Source code for networkx.readwrite.sparse6

# Original author: D. Eppstein, UC Irvine, August 12, 2003.
# The original code at http://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: http://users.cecs.anu.edu.au/~bdm/data/formats.html

"""
import networkx as nx
from networkx.exception import NetworkXError
from networkx.utils import open_file, not_implemented_for
from networkx.readwrite.graph6 import data_to_n, n_to_data

__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"


[docs]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 <http://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
[docs]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 <http://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))
[docs]@open_file(0, mode="rb") 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() 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 <http://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
[docs]@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() 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 <http://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)