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This documents an unmaintained version of NetworkX. Please upgrade to a maintained version and see the current NetworkX documentation.

Source code for networkx.readwrite.pajek

#    Copyright (C) 2008-2014 by
#    Aric Hagberg <hagberg@lanl.gov>
#    Dan Schult <dschult@colgate.edu>
#    Pieter Swart <swart@lanl.gov>
#    All rights reserved.
#    BSD license.
#
# Authors: Aric Hagberg (hagberg@lanl.gov)
"""
*****
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 is_string_like, open_file, make_str

__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 '*vertices %s' % (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) id = int(na.pop('id', nodenumber[n])) 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 is_string_like(v) and v.strip() != '': s += ' %s %s' % (make_qstr(k), make_qstr(v)) else: warnings.warn('Node attribute %s is not processed. %s.' % (k, 'Empty attribute' if is_string_like(v) 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 is_string_like(v) and v.strip() != '': s += ' %s %s' % (make_qstr(k), make_qstr(v)) else: warnings.warn('Edge attribute %s is not processed. %s.' % (k, 'Empty attribute' if is_string_like(v) 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 is_string_like(lines): 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(make_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(make_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): """Return the string representation of t. Add outer double-quotes if the string has a space. """ if not is_string_like(t): t = str(t) if " " in t: t = r'"%s"' % t return t # fixture for nose tests def teardown_module(module): import os os.unlink('test.net')