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annotate planemo/lib/python3.7/site-packages/networkx/drawing/nx_pydot.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 """
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2 *****
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3 Pydot
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4 *****
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5
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6 Import and export NetworkX graphs in Graphviz dot format using pydot.
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7
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8 Either this module or nx_agraph can be used to interface with graphviz.
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9
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10 See Also
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11 --------
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12 pydot: https://github.com/erocarrera/pydot
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13 Graphviz: https://www.graphviz.org
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14 DOT Language: http://www.graphviz.org/doc/info/lang.html
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15 """
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16 # Author: Aric Hagberg (aric.hagberg@gmail.com)
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17
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18 # Copyright (C) 2004-2019 by
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19 # Aric Hagberg <hagberg@lanl.gov>
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20 # Dan Schult <dschult@colgate.edu>
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21 # Pieter Swart <swart@lanl.gov>
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22 # Cecil Curry <leycec@gmail.com>
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23 # All rights reserved.
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24 # BSD license.
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25 from locale import getpreferredencoding
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26 from networkx.utils import open_file, make_str
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27 import networkx as nx
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28
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29 __all__ = ['write_dot', 'read_dot', 'graphviz_layout', 'pydot_layout',
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30 'to_pydot', 'from_pydot']
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31
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32 # 2.x/3.x compatibility
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33 try:
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34 basestring
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35 except NameError:
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36 basestring = str
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37 unicode = str
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38
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39
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40 @open_file(1, mode='w')
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41 def write_dot(G, path):
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42 """Write NetworkX graph G to Graphviz dot format on path.
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43
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44 Path can be a string or a file handle.
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45 """
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46 P = to_pydot(G)
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47 path.write(P.to_string())
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48 return
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49
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50
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51 @open_file(0, mode='r')
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52 def read_dot(path):
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53 """Returns a NetworkX :class:`MultiGraph` or :class:`MultiDiGraph` from the
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54 dot file with the passed path.
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55
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56 If this file contains multiple graphs, only the first such graph is
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57 returned. All graphs _except_ the first are silently ignored.
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58
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59 Parameters
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60 ----------
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61 path : str or file
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62 Filename or file handle.
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63
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64 Returns
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65 -------
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66 G : MultiGraph or MultiDiGraph
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67 A :class:`MultiGraph` or :class:`MultiDiGraph`.
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68
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69 Notes
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70 -----
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71 Use `G = nx.Graph(read_dot(path))` to return a :class:`Graph` instead of a
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72 :class:`MultiGraph`.
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73 """
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74 import pydot
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75 data = path.read()
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76
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77 # List of one or more "pydot.Dot" instances deserialized from this file.
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78 P_list = pydot.graph_from_dot_data(data)
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79
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80 # Convert only the first such instance into a NetworkX graph.
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81 return from_pydot(P_list[0])
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82
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83
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84 def from_pydot(P):
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85 """Returns a NetworkX graph from a Pydot graph.
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86
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87 Parameters
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88 ----------
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89 P : Pydot graph
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90 A graph created with Pydot
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91
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92 Returns
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93 -------
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94 G : NetworkX multigraph
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95 A MultiGraph or MultiDiGraph.
