annotate env/lib/python3.9/site-packages/networkx/algorithms/simple_paths.py @ 0:4f3585e2f14b draft default tip

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author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 from heapq import heappush, heappop
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2 from itertools import count
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3
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4 import networkx as nx
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5 from networkx.utils import not_implemented_for
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6 from networkx.utils import pairwise
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7 from networkx.utils import empty_generator
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8 from networkx.algorithms.shortest_paths.weighted import _weight_function
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9
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10 __all__ = [
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11 "all_simple_paths",
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12 "is_simple_path",
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13 "shortest_simple_paths",
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14 "all_simple_edge_paths",
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15 ]
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16
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17
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18 def is_simple_path(G, nodes):
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19 """Returns True if and only if `nodes` form a simple path in `G`.
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20
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21 A *simple path* in a graph is a nonempty sequence of nodes in which
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22 no node appears more than once in the sequence, and each adjacent
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23 pair of nodes in the sequence is adjacent in the graph.
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24
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25 Parameters
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26 ----------
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27 nodes : list
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28 A list of one or more nodes in the graph `G`.
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29
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30 Returns
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31 -------
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32 bool
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33 Whether the given list of nodes represents a simple path in `G`.
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34
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35 Notes
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36 -----
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37 An empty list of nodes is not a path but a list of one node is a
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38 path. Here's an explanation why.
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39
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40 This function operates on *node paths*. One could also consider
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41 *edge paths*. There is a bijection between node paths and edge
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42 paths.
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43
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44 The *length of a path* is the number of edges in the path, so a list
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45 of nodes of length *n* corresponds to a path of length *n* - 1.
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46 Thus the smallest edge path would be a list of zero edges, the empty
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47 path. This corresponds to a list of one node.
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48
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49 To convert between a node path and an edge path, you can use code
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50 like the following::
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51
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52 >>> from networkx.utils import pairwise
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53 >>> nodes = [0, 1, 2, 3]
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54 >>> edges = list(pairwise(nodes))
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55 >>> edges
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56 [(0, 1), (1, 2), (2, 3)]
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57 >>> nodes = [edges[0][0]] + [v for u, v in edges]
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58 >>> nodes
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59 [0, 1, 2, 3]
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60
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61 Examples
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62 --------
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63 >>> G = nx.cycle_graph(4)
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64 >>> nx.is_simple_path(G, [2, 3, 0])
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65 True
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66 >>> nx.is_simple_path(G, [0, 2])
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67 False
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68
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69 """
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70 # The empty list is not a valid path. Could also return
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71 # NetworkXPointlessConcept here.
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72 if len(nodes) == 0:
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73 return False
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74 # If the list is a single node, just check that the node is actually
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75 # in the graph.
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76 if len(nodes) == 1:
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77 return nodes[0] in G
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78 # Test that no node appears more than once, and that each
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79 # adjacent pair of nodes is adjacent.
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80 return len(set(nodes)) == len(nodes) and all(v in G[u] for u, v in pairwise(nodes))
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81
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82
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83 def all_simple_paths(G, source, target, cutoff=None):
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84 """Generate all simple paths in the graph G from source to target.
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85
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86 A simple path is a path with no repeated nodes.
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87
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88 Parameters
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89 ----------
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90 G : NetworkX graph
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91
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92 source : node
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93 Starting node for path
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94
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95 target : nodes
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96 Single node or iterable of nodes at which to end path
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97
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98 cutoff : integer, optional
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99 Depth to stop the search. Only paths of length <= cutoff are returned.
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100
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101 Returns
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102 -------
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103 path_generator: generator
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104 A generator that produces lists of simple paths. If there are no paths
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105 between the source and target within the given cutoff the generator
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106 produces no output.
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107
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108 Examples
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109 --------
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110 This iterator generates lists of nodes::
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111
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112 >>> G = nx.complete_graph(4)
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113 >>> for path in nx.all_simple_paths(G, source=0, target=3):
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114 ... print(path)
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115 ...
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116 [0, 1, 2, 3]
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117 [0, 1, 3]
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118 [0, 2, 1, 3]
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119 [0, 2, 3]
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120 [0, 3]
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121
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122 You can generate only those paths that are shorter than a certain
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123 length by using the `cutoff` keyword argument::
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124
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125 >>> paths = nx.all_simple_paths(G, source=0, target=3, cutoff=2)
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126 >>> print(list(paths))
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127 [[0, 1, 3], [0, 2, 3], [0, 3]]
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128
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129 To get each path as the corresponding list of edges, you can use the
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130 :func:`networkx.utils.pairwise` helper function::
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131
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132 >>> paths = nx.all_simple_paths(G, source=0, target=3)
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133 >>> for path in map(nx.utils.pairwise, paths):
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134 ... print(list(path))
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135 [(0, 1), (1, 2), (2, 3)]
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136 [(0, 1), (1, 3)]
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137 [(0, 2), (2, 1), (1, 3)]
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138 [(0, 2), (2, 3)]
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139 [(0, 3)]
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140
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141 Pass an iterable of nodes as target to generate all paths ending in any of several nodes::
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142
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143 >>> G = nx.complete_graph(4)
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144 >>> for path in nx.all_simple_paths(G, source=0, target=[3, 2]):
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145 ... print(path)
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146 ...
