Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/sitepackages/networkx/readwrite/graph6.py @ 0:4f3585e2f14b draft default tip
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author  shellac 

date  Mon, 22 Mar 2021 18:12:50 +0000 
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rev  line source 

0
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1 # Original author: D. Eppstein, UC Irvine, August 12, 2003. 
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2 # The original code at http://www.ics.uci.edu/~eppstein/PADS/ is public domain. 
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3 """Functions for reading and writing graphs in the *graph6* format. 
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4 
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5 The *graph6* file format is suitable for small graphs or large dense 
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6 graphs. For large sparse graphs, use the *sparse6* format. 
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7 
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8 For more information, see the `graph6`_ homepage. 
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9 
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10 .. _graph6: http://users.cecs.anu.edu.au/~bdm/data/formats.html 
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11 
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12 """ 
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13 from itertools import islice 
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14 
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15 import networkx as nx 
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16 from networkx.exception import NetworkXError 
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17 from networkx.utils import open_file, not_implemented_for 
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18 
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19 __all__ = ["from_graph6_bytes", "read_graph6", "to_graph6_bytes", "write_graph6"] 
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20 
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21 
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22 def _generate_graph6_bytes(G, nodes, header): 
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23 """Yield bytes in the graph6 encoding of a graph. 
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24 
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25 `G` is an undirected simple graph. `nodes` is the list of nodes for 
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26 which the nodeinduced subgraph will be encoded; if `nodes` is the 
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27 list of all nodes in the graph, the entire graph will be 
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28 encoded. `header` is a Boolean that specifies whether to generate 
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29 the header ``b'>>graph6<<'`` before the remaining data. 
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30 
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31 This function generates `bytes` objects in the following order: 
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32 
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33 1. the header (if requested), 
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34 2. the encoding of the number of nodes, 
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35 3. each character, oneatatime, in the encoding of the requested 
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36 nodeinduced subgraph, 
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37 4. a newline character. 
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38 
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39 This function raises :exc:`ValueError` if the graph is too large for 
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40 the graph6 format (that is, greater than ``2 ** 36`` nodes). 
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41 
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42 """ 
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43 n = len(G) 
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44 if n >= 2 ** 36: 
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45 raise ValueError( 
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46 "graph6 is only defined if number of nodes is less " "than 2 ** 36" 
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47 ) 
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48 if header: 
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49 yield b">>graph6<<" 
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50 for d in n_to_data(n): 
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51 yield str.encode(chr(d + 63)) 
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52 # This generates the same as `(v in G[u] for u, v in combinations(G, 2))`, 
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53 # but in "columnmajor" order instead of "rowmajor" order. 
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54 bits = (nodes[j] in G[nodes[i]] for j in range(1, n) for i in range(j)) 
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55 chunk = list(islice(bits, 6)) 
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56 while chunk: 
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57 d = sum(b << 5  i for i, b in enumerate(chunk)) 
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58 yield str.encode(chr(d + 63)) 
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59 chunk = list(islice(bits, 6)) 
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60 yield b"\n" 
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61 
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62 
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63 def from_graph6_bytes(bytes_in): 
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64 """Read a simple undirected graph in graph6 format from bytes. 
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65 
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66 Parameters 
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67  
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68 bytes_in : bytes 
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69 Data in graph6 format, without a trailing newline. 
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70 
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71 Returns 
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72  
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73 G : Graph 
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74 
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75 Raises 
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76  
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77 NetworkXError 
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78 If bytes_in is unable to be parsed in graph6 format 
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79 
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80 ValueError 
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81 If any character ``c`` in bytes_in does not satisfy 
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82 ``63 <= ord(c) < 127``. 
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83 
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84 Examples 
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85  
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86 >>> G = nx.from_graph6_bytes(b"A_") 
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87 >>> sorted(G.edges()) 
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88 [(0, 1)] 
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89 
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90 See Also 
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91  
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92 read_graph6, write_graph6 
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93 
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94 References 
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95  
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96 .. [1] Graph6 specification 
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97 <http://users.cecs.anu.edu.au/~bdm/data/formats.html> 
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98 
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99 """ 
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100 
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101 def bits(): 
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102 """Returns sequence of individual bits from 6bitpervalue 
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103 list of data values.""" 
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104 for d in data: 
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105 for i in [5, 4, 3, 2, 1, 0]: 
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106 yield (d >> i) & 1 
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107 
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108 if bytes_in.startswith(b">>graph6<<"): 
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109 bytes_in = bytes_in[10:] 
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110 
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111 data = [c  63 for c in bytes_in] 
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112 if any(c > 63 for c in data): 
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113 raise ValueError("each input character must be in range(63, 127)") 
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114 
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115 n, data = data_to_n(data) 
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116 nd = (n * (n  1) // 2 + 5) // 6 
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117 if len(data) != nd: 
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118 raise NetworkXError( 
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119 f"Expected {n * (n  1) // 2} bits but got {len(data) * 6} in graph6" 
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120 ) 
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121 
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122 G = nx.Graph() 
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123 G.add_nodes_from(range(n)) 
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124 for (i, j), b in zip([(i, j) for j in range(1, n) for i in range(j)], bits()): 
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125 if b: 
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126 G.add_edge(i, j) 
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127 
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128 return G 
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129 
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130 
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131 def to_graph6_bytes(G, nodes=None, header=True): 
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132 """Convert a simple undirected graph to bytes in graph6 format. 
