(self, key: str) -> Any:
# `data.*_dict` => Link to node and edge stores.
# `data.*` => Link to the `_global_store`.
# Using `data.*_dict` is the same as using `collect()` for collecting
# nodes and edges features.
if hasattr(self._global_store, key):
return getattr(self._global_store, key)
elif bool(re.search('_dict$', key)):
return self.collect(key[:-5])
raise AttributeError(f"'{self.__class__.__name__}' has no "
f"attribute '{key}'")
def __setattr__(self, key: str, value: Any):
# NOTE: We aim to prevent duplicates in node or edge types.
if key in self.node_types:
raise AttributeError(f"'{key}' is already present as a node type")
elif key in self.edge_types:
raise AttributeError(f"'{key}' is already present as an edge type")
setattr(self._global_store, key, value)
def __delattr__(self, key: str):
delattr(self._global_store, key)
def __getitem__(self, *args: QueryType) -> Any:
# `data[*]` => Link to either `_global_store`, _node_store_dict` or
# `_edge_store_dict`.
# If neither is present, we create a new `Storage` object for the given
# node/edge-type.
key = self._to_canonical(*args)
out = self._global_store.get(key, None)
if out is not None:
return out
if isinstance(key, tuple):
return self.get_edge_store(*key)
else:
return self.get_node_store(key)
def __setitem__(self, key: str, value: Any):
if key in self.node_types:
raise AttributeError(f"'{key}' is already present as a node type")
elif key in self.edge_types:
raise AttributeError(f"'{key}' is already present as an edge type")
self._global_store[key] = value
def __delitem__(self, *args: QueryType):
# `del data[*]` => Link to `_node_store_dict` or `_edge_store_dict`.
key = self._to_canonical(*args)
if key in self.edge_types:
del self._edge_store_dict[key]
elif key in self.node_types:
del self._node_store_dict[key]
else:
del self._global_store[key]
def __copy__(self):
out = self.__class__.__new__(self.__class__)
for key, value in self.__dict__.items():
out.__dict__[key] = value
out.__dict__['_global_store'] = copy.copy(self._global_store)
out._global_store._parent = out
out.__dict__['_node_store_dict'] = {}
for key, store in self._node_store_dict.items():
out._node_store_dict[key] = copy.copy(store)
out._node_store_dict[key]._parent = out
out.__dict__['_edge_store_dict'] = {}
for key, store in self._edge_store_dict.items():
out._edge_store_dict[key] = copy.copy(store)
out._edge_store_dict[key]._parent = out
return out
def __deepcopy__(self, memo):
out = self.__class__.__new__(self.__class__)
for key, value in self.__dict__.items():
out.__dict__[key] = copy.deepcopy(value, memo)
out._global_store._parent = out
for key in self._node_store_dict.keys():
out._node_store_dict[key]._parent = out
for key in out._edge_store_dict.keys():
out._edge_store_dict[key]._parent = out
return out
def __repr__(self) -> str:
info1 = [size_repr(k, v, 2) for k, v in self._global_store.items()]
info2 = [size_repr(k, v, 2) for k, v in self._node_store_dict.items()]
info3 = [size_repr(k, v, 2) for k, v in self._edge_store_dict.items()]
info = ',\n'.join(info1 + info2 + info3)
info = f'\n{info}\n' if len(info) > 0 else info
return f'{self.__class__.__name__}({info})'
def stores_as(self, data: Self):
for node_type in data.node_types:
self.get_node_store(node_type)
for edge_type in data.edge_types:
self.get_edge_store(*edge_type)
return self
@property
def stores(self) -> List[BaseStorage]:
r"""Returns a list of all storages of the graph."""
return ([self._global_store] + list(self.node_stores) +
list(self.edge_stores))
@property
def node_types(self) -> List[NodeType]:
r"""Returns a list of all node types of the graph."""
return list(self._node_store_dict.keys())
@property
def node_stores(self) -> List[NodeStorage]:
r"""Returns a list of all node storages of the graph."""
return list(self._node_store_dict.values())
@property
def edge_types(self) -> List[EdgeType]:
r"""Returns a list of all edge types of the graph."""
return list(self._edge_store_dict.keys())
@property
def edge_stores(self) -> List[EdgeStorage]:
r"""Returns a list of all edge storages of the graph."""
return list(self._edge_store_dict.values())
[docs] def node_items(self) -> List[Tuple[NodeType, NodeStorage]]:
r"""Returns a list of node type and node storage pairs."""
