Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/edgelist.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 """ |
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2 ********** |
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3 Edge Lists |
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4 ********** |
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5 Read and write NetworkX graphs as edge lists. |
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6 |
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7 The multi-line adjacency list format is useful for graphs with nodes |
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8 that can be meaningfully represented as strings. With the edgelist |
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9 format simple edge data can be stored but node or graph data is not. |
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10 There is no way of representing isolated nodes unless the node has a |
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11 self-loop edge. |
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12 |
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13 Format |
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14 ------ |
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15 You can read or write three formats of edge lists with these functions. |
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16 |
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17 Node pairs with no data:: |
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18 |
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19 1 2 |
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20 |
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21 Python dictionary as data:: |
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22 |
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23 1 2 {'weight':7, 'color':'green'} |
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24 |
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25 Arbitrary data:: |
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26 |
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27 1 2 7 green |
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28 """ |
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29 |
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30 __all__ = [ |
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31 "generate_edgelist", |
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32 "write_edgelist", |
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33 "parse_edgelist", |
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34 "read_edgelist", |
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35 "read_weighted_edgelist", |
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36 "write_weighted_edgelist", |
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37 ] |
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38 |
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39 from networkx.utils import open_file |
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40 import networkx as nx |
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41 |
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42 |
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43 def generate_edgelist(G, delimiter=" ", data=True): |
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44 """Generate a single line of the graph G in edge list format. |
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45 |
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46 Parameters |
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47 ---------- |
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48 G : NetworkX graph |
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49 |
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50 delimiter : string, optional |
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51 Separator for node labels |
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52 |
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53 data : bool or list of keys |
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54 If False generate no edge data. If True use a dictionary |
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55 representation of edge data. If a list of keys use a list of data |
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56 values corresponding to the keys. |
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57 |
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58 Returns |
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59 ------- |
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60 lines : string |
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61 Lines of data in adjlist format. |
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62 |
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63 Examples |
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64 -------- |
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65 >>> G = nx.lollipop_graph(4, 3) |
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66 >>> G[1][2]["weight"] = 3 |
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67 >>> G[3][4]["capacity"] = 12 |
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68 >>> for line in nx.generate_edgelist(G, data=False): |
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69 ... print(line) |
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70 0 1 |
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71 0 2 |
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72 0 3 |
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73 1 2 |
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74 1 3 |
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75 2 3 |
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76 3 4 |
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77 4 5 |
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78 5 6 |
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79 |
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80 >>> for line in nx.generate_edgelist(G): |
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81 ... print(line) |
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82 0 1 {} |
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83 0 2 {} |
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84 0 3 {} |
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85 1 2 {'weight': 3} |
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86 1 3 {} |
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87 2 3 {} |
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88 3 4 {'capacity': 12} |
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89 4 5 {} |
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90 5 6 {} |
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91 |
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92 >>> for line in nx.generate_edgelist(G, data=["weight"]): |
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93 ... print(line) |
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94 0 1 |
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95 0 2 |
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96 0 3 |
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97 1 2 3 |
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98 1 3 |
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99 2 3 |
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100 3 4 |
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101 4 5 |
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102 5 6 |
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103 |
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104 See Also |
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105 -------- |
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106 write_adjlist, read_adjlist |
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107 """ |
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108 if data is True: |
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109 for u, v, d in G.edges(data=True): |
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110 e = u, v, dict(d) |
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111 yield delimiter.join(map(str, e)) |
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112 elif data is False: |
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113 for u, v in G.edges(data=False): |
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114 e = u, v |
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115 yield delimiter.join(map(str, e)) |
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116 else: |
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117 for u, v, d in G.edges(data=True): |
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118 e = [u, v] |
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119 try: |
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120 e.extend(d[k] for k in data) |
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121 except KeyError: |
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122 pass # missing data for this edge, should warn? |
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123 yield delimiter.join(map(str, e)) |
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124 |
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125 |
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126 @open_file(1, mode="wb") |
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127 def write_edgelist(G, path, comments="#", delimiter=" ", data=True, encoding="utf-8"): |
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128 """Write graph as a list of edges. |
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129 |
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130 Parameters |
