Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/graph6.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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 node-induced 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, one-at-a-time, in the encoding of the requested |
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36 node-induced 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 "column-major" order instead of "row-major" 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 6-bit-per-value |
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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...n-1 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 file-like 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...n-1 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 file-like 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 : file-like 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...n-1 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 file-like 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 eight-unit 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 eight-unit 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 ] |