Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/networkx/linalg/spectrum.py @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author | shellac |
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date | Thu, 14 May 2020 14:56:58 -0400 |
parents | 26e78fe6e8c4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/networkx/linalg/spectrum.py Thu May 14 14:56:58 2020 -0400 @@ -0,0 +1,172 @@ +""" +Eigenvalue spectrum of graphs. +""" +# Copyright (C) 2004-2019 by +# Aric Hagberg <hagberg@lanl.gov> +# Dan Schult <dschult@colgate.edu> +# Pieter Swart <swart@lanl.gov> +# All rights reserved. +# BSD license. +import networkx as nx +__author__ = "\n".join(['Aric Hagberg <aric.hagberg@gmail.com>', + 'Pieter Swart (swart@lanl.gov)', + 'Dan Schult(dschult@colgate.edu)', + 'Jean-Gabriel Young (jean.gabriel.young@gmail.com)']) + +__all__ = ['laplacian_spectrum', 'adjacency_spectrum', 'modularity_spectrum', + 'normalized_laplacian_spectrum', 'bethe_hessian_spectrum'] + + +def laplacian_spectrum(G, weight='weight'): + """Returns eigenvalues of the Laplacian of G + + Parameters + ---------- + G : graph + A NetworkX graph + + weight : string or None, optional (default='weight') + The edge data key used to compute each value in the matrix. + If None, then each edge has weight 1. + + Returns + ------- + evals : NumPy array + Eigenvalues + + Notes + ----- + For MultiGraph/MultiDiGraph, the edges weights are summed. + See to_numpy_matrix for other options. + + See Also + -------- + laplacian_matrix + """ + from scipy.linalg import eigvalsh + return eigvalsh(nx.laplacian_matrix(G, weight=weight).todense()) + + +def normalized_laplacian_spectrum(G, weight='weight'): + """Return eigenvalues of the normalized Laplacian of G + + Parameters + ---------- + G : graph + A NetworkX graph + + weight : string or None, optional (default='weight') + The edge data key used to compute each value in the matrix. + If None, then each edge has weight 1. + + Returns + ------- + evals : NumPy array + Eigenvalues + + Notes + ----- + For MultiGraph/MultiDiGraph, the edges weights are summed. + See to_numpy_matrix for other options. + + See Also + -------- + normalized_laplacian_matrix + """ + from scipy.linalg import eigvalsh + return eigvalsh(nx.normalized_laplacian_matrix(G, weight=weight).todense()) + + +def adjacency_spectrum(G, weight='weight'): + """Returns eigenvalues of the adjacency matrix of G. + + Parameters + ---------- + G : graph + A NetworkX graph + + weight : string or None, optional (default='weight') + The edge data key used to compute each value in the matrix. + If None, then each edge has weight 1. + + Returns + ------- + evals : NumPy array + Eigenvalues + + Notes + ----- + For MultiGraph/MultiDiGraph, the edges weights are summed. + See to_numpy_matrix for other options. + + See Also + -------- + adjacency_matrix + """ + from scipy.linalg import eigvals + return eigvals(nx.adjacency_matrix(G, weight=weight).todense()) + + +def modularity_spectrum(G): + """Returns eigenvalues of the modularity matrix of G. + + Parameters + ---------- + G : Graph + A NetworkX Graph or DiGraph + + Returns + ------- + evals : NumPy array + Eigenvalues + + See Also + -------- + modularity_matrix + + References + ---------- + .. [1] M. E. J. Newman, "Modularity and community structure in networks", + Proc. Natl. Acad. Sci. USA, vol. 103, pp. 8577-8582, 2006. + """ + from scipy.linalg import eigvals + if G.is_directed(): + return eigvals(nx.directed_modularity_matrix(G)) + else: + return eigvals(nx.modularity_matrix(G)) + + +def bethe_hessian_spectrum(G, r=None): + """Returns eigenvalues of the Bethe Hessian matrix of G. + + Parameters + ---------- + G : Graph + A NetworkX Graph or DiGraph + + r : float + Regularizer parameter + + Returns + ------- + evals : NumPy array + Eigenvalues + + See Also + -------- + bethe_hessian_matrix + + References + ---------- + .. [1] A. Saade, F. Krzakala and L. Zdeborová + "Spectral clustering of graphs with the bethe hessian", + Advances in Neural Information Processing Systems. 2014. + """ + from scipy.linalg import eigvalsh + return eigvalsh(nx.bethe_hessian_matrix(G, r).todense()) + + +# fixture for pytest +def setup_module(module): + import pytest + scipy.linalg = pytest.importorskip('scipy.linalg')