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147 [0, 1, 2]
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148 [0, 1, 2, 3]
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149 [0, 1, 3]
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150 [0, 1, 3, 2]
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151 [0, 2]
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152 [0, 2, 1, 3]
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153 [0, 2, 3]
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154 [0, 3]
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155 [0, 3, 1, 2]
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156 [0, 3, 2]
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157
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158 Iterate over each path from the root nodes to the leaf nodes in a
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159 directed acyclic graph using a functional programming approach::
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160
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161 >>> from itertools import chain
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162 >>> from itertools import product
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163 >>> from itertools import starmap
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164 >>> from functools import partial
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165 >>>
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166 >>> chaini = chain.from_iterable
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167 >>>
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168 >>> G = nx.DiGraph([(0, 1), (1, 2), (0, 3), (3, 2)])
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169 >>> roots = (v for v, d in G.in_degree() if d == 0)
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170 >>> leaves = (v for v, d in G.out_degree() if d == 0)
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171 >>> all_paths = partial(nx.all_simple_paths, G)
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172 >>> list(chaini(starmap(all_paths, product(roots, leaves))))
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173 [[0, 1, 2], [0, 3, 2]]
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174
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175 The same list computed using an iterative approach::
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176
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177 >>> G = nx.DiGraph([(0, 1), (1, 2), (0, 3), (3, 2)])
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178 >>> roots = (v for v, d in G.in_degree() if d == 0)
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179 >>> leaves = (v for v, d in G.out_degree() if d == 0)
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180 >>> all_paths = []
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181 >>> for root in roots:
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182 ... for leaf in leaves:
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183 ... paths = nx.all_simple_paths(G, root, leaf)
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184 ... all_paths.extend(paths)
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185 >>> all_paths
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186 [[0, 1, 2], [0, 3, 2]]
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187
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188 Iterate over each path from the root nodes to the leaf nodes in a
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189 directed acyclic graph passing all leaves together to avoid unnecessary
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190 compute::
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191
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192 >>> G = nx.DiGraph([(0, 1), (2, 1), (1, 3), (1, 4)])
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193 >>> roots = (v for v, d in G.in_degree() if d == 0)
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194 >>> leaves = [v for v, d in G.out_degree() if d == 0]
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195 >>> all_paths = []
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196 >>> for root in roots:
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197 ... paths = nx.all_simple_paths(G, root, leaves)
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198 ... all_paths.extend(paths)
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199 >>> all_paths
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200 [[0, 1, 3], [0, 1, 4], [2, 1, 3], [2, 1, 4]]
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201
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202 Notes
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203 -----
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204 This algorithm uses a modified depth-first search to generate the
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205 paths [1]_. A single path can be found in $O(V+E)$ time but the
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206 number of simple paths in a graph can be very large, e.g. $O(n!)$ in
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207 the complete graph of order $n$.
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208
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209 References
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210 ----------
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211 .. [1] R. Sedgewick, "Algorithms in C, Part 5: Graph Algorithms",
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212 Addison Wesley Professional, 3rd ed., 2001.
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213
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214 See Also
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215 --------
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216 all_shortest_paths, shortest_path
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217
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218 """
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219 if source not in G:
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220 raise nx.NodeNotFound(f"source node {source} not in graph")
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221 if target in G:
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222 targets = {target}
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223 else:
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224 try:
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225 targets = set(target)
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226 except TypeError as e:
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227 raise nx.NodeNotFound(f"target node {target} not in graph") from e
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228 if source in targets:
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229 return empty_generator()
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230 if cutoff is None:
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231 cutoff = len(G) - 1
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232 if cutoff < 1:
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233 return empty_generator()
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234 if G.is_multigraph():
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235 return _all_simple_paths_multigraph(G, source, targets, cutoff)
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236 else:
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237 return _all_simple_paths_graph(G, source, targets, cutoff)
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238
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239
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240 def _all_simple_paths_graph(G, source, targets, cutoff):
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241 visited = dict.fromkeys([source])
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242 stack = [iter(G[source])]
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243 while stack:
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244 children = stack[-1]
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245 child = next(children, None)
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246 if child is None:
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247 stack.pop()
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248 visited.popitem()
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249 elif len(visited) < cutoff:
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250 if child in visited:
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251 continue
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252 if child in targets:
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253 yield list(visited) + [child]
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254 visited[child] = None
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255 if targets - set(visited.keys()): # expand stack until find all targets
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256 stack.append(iter(G[child]))
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257 else:
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258 visited.popitem() # maybe other ways to child
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259 else: # len(visited) == cutoff:
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260 for target in (targets & (set(children) | {child})) - set(visited.keys()):
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261 yield list(visited) + [target]
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262 stack.pop()
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263 visited.popitem()
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264
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265
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266 def _all_simple_paths_multigraph(G, source, targets, cutoff):
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267 visited = dict.fromkeys([source])
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268 stack = [(v for u, v in G.edges(source))]
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269 while stack:
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270 children = stack[-1]
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271 child = next(children, None)
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272 if child is None:
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273 stack.pop()
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274 visited.popitem()
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275 elif len(visited) < cutoff:
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276 if child in visited:
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277 continue
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278 if child in targets:
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279 yield list(visited) + [child]
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280 visited[child] = None
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281 if targets - set(visited.keys()):
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282 stack.append((v for u, v in G.edges(child)))
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283 else:
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284 visited.popitem()
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285 else: # len(visited) == cutoff:
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286 for target in targets - set(visited.keys()):
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287 count = ([child] + list(children)).count(target)
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288 for i in range(count):
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289 yield list(visited) + [target]
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290 stack.pop()
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291 visited.popitem()
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292
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293
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294 def all_simple_edge_paths(G, source, target, cutoff=None):
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295 """Generate lists of edges for all simple paths in G from source to target.
