def add_edge(self, s, t, attrs=None, **attr):
"""Add an edge to a graph.
Parameters
----------
graph : networkx.(Di)Graph
s : hashable, source node id.
t : hashable, target node id.
attrs : dict
Edge attributes.
"""
if attrs is None:
attrs = attr
else:
try:
attrs.update(attr)
except AttributeError:
raise ReGraphError(
"The attr_dict argument must be a dictionary.")
new_attrs = safe_deepcopy_dict(attrs)
if s not in self.nodes():
raise GraphError("Node '{}' does not exist!".format(s))
if t not in self.nodes():
raise GraphError("Node '{}' does not exist!".format(t))
normalize_attrs(new_attrs)
if (s, t) in self.edges():
raise GraphError("Edge '{}'->'{}' already exists!".format(s, t))
self._graph.add_edge(s, t, **new_attrs)
def clone_node(self, node_id, name=None):
"""Clone node.
Create a new node, a copy of a node with `node_id`, and reconnect it
with all the adjacent nodes of `node_id`.
Parameters
----------
node_id : hashable,
Id of a node to clone.
name : hashable, optional
Id for the clone, if is not specified, new id will be generated.
Returns
-------
new_node : hashable
Id of the new node corresponding to the clone
Raises
------
GraphError
If node wiht `node_id` does not exists or a node with
`name` (clone's name) already exists.
"""
if node_id not in self.nodes():
raise GraphError("Node '{}' does not exist!".format(node_id))
# generate new name for a clone
if name is None:
i = 1
new_node = str(node_id) + str(i)
while new_node in self.nodes():
i += 1
new_node = str(node_id) + str(i)
else:
if name in self.nodes():
raise GraphError("Node '{}' already exists!".format(name))
else:
new_node = name
self.add_node(new_node, self.get_node(node_id))
# Connect all the edges
self.add_edges_from(
set([(n, new_node) for n, _ in self.in_edges(node_id)
if (n, new_node) not in self.edges()]))
self.add_edges_from(
set([(new_node, n) for _, n in self.out_edges(node_id)
if (new_node, n) not in self.edges()]))
# Copy the attributes of the edges
for s, t in self.in_edges(node_id):
self.set_edge(s, new_node, safe_deepcopy_dict(self.get_edge(s, t)))
for s, t in self.out_edges(node_id):
self.set_edge(new_node, t, safe_deepcopy_dict(self.get_edge(s, t)))
return new_node
def add_edge(graph, s, t, attrs=None, **attr):
"""Add an edge to a graph.
Parameters
----------
graph : networkx.(Di)Graph
s : hashable, source node id.
t : hashable, target node id.
attrs : dict
Edge attributes.
Raises
------
ReGraphError
If `attrs` is not a dictionary
GraphError
If either one of the nodes does not exist in the graph or
an edge between `s` and `t` already
exists.
"""
# Set up attribute dict (from Networkx to preserve the signature).
if attrs is None:
attrs = attr
else:
try:
attrs.update(attr)
except AttributeError:
raise ReGraphError(
"The attr_dict argument must be a dictionary."
)
new_attrs = deepcopy(attrs)
if s not in graph.nodes():
raise GraphError("Node '%s' does not exist!" % s)
if t not in graph.nodes():
raise GraphError("Node '%s' does not exist!" % t)
normalize_attrs(new_attrs)
if graph.is_directed():
if (s, t) in graph.edges():
raise GraphError(
"Edge '%s'->'%s' already exists!" %
(s, t)
)
graph.add_edge(s, t, new_attrs)
else:
if (s, t) in graph.edges() or (t, s) in graph.edges():
raise GraphError(
"Edge '%s'->'%s' already exists!" %
(s, t)
)
graph.add_edge(s, t)
graph.edge[s][t] = new_attrs
graph.edge[t][s] = new_attrs
def remove_node_attrs(self, node_id, attrs):
"""Remove attrs of a node specified by attrs_dict.
Parameters
----------
node_id : hashable
Node whose attributes to remove.
attrs : dict
Dictionary with attributes to remove.
Raises
------
GraphError
If a node with the specified id does not exist.
