Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/sitepackages/networkx/drawing/nx_agraph.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author  shellac 

date  Mon, 22 Mar 2021 18:12:50 +0000 
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0
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1 """ 
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2 *************** 
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3 Graphviz AGraph 
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4 *************** 
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5 
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6 Interface to pygraphviz AGraph class. 
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7 
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8 Examples 
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9  
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10 >>> G = nx.complete_graph(5) 
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11 >>> A = nx.nx_agraph.to_agraph(G) 
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12 >>> H = nx.nx_agraph.from_agraph(A) 
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13 
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14 See Also 
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15  
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16 Pygraphviz: http://pygraphviz.github.io/ 
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17 """ 
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18 import os 
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19 import tempfile 
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20 import networkx as nx 
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21 
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22 __all__ = [ 
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23 "from_agraph", 
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24 "to_agraph", 
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25 "write_dot", 
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26 "read_dot", 
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27 "graphviz_layout", 
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28 "pygraphviz_layout", 
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29 "view_pygraphviz", 
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30 ] 
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31 
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32 
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33 def from_agraph(A, create_using=None): 
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34 """Returns a NetworkX Graph or DiGraph from a PyGraphviz graph. 
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35 
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36 Parameters 
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37  
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38 A : PyGraphviz AGraph 
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39 A graph created with PyGraphviz 
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40 
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41 create_using : NetworkX graph constructor, optional (default=None) 
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42 Graph type to create. If graph instance, then cleared before populated. 
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43 If `None`, then the appropriate Graph type is inferred from `A`. 
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44 
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45 Examples 
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46  
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47 >>> K5 = nx.complete_graph(5) 
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48 >>> A = nx.nx_agraph.to_agraph(K5) 
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49 >>> G = nx.nx_agraph.from_agraph(A) 
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50 
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51 Notes 
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52  
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53 The Graph G will have a dictionary G.graph_attr containing 
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54 the default graphviz attributes for graphs, nodes and edges. 
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55 
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56 Default node attributes will be in the dictionary G.node_attr 
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57 which is keyed by node. 
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58 
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59 Edge attributes will be returned as edge data in G. With 
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60 edge_attr=False the edge data will be the Graphviz edge weight 
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61 attribute or the value 1 if no edge weight attribute is found. 
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62 
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63 """ 
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64 if create_using is None: 
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65 if A.is_directed(): 
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66 if A.is_strict(): 
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67 create_using = nx.DiGraph 
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68 else: 
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69 create_using = nx.MultiDiGraph 
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70 else: 
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71 if A.is_strict(): 
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72 create_using = nx.Graph 
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73 else: 
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74 create_using = nx.MultiGraph 
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75 
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76 # assign defaults 
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77 N = nx.empty_graph(0, create_using) 
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78 if A.name is not None: 
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79 N.name = A.name 
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80 
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81 # add graph attributes 
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82 N.graph.update(A.graph_attr) 
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83 
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84 # add nodes, attributes to N.node_attr 
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85 for n in A.nodes(): 
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86 str_attr = {str(k): v for k, v in n.attr.items()} 
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87 N.add_node(str(n), **str_attr) 
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88 
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89 # add edges, assign edge data as dictionary of attributes 
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90 for e in A.edges(): 
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91 u, v = str(e[0]), str(e[1]) 
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92 attr = dict(e.attr) 
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93 str_attr = {str(k): v for k, v in attr.items()} 
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94 if not N.is_multigraph(): 
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95 if e.name is not None: 
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96 str_attr["key"] = e.name 
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97 N.add_edge(u, v, **str_attr) 
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98 else: 
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99 N.add_edge(u, v, key=e.name, **str_attr) 
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100 
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101 # add default attributes for graph, nodes, and edges 
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102 # hang them on N.graph_attr 
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103 N.graph["graph"] = dict(A.graph_attr) 
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104 N.graph["node"] = dict(A.node_attr) 
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105 N.graph["edge"] = dict(A.edge_attr) 
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106 return N 
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107 
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108 
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109 def to_agraph(N): 
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110 """Returns a pygraphviz graph from a NetworkX graph N. 