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296
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297 A simple path is a path with no repeated nodes.
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298
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299 Parameters
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300 ----------
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301 G : NetworkX graph
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302
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303 source : node
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304 Starting node for path
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305
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306 target : nodes
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307 Single node or iterable of nodes at which to end path
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308
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309 cutoff : integer, optional
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310 Depth to stop the search. Only paths of length <= cutoff are returned.
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311
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312 Returns
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313 -------
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314 path_generator: generator
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315 A generator that produces lists of simple paths. If there are no paths
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316 between the source and target within the given cutoff the generator
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317 produces no output.
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318 For multigraphs, the list of edges have elements of the form `(u,v,k)`.
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319 Where `k` corresponds to the edge key.
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320
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321 Examples
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322 --------
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323
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324 Print the simple path edges of a Graph::
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325
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326 >>> g = nx.Graph([(1, 2), (2, 4), (1, 3), (3, 4)])
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327 >>> for path in sorted(nx.all_simple_edge_paths(g, 1, 4)):
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328 ... print(path)
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329 [(1, 2), (2, 4)]
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330 [(1, 3), (3, 4)]
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331
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332 Print the simple path edges of a MultiGraph. Returned edges come with
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333 their associated keys::
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334
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335 >>> mg = nx.MultiGraph()
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336 >>> mg.add_edge(1, 2, key="k0")
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337 'k0'
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338 >>> mg.add_edge(1, 2, key="k1")
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339 'k1'
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340 >>> mg.add_edge(2, 3, key="k0")
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341 'k0'
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342 >>> for path in sorted(nx.all_simple_edge_paths(mg, 1, 3)):
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343 ... print(path)
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344 [(1, 2, 'k0'), (2, 3, 'k0')]
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345 [(1, 2, 'k1'), (2, 3, 'k0')]
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346
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347
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348 Notes
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349 -----
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350 This algorithm uses a modified depth-first search to generate the
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351 paths [1]_. A single path can be found in $O(V+E)$ time but the
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352 number of simple paths in a graph can be very large, e.g. $O(n!)$ in
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353 the complete graph of order $n$.
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354
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355 References
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356 ----------
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357 .. [1] R. Sedgewick, "Algorithms in C, Part 5: Graph Algorithms",
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358 Addison Wesley Professional, 3rd ed., 2001.
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359
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360 See Also
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361 --------
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362 all_shortest_paths, shortest_path, all_simple_paths
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363
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364 """
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365 if source not in G:
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366 raise nx.NodeNotFound("source node %s not in graph" % source)
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367 if target in G:
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368 targets = {target}
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369 else:
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370 try:
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371 targets = set(target)
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372 except TypeError:
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373 raise nx.NodeNotFound("target node %s not in graph" % target)
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374 if source in targets:
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375 return []
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376 if cutoff is None:
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377 cutoff = len(G) - 1
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378 if cutoff < 1:
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379 return []
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380 if G.is_multigraph():
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381 for simp_path in _all_simple_edge_paths_multigraph(G, source, targets, cutoff):
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382 yield simp_path
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parents:
diff changeset
383 else:
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parents:
diff changeset
384 for simp_path in _all_simple_paths_graph(G, source, targets, cutoff):
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parents:
diff changeset
385 yield list(zip(simp_path[:-1], simp_path[1:]))
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parents:
diff changeset
386
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parents:
diff changeset
387
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parents:
diff changeset
388 def _all_simple_edge_paths_multigraph(G, source, targets, cutoff):
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parents:
diff changeset
389 if not cutoff or cutoff < 1:
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parents:
diff changeset
390 return []
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parents:
diff changeset
391 visited = [source]
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parents:
diff changeset
392 stack = [iter(G.edges(source, keys=True))]
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parents:
diff changeset
393
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parents:
diff changeset
394 while stack:
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parents:
diff changeset
395 children = stack[-1]
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diff changeset
396 child = next(children, None)
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parents:
diff changeset
397 if child is None:
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parents:
diff changeset
398 stack.pop()
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parents:
diff changeset
399 visited.pop()
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parents:
diff changeset
400 elif len(visited) < cutoff:
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parents:
diff changeset
401 if child[1] in targets:
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parents:
diff changeset
402 yield visited[1:] + [child]
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parents:
diff changeset
403 elif child[1] not in [v[0] for v in visited[1:]]:
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parents:
diff changeset
404 visited.append(child)
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diff changeset
405 stack.append(iter(G.edges(child[1], keys=True)))
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parents:
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406 else: # len(visited) == cutoff:
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parents:
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407 for (u, v, k) in [child] + list(children):
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parents:
diff changeset
408 if v in targets:
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409 yield visited[1:] + [(u, v, k)]
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parents:
diff changeset
410 stack.pop()
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parents:
diff changeset
411 visited.pop()
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parents:
diff changeset
412
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parents:
diff changeset
413
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414 @not_implemented_for("multigraph")
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diff changeset
415 def shortest_simple_paths(G, source, target, weight=None):
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parents:
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416 """Generate all simple paths in the graph G from source to target,
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parents:
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417 starting from shortest ones.
