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annotate planemo/lib/python3.7/site-packages/networkx/drawing/nx_agraph.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1 # Copyright (C) 2004-2019 by
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2 # Aric Hagberg <hagberg@lanl.gov>
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3 # Dan Schult <dschult@colgate.edu>
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4 # Pieter Swart <swart@lanl.gov>
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5 # All rights reserved.
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6 # BSD license.
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7 #
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8 # Author: Aric Hagberg (hagberg@lanl.gov)
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9 """
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10 ***************
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11 Graphviz AGraph
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12 ***************
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13
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14 Interface to pygraphviz AGraph class.
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15
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16 Examples
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17 --------
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18 >>> G = nx.complete_graph(5)
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19 >>> A = nx.nx_agraph.to_agraph(G)
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20 >>> H = nx.nx_agraph.from_agraph(A)
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21
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22 See Also
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23 --------
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24 Pygraphviz: http://pygraphviz.github.io/
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25 """
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26 import os
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27 import tempfile
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28 import networkx as nx
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29
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30 __all__ = ['from_agraph', 'to_agraph',
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31 'write_dot', 'read_dot',
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32 'graphviz_layout',
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33 'pygraphviz_layout',
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34 'view_pygraphviz']
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35
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36
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37 def from_agraph(A, create_using=None):
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38 """Returns a NetworkX Graph or DiGraph from a PyGraphviz graph.
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39
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40 Parameters
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41 ----------
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42 A : PyGraphviz AGraph
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43 A graph created with PyGraphviz
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44
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45 create_using : NetworkX graph constructor, optional (default=nx.Graph)
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46 Graph type to create. If graph instance, then cleared before populated.
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47
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48 Examples
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49 --------
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50 >>> K5 = nx.complete_graph(5)
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51 >>> A = nx.nx_agraph.to_agraph(K5)
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52 >>> G = nx.nx_agraph.from_agraph(A)
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53
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54 Notes
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55 -----
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56 The Graph G will have a dictionary G.graph_attr containing
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57 the default graphviz attributes for graphs, nodes and edges.
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58
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59 Default node attributes will be in the dictionary G.node_attr
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60 which is keyed by node.
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61
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62 Edge attributes will be returned as edge data in G. With
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63 edge_attr=False the edge data will be the Graphviz edge weight
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64 attribute or the value 1 if no edge weight attribute is found.
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65
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66 """
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67 if create_using is None:
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68 if A.is_directed():
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69 if A.is_strict():
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70 create_using = nx.DiGraph
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71 else:
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72 create_using = nx.MultiDiGraph
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73 else:
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74 if A.is_strict():
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75 create_using = nx.Graph
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76 else:
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77 create_using = nx.MultiGraph
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78
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79 # assign defaults
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80 N = nx.empty_graph(0, create_using)
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81 if A.name is not None:
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82 N.name = A.name
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83
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84 # add graph attributes
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85 N.graph.update(A.graph_attr)
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86
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87 # add nodes, attributes to N.node_attr
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88 for n in A.nodes():
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89 str_attr = {str(k): v for k, v in n.attr.items()}
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90 N.add_node(str(n), **str_attr)
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91
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92 # add edges, assign edge data as dictionary of attributes
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93 for e in A.edges():
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94 u, v = str(e[0]), str(e[1])
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95 attr = dict(e.attr)
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96 str_attr = {str(k): v for k, v in attr.items()}
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97 if not N.is_multigraph():
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98 if e.name is not None:
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99 str_attr['key'] = e.name
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100 N.add_edge(u, v, **str_attr)
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101 else:
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102 N.add_edge(u, v, key=e.name, **str_attr)
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103
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104 # add default attributes for graph, nodes, and edges
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105 # hang them on N.graph_attr
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106 N.graph['graph'] = dict(A.graph_attr)
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107 N.graph['node'] = dict(A.node_attr)
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108 N.graph['edge'] = dict(A.edge_attr)
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109 return N
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110
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111
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112 def to_agraph(N):
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113 """Returns a pygraphviz graph from a NetworkX graph N.