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111 
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112 Parameters 
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113  
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114 N : NetworkX graph 
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115 A graph created with NetworkX 
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116 
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117 Examples 
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118  
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119 >>> K5 = nx.complete_graph(5) 
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120 >>> A = nx.nx_agraph.to_agraph(K5) 
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121 
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122 Notes 
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123  
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124 If N has an dict N.graph_attr an attempt will be made first 
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125 to copy properties attached to the graph (see from_agraph) 
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126 and then updated with the calling arguments if any. 
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127 
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128 """ 
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129 try: 
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130 import pygraphviz 
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131 except ImportError as e: 
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132 raise ImportError("requires pygraphviz " "http://pygraphviz.github.io/") from e 
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133 directed = N.is_directed() 
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134 strict = nx.number_of_selfloops(N) == 0 and not N.is_multigraph() 
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135 A = pygraphviz.AGraph(name=N.name, strict=strict, directed=directed) 
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136 
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137 # default graph attributes 
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138 A.graph_attr.update(N.graph.get("graph", {})) 
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139 A.node_attr.update(N.graph.get("node", {})) 
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140 A.edge_attr.update(N.graph.get("edge", {})) 
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141 
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142 A.graph_attr.update( 
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143 (k, v) for k, v in N.graph.items() if k not in ("graph", "node", "edge") 
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144 ) 
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145 
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146 # add nodes 
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147 for n, nodedata in N.nodes(data=True): 
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148 A.add_node(n) 
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149 # Add node data 
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150 a = A.get_node(n) 
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151 a.attr.update({k: str(v) for k, v in nodedata.items()}) 
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152 
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153 # loop over edges 
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154 if N.is_multigraph(): 
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155 for u, v, key, edgedata in N.edges(data=True, keys=True): 
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156 str_edgedata = {k: str(v) for k, v in edgedata.items() if k != "key"} 
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157 A.add_edge(u, v, key=str(key)) 
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158 # Add edge data 
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159 a = A.get_edge(u, v) 
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160 a.attr.update(str_edgedata) 
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161 
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162 else: 
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163 for u, v, edgedata in N.edges(data=True): 
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164 str_edgedata = {k: str(v) for k, v in edgedata.items()} 
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165 A.add_edge(u, v) 
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166 # Add edge data 
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167 a = A.get_edge(u, v) 
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168 a.attr.update(str_edgedata) 
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169 
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170 return A 
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171 
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172 
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173 def write_dot(G, path): 
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174 """Write NetworkX graph G to Graphviz dot format on path. 
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175 
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176 Parameters 
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177  
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178 G : graph 
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179 A networkx graph 
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180 path : filename 
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181 Filename or file handle to write 
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182 """ 
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183 A = to_agraph(G) 
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184 A.write(path) 
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185 A.clear() 
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186 return 
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187 
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188 
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189 def read_dot(path): 
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190 """Returns a NetworkX graph from a dot file on path. 
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191 
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192 Parameters 
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193  
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194 path : file or string 
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195 File name or file handle to read. 
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196 """ 
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197 try: 
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198 import pygraphviz 
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199 except ImportError as e: 
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200 raise ImportError( 
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201 "read_dot() requires pygraphviz " "http://pygraphviz.github.io/" 
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202 ) from e 
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203 A = pygraphviz.AGraph(file=path) 
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204 gr = from_agraph(A) 
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205 A.clear() 
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206 return gr 
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207 
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208 
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209 def graphviz_layout(G, prog="neato", root=None, args=""): 
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210 """Create node positions for G using Graphviz. 
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211 
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212 Parameters 
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213  
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214 G : NetworkX graph 
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215 A graph created with NetworkX 
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216 prog : string 
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217 Name of Graphviz layout program 
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218 root : string, optional 
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219 Root node for twopi layout 
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220 args : string, optional 
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221 Extra arguments to Graphviz layout program 
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222 
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223 Returns 
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224  
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225 Dictionary of x, y, positions keyed by node. 