"""
if node_id not in self.nodes():
raise GraphError("Node '%s' does not exist!" % str(node_id))
elif attrs is None:
warnings.warn(
"You want to remove attrs from '{}' with an empty attrs_dict!".
format(node_id), GraphAttrsWarning)
node_attrs = safe_deepcopy_dict(self.get_node(node_id))
remove_attrs(node_attrs, attrs, normalize=True)
self.update_node_attrs(node_id, node_attrs)
def update_edge_attrs(graph, s, t, attrs):
"""Update attributes of an edge.
Parameters
----------
graph : networkx.(Di)Graph
s : hashable, source node id.
t : hashable, target node id.
attrs : dict
New attributes to assign to the edge
Raises
------
GraphError
If an edge between `s` and `t` does not exist.
"""
if not graph.has_edge(s, t):
raise GraphError("Edge '%s->%s' does not exist!" % (str(s), str(t)))
elif attrs is None:
warnings.warn(
"You want to update '%s->%s' attrs with an empty attrs_dict" %
(str(s), str(t)), GraphAttrsWarning)
else:
new_attrs = deepcopy(attrs)
normalize_attrs(new_attrs)
graph.edge[s][t] = new_attrs
if not graph.is_directed():
graph.edge[t][s] = new_attrs
def set_node_attrs(self, node_id, attrs, normalize=True, update=True):
"""Set node attrs.
Parameters
----------
node_id : hashable
Id of the node to update
attrs : dict
Dictionary with new attributes to set
normalize : bool, optional
Flag, when set to True attributes are normalized to be set-valued.
True by default
update : bool, optional
Flag, when set to True attributes whose keys are not present
in attrs are removed, True by default
Raises
------
GraphError
If a node `node_id` does not exist.
"""
if node_id not in self.nodes():
raise GraphError("Node '{}' does not exist!".format(node_id))
node_attrs = safe_deepcopy_dict(self.get_node(node_id))
set_attrs(node_attrs, attrs, normalize, update)
self.update_node_attrs(node_id, node_attrs, normalize)
def update_node_attrs(graph, node_id, attrs):
"""Update attributes of a node.
Parameters
----------
graph : networkx.(Di)Graph
node_id : hashable, node to update.
attrs : dict
New attributes to assign to the node
Raises
------
GraphError
If a node with the specified id does not exist.
"""
new_attrs = deepcopy(attrs)
if node_id not in graph.nodes():
raise GraphError("Node '%s' does not exist!" % str(node_id))
elif new_attrs is None:
warnings.warn(
"You want to update '%s' attrs with an empty attrs_dict!" %
node_id, GraphAttrsWarning)
else:
normalize_attrs(new_attrs)
graph.node[node_id] = new_attrs
def remove_edge_attrs(graph, s, t, attrs):
"""Remove attrs of an edge specified by attrs.
Parameters
----------
graph : networkx.(Di)Graph
s : hashable, source node id.
t : hashable, target node id.
attrs : dict
Dictionary with attributes to remove.
Raises
------
GraphError
If an edge between `s` and `t` does not exist.
"""
if not graph.has_edge(s, t):
raise GraphError("Edge %s-%s does not exist" % (str(s), str(t)))
else:
normalize_attrs(attrs)
old_attrs = get_edge(graph, s, t)
for key, value in attrs.items():
if key in old_attrs:
new_set = old_attrs[key].difference(value)
if new_set:
old_attrs[key] = new_set
else:
del old_attrs[key]
set_edge(graph, s, t, old_attrs)
def predecessors(self, node_id):
"""Return the set of predecessors."""
if node_id not in self.nodes():
raise GraphError(
"Node '{}' does not exist in the graph".format(node_id))
return self._graph.predecessors(node_id)
def update_edge_attrs(self, s, t, attrs, normalize=True):
"""Update attributes of a node.
Parameters
----------
s : hashable, source node of the edge to update.
t : hashable, target node of the edge to update.
attrs : dict
New attributes to assign to the node
"""
if not self._graph.has_edge(s, t):
raise GraphError("Edge '{}->{}' does not exist!".format(s, t))
if attrs is None:
warnings.warn(
"You want to update '{}->{}' attrs with an empty attrs_dict".
format(s, t), GraphAttrsWarning)
if normalize is True:
normalize_attrs(attrs)
attrs_to_remove = set()
for k in self._graph.adj[s][t].keys():
if k not in attrs.keys():
attrs_to_remove.add(k)
self._graph.add_edge(s, t, **attrs)
for k in attrs_to_remove:
del self._graph.adj[s][t][k]
def update_node_attrs(self, node_id, attrs, normalize=True):
"""Update attributes of a node.
