377 lines
10 KiB
Python
377 lines
10 KiB
Python
# Original author: D. Eppstein, UC Irvine, August 12, 2003.
|
|
# The original code at https://www.ics.uci.edu/~eppstein/PADS/ is public domain.
|
|
"""Functions for reading and writing graphs in the *sparse6* format.
|
|
|
|
The *sparse6* file format is a space-efficient format for large sparse
|
|
graphs. For small graphs or large dense graphs, use the *graph6* file
|
|
format.
|
|
|
|
For more information, see the `sparse6`_ homepage.
|
|
|
|
.. _sparse6: https://users.cecs.anu.edu.au/~bdm/data/formats.html
|
|
|
|
"""
|
|
import networkx as nx
|
|
from networkx.exception import NetworkXError
|
|
from networkx.readwrite.graph6 import data_to_n, n_to_data
|
|
from networkx.utils import not_implemented_for, open_file
|
|
|
|
__all__ = ["from_sparse6_bytes", "read_sparse6", "to_sparse6_bytes", "write_sparse6"]
|
|
|
|
|
|
def _generate_sparse6_bytes(G, nodes, header):
|
|
"""Yield bytes in the sparse6 encoding of a graph.
|
|
|
|
`G` is an undirected simple graph. `nodes` is the list of nodes for
|
|
which the node-induced subgraph will be encoded; if `nodes` is the
|
|
list of all nodes in the graph, the entire graph will be
|
|
encoded. `header` is a Boolean that specifies whether to generate
|
|
the header ``b'>>sparse6<<'`` before the remaining data.
|
|
|
|
This function generates `bytes` objects in the following order:
|
|
|
|
1. the header (if requested),
|
|
2. the encoding of the number of nodes,
|
|
3. each character, one-at-a-time, in the encoding of the requested
|
|
node-induced subgraph,
|
|
4. a newline character.
|
|
|
|
This function raises :exc:`ValueError` if the graph is too large for
|
|
the graph6 format (that is, greater than ``2 ** 36`` nodes).
|
|
|
|
"""
|
|
n = len(G)
|
|
if n >= 2**36:
|
|
raise ValueError(
|
|
"sparse6 is only defined if number of nodes is less than 2 ** 36"
|
|
)
|
|
if header:
|
|
yield b">>sparse6<<"
|
|
yield b":"
|
|
for d in n_to_data(n):
|
|
yield str.encode(chr(d + 63))
|
|
|
|
k = 1
|
|
while 1 << k < n:
|
|
k += 1
|
|
|
|
def enc(x):
|
|
"""Big endian k-bit encoding of x"""
|
|
return [1 if (x & 1 << (k - 1 - i)) else 0 for i in range(k)]
|
|
|
|
edges = sorted((max(u, v), min(u, v)) for u, v in G.edges())
|
|
bits = []
|
|
curv = 0
|
|
for v, u in edges:
|
|
if v == curv: # current vertex edge
|
|
bits.append(0)
|
|
bits.extend(enc(u))
|
|
elif v == curv + 1: # next vertex edge
|
|
curv += 1
|
|
bits.append(1)
|
|
bits.extend(enc(u))
|
|
else: # skip to vertex v and then add edge to u
|
|
curv = v
|
|
bits.append(1)
|
|
bits.extend(enc(v))
|
|
bits.append(0)
|
|
bits.extend(enc(u))
|
|
if k < 6 and n == (1 << k) and ((-len(bits)) % 6) >= k and curv < (n - 1):
|
|
# Padding special case: small k, n=2^k,
|
|
# more than k bits of padding needed,
|
|
# current vertex is not (n-1) --
|
|
# appending 1111... would add a loop on (n-1)
|
|
bits.append(0)
|
|
bits.extend([1] * ((-len(bits)) % 6))
|
|
else:
|
|
bits.extend([1] * ((-len(bits)) % 6))
|
|
|
|
data = [
|
|
(bits[i + 0] << 5)
|
|
+ (bits[i + 1] << 4)
|
|
+ (bits[i + 2] << 3)
|
|
+ (bits[i + 3] << 2)
|
|
+ (bits[i + 4] << 1)
|
|
+ (bits[i + 5] << 0)
|
|
for i in range(0, len(bits), 6)
|
|
]
|
|
|
|
for d in data:
|
|
yield str.encode(chr(d + 63))
|
|
yield b"\n"
|
|
|
|
|
|
@nx._dispatchable(graphs=None, returns_graph=True)
|
|
def from_sparse6_bytes(string):
|
|
"""Read an undirected graph in sparse6 format from string.
