# -*- coding: utf-8 -*-
# Copyright (C) 2006-2018 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
#
# Authors:
# Aric Hagberg <aric.hagberg@gmail.com>
# Dan Schult <dschult@colgate.edu>
# Ben Edwards <bedwards@cs.unm.edu>
# Neil Girdhar <neil.girdhar@mcgill.ca>
#
"""Algorithms for directed acyclic graphs (DAGs).
Note that most of these functions are only guaranteed to work for DAGs.
In general, these functions do not check for acyclic-ness, so it is up
to the user to check for that.
"""
from collections import defaultdict
from fractions import gcd
from functools import partial
from itertools import chain
from itertools import product
from itertools import starmap
import heapq
import networkx as nx
from networkx.generators.trees import NIL
from networkx.utils import arbitrary_element
from networkx.utils import consume
from networkx.utils import pairwise
from networkx.utils import generate_unique_node
from networkx.utils import not_implemented_for
__all__ = ['descendants',
'ancestors',
'topological_sort',
'lexicographical_topological_sort',
'is_directed_acyclic_graph',
'is_aperiodic',
'transitive_closure',
'transitive_reduction',
'antichains',
'dag_longest_path',
'dag_longest_path_length',
'dag_to_branching']
chaini = chain.from_iterable
[docs]def descendants(G, source):
"""Return all nodes reachable from `source` in `G`.
Parameters
----------
G : NetworkX DiGraph
A directed acyclic graph (DAG)
source : node in `G`
Returns
-------
set()
The descendants of `source` in `G`
"""
if not G.has_node(source):
raise nx.NetworkXError("The node %s is not in the graph." % source)
des = set(n for n, d in nx.shortest_path_length(G, source=source).items())
return des - {source}
[docs]def ancestors(G, source):
"""Return all nodes having a path to `source` in `G`.
Parameters
----------
G : NetworkX DiGraph
A directed acyclic graph (DAG)
source : node in `G`
Returns
-------
set()
The ancestors of source in G
"""
if not G.has_node(source):
raise nx.NetworkXError("The node %s is not in the graph." % source)
anc = set(n for n, d in nx.shortest_path_length(G, target=source).items())
return anc - {source}
def has_cycle(G):
"""Decides whether the directed graph has a cycle."""
try:
consume(topological_sort(G))
except nx.NetworkXUnfeasible:
return True
else:
return False
[docs]def is_directed_acyclic_graph(G):
"""Return True if the graph `G` is a directed acyclic graph (DAG) or
False if not.
Parameters
----------
G : NetworkX graph
Returns
-------
bool
True if `G` is a DAG, False otherwise
"""
return G.is_directed() and not has_cycle(G)
[docs]def topological_sort(G):
"""Return a generator of nodes in topologically sorted order.
A topological sort is a nonunique permutation of the nodes such that an
edge from u to v implies that u appears before v in the topological sort
order.
Parameters
----------
G : NetworkX digraph
A directed acyclic graph (DAG)
Returns
-------
iterable
An iterable of node names in topological sorted order.
Raises
------
NetworkXError
Topological sort is defined for directed graphs only. If the graph `G`
is undirected, a :exc:`NetworkXError` is raised.
NetworkXUnfeasible
If `G` is not a directed acyclic graph (DAG) no topological sort exists
and a :exc:`NetworkXUnfeasible` exception is raised. This can also be
raised if `G` is changed while the returned iterator is being processed.
RuntimeError
If `G` is changed while the returned iterator is being processed.
Examples
--------
To get the reverse order of the topological sort:
>>> DG = nx.DiGraph([(1, 2), (2, 3)])
>>> list(reversed(list(nx.topological_sort(DG))))
[3, 2, 1]
Notes
-----
This algorithm is based on a description and proof in
"Introduction to Algorithms: A Creative Approach" [1]_ .
See also
--------
is_directed_acyclic_graph, lexicographical_topological_sort
References
----------
.. [1] Manber, U. (1989).
*Introduction to Algorithms - A Creative Approach.* Addison-Wesley.
