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heterograph.py
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heterograph.py
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"""Classes for heterogeneous graphs."""
import copy
import itertools
import numbers
# pylint: disable= too-many-lines
from collections import defaultdict
from collections.abc import Iterable, Mapping
from contextlib import contextmanager
import networkx as nx
import numpy as np
from . import backend as F, core, graph_index, heterograph_index, utils
from ._ffi.function import _init_api
from .base import (
ALL,
dgl_warning,
DGLError,
EID,
ETYPE,
is_all,
NID,
NTYPE,
SLICE_FULL,
)
from .frame import Frame
from .ops import segment
from .view import (
HeteroEdgeDataView,
HeteroEdgeView,
HeteroNodeDataView,
HeteroNodeView,
)
__all__ = ["DGLGraph", "combine_names"]
class DGLGraph(object):
"""Class for storing graph structure and node/edge feature data.
There are a few ways to create a DGLGraph:
* To create a homogeneous graph from Tensor data, use :func:`dgl.graph`.
* To create a heterogeneous graph from Tensor data, use :func:`dgl.heterograph`.
* To create a graph from other data sources, use ``dgl.*`` create ops. See
:ref:`api-graph-create-ops`.
Read the user guide chapter :ref:`guide-graph` for an in-depth explanation about its
usage.
"""
is_block = False
# pylint: disable=unused-argument, dangerous-default-value
def __init__(
self,
gidx=[],
ntypes=["_N"],
etypes=["_E"],
node_frames=None,
edge_frames=None,
**deprecate_kwargs
):
"""Internal constructor for creating a DGLGraph.
Parameters
----------
gidx : HeteroGraphIndex
Graph index object.
ntypes : list of str, pair of list of str
Node type list. ``ntypes[i]`` stores the name of node type i.
If a pair is given, the graph created is a uni-directional bipartite graph,
and its SRC node types and DST node types are given as in the pair.
etypes : list of str
Edge type list. ``etypes[i]`` stores the name of edge type i.
node_frames : list[Frame], optional
Node feature storage. If None, empty frame is created.
Otherwise, ``node_frames[i]`` stores the node features
of node type i. (default: None)
edge_frames : list[Frame], optional
Edge feature storage. If None, empty frame is created.
Otherwise, ``edge_frames[i]`` stores the edge features
of edge type i. (default: None)
"""
if isinstance(gidx, DGLGraph):
raise DGLError(
"The input is already a DGLGraph. No need to create it again."
)
if not isinstance(gidx, heterograph_index.HeteroGraphIndex):
dgl_warning(
"Recommend creating graphs by `dgl.graph(data)`"
" instead of `dgl.DGLGraph(data)`."
)
(sparse_fmt, arrays), num_src, num_dst = utils.graphdata2tensors(
gidx
)
if sparse_fmt == "coo":
gidx = heterograph_index.create_unitgraph_from_coo(
1,
num_src,
num_dst,
arrays[0],
arrays[1],
["coo", "csr", "csc"],
)
else:
gidx = heterograph_index.create_unitgraph_from_csr(
1,
num_src,
num_dst,
arrays[0],
arrays[1],
arrays[2],
["coo", "csr", "csc"],
sparse_fmt == "csc",
)
if len(deprecate_kwargs) != 0:
dgl_warning(
"Keyword arguments {} are deprecated in v0.5, and can be safely"
" removed in all cases.".format(list(deprecate_kwargs.keys()))
)
self._init(gidx, ntypes, etypes, node_frames, edge_frames)
def _init(self, gidx, ntypes, etypes, node_frames, edge_frames):
"""Init internal states."""
self._graph = gidx
self._canonical_etypes = None
self._batch_num_nodes = None
self._batch_num_edges = None
# Handle node types
if isinstance(ntypes, tuple):
if len(ntypes) != 2:
errmsg = "Invalid input. Expect a pair (srctypes, dsttypes) but got {}".format(
ntypes
)
raise TypeError(errmsg)
if not self._graph.is_metagraph_unibipartite():
raise ValueError(
"Invalid input. The metagraph must be a uni-directional"
" bipartite graph."