|
|
|
|
Parameters
|
|
----------
|
|
string : string
|
|
Data in sparse6 format
|
|
|
|
Returns
|
|
-------
|
|
G : Graph
|
|
|
|
Raises
|
|
------
|
|
NetworkXError
|
|
If the string is unable to be parsed in sparse6 format
|
|
|
|
Examples
|
|
--------
|
|
>>> G = nx.from_sparse6_bytes(b":A_")
|
|
>>> sorted(G.edges())
|
|
[(0, 1), (0, 1), (0, 1)]
|
|
|
|
See Also
|
|
--------
|
|
read_sparse6, write_sparse6
|
|
|
|
References
|
|
----------
|
|
.. [1] Sparse6 specification
|
|
<https://users.cecs.anu.edu.au/~bdm/data/formats.html>
|
|
|
|
"""
|
|
if string.startswith(b">>sparse6<<"):
|
|
string = string[11:]
|
|
if not string.startswith(b":"):
|
|
raise NetworkXError("Expected leading colon in sparse6")
|
|
|
|
chars = [c - 63 for c in string[1:]]
|
|
n, data = data_to_n(chars)
|
|
k = 1
|
|
while 1 << k < n:
|
|
k += 1
|
|
|
|
def parseData():
|
|
"""Returns stream of pairs b[i], x[i] for sparse6 format."""
|
|
chunks = iter(data)
|
|
d = None # partial data word
|
|
dLen = 0 # how many unparsed bits are left in d
|
|
|
|
while 1:
|
|
if dLen < 1:
|
|
try:
|
|
d = next(chunks)
|
|
except StopIteration:
|
|
return
|
|
dLen = 6
|
|
dLen -= 1
|
|
b = (d >> dLen) & 1 # grab top remaining bit
|
|
|
|
x = d & ((1 << dLen) - 1) # partially built up value of x
|
|
xLen = dLen # how many bits included so far in x
|
|
while xLen < k: # now grab full chunks until we have enough
|
|
try:
|
|
d = next(chunks)
|
|
except StopIteration:
|
|
return
|
|
dLen = 6
|
|
x = (x << 6) + d
|
|
xLen += 6
|
|
x = x >> (xLen - k) # shift back the extra bits
|
|
dLen = xLen - k
|
|
yield b, x
|
|
|
|
v = 0
|
|
|
|
G = nx.MultiGraph()
|
|
G.add_nodes_from(range(n))
|
|
|
|
multigraph = False
|
|
for b, x in parseData():
|
|
if b == 1:
|
|
v += 1
|
|
# padding with ones can cause overlarge number here
|
|
if x >= n or v >= n:
|
|
break
|
|
elif x > v:
|
|
v = x
|
|
else:
|
|
if G.has_edge(x, v):
|
|
multigraph = True
|
|
G.add_edge(x, v)
|
|
if not multigraph:
|
|
G = nx.Graph(G)
|
|
return G
|
|
|
|
|
|
def to_sparse6_bytes(G, nodes=None, header=True):
|
|
"""Convert an undirected graph to bytes in sparse6 format.
|
|
|
|
Parameters
|
|
----------
|
|
G : Graph (undirected)
|
|
|
|
nodes: list or iterable
|
|
Nodes are labeled 0...n-1 in the order provided. If None the ordering
|
|
given by ``G.nodes()`` is used.
|
|
|
|
header: bool
|
|
If True add '>>sparse6<<' bytes to head of data.
|
|
|
|
Raises
|
|
------
|
|
NetworkXNotImplemented
|
|
If the graph is directed.
|
|
|
|
ValueError
|
|
If the graph has at least ``2 ** 36`` nodes; the sparse6 format
|
|
is only defined for graphs of order less than ``2 ** 36``.
|
|
|
|
Examples
|
|
--------
|
|
>>> nx.to_sparse6_bytes(nx.path_graph(2))
|
|
b'>>sparse6<<:An\\n'
|
|
|
|
See Also
|
|
--------
|
|
to_sparse6_bytes, read_sparse6, write_sparse6_bytes
|
|
|
|
Notes
|
|
-----
|
|
The returned bytes end with a newline character.
|
|
|
|
The format does not support edge or node labels.