Parameters
----------
node_id : hashable, node to update.
attrs : dict
New attributes to assign to the node
"""
new_attrs = safe_deepcopy_dict(attrs)
if node_id not in self.nodes():
raise GraphError("Node '{}' does not exist!".format(node_id))
elif new_attrs is None:
warnings.warn(
"You want to update '{}' attrs with an empty attrs_dict!".
format(node_id), GraphAttrsWarning)
else:
if normalize is True:
normalize_attrs(new_attrs)
attrs_to_remove = set()
for k in self._graph.nodes[node_id].keys():
if k not in new_attrs.keys():
attrs_to_remove.add(k)
self._graph.add_node(node_id, **new_attrs)
for k in attrs_to_remove:
del self._graph.nodes[node_id][k]
def set_edge(graph, s, t, attrs):
"""Set edge attrs.
Parameters
----------
graph : networkx.(Di)Graph
s : hashable, source node id.
t : hashable, target node id.
attrs : dictionary
Dictionary with attributes to set.
Raises
------
GraphError
If an edge between `s` and `t` does not exist.
"""
new_attrs = deepcopy(attrs)
if not graph.has_edge(s, t):
raise GraphError(
"Edge %s->%s does not exist" % (str(s), str(t)))
normalize_attrs(new_attrs)
graph.edge[s][t] = new_attrs
if not graph.is_directed():
graph.edge[t][s] = new_attrs
def set_edge_attrs(self, s, t, attrs, normalize=True, update=True):
"""Set edge attrs.
Parameters
----------
attrs : dict
Dictionary with new attributes to set
normalize : bool, optional
Flag, when set to True attributes are normalized to be set-valued.
True by default
update : bool, optional
Flag, when set to True attributes whose keys are not present
in attrs are removed, True by default
Raises
------
GraphError
If an edge between `s` and `t` does not exist.
"""
if not self.exists_edge(s, t):
raise GraphError("Edge {}->{} does not exist".format(s, t))
edge_attrs = safe_deepcopy_dict(self.get_edge(s, t))
set_attrs(edge_attrs, attrs, normalize, update)
self.update_edge_attrs(s, t, edge_attrs, normalize=normalize)
def add_node(graph, node_id, attrs=None):
"""Add a node to a graph.
Parameters
----------
graph : networkx.(Di)Graph
node_id : hashable
Prefix that is prepended to the new unique name.
attrs : dict, optional
Node attributes.
Raises
-------
regraph.exceptions.GraphError
Raises an error if node already exists in the graph.
"""
new_attrs = deepcopy(attrs)
if new_attrs is None:
new_attrs = dict()
if node_id not in graph.nodes():
graph.add_node(node_id)
normalize_attrs(new_attrs)
graph.node[node_id] = new_attrs
else:
raise GraphError("Node '%s' already exists!" % node_id)
def add_node_attrs(graph, node, attrs):
"""Add new attributes to a node.
Parameters
----------
graph : networkx.(Di)Graph
node : hashable
Id of a node to add attributes to.
attrs : dict
Attributes to add.
Raises
------
GraphError
If a node with the specified id does not exist.
"""
if node not in graph.nodes():
raise GraphError("Node '%s' does not exist!" % str(node))
normalize_attrs(attrs)
node_attrs = graph.node[node]
if node_attrs is None:
graph.node[node] = copy.deepcopy(attrs)
else:
for key in attrs:
if key in node_attrs:
# node_attrs[key] = hyb_union(node_attrs[key], attrs_dict[key])
node_attrs[key] = node_attrs[key].union(attrs[key])
else:
node_attrs[key] = attrs[key]
def remove_node_attrs(graph, node_id, attrs):
"""Remove attrs of a node specified by attrs_dict.
Parameters
----------
graph : networkx.(Di)Graph
node_id : hashable
Node whose attributes to remove.
attrs : dict
Dictionary with attributes to remove.