)
self._ntypes = ntypes[0] + ntypes[1]
self._srctypes_invmap = {t: i for i, t in enumerate(ntypes[0])}
self._dsttypes_invmap = {
t: i + len(ntypes[0]) for i, t in enumerate(ntypes[1])
}
self._is_unibipartite = True
if len(ntypes[0]) == 1 and len(ntypes[1]) == 1 and len(etypes) == 1:
self._canonical_etypes = [
(ntypes[0][0], etypes[0], ntypes[1][0])
]
else:
self._ntypes = ntypes
if len(ntypes) == 1:
src_dst_map = None
else:
src_dst_map = find_src_dst_ntypes(
self._ntypes, self._graph.metagraph
)
self._is_unibipartite = src_dst_map is not None
if self._is_unibipartite:
self._srctypes_invmap, self._dsttypes_invmap = src_dst_map
else:
self._srctypes_invmap = {
t: i for i, t in enumerate(self._ntypes)
}
self._dsttypes_invmap = self._srctypes_invmap
# Handle edge types
self._etypes = etypes
if self._canonical_etypes is None:
if len(etypes) == 1 and len(ntypes) == 1:
self._canonical_etypes = [(ntypes[0], etypes[0], ntypes[0])]
else:
self._canonical_etypes = make_canonical_etypes(
self._etypes, self._ntypes, self._graph.metagraph
)
# An internal map from etype to canonical etype tuple.
# If two etypes have the same name, an empty tuple is stored instead to indicate
# ambiguity.
self._etype2canonical = {}
for i, ety in enumerate(self._etypes):
if ety in self._etype2canonical:
self._etype2canonical[ety] = tuple()
else:
self._etype2canonical[ety] = self._canonical_etypes[i]
self._etypes_invmap = {
t: i for i, t in enumerate(self._canonical_etypes)
}
# node and edge frame
if node_frames is None:
node_frames = [None] * len(self._ntypes)
node_frames = [
Frame(num_rows=self._graph.number_of_nodes(i))
if frame is None
else frame
for i, frame in enumerate(node_frames)
]
self._node_frames = node_frames
if edge_frames is None:
edge_frames = [None] * len(self._etypes)
edge_frames = [
Frame(num_rows=self._graph.number_of_edges(i))
if frame is None
else frame
for i, frame in enumerate(edge_frames)
]
self._edge_frames = edge_frames
def __setstate__(self, state):
# Compatibility check
# TODO: version the storage
if isinstance(state, dict):
# Since 0.5 we use the default __dict__ method
self.__dict__.update(state)
elif isinstance(state, tuple) and len(state) == 5:
# DGL == 0.4.3
dgl_warning(
"The object is pickled with DGL == 0.4.3. "
"Some of the original attributes are ignored."
)
self._init(*state)
elif isinstance(state, dict):
# DGL <= 0.4.2
dgl_warning(
"The object is pickled with DGL <= 0.4.2. "
"Some of the original attributes are ignored."
)
self._init(
state["_graph"],
state["_ntypes"],
state["_etypes"],
state["_node_frames"],
state["_edge_frames"],
)
else:
raise IOError("Unrecognized pickle format.")
def __repr__(self):
if len(self.ntypes) == 1 and len(self.etypes) == 1:
ret = (
"Graph(num_nodes={node}, num_edges={edge},\n"
" ndata_schemes={ndata}\n"
" edata_schemes={edata})"
)
return ret.format(
node=self.number_of_nodes(),
edge=self.number_of_edges(),
ndata=str(self.node_attr_schemes()),
edata=str(self.edge_attr_schemes()),
)
else:
ret = (
"Graph(num_nodes={node},\n"
" num_edges={edge},\n"
" metagraph={meta})"
)
nnode_dict = {
self.ntypes[i]: self._graph.number_of_nodes(i)
for i in range(len(self.ntypes))
}
nedge_dict = {
self.canonical_etypes[i]: self._graph.number_of_edges(i)
for i in range(len(self.etypes))
}
meta = str(self.metagraph().edges(keys=True))
return ret.format(node=nnode_dict, edge=nedge_dict, meta=meta)
def __copy__(self):
"""Shallow copy implementation."""