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96
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97 Examples
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98 --------
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99 >>> K5 = nx.complete_graph(5)
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100 >>> A = nx.nx_pydot.to_pydot(K5)
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101 >>> G = nx.nx_pydot.from_pydot(A) # return MultiGraph
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102
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103 # make a Graph instead of MultiGraph
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104 >>> G = nx.Graph(nx.nx_pydot.from_pydot(A))
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105
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106 """
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107 if P.get_strict(None): # pydot bug: get_strict() shouldn't take argument
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108 multiedges = False
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109 else:
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110 multiedges = True
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111
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112 if P.get_type() == 'graph': # undirected
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113 if multiedges:
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114 N = nx.MultiGraph()
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115 else:
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116 N = nx.Graph()
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117 else:
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118 if multiedges:
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119 N = nx.MultiDiGraph()
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120 else:
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121 N = nx.DiGraph()
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122
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123 # assign defaults
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124 name = P.get_name().strip('"')
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125 if name != '':
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126 N.name = name
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127
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128 # add nodes, attributes to N.node_attr
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129 for p in P.get_node_list():
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130 n = p.get_name().strip('"')
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131 if n in ('node', 'graph', 'edge'):
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132 continue
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133 N.add_node(n, **p.get_attributes())
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134
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135 # add edges
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136 for e in P.get_edge_list():
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137 u = e.get_source()
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138 v = e.get_destination()
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139 attr = e.get_attributes()
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140 s = []
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141 d = []
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142
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143 if isinstance(u, basestring):
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144 s.append(u.strip('"'))
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145 else:
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146 for unodes in u['nodes']:
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147 s.append(unodes.strip('"'))
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148
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149 if isinstance(v, basestring):
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150 d.append(v.strip('"'))
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151 else:
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152 for vnodes in v['nodes']:
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153 d.append(vnodes.strip('"'))
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154
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155 for source_node in s:
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156 for destination_node in d:
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157 N.add_edge(source_node, destination_node, **attr)
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158
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159 # add default attributes for graph, nodes, edges
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160 pattr = P.get_attributes()
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161 if pattr:
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162 N.graph['graph'] = pattr
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163 try:
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164 N.graph['node'] = P.get_node_defaults()[0]
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165 except (IndexError, TypeError):
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166 pass # N.graph['node']={}
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167 try:
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168 N.graph['edge'] = P.get_edge_defaults()[0]
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169 except (IndexError, TypeError):
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170 pass # N.graph['edge']={}
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171 return N
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172
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173
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174 def to_pydot(N):
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175 """Returns a pydot graph from a NetworkX graph N.
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176
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177 Parameters
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178 ----------
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179 N : NetworkX graph
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180 A graph created with NetworkX
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181
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182 Examples
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183 --------
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184 >>> K5 = nx.complete_graph(5)
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185 >>> P = nx.nx_pydot.to_pydot(K5)
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186
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187 Notes
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188 -----
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189
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190 """
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191 import pydot
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192
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193 # set Graphviz graph type
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194 if N.is_directed():
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195 graph_type = 'digraph'
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196 else:
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197 graph_type = 'graph'
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198 strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph()
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199
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200 name = N.name
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201 graph_defaults = N.graph.get('graph', {})
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202 if name == '':
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203 P = pydot.Dot('', graph_type=graph_type, strict=strict,
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204 **graph_defaults)
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205 else:
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206 P = pydot.Dot('"%s"' % name, graph_type=graph_type, strict=strict,
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207 **graph_defaults)
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208 try:
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209 P.set_node_defaults(**N.graph['node'])
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210 except KeyError:
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211 pass
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212 try:
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213 P.set_edge_defaults(**N.graph['edge'])
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214 except KeyError:
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215 pass
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216
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217 for n, nodedata in N.nodes(data=True):
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218 str_nodedata = dict((k, make_str(v)) for k, v in nodedata.items())
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219 p = pydot.Node(make_str(n), **str_nodedata)
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220 P.add_node(p)
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221
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222 if N.is_multigraph():
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223 for u, v, key, edgedata in N.edges(data=True, keys=True):
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224 str_edgedata = dict((k, make_str(v)) for k, v in edgedata.items()
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225 if k != 'key')
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226 edge = pydot.Edge(make_str(u), make_str(v),
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227 key=make_str(key), **str_edgedata)
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228 P.add_edge(edge)
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229
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230 else:
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231 for u, v, edgedata in N.edges(data=True):
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232 str_edgedata = dict((k, make_str(v)) for k, v in edgedata.items())
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233 edge = pydot.Edge(make_str(u), make_str(v), **str_edgedata)
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234 P.add_edge(edge)
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235 return P
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236
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237
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238 def graphviz_layout(G, prog='neato', root=None):
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239 """Create node positions using Pydot and Graphviz.
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240
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241 Returns a dictionary of positions keyed by node.
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242
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243 Parameters
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244 ----------
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245 G : NetworkX Graph
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246 The graph for which the layout is computed.