Raises
------
GraphError
If a node with the specified id does not exist.
"""
if node_id not in graph.nodes():
raise GraphError("Node '%s' does not exist!" % str(node_id))
elif attrs is None:
warnings.warn(
"You want to remove attrs from '%s' with an empty attrs_dict!" %
node_id, GraphAttrsWarning)
elif graph.node[node_id] is None:
warnings.warn("Node '%s' does not have any attribute!" % node_id,
GraphAttrsWarning)
else:
normalize_attrs(attrs)
old_attrs = graph.node[node_id]
for key, value in attrs.items():
if key in old_attrs:
new_set = old_attrs[key].difference(value)
if not new_set:
del old_attrs[key]
else:
old_attrs[key] = new_set
def add_edge_attrs(graph, s, t, attrs):
"""Add attributes of an edge in a graph.
Parameters
----------
graph : networkx.(Di)Graph
s : hashable, source node id.
t : hashable, target node id.
attrs : dict
Dictionary with attributes to remove.
Raises
------
GraphError
If an edge between `s` and `t` does not exist.
"""
new_attrs = deepcopy(attrs)
if not graph.has_edge(s, t):
raise (GraphError("Edge '%s->%s' does not exist" % (str(s), str(t))))
elif new_attrs is None:
pass
else:
normalize_attrs(new_attrs)
edge_attrs = get_edge(graph, s, t)
for key, value in new_attrs.items():
if key in edge_attrs:
edge_attrs[key] = edge_attrs[key].union(value)
else:
edge_attrs[key] = value
set_edge(graph, s, t, edge_attrs)
def get_relabeled_graph(graph, mapping):
"""Return a graph with node labeling specified in the mapping.
Similar to networkx.relabel.relabel_nodes:
https://networkx.github.io/documentation/development/_modules/networkx/relabel.html
Parameters
----------
graph : networkx.(Di)Graph
mapping: dict
A dictionary with keys being old node ids and their values
being new id's of the respective nodes.
Returns
-------
g : networkx.(Di)Graph
New graph object isomorphic to the `graph` with the relabled nodes.
Raises
------
ReGraphError
If new id's do not define a set of distinct node id's.
See also
--------
regraph.primitives.relabel_nodes
"""
g = type(graph)()
old_nodes = set(mapping.keys())
for old_node in old_nodes:
try:
new_node = mapping[old_node]
except KeyError:
continue
try:
g.add_node(new_node, graph.node[old_node])
except KeyError:
raise GraphError("Node '%s' does not exist!" % old_node)
new_edges = list()
attributes = dict()
for s, t in graph.edges():
new_edges.append((mapping[s], mapping[t]))
attributes[(mapping[s], mapping[t])] =\
graph.edge[s][t]
add_edges_from(g, new_edges)
for s, t in g.edges():
if g.is_directed():
set_edge(g, s, t, attributes[(s, t)])
else:
if (s, t) in attributes.keys():
set_edge(g, s, t, attributes[(s, t)])
else:
set_edge(g, s, t, attributes[(t, s)])
return g
def remove_edge(self, s, t):
"""Remove edge from the graph.
Parameters
----------
graph : networkx.(Di)Graph
s : hashable, source node id.
t : hashable, target node id.
"""
if (s, t) not in self.edges():
raise GraphError("Edge '{}->{}' does not exist!".format(s, t))
self._graph.remove_edge(s, t)
def remove_node(self, node_id):
"""Remove node.
Parameters
----------
graph : networkx.(Di)Graph
node_id : hashable, node to remove.
"""
if node_id in self.nodes():
self._graph.remove_node(node_id)
else:
raise GraphError("Node '{}' does not exist!".format(node_id))
return
def get_relabeled_graph(graph, mapping):
"""Return a graph with node labeling specified in the mapping.
Parameters
----------
graph : networkx.(Di)Graph
mapping: dict
A dictionary with keys being old node ids and their values
being new id's of the respective nodes.
Returns
-------
g : networkx.(Di)Graph
New graph object isomorphic to the `graph` with the relabled nodes.
Raises
------
ReGraphError
If new id's do not define a set of distinct node id's.