# TODO(minjie): too many states in python; should clean up and lower to C
cls = type(self)
obj = cls.__new__(cls)
obj.__dict__.update(self.__dict__)
return obj
#################################################################
# Mutation operations
#################################################################
def add_nodes(self, num, data=None, ntype=None):
r"""Add new nodes of the same node type
Parameters
----------
num : int
Number of nodes to add.
data : dict, optional
Feature data of the added nodes.
ntype : str, optional
The type of the new nodes. Can be omitted if there is
only one node type in the graph.
Notes
-----
* Inplace update is applied to the current graph.
* If the key of ``data`` does not contain some existing feature fields,
those features for the new nodes will be created by initializers
defined with :func:`set_n_initializer` (default initializer fills zeros).
* If the key of ``data`` contains new feature fields, those features for
the old nodes will be created by initializers defined with
:func:`set_n_initializer` (default initializer fills zeros).
* This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
**Homogeneous Graphs or Heterogeneous Graphs with A Single Node Type**
>>> g = dgl.graph((torch.tensor([0, 1]), torch.tensor([1, 2])))
>>> g.num_nodes()
3
>>> g.add_nodes(2)
>>> g.num_nodes()
5
If the graph has some node features and new nodes are added without
features, their features will be created by initializers defined
with :func:`set_n_initializer`.
>>> g.ndata['h'] = torch.ones(5, 1)
>>> g.add_nodes(1)
>>> g.ndata['h']
tensor([[1.], [1.], [1.], [1.], [1.], [0.]])
We can also assign features for the new nodes in adding new nodes.
>>> g.add_nodes(1, {'h': torch.ones(1, 1), 'w': torch.ones(1, 1)})
>>> g.ndata['h']
tensor([[1.], [1.], [1.], [1.], [1.], [0.], [1.]])
Since ``data`` contains new feature fields, the features for old nodes
will be created by initializers defined with :func:`set_n_initializer`.
>>> g.ndata['w']
tensor([[0.], [0.], [0.], [0.], [0.], [0.], [1.]])
**Heterogeneous Graphs with Multiple Node Types**
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): (torch.tensor([0, 1, 1, 2]),
... torch.tensor([0, 0, 1, 1])),
... ('developer', 'develops', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))
... })
>>> g.add_nodes(2)
DGLError: Node type name must be specified
if there are more than one node types.
>>> g.num_nodes('user')
3
>>> g.add_nodes(2, ntype='user')
>>> g.num_nodes('user')
5
See Also
--------
remove_nodes
add_edges
remove_edges
"""
# TODO(xiangsx): block do not support add_nodes
if ntype is None:
if self._graph.number_of_ntypes() != 1:
raise DGLError(
"Node type name must be specified if there are more than one "
"node types."
)
# nothing happen
if num == 0:
return
assert num > 0, "Number of new nodes should be larger than one."