"""
if not G.is_directed():
raise nx.NetworkXError(
"Topological sort not defined on undirected graphs.")
indegree_map = {v: d for v, d in G.in_degree() if d > 0}
# These nodes have zero indegree and ready to be returned.
zero_indegree = [v for v, d in G.in_degree() if d == 0]
while zero_indegree:
node = zero_indegree.pop()
if node not in G:
raise RuntimeError("Graph changed during iteration")
for _, child in G.edges(node):
try:
indegree_map[child] -= 1
except KeyError:
raise RuntimeError("Graph changed during iteration")
if indegree_map[child] == 0:
zero_indegree.append(child)
del indegree_map[child]
yield node
if indegree_map:
raise nx.NetworkXUnfeasible("Graph contains a cycle or graph changed "
"during iteration")
[docs]def lexicographical_topological_sort(G, key=None):
"""Return a generator of nodes in lexicographically topologically sorted
order.
A topological sort is a nonunique permutation of the nodes such that an
edge from u to v implies that u appears before v in the topological sort
order.
Parameters
----------
G : NetworkX digraph
A directed acyclic graph (DAG)
key : function, optional
This function maps nodes to keys with which to resolve ambiguities in
the sort order. Defaults to the identity function.
Returns
-------
iterable
An iterable of node names in lexicographical topological sort order.
Raises
------
NetworkXError
Topological sort is defined for directed graphs only. If the graph `G`
is undirected, a :exc:`NetworkXError` is raised.
NetworkXUnfeasible
If `G` is not a directed acyclic graph (DAG) no topological sort exists
and a :exc:`NetworkXUnfeasible` exception is raised. This can also be
raised if `G` is changed while the returned iterator is being processed.
RuntimeError
If `G` is changed while the returned iterator is being processed.
Notes
-----
This algorithm is based on a description and proof in
"Introduction to Algorithms: A Creative Approach" [1]_ .
See also
--------
topological_sort
References
----------
.. [1] Manber, U. (1989).
*Introduction to Algorithms - A Creative Approach.* Addison-Wesley.
"""
if not G.is_directed():
raise nx.NetworkXError(
"Topological sort not defined on undirected graphs.")
if key is None:
def key(x): return x
def create_tuple(node):
return key(node), node
indegree_map = {v: d for v, d in G.in_degree() if d > 0}
# These nodes have zero indegree and ready to be returned.
zero_indegree = [create_tuple(v) for v, d in G.in_degree() if d == 0]
heapq.heapify(zero_indegree)
while zero_indegree:
_, node = heapq.heappop(zero_indegree)
if node not in G:
raise RuntimeError("Graph changed during iteration")
for _, child in G.edges(node):
try:
indegree_map[child] -= 1
except KeyError:
raise RuntimeError("Graph changed during iteration")
if indegree_map[child] == 0:
heapq.heappush(zero_indegree, create_tuple(child))
del indegree_map[child]
yield node
if indegree_map:
raise nx.NetworkXUnfeasible("Graph contains a cycle or graph changed "
"during iteration")
[docs]def is_aperiodic(G):
"""Return True if `G` is aperiodic.
A directed graph is aperiodic if there is no integer k > 1 that
divides the length of every cycle in the graph.
Parameters
----------
G : NetworkX DiGraph
A directed graph
Returns
-------
bool
True if the graph is aperiodic False otherwise
Raises
------
NetworkXError
If `G` is not directed
Notes
-----
This uses the method outlined in [1]_, which runs in $O(m)$ time
given $m$ edges in `G`. Note that a graph is not aperiodic if it is
acyclic as every integer trivial divides length 0 cycles.
References
----------
.. [1] Jarvis, J. P.; Shier, D. R. (1996),
"Graph-theoretic analysis of finite Markov chains,"
in Shier, D. R.; Wallenius, K. T., Applied Mathematical Modeling:
A Multidisciplinary Approach, CRC Press.
"""
if not G.is_directed():
raise nx.NetworkXError(
"is_aperiodic not defined for undirected graphs")
s = arbitrary_element(G)
levels = {s: 0}
this_level = [s]
g = 0
l = 1
while this_level:
next_level = []
for u in this_level:
for v in G[u]:
if v in levels: # Non-Tree Edge
g = gcd(g, levels[u] - levels[v] + 1)
else: # Tree Edge
next_level.append(v)
levels[v] = l
this_level = next_level
l += 1
if len(levels) == len(G): # All nodes in tree
return g == 1
else:
return g == 1 and nx.is_aperiodic(G.subgraph(set(G) - set(levels)))
[docs]@not_implemented_for('undirected')
def transitive_closure(G):
""" Returns transitive closure of a directed graph
The transitive closure of G = (V,E) is a graph G+ = (V,E+) such that
for all v,w in V there is an edge (v,w) in E+ if and only if there
is a non-null path from v to w in G.
