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 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 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 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(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 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 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 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_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(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!")