ntid = self.get_ntype_id(ntype)
# update graph idx
metagraph = self._graph.metagraph
num_nodes_per_type = []
for c_ntype in self.ntypes:
if self.get_ntype_id(c_ntype) == ntid:
num_nodes_per_type.append(self.number_of_nodes(c_ntype) + num)
else:
num_nodes_per_type.append(self.number_of_nodes(c_ntype))
relation_graphs = []
for c_etype in self.canonical_etypes:
# src or dst == ntype, update the relation graph
if (
self.get_ntype_id(c_etype[0]) == ntid
or self.get_ntype_id(c_etype[2]) == ntid
):
u, v = self.edges(form="uv", order="eid", etype=c_etype)
hgidx = heterograph_index.create_unitgraph_from_coo(
1 if c_etype[0] == c_etype[2] else 2,
self.number_of_nodes(c_etype[0])
+ (num if self.get_ntype_id(c_etype[0]) == ntid else 0),
self.number_of_nodes(c_etype[2])
+ (num if self.get_ntype_id(c_etype[2]) == ntid else 0),
u,
v,
["coo", "csr", "csc"],
)
relation_graphs.append(hgidx)
else:
# do nothing
relation_graphs.append(
self._graph.get_relation_graph(self.get_etype_id(c_etype))
)
hgidx = heterograph_index.create_heterograph_from_relations(
metagraph,
relation_graphs,
utils.toindex(num_nodes_per_type, "int64"),
)
self._graph = hgidx
# update data frames
if data is None:
# Initialize feature with :func:`set_n_initializer`
self._node_frames[ntid].add_rows(num)
else:
self._node_frames[ntid].append(data)
self._reset_cached_info()
def add_edges(self, u, v, data=None, etype=None):
r"""Add multiple new edges for the specified edge type
The i-th new edge will be from ``u[i]`` to ``v[i]``.
Parameters
----------
u : int, tensor, numpy.ndarray, list
Source node IDs, ``u[i]`` gives the source node for the i-th new edge.
v : int, tensor, numpy.ndarray, list
Destination node IDs, ``v[i]`` gives the destination node for the i-th new edge.
data : dict, optional
Feature data of the added edges. The i-th row of the feature data
corresponds to the i-th new edge.
etype : str or tuple of str, optional
The type of the new edges. Can be omitted if there is
only one edge type in the graph.
Notes
-----
* Inplace update is applied to the current graph.
* If end nodes of adding edges does not exists, add_nodes is invoked
to add new nodes. The node features of the new nodes will be created
by initializers defined with :func:`set_n_initializer` (default
initializer fills zeros). In certain cases, it is recommanded to
add_nodes first and then add_edges.
* If the key of ``data`` does not contain some existing feature fields,
those features for the new edges will be created by initializers
defined with :func:`set_n_initializer` (default initializer fills zeros).
* If the key of ``data`` contains new feature fields, those features for
the old edges will be created by initializers defined with
:func:`set_n_initializer` (default initializer fills zeros).
* This function discards the batch information. Please use
:func:`dgl.DGLGraph.set_batch_num_nodes`
and :func:`dgl.DGLGraph.set_batch_num_edges` on the transformed graph
to maintain the information.
Examples
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch
**Homogeneous Graphs or Heterogeneous Graphs with A Single Edge Type**
>>> g = dgl.graph((torch.tensor([0, 1]), torch.tensor([1, 2])))
>>> g.num_edges()
2
>>> g.add_edges(torch.tensor([1, 3]), torch.tensor([0, 1]))
>>> g.num_edges()
4
Since ``u`` or ``v`` contains a non-existing node ID, the nodes are
added implicitly.
>>> g.num_nodes()
4
If the graph has some edge features and new edges are added without
features, their features will be created by initializers defined
with :func:`set_n_initializer`.
>>> g.edata['h'] = torch.ones(4, 1)
>>> g.add_edges(torch.tensor([1]), torch.tensor([1]))
>>> g.edata['h']
tensor([[1.], [1.], [1.], [1.], [0.]])
We can also assign features for the new edges in adding new edges.
>>> g.add_edges(torch.tensor([0, 0]), torch.tensor([2, 2]),
... {'h': torch.tensor([[1.], [2.]]), 'w': torch.ones(2, 1)})
>>> g.edata['h']
tensor([[1.], [1.], [1.], [1.], [0.], [1.], [2.]])
Since ``data`` contains new feature fields, the features for old edges
will be created by initializers defined with :func:`set_n_initializer`.
>>> g.edata['w']
tensor([[0.], [0.], [0.], [0.], [0.], [1.], [1.]])