Parameters
----------
G : NetworkX DiGraph
A directed graph
Returns
-------
NetworkX DiGraph
The transitive closure of `G`
Raises
------
NetworkXNotImplemented
If `G` is not directed
References
----------
.. [1] http://www.ics.uci.edu/~eppstein/PADS/PartialOrder.py
"""
TC = G.copy()
for v in G:
TC.add_edges_from((v, u) for u in nx.dfs_preorder_nodes(G, source=v)
if v != u)
return TC
[docs]@not_implemented_for('undirected')
def transitive_reduction(G):
""" Returns transitive reduction of a directed graph
The transitive reduction of G = (V,E) is a graph G- = (V,E-) such that
for all v,w in V there is an edge (v,w) in E- if and only if (v,w) is
in E and there is no path from v to w in G with length greater than 1.
Parameters
----------
G : NetworkX DiGraph
A directed acyclic graph (DAG)
Returns
-------
NetworkX DiGraph
The transitive reduction of `G`
Raises
------
NetworkXError
If `G` is not a directed acyclic graph (DAG) transitive reduction is
not uniquely defined and a :exc:`NetworkXError` exception is raised.
References
----------
https://en.wikipedia.org/wiki/Transitive_reduction
"""
if not is_directed_acyclic_graph(G):
raise nx.NetworkXError(
"Transitive reduction only uniquely defined on directed acyclic graphs.")
TR = nx.DiGraph()
TR.add_nodes_from(G.nodes())
for u in G:
u_edges = set(G[u])
for v in G[u]:
u_edges -= {y for x, y in nx.dfs_edges(G, v)}
TR.add_edges_from((u, v) for v in u_edges)
return TR
[docs]@not_implemented_for('undirected')
def antichains(G):
"""Generates antichains from a directed acyclic graph (DAG).
An antichain is a subset of a partially ordered set such that any
two elements in the subset are incomparable.
Parameters
----------
G : NetworkX DiGraph
A directed acyclic graph (DAG)
Returns
-------
generator object
Raises
------
NetworkXNotImplemented
If `G` is not directed
NetworkXUnfeasible
If `G` contains a cycle
Notes
-----
This function was originally developed by Peter Jipsen and Franco Saliola
for the SAGE project. It's included in NetworkX with permission from the
authors. Original SAGE code at:
https://github.com/sagemath/sage/blob/master/src/sage/combinat/posets/hasse_diagram.py
References
----------
.. [1] Free Lattices, by R. Freese, J. Jezek and J. B. Nation,
AMS, Vol 42, 1995, p. 226.
"""
TC = nx.transitive_closure(G)
antichains_stacks = [([], list(reversed(list(nx.topological_sort(G)))))]
while antichains_stacks:
(antichain, stack) = antichains_stacks.pop()
# Invariant:
# - the elements of antichain are independent
# - the elements of stack are independent from those of antichain
yield antichain
while stack:
x = stack.pop()
new_antichain = antichain + [x]
new_stack = [
t for t in stack if not ((t in TC[x]) or (x in TC[t]))]
antichains_stacks.append((new_antichain, new_stack))
[docs]@not_implemented_for('undirected')
def dag_longest_path(G, weight='weight', default_weight=1):
"""Returns the longest path in a directed acyclic graph (DAG).
If `G` has edges with `weight` attribute the edge data are used as
weight values.
Parameters
----------
G : NetworkX DiGraph
A directed acyclic graph (DAG)
weight : str, optional
Edge data key to use for weight
default_weight : int, optional
The weight of edges that do not have a weight attribute
Returns
-------
list
Longest path
Raises
------
NetworkXNotImplemented
If `G` is not directed
See also
--------
dag_longest_path_length
"""
if not G:
return []
dist = {} # stores {v : (length, u)}
for v in nx.topological_sort(G):
us = [(dist[u][0] + data.get(weight, default_weight), u)
for u, data in G.pred[v].items()]
