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subhabangalore@gmail.com 01-13-2013 08:05 PM

Subgraph Drawing
 
Dear Group,

I have two questions, if I take a subseries of the matrix as in eigenvalue here,
provided I have one graph of the full form in G, how may I show it, as if I do the nx.draw(G) it takes only the original graph.

>>> import numpy
>>> import networkx as nx
>>> import matplotlib.pyplot as plt
>>> G=nx.Graph()
>>> G.add_edges_from([(1,2),(1,3),(1,3),(1,4),(1,5),(1,6),(1,7),(1,8)])
>>> L =nx.laplacian(G)
>>> print L

[[ 7. -1. -1. -1. -1. -1. -1. -1.]
[-1. 1. 0. 0. 0. 0. 0. 0.]
[-1. 0. 1. 0. 0. 0. 0. 0.]
[-1. 0. 0. 1. 0. 0. 0. 0.]
[-1. 0. 0. 0. 1. 0. 0. 0.]
[-1. 0. 0. 0. 0. 1. 0. 0.]
[-1. 0. 0. 0. 0. 0. 1. 0.]
[-1. 0. 0. 0. 0. 0. 0. 1.]]
>>> print numpy.linalg.eigvals(L)

[ 8.00000000e+00 2.22044605e-16 1.00000000e+00 1.00000000e+00
1.00000000e+00 1.00000000e+00 1.00000000e+00 1.00000000e+00]

for more than 1000 nodes it is coming too slow on Windows 7 machine with 3GB RAM.

If any one of the learned members can help.

Apology for any indentation error etc.

Thanking all in Advance,

Regards,
Subhabrata Banerjee.

Oscar Benjamin 01-13-2013 11:26 PM

Re: Subgraph Drawing
 
On 13 January 2013 20:05, <subhabangalore@gmail.com> wrote:
> Dear Group,
>
> I have two questions, if I take a subseries of the matrix as in eigenvalue here,
> provided I have one graph of the full form in G, how may I show it, as if I do the nx.draw(G) it takes only the original graph.


I'm sorry, but I really don't understand what you mean. When you say
"subseries" do you mean "subgraph"? Or do you mean a subset of the
eigenvalues?

It would be good if you could give a simple example of what you mean
using code and showing the expected/desired output.

>
>>>> import numpy
>>>> import networkx as nx
>>>> import matplotlib.pyplot as plt
>>>> G=nx.Graph()
>>>> G.add_edges_from([(1,2),(1,3),(1,3),(1,4),(1,5),(1,6),(1,7),(1,8)])
>>>> L =nx.laplacian(G)
>>>> print L

> [[ 7. -1. -1. -1. -1. -1. -1. -1.]
> [-1. 1. 0. 0. 0. 0. 0. 0.]
> [-1. 0. 1. 0. 0. 0. 0. 0.]
> [-1. 0. 0. 1. 0. 0. 0. 0.]
> [-1. 0. 0. 0. 1. 0. 0. 0.]
> [-1. 0. 0. 0. 0. 1. 0. 0.]
> [-1. 0. 0. 0. 0. 0. 1. 0.]
> [-1. 0. 0. 0. 0. 0. 0. 1.]]
>>>> print numpy.linalg.eigvals(L)

> [ 8.00000000e+00 2.22044605e-16 1.00000000e+00 1.00000000e+00
> 1.00000000e+00 1.00000000e+00 1.00000000e+00 1.00000000e+00]
>
> for more than 1000 nodes it is coming too slow on Windows 7 machine with 3GB RAM.


What is too slow?


Oscar

Steven D'Aprano 01-14-2013 12:35 AM

Re: Subgraph Drawing
 
On Sun, 13 Jan 2013 12:05:54 -0800, subhabangalore wrote:

> Dear Group,
>
> I have two questions, if I take a subseries of the matrix as in
> eigenvalue here, provided I have one graph of the full form in G, how
> may I show it, as if I do the nx.draw(G) it takes only the original
> graph.