**Heterogeneous Graphs with Multiple Edge Types**
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): (torch.tensor([0, 1, 1, 2]),
... torch.tensor([0, 0, 1, 1])),
... ('developer', 'develops', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))
... })
>>> g.add_edges(torch.tensor([3]), torch.tensor([3]))
DGLError: Edge type name must be specified
if there are more than one edge types.
>>> g.number_of_edges('plays')
4
>>> g.add_edges(torch.tensor([3]), torch.tensor([3]), etype='plays')
>>> g.number_of_edges('plays')
5
See Also
--------
add_nodes
remove_nodes
remove_edges
"""
# TODO(xiangsx): block do not support add_edges
u = utils.prepare_tensor(self, u, "u")
v = utils.prepare_tensor(self, v, "v")
if etype is None:
if self._graph.number_of_etypes() != 1:
raise DGLError(
"Edge type name must be specified if there are more than one "
"edge types."
)
# nothing changed
if len(u) == 0 or len(v) == 0:
return
assert len(u) == len(v) or len(u) == 1 or len(v) == 1, (
"The number of source nodes and the number of destination nodes should be same, "
"or either the number of source nodes or the number of destination nodes is 1."
)
if len(u) == 1 and len(v) > 1:
u = F.full_1d(
len(v), F.as_scalar(u), dtype=F.dtype(u), ctx=F.context(u)
)
if len(v) == 1 and len(u) > 1:
v = F.full_1d(
len(u), F.as_scalar(v), dtype=F.dtype(v), ctx=F.context(v)
)
u_type, e_type, v_type = self.to_canonical_etype(etype)
# if end nodes of adding edges does not exists
# use add_nodes to add new nodes first.
num_of_u = self.number_of_nodes(u_type)
num_of_v = self.number_of_nodes(v_type)
u_max = F.as_scalar(F.max(u, dim=0)) + 1
v_max = F.as_scalar(F.max(v, dim=0)) + 1
if u_type == v_type:
num_nodes = max(u_max, v_max)
if num_nodes > num_of_u:
self.add_nodes(num_nodes - num_of_u, ntype=u_type)
else:
if u_max > num_of_u:
self.add_nodes(u_max - num_of_u, ntype=u_type)
if v_max > num_of_v:
self.add_nodes(v_max - num_of_v, ntype=v_type)
# metagraph is not changed
metagraph = self._graph.metagraph
num_nodes_per_type = []
for ntype in self.ntypes:
num_nodes_per_type.append(self.number_of_nodes(ntype))
# update graph idx
relation_graphs = []
for c_etype in self.canonical_etypes:
# the target edge type
if c_etype == (u_type, e_type, v_type):
old_u, old_v = self.edges(form="uv", order="eid", etype=c_etype)
hgidx = heterograph_index.create_unitgraph_from_coo(
1 if u_type == v_type else 2,
self.number_of_nodes(u_type),
self.number_of_nodes(v_type),
F.cat([old_u, u], dim=0),
F.cat([old_v, v], dim=0),
["coo", "csr", "csc"],
)
relation_graphs.append(hgidx)
else:
# do nothing
# Note: node range change has been handled in add_nodes()
relation_graphs.append(
self._graph.get_relation_graph(self.get_etype_id(c_etype))
)
hgidx = heterograph_index.create_heterograph_from_relations(
metagraph,
relation_graphs,
utils.toindex(num_nodes_per_type, "int64"),
)
self._graph = hgidx
# handle data
etid = self.get_etype_id(etype)
if data is None:
self._edge_frames[etid].add_rows(len(u))
else:
self._edge_frames[etid].append(data)
self._reset_cached_info()
def remove_edges(self, eids, etype=None, store_ids=False):
r"""Remove multiple edges with the specified edge type
Nodes will not be removed. After removing edges, the rest
edges will be re-indexed using consecutive integers from 0,
with their relative order preserved.
The features for the removed edges will be removed accordingly.