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133 
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134 Parameters 
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135  
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136 G : Graph (undirected) 
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137 
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138 nodes: list or iterable 
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139 Nodes are labeled 0...n1 in the order provided. If None the ordering 
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140 given by ``G.nodes()`` is used. 
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141 
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142 header: bool 
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143 If True add '>>graph6<<' bytes to head of data. 
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144 
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145 Raises 
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146  
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147 NetworkXNotImplemented 
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148 If the graph is directed or is a multigraph. 
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149 
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150 ValueError 
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151 If the graph has at least ``2 ** 36`` nodes; the graph6 format 
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152 is only defined for graphs of order less than ``2 ** 36``. 
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153 
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154 Examples 
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155  
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156 >>> nx.to_graph6_bytes(nx.path_graph(2)) 
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157 b'>>graph6<<A_\\n' 
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158 
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159 See Also 
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160  
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161 from_graph6_bytes, read_graph6, write_graph6_bytes 
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162 
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163 Notes 
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164  
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165 The returned bytes end with a newline character. 
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166 
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167 The format does not support edge or node labels, parallel edges or 
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168 self loops. If self loops are present they are silently ignored. 
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169 
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170 References 
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171  
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172 .. [1] Graph6 specification 
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173 <http://users.cecs.anu.edu.au/~bdm/data/formats.html> 
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174 
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175 """ 
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176 if nodes is not None: 
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177 G = G.subgraph(nodes) 
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178 H = nx.convert_node_labels_to_integers(G) 
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179 nodes = sorted(H.nodes()) 
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180 return b"".join(_generate_graph6_bytes(H, nodes, header)) 
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181 
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182 
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183 @open_file(0, mode="rb") 
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184 def read_graph6(path): 
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185 """Read simple undirected graphs in graph6 format from path. 
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186 
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187 Parameters 
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188  
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189 path : file or string 
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190 File or filename to write. 
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191 
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192 Returns 
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193  
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194 G : Graph or list of Graphs 
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195 If the file contains multiple lines then a list of graphs is returned 
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196 
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197 Raises 
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198  
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199 NetworkXError 
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200 If the string is unable to be parsed in graph6 format 
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201 
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202 Examples 
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203  
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204 You can read a graph6 file by giving the path to the file:: 
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205 
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206 >>> import tempfile 
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207 >>> with tempfile.NamedTemporaryFile() as f: 
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208 ... _ = f.write(b">>graph6<<A_\\n") 
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209 ... _ = f.seek(0) 
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210 ... G = nx.read_graph6(f.name) 
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211 >>> list(G.edges()) 
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212 [(0, 1)] 
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213 
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214 You can also read a graph6 file by giving an open filelike object:: 
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215 
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216 >>> import tempfile 
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217 >>> with tempfile.NamedTemporaryFile() as f: 
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218 ... _ = f.write(b">>graph6<<A_\\n") 
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219 ... _ = f.seek(0) 
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220 ... G = nx.read_graph6(f) 
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221 >>> list(G.edges()) 
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222 [(0, 1)] 
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223 
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224 See Also 
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225  
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226 from_graph6_bytes, write_graph6 
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227 
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228 References 
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229  
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230 .. [1] Graph6 specification 
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231 <http://users.cecs.anu.edu.au/~bdm/data/formats.html> 
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232 
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233 """ 
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234 glist = [] 
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235 for line in path: 
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236 line = line.strip() 
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237 if not len(line): 
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238 continue 
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239 glist.append(from_graph6_bytes(line)) 
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240 if len(glist) == 1: 
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241 return glist[0] 
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242 else: 
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243 return glist 
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244 
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245 
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246 @not_implemented_for("directed") 
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247 @not_implemented_for("multigraph") 
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248 @open_file(1, mode="wb") 
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249 def write_graph6(G, path, nodes=None, header=True): 
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250 """Write a simple undirected graph to a path in graph6 format. 
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251 
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252 Parameters 
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253  
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254 G : Graph (undirected) 
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255 
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256 path : str 
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257 The path naming the file to which to write the graph. 
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258 
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259 nodes: list or iterable 
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260 Nodes are labeled 0...n1 in the order provided. If None the ordering 
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261 given by ``G.nodes()`` is used. 
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262 
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263 header: bool 
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264 If True add '>>graph6<<' string to head of data 
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265 
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266 Raises 
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267  
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268 NetworkXNotImplemented 
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269 If the graph is directed or is a multigraph. 
