import re
import copy
import logging
import torch
import torch_geometric
from torch_sparse import coalesce, SparseTensor
from torch_geometric.utils import (contains_isolated_nodes,
contains_self_loops, is_undirected)
from ..utils.num_nodes import maybe_num_nodes
__num_nodes_warn_msg__ = (
'The number of nodes in your data object can only be inferred by its {} '
'indices, and hence may result in unexpected batch-wise behavior, e.g., '
'in case there exists isolated nodes. Please consider explicitly setting '
'the number of nodes for this data object by assigning it to '
'data.num_nodes.')
def size_repr(key, item, indent=0):
indent_str = ' ' * indent
if torch.is_tensor(item) and item.dim() == 0:
out = item.item()
elif torch.is_tensor(item):
out = str(list(item.size()))
elif isinstance(item, SparseTensor):
out = str(item.sizes())[:-1] + f', nnz={item.nnz()}]'
elif isinstance(item, list) or isinstance(item, tuple):
out = str([len(item)])
elif isinstance(item, dict):
lines = [indent_str + size_repr(k, v, 2) for k, v in item.items()]
out = '{\n' + ',\n'.join(lines) + '\n' + indent_str + '}'
elif isinstance(item, str):
out = f'"{item}"'
else:
out = str(item)
return f'{indent_str}{key}={out}'
class Data(object):
r"""A plain old python object modeling a single graph with various
(optional) attributes:
Args:
x (Tensor, optional): Node feature matrix with shape :obj:`[num_nodes,
num_node_features]`. (default: :obj:`None`)
edge_index (LongTensor, optional): Graph connectivity in COO format
with shape :obj:`[2, num_edges]`. (default: :obj:`None`)
edge_attr (Tensor, optional): Edge feature matrix with shape
:obj:`[num_edges, num_edge_features]`. (default: :obj:`None`)
y (Tensor, optional): Graph or node targets with arbitrary shape.
(default: :obj:`None`)
pos (Tensor, optional): Node position matrix with shape
:obj:`[num_nodes, num_dimensions]`. (default: :obj:`None`)
norm (Tensor, optional): Normal vector matrix with shape
:obj:`[num_nodes, num_dimensions]`. (default: :obj:`None`)
face (LongTensor, optional): Face adjacency matrix with shape
:obj:`[3, num_faces]`. (default: :obj:`None`)
The data object is not restricted to these attributes and can be extented
by any other additional data.
Example::
data = Data(x=x, edge_index=edge_index)
data.train_idx = torch.tensor([...], dtype=torch.long)
data.test_mask = torch.tensor([...], dtype=torch.bool)
"""
def __init__(self, x=None, edge_index=None, edge_attr=None, y=None,
pos=None, norm=None, face=None, **kwargs):
self.x = x
self.edge_index = edge_index
self.edge_attr = edge_attr
self.y = y
self.pos = pos
self.norm = norm
self.face = face
for key, item in kwargs.items():
if key == 'num_nodes':
self.__num_nodes__ = item
else:
self[key] = item
if edge_index is not None and edge_index.dtype != torch.long:
raise ValueError(
(f'Argument `edge_index` needs to be of type `torch.long` but '
f'found type `{edge_index.dtype}`.'))
if face is not None and face.dtype != torch.long:
raise ValueError(
(f'Argument `face` needs to be of type `torch.long` but found '
f'type `{face.dtype}`.'))
if torch_geometric.is_debug_enabled():
self.debug()
@classmethod
def from_dict(cls, dictionary):
r"""Creates a data object from a python dictionary."""
data = cls()
for key, item in dictionary.items():
data[key] = item
if torch_geometric.is_debug_enabled():
data.debug()
return data
def __getitem__(self, key):
r"""Gets the data of the attribute :obj:`key`."""
return getattr(self, key, None)
def __setitem__(self, key, value):
"""Sets the attribute :obj:`key` to :obj:`value`."""
setattr(self, key, value)
@property
def keys(self):
r"""Returns all names of graph attributes."""
keys = [key for key in self.__dict__.keys() if self[key] is not None]
keys = [key for key in keys if key[:2] != '__' and key[-2:] != '__']
return keys
def __len__(self):
r"""Returns the number of all present attributes."""
return len(self.keys)
def __contains__(self, key):
r"""Returns :obj:`True`, if the attribute :obj:`key` is present in the
data."""
return key in self.keys
def __iter__(self):
r"""Iterates over all present attributes in the data, yielding their
attribute names and content."""
for key in sorted(self.keys):
yield key, self[key]
def __call__(self, *keys):
r"""Iterates over all attributes :obj:`*keys` in the data, yielding
their attribute names and content.
