Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/sparse6.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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 *sparse6* format. |
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4 |
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5 The *sparse6* file format is a space-efficient format for large sparse |
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6 graphs. For small graphs or large dense graphs, use the *graph6* file |
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7 format. |
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8 |
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9 For more information, see the `sparse6`_ homepage. |
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10 |
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11 .. _sparse6: http://users.cecs.anu.edu.au/~bdm/data/formats.html |
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12 |
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13 """ |
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14 import networkx as nx |
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15 from networkx.exception import NetworkXError |
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16 from networkx.utils import open_file, not_implemented_for |
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17 from networkx.readwrite.graph6 import data_to_n, n_to_data |
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18 |
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19 __all__ = ["from_sparse6_bytes", "read_sparse6", "to_sparse6_bytes", "write_sparse6"] |
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20 |
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21 |
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22 def _generate_sparse6_bytes(G, nodes, header): |
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23 """Yield bytes in the sparse6 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'>>sparse6<<'`` 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 "sparse6 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">>sparse6<<" |
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50 yield b":" |
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51 for d in n_to_data(n): |
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52 yield str.encode(chr(d + 63)) |
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53 |
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54 k = 1 |
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55 while 1 << k < n: |
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56 k += 1 |
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57 |
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58 def enc(x): |
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59 """Big endian k-bit encoding of x""" |
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60 return [1 if (x & 1 << (k - 1 - i)) else 0 for i in range(k)] |
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61 |
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62 edges = sorted((max(u, v), min(u, v)) for u, v in G.edges()) |
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63 bits = [] |
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64 curv = 0 |
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65 for (v, u) in edges: |
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66 if v == curv: # current vertex edge |
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67 bits.append(0) |
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68 bits.extend(enc(u)) |
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69 elif v == curv + 1: # next vertex edge |
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70 curv += 1 |
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71 bits.append(1) |
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72 bits.extend(enc(u)) |
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73 else: # skip to vertex v and then add edge to u |
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74 curv = v |
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75 bits.append(1) |
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76 bits.extend(enc(v)) |
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77 bits.append(0) |
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78 bits.extend(enc(u)) |
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79 if k < 6 and n == (1 << k) and ((-len(bits)) % 6) >= k and curv < (n - 1): |
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80 # Padding special case: small k, n=2^k, |
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81 # more than k bits of padding needed, |
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82 # current vertex is not (n-1) -- |
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83 # appending 1111... would add a loop on (n-1) |
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84 bits.append(0) |
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85 bits.extend([1] * ((-len(bits)) % 6)) |
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86 else: |
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87 bits.extend([1] * ((-len(bits)) % 6)) |
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88 |
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89 data = [ |
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90 (bits[i + 0] << 5) |
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91 + (bits[i + 1] << 4) |
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92 + (bits[i + 2] << 3) |
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93 + (bits[i + 3] << 2) |
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94 + (bits[i + 4] << 1) |
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95 + (bits[i + 5] << 0) |
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96 for i in range(0, len(bits), 6) |
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97 ] |
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98 |
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99 for d in data: |
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100 yield str.encode(chr(d + 63)) |
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101 yield b"\n" |
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102 |
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103 |
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104 def from_sparse6_bytes(string): |
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105 """Read an undirected graph in sparse6 format from string. |
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106 |
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107 Parameters |
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108 ---------- |
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109 string : string |
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110 Data in sparse6 format |
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111 |
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112 Returns |
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113 ------- |
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114 G : Graph |
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115 |
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116 Raises |
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117 ------ |
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118 NetworkXError |
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119 If the string is unable to be parsed in sparse6 format |
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120 |
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121 Examples |
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122 -------- |
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123 >>> G = nx.from_sparse6_bytes(b":A_") |
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124 >>> sorted(G.edges()) |
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125 [(0, 1), (0, 1), (0, 1)] |
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126 |
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127 See Also |
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128 -------- |
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129 read_sparse6, write_sparse6 |
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130 |
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131 References |
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132 ---------- |
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133 .. [1] Sparse6 specification |
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134 <http://users.cecs.anu.edu.au/~bdm/data/formats.html> |
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135 |
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136 """ |
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137 if string.startswith(b">>sparse6<<"): |
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138 string = string[11:] |
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139 if not string.startswith(b":"): |
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140 raise NetworkXError("Expected leading colon in sparse6") |