return list(self._node_store_dict.items())
[docs] def edge_items(self) -> List[Tuple[EdgeType, EdgeStorage]]:
r"""Returns a list of edge type and edge storage pairs."""
return list(self._edge_store_dict.items())
[docs] def to_dict(self) -> Dict[str, Any]:
out_dict: Dict[str, Any] = {}
out_dict['_global_store'] = self._global_store.to_dict()
for key, store in chain(self._node_store_dict.items(),
self._edge_store_dict.items()):
out_dict[key] = store.to_dict()
return out_dict
[docs] def to_namedtuple(self) -> NamedTuple:
field_names = list(self._global_store.keys())
field_values = list(self._global_store.values())
field_names += [
'__'.join(key) if isinstance(key, tuple) else key
for key in self.node_types + self.edge_types
]
field_values += [
store.to_namedtuple()
for store in self.node_stores + self.edge_stores
]
DataTuple = namedtuple('DataTuple', field_names)
return DataTuple(*field_values)
[docs] def set_value_dict(
self,
key: str,
value_dict: Dict[str, Any],
) -> Self:
r"""Sets the values in the dictionary :obj:`value_dict` to the
attribute with name :obj:`key` to all node/edge types present in the
dictionary.
.. code-block:: python
data = HeteroData()
data.set_value_dict('x', {
'paper': torch.randn(4, 16),
'author': torch.randn(8, 32),
})
print(data['paper'].x)
"""
for k, v in (value_dict or {}).items():
self[k][key] = v
return self
[docs] def update(self, data: Self) -> Self:
for store in data.stores:
for key, value in store.items():
self[store._key][key] = value
return self
[docs] def __cat_dim__(self, key: str, value: Any,
store: Optional[NodeOrEdgeStorage] = None, *args,
**kwargs) -> Any:
if is_sparse(value) and 'adj' in key:
return (0, 1)
elif isinstance(store, EdgeStorage) and 'index' in key:
return -1
return 0
[docs] def __inc__(self, key: str, value: Any,
store: Optional[NodeOrEdgeStorage] = None, *args,
**kwargs) -> Any:
if 'batch' in key and isinstance(value, Tensor):
return int(value.max()) + 1
elif isinstance(store, EdgeStorage) and 'index' in key:
return torch.tensor(store.size()).view(2, 1)
else:
return 0
@property
def num_nodes(self) -> Optional[int]:
r"""Returns the number of nodes in the graph."""
return super().num_nodes
@property
def num_node_features(self) -> Dict[NodeType, int]:
r"""Returns the number of features per node type in the graph."""
return {
key: store.num_node_features
for key, store in self._node_store_dict.items()
}
@property
def num_features(self) -> Dict[NodeType, int]:
r"""Returns the number of features per node type in the graph.
Alias for :py:attr:`~num_node_features`.
"""
return self.num_node_features
@property
def num_edge_features(self) -> Dict[EdgeType, int]:
r"""Returns the number of features per edge type in the graph."""
return {
key: store.num_edge_features
for key, store in self._edge_store_dict.items()
}
[docs] def has_isolated_nodes(self) -> bool:
r"""Returns :obj:`True` if the graph contains isolated nodes."""
edge_index, _, _ = to_homogeneous_edge_index(self)
return contains_isolated_nodes(edge_index, num_nodes=self.num_nodes)
[docs] def is_undirected(self) -> bool:
r"""Returns :obj:`True` if graph edges are undirected."""
edge_index, _, _ = to_homogeneous_edge_index(self)
return is_undirected(edge_index, num_nodes=self.num_nodes)
[docs] def validate(self, raise_on_error: bool = True) -> bool:
r"""Validates the correctness of the data."""
cls_name = self.__class__.__name__
status = True
node_types = set(self.node_types)
num_src_node_types = {src for src, _, _ in self.edge_types}
num_dst_node_types = {dst for _, _, dst in self.edge_types}
dangling_types = (num_src_node_types | num_dst_node_types) - node_types
if len(dangling_types) > 0:
status = False
warn_or_raise(
f"The node types {dangling_types} are referenced in edge "
f"types but do not exist as node types", raise_on_error)
dangling_types = node_types - (num_src_node_types | num_dst_node_types)
if len(dangling_types) > 0:
warn_or_raise( # May be intended.
