305 lines
8.2 KiB
Python
305 lines
8.2 KiB
Python
|
# -*- coding: utf-8 -*-
|
||
|
|
"""
|
||
|
|
**************
|
||
|
|
Adjacency List
|
||
|
|
**************
|
||
|
|
Read and write NetworkX graphs as adjacency lists.
|
||
|
|
|
||
|
|
Adjacency list format is useful for graphs without data associated
|
||
|
|
with nodes or edges and for nodes that can be meaningfully represented
|
||
|
|
as strings.
|
||
|
|
|
||
|
|
Format
|
||
|
|
------
|
||
|
|
The adjacency list format consists of lines with node labels. The
|
||
|
|
first label in a line is the source node. Further labels in the line
|
||
|
|
are considered target nodes and are added to the graph along with an edge
|
||
|
|
between the source node and target node.
|
||
|
|
|
||
|
|
The graph with edges a-b, a-c, d-e can be represented as the following
|
||
|
|
adjacency list (anything following the # in a line is a comment)::
|
||
|
|
|
||
|
|
a b c # source target target
|
||
|
|
d e
|
||
|
|
"""
|
||
|
|
__author__ = '\n'.join(['Aric Hagberg <hagberg@lanl.gov>',
|
||
|
|
'Dan Schult <dschult@colgate.edu>',
|
||
|
|
'Loïc Séguin-C. <loicseguin@gmail.com>'])
|
||
|
|
# Copyright (C) 2004-2019 by
|
||
|
|
# Aric Hagberg <hagberg@lanl.gov>
|
||
|
|
# Dan Schult <dschult@colgate.edu>
|
||
|
|
# Pieter Swart <swart@lanl.gov>
|
||
|
|
# All rights reserved.
|
||
|
|
# BSD license.
|
||
|
|
|
||
|
|
__all__ = ['generate_adjlist',
|
||
|
|
'write_adjlist',
|
||
|
|
'parse_adjlist',
|
||
|
|
'read_adjlist']
|
||
|
|
|
||
|
|
from networkx.utils import make_str, open_file
|
||
|
|
import networkx as nx
|
||
|
|
|
||
|
|
|
||
|
|
def generate_adjlist(G, delimiter=' '):
|
||
|
|
"""Generate a single line of the graph G in adjacency list format.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
G : NetworkX graph
|
||
|
|
|
||
|
|
delimiter : string, optional
|
||
|
|
Separator for node labels
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
lines : string
|
||
|
|
Lines of data in adjlist format.
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> G = nx.lollipop_graph(4, 3)
|
||
|
|
>>> for line in nx.generate_adjlist(G):
|
||
|
|
... print(line)
|
||
|
|
0 1 2 3
|
||
|
|
1 2 3
|
||
|
|
2 3
|
||
|
|
3 4
|
||
|
|
4 5
|
||
|
|
5 6
|
||
|
|
6
|
||
|
|
|
||
|
|
See Also
|
||
|
|
--------
|
||
|
|
write_adjlist, read_adjlist
|
||
|
|
|
||
|
|
"""
|
||
|
|
directed = G.is_directed()
|
||
|
|
seen = set()
|
||
|
|
for s, nbrs in G.adjacency():
|
||
|
|
line = make_str(s) + delimiter
|
||
|
|
for t, data in nbrs.items():
|
||
|
|
if not directed and t in seen:
|
||
|
|
continue
|
||
|
|
if G.is_multigraph():
|
||
|
|
for d in data.values():
|
||
|
|
line += make_str(t) + delimiter
|
||
|
|
else:
|
||
|
|
line += make_str(t) + delimiter
|
||
|
|
if not directed:
|
||
|
|
seen.add(s)
|
||
|
|
yield line[:-len(delimiter)]
|
||
|
|
|
||
|
|
|
||
|
|
@open_file(1, mode='wb')
|
||
|
|
def write_adjlist(G, path, comments="#", delimiter=' ', encoding='utf-8'):
|
||
|
|
"""Write graph G in single-line adjacency-list format to path.
|
||
|
|
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
G : NetworkX graph
|
||
|
|
|
||
|
|
path : string or file
|
||
|
|
Filename or file handle for data output.
|
||
|
|
Filenames ending in .gz or .bz2 will be compressed.
|
||
|
|
|
||
|
|
comments : string, optional
|
||
|
|
Marker for comment lines
|
||
|
|
|
||
|
|
delimiter : string, optional
|
||
|
|
Separator for node labels
|
||
|
|
|
||
|
|
encoding : string, optional
|
||
|
|
Text encoding.