See also
--------
regraph.primitives.relabel_nodes
"""
g = nx.DiGraph()
old_nodes = set(mapping.keys())
for old_node in old_nodes:
try:
new_node = mapping[old_node]
except KeyError:
continue
try:
g.add_node(new_node, **graph.get_node(old_node))
except KeyError:
raise GraphError("Node '%s' does not exist!" % old_node)
new_edges = list()
attributes = dict()
for s, t in graph.edges():
new_edges.append((mapping[s], mapping[t]))
attributes[(mapping[s], mapping[t])] =\
graph.get_edge(s, t)
g.add_edges_from(new_edges)
for s, t in g.edges():
nx.set_edge_attributes(g, {(s, t): attributes[(s, t)]})
return g
def add_node(self, node_id, attrs=None):
"""Abstract method for adding a node.
Parameters
----------
node_id : hashable
Prefix that is prepended to the new unique name.
attrs : dict, optional
Node attributes.
"""
if attrs is None:
new_attrs = dict()
else:
new_attrs = safe_deepcopy_dict(attrs)
normalize_attrs(new_attrs)
if node_id not in self.nodes():
self._graph.add_node(node_id, **new_attrs)
return node_id
else:
raise GraphError("Node '{}' already exists!".format(node_id))
def remove_edge(graph, s, t):
"""Remove edge from a graph.
Parameters
----------
graph : networkx.(Di)Graph
s : hashable, source node id.
t : hashable, target node id.
Raises
------
GraphError
If edge between `s` and `t` does not exist.
"""
if graph.is_directed():
if (s, t) not in graph.edges():
raise GraphError("Edge '%s->%s' does not exist!" %
(str(s), str(t)))
graph.remove_edge(s, t)
def add_node_attrs(self, node, attrs):
"""Add new attributes to a node.
Parameters
----------
node : hashable
Id of a node to add attributes to.
attrs : dict
Attributes to add.
Raises
------
GraphError
If a node `node_id` does not exist.
"""
if node not in self.nodes():
raise GraphError("Node '{}' does not exist!".format(node))
node_attrs = safe_deepcopy_dict(self.get_node(node))
add_attrs(node_attrs, attrs, normalize=True)
self.update_node_attrs(node, node_attrs)
def remove_node(graph, node_id):
"""Remove node.
Parameters
----------
graph : networkx.(Di)Graph
node_id : hashable, node to remove.
Raises
------
GraphError
If a node with the specified id does not exist.
"""
if node_id in graph.nodes():
neighbors = set(graph.__getitem__(node_id).keys())
neighbors -= {node_id}
graph.remove_node(node_id)
else:
raise GraphError("Node %s does not exist!" % str(node_id))
return
def remove_edge_attrs(self, s, t, attrs):
"""Remove attrs of an edge specified by attrs.
Parameters
----------
s : hashable
Source node id.
t : hashable
Target node id.
attrs : dict
Dictionary with attributes to remove.
Raises
------
GraphError
If an edge between `s` and `t` does not exist.
"""
if not self.exists_edge(s, t):
raise GraphError("Edge {}->{} does not exist".format(s, t))
edge_attrs = safe_deepcopy_dict(self.get_edge(s, t))
remove_attrs(edge_attrs, attrs, normalize=True)
self.update_edge_attrs(s, t, edge_attrs)
def merge_nodes(graph,
nodes,
node_id=None,
method="union",
edge_method="union"):
"""Merge a list of nodes.
Parameters
----------
graph : nx.(Di)Graph
nodes : iterable
Collection of node id's to merge.
node_id : hashable, optional
Id of a new node corresponding to the result of merge.
method : optional
Method of node attributes merge: if `"union"` the resulting node
will contain the union of all attributes of the merged nodes,
if `"intersection"`, the resulting node will contain their
intersection. Default value is `"union"`.
edge_method : optional
Method of edge attributes merge: if `"union"` the edges that were
merged will contain the union of all attributes,
if `"intersection"` -- their ntersection. Default value is `"union"`.
Returns
-------
node_id : hashable
Id of a new node corresponding to the result of merge.
Raises
------
ReGraphError
If unknown merging method is provided
GraphError
If some nodes from `nodes` do not exist in the graph.