f"The node types {dangling_types} are isolated and are not "
f"referenced by any edge type ", raise_on_error=False)
for edge_type, store in self._edge_store_dict.items():
src, _, dst = edge_type
num_src_nodes = self[src].num_nodes
num_dst_nodes = self[dst].num_nodes
if num_src_nodes is None:
status = False
warn_or_raise(
f"'num_nodes' is undefined in node type '{src}' of "
f"'{cls_name}'", raise_on_error)
if num_dst_nodes is None:
status = False
warn_or_raise(
f"'num_nodes' is undefined in node type '{dst}' of "
f"'{cls_name}'", raise_on_error)
if 'edge_index' in store:
if (store.edge_index.dim() != 2
or store.edge_index.size(0) != 2):
status = False
warn_or_raise(
f"'edge_index' of edge type {edge_type} needs to be "
f"of shape [2, num_edges] in '{cls_name}' (found "
f"{store.edge_index.size()})", raise_on_error)
if 'edge_index' in store and store.edge_index.numel() > 0:
if store.edge_index.min() < 0:
status = False
warn_or_raise(
f"'edge_index' of edge type {edge_type} contains "
f"negative indices in '{cls_name}' "
f"(found {int(store.edge_index.min())})",
raise_on_error)
if (num_src_nodes is not None
and store.edge_index[0].max() >= num_src_nodes):
status = False
warn_or_raise(
f"'edge_index' of edge type {edge_type} contains "
f"larger source indices than the number of nodes "
f"({num_src_nodes}) of this node type in '{cls_name}' "
f"(found {int(store.edge_index[0].max())})",
raise_on_error)
if (num_dst_nodes is not None
and store.edge_index[1].max() >= num_dst_nodes):
status = False
warn_or_raise(
f"'edge_index' of edge type {edge_type} contains "
f"larger destination indices than the number of nodes "
f"({num_dst_nodes}) of this node type in '{cls_name}' "
f"(found {int(store.edge_index[1].max())})",
raise_on_error)
return status
def debug(self):
pass # TODO
###########################################################################
def _to_canonical(self, *args: QueryType) -> NodeOrEdgeType:
# Converts a given `QueryType` to its "canonical type":
# 1. `relation_type` will get mapped to the unique
# `(src_node_type, relation_type, dst_node_type)` tuple.
# 2. `(src_node_type, dst_node_type)` will get mapped to the unique
# `(src_node_type, *, dst_node_type)` tuple, and
# `(src_node_type, 'to', dst_node_type)` otherwise.
if len(args) == 1:
args = args[0]
if isinstance(args, str):
node_types = [key for key in self.node_types if key == args]
if len(node_types) == 1:
args = node_types[0]
return args
# Try to map to edge type based on unique relation type:
edge_types = [key for key in self.edge_types if key[1] == args]
if len(edge_types) == 1:
args = edge_types[0]
return args
elif len(args) == 2:
# Try to find the unique source/destination node tuple:
edge_types = [
key for key in self.edge_types
if key[0] == args[0] and key[-1] == args[-1]
]
if len(edge_types) == 1:
args = edge_types[0]
return args
elif len(edge_types) == 0:
args = (args[0], DEFAULT_REL, args[1])
return args
return args
[docs] def collect(
self,
key: str,
allow_empty: bool = False,
) -> Dict[NodeOrEdgeType, Any]:
r"""Collects the attribute :attr:`key` from all node and edge types.
.. code-block:: python
data = HeteroData()
data['paper'].x = ...
data['author'].x = ...
print(data.collect('x'))
>>> { 'paper': ..., 'author': ...}
.. note::
This is equivalent to writing :obj:`data.x_dict`.
Args:
key (str): The attribute to collect from all node and ege types.
allow_empty (bool, optional): If set to :obj:`True`, will not raise
an error in case the attribute does not exit in any node or
edge type. (default: :obj:`False`)
"""
mapping = {}
for subtype, store in chain(self._node_store_dict.items(),
self._edge_store_dict.items()):
if hasattr(store, key):
mapping[subtype] = getattr(store, key)
if not allow_empty and len(mapping) == 0:
raise KeyError(f"Tried to collect '{key}' but did not find any "
f"occurrences of it in any node and/or edge type")
return mapping
def _check_type_name(self, name: str):
if '__' in name:
warnings.warn(f"The type '{name}' contains double underscores "
f"('__') which may lead to unexpected behavior. "
f"To avoid any issues, ensure that your type names "
f"only contain single underscores.")