If :obj:`*keys` is not given this method will iterative over all
present attributes."""
for key in sorted(self.keys) if not keys else keys:
if key in self:
yield key, self[key]
def __cat_dim__(self, key, value):
r"""Returns the dimension for which :obj:`value` of attribute
:obj:`key` will get concatenated when creating batches.
.. note::
This method is for internal use only, and should only be overridden
if the batch concatenation process is corrupted for a specific data
attribute.
"""
# Concatenate `*index*` and `*face*` attributes in the last dimension.
if bool(re.search('(index|face)', key)):
return -1
# By default, concatenate sparse matrices diagonally.
elif isinstance(value, SparseTensor):
return (0, 1)
return 0
def __inc__(self, key, value):
r"""Returns the incremental count to cumulatively increase the value
of the next attribute of :obj:`key` when creating batches.
.. note::
This method is for internal use only, and should only be overridden
if the batch concatenation process is corrupted for a specific data
attribute.
"""
# Only `*index*` and `*face*` attributes should be cumulatively summed
# up when creating batches.
return self.num_nodes if bool(re.search('(index|face)', key)) else 0
@property
def num_nodes(self):
r"""Returns or sets the number of nodes in the graph.
.. note::
The number of nodes in your data object is typically automatically
inferred, *e.g.*, when node features :obj:`x` are present.
In some cases however, a graph may only be given by its edge
indices :obj:`edge_index`.
PyTorch Geometric then *guesses* the number of nodes
according to :obj:`edge_index.max().item() + 1`, but in case there
exists isolated nodes, this number has not to be correct and can
therefore result in unexpected batch-wise behavior.
Thus, we recommend to set the number of nodes in your data object
explicitly via :obj:`data.num_nodes = ...`.
You will be given a warning that requests you to do so.
"""
if hasattr(self, '__num_nodes__'):
return self.__num_nodes__
for key, item in self('x', 'pos', 'norm', 'batch'):
return item.size(self.__cat_dim__(key, item))
if hasattr(self, 'adj'):
return self.adj.size(0)
if hasattr(self, 'adj_t'):
return self.adj_t.size(1)
if self.face is not None:
logging.warning(__num_nodes_warn_msg__.format('face'))
return maybe_num_nodes(self.face)
if self.edge_index is not None:
logging.warning(__num_nodes_warn_msg__.format('edge'))
return maybe_num_nodes(self.edge_index)
return None
@num_nodes.setter
def num_nodes(self, num_nodes):
self.__num_nodes__ = num_nodes
@property
def num_edges(self):
r"""Returns the number of edges in the graph."""
for key, item in self('edge_index', 'edge_attr'):
return item.size(self.__cat_dim__(key, item))
return None
@property
def num_faces(self):
r"""Returns the number of faces in the mesh."""
if self.face is not None:
return self.face.size(self.__cat_dim__('face', self.face))
return None
@property
def num_node_features(self):
r"""Returns the number of features per node in the graph."""
if self.x is None:
return 0
return 1 if self.x.dim() == 1 else self.x.size(1)
@property
def num_features(self):
r"""Alias for :py:attr:`~num_node_features`."""
return self.num_node_features
@property
def num_edge_features(self):
r"""Returns the number of features per edge in the graph."""
if self.edge_attr is None:
return 0
return 1 if self.edge_attr.dim() == 1 else self.edge_attr.size(1)
def is_coalesced(self):
r"""Returns :obj:`True`, if edge indices are ordered and do not contain
duplicate entries."""
edge_index, _ = coalesce(self.edge_index, None, self.num_nodes,
self.num_nodes)
return self.edge_index.numel() == edge_index.numel() and (
self.edge_index != edge_index).sum().item() == 0
def coalesce(self):
r""""Orders and removes duplicated entries from edge indices."""
self.edge_index, self.edge_attr = coalesce(self.edge_index,
self.edge_attr,
self.num_nodes,
self.num_nodes)
return self
def contains_isolated_nodes(self):
r"""Returns :obj:`True`, if the graph contains isolated nodes."""
return contains_isolated_nodes(self.edge_index, self.num_nodes)
def contains_self_loops(self):
"""Returns :obj:`True`, if the graph contains self-loops."""
return contains_self_loops(self.edge_index)
def is_undirected(self):
r"""Returns :obj:`True`, if graph edges are undirected."""
return is_undirected(self.edge_index, self.edge_attr, self.num_nodes)
def is_directed(self):
r"""Returns :obj:`True`, if graph edges are directed."""
return not self.is_undirected()
def __apply__(self, item, func):
if torch.is_tensor(item):
return func(item)
elif isinstance(item, SparseTensor):
# Not all apply methods are supported for `SparseTensor`, e.g.,
# `contiguous()`. We can get around it by capturing the exception.
try:
return func(item)
except AttributeError:
return item
elif isinstance(item, (tuple, list)):
return [self.__apply__(v, func) for v in item]
elif isinstance(item, dict):
return {k: self.__apply__(v, func) for k, v in item.items()}
else:
return item
def apply(self, func, *keys):
r"""Applies the function :obj:`func` to all tensor attributes
:obj:`*keys`. If :obj:`*keys` is not given, :obj:`func` is applied to
all present attributes.