Examples
--------
>>> g = nx.DiGraph()
>>> add_nodes_from(g, [(1, {"a": 1, "b": 1}), 2, (3, {"a": 3, "c": 3})])
>>> add_edges_from(g, [(1, 3), (1, 2), (2, 3)])
>>> merge_nodes(g, [1, 3], "merged_node")
>>> g.nodes()
["merged_node", 2]
>>> g.edges()
[("merged_node", "merged_node"), ("merged_node", 2), (2, "merged_node")]
>>> g.node["merged_node"]
{"a": {1, 3}, "b": {1}, "c": {3}}
"""
if len(nodes) == 1:
if node_id is not None:
relabel_node(graph, nodes[0], node_id)
elif len(nodes) > 1:
if method is None:
method = "union"
if edge_method is None:
method = "union"
# Generate name for new node
if node_id is None:
node_id = "_".join([str(n) for n in nodes])
elif node_id in graph.nodes() and (node_id not in nodes):
raise GraphError("New name for merged node is not valid: "
"node with name '%s' already exists!" % node_id)
# Merge data attached to node according to the method specified
# restore proper connectivity
if method == "union":
attr_accumulator = {}
elif method == "intersection":
attr_accumulator = deepcopy(graph.node[nodes[0]])
else:
raise ReGraphError("Merging method '%s' is not defined!" % method)
self_loop = False
self_loop_attrs = {}
if graph.is_directed():
source_nodes = set()
target_nodes = set()
source_dict = {}
target_dict = {}
else:
neighbors = set()
neighbors_dict = {}
all_neighbors = set()
for node in nodes:
all_neighbors |= set(graph.__getitem__(node).keys())
attr_accumulator = merge_attributes(attr_accumulator,
graph.node[node], method)
if graph.is_directed():
in_edges = graph.in_edges(node)
out_edges = graph.out_edges(node)
# manage self loops
for s, t in in_edges:
if s in nodes:
self_loop = True
if len(self_loop_attrs) == 0:
self_loop_attrs = graph.edge[s][t]
else:
self_loop_attrs = merge_attributes(
self_loop_attrs, graph.edge[s][t], edge_method)
for s, t in out_edges:
if t in nodes:
self_loop = True
if len(self_loop_attrs) == 0:
self_loop_attrs = graph.edge[s][t]
else:
self_loop_attrs = merge_attributes(
self_loop_attrs, graph.edge[s][t], edge_method)
source_nodes.update(
[n if n not in nodes else node_id for n, _ in in_edges])
target_nodes.update(
[n if n not in nodes else node_id for _, n in out_edges])
for edge in in_edges:
if not edge[0] in source_dict.keys():
attrs = graph.edge[edge[0]][edge[1]]
source_dict.update({edge[0]: attrs})
else:
attrs = merge_attributes(source_dict[edge[0]],
graph.edge[edge[0]][edge[1]],
edge_method)
source_dict.update({edge[0]: attrs})
for edge in out_edges:
if not edge[1] in target_dict.keys():
attrs = graph.edge[edge[0]][edge[1]]
target_dict.update({edge[1]: attrs})
else:
attrs = merge_attributes(target_dict[edge[1]],
graph.edge[edge[0]][edge[1]],
edge_method)
target_dict.update({edge[1]: attrs})
else:
for n in graph.neighbors(node):
if n in nodes:
self_loop = True
if len(self_loop_attrs) == 0:
self_loop_attrs = graph.edge[n][node]
else:
self_loop_attrs = merge_attributes(
self_loop_attrs, graph.edge[n][node],
edge_method)
neighbors.update(
[n for n in graph.neighbors(node) if n not in nodes])
for n in graph.neighbors(node):
if n not in nodes:
if n not in neighbors_dict.keys():
attrs = graph.edge[n][node]
neighbors_dict.update({n: attrs})
else:
attrs = merge_attributes(neighbors_dict[n],
graph.edge[n][node],
edge_method)
neighbors_dict.update({n: attrs})
graph.remove_node(node)
all_neighbors -= {node}
add_node(graph, node_id, attr_accumulator)
all_neighbors.add(node_id)
if graph.is_directed():
if self_loop:
add_edges_from(graph, [(node_id, node_id)])
graph.edge[node_id][node_id] = self_loop_attrs
for n in source_nodes:
if not exists_edge(graph, n, node_id):
add_edge(graph, n, node_id)
for n in target_nodes:
if not exists_edge(graph, node_id, n):
add_edge(graph, node_id, n)
# Attach accumulated attributes to edges
for node, attrs in source_dict.items():
if node not in nodes:
graph.edge[node][node_id] = attrs
for node, attrs in target_dict.items():
if node not in nodes:
graph.edge[node_id][node] = attrs
else:
if self_loop:
add_edges_from(graph, [(node_id, node_id)])
graph.edge[node_id][node_id] = self_loop_attrs
add_edges_from(graph, [(n, node_id) for n in neighbors])
# Attach accumulated attributes to edges
for node, attrs in neighbors_dict.items():
if node not in nodes:
graph.edge[node][node_id] = attrs
graph.edge[node_id][node] = attrs
return node_id
def get_relabeled_graph(self, mapping, raw=False):
"""Return a graph with node labeling specified in the mapping.
