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Networkx "generalized_laplacian ()" is no longer working?

This example (from the Networkx manual http://networkx.imtqy.com/documentation/latest/examples/advanced/eigenvalues.html ):

#!/usr/bin/env python
"""
Create an G{n,m} random graph and compute the eigenvalues.

Requires numpy or LinearAlgebra package from Numeric Python.

Uses optional pylab plotting to produce histogram of eigenvalues.

"""
__author__ = """Aric Hagberg (hagberg@lanl.gov)"""
__credits__ = """"""
#    Copyright (C) 2004-2006 by
#    Aric Hagberg <hagberg@lanl.gov>
#    Dan Schult <dschult@colgate.edu>
#    Pieter Swart <swart@lanl.gov>
#    All rights reserved.
#    BSD license.

from networkx import *
try:
    import numpy.linalg
    eigenvalues=numpy.linalg.eigvals
except ImportError:
    raise ImportError("numpy can not be imported.")

try:
    from pylab import *
except:
    pass

n=1000 # 1000 nodes
m=5000 # 5000 edges

G=gnm_random_graph(n,m)

L=generalized_laplacian(G)
e=eigenvalues(L)
print("Largest eigenvalue:", max(e))
print("Smallest eigenvalue:", min(e))
# plot with matplotlib if we have it
# shows "semicircle" distribution of eigenvalues
try:
    hist(e,bins=100) # histogram with 100 bins
    xlim(0,2)  # eigenvalues between 0 and 2
    show()
except:
    pass

Causes the following error with the latest version of networkx:

Traceback (most recent call last):
  File "Untitled 2.py", line 36, in <module>
    L=generalized_laplacian(G)
NameError: name 'generalized_laplacian' is not defined

How do I go to make it work?

+4
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2 answers

This example is definitely broken with newer versions of NetworkX. Here's what works:

import networkx as nx
import numpy.linalg
import matplotlib.pyplot as plt

n = 1000 # 1000 nodes
m = 5000 # 5000 edges
G = nx.gnm_random_graph(n,m)

L = nx.normalized_laplacian_matrix(G)
e = numpy.linalg.eigvals(L.A)
print("Largest eigenvalue:", max(e))
print("Smallest eigenvalue:", min(e))
plt.hist(e,bins=100) # histogram with 100 bins
plt.xlim(0,2)  # eigenvalues between 0 and 2
plt.show()
+5
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I think the name has been removed in this commit :

Deprecate non-"matrix" names in laplacian.

Use laplacian_matrix, directed_laplacian_matrix, and normalized_laplacian_matrix only and deprecate other name aliases.

The lines that he changed from networkx/linalg/laplacianmatrix.pyinclude

-combinatorial_laplacian=laplacian_matrix
-generalized_laplacian=normalized_laplacian_matrix
-normalized_laplacian=normalized_laplacian_matrix
-laplacian=laplacian_matrix

So, I think you can use normalized_laplacian_matrixinstead:

>>> normalized_laplacian_matrix(G)
<1000x1000 sparse matrix of type '<type 'numpy.float64'>'
    with 11000 stored elements in Compressed Sparse Row format>
+1

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