Parameters
----------
eids : int, tensor, numpy.ndarray, list
IDs for the edges to remove.
etype : str or tuple of str, optional
The type of the edges to remove. Can be omitted if there is
only one edge type in the graph.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted nodes and edges in the ``ndata``
and ``edata`` of the resulting graph under name ``dgl.NID`` and ``dgl.EID``,
respectively.
Notes
-----
This function preserves the batch information.
Examples
--------
>>> import dgl
>>> import torch
**Homogeneous Graphs or Heterogeneous Graphs with A Single Edge Type**
>>> g = dgl.graph((torch.tensor([0, 0, 2]), torch.tensor([0, 1, 2])))
>>> g.edata['he'] = torch.arange(3).float().reshape(-1, 1)
>>> g.remove_edges(torch.tensor([0, 1]))
>>> g
Graph(num_nodes=3, num_edges=1,
ndata_schemes={}
edata_schemes={'he': Scheme(shape=(1,), dtype=torch.float32)})
>>> g.edges('all')
(tensor([2]), tensor([2]), tensor([0]))
>>> g.edata['he']
tensor([[2.]])
Removing edges from a batched graph preserves batch information.
>>> g = dgl.graph((torch.tensor([0, 0, 2]), torch.tensor([0, 1, 2])))
>>> g2 = dgl.graph((torch.tensor([1, 2, 3]), torch.tensor([1, 3, 4])))
>>> bg = dgl.batch([g, g2])
>>> bg.batch_num_edges()
tensor([3, 3])
>>> bg.remove_edges([1, 4])
>>> bg.batch_num_edges()
tensor([2, 2])
**Heterogeneous Graphs with Multiple Edge Types**
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): (torch.tensor([0, 1, 1, 2]),
... torch.tensor([0, 0, 1, 1])),
... ('developer', 'develops', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))
... })
>>> g.remove_edges(torch.tensor([0, 1]))
DGLError: Edge type name must be specified
if there are more than one edge types.
>>> g.remove_edges(torch.tensor([0, 1]), 'plays')
>>> g.edges('all', etype='plays')
(tensor([0, 1]), tensor([0, 0]), tensor([0, 1]))
See Also
--------
add_nodes
add_edges
remove_nodes
"""
# TODO(xiangsx): block do not support remove_edges
if etype is None:
if self._graph.number_of_etypes() != 1:
raise DGLError(
"Edge type name must be specified if there are more than one "
"edge types."
)
eids = utils.prepare_tensor(self, eids, "u")
if len(eids) == 0:
# no edge to delete
return
assert self.number_of_edges(etype) > F.as_scalar(
F.max(eids, dim=0)
), "The input eid {} is out of the range [0:{})".format(
F.as_scalar(F.max(eids, dim=0)), self.number_of_edges(etype)
)
# edge_subgraph
edges = {}
u_type, e_type, v_type = self.to_canonical_etype(etype)
for c_etype in self.canonical_etypes:
# the target edge type
if c_etype == (u_type, e_type, v_type):
origin_eids = self.edges(form="eid", order="eid", etype=c_etype)
edges[c_etype] = utils.compensate(eids, origin_eids)
else:
edges[c_etype] = self.edges(
form="eid", order="eid", etype=c_etype
)
# If the graph is batched, update batch_num_edges
batched = self._batch_num_edges is not None
if batched:
c_etype = (u_type, e_type, v_type)
one_hot_removed_edges = F.zeros(
(self.num_edges(c_etype),), F.float32, self.device
)
one_hot_removed_edges = F.scatter_row(
one_hot_removed_edges,
eids,
F.full_1d(len(eids), 1.0, F.float32, self.device),
)
c_etype_batch_num_edges = self._batch_num_edges[c_etype]
batch_num_removed_edges = segment.segment_reduce(
c_etype_batch_num_edges, one_hot_removed_edges, reducer="sum"
)
self._batch_num_edges[c_etype] = c_etype_batch_num_edges - F.astype(
batch_num_removed_edges, F.int64
)
sub_g = self.edge_subgraph(
edges, relabel_nodes=False, store_ids=store_ids
)
self._graph = sub_g._graph
self._node_frames = sub_g._node_frames
self._edge_frames = sub_g._edge_frames
def remove_nodes(self, nids, ntype=None, store_ids=False):
r"""Remove multiple nodes with the specified node type
Edges that connect to the nodes will be removed as well. After removing
nodes and edges, the rest nodes and edges will be re-indexed using
consecutive integers from 0, with their relative order preserved.
