Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/pajek.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 """ |
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2 ***** |
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3 Pajek |
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4 ***** |
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5 Read graphs in Pajek format. |
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6 |
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7 This implementation handles directed and undirected graphs including |
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8 those with self loops and parallel edges. |
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9 |
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10 Format |
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11 ------ |
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12 See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm |
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13 for format information. |
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14 |
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15 """ |
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16 |
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17 import warnings |
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18 |
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19 import networkx as nx |
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20 from networkx.utils import open_file |
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21 |
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22 __all__ = ["read_pajek", "parse_pajek", "generate_pajek", "write_pajek"] |
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23 |
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24 |
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25 def generate_pajek(G): |
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26 """Generate lines in Pajek graph format. |
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27 |
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28 Parameters |
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29 ---------- |
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30 G : graph |
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31 A Networkx graph |
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32 |
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33 References |
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34 ---------- |
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35 See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm |
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36 for format information. |
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37 """ |
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38 if G.name == "": |
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39 name = "NetworkX" |
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40 else: |
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41 name = G.name |
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42 # Apparently many Pajek format readers can't process this line |
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43 # So we'll leave it out for now. |
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44 # yield '*network %s'%name |
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45 |
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46 # write nodes with attributes |
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47 yield f"*vertices {G.order()}" |
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48 nodes = list(G) |
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49 # make dictionary mapping nodes to integers |
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50 nodenumber = dict(zip(nodes, range(1, len(nodes) + 1))) |
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51 for n in nodes: |
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52 # copy node attributes and pop mandatory attributes |
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53 # to avoid duplication. |
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54 na = G.nodes.get(n, {}).copy() |
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55 x = na.pop("x", 0.0) |
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56 y = na.pop("y", 0.0) |
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57 try: |
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58 id = int(na.pop("id", nodenumber[n])) |
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59 except ValueError as e: |
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60 e.args += ( |
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61 ( |
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62 "Pajek format requires 'id' to be an int()." |
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63 " Refer to the 'Relabeling nodes' section." |
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64 ), |
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65 ) |
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66 raise |
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67 nodenumber[n] = id |
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68 shape = na.pop("shape", "ellipse") |
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69 s = " ".join(map(make_qstr, (id, n, x, y, shape))) |
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70 # only optional attributes are left in na. |
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71 for k, v in na.items(): |
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72 if isinstance(v, str) and v.strip() != "": |
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73 s += f" {make_qstr(k)} {make_qstr(v)}" |
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74 else: |
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75 warnings.warn( |
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76 f"Node attribute {k} is not processed. {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}." |
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77 ) |
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78 yield s |
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79 |
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80 # write edges with attributes |
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81 if G.is_directed(): |
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82 yield "*arcs" |
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83 else: |
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84 yield "*edges" |
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85 for u, v, edgedata in G.edges(data=True): |
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86 d = edgedata.copy() |
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87 value = d.pop("weight", 1.0) # use 1 as default edge value |
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88 s = " ".join(map(make_qstr, (nodenumber[u], nodenumber[v], value))) |
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89 for k, v in d.items(): |
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90 if isinstance(v, str) and v.strip() != "": |
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91 s += f" {make_qstr(k)} {make_qstr(v)}" |
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92 else: |
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93 warnings.warn( |
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94 f"Edge attribute {k} is not processed. {('Empty attribute' if isinstance(v, str) else 'Non-string attribute')}." |
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95 ) |
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96 yield s |
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97 |
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98 |
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99 @open_file(1, mode="wb") |
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100 def write_pajek(G, path, encoding="UTF-8"): |
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101 """Write graph in Pajek format to path. |
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102 |
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103 Parameters |
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104 ---------- |
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105 G : graph |
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106 A Networkx graph |
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107 path : file or string |
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108 File or filename to write. |
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109 Filenames ending in .gz or .bz2 will be compressed. |
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110 |
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111 Examples |
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112 -------- |
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113 >>> G = nx.path_graph(4) |
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114 >>> nx.write_pajek(G, "test.net") |
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115 |
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116 Warnings |
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117 -------- |
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118 Optional node attributes and edge attributes must be non-empty strings. |
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119 Otherwise it will not be written into the file. You will need to |
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120 convert those attributes to strings if you want to keep them. |
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121 |
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122 References |
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123 ---------- |
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124 See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm |
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125 for format information. |
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126 """ |
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127 for line in generate_pajek(G): |
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128 line += "\n" |
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129 path.write(line.encode(encoding)) |
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130 |
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131 |
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132 @open_file(0, mode="rb") |
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133 def read_pajek(path, encoding="UTF-8"): |
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134 """Read graph in Pajek format from path. |
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135 |
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136 Parameters |
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137 ---------- |
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138 path : file or string |
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139 File or filename to write. |
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140 Filenames ending in .gz or .bz2 will be uncompressed. |
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141 |
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142 Returns |