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226 
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227 Examples 
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228  
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229 >>> G = nx.petersen_graph() 
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230 >>> pos = nx.nx_agraph.graphviz_layout(G) 
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231 >>> pos = nx.nx_agraph.graphviz_layout(G, prog="dot") 
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232 
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233 Notes 
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234  
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235 This is a wrapper for pygraphviz_layout. 
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236 """ 
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237 return pygraphviz_layout(G, prog=prog, root=root, args=args) 
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238 
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239 
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240 def pygraphviz_layout(G, prog="neato", root=None, args=""): 
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241 """Create node positions for G using Graphviz. 
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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 A graph created with NetworkX 
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247 prog : string 
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248 Name of Graphviz layout program 
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249 root : string, optional 
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250 Root node for twopi layout 
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251 args : string, optional 
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252 Extra arguments to Graphviz layout program 
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253 
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254 Returns 
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255  
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256 node_pos : dict 
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257 Dictionary of x, y, positions keyed by node. 
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258 
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259 Examples 
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260  
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261 >>> G = nx.petersen_graph() 
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262 >>> pos = nx.nx_agraph.graphviz_layout(G) 
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263 >>> pos = nx.nx_agraph.graphviz_layout(G, prog="dot") 
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264 
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265 Notes 
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266  
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267 If you use complex node objects, they may have the same string 
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268 representation and GraphViz could treat them as the same node. 
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269 The layout may assign both nodes a single location. See Issue #1568 
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270 If this occurs in your case, consider relabeling the nodes just 
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271 for the layout computation using something similar to:: 
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272 
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273 >>> H = nx.convert_node_labels_to_integers(G, label_attribute="node_label") 
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274 >>> H_layout = nx.nx_agraph.pygraphviz_layout(G, prog="dot") 
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275 >>> G_layout = {H.nodes[n]["node_label"]: p for n, p in H_layout.items()} 
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276 
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277 """ 
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278 try: 
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279 import pygraphviz 
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280 except ImportError as e: 
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281 raise ImportError("requires pygraphviz " "http://pygraphviz.github.io/") from e 
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282 if root is not None: 
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283 args += f"Groot={root}" 
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284 A = to_agraph(G) 
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285 A.layout(prog=prog, args=args) 
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286 node_pos = {} 
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287 for n in G: 
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288 node = pygraphviz.Node(A, n) 
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289 try: 
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290 xs = node.attr["pos"].split(",") 
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291 node_pos[n] = tuple(float(x) for x in xs) 
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292 except: 
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293 print("no position for node", n) 
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294 node_pos[n] = (0.0, 0.0) 
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295 return node_pos 
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296 
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297 
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298 @nx.utils.open_file(5, "w+b") 
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299 def view_pygraphviz( 
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300 G, edgelabel=None, prog="dot", args="", suffix="", path=None, show=True 
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301 ): 
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302 """Views the graph G using the specified layout algorithm. 
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303 
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304 Parameters 
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305  
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306 G : NetworkX graph 
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307 The machine to draw. 
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308 edgelabel : str, callable, None 
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309 If a string, then it specifes the edge attribute to be displayed 
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310 on the edge labels. If a callable, then it is called for each 
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311 edge and it should return the string to be displayed on the edges. 
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312 The function signature of `edgelabel` should be edgelabel(data), 
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313 where `data` is the edge attribute dictionary. 
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314 prog : string 
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315 Name of Graphviz layout program. 
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316 args : str 
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317 Additional arguments to pass to the Graphviz layout program. 
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318 suffix : str 
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319 If `filename` is None, we save to a temporary file. The value of 
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320 `suffix` will appear at the tail end of the temporary filename. 
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321 path : str, None 
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322 The filename used to save the image. If None, save to a temporary 
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323 file. File formats are the same as those from pygraphviz.agraph.draw. 
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324 show : bool, default = True 
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325 Whether to display the graph with `networkx.utils.default_opener`, 
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326 default is `True`. If `False`, the rendered graph is still available 
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327 at `path`. 