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diff changeset
418
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419 A simple path is a path with no repeated nodes.
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parents:
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420
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421 If a weighted shortest path search is to be used, no negative weights
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parents:
diff changeset
422 are allowed.
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parents:
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423
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424 Parameters
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parents:
diff changeset
425 ----------
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parents:
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426 G : NetworkX graph
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diff changeset
427
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428 source : node
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parents:
diff changeset
429 Starting node for path
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parents:
diff changeset
430
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431 target : node
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parents:
diff changeset
432 Ending node for path
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parents:
diff changeset
433
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434 weight : string or function
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parents:
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435 If it is a string, it is the name of the edge attribute to be
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parents:
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436 used as a weight.
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parents:
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437
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438 If it is a function, the weight of an edge is the value returned
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439 by the function. The function must accept exactly three positional
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440 arguments: the two endpoints of an edge and the dictionary of edge
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441 attributes for that edge. The function must return a number.
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442
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443 If None all edges are considered to have unit weight. Default
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parents:
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444 value None.
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diff changeset
445
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446 Returns
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parents:
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447 -------
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parents:
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448 path_generator: generator
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449 A generator that produces lists of simple paths, in order from
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parents:
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450 shortest to longest.
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parents:
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451
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parents:
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452 Raises
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parents:
diff changeset
453 ------
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454 NetworkXNoPath
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diff changeset
455 If no path exists between source and target.
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parents:
diff changeset
456
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parents:
diff changeset
457 NetworkXError
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parents:
diff changeset
458 If source or target nodes are not in the input graph.
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parents:
diff changeset
459
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parents:
diff changeset
460 NetworkXNotImplemented
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parents:
diff changeset
461 If the input graph is a Multi[Di]Graph.
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parents:
diff changeset
462
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parents:
diff changeset
463 Examples
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parents:
diff changeset
464 --------
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diff changeset
465
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parents:
diff changeset
466 >>> G = nx.cycle_graph(7)
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parents:
diff changeset
467 >>> paths = list(nx.shortest_simple_paths(G, 0, 3))
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parents:
diff changeset
468 >>> print(paths)
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parents:
diff changeset
469 [[0, 1, 2, 3], [0, 6, 5, 4, 3]]
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parents:
diff changeset
470
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parents:
diff changeset
471 You can use this function to efficiently compute the k shortest/best
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parents:
diff changeset
472 paths between two nodes.
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parents:
diff changeset
473
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shellac
parents:
diff changeset
474 >>> from itertools import islice
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shellac
parents:
diff changeset
475 >>> def k_shortest_paths(G, source, target, k, weight=None):
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parents:
diff changeset
476 ... return list(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
477 ... islice(nx.shortest_simple_paths(G, source, target, weight=weight), k)
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parents:
diff changeset
478 ... )
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parents:
diff changeset
479 >>> for path in k_shortest_paths(G, 0, 3, 2):
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shellac
parents:
diff changeset
480 ... print(path)
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shellac
parents:
diff changeset
481 [0, 1, 2, 3]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
482 [0, 6, 5, 4, 3]
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shellac
parents:
diff changeset
483
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shellac
parents:
diff changeset
484 Notes
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shellac
parents:
diff changeset
485 -----
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shellac
parents:
diff changeset
486 This procedure is based on algorithm by Jin Y. Yen [1]_. Finding
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shellac
parents:
diff changeset
487 the first $K$ paths requires $O(KN^3)$ operations.
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shellac
parents:
diff changeset
488
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shellac
parents:
diff changeset
489 See Also
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parents:
diff changeset
490 --------
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parents:
diff changeset
491 all_shortest_paths
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parents:
diff changeset
492 shortest_path
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parents:
diff changeset
493 all_simple_paths
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parents:
diff changeset
494
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shellac
parents:
diff changeset
495 References
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parents:
diff changeset
496 ----------
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parents:
diff changeset
497 .. [1] Jin Y. Yen, "Finding the K Shortest Loopless Paths in a
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shellac
parents:
diff changeset
498 Network", Management Science, Vol. 17, No. 11, Theory Series
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shellac
parents:
diff changeset
499 (Jul., 1971), pp. 712-716.