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> G=nx.path_graph(4)
|
||
|
|
>>> nx.write_adjlist(G,"test.adjlist")
|
||
|
|
|
||
|
|
The path can be a filehandle or a string with the name of the file. If a
|
||
|
|
filehandle is provided, it has to be opened in 'wb' mode.
|
||
|
|
|
||
|
|
>>> fh=open("test.adjlist",'wb')
|
||
|
|
>>> nx.write_adjlist(G, fh)
|
||
|
|
|
||
|
|
Notes
|
||
|
|
-----
|
||
|
|
This format does not store graph, node, or edge data.
|
||
|
|
|
||
|
|
See Also
|
||
|
|
--------
|
||
|
|
read_adjlist, generate_adjlist
|
||
|
|
"""
|
||
|
|
import sys
|
||
|
|
import time
|
||
|
|
pargs = comments + " ".join(sys.argv) + '\n'
|
||
|
|
header = (pargs
|
||
|
|
+ comments + " GMT {}\n".format(time.asctime(time.gmtime()))
|
||
|
|
+ comments + " {}\n".format(G.name))
|
||
|
|
path.write(header.encode(encoding))
|
||
|
|
|
||
|
|
for line in generate_adjlist(G, delimiter):
|
||
|
|
line += '\n'
|
||
|
|
path.write(line.encode(encoding))
|
||
|
|
|
||
|
|
|
||
|
|
def parse_adjlist(lines, comments='#', delimiter=None,
|
||
|
|
create_using=None, nodetype=None):
|
||
|
|
"""Parse lines of a graph adjacency list representation.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
lines : list or iterator of strings
|
||
|
|
Input data in adjlist format
|
||
|
|
|
||
|
|
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
||
|
|
Graph type to create. If graph instance, then cleared before populated.
|
||
|
|
|
||
|
|
nodetype : Python type, optional
|
||
|
|
Convert nodes to this type.
|
||
|
|
|
||
|
|
comments : string, optional
|
||
|
|
Marker for comment lines
|
||
|
|
|
||
|
|
delimiter : string, optional
|
||
|
|
Separator for node labels. The default is whitespace.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
G: NetworkX graph
|
||
|
|
The graph corresponding to the lines in adjacency list format.
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> lines = ['1 2 5',
|
||
|
|
... '2 3 4',
|
||
|
|
... '3 5',
|
||
|
|
... '4',
|
||
|
|
... '5']
|
||
|
|
>>> G = nx.parse_adjlist(lines, nodetype=int)
|
||
|
|
>>> nodes = [1, 2, 3, 4, 5]
|
||
|
|
>>> all(node in G for node in nodes)
|
||
|
|
True
|
||
|
|
>>> edges = [(1, 2), (1, 5), (2, 3), (2, 4), (3, 5)]
|
||
|
|
>>> all((u, v) in G.edges() or (v, u) in G.edges() for (u, v) in edges)
|
||
|
|
True
|
||
|
|
|
||
|
|
See Also
|
||
|
|
--------
|
||
|
|
read_adjlist
|
||
|
|
|
||
|
|
"""
|
||
|
|
G = nx.empty_graph(0, create_using)
|
||
|
|
for line in lines:
|
||
|
|
p = line.find(comments)
|
||
|
|
if p >= 0:
|
||
|
|
line = line[:p]
|
||
|
|
if not len(line):
|
||
|
|
continue
|
||
|
|
vlist = line.strip().split(delimiter)
|
||
|
|
u = vlist.pop(0)
|
||
|
|
# convert types
|
||
|
|
if nodetype is not None:
|
||
|
|
try:
|
||
|
|
u = nodetype(u)
|
||
|
|
except:
|
||
|
|
raise TypeError("Failed to convert node ({}) to type {}"
|
||
|
|
.format(u, nodetype))
|
||
|
|
G.add_node(u)
|
||
|
|
if nodetype is not None:
|
||
|
|
try:
|
||
|
|
vlist = map(nodetype, vlist)
|
||
|
|
except:
|
||
|
|
raise TypeError("Failed to convert nodes ({}) to type {}"
|
||
|
|
.format(','.join(vlist), nodetype))
|
||
|
|
G.add_edges_from([(u, v) for v in vlist])
|
||
|
|
return G
|
||
|
|
|
||
|
|
|
||
|
|
@open_file(0, mode='rb')
|
||
|
|
def read_adjlist(path, comments="#", delimiter=None, create_using=None,
|
||
|
|
nodetype=None, encoding='utf-8'):
|
||
|
|
"""Read graph in adjacency list format from path.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
path : string or file
|
||
|
|
Filename or file handle to read.