# Use the best predecessor if there is one and its distance is
# non-negative, otherwise terminate.
maxu = max(us, key=lambda x: x[0]) if us else (0, v)
dist[v] = maxu if maxu[0] >= 0 else (0, v)
u = None
v = max(dist, key=lambda x: dist[x][0])
path = []
while u != v:
path.append(v)
u = v
v = dist[v][1]
path.reverse()
return path
[docs]@not_implemented_for('undirected')
def dag_longest_path_length(G, weight='weight', default_weight=1):
"""Returns the longest path length in a DAG
Parameters
----------
G : NetworkX DiGraph
A directed acyclic graph (DAG)
weight : string, optional
Edge data key to use for weight
default_weight : int, optional
The weight of edges that do not have a weight attribute
Returns
-------
int
Longest path length
Raises
------
NetworkXNotImplemented
If `G` is not directed
See also
--------
dag_longest_path
"""
path = nx.dag_longest_path(G, weight, default_weight)
path_length = 0
for (u, v) in pairwise(path):
path_length += G[u][v].get(weight, default_weight)
return path_length
def root_to_leaf_paths(G):
"""Yields root-to-leaf paths in a directed acyclic graph.
`G` must be a directed acyclic graph. If not, the behavior of this
function is undefined. A "root" in this graph is a node of in-degree
zero and a "leaf" a node of out-degree zero.
When invoked, this function iterates over each path from any root to
any leaf. A path is a list of nodes.
"""
roots = (v for v, d in G.in_degree() if d == 0)
leaves = (v for v, d in G.out_degree() if d == 0)
all_paths = partial(nx.all_simple_paths, G)
# TODO In Python 3, this would be better as `yield from ...`.
return chaini(starmap(all_paths, product(roots, leaves)))
[docs]@not_implemented_for('multigraph')
@not_implemented_for('undirected')
def dag_to_branching(G):
"""Returns a branching representing all (overlapping) paths from
root nodes to leaf nodes in the given directed acyclic graph.
As described in :mod:`networkx.algorithms.tree.recognition`, a
*branching* is a directed forest in which each node has at most one
parent. In other words, a branching is a disjoint union of
*arborescences*. For this function, each node of in-degree zero in
`G` becomes a root of one of the arborescences, and there will be
one leaf node for each distinct path from that root to a leaf node
in `G`.
Each node `v` in `G` with *k* parents becomes *k* distinct nodes in
the returned branching, one for each parent, and the sub-DAG rooted
at `v` is duplicated for each copy. The algorithm then recurses on
the children of each copy of `v`.
Parameters
----------
G : NetworkX graph
A directed acyclic graph.
Returns
-------
DiGraph
The branching in which there is a bijection between root-to-leaf
paths in `G` (in which multiple paths may share the same leaf)
and root-to-leaf paths in the branching (in which there is a
unique path from a root to a leaf).
Each node has an attribute 'source' whose value is the original
node to which this node corresponds. No other graph, node, or
edge attributes are copied into this new graph.
Raises
------
NetworkXNotImplemented
If `G` is not directed, or if `G` is a multigraph.
HasACycle
If `G` is not acyclic.
Examples
--------
To examine which nodes in the returned branching were produced by
which original node in the directed acyclic graph, we can collect
the mapping from source node to new nodes into a dictionary. For
example, consider the directed diamond graph::
>>> from collections import defaultdict
>>> from operator import itemgetter
>>>
>>> G = nx.DiGraph(nx.utils.pairwise('abd'))
>>> G.add_edges_from(nx.utils.pairwise('acd'))
>>> B = nx.dag_to_branching(G)
>>>
>>> sources = defaultdict(set)
>>> for v, source in B.nodes(data='source'):
... sources[source].add(v)
>>> len(sources['a'])
1
>>> len(sources['d'])
2
To copy node attributes from the original graph to the new graph,
you can use a dictionary like the one constructed in the above
example::
>>> for source, nodes in sources.items():
... for v in nodes:
... B.node[v].update(G.node[source])
Notes
-----
This function is not idempotent in the sense that the node labels in
the returned branching may be uniquely generated each time the
function is invoked. In fact, the node labels may not be integers;
in order to relabel the nodes to be more readable, you can use the
:func:`networkx.convert_node_labels_to_integers` function.
The current implementation of this function uses
:func:`networkx.prefix_tree`, so it is subject to the limitations of
that function.
"""
if has_cycle(G):
msg = 'dag_to_branching is only defined for acyclic graphs'
raise nx.HasACycle(msg)
paths = root_to_leaf_paths(G)
B, root = nx.prefix_tree(paths)
# Remove the synthetic `root` and `NIL` nodes in the prefix tree.
B.remove_node(root)
B.remove_node(NIL)
return B