The features for the removed nodes/edges will be removed accordingly.
Parameters
----------
nids : int, tensor, numpy.ndarray, list
Nodes to remove.
ntype : str, optional
The type of the nodes to remove. Can be omitted if there is
only one node type in the graph.
store_ids : bool, optional
If True, it will store the raw IDs of the extracted nodes and edges in the ``ndata``
and ``edata`` of the resulting graph under name ``dgl.NID`` and ``dgl.EID``,
respectively.
Notes
-----
This function preserves the batch information.
Examples
--------
>>> import dgl
>>> import torch
**Homogeneous Graphs or Heterogeneous Graphs with A Single Node Type**
>>> g = dgl.graph((torch.tensor([0, 0, 2]), torch.tensor([0, 1, 2])))
>>> g.ndata['hv'] = torch.arange(3).float().reshape(-1, 1)
>>> g.edata['he'] = torch.arange(3).float().reshape(-1, 1)
>>> g.remove_nodes(torch.tensor([0, 1]))
>>> g
Graph(num_nodes=1, num_edges=1,
ndata_schemes={'hv': Scheme(shape=(1,), dtype=torch.float32)}
edata_schemes={'he': Scheme(shape=(1,), dtype=torch.float32)})
>>> g.ndata['hv']
tensor([[2.]])
>>> g.edata['he']
tensor([[2.]])
Removing nodes from a batched graph preserves batch information.
>>> g = dgl.graph((torch.tensor([0, 0, 2]), torch.tensor([0, 1, 2])))
>>> g2 = dgl.graph((torch.tensor([1, 2, 3]), torch.tensor([1, 3, 4])))
>>> bg = dgl.batch([g, g2])
>>> bg.batch_num_nodes()
tensor([3, 5])
>>> bg.remove_nodes([1, 4])
>>> bg.batch_num_nodes()
tensor([2, 4])
>>> bg.batch_num_edges()
tensor([2, 2])
**Heterogeneous Graphs with Multiple Node Types**
>>> g = dgl.heterograph({
... ('user', 'plays', 'game'): (torch.tensor([0, 1, 1, 2]),
... torch.tensor([0, 0, 1, 1])),
... ('developer', 'develops', 'game'): (torch.tensor([0, 1]),
... torch.tensor([0, 1]))
... })
>>> g.remove_nodes(torch.tensor([0, 1]))
DGLError: Node type name must be specified
if there are more than one node types.
>>> g.remove_nodes(torch.tensor([0, 1]), ntype='game')
>>> g.num_nodes('user')
3
>>> g.num_nodes('game')
0
>>> g.num_edges('plays')
0
See Also
--------
add_nodes
add_edges
remove_edges
"""
# TODO(xiangsx): block do not support remove_nodes
if ntype is None:
if self._graph.number_of_ntypes() != 1:
raise DGLError(
"Node type name must be specified if there are more than one "
"node types."