[docs] def get_node_store(self, key: NodeType) -> NodeStorage:
r"""Gets the :class:`~torch_geometric.data.storage.NodeStorage` object
of a particular node type :attr:`key`.
If the storage is not present yet, will create a new
:class:`torch_geometric.data.storage.NodeStorage` object for the given
node type.
.. code-block:: python
data = HeteroData()
node_storage = data.get_node_store('paper')
"""
out = self._node_store_dict.get(key, None)
if out is None:
self._check_type_name(key)
out = NodeStorage(_parent=self, _key=key)
self._node_store_dict[key] = out
return out
[docs] def get_edge_store(self, src: str, rel: str, dst: str) -> EdgeStorage:
r"""Gets the :class:`~torch_geometric.data.storage.EdgeStorage` object
of a particular edge type given by the tuple :obj:`(src, rel, dst)`.
If the storage is not present yet, will create a new
:class:`torch_geometric.data.storage.EdgeStorage` object for the given
edge type.
.. code-block:: python
data = HeteroData()
edge_storage = data.get_edge_store('author', 'writes', 'paper')
"""
key = (src, rel, dst)
out = self._edge_store_dict.get(key, None)
if out is None:
self._check_type_name(rel)
out = EdgeStorage(_parent=self, _key=key)
self._edge_store_dict[key] = out
return out
[docs] def rename(self, name: NodeType, new_name: NodeType) -> Self:
r"""Renames the node type :obj:`name` to :obj:`new_name` in-place."""
node_store = self._node_store_dict.pop(name)
node_store._key = new_name
self._node_store_dict[new_name] = node_store
for edge_type in self.edge_types:
src, rel, dst = edge_type
if src == name or dst == name:
edge_store = self._edge_store_dict.pop(edge_type)
src = new_name if src == name else src
dst = new_name if dst == name else dst
edge_type = (src, rel, dst)
edge_store._key = edge_type
self._edge_store_dict[edge_type] = edge_store
return self
[docs] def subgraph(self, subset_dict: Dict[NodeType, Tensor]) -> Self:
r"""Returns the induced subgraph containing the node types and
corresponding nodes in :obj:`subset_dict`.
If a node type is not a key in :obj:`subset_dict` then all nodes of
that type remain in the graph.
.. code-block:: python
data = HeteroData()
data['paper'].x = ...
data['author'].x = ...
data['conference'].x = ...
data['paper', 'cites', 'paper'].edge_index = ...
data['author', 'paper'].edge_index = ...
data['paper', 'conference'].edge_index = ...
print(data)
>>> HeteroData(
paper={ x=[10, 16] },
author={ x=[5, 32] },
conference={ x=[5, 8] },
(paper, cites, paper)={ edge_index=[2, 50] },
(author, to, paper)={ edge_index=[2, 30] },
(paper, to, conference)={ edge_index=[2, 25] }
)
subset_dict = {
'paper': torch.tensor([3, 4, 5, 6]),
'author': torch.tensor([0, 2]),
}
print(data.subgraph(subset_dict))
>>> HeteroData(
paper={ x=[4, 16] },
author={ x=[2, 32] },
conference={ x=[5, 8] },
(paper, cites, paper)={ edge_index=[2, 24] },
(author, to, paper)={ edge_index=[2, 5] },
(paper, to, conference)={ edge_index=[2, 10] }
)
Args:
subset_dict (Dict[str, LongTensor or BoolTensor]): A dictionary
holding the nodes to keep for each node type.
"""
data = copy.copy(self)
subset_dict = copy.copy(subset_dict)
for node_type, subset in subset_dict.items():
for key, value in self[node_type].items():
if key == 'num_nodes':
if subset.dtype == torch.bool:
data[node_type].num_nodes = int(subset.sum())
else:
data[node_type].num_nodes = subset.size(0)
elif self[node_type].is_node_attr(key):
data[node_type][key] = value[subset]
else:
data[node_type][key] = value
for edge_type in self.edge_types:
if 'edge_index' not in self[edge_type]:
continue
src, _, dst = edge_type
src_subset = subset_dict.get(src)
if src_subset is None:
src_subset = torch.arange(data[src].num_nodes)
dst_subset = subset_dict.get(dst)
if dst_subset is None:
dst_subset = torch.arange(data[dst].num_nodes)
edge_index, _, edge_mask = bipartite_subgraph(
(src_subset, dst_subset),
self[edge_type].edge_index,
relabel_nodes=True,
size=(self[src].num_nodes, self[dst].num_nodes),
return_edge_mask=True,
)
for key, value in self[edge_type].items():
if key == 'edge_index':
data[edge_type].edge_index = edge_index
elif self[edge_type].is_edge_attr(key):
data[edge_type][key] = value[edge_mask]
else:
data[edge_type][key] = value
return data
[docs] def edge_subgraph(
self,
subset_dict: Dict[EdgeType, Tensor],
) -> Self:
r"""Returns the induced subgraph given by the edge indices in
:obj:`subset_dict` for certain edge types.