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131 ---------- |
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132 G : graph |
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133 A NetworkX graph |
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134 path : file or string |
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135 File or filename to write. If a file is provided, it must be |
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136 opened in 'wb' mode. Filenames ending in .gz or .bz2 will be compressed. |
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137 comments : string, optional |
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138 The character used to indicate the start of a comment |
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139 delimiter : string, optional |
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140 The string used to separate values. The default is whitespace. |
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141 data : bool or list, optional |
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142 If False write no edge data. |
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143 If True write a string representation of the edge data dictionary.. |
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144 If a list (or other iterable) is provided, write the keys specified |
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145 in the list. |
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146 encoding: string, optional |
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147 Specify which encoding to use when writing file. |
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148 |
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149 Examples |
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150 -------- |
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151 >>> G = nx.path_graph(4) |
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152 >>> nx.write_edgelist(G, "test.edgelist") |
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153 >>> G = nx.path_graph(4) |
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154 >>> fh = open("test.edgelist", "wb") |
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155 >>> nx.write_edgelist(G, fh) |
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156 >>> nx.write_edgelist(G, "test.edgelist.gz") |
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157 >>> nx.write_edgelist(G, "test.edgelist.gz", data=False) |
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158 |
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159 >>> G = nx.Graph() |
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160 >>> G.add_edge(1, 2, weight=7, color="red") |
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161 >>> nx.write_edgelist(G, "test.edgelist", data=False) |
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162 >>> nx.write_edgelist(G, "test.edgelist", data=["color"]) |
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163 >>> nx.write_edgelist(G, "test.edgelist", data=["color", "weight"]) |
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164 |
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165 See Also |
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166 -------- |
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167 read_edgelist |
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168 write_weighted_edgelist |
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169 """ |
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170 |
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171 for line in generate_edgelist(G, delimiter, data): |
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172 line += "\n" |
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173 path.write(line.encode(encoding)) |
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174 |
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175 |
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176 def parse_edgelist( |
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177 lines, comments="#", delimiter=None, create_using=None, nodetype=None, data=True |
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178 ): |
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179 """Parse lines of an edge list representation of a graph. |
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180 |
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181 Parameters |
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182 ---------- |
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183 lines : list or iterator of strings |
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184 Input data in edgelist format |
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185 comments : string, optional |
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186 Marker for comment lines. Default is `'#'` |
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187 delimiter : string, optional |
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188 Separator for node labels. Default is `None`, meaning any whitespace. |
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189 create_using : NetworkX graph constructor, optional (default=nx.Graph) |
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190 Graph type to create. If graph instance, then cleared before populated. |
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191 nodetype : Python type, optional |
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192 Convert nodes to this type. Default is `None`, meaning no conversion is |
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193 performed. |
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194 data : bool or list of (label,type) tuples |
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195 If `False` generate no edge data or if `True` use a dictionary |
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196 representation of edge data or a list tuples specifying dictionary |
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197 key names and types for edge data. |
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198 |
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199 Returns |
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200 ------- |
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201 G: NetworkX Graph |
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202 The graph corresponding to lines |
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203 |
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204 Examples |
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205 -------- |
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206 Edgelist with no data: |
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207 |
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208 >>> lines = ["1 2", "2 3", "3 4"] |
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209 >>> G = nx.parse_edgelist(lines, nodetype=int) |
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210 >>> list(G) |
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211 [1, 2, 3, 4] |
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212 >>> list(G.edges()) |
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213 [(1, 2), (2, 3), (3, 4)] |
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214 |
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215 Edgelist with data in Python dictionary representation: |
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216 |
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217 >>> lines = ["1 2 {'weight': 3}", "2 3 {'weight': 27}", "3 4 {'weight': 3.0}"] |
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218 >>> G = nx.parse_edgelist(lines, nodetype=int) |
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219 >>> list(G) |
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220 [1, 2, 3, 4] |
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221 >>> list(G.edges(data=True)) |
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222 [(1, 2, {'weight': 3}), (2, 3, {'weight': 27}), (3, 4, {'weight': 3.0})] |
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223 |
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224 Edgelist with data in a list: |
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225 |
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226 >>> lines = ["1 2 3", "2 3 27", "3 4 3.0"] |
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227 >>> G = nx.parse_edgelist(lines, nodetype=int, data=(("weight", float),)) |
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228 >>> list(G) |
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229 [1, 2, 3, 4] |
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230 >>> list(G.edges(data=True)) |
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231 [(1, 2, {'weight': 3.0}), (2, 3, {'weight': 27.0}), (3, 4, {'weight': 3.0})] |
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232 |
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233 See Also |
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234 -------- |
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235 read_weighted_edgelist |
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236 """ |
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237 from ast import literal_eval |
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238 |
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239 G = nx.empty_graph(0, create_using) |
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240 for line in lines: |
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241 p = line.find(comments) |
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242 if p >= 0: |
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243 line = line[:p] |
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244 if not line: |