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247 prog : string (default: 'neato')
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248 The name of the GraphViz program to use for layout.
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249 Options depend on GraphViz version but may include:
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250 'dot', 'twopi', 'fdp', 'sfdp', 'circo'
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251 root : Node from G or None (default: None)
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252 The node of G from which to start some layout algorithms.
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253
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254 Returns
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255 -------
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256 Dictionary of (x, y) positions keyed by node.
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257
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258 Examples
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259 --------
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260 >>> G = nx.complete_graph(4)
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261 >>> pos = nx.nx_pydot.graphviz_layout(G)
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262 >>> pos = nx.nx_pydot.graphviz_layout(G, prog='dot')
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263
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264 Notes
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265 -----
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266 This is a wrapper for pydot_layout.
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267 """
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268 return pydot_layout(G=G, prog=prog, root=root)
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269
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270
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271 def pydot_layout(G, prog='neato', root=None):
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272 """Create node positions using :mod:`pydot` and Graphviz.
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273
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274 Parameters
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275 --------
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276 G : Graph
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277 NetworkX graph to be laid out.
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278 prog : string (default: 'neato')
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279 Name of the GraphViz command to use for layout.
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280 Options depend on GraphViz version but may include:
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281 'dot', 'twopi', 'fdp', 'sfdp', 'circo'
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282 root : Node from G or None (default: None)
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283 The node of G from which to start some layout algorithms.
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284
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285 Returns
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286 --------
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287 dict
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288 Dictionary of positions keyed by node.
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289
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290 Examples
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291 --------
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292 >>> G = nx.complete_graph(4)
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293 >>> pos = nx.nx_pydot.pydot_layout(G)
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294 >>> pos = nx.nx_pydot.pydot_layout(G, prog='dot')
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295
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296 Notes
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297 -----
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298 If you use complex node objects, they may have the same string
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299 representation and GraphViz could treat them as the same node.
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300 The layout may assign both nodes a single location. See Issue #1568
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301 If this occurs in your case, consider relabeling the nodes just
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302 for the layout computation using something similar to:
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303
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304 H = nx.convert_node_labels_to_integers(G, label_attribute='node_label')
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305 H_layout = nx.nx_pydot.pydot_layout(G, prog='dot')
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306 G_layout = {H.nodes[n]['node_label']: p for n, p in H_layout.items()}
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307
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308 """
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309 import pydot
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310 P = to_pydot(G)
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311 if root is not None:
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312 P.set("root", make_str(root))
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313
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314 # List of low-level bytes comprising a string in the dot language converted
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315 # from the passed graph with the passed external GraphViz command.
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316 D_bytes = P.create_dot(prog=prog)
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317
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318 # Unique string decoded from these bytes with the preferred locale encoding
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319 D = unicode(D_bytes, encoding=getpreferredencoding())
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320
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321 if D == "": # no data returned
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322 print("Graphviz layout with %s failed" % (prog))
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323 print()
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324 print("To debug what happened try:")
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325 print("P = nx.nx_pydot.to_pydot(G)")
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326 print("P.write_dot(\"file.dot\")")
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327 print("And then run %s on file.dot" % (prog))
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328 return
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329
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330 # List of one or more "pydot.Dot" instances deserialized from this string.
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331 Q_list = pydot.graph_from_dot_data(D)
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332 assert len(Q_list) == 1
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333
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334 # The first and only such instance, as guaranteed by the above assertion.
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335 Q = Q_list[0]
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336
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337 node_pos = {}
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338 for n in G.nodes():
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339 pydot_node = pydot.Node(make_str(n)).get_name()
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340 node = Q.get_node(pydot_node)
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341
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342 if isinstance(node, list):
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343 node = node[0]
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344 pos = node.get_pos()[1:-1] # strip leading and trailing double quotes
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345 if pos is not None:
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346 xx, yy = pos.split(",")
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347 node_pos[n] = (float(xx), float(yy))
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348 return node_pos
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349
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350
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351 # fixture for pytest
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352 def setup_module(module):
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353 import pytest
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354 pytdot = pytest.importorskip('pytdot')