)
nids = utils.prepare_tensor(self, nids, "u")
if len(nids) == 0:
# no node to delete
return
assert self.number_of_nodes(ntype) > F.as_scalar(
F.max(nids, dim=0)
), "The input nids {} is out of the range [0:{})".format(
F.as_scalar(F.max(nids, dim=0)), self.number_of_nodes(ntype)
)
ntid = self.get_ntype_id(ntype)
nodes = {}
for c_ntype in self.ntypes:
if self.get_ntype_id(c_ntype) == ntid:
target_ntype = c_ntype
original_nids = self.nodes(c_ntype)
nodes[c_ntype] = utils.compensate(nids, original_nids)
else:
nodes[c_ntype] = self.nodes(c_ntype)
# If the graph is batched, update batch_num_nodes
batched = self._batch_num_nodes is not None
if batched:
one_hot_removed_nodes = F.zeros(
(self.num_nodes(target_ntype),), F.float32, self.device
)
one_hot_removed_nodes = F.scatter_row(
one_hot_removed_nodes,
nids,
F.full_1d(len(nids), 1.0, F.float32, self.device),
)
c_ntype_batch_num_nodes = self._batch_num_nodes[target_ntype]
batch_num_removed_nodes = segment.segment_reduce(
c_ntype_batch_num_nodes, one_hot_removed_nodes, reducer="sum"
)
self._batch_num_nodes[
target_ntype
] = c_ntype_batch_num_nodes - F.astype(
batch_num_removed_nodes, F.int64
)
# Record old num_edges to check later whether some edges were removed
old_num_edges = {
c_etype: self._graph.number_of_edges(self.get_etype_id(c_etype))
for c_etype in self.canonical_etypes
}
# node_subgraph
# If batch_num_edges is to be updated, record the original edge IDs
sub_g = self.subgraph(nodes, store_ids=store_ids or batched)
self._graph = sub_g._graph
self._node_frames = sub_g._node_frames
self._edge_frames = sub_g._edge_frames
# If the graph is batched, update batch_num_edges
if batched:
canonical_etypes = [
c_etype
for c_etype in self.canonical_etypes
if self._graph.number_of_edges(self.get_etype_id(c_etype))
!= old_num_edges[c_etype]
]
for c_etype in canonical_etypes:
if self._graph.number_of_edges(self.get_etype_id(c_etype)) == 0:
self._batch_num_edges[c_etype] = F.zeros(
(self.batch_size,), F.int64, self.device
)
continue
one_hot_left_edges = F.zeros(
(old_num_edges[c_etype],), F.float32, self.device
)
eids = self.edges[c_etype].data[EID]
one_hot_left_edges = F.scatter_row(
one_hot_left_edges,
eids,
F.full_1d(len(eids), 1.0, F.float32, self.device),
)
batch_num_left_edges = segment.segment_reduce(
self._batch_num_edges[c_etype],
one_hot_left_edges,
reducer="sum",
)
self._batch_num_edges[c_etype] = F.astype(
batch_num_left_edges, F.int64
)
if batched and not store_ids:
for c_ntype in self.ntypes:
self.nodes[c_ntype].data.pop(NID)
for c_etype in self.canonical_etypes:
self.edges[c_etype].data.pop(EID)
def _reset_cached_info(self):
"""Some info like batch_num_nodes may be stale after mutation
Clean these cached info
"""
self._batch_num_nodes = None
self._batch_num_edges = None
#################################################################
# Metagraph query
#################################################################
@property
def is_unibipartite(self):
"""Return whether the graph is a uni-bipartite graph.
A uni-bipartite heterograph can further divide its node types into two sets:
SRC and DST. All edges are from nodes in SRC to nodes in DST. The following APIs
can be used to get the type, data, and nodes that belong to SRC and DST sets:
* :func:`srctype` and :func:`dsttype`
* :func:`srcdata` and :func:`dstdata`
* :func:`srcnodes` and :func:`dstnodes`
Note that we allow two node types to have the same name as long as one
belongs to SRC while the other belongs to DST. To distinguish them, prepend
the name with ``"SRC/"`` or ``"DST/"`` when specifying a node type.
"""
return self._is_unibipartite
@property
def ntypes(self):
"""Return all the node type names in the graph.
Returns
-------
list[str]
All the node type names in a list.
Notes
-----
DGL internally assigns an integer ID for each node type. The returned
node type names are sorted according to their IDs.
Examples
--------
The following example uses PyTorch backend.
>>> import dgl
>>> import torch