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245 continue |
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246 # split line, should have 2 or more |
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247 s = line.strip().split(delimiter) |
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248 if len(s) < 2: |
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249 continue |
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250 u = s.pop(0) |
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251 v = s.pop(0) |
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252 d = s |
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253 if nodetype is not None: |
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254 try: |
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255 u = nodetype(u) |
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256 v = nodetype(v) |
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257 except Exception as e: |
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258 raise TypeError( |
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259 f"Failed to convert nodes {u},{v} to type {nodetype}." |
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260 ) from e |
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261 |
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262 if len(d) == 0 or data is False: |
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263 # no data or data type specified |
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264 edgedata = {} |
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265 elif data is True: |
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266 # no edge types specified |
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267 try: # try to evaluate as dictionary |
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268 if delimiter == ",": |
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269 edgedata_str = ",".join(d) |
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270 else: |
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271 edgedata_str = " ".join(d) |
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272 edgedata = dict(literal_eval(edgedata_str.strip())) |
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273 except Exception as e: |
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274 raise TypeError( |
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275 f"Failed to convert edge data ({d}) to dictionary." |
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276 ) from e |
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277 else: |
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278 # convert edge data to dictionary with specified keys and type |
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279 if len(d) != len(data): |
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280 raise IndexError( |
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281 f"Edge data {d} and data_keys {data} are not the same length" |
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282 ) |
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283 edgedata = {} |
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284 for (edge_key, edge_type), edge_value in zip(data, d): |
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285 try: |
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286 edge_value = edge_type(edge_value) |
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287 except Exception as e: |
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288 raise TypeError( |
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289 f"Failed to convert {edge_key} data {edge_value} " |
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290 f"to type {edge_type}." |
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291 ) from e |
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292 edgedata.update({edge_key: edge_value}) |
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293 G.add_edge(u, v, **edgedata) |
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294 return G |
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295 |
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296 |
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297 @open_file(0, mode="rb") |
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298 def read_edgelist( |
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299 path, |
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300 comments="#", |
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301 delimiter=None, |
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302 create_using=None, |
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303 nodetype=None, |
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304 data=True, |
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305 edgetype=None, |
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306 encoding="utf-8", |
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307 ): |
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308 """Read a graph from a list of edges. |
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309 |
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310 Parameters |
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311 ---------- |
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312 path : file or string |
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313 File or filename to read. If a file is provided, it must be |
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314 opened in 'rb' mode. |
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315 Filenames ending in .gz or .bz2 will be uncompressed. |
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316 comments : string, optional |
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317 The character used to indicate the start of a comment. |
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318 delimiter : string, optional |
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319 The string used to separate values. The default is whitespace. |
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320 create_using : NetworkX graph constructor, optional (default=nx.Graph) |
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321 Graph type to create. If graph instance, then cleared before populated. |
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322 nodetype : int, float, str, Python type, optional |
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323 Convert node data from strings to specified type |
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324 data : bool or list of (label,type) tuples |
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325 Tuples specifying dictionary key names and types for edge data |
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326 edgetype : int, float, str, Python type, optional OBSOLETE |
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327 Convert edge data from strings to specified type and use as 'weight' |
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328 encoding: string, optional |
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329 Specify which encoding to use when reading file. |
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330 |
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331 Returns |
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332 ------- |
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333 G : graph |
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334 A networkx Graph or other type specified with create_using |
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335 |
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336 Examples |
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337 -------- |
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338 >>> nx.write_edgelist(nx.path_graph(4), "test.edgelist") |
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339 >>> G = nx.read_edgelist("test.edgelist") |
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340 |
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341 >>> fh = open("test.edgelist", "rb") |
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342 >>> G = nx.read_edgelist(fh) |
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343 >>> fh.close() |
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344 |
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345 >>> G = nx.read_edgelist("test.edgelist", nodetype=int) |
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346 >>> G = nx.read_edgelist("test.edgelist", create_using=nx.DiGraph) |
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347 |
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348 Edgelist with data in a list: |
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349 |
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350 >>> textline = "1 2 3" |
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351 >>> fh = open("test.edgelist", "w") |
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352 >>> d = fh.write(textline) |
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353 >>> fh.close() |
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354 >>> G = nx.read_edgelist("test.edgelist", nodetype=int, data=(("weight", float),)) |
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355 >>> list(G) |
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356 [1, 2] |
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357 >>> list(G.edges(data=True)) |
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358 [(1, 2, {'weight': 3.0})] |
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359 |
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360 See parse_edgelist() for more examples of formatting. |
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361 |