Will currently preserve all the nodes in the graph, even if they are
isolated after subgraph computation.
Args:
subset_dict (Dict[Tuple[str, str, str], LongTensor or BoolTensor]):
A dictionary holding the edges to keep for each edge type.
"""
data = copy.copy(self)
for edge_type, subset in subset_dict.items():
edge_store, new_edge_store = self[edge_type], data[edge_type]
for key, value in edge_store.items():
if edge_store.is_edge_attr(key):
dim = self.__cat_dim__(key, value, edge_store)
if subset.dtype == torch.bool:
new_edge_store[key] = mask_select(value, dim, subset)
else:
new_edge_store[key] = value.index_select(dim, subset)
return data
[docs] def node_type_subgraph(self, node_types: List[NodeType]) -> Self:
r"""Returns the subgraph induced by the given :obj:`node_types`, *i.e.*
the returned :class:`HeteroData` object only contains the node types
which are included in :obj:`node_types`, and only contains the edge
types where both end points are included in :obj:`node_types`.
"""
data = copy.copy(self)
for edge_type in self.edge_types:
src, _, dst = edge_type
if src not in node_types or dst not in node_types:
del data[edge_type]
for node_type in self.node_types:
if node_type not in node_types:
del data[node_type]
return data
[docs] def edge_type_subgraph(self, edge_types: List[EdgeType]) -> Self:
r"""Returns the subgraph induced by the given :obj:`edge_types`, *i.e.*
the returned :class:`HeteroData` object only contains the edge types
which are included in :obj:`edge_types`, and only contains the node
types of the end points which are included in :obj:`node_types`.
"""
edge_types = [self._to_canonical(e) for e in edge_types]
data = copy.copy(self)
for edge_type in self.edge_types:
if edge_type not in edge_types:
del data[edge_type]
node_types = set(e[0] for e in edge_types)
node_types |= set(e[-1] for e in edge_types)
for node_type in self.node_types:
if node_type not in node_types:
del data[node_type]
return data
[docs] def to_homogeneous(
self,
node_attrs: Optional[List[str]] = None,
edge_attrs: Optional[List[str]] = None,
add_node_type: bool = True,
add_edge_type: bool = True,
dummy_values: bool = True,
) -> Data:
"""Converts a :class:`~torch_geometric.data.HeteroData` object to a
homogeneous :class:`~torch_geometric.data.Data` object.
By default, all features with same feature dimensionality across
different types will be merged into a single representation, unless
otherwise specified via the :obj:`node_attrs` and :obj:`edge_attrs`
arguments.
Furthermore, attributes named :obj:`node_type` and :obj:`edge_type`
will be added to the returned :class:`~torch_geometric.data.Data`
object, denoting node-level and edge-level vectors holding the
node and edge type as integers, respectively.
Args:
node_attrs (List[str], optional): The node features to combine
across all node types. These node features need to be of the
same feature dimensionality. If set to :obj:`None`, will
automatically determine which node features to combine.
(default: :obj:`None`)
edge_attrs (List[str], optional): The edge features to combine
across all edge types. These edge features need to be of the
same feature dimensionality. If set to :obj:`None`, will
automatically determine which edge features to combine.
(default: :obj:`None`)
add_node_type (bool, optional): If set to :obj:`False`, will not
add the node-level vector :obj:`node_type` to the returned
:class:`~torch_geometric.data.Data` object.
(default: :obj:`True`)
add_edge_type (bool, optional): If set to :obj:`False`, will not
add the edge-level vector :obj:`edge_type` to the returned
:class:`~torch_geometric.data.Data` object.
(default: :obj:`True`)
dummy_values (bool, optional): If set to :obj:`True`, will fill
attributes of remaining types with dummy values.
