Re: [igraph] MCL Algorithm

[Gábor Csárdi]

Thanks Chris, I've added your code to the (experimental and rather
empty) igraph wiki:
http://igraph.wikidot.com/community-detection-in-python
I hope you don't mind.

G.

On Wed, Dec 31, 2008 at 5:11 PM, Chris Wj <address@hidden> wrote:
> Well we certainly appreciate all the work you put in to the library.
>
> Quick Python code snippet I whipped up to test using MLC with igraph (uses
> subprocess and pipes):
>
> import igraph
>
> def igraph_to_mcl_matrix():
>     from subprocess import Popen, PIPE
>     from cStringIO import StringIO
>     G1 = igraph.Graph(n=3)
>     G1.add_edges(((0,1),(0,2),(1,2)))
>     mcifile = StringIO()
>     mclheader = (
>         ("\n(mclheader\n"),
>         ("mcltype matrix\n"),
>         ( "dimensions %sx%s\n)\n" % (G1.vcount(), G1.vcount()) ),
>         ("(mclmatrix\n"),
>         ("begin\n")
>     )
>     mcifile.writelines(mclheader)
>     for v in G1.vs:
>         mcifile.write(str(v.index) + " ")
>         for n in G1.neighbors(v.index):
>             mcifile.write(str(n) + " ")
>         mcifile.write(" $\n")
>     mcifile.write(")\n")
>     mcifile.seek(0)
>     cmd = "mcl - -o -"
>     p = Popen(cmd, stdout=PIPE, stdin=PIPE, stderr=PIPE)
>     sout,serr = p.communicate(mcifile.read())
>     p.wait()
>     #print "return code: %i\n" % p.returncode
>     if p.returncode==0 and len(sout)>0:
>         lines = sout.splitlines()
>         idx_begin = lines.index("begin")+1
>         idx_end = lines[idx_begin:].index(")")+idx_begin
>         for line in lines[idx_begin:idx_end]:
>             print line
>
> I used StringIO because I originally was using file IO before piping and it
> was easier to switch the code back and forth between string and file
> objects.
>
> On Wed, Dec 31, 2008 at 3:43 AM, Gábor Csárdi <address@hidden> wrote:
>>
>> Chris,
>>
>> this is always a difficult decision, the main problem is, that it is
>> not easy to do it in a way that allows us to include future updates as
>> well. Furthermore we