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parents:
diff changeset
500
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shellac
parents:
diff changeset
501 """
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shellac
parents:
diff changeset
502 if source not in G:
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parents:
diff changeset
503 raise nx.NodeNotFound(f"source node {source} not in graph")
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parents:
diff changeset
504
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parents:
diff changeset
505 if target not in G:
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parents:
diff changeset
506 raise nx.NodeNotFound(f"target node {target} not in graph")
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parents:
diff changeset
507
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parents:
diff changeset
508 if weight is None:
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parents:
diff changeset
509 length_func = len
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parents:
diff changeset
510 shortest_path_func = _bidirectional_shortest_path
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parents:
diff changeset
511 else:
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parents:
diff changeset
512 wt = _weight_function(G, weight)
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parents:
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513
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514 def length_func(path):
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parents:
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515 return sum(
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parents:
diff changeset
516 wt(u, v, G.get_edge_data(u, v)) for (u, v) in zip(path, path[1:])
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parents:
diff changeset
517 )
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parents:
diff changeset
518
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parents:
diff changeset
519 shortest_path_func = _bidirectional_dijkstra
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520
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521 listA = list()
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parents:
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522 listB = PathBuffer()
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523 prev_path = None
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parents:
diff changeset
524 while True:
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parents:
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525 if not prev_path:
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parents:
diff changeset
526 length, path = shortest_path_func(G, source, target, weight=weight)
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parents:
diff changeset
527 listB.push(length, path)
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diff changeset
528 else:
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diff changeset
529 ignore_nodes = set()
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530 ignore_edges = set()
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parents:
diff changeset
531 for i in range(1, len(prev_path)):
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parents:
diff changeset
532 root = prev_path[:i]
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parents:
diff changeset
533 root_length = length_func(root)
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parents:
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534 for path in listA:
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parents:
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535 if path[:i] == root:
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parents:
diff changeset
536 ignore_edges.add((path[i - 1], path[i]))
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parents:
diff changeset
537 try:
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parents:
diff changeset
538 length, spur = shortest_path_func(
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parents:
diff changeset
539 G,
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parents:
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540 root[-1],
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parents:
diff changeset
541 target,
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parents:
diff changeset
542 ignore_nodes=ignore_nodes,
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parents:
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543 ignore_edges=ignore_edges,
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parents:
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544 weight=weight,
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parents:
diff changeset
545 )
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parents:
diff changeset
546 path = root[:-1] + spur
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parents:
diff changeset
547 listB.push(root_length + length, path)
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parents:
diff changeset
548 except nx.NetworkXNoPath:
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parents:
diff changeset
549 pass
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parents:
diff changeset
550 ignore_nodes.add(root[-1])
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parents:
diff changeset
551
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parents:
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552 if listB:
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parents:
diff changeset
553 path = listB.pop()
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parents:
diff changeset
554 yield path
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parents:
diff changeset
555 listA.append(path)
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parents:
diff changeset
556 prev_path = path
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parents:
diff changeset
557 else:
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parents:
diff changeset
558 break
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parents:
diff changeset
559
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parents:
diff changeset
560
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561 class PathBuffer:
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parents:
diff changeset
562 def __init__(self):
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parents:
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563 self.paths = set()
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564 self.sortedpaths = list()
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parents:
diff changeset
565 self.counter = count()
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parents:
diff changeset
566
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567 def __len__(self):
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parents:
diff changeset
568 return len(self.sortedpaths)
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shellac
parents:
diff changeset
569
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parents:
diff changeset
570 def push(self, cost, path):
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parents:
diff changeset
571 hashable_path = tuple(path)
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parents:
diff changeset
572 if hashable_path not in self.paths:
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parents:
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573 heappush(self.sortedpaths, (cost, next(self.counter), path))
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parents:
diff changeset
574 self.paths.add(hashable_path)
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parents:
diff changeset
575
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parents:
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576 def pop(self):
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parents:
diff changeset
577 (cost, num, path) = heappop(self.sortedpaths)
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parents:
diff changeset
578 hashable_path = tuple(path)
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shellac
parents:
diff changeset
579 self.paths.remove(hashable_path)
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parents:
diff changeset
580 return path
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shellac
parents:
diff changeset
581
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parents:
diff changeset
582
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shellac
parents:
diff changeset
583 def _bidirectional_shortest_path(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
584 G, source, target, ignore_nodes=None, ignore_edges=None, weight=None
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shellac
parents:
diff changeset
585 ):
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parents:
diff changeset
586 """Returns the shortest path between source and target ignoring
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parents:
diff changeset
587 nodes and edges in the containers ignore_nodes and ignore_edges.