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114
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115 Parameters
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116 ----------
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117 N : NetworkX graph
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118 A graph created with NetworkX
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119
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120 Examples
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121 --------
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122 >>> K5 = nx.complete_graph(5)
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123 >>> A = nx.nx_agraph.to_agraph(K5)
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124
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125 Notes
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126 -----
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127 If N has an dict N.graph_attr an attempt will be made first
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128 to copy properties attached to the graph (see from_agraph)
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129 and then updated with the calling arguments if any.
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130
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131 """
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132 try:
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133 import pygraphviz
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134 except ImportError:
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135 raise ImportError('requires pygraphviz ',
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136 'http://pygraphviz.github.io/')
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137 directed = N.is_directed()
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138 strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph()
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139 A = pygraphviz.AGraph(name=N.name, strict=strict, directed=directed)
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140
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141 # default graph attributes
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142 A.graph_attr.update(N.graph.get('graph', {}))
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143 A.node_attr.update(N.graph.get('node', {}))
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144 A.edge_attr.update(N.graph.get('edge', {}))
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145
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146 A.graph_attr.update((k, v) for k, v in N.graph.items()
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147 if k not in ('graph', 'node', 'edge'))
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148
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149 # add nodes
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150 for n, nodedata in N.nodes(data=True):
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151 A.add_node(n)
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152 if nodedata is not None:
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153 a = A.get_node(n)
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154 a.attr.update({k: str(v) for k, v in nodedata.items()})
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155
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156 # loop over edges
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157 if N.is_multigraph():
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158 for u, v, key, edgedata in N.edges(data=True, keys=True):
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159 str_edgedata = {k: str(v) for k, v in edgedata.items()
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160 if k != 'key'}
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161 A.add_edge(u, v, key=str(key))
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162 if edgedata is not None:
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163 a = A.get_edge(u, v)
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164 a.attr.update(str_edgedata)
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165
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166 else:
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167 for u, v, edgedata in N.edges(data=True):
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168 str_edgedata = {k: str(v) for k, v in edgedata.items()}
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169 A.add_edge(u, v)
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170 if edgedata is not None:
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171 a = A.get_edge(u, v)
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172 a.attr.update(str_edgedata)
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173
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174 return A
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175
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176
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177 def write_dot(G, path):
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178 """Write NetworkX graph G to Graphviz dot format on path.
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179
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180 Parameters
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181 ----------
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182 G : graph
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183 A networkx graph
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184 path : filename
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185 Filename or file handle to write
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186 """
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187 try:
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188 import pygraphviz
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189 except ImportError:
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190 raise ImportError('requires pygraphviz ',
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191 'http://pygraphviz.github.io/')
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192 A = to_agraph(G)
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193 A.write(path)
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194 A.clear()
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195 return
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196
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197
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198 def read_dot(path):
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199 """Returns a NetworkX graph from a dot file on path.
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200
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201 Parameters
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202 ----------
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203 path : file or string
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204 File name or file handle to read.
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205 """
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206 try:
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207 import pygraphviz
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208 except ImportError:
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209 raise ImportError('read_dot() requires pygraphviz ',
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210 'http://pygraphviz.github.io/')
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211 A = pygraphviz.AGraph(file=path)
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212 return from_agraph(A)
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213
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214
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215 def graphviz_layout(G, prog='neato', root=None, args=''):
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216 """Create node positions for G using Graphviz.
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217
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218 Parameters
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219 ----------
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220 G : NetworkX graph
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221 A graph created with NetworkX
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222 prog : string
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223 Name of Graphviz layout program
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224 root : string, optional
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225 Root node for twopi layout
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226 args : string, optional
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227 Extra arguments to Graphviz layout program
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228
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229 Returns
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230 -------
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231 Dictionary of x, y, positions keyed by node.
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232
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233 Examples
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234 --------
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235 >>> G = nx.petersen_graph()
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236 >>> pos = nx.nx_agraph.graphviz_layout(G)
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237 >>> pos = nx.nx_agraph.graphviz_layout(G, prog='dot')
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238
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239 Notes
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240 -----
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241 This is a wrapper for pygraphviz_layout.