"""
for key, item in self(*keys):
self[key] = self.__apply__(item, func)
return self
def contiguous(self, *keys):
r"""Ensures a contiguous memory layout for all attributes :obj:`*keys`.
If :obj:`*keys` is not given, all present attributes are ensured to
have a contiguous memory layout."""
return self.apply(lambda x: x.contiguous(), *keys)
def to(self, device, *keys, **kwargs):
r"""Performs tensor dtype and/or device conversion to all attributes
:obj:`*keys`.
If :obj:`*keys` is not given, the conversion is applied to all present
attributes."""
return self.apply(lambda x: x.to(device, **kwargs), *keys)
def clone(self):
return self.__class__.from_dict({
k: v.clone() if torch.is_tensor(v) else copy.deepcopy(v)
for k, v in self.__dict__.items()
})
def debug(self):
if self.edge_index is not None:
if self.edge_index.dtype != torch.long:
raise RuntimeError(
('Expected edge indices of dtype {}, but found dtype '
' {}').format(torch.long, self.edge_index.dtype))
if self.face is not None:
if self.face.dtype != torch.long:
raise RuntimeError(
('Expected face indices of dtype {}, but found dtype '
' {}').format(torch.long, self.face.dtype))
if self.edge_index is not None:
if self.edge_index.dim() != 2 or self.edge_index.size(0) != 2:
raise RuntimeError(
('Edge indices should have shape [2, num_edges] but found'
' shape {}').format(self.edge_index.size()))
if self.edge_index is not None and self.num_nodes is not None:
if self.edge_index.numel() > 0:
min_index = self.edge_index.min()
max_index = self.edge_index.max()
else:
min_index = max_index = 0
if min_index < 0 or max_index > self.num_nodes - 1:
raise RuntimeError(
('Edge indices must lay in the interval [0, {}]'
' but found them in the interval [{}, {}]').format(
self.num_nodes - 1, min_index, max_index))
if self.face is not None:
if self.face.dim() != 2 or self.face.size(0) != 3:
raise RuntimeError(
('Face indices should have shape [3, num_faces] but found'
' shape {}').format(self.face.size()))
if self.face is not None and self.num_nodes is not None:
if self.face.numel() > 0:
min_index = self.face.min()
max_index = self.face.max()
else:
min_index = max_index = 0
if min_index < 0 or max_index > self.num_nodes - 1:
raise RuntimeError(
('Face indices must lay in the interval [0, {}]'
' but found them in the interval [{}, {}]').format(
self.num_nodes - 1, min_index, max_index))
if self.edge_index is not None and self.edge_attr is not None:
if self.edge_index.size(1) != self.edge_attr.size(0):
raise RuntimeError(
('Edge indices and edge attributes hold a differing '
'number of edges, found {} and {}').format(
self.edge_index.size(), self.edge_attr.size()))
if self.x is not None and self.num_nodes is not None:
if self.x.size(0) != self.num_nodes:
raise RuntimeError(
('Node features should hold {} elements in the first '
'dimension but found {}').format(self.num_nodes,
self.x.size(0)))
if self.pos is not None and self.num_nodes is not None:
if self.pos.size(0) != self.num_nodes:
raise RuntimeError(
('Node positions should hold {} elements in the first '
'dimension but found {}').format(self.num_nodes,
self.pos.size(0)))
if self.norm is not None and self.num_nodes is not None:
if self.norm.size(0) != self.num_nodes:
raise RuntimeError(
('Node normals should hold {} elements in the first '
'dimension but found {}').format(self.num_nodes,
self.norm.size(0)))
def __repr__(self):
cls = str(self.__class__.__name__)
has_dict = any([isinstance(item, dict) for _, item in self])
if not has_dict:
info = [size_repr(key, item) for key, item in self]
return '{}({})'.format(cls, ', '.join(info))
else:
info = [size_repr(key, item, indent=2) for key, item in self]
return '{}(\n{}\n)'.format(cls, ',\n'.join(info))