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shellac
parents:
diff changeset
588
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shellac
parents:
diff changeset
589 This is a custom modification of the standard bidirectional shortest
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
590 path implementation at networkx.algorithms.unweighted
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shellac
parents:
diff changeset
591
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parents:
diff changeset
592 Parameters
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parents:
diff changeset
593 ----------
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parents:
diff changeset
594 G : NetworkX graph
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parents:
diff changeset
595
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shellac
parents:
diff changeset
596 source : node
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shellac
parents:
diff changeset
597 starting node for path
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shellac
parents:
diff changeset
598
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parents:
diff changeset
599 target : node
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parents:
diff changeset
600 ending node for path
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shellac
parents:
diff changeset
601
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shellac
parents:
diff changeset
602 ignore_nodes : container of nodes
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parents:
diff changeset
603 nodes to ignore, optional
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shellac
parents:
diff changeset
604
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shellac
parents:
diff changeset
605 ignore_edges : container of edges
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shellac
parents:
diff changeset
606 edges to ignore, optional
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
607
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
608 weight : None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
609 This function accepts a weight argument for convenience of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
610 shortest_simple_paths function. It will be ignored.
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shellac
parents:
diff changeset
611
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shellac
parents:
diff changeset
612 Returns
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
613 -------
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
614 path: list
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
615 List of nodes in a path from source to target.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
616
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
617 Raises
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
618 ------
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
619 NetworkXNoPath
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
620 If no path exists between source and target.
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shellac
parents:
diff changeset
621
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
622 See Also
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
623 --------
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
624 shortest_path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
625
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
626 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
627 # call helper to do the real work
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parents:
diff changeset
628 results = _bidirectional_pred_succ(G, source, target, ignore_nodes, ignore_edges)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
629 pred, succ, w = results
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
630
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parents:
diff changeset
631 # build path from pred+w+succ
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parents:
diff changeset
632 path = []
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parents:
diff changeset
633 # from w to target
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shellac
parents:
diff changeset
634 while w is not None:
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shellac
parents:
diff changeset
635 path.append(w)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
636 w = succ[w]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
637 # from source to w
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
638 w = pred[path[0]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
639 while w is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
640 path.insert(0, w)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
641 w = pred[w]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
642
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
643 return len(path), path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
644
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645
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parents:
diff changeset
646 def _bidirectional_pred_succ(G, source, target, ignore_nodes=None, ignore_edges=None):
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parents:
diff changeset
647 """Bidirectional shortest path helper.
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parents:
diff changeset
648 Returns (pred,succ,w) where
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parents:
diff changeset
649 pred is a dictionary of predecessors from w to the source, and
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parents:
diff changeset
650 succ is a dictionary of successors from w to the target.
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parents:
diff changeset
651 """
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parents:
diff changeset
652 # does BFS from both source and target and meets in the middle
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parents:
diff changeset
653 if ignore_nodes and (source in ignore_nodes or target in ignore_nodes):
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parents:
diff changeset
654 raise nx.NetworkXNoPath(f"No path between {source} and {target}.")
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parents:
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655 if target == source:
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parents:
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656 return ({target: None}, {source: None}, source)
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parents:
diff changeset
657
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parents:
diff changeset
658 # handle either directed or undirected
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parents:
diff changeset
659 if G.is_directed():
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parents:
diff changeset
660 Gpred = G.predecessors
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parents:
diff changeset
661 Gsucc = G.successors
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parents:
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662 else:
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parents:
diff changeset
663 Gpred = G.neighbors
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parents:
diff changeset
664 Gsucc = G.neighbors
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parents:
diff changeset
665
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parents:
diff changeset
666 # support optional nodes filter
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667 if ignore_nodes:
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parents:
diff changeset
668
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diff changeset
669 def filter_iter(nodes):
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parents:
diff changeset
670 def iterate(v):
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parents:
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671 for w in nodes(v):
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parents:
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672 if w not in ignore_nodes:
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parents:
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673 yield w
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parents:
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674
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parents:
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675 return iterate
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parents:
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676
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parents:
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677 Gpred = filter_iter(Gpred)
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parents:
diff changeset
678 Gsucc = filter_iter(Gsucc)
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parents:
diff changeset
679
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parents:
diff changeset
680 # support optional edges filter
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parents:
diff changeset
681 if ignore_edges:
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parents:
diff changeset
682 if G.is_directed():
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parents:
diff changeset
683
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parents:
diff changeset
684 def filter_pred_iter(pred_iter):
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parents:
diff changeset
685 def iterate(v):
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parents:
diff changeset
686 for w in pred_iter(v):
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parents:
diff changeset
687 if (w, v) not in ignore_edges:
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parents:
diff changeset
688 yield w
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parents:
diff changeset
689
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parents:
diff changeset
690 return iterate
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parents:
diff changeset
691
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parents:
diff changeset
692 def filter_succ_iter(succ_iter):
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parents:
diff changeset
693 def iterate(v):
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parents:
diff changeset
694 for w in succ_iter(v):
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shellac
parents:
diff changeset
695 if (v, w) not in ignore_edges:
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parents:
diff changeset
696 yield w
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parents:
diff changeset
697
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parents:
diff changeset
698 return iterate
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parents:
diff changeset
699
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parents:
diff changeset
700 Gpred = filter_pred_iter(Gpred)
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shellac
parents:
diff changeset
701 Gsucc = filter_succ_iter(Gsucc)
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parents:
diff changeset
702
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parents:
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703 else:
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parents:
diff changeset
704
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parents:
diff changeset
705 def filter_iter(nodes):
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parents:
diff changeset
706 def iterate(v):
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parents:
diff changeset
707 for w in nodes(v):
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parents:
diff changeset
708 if (v, w) not in ignore_edges and (w, v) not in ignore_edges:
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shellac
parents:
diff changeset
709 yield w
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shellac
parents:
diff changeset
710
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shellac
parents:
diff changeset
711 return iterate
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shellac
parents:
diff changeset
712
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shellac
parents:
diff changeset
713 Gpred = filter_iter(Gpred)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
714 Gsucc = filter_iter(Gsucc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
715
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shellac
parents:
diff changeset
716 # predecesssor and successors in search
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
717 pred = {source: None}
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shellac
parents:
diff changeset
718 succ = {target: None}
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shellac
parents:
diff changeset
719
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
720 # initialize fringes, start with forward
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
721 forward_fringe = [source]
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shellac
parents:
diff changeset
722 reverse_fringe = [target]
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shellac
parents:
diff changeset
723
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shellac
parents:
diff changeset
724 while forward_fringe and reverse_fringe:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
725 if len(forward_fringe) <= len(reverse_fringe):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
726 this_level = forward_fringe
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
727 forward_fringe = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
728 for v in this_level:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
729 for w in Gsucc(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
730 if w not in pred:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
731 forward_fringe.append(w)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
732 pred[w] = v
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
733 if w in succ:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
734 # found path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
735 return pred, succ, w
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
736 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
737 this_level = reverse_fringe
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
738 reverse_fringe = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
739 for v in this_level:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
740 for w in Gpred(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
741 if w not in succ:
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shellac
parents:
diff changeset
742 succ[w] = v
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shellac
parents:
diff changeset
743 reverse_fringe.append(w)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
744 if w in pred:
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shellac
parents:
diff changeset
745 # found path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
746 return pred, succ, w
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
747
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
748 raise nx.NetworkXNoPath(f"No path between {source} and {target}.")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
749
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
750
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751 def _bidirectional_dijkstra(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
752 G, source, target, weight="weight", ignore_nodes=None, ignore_edges=None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
753 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
754 """Dijkstra's algorithm for shortest paths using bidirectional search.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
755
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
756 This function returns the shortest path between source and target
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757 ignoring nodes and edges in the containers ignore_nodes and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
758 ignore_edges.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
759
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
760 This is a custom modification of the standard Dijkstra bidirectional
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
761 shortest path implementation at networkx.algorithms.weighted
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
762
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
763 Parameters
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
764 ----------
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
765 G : NetworkX graph
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
766
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
767 source : node
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
768 Starting node.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
769
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shellac
parents:
diff changeset
770 target : node
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
771 Ending node.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
772
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
773 weight: string, function, optional (default='weight')
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
774 Edge data key or weight function corresponding to the edge weight
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
775
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
776 ignore_nodes : container of nodes
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
777 nodes to ignore, optional
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
778
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
779 ignore_edges : container of edges
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
780 edges to ignore, optional
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
781
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
782 Returns
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
783 -------
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
784 length : number
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
785 Shortest path length.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
786
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
787 Returns a tuple of two dictionaries keyed by node.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
788 The first dictionary stores distance from the source.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
789 The second stores the path from the source to that node.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
790
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
791 Raises
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
792 ------
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
793 NetworkXNoPath
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
794 If no path exists between source and target.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
795
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
796 Notes
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
797 -----
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
798 Edge weight attributes must be numerical.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
799 Distances are calculated as sums of weighted edges traversed.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
800
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
801 In practice bidirectional Dijkstra is much more than twice as fast as
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
802 ordinary Dijkstra.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
803
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
804 Ordinary Dijkstra expands nodes in a sphere-like manner from the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
805 source. The radius of this sphere will eventually be the length
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
806 of the shortest path. Bidirectional Dijkstra will expand nodes
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
807 from both the source and the target, making two spheres of half
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
808 this radius. Volume of the first sphere is pi*r*r while the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
809 others are 2*pi*r/2*r/2, making up half the volume.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
810
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
811 This algorithm is not guaranteed to work if edge weights
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
812 are negative or are floating point numbers
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
813 (overflows and roundoff errors can cause problems).
