Proper working implementation of a cycle detection algorithm, that
returns the cycles (rather than printing them) by constructing the
path between the two nodes that were found to be cyclic.
Patch by: Sverre Rabbelier
# Copyright (c) 2007-2008 Pedro Matiello <pmatiello@gmail.com>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation
# files (the "Software"), to deal in the Software without
# restriction, including without limitation the rights to use,
# copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following
# conditions:
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
# HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
# OTHER DEALINGS IN THE SOFTWARE.
"""
Functions for reading and writing graphs.
@sort: read_xml, write_xml, write_dot_graph, write_dot_digraph, write_dot_hypergraph
"""
# Imports
from xml.dom.minidom import Document, parseString
# Values
colors = ['aquamarine4', 'blue4', 'brown4', 'cornflowerblue', 'cyan4',
'darkgreen', 'darkorange3', 'darkorchid4', 'darkseagreen4', 'darkslategray',
'deeppink4', 'deepskyblue4', 'firebrick3', 'hotpink3', 'indianred3',
'indigo', 'lightblue4', 'lightseagreen', 'lightskyblue4', 'magenta4',
'maroon', 'palevioletred3', 'steelblue', 'violetred3']
# XML
def write_xml(graph):
"""
Return a string specifying the given graph as a XML document.
@type graph: graph
@param graph: Graph.
@rtype: string
@return: String specifying the graph as a XML document.
"""
# Document root
grxml = Document()
grxmlr = grxml.createElement('graph')
grxml.appendChild(grxmlr)
# Each node...
for each_node in graph.nodes():
node = grxml.createElement('node')
node.setAttribute('id',str(each_node))
grxmlr.appendChild(node)
for each_attr in graph.get_node_attributes(each_node):
attr = grxml.createElement('attribute')
attr.setAttribute('attr', each_attr[0])
attr.setAttribute('value', each_attr[1])
node.appendChild(attr)
# Each edge...
for edge_from, edge_to in graph.edges():
edge = grxml.createElement('edge')
edge.setAttribute('from',str(edge_from))
edge.setAttribute('to',str(edge_to))
edge.setAttribute('wt',str(graph.get_edge_weight(edge_from, edge_to)))
edge.setAttribute('label',str(graph.get_edge_label(edge_from, edge_to)))
grxmlr.appendChild(edge)
for attr_name, attr_value in graph.get_edge_attributes(edge_from, edge_to):
attr = grxml.createElement('attribute')
attr.setAttribute('attr', attr_name)
attr.setAttribute('value', attr_value)
edge.appendChild(attr)
return grxml.toprettyxml()
def write_xml_hypergraph(hypergraph):
"""
Return a string specifying the given hypergraph as a XML document.
@type hypergraph: hypergraph
@param hypergraph: Hypergraph.
@rtype: string
@return: String specifying the graph as a XML document.
"""
# Document root
grxml = Document()
grxmlr = grxml.createElement('hypergraph')
grxml.appendChild(grxmlr)
# Each node...
nodes = hypergraph.nodes()
hyperedges = hypergraph.get_hyperedges()
for each_node in (nodes + hyperedges):
if (each_node in nodes):
node = grxml.createElement('node')
else:
node = grxml.createElement('hyperedge')
node.setAttribute('id',str(each_node))
grxmlr.appendChild(node)
# and its outgoing edge
for each_edge in hypergraph.get_links(each_node):
edge = grxml.createElement('link')
edge.setAttribute('to',str(each_edge))
node.appendChild(edge)
return grxml.toprettyxml()
def read_xml(graph, string):
"""
Read a graph from a XML document. Nodes and edges specified in the input will be added to the current graph.
@type graph: graph
@param graph: Graph
@type string: string
@param string: Input string in XML format specifying a graph.
"""
dom = parseString(string)
# Read nodes...
for each_node in dom.getElementsByTagName("node"):
graph.add_node(each_node.getAttribute('id'))
for each_attr in each_node.getElementsByTagName("attribute"):
graph.add_node_attribute(each_node.getAttribute('id'), (each_attr.getAttribute('attr'),
each_attr.getAttribute('value')))
# Read edges...
for each_edge in dom.getElementsByTagName("edge"):
graph.add_edge(each_edge.getAttribute('from'), each_edge.getAttribute('to'), \
wt=float(each_edge.getAttribute('wt')), label=each_edge.getAttribute('label'))
for each_attr in each_edge.getElementsByTagName("attribute"):
attr_tuple = (each_attr.getAttribute('attr'), each_attr.getAttribute('value'))
if (attr_tuple not in graph.get_edge_attributes(each_edge.getAttribute('from'), \
each_edge.getAttribute('to'))):
graph.add_edge_attribute(each_edge.getAttribute('from'), \
each_edge.getAttribute('to'), attr_tuple)
def read_xml_hypergraph(hypergraph, string):
"""
Read a graph from a XML document. Nodes and hyperedges specified in the input will be added to the current graph.