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242 """
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243 return pygraphviz_layout(G, prog=prog, root=root, args=args)
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244
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245
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246 def pygraphviz_layout(G, prog='neato', root=None, args=''):
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247 """Create node positions for G using Graphviz.
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248
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249 Parameters
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250 ----------
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251 G : NetworkX graph
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252 A graph created with NetworkX
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253 prog : string
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254 Name of Graphviz layout program
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255 root : string, optional
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256 Root node for twopi layout
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257 args : string, optional
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258 Extra arguments to Graphviz layout program
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259
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260 Returns : dictionary
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261 Dictionary of x, y, positions keyed by node.
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262
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263 Examples
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264 --------
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265 >>> G = nx.petersen_graph()
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266 >>> pos = nx.nx_agraph.graphviz_layout(G)
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267 >>> pos = nx.nx_agraph.graphviz_layout(G, prog='dot')
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268
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269 Notes
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270 -----
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271 If you use complex node objects, they may have the same string
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272 representation and GraphViz could treat them as the same node.
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273 The layout may assign both nodes a single location. See Issue #1568
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274 If this occurs in your case, consider relabeling the nodes just
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275 for the layout computation using something similar to:
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276
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277 H = nx.convert_node_labels_to_integers(G, label_attribute='node_label')
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278 H_layout = nx.nx_agraph.pygraphviz_layout(G, prog='dot')
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279 G_layout = {H.nodes[n]['node_label']: p for n, p in H_layout.items()}
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280
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281 """
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282 try:
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283 import pygraphviz
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284 except ImportError:
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285 raise ImportError('requires pygraphviz ',
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286 'http://pygraphviz.github.io/')
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287 if root is not None:
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288 args += "-Groot=%s" % root
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289 A = to_agraph(G)
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290 A.layout(prog=prog, args=args)
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291 node_pos = {}
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292 for n in G:
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293 node = pygraphviz.Node(A, n)
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294 try:
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295 xs = node.attr["pos"].split(',')
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296 node_pos[n] = tuple(float(x) for x in xs)
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297 except:
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298 print("no position for node", n)
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299 node_pos[n] = (0.0, 0.0)
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300 return node_pos
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301
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302
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303 @nx.utils.open_file(5, 'w+b')
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304 def view_pygraphviz(G, edgelabel=None, prog='dot', args='',
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305 suffix='', path=None):
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306 """Views the graph G using the specified layout algorithm.
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307
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308 Parameters
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309 ----------
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310 G : NetworkX graph
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311 The machine to draw.
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312 edgelabel : str, callable, None
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313 If a string, then it specifes the edge attribute to be displayed
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314 on the edge labels. If a callable, then it is called for each
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315 edge and it should return the string to be displayed on the edges.
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316 The function signature of `edgelabel` should be edgelabel(data),
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317 where `data` is the edge attribute dictionary.
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318 prog : string
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319 Name of Graphviz layout program.
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320 args : str
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321 Additional arguments to pass to the Graphviz layout program.
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322 suffix : str
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323 If `filename` is None, we save to a temporary file. The value of
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324 `suffix` will appear at the tail end of the temporary filename.
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325 path : str, None
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326 The filename used to save the image. If None, save to a temporary
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327 file. File formats are the same as those from pygraphviz.agraph.draw.
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328
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329 Returns
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330 -------
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331 path : str
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332 The filename of the generated image.
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333 A : PyGraphviz graph
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334 The PyGraphviz graph instance used to generate the image.
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335
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336 Notes
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337 -----
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338 If this function is called in succession too quickly, sometimes the
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339 image is not displayed. So you might consider time.sleep(.5) between
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340 calls if you experience problems.
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341
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342 """
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343 if not len(G):
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344 raise nx.NetworkXException("An empty graph cannot be drawn.")
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345
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346 import pygraphviz
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347
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348 # If we are providing default values for graphviz, these must be set
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349 # before any nodes or edges are added to the PyGraphviz graph object.
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350 # The reason for this is that default values only affect incoming objects.
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351 # If you change the default values after the objects have been added,
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352 # then they inherit no value and are set only if explicitly set.
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353
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354 # to_agraph() uses these values.
