Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
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285 lines
8.4 KiB
285 lines
8.4 KiB
4 years ago
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"""
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*****
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Pajek
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*****
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Read graphs in Pajek format.
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This implementation handles directed and undirected graphs including
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those with self loops and parallel edges.
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Format
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------
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See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
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for format information.
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"""
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import warnings
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import networkx as nx
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from networkx.utils import open_file
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__all__ = ["read_pajek", "parse_pajek", "generate_pajek", "write_pajek"]
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def generate_pajek(G):
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"""Generate lines in Pajek graph format.
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Parameters
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----------
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G : graph
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A Networkx graph
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References
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----------
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See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
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for format information.
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"""
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if G.name == "":
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name = "NetworkX"
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else:
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name = G.name
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# Apparently many Pajek format readers can't process this line
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# So we'll leave it out for now.
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# yield '*network %s'%name
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# write nodes with attributes
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yield f"*vertices {G.order()}"
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nodes = list(G)
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# make dictionary mapping nodes to integers
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nodenumber = dict(zip(nodes, range(1, len(nodes) + 1)))
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for n in nodes:
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# copy node attributes and pop mandatory attributes
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# to avoid duplication.
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na = G.nodes.get(n, {}).copy()
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x = na.pop("x", 0.0)
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y = na.pop("y", 0.0)
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try:
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id = int(na.pop("id", nodenumber[n]))
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except ValueError as e:
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e.args += (
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(
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"Pajek format requires 'id' to be an int()."
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" Refer to the 'Relabeling nodes' section."
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),
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)
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raise
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nodenumber[n] = id
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shape = na.pop("shape", "ellipse")
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s = " ".join(map(make_qstr, (id, n, x, y, shape)))
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# only optional attributes are left in na.
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for k, v in na.items():
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if isinstance(v, str) and v.strip() != "":
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s += f" {make_qstr(k)} {make_qstr(v)}"
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else:
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warnings.warn(
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f"Node attribute {k} is not processed. {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}."
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)
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yield s
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# write edges with attributes
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if G.is_directed():
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yield "*arcs"
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else:
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yield "*edges"
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for u, v, edgedata in G.edges(data=True):
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d = edgedata.copy()
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value = d.pop("weight", 1.0) # use 1 as default edge value
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s = " ".join(map(make_qstr, (nodenumber[u], nodenumber[v], value)))
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for k, v in d.items():
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if isinstance(v, str) and v.strip() != "":
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s += f" {make_qstr(k)} {make_qstr(v)}"
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else:
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warnings.warn(
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f"Edge attribute {k} is not processed. {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}."
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)
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yield s
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@open_file(1, mode="wb")
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def write_pajek(G, path, encoding="UTF-8"):
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"""Write graph in Pajek format to path.
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Parameters
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----------
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G : graph
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A Networkx graph
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path : file or string
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File or filename to write.
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Filenames ending in .gz or .bz2 will be compressed.
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Examples
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--------
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>>> G = nx.path_graph(4)
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>>> nx.write_pajek(G, "test.net")
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Warnings
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--------
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Optional node attributes and edge attributes must be non-empty strings.
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Otherwise it will not be written into the file. You will need to
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convert those attributes to strings if you want to keep them.
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References
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----------
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See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
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for format information.
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"""
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for line in generate_pajek(G):
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line += "\n"
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path.write(line.encode(encoding))
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@open_file(0, mode="rb")
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def read_pajek(path, encoding="UTF-8"):
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"""Read graph in Pajek 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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Filenames ending in .gz or .bz2 will be uncompressed.
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Returns
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-------
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G : NetworkX MultiGraph or MultiDiGraph.
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Examples
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--------
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>>> G = nx.path_graph(4)
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>>> nx.write_pajek(G, "test.net")
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>>> G = nx.read_pajek("test.net")
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To create a Graph instead of a MultiGraph use
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>>> G1 = nx.Graph(G)
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References
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----------
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See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
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for format information.
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"""
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lines = (line.decode(encoding) for line in path)
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return parse_pajek(lines)
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def parse_pajek(lines):
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"""Parse Pajek format graph from string or iterable.
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Parameters
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----------
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lines : string or iterable
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Data in Pajek format.
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Returns
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-------
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G : NetworkX graph
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See Also
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--------
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read_pajek()
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"""
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import shlex
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# multigraph=False
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if isinstance(lines, str):
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lines = iter(lines.split("\n"))
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lines = iter([line.rstrip("\n") for line in lines])
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G = nx.MultiDiGraph() # are multiedges allowed in Pajek? assume yes
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labels = [] # in the order of the file, needed for matrix
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while lines:
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try:
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l = next(lines)
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except: # EOF
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break
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if l.lower().startswith("*network"):
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try:
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label, name = l.split(None, 1)
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except ValueError:
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# Line was not of the form: *network NAME
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pass
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else:
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G.graph["name"] = name
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elif l.lower().startswith("*vertices"):
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nodelabels = {}
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l, nnodes = l.split()
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for i in range(int(nnodes)):
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l = next(lines)
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try:
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splitline = [
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x.decode("utf-8") for x in shlex.split(str(l).encode("utf-8"))
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]
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except AttributeError:
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splitline = shlex.split(str(l))
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id, label = splitline[0:2]
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labels.append(label)
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G.add_node(label)
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nodelabels[id] = label
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G.nodes[label]["id"] = id
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try:
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x, y, shape = splitline[2:5]
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G.nodes[label].update(
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{"x": float(x), "y": float(y), "shape": shape}
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)
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except:
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pass
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extra_attr = zip(splitline[5::2], splitline[6::2])
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G.nodes[label].update(extra_attr)
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elif l.lower().startswith("*edges") or l.lower().startswith("*arcs"):
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if l.lower().startswith("*edge"):
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# switch from multidigraph to multigraph
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G = nx.MultiGraph(G)
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if l.lower().startswith("*arcs"):
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# switch to directed with multiple arcs for each existing edge
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G = G.to_directed()
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for l in lines:
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try:
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splitline = [
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x.decode("utf-8") for x in shlex.split(str(l).encode("utf-8"))
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]
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except AttributeError:
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splitline = shlex.split(str(l))
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if len(splitline) < 2:
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continue
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ui, vi = splitline[0:2]
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u = nodelabels.get(ui, ui)
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v = nodelabels.get(vi, vi)
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# parse the data attached to this edge and put in a dictionary
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edge_data = {}
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try:
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# there should always be a single value on the edge?
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w = splitline[2:3]
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edge_data.update({"weight": float(w[0])})
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except:
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pass
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# if there isn't, just assign a 1
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# edge_data.update({'value':1})
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extra_attr = zip(splitline[3::2], splitline[4::2])
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edge_data.update(extra_attr)
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# if G.has_edge(u,v):
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# multigraph=True
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G.add_edge(u, v, **edge_data)
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elif l.lower().startswith("*matrix"):
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G = nx.DiGraph(G)
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adj_list = (
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(labels[row], labels[col], {"weight": int(data)})
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for (row, line) in enumerate(lines)
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for (col, data) in enumerate(line.split())
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if int(data) != 0
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)
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G.add_edges_from(adj_list)
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return G
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def make_qstr(t):
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"""Returns the string representation of t.
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Add outer double-quotes if the string has a space.
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"""
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if not isinstance(t, str):
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t = str(t)
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if " " in t:
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t = f'"{t}"'
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return t
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