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270 
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271 ValueError 
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272 If the graph has at least ``2 ** 36`` nodes; the graph6 format 
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273 is only defined for graphs of order less than ``2 ** 36``. 
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274 
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275 Examples 
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276  
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277 You can write a graph6 file by giving the path to a file:: 
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278 
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279 >>> import tempfile 
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280 >>> with tempfile.NamedTemporaryFile() as f: 
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281 ... nx.write_graph6(nx.path_graph(2), f.name) 
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282 ... _ = f.seek(0) 
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283 ... print(f.read()) 
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284 b'>>graph6<<A_\\n' 
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285 
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286 See Also 
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287  
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288 from_graph6_bytes, read_graph6 
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289 
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290 Notes 
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291  
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292 The function writes a newline character after writing the encoding 
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293 of the graph. 
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294 
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295 The format does not support edge or node labels, parallel edges or 
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296 self loops. If self loops are present they are silently ignored. 
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297 
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298 References 
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299  
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300 .. [1] Graph6 specification 
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301 <http://users.cecs.anu.edu.au/~bdm/data/formats.html> 
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302 
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303 """ 
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304 return write_graph6_file(G, path, nodes=nodes, header=header) 
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305 
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306 
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307 @not_implemented_for("directed") 
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308 @not_implemented_for("multigraph") 
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309 def write_graph6_file(G, f, nodes=None, header=True): 
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310 """Write a simple undirected graph to a filelike object in graph6 format. 
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311 
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312 Parameters 
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313  
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314 G : Graph (undirected) 
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315 
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316 f : filelike object 
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317 The file to write. 
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318 
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319 nodes: list or iterable 
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320 Nodes are labeled 0...n1 in the order provided. If None the ordering 
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321 given by ``G.nodes()`` is used. 
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322 
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323 header: bool 
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324 If True add '>>graph6<<' string to head of data 
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325 
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326 Raises 
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327  
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328 NetworkXNotImplemented 
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329 If the graph is directed or is a multigraph. 
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330 
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331 ValueError 
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332 If the graph has at least ``2 ** 36`` nodes; the graph6 format 
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333 is only defined for graphs of order less than ``2 ** 36``. 
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334 
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335 Examples 
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336  
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337 You can write a graph6 file by giving an open filelike object:: 
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338 
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339 >>> import tempfile 
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340 >>> with tempfile.NamedTemporaryFile() as f: 
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341 ... nx.write_graph6(nx.path_graph(2), f) 
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342 ... _ = f.seek(0) 
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343 ... print(f.read()) 
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344 b'>>graph6<<A_\\n' 
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345 
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346 See Also 
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347  
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348 from_graph6_bytes, read_graph6 
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349 
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350 Notes 
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351  
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352 The function writes a newline character after writing the encoding 
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353 of the graph. 
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354 
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355 The format does not support edge or node labels, parallel edges or 
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356 self loops. If self loops are present they are silently ignored. 
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357 
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358 References 
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359  
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360 .. [1] Graph6 specification 
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361 <http://users.cecs.anu.edu.au/~bdm/data/formats.html> 
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362 
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363 """ 
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364 if nodes is not None: 
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365 G = G.subgraph(nodes) 
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366 H = nx.convert_node_labels_to_integers(G) 
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367 nodes = sorted(H.nodes()) 
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368 for b in _generate_graph6_bytes(H, nodes, header): 
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369 f.write(b) 
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370 
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371 
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372 def data_to_n(data): 
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373 """Read initial one, four or eightunit value from graph6 
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374 integer sequence. 
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375 
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376 Return (value, rest of seq.)""" 
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377 if data[0] <= 62: 
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378 return data[0], data[1:] 
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379 if data[1] <= 62: 
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380 return (data[1] << 12) + (data[2] << 6) + data[3], data[4:] 
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381 return ( 
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382 (data[2] << 30) 
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383 + (data[3] << 24) 
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384 + (data[4] << 18) 
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385 + (data[5] << 12) 
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386 + (data[6] << 6) 
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387 + data[7], 
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388 data[8:], 
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389 ) 
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390 
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391 
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392 def n_to_data(n): 
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393 """Convert an integer to one, four or eightunit graph6 sequence. 
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394 
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395 This function is undefined if `n` is not in ``range(2 ** 36)``. 
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396 
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397 """ 
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398 if n <= 62: 
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399 return [n] 
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400 elif n <= 258047: 
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401 return [63, (n >> 12) & 0x3F, (n >> 6) & 0x3F, n & 0x3F] 
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402 else: # if n <= 68719476735: 
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403 return [ 
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404 63, 
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405 63, 
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406 (n >> 30) & 0x3F, 
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407 (n >> 24) & 0x3F, 
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408 (n >> 18) & 0x3F, 
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409 (n >> 12) & 0x3F, 
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410 (n >> 6) & 0x3F, 
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411 n & 0x3F, 
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412 ] 