Parameters
----------
graph : networkx.(Di)Graph
mapping: dict
A dictionary with keys being old node ids and their values
being new id's of the respective nodes.
Returns
-------
g : networkx.(Di)Graph
New graph object isomorphic to the `graph` with the relabled nodes.
Raises
------
ReGraphError
If new id's do not define a set of distinct node id's.
See also
--------
regraph.primitives.relabel_nodes
"""
g = nx.DiGraph()
old_nodes = set(mapping.keys())
for old_node in old_nodes:
try:
new_node = mapping[old_node]
except KeyError:
pass
try:
g.add_node(new_node, **self.get_node(old_node))
except KeyError:
raise GraphError("Node '%s' does not exist!" % old_node)
new_edges = list()
attributes = dict()
for s, t in self.edges():
new_s = None
new_t = None
try:
new_s = mapping[s]
except KeyError:
pass
try:
new_t = mapping[t]
except KeyError:
pass
if new_s and new_t:
new_edges.append((new_s, new_t))
attributes[(new_s, new_t)] = self.get_edge(s, t)
g.add_edges_from(new_edges)
for s, t in g.edges():
for k, v in attributes[(s, t)].items():
g.adj[s][t][k] = v
if not raw:
new_obj = NXGraph()
new_obj._graph = g
return new_obj
return g
def clone_node(graph, node_id, name=None):
"""Clone node.
Create a new node, a copy of a node with `node_id`, and reconnect it
with all the adjacent nodes of `node_id`.
Parameters
----------
graph : networkx.(Di)Graph
node_id : id of a node to clone.
name : id for the clone, optional
If is not specified, new id will be generated.
Returns
-------
new_node : hashable, clone's id
Raises
------
GraphError
If node wiht `node_id` does not exists or a node with
`name` (clone's name) already exists.
Examples
--------
>>> g = nx.DiGraph()
>>> add_nodes_from(g, [1, 2, 3])
>>> add_edges_from(g, [(1, 2), (3, 2)])
>>> clone_node(g, 2, "2_clone")
>>> g.nodes()
[1, 2, "2_clone", 3]
>>> g.edges()
[(1, 2), (1, "2_clone"), (3, 2), (3, "2_clone")]
"""
if node_id not in graph.nodes():
raise GraphError("Node '%s' does not exist!" % str(node_id))
# generate new name for a clone
if name is None:
i = 1
new_node = str(node_id) + str(i)
while new_node in graph.nodes():
i += 1
new_node = str(node_id) + str(i)
else:
if name in graph.nodes():
raise GraphError("Node '%s' already exists!" % str(name))
else:
new_node = name
graph.add_node(new_node, deepcopy(graph.node[node_id]))
# Connect all the edges
if graph.is_directed():
add_edges_from(graph,
[(n, new_node) for n, _ in graph.in_edges(node_id)])
add_edges_from(graph,
[(new_node, n) for _, n in graph.out_edges(node_id)])
# Copy the attributes of the edges
for s, t in graph.in_edges(node_id):
graph.edge[s][new_node] = deepcopy(graph.edge[s][t])
for s, t in graph.out_edges(node_id):
graph.edge[new_node][t] = deepcopy(graph.edge[s][t])
else:
add_edges_from(graph,
[(n, new_node) for n in graph.neighbors(node_id)])
# Copy the attributes of the edges
for n in graph.neighbors(node_id):
graph.edge[new_node][n] = deepcopy(graph.edge[n][node_id])
graph.edge[n][new_node] = graph.edge[new_node][n]
return new_node
def merge_nodes(self,
nodes,
node_id=None,
method="union",
edge_method="union"):
"""Merge a list of nodes.