Dummy values are :obj:`NaN` for floating point attributes,
:obj:`False` for booleans, and :obj:`-1` for integers.
(default: :obj:`True`)
"""
def get_sizes(stores: List[BaseStorage]) -> Dict[str, List[Tuple]]:
sizes_dict = defaultdict(list)
for store in stores:
for key, value in store.items():
if key in [
'edge_index', 'edge_label_index', 'adj', 'adj_t'
]:
continue
if isinstance(value, Tensor):
dim = self.__cat_dim__(key, value, store)
size = value.size()[:dim] + value.size()[dim + 1:]
sizes_dict[key].append(tuple(size))
return sizes_dict
def fill_dummy_(stores: List[BaseStorage],
keys: Optional[List[str]] = None):
sizes_dict = get_sizes(stores)
if keys is not None:
sizes_dict = {
key: sizes
for key, sizes in sizes_dict.items() if key in keys
}
sizes_dict = {
key: sizes
for key, sizes in sizes_dict.items() if len(set(sizes)) == 1
}
for store in stores: # Fill stores with dummy features:
for key, sizes in sizes_dict.items():
if key not in store:
ref = list(self.collect(key).values())[0]
dim = self.__cat_dim__(key, ref, store)
if ref.is_floating_point():
dummy = float('NaN')
elif ref.dtype == torch.bool:
dummy = False
else:
dummy = -1
if isinstance(store, NodeStorage):
dim_size = store.num_nodes
else:
dim_size = store.num_edges
shape = sizes[0][:dim] + (dim_size, ) + sizes[0][dim:]
store[key] = torch.full(shape, dummy, dtype=ref.dtype,
device=ref.device)
def _consistent_size(stores: List[BaseStorage]) -> List[str]:
sizes_dict = get_sizes(stores)
keys = []
for key, sizes in sizes_dict.items():
# The attribute needs to exist in all types:
if len(sizes) != len(stores):
continue
# The attributes needs to have the same number of dimensions:
lengths = set([len(size) for size in sizes])
if len(lengths) != 1:
continue
# The attributes needs to have the same size in all dimensions:
if len(sizes[0]) != 1 and len(set(sizes)) != 1:
continue
keys.append(key)
# Check for consistent column names in `TensorFrame`:
tf_cols = defaultdict(list)
for store in stores:
for key, value in store.items():
if isinstance(value, TensorFrame):
cols = tuple(chain(*value.col_names_dict.values()))
tf_cols[key].append(cols)
for key, cols in tf_cols.items():
# The attribute needs to exist in all types:
if len(cols) != len(stores):
continue
# The attributes needs to have the same column names:
lengths = set(cols)
if len(lengths) != 1:
continue
keys.append(key)
return keys
if dummy_values:
self = copy.copy(self)
fill_dummy_(self.node_stores, node_attrs)
fill_dummy_(self.edge_stores, edge_attrs)
edge_index, node_slices, edge_slices = to_homogeneous_edge_index(self)
device = edge_index.device if edge_index is not None else None
data = Data(**self._global_store.to_dict())
if edge_index is not None:
data.edge_index = edge_index
data._node_type_names = list(node_slices.keys())
data._edge_type_names = list(edge_slices.keys())
# Combine node attributes into a single tensor:
if node_attrs is None:
node_attrs = _consistent_size(self.node_stores)
for key in node_attrs:
if key in {'ptr'}:
continue
values = [store[key] for store in self.node_stores]
if isinstance(values[0], TensorFrame):
value = torch_frame.cat(values, dim=0)
else:
dim = self.__cat_dim__(key, values[0], self.node_stores[0])
dim = values[0].dim() + dim if dim < 0 else dim
# For two-dimensional features, we allow arbitrary shapes and
# pad them with zeros if necessary in case their size doesn't
# match:
if values[0].dim() == 2 and dim == 0:
_max = max([value.size(-1) for value in values])
for i, v in enumerate(values):
if v.size(-1) < _max:
pad = v.new_zeros(v.size(0), _max - v.size(-1))
values[i] = torch.cat([v, pad], dim=-1)
value = torch.cat(values, dim)
data[key] = value
if not data.can_infer_num_nodes:
data.num_nodes = list(node_slices.values())[-1][1]
# Combine edge attributes into a single tensor:
if edge_attrs is None:
edge_attrs = _consistent_size(self.edge_stores)
for key in edge_attrs:
values = [store[key] for store in self.edge_stores]
dim = self.__cat_dim__(key, values[0], self.edge_stores[0])
value = torch.cat(values, dim) if len(values) > 1 else values[0]
data[key] = value
if 'edge_label_index' in self:
edge_label_index_dict = self.edge_label_index_dict
for edge_type, edge_label_index in edge_label_index_dict.items():
edge_label_index = edge_label_index.clone()
edge_label_index[0] += node_slices[edge_type[0]][0]
edge_label_index[1] += node_slices[edge_type[-1]][0]
edge_label_index_dict[edge_type] = edge_label_index
data.edge_label_index = torch.cat(
list(edge_label_index_dict.values()), dim=-1)
if add_node_type:
sizes = [offset[1] - offset[0] for offset in node_slices.values()]
sizes = torch.tensor(sizes, dtype=torch.long, device=device)
node_type = torch.arange(len(sizes), device=device)
data.node_type = node_type.repeat_interleave(sizes)
if add_edge_type and edge_index is not None:
sizes = [offset[1] - offset[0] for offset in edge_slices.values()]
sizes = torch.tensor(sizes, dtype=torch.long, device=device)
edge_type = torch.arange(len(sizes), device=device)
data.edge_type = edge_type.repeat_interleave(sizes)
return data
# FeatureStore interface ##################################################
def _put_tensor(self, tensor: FeatureTensorType, attr: TensorAttr) -> bool:
if not attr.is_set('index'):
attr.index = None
out = self._node_store_dict.get(attr.group_name, None)
if out:
# Group name exists, handle index or create new attribute name:
val = getattr(out, attr.attr_name, None)
if val is not None:
val[attr.index] = tensor
else:
assert attr.index is None
setattr(self[attr.group_name], attr.attr_name, tensor)
else:
# No node storage found, just store tensor in new one:
setattr(self[attr.group_name], attr.attr_name, tensor)
return True
def _get_tensor(self, attr: TensorAttr) -> Optional[FeatureTensorType]:
# Retrieve tensor and index accordingly:
tensor = getattr(self[attr.group_name], attr.attr_name, None)
if tensor is not None:
# TODO this behavior is a bit odd, since TensorAttr requires that
# we set `index`. So, we assume here that indexing by `None` is
# equivalent to not indexing at all, which is not in line with
# Python semantics.
return tensor[attr.index] if attr.index is not None else tensor
return None
def _remove_tensor(self, attr: TensorAttr) -> bool:
# Remove tensor entirely:
if hasattr(self[attr.group_name], attr.attr_name):
delattr(self[attr.group_name], attr.attr_name)
return True
return False
def _get_tensor_size(self, attr: TensorAttr) -> Tuple:
return self._get_tensor(attr).size()
[docs] def get_all_tensor_attrs(self) -> List[TensorAttr]:
out = []
for group_name, group in self.node_items():
for attr_name in group:
if group.is_node_attr(attr_name):
out.append(TensorAttr(group_name, attr_name))
return out
# GraphStore interface ####################################################
def _put_edge_index(self, edge_index: EdgeTensorType,
edge_attr: EdgeAttr) -> bool:
if not hasattr(self, '_edge_attrs'):
self._edge_attrs = {}
self._edge_attrs[(edge_attr.edge_type, edge_attr.layout)] = edge_attr
row, col = edge_index
store = self[edge_attr.edge_type]
if edge_attr.layout == EdgeLayout.COO:
store.edge_index = torch.stack([row, col], dim=0)
elif edge_attr.layout == EdgeLayout.CSR:
store.adj = SparseTensor(
rowptr=row,
col=col,
sparse_sizes=edge_attr.size,
is_sorted=True,
trust_data=True,
)
else: # edge_attr.layout == EdgeLayout.CSC:
size = edge_attr.size[::-1] if edge_attr.size is not None else None
store.adj_t = SparseTensor(
rowptr=col,
col=row,
sparse_sizes=size,
is_sorted=True,
trust_data=True,
)
return True
def _get_edge_index(self, edge_attr: EdgeAttr) -> Optional[EdgeTensorType]:
r"""Gets an edge index from edge storage, in the specified layout."""
