Source code for networkx.readwrite.pajek

"""
*****
Pajek
*****
Read graphs in Pajek format.

This implementation handles directed and undirected graphs including
those with self loops and parallel edges.

Format
------
See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
for format information.

"""

import warnings

import networkx as nx
from networkx.utils import open_file

__all__ = ["read_pajek", "parse_pajek", "generate_pajek", "write_pajek"]


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