Parameters
----------
nodes : iterable
Collection of node id's to merge.
node_id : hashable, optional
Id of a new node corresponding to the result of merge.
method : optional
Method of node attributes merge: if `"union"` the resulting node
will contain the union of all attributes of the merged nodes,
if `"intersection"`, the resulting node will contain their
intersection. Default value is `"union"`.
edge_method : optional
Method of edge attributes merge: if `"union"` the edges that were
merged will contain the union of all attributes,
if `"intersection"` -- their ntersection.
Default value is `"union"`.
"""
if len(nodes) > 1:
if method is None:
method = "union"
if edge_method is None:
method = "union"
# Generate name for new node
if node_id is None:
node_id = "_".join(sorted([str(n) for n in nodes]))
if node_id in self.nodes():
node_id = self.generate_new_node_id(node_id)
elif node_id in self.nodes() and (node_id not in nodes):
raise GraphError("New name for merged node is not valid: "
"node with name '%s' already exists!" %
node_id)
# Merge data attached to node according to the method specified
# restore proper connectivity
if method == "union":
attr_accumulator = {}
elif method == "intersection":
attr_accumulator = safe_deepcopy_dict(self.get_node(nodes[0]))
else:
raise ReGraphError(
"Merging method '{}' is not defined!".format(method))
self_loop = False
self_loop_attrs = {}
source_nodes = set()
target_nodes = set()
source_dict = {}
target_dict = {}
for node in nodes:
attr_accumulator = merge_attributes(attr_accumulator,
self.get_node(node),
method)
in_edges = self.in_edges(node)
out_edges = self.out_edges(node)
# manage self loops
for s, t in in_edges:
if s in nodes:
self_loop = True
if len(self_loop_attrs) == 0:
self_loop_attrs = self.get_edge(s, t)
else:
self_loop_attrs = merge_attributes(
self_loop_attrs, self.get_edge(s, t),
edge_method)
for s, t in out_edges:
if t in nodes:
self_loop = True
if len(self_loop_attrs) == 0:
self_loop_attrs = self.get_edge(s, t)
else:
self_loop_attrs = merge_attributes(
self_loop_attrs, self.get_edge(s, t),
edge_method)
source_nodes.update(
[n if n not in nodes else node_id for n, _ in in_edges])
target_nodes.update(
[n if n not in nodes else node_id for _, n in out_edges])
for edge in in_edges:
if not edge[0] in source_dict.keys():
attrs = self.get_edge(edge[0], edge[1])
source_dict.update({edge[0]: attrs})
else:
attrs = merge_attributes(
source_dict[edge[0]],
self.get_edge(edge[0], edge[1]), edge_method)
source_dict.update({edge[0]: attrs})
for edge in out_edges:
if not edge[1] in target_dict.keys():
attrs = self.get_edge(edge[0], edge[1])
target_dict.update({edge[1]: attrs})
else:
attrs = merge_attributes(
target_dict[edge[1]],
self.get_edge(edge[0], edge[1]), edge_method)
target_dict.update({edge[1]: attrs})
self.remove_node(node)
self.add_node(node_id, attr_accumulator)
if self_loop:
self.add_edges_from([(node_id, node_id)])
self.set_edge(node_id, node_id, self_loop_attrs)
for n in source_nodes:
if not self.exists_edge(n, node_id):
self.add_edge(n, node_id)
for n in target_nodes:
if not self.exists_edge(node_id, n):
self.add_edge(node_id, n)
# Attach accumulated attributes to edges
for node, attrs in source_dict.items():
if node not in nodes:
self.set_edge(node, node_id, attrs)
for node, attrs in target_dict.items():
if node not in nodes:
self.set_edge(node_id, node, attrs)
return node_id
else:
raise ReGraphError(
"More than two nodes should be specified for merging!")