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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 # If we are providing default values for graphviz, these must be set 
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347 # before any nodes or edges are added to the PyGraphviz graph object. 
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348 # The reason for this is that default values only affect incoming objects. 
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349 # If you change the default values after the objects have been added, 
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350 # then they inherit no value and are set only if explicitly set. 
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351 
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352 # to_agraph() uses these values. 
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353 attrs = ["edge", "node", "graph"] 
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354 for attr in attrs: 
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355 if attr not in G.graph: 
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356 G.graph[attr] = {} 
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357 
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358 # These are the default values. 
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359 edge_attrs = {"fontsize": "10"} 
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360 node_attrs = { 
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361 "style": "filled", 
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362 "fillcolor": "#0000FF40", 
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363 "height": "0.75", 
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364 "width": "0.75", 
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365 "shape": "circle", 
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366 } 
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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 
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401 def func(data): 
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402 return "".join([" ", str(data[edgelabel]), " "]) 
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403 
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404 else: 
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405 func = edgelabel 
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406 
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407 # update all the edge labels 
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408 if G.is_multigraph(): 
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409 for u, v, key, data in G.edges(keys=True, data=True): 
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410 # PyGraphviz doesn't convert the key to a string. See #339 
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411 edge = A.get_edge(u, v, str(key)) 
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412 edge.attr["label"] = str(func(data)) 
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413 else: 
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414 for u, v, data in G.edges(data=True): 
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415 edge = A.get_edge(u, v) 
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416 edge.attr["label"] = str(func(data)) 
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417 
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418 if path is None: 
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419 ext = "png" 
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420 if suffix: 
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421 suffix = f"_{suffix}.{ext}" 
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422 else: 
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423 suffix = f".{ext}" 
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424 path = tempfile.NamedTemporaryFile(suffix=suffix, delete=False) 
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425 else: 
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426 # Assume the decorator worked and it is a fileobject. 
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427 pass 
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428 
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429 # Write graph to file 
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430 A.draw(path=path, format=None, prog=prog, args=args) 
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431 path.close() 
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432 
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433 # Show graph in a new window (depends on platform configuration) 
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434 if show: 
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435 nx.utils.default_opener(path.name) 
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436 
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437 return path.name, A 
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438 
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439 
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440 def display_pygraphviz(graph, path, format=None, prog=None, args=""): 
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441 """Internal function to display a graph in OS dependent manner. 
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442 
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443 Parameters 
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444  
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445 graph : PyGraphviz graph 
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446 A PyGraphviz AGraph instance. 
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447 path : file object 
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448 An already opened file object that will be closed. 
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449 format : str, None 
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450 An attempt is made to guess the output format based on the extension 
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451 of the filename. If that fails, the value of `format` is used. 
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452 prog : string 
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453 Name of Graphviz layout program. 
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454 args : str 
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455 Additional arguments to pass to the Graphviz layout program. 
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456 
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457 Notes 
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458  
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459 If this function is called in succession too quickly, sometimes the 
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460 image is not displayed. So you might consider time.sleep(.5) between 
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461 calls if you experience problems. 
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462 
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463 """ 
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464 import warnings 
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465 
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466 warnings.warn( 
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467 "display_pygraphviz is deprecated and will be removed in NetworkX 3.0. " 
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468 "To view a graph G using pygraphviz, use nx.nx_agraph.view_pygraphviz(G). " 
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469 "To view a graph from file, consider nx.utils.default_opener(filename).", 
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470 DeprecationWarning, 
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471 ) 
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472 if format is None: 
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473 filename = path.name 
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474 format = os.path.splitext(filename)[1].lower()[1:] 
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475 if not format: 
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476 # Let the draw() function use its default 
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477 format = None 
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478 
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479 # Save to a file and display in the default viewer. 
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480 # We must close the file before viewing it. 
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481 graph.draw(path, format, prog, args) 
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482 path.close() 
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483 nx.utils.default_opener(filename) 