@type hypergraph: hypergraph
@param hypergraph: Hypergraph
@type string: string
@param string: Input string in XML format specifying a graph.
"""
dom = parseString(string)
for each_node in dom.getElementsByTagName("node"):
hypergraph.add_nodes(each_node.getAttribute('id'))
for each_node in dom.getElementsByTagName("hyperedge"):
hypergraph.add_hyperedges(each_node.getAttribute('id'))
dom = parseString(string)
for each_node in dom.getElementsByTagName("node"):
for each_edge in each_node.getElementsByTagName("link"):
hypergraph.link(each_node.getAttribute('id'), each_edge.getAttribute('to'))
# DOT Language
def _dot_node_str(graph, node, wt):
line = '\t"%s" [ ' % str(node)
attrlist = graph.get_node_attributes(node)
for each in attrlist:
attr = '%s="%s" ' % (each[0], each[1])
line = line + attr
line = line + ']\n'
return line
def _dot_edge_str(graph, u, v, wt):
line = '\t"%s" -- "%s" [ ' % (str(u), str(v))
attrlist = graph.get_edge_attributes(u, v) + [('label',graph.get_edge_label(u, v))]
for each in attrlist:
attr = '%s="%s" ' % (each[0], each[1])
line = line + attr
line = line + ']\n'
return line
def _dot_arrow_str(graph, u, v, wt):
line = '\t"%s" -> "%s" [ ' % (str(u), str(v))
attrlist = graph.get_edge_attributes(u, v) + [('label',graph.get_edge_label(u, v))]
for each in attrlist:
attr = '%s="%s" ' % (each[0], each[1])
line = line + attr
line = line + ']\n'
return line
def write_dot_graph(graph, wt):
"""
Return a string specifying the given graph in DOT Language.
@type graph: graph
@param graph: Graph.
@type wt: boolean
@param wt: Whether edges should be labelled with its weight.
@rtype: string
@return: String specifying the graph in DOT Language.
"""
doc = 'graph graphname \n{\n'
for node in graph:
doc = doc + _dot_node_str(graph, node, wt)
for edge in graph[node]:
if (node >= edge):
doc = doc + _dot_edge_str(graph, node, edge, wt)
doc = doc + '}'
return doc
def write_dot_digraph(graph, wt):
"""
Return a string specifying the given digraph in DOT Language.
@type graph: graph
@param graph: Graph.
@type wt: boolean
@param wt: Whether arrows should be labelled with its weight.
@rtype: string
@return: String specifying the graph in DOT Language.
"""
doc = 'digraph graphname \n{\n'
for node in graph:
doc = doc + _dot_node_str(graph, node, wt)
for edge in graph[node]:
doc = doc + _dot_arrow_str(graph, node, edge, wt)
doc = doc + '}'
return doc
def write_dot_hypergraph(hypergraph, coloured=False):
"""
Return a string specifying the given hypergraph in DOT Language.
@type hypergraph: hypergraph
@param hypergraph: Hypergraph.
@type coloured: boolean
@param coloured: Whether hyperedges should be coloured.
@rtype: string
@return: String specifying the hypergraph in DOT Language.
"""
# Start document
doc = ""
doc = doc + "graph graphname" + "\n{\n"
colortable = {}
colorcount = 0
# Add hyperedges
color = ''
for each_hyperedge in hypergraph.hyperedges():
colortable[each_hyperedge] = colors[colorcount % len(colors)]
colorcount = colorcount + 1
if (coloured):
color = " color=%s" % colortable[each_hyperedge]
vars = {
'hyperedge' : str(each_hyperedge),
'color' : color
}
doc = doc + '\t"%(hyperedge)s" [shape=point %(color)s]\n' % vars
color = "\n"
# Add nodes and links
for each_node in hypergraph.nodes():
doc = doc + "\t\"%s\"\n" % str(each_node)
for each_link in hypergraph.links(each_node):
if (coloured):
color = " [color=%s]\n" % colortable[each_link]
linkvars = {
'node' : str(each_node),
'hyperedge' : str(each_link)
}
doc = doc + '\t %(node)s -- %(hyperedge)s' % linkvars + color
doc = doc + "}"
return doc