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143 ------- |
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144 G : NetworkX MultiGraph or MultiDiGraph. |
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145 |
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146 Examples |
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147 -------- |
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148 >>> G = nx.path_graph(4) |
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149 >>> nx.write_pajek(G, "test.net") |
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150 >>> G = nx.read_pajek("test.net") |
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151 |
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152 To create a Graph instead of a MultiGraph use |
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153 |
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154 >>> G1 = nx.Graph(G) |
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155 |
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156 References |
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157 ---------- |
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158 See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm |
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159 for format information. |
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160 """ |
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161 lines = (line.decode(encoding) for line in path) |
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162 return parse_pajek(lines) |
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163 |
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164 |
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165 def parse_pajek(lines): |
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166 """Parse Pajek format graph from string or iterable. |
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167 |
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168 Parameters |
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169 ---------- |
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170 lines : string or iterable |
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171 Data in Pajek format. |
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172 |
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173 Returns |
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174 ------- |
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175 G : NetworkX graph |
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176 |
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177 See Also |
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178 -------- |
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179 read_pajek() |
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180 |
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181 """ |
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182 import shlex |
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183 |
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184 # multigraph=False |
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185 if isinstance(lines, str): |
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186 lines = iter(lines.split("\n")) |
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187 lines = iter([line.rstrip("\n") for line in lines]) |
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188 G = nx.MultiDiGraph() # are multiedges allowed in Pajek? assume yes |
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189 labels = [] # in the order of the file, needed for matrix |
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190 while lines: |
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191 try: |
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192 l = next(lines) |
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193 except: # EOF |
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194 break |
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195 if l.lower().startswith("*network"): |
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196 try: |
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197 label, name = l.split(None, 1) |
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198 except ValueError: |
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199 # Line was not of the form: *network NAME |
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200 pass |
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201 else: |
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202 G.graph["name"] = name |
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203 elif l.lower().startswith("*vertices"): |
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204 nodelabels = {} |
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205 l, nnodes = l.split() |
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206 for i in range(int(nnodes)): |
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207 l = next(lines) |
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208 try: |
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209 splitline = [ |
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210 x.decode("utf-8") for x in shlex.split(str(l).encode("utf-8")) |
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211 ] |
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212 except AttributeError: |
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213 splitline = shlex.split(str(l)) |
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214 id, label = splitline[0:2] |
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215 labels.append(label) |
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216 G.add_node(label) |
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217 nodelabels[id] = label |
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218 G.nodes[label]["id"] = id |
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219 try: |
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220 x, y, shape = splitline[2:5] |
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221 G.nodes[label].update( |
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222 {"x": float(x), "y": float(y), "shape": shape} |
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223 ) |
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224 except: |
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225 pass |
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226 extra_attr = zip(splitline[5::2], splitline[6::2]) |
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227 G.nodes[label].update(extra_attr) |
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228 elif l.lower().startswith("*edges") or l.lower().startswith("*arcs"): |
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229 if l.lower().startswith("*edge"): |
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230 # switch from multidigraph to multigraph |
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231 G = nx.MultiGraph(G) |
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232 if l.lower().startswith("*arcs"): |
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233 # switch to directed with multiple arcs for each existing edge |
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234 G = G.to_directed() |
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235 for l in lines: |
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236 try: |
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237 splitline = [ |
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238 x.decode("utf-8") for x in shlex.split(str(l).encode("utf-8")) |
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239 ] |
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240 except AttributeError: |
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241 splitline = shlex.split(str(l)) |
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242 |
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243 if len(splitline) < 2: |
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244 continue |
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245 ui, vi = splitline[0:2] |
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246 u = nodelabels.get(ui, ui) |
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247 v = nodelabels.get(vi, vi) |
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248 # parse the data attached to this edge and put in a dictionary |
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249 edge_data = {} |
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250 try: |
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251 # there should always be a single value on the edge? |
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252 w = splitline[2:3] |
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253 edge_data.update({"weight": float(w[0])}) |
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254 except: |
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255 pass |
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256 # if there isn't, just assign a 1 |
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257 # edge_data.update({'value':1}) |
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258 extra_attr = zip(splitline[3::2], splitline[4::2]) |
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259 edge_data.update(extra_attr) |
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260 # if G.has_edge(u,v): |
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261 # multigraph=True |
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262 G.add_edge(u, v, **edge_data) |
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263 elif l.lower().startswith("*matrix"): |
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264 G = nx.DiGraph(G) |
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265 adj_list = ( |
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266 (labels[row], labels[col], {"weight": int(data)}) |
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267 for (row, line) in enumerate(lines) |
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268 for (col, data) in enumerate(line.split()) |
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269 if int(data) != 0 |
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270 ) |
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271 G.add_edges_from(adj_list) |
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272 |
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273 return G |
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274 |
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275 |
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276 def make_qstr(t): |
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277 """Returns the string representation of t. |
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278 Add outer double-quotes if the string has a space. |
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279 """ |
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280 if not isinstance(t, str): |
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281 t = str(t) |
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282 if " " in t: |
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283 t = f'"{t}"' |
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284 return t |