|
||
|
|
Filenames ending in .gz or .bz2 will be uncompressed.
|
||
|
|
|
||
|
|
create_using : NetworkX graph constructor, optional (default=nx.Graph)
|
||
|
|
Graph type to create. If graph instance, then cleared before populated.
|
||
|
|
|
||
|
|
nodetype : Python type, optional
|
||
|
|
Convert nodes to this type.
|
||
|
|
|
||
|
|
comments : string, optional
|
||
|
|
Marker for comment lines
|
||
|
|
|
||
|
|
delimiter : string, optional
|
||
|
|
Separator for node labels. The default is whitespace.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
G: NetworkX graph
|
||
|
|
The graph corresponding to the lines in adjacency list format.
|
||
|
|
|
||
|
|
Examples
|
||
|
|
--------
|
||
|
|
>>> G=nx.path_graph(4)
|
||
|
|
>>> nx.write_adjlist(G, "test.adjlist")
|
||
|
|
>>> G=nx.read_adjlist("test.adjlist")
|
||
|
|
|
||
|
|
The path can be a filehandle or a string with the name of the file. If a
|
||
|
|
filehandle is provided, it has to be opened in 'rb' mode.
|
||
|
|
|
||
|
|
>>> fh=open("test.adjlist", 'rb')
|
||
|
|
>>> G=nx.read_adjlist(fh)
|
||
|
|
|
||
|
|
Filenames ending in .gz or .bz2 will be compressed.
|
||
|
|
|
||
|
|
>>> nx.write_adjlist(G,"test.adjlist.gz")
|
||
|
|
>>> G=nx.read_adjlist("test.adjlist.gz")
|
||
|
|
|
||
|
|
The optional nodetype is a function to convert node strings to nodetype.
|
||
|
|
|
||
|
|
For example
|
||
|
|
|
||
|
|
>>> G=nx.read_adjlist("test.adjlist", nodetype=int)
|
||
|
|
|
||
|
|
will attempt to convert all nodes to integer type.
|
||
|
|
|
||
|
|
Since nodes must be hashable, the function nodetype must return hashable
|
||
|
|
types (e.g. int, float, str, frozenset - or tuples of those, etc.)
|
||
|
|
|
||
|
|
The optional create_using parameter indicates the type of NetworkX graph
|
||
|
|
created. The default is `nx.Graph`, an undirected graph.
|
||
|
|
To read the data as a directed graph use
|
||
|
|
|
||
|
|
>>> G=nx.read_adjlist("test.adjlist", create_using=nx.DiGraph)
|
||
|
|
|
||
|
|
Notes
|
||
|
|
-----
|
||
|
|
This format does not store graph or node data.
|
||
|
|
|
||
|
|
See Also
|
||
|
|
--------
|
||
|
|
write_adjlist
|
||
|
|
"""
|
||
|
|
lines = (line.decode(encoding) for line in path)
|
||
|
|
return parse_adjlist(lines,
|
||
|
|
comments=comments,
|
||
|
|
delimiter=delimiter,
|
||
|
|
create_using=create_using,
|
||
|
|
nodetype=nodetype)
|
||
|
|
|
||
|
|
|
||
|
|
# fixture for pytest
|
||
|
|
def teardown_module(module):
|
||
|
|
import os
|
||
|
|
for fname in ['test.adjlist', 'test.adjlist.gz']:
|
||
|
|
if os.path.isfile(fname):
|
||
|
|
os.unlink(fname)
|