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141 |
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142 chars = [c - 63 for c in string[1:]] |
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143 n, data = data_to_n(chars) |
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144 k = 1 |
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145 while 1 << k < n: |
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146 k += 1 |
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147 |
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148 def parseData(): |
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149 """Returns stream of pairs b[i], x[i] for sparse6 format.""" |
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150 chunks = iter(data) |
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151 d = None # partial data word |
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152 dLen = 0 # how many unparsed bits are left in d |
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153 |
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154 while 1: |
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155 if dLen < 1: |
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156 try: |
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157 d = next(chunks) |
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158 except StopIteration: |
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159 return |
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160 dLen = 6 |
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161 dLen -= 1 |
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162 b = (d >> dLen) & 1 # grab top remaining bit |
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163 |
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164 x = d & ((1 << dLen) - 1) # partially built up value of x |
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165 xLen = dLen # how many bits included so far in x |
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166 while xLen < k: # now grab full chunks until we have enough |
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167 try: |
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168 d = next(chunks) |
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169 except StopIteration: |
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170 return |
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171 dLen = 6 |
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172 x = (x << 6) + d |
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173 xLen += 6 |
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174 x = x >> (xLen - k) # shift back the extra bits |
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175 dLen = xLen - k |
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176 yield b, x |
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177 |
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178 v = 0 |
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179 |
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180 G = nx.MultiGraph() |
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181 G.add_nodes_from(range(n)) |
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182 |
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183 multigraph = False |
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184 for b, x in parseData(): |
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185 if b == 1: |
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186 v += 1 |
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187 # padding with ones can cause overlarge number here |
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188 if x >= n or v >= n: |
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189 break |
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190 elif x > v: |
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191 v = x |
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192 else: |
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193 if G.has_edge(x, v): |
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194 multigraph = True |
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195 G.add_edge(x, v) |
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196 if not multigraph: |
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197 G = nx.Graph(G) |
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198 return G |
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199 |
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200 |
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201 def to_sparse6_bytes(G, nodes=None, header=True): |
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202 """Convert an undirected graph to bytes in sparse6 format. |
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203 |
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204 Parameters |
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205 ---------- |
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206 G : Graph (undirected) |
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207 |
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208 nodes: list or iterable |
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209 Nodes are labeled 0...n-1 in the order provided. If None the ordering |
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210 given by ``G.nodes()`` is used. |
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211 |
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212 header: bool |
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213 If True add '>>sparse6<<' bytes to head of data. |
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214 |
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215 Raises |
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216 ------ |
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217 NetworkXNotImplemented |
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218 If the graph is directed. |
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219 |
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220 ValueError |
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221 If the graph has at least ``2 ** 36`` nodes; the sparse6 format |
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222 is only defined for graphs of order less than ``2 ** 36``. |
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223 |
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224 Examples |
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225 -------- |
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226 >>> nx.to_sparse6_bytes(nx.path_graph(2)) |
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227 b'>>sparse6<<:An\\n' |
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228 |
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229 See Also |
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230 -------- |
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231 to_sparse6_bytes, read_sparse6, write_sparse6_bytes |
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232 |
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233 Notes |
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234 ----- |
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235 The returned bytes end with a newline character. |
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236 |
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237 The format does not support edge or node labels. |
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238 |
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239 References |
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240 ---------- |
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241 .. [1] Graph6 specification |
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242 <http://users.cecs.anu.edu.au/~bdm/data/formats.html> |
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243 |
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244 """ |
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245 if nodes is not None: |
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246 G = G.subgraph(nodes) |
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247 G = nx.convert_node_labels_to_integers(G, ordering="sorted") |
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248 return b"".join(_generate_sparse6_bytes(G, nodes, header)) |
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249 |
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250 |
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251 @open_file(0, mode="rb") |
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252 def read_sparse6(path): |
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253 """Read an undirected graph in sparse6 format from path. |
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254 |
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255 Parameters |
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256 ---------- |
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257 path : file or string |
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258 File or filename to write. |