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362 See Also |
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363 -------- |
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364 parse_edgelist |
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365 write_edgelist |
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366 |
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367 Notes |
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368 ----- |
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369 Since nodes must be hashable, the function nodetype must return hashable |
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370 types (e.g. int, float, str, frozenset - or tuples of those, etc.) |
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371 """ |
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372 lines = (line if isinstance(line, str) else line.decode(encoding) for line in path) |
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373 return parse_edgelist( |
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374 lines, |
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375 comments=comments, |
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376 delimiter=delimiter, |
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377 create_using=create_using, |
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378 nodetype=nodetype, |
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379 data=data, |
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380 ) |
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381 |
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382 |
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383 def write_weighted_edgelist(G, path, comments="#", delimiter=" ", encoding="utf-8"): |
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384 """Write graph G as a list of edges with numeric weights. |
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385 |
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386 Parameters |
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387 ---------- |
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388 G : graph |
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389 A NetworkX graph |
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390 path : file or string |
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391 File or filename to write. If a file is provided, it must be |
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392 opened in 'wb' mode. |
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393 Filenames ending in .gz or .bz2 will be compressed. |
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394 comments : string, optional |
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395 The character used to indicate the start of a comment |
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396 delimiter : string, optional |
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397 The string used to separate values. The default is whitespace. |
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398 encoding: string, optional |
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399 Specify which encoding to use when writing file. |
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400 |
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401 Examples |
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402 -------- |
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403 >>> G = nx.Graph() |
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404 >>> G.add_edge(1, 2, weight=7) |
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405 >>> nx.write_weighted_edgelist(G, "test.weighted.edgelist") |
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406 |
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407 See Also |
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408 -------- |
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409 read_edgelist |
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410 write_edgelist |
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411 read_weighted_edgelist |
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412 """ |
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413 write_edgelist( |
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414 G, |
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415 path, |
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416 comments=comments, |
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417 delimiter=delimiter, |
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418 data=("weight",), |
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419 encoding=encoding, |
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420 ) |
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421 |
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422 |
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423 def read_weighted_edgelist( |
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424 path, |
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425 comments="#", |
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426 delimiter=None, |
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427 create_using=None, |
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428 nodetype=None, |
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429 encoding="utf-8", |
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430 ): |
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431 """Read a graph as list of edges with numeric weights. |
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432 |
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433 Parameters |
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434 ---------- |
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435 path : file or string |
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436 File or filename to read. If a file is provided, it must be |
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437 opened in 'rb' mode. |
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438 Filenames ending in .gz or .bz2 will be uncompressed. |
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439 comments : string, optional |
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440 The character used to indicate the start of a comment. |
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441 delimiter : string, optional |
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442 The string used to separate values. The default is whitespace. |
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443 create_using : NetworkX graph constructor, optional (default=nx.Graph) |
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444 Graph type to create. If graph instance, then cleared before populated. |
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445 nodetype : int, float, str, Python type, optional |
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446 Convert node data from strings to specified type |
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447 encoding: string, optional |
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448 Specify which encoding to use when reading file. |
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449 |
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450 Returns |
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451 ------- |
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452 G : graph |
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453 A networkx Graph or other type specified with create_using |
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454 |
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455 Notes |
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456 ----- |
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457 Since nodes must be hashable, the function nodetype must return hashable |
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458 types (e.g. int, float, str, frozenset - or tuples of those, etc.) |
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459 |
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460 Example edgelist file format. |
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461 |
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462 With numeric edge data:: |
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463 |
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464 # read with |
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465 # >>> G=nx.read_weighted_edgelist(fh) |
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466 # source target data |
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467 a b 1 |
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468 a c 3.14159 |
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469 d e 42 |
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470 |
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471 See Also |
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472 -------- |
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473 write_weighted_edgelist |
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474 """ |
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475 return read_edgelist( |
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476 path, |
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477 comments=comments, |
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478 delimiter=delimiter, |
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479 create_using=create_using, |
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480 nodetype=nodetype, |
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481 data=(("weight", float),), |
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482 encoding=encoding, |
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483 ) |