Is this what you mean? If not, you will have to explain your question
better.


L = = nx.laplacian(G)
E = numpy.linalg.eigvals(L)
nx.draw(E)


> >>> print numpy.linalg.eigvals(L)

> [ 8.00000000e+00 2.22044605e-16 1.00000000e+00 1.00000000e+00
> 1.00000000e+00 1.00000000e+00 1.00000000e+00 1.00000000e+00]
> for more than 1000 nodes it is coming too slow on Windows 7 machine with
> 3GB RAM.


Get a faster machine. Or use fewer nodes. Or be patient and wait.

Solving a graph problem with 1000 nodes is a fairly big problem for a
desktop PC. It will take time. Calculations don't just happen instantly,
the more work you have to do the longer they take.

The last alternative is to ask on a specialist numpy list. But I expect
they will probably tell you the same thing.


--
Steven

subhabangalore@gmail.com 01-14-2013 04:01 AM

Re: Subgraph Drawing
 
On Monday, January 14, 2013 6:05:49 AM UTC+5:30, Steven D'Aprano wrote:
> On Sun, 13 Jan 2013 12:05:54 -0800, subhabangalore wrote:
>
>
>
> > Dear Group,

>
> >

>
> > I have two questions, if I take a subseries of the matrix as in

>
> > eigenvalue here, provided I have one graph of the full form in G, how

>
> > may I show it, as if I do the nx.draw(G) it takes only the original

>
> > graph.

>
>
>
> Is this what you mean? If not, you will have to explain your question
>
> better.
>
>
>
>
>
> L = = nx.laplacian(G)
>
> E = numpy.linalg.eigvals(L)
>
> nx.draw(E)
>
>
>
>
>
> > >>> print numpy.linalg.eigvals(L)

>
> > [ 8.00000000e+00 2.22044605e-16 1.00000000e+00 1.00000000e+00

>
> > 1.00000000e+00 1.00000000e+00 1.00000000e+00 1.00000000e+00]

>
> > for more than 1000 nodes it is coming too slow on Windows 7 machine with

>
> > 3GB RAM.

>
>
>
> Get a faster machine. Or use fewer nodes. Or be patient and wait.
>
>
>
> Solving a graph problem with 1000 nodes is a fairly big problem for a
>
> desktop PC. It will take time. Calculations don't just happen instantly,
>
> the more work you have to do the longer they take.
>
>
>
> The last alternative is to ask on a specialist numpy list. But I expect
>
> they will probably tell you the same thing.
>
>
>
>
>
> --
>
> Steven


Dear Steven,

Thank you for your kind effort. You got the problem right. But it is giving following error,
Traceback (most recent call last):
File "<pyshell#5>", line 1, in <module>
nx.draw(E)
File "C:\Python27\lib\site-packages\networkx\drawing\nx_pylab.py", line 138, in draw
draw_networkx(G,pos=pos,ax=ax,**kwds)
File "C:\Python27\lib\site-packages\networkx\drawing\nx_pylab.py", line 267, in draw_networkx
pos=nx.drawing.spring_layout(G) # default to spring layout
File "C:\Python27\lib\site-packages\networkx\drawing\layout.py", line 241, in fruchterman_reingold_layout
A=nx.to_numpy_matrix(G,weight=weight)
File "C:\Python27\lib\site-packages\networkx\convert.py", line 492, in to_numpy_matrix
nodelist = G.nodes()
AttributeError: 'numpy.ndarray' object has no attribute 'nodes'
>>>


there are other solution of converting back the matrix to graph should I try that?

Regards,
Subhabrata.

Steven D'Aprano 01-14-2013 04:13 AM

Re: Subgraph Drawing
 
On Sun, 13 Jan 2013 20:01:21 -0800, subhabangalore wrote:

> there are other solution of converting back the matrix to graph should I
> try that?


Yes.

--
Steven


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