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259 |
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260 Returns |
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261 ------- |
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262 G : Graph/Multigraph or list of Graphs/MultiGraphs |
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263 If the file contains multiple lines then a list of graphs is returned |
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264 |
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265 Raises |
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266 ------ |
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267 NetworkXError |
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268 If the string is unable to be parsed in sparse6 format |
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269 |
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270 Examples |
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271 -------- |
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272 You can read a sparse6 file by giving the path to the file:: |
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273 |
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274 >>> import tempfile |
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275 >>> with tempfile.NamedTemporaryFile() as f: |
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276 ... _ = f.write(b">>sparse6<<:An\\n") |
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277 ... _ = f.seek(0) |
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278 ... G = nx.read_sparse6(f.name) |
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279 >>> list(G.edges()) |
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280 [(0, 1)] |
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281 |
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282 You can also read a sparse6 file by giving an open file-like object:: |
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283 |
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284 >>> import tempfile |
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285 >>> with tempfile.NamedTemporaryFile() as f: |
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286 ... _ = f.write(b">>sparse6<<:An\\n") |
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287 ... _ = f.seek(0) |
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288 ... G = nx.read_sparse6(f) |
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289 >>> list(G.edges()) |
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290 [(0, 1)] |
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291 |
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292 See Also |
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293 -------- |
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294 read_sparse6, from_sparse6_bytes |
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295 |
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296 References |
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297 ---------- |
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298 .. [1] Sparse6 specification |
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299 <http://users.cecs.anu.edu.au/~bdm/data/formats.html> |
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300 |
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301 """ |
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302 glist = [] |
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303 for line in path: |
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304 line = line.strip() |
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305 if not len(line): |
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306 continue |
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307 glist.append(from_sparse6_bytes(line)) |
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308 if len(glist) == 1: |
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309 return glist[0] |
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310 else: |
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311 return glist |
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312 |
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313 |
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314 @not_implemented_for("directed") |
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315 @open_file(1, mode="wb") |
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316 def write_sparse6(G, path, nodes=None, header=True): |
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317 """Write graph G to given path in sparse6 format. |
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318 |
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319 Parameters |
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320 ---------- |
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321 G : Graph (undirected) |
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322 |
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323 path : file or string |
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324 File or filename to write |
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325 |
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326 nodes: list or iterable |
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327 Nodes are labeled 0...n-1 in the order provided. If None the ordering |
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328 given by G.nodes() is used. |
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329 |
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330 header: bool |
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331 If True add '>>sparse6<<' string to head of data |
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332 |
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333 Raises |
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334 ------ |
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335 NetworkXError |
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336 If the graph is directed |
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337 |
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338 Examples |
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339 -------- |
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340 You can write a sparse6 file by giving the path to the file:: |
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341 |
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342 >>> import tempfile |
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343 >>> with tempfile.NamedTemporaryFile() as f: |
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344 ... nx.write_sparse6(nx.path_graph(2), f.name) |
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345 ... print(f.read()) |
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346 b'>>sparse6<<:An\\n' |
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347 |
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348 You can also write a sparse6 file by giving an open file-like object:: |
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349 |
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350 >>> with tempfile.NamedTemporaryFile() as f: |
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351 ... nx.write_sparse6(nx.path_graph(2), f) |
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352 ... _ = f.seek(0) |
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353 ... print(f.read()) |
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354 b'>>sparse6<<:An\\n' |
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355 |
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356 See Also |
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357 -------- |
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358 read_sparse6, from_sparse6_bytes |
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359 |
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360 Notes |
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361 ----- |
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362 The format does not support edge or node labels. |
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363 |
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364 References |
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365 ---------- |
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366 .. [1] Sparse6 specification |
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367 <http://users.cecs.anu.edu.au/~bdm/data/formats.html> |
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368 |
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369 """ |
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370 if nodes is not None: |
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371 G = G.subgraph(nodes) |
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372 G = nx.convert_node_labels_to_integers(G, ordering="sorted") |
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373 for b in _generate_sparse6_bytes(G, nodes, header): |
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374 path.write(b) |