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355 attrs = ['edge', 'node', 'graph']
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356 for attr in attrs:
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357 if attr not in G.graph:
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358 G.graph[attr] = {}
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359
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360 # These are the default values.
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361 edge_attrs = {'fontsize': '10'}
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362 node_attrs = {'style': 'filled',
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363 'fillcolor': '#0000FF40',
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364 'height': '0.75',
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365 'width': '0.75',
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366 'shape': 'circle'}
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367 graph_attrs = {}
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368
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369 def update_attrs(which, attrs):
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370 # Update graph attributes. Return list of those which were added.
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371 added = []
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372 for k, v in attrs.items():
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373 if k not in G.graph[which]:
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374 G.graph[which][k] = v
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375 added.append(k)
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376
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377 def clean_attrs(which, added):
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378 # Remove added attributes
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379 for attr in added:
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380 del G.graph[which][attr]
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381 if not G.graph[which]:
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382 del G.graph[which]
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383
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384 # Update all default values
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385 update_attrs('edge', edge_attrs)
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386 update_attrs('node', node_attrs)
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387 update_attrs('graph', graph_attrs)
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388
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389 # Convert to agraph, so we inherit default values
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390 A = to_agraph(G)
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391
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392 # Remove the default values we added to the original graph.
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393 clean_attrs('edge', edge_attrs)
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394 clean_attrs('node', node_attrs)
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395 clean_attrs('graph', graph_attrs)
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396
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397 # If the user passed in an edgelabel, we update the labels for all edges.
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398 if edgelabel is not None:
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399 if not hasattr(edgelabel, '__call__'):
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400 def func(data):
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401 return ''.join([" ", str(data[edgelabel]), " "])
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402 else:
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403 func = edgelabel
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404
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405 # update all the edge labels
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406 if G.is_multigraph():
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407 for u, v, key, data in G.edges(keys=True, data=True):
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408 # PyGraphviz doesn't convert the key to a string. See #339
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409 edge = A.get_edge(u, v, str(key))
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410 edge.attr['label'] = str(func(data))
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411 else:
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412 for u, v, data in G.edges(data=True):
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413 edge = A.get_edge(u, v)
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414 edge.attr['label'] = str(func(data))
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415
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416 if path is None:
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417 ext = 'png'
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418 if suffix:
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419 suffix = '_%s.%s' % (suffix, ext)
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420 else:
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421 suffix = '.%s' % (ext,)
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422 path = tempfile.NamedTemporaryFile(suffix=suffix, delete=False)
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423 else:
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424 # Assume the decorator worked and it is a file-object.
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425 pass
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426
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427 display_pygraphviz(A, path=path, prog=prog, args=args)
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428
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429 return path.name, A
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430
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431
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432 def display_pygraphviz(graph, path, format=None, prog=None, args=''):
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433 """Internal function to display a graph in OS dependent manner.
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434
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435 Parameters
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436 ----------
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437 graph : PyGraphviz graph
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438 A PyGraphviz AGraph instance.
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439 path : file object
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440 An already opened file object that will be closed.
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441 format : str, None
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442 An attempt is made to guess the output format based on the extension
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443 of the filename. If that fails, the value of `format` is used.
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444 prog : string
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445 Name of Graphviz layout program.
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446 args : str
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447 Additional arguments to pass to the Graphviz layout program.
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448
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449 Notes
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450 -----
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451 If this function is called in succession too quickly, sometimes the
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452 image is not displayed. So you might consider time.sleep(.5) between
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453 calls if you experience problems.
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454
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455 """
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456 if format is None:
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457 filename = path.name
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458 format = os.path.splitext(filename)[1].lower()[1:]
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459 if not format:
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460 # Let the draw() function use its default
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461 format = None
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462
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463 # Save to a file and display in the default viewer.
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464 # We must close the file before viewing it.
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465 graph.draw(path, format, prog, args)
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466 path.close()
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467 nx.utils.default_opener(filename)
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468
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469
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470 # fixture for pytest
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471 def setup_module(module):
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472 import pytest
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473 pygraphviz = pytest.importorskip('pygraphviz')