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
814
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
815 See Also
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
816 --------
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
817 shortest_path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
818 shortest_path_length
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
819 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
820 if ignore_nodes and (source in ignore_nodes or target in ignore_nodes):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
821 raise nx.NetworkXNoPath(f"No path between {source} and {target}.")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
822 if source == target:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
823 return (0, [source])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
824
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
825 # handle either directed or undirected
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
826 if G.is_directed():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
827 Gpred = G.predecessors
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
828 Gsucc = G.successors
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
829 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
830 Gpred = G.neighbors
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
831 Gsucc = G.neighbors
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
832
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
833 # support optional nodes filter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
834 if ignore_nodes:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
835
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
836 def filter_iter(nodes):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
837 def iterate(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
838 for w in nodes(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
839 if w not in ignore_nodes:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
840 yield w
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
841
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
842 return iterate
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
843
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
844 Gpred = filter_iter(Gpred)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
845 Gsucc = filter_iter(Gsucc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
846
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
847 # support optional edges filter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
848 if ignore_edges:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
849 if G.is_directed():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
850
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
851 def filter_pred_iter(pred_iter):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
852 def iterate(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
853 for w in pred_iter(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
854 if (w, v) not in ignore_edges:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
855 yield w
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
856
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
857 return iterate
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
858
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
859 def filter_succ_iter(succ_iter):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
860 def iterate(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
861 for w in succ_iter(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
862 if (v, w) not in ignore_edges:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
863 yield w
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
864
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
865 return iterate
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
866
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
867 Gpred = filter_pred_iter(Gpred)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
868 Gsucc = filter_succ_iter(Gsucc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
869
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
870 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
871
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
872 def filter_iter(nodes):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
873 def iterate(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
874 for w in nodes(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
875 if (v, w) not in ignore_edges and (w, v) not in ignore_edges:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
876 yield w
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
877
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
878 return iterate
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
879
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
880 Gpred = filter_iter(Gpred)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
881 Gsucc = filter_iter(Gsucc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
882
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
883 push = heappush
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
884 pop = heappop
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
885 # Init: Forward Backward
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
886 dists = [{}, {}] # dictionary of final distances
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
887 paths = [{source: [source]}, {target: [target]}] # dictionary of paths
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
888 fringe = [[], []] # heap of (distance, node) tuples for
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
889 # extracting next node to expand
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
890 seen = [{source: 0}, {target: 0}] # dictionary of distances to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
891 # nodes seen
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
892 c = count()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
893 # initialize fringe heap
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
894 push(fringe[0], (0, next(c), source))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
895 push(fringe[1], (0, next(c), target))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
896 # neighs for extracting correct neighbor information
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
897 neighs = [Gsucc, Gpred]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
898 # variables to hold shortest discovered path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
899 # finaldist = 1e30000
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
900 finalpath = []
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
901 dir = 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
902 while fringe[0] and fringe[1]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
903 # choose direction
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
904 # dir == 0 is forward direction and dir == 1 is back
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
905 dir = 1 - dir
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
906 # extract closest to expand
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shellac
parents:
diff changeset
907 (dist, _, v) = pop(fringe[dir])
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shellac
parents:
diff changeset
908 if v in dists[dir]:
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shellac
parents:
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909 # Shortest path to v has already been found
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shellac
parents:
diff changeset
910 continue
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shellac
parents:
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911 # update distance
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shellac
parents:
diff changeset
912 dists[dir][v] = dist # equal to seen[dir][v]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
913 if v in dists[1 - dir]:
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shellac
parents:
diff changeset
914 # if we have scanned v in both directions we are done
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shellac
parents:
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915 # we have now discovered the shortest path
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shellac
parents:
diff changeset
916 return (finaldist, finalpath)
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shellac
parents:
diff changeset
917
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shellac
parents:
diff changeset
918 wt = _weight_function(G, weight)
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shellac
parents:
diff changeset
919 for w in neighs[dir](v):
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shellac
parents:
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920 if dir == 0: # forward
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shellac
parents:
diff changeset
921 minweight = wt(v, w, G.get_edge_data(v, w))
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shellac
parents:
diff changeset
922 vwLength = dists[dir][v] + minweight
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shellac
parents:
diff changeset
923 else: # back, must remember to change v,w->w,v
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shellac
parents:
diff changeset
924 minweight = wt(w, v, G.get_edge_data(w, v))
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shellac
parents:
diff changeset
925 vwLength = dists[dir][v] + minweight
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shellac
parents:
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926
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shellac
parents:
diff changeset
927 if w in dists[dir]:
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shellac
parents:
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928 if vwLength < dists[dir][w]:
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shellac
parents:
diff changeset
929 raise ValueError("Contradictory paths found: negative weights?")
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shellac
parents:
diff changeset
930 elif w not in seen[dir] or vwLength < seen[dir][w]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
931 # relaxing
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
932 seen[dir][w] = vwLength
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
933 push(fringe[dir], (vwLength, next(c), w))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
934 paths[dir][w] = paths[dir][v] + [w]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
935 if w in seen[0] and w in seen[1]:
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shellac
parents:
diff changeset
936 # see if this path is better than than the already
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shellac
parents:
diff changeset
937 # discovered shortest path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
938 totaldist = seen[0][w] + seen[1][w]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
939 if finalpath == [] or finaldist > totaldist:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
940 finaldist = totaldist
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
941 revpath = paths[1][w][:]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
942 revpath.reverse()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
943 finalpath = paths[0][w] + revpath[1:]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
944 raise nx.NetworkXNoPath(f"No path between {source} and {target}.")