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 Superseded by reCTBN.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