store = self[edge_attr.edge_type]
edge_attrs = getattr(self, '_edge_attrs', {})
if (edge_attr.edge_type, edge_attr.layout) in edge_attrs:
edge_attr = edge_attrs[(edge_attr.edge_type, edge_attr.layout)]
if edge_attr.size is None:
edge_attr.size = store.size() # Modify in-place.
if edge_attr.layout == EdgeLayout.COO and 'edge_index' in store:
row, col = store.edge_index
return row, col
elif edge_attr.layout == EdgeLayout.CSR and 'adj' in store:
rowptr, col, _ = store.adj.csr()
return rowptr, col
elif edge_attr.layout == EdgeLayout.CSC and 'adj_t' in store:
colptr, row, _ = store.adj_t.csr()
return row, colptr
return None
def _remove_edge_index(self, edge_attr: EdgeAttr) -> bool:
edge_type = edge_attr.edge_type
store = self[edge_type]
if edge_attr.layout == EdgeLayout.COO and 'edge_index' in store:
del store.edge_index
if hasattr(self, '_edge_attrs'):
self._edge_attrs.pop((edge_type, EdgeLayout.COO), None)
return True
elif edge_attr.layout == EdgeLayout.CSR and 'adj' in store:
del store.adj
if hasattr(self, '_edge_attrs'):
self._edge_attrs.pop((edge_type, EdgeLayout.CSR), None)
return True
elif edge_attr.layout == EdgeLayout.CSC and 'adj_t' in store:
del store.adj_t
if hasattr(self, '_edge_attrs'):
self._edge_attrs.pop((edge_type, EdgeLayout.CSC), None)
return True
return False
[docs] def get_all_edge_attrs(self) -> List[EdgeAttr]:
edge_attrs = getattr(self, '_edge_attrs', {})
for store in self.edge_stores:
if ('edge_index' in store
and (store._key, EdgeLayout.COO) not in edge_attrs):
edge_attrs[(store._key, EdgeLayout.COO)] = EdgeAttr(
store._key, 'coo', is_sorted=False)
if ('adj' in store
and (store._key, EdgeLayout.CSR) not in edge_attrs):
size = store.adj.sparse_sizes()
edge_attrs[(store._key, EdgeLayout.CSR)] = EdgeAttr(
store._key, 'csr', size=size)
if ('adj_t' in store
and (store._key, EdgeLayout.CSC) not in edge_attrs):
size = store.adj_t.sparse_sizes()[::-1]
edge_attrs[(store._key, EdgeLayout.CSC)] = EdgeAttr(
store._key, 'csc', size=size)
return list(edge_attrs.values())
# Helper functions ############################################################
def get_node_slices(num_nodes: Dict[str, int]) -> Dict[str, Tuple[int, int]]:
r"""Returns the boundaries of each node type in a graph."""
node_slices: Dict[NodeType, Tuple[int, int]] = {}
cumsum = 0
for node_type, N in num_nodes.items():
node_slices[node_type] = (cumsum, cumsum + N)
cumsum += N
return node_slices
def offset_edge_index(
node_slices: Dict[NodeType, Tuple[int, int]],
edge_type: EdgeType,
edge_index: Tensor,
) -> Tensor:
r"""Increases the edge indices by the offsets of source and destination
node types.
"""
src, _, dst = edge_type
offset = [[node_slices[src][0]], [node_slices[dst][0]]]
offset = torch.tensor(offset, device=edge_index.device)
return edge_index + offset
def to_homogeneous_edge_index(
data: HeteroData,
) -> Tuple[Optional[Tensor], Dict[NodeType, Any], Dict[EdgeType, Any]]:
r"""Converts a heterogeneous graph into a homogeneous typed graph."""
# Record slice information per node type:
node_slices = get_node_slices(data.num_nodes_dict)
# Record edge indices and slice information per edge type:
cumsum = 0
edge_indices: List[Tensor] = []
edge_slices: Dict[EdgeType, Tuple[int, int]] = {}
for edge_type, edge_index in data.collect('edge_index', True).items():
edge_index = offset_edge_index(node_slices, edge_type, edge_index)
edge_indices.append(edge_index)
edge_slices[edge_type] = (cumsum, cumsum + edge_index.size(1))
cumsum += edge_index.size(1)
edge_index: Optional[Tensor] = None
if len(edge_indices) == 1: # Memory-efficient `torch.cat`:
edge_index = edge_indices[0]
elif len(edge_indices) > 1:
edge_index = torch.cat(edge_indices, dim=-1)
return edge_index, node_slices, edge_slices