|
|
|
|
References
|
|
----------
|
|
.. [1] Graph6 specification
|
|
<https://users.cecs.anu.edu.au/~bdm/data/formats.html>
|
|
|
|
"""
|
|
if nodes is not None:
|
|
G = G.subgraph(nodes)
|
|
G = nx.convert_node_labels_to_integers(G, ordering="sorted")
|
|
return b"".join(_generate_sparse6_bytes(G, nodes, header))
|
|
|
|
|
|
@open_file(0, mode="rb")
|
|
@nx._dispatchable(graphs=None, returns_graph=True)
|
|
def read_sparse6(path):
|
|
"""Read an undirected graph in sparse6 format from path.
|
|
|
|
Parameters
|
|
----------
|
|
path : file or string
|
|
File or filename to write.
|
|
|
|
Returns
|
|
-------
|
|
G : Graph/Multigraph or list of Graphs/MultiGraphs
|
|
If the file contains multiple lines then a list of graphs is returned
|
|
|
|
Raises
|
|
------
|
|
NetworkXError
|
|
If the string is unable to be parsed in sparse6 format
|
|
|
|
Examples
|
|
--------
|
|
You can read a sparse6 file by giving the path to the file::
|
|
|
|
>>> import tempfile
|
|
>>> with tempfile.NamedTemporaryFile(delete=False) as f:
|
|
... _ = f.write(b">>sparse6<<:An\\n")
|
|
... _ = f.seek(0)
|
|
... G = nx.read_sparse6(f.name)
|
|
>>> list(G.edges())
|
|
[(0, 1)]
|
|
|
|
You can also read a sparse6 file by giving an open file-like object::
|
|
|
|
>>> import tempfile
|
|
>>> with tempfile.NamedTemporaryFile() as f:
|
|
... _ = f.write(b">>sparse6<<:An\\n")
|
|
... _ = f.seek(0)
|
|
... G = nx.read_sparse6(f)
|
|
>>> list(G.edges())
|
|
[(0, 1)]
|
|
|
|
See Also
|
|
--------
|
|
read_sparse6, from_sparse6_bytes
|
|
|
|
References
|
|
----------
|
|
.. [1] Sparse6 specification
|
|
<https://users.cecs.anu.edu.au/~bdm/data/formats.html>
|
|
|
|
"""
|
|
glist = []
|
|
for line in path:
|
|
line = line.strip()
|
|
if not len(line):
|
|
continue
|
|
glist.append(from_sparse6_bytes(line))
|
|
if len(glist) == 1:
|
|
return glist[0]
|
|
else:
|
|
return glist
|
|
|
|
|
|
@not_implemented_for("directed")
|
|
@open_file(1, mode="wb")
|
|
def write_sparse6(G, path, nodes=None, header=True):
|
|
"""Write graph G to given path in sparse6 format.
|
|
|
|
Parameters
|
|
----------
|
|
G : Graph (undirected)
|
|
|
|
path : file or string
|
|
File or filename to write
|
|
|
|
nodes: list or iterable
|
|
Nodes are labeled 0...n-1 in the order provided. If None the ordering
|
|
given by G.nodes() is used.
|
|
|
|
header: bool
|
|
If True add '>>sparse6<<' string to head of data
|
|
|
|
Raises
|
|
------
|
|
NetworkXError
|
|
If the graph is directed
|
|
|
|
Examples
|
|
--------
|
|
You can write a sparse6 file by giving the path to the file::
|
|
|
|
>>> import tempfile
|
|
>>> with tempfile.NamedTemporaryFile(delete=False) as f:
|
|
... nx.write_sparse6(nx.path_graph(2), f.name)
|
|
... print(f.read())
|
|
b'>>sparse6<<:An\\n'
|
|
|
|
You can also write a sparse6 file by giving an open file-like object::
|
|
|
|
>>> with tempfile.NamedTemporaryFile() as f:
|
|
... nx.write_sparse6(nx.path_graph(2), f)
|
|
... _ = f.seek(0)
|
|
... print(f.read())
|
|
b'>>sparse6<<:An\\n'
|
|
|
|
See Also
|
|
--------
|
|
read_sparse6, from_sparse6_bytes
|
|
|
|
Notes
|
|
-----
|
|
The format does not support edge or node labels.
|
|
|
|
References
|
|
----------
|
|
.. [1] Sparse6 specification
|
|
<https://users.cecs.anu.edu.au/~bdm/data/formats.html>
|
|
|
|
"""
|
|
if nodes is not None:
|
|
G = G.subgraph(nodes)
|
|
G = nx.convert_node_labels_to_integers(G, ordering="sorted")
|
|
for b in _generate_sparse6_bytes(G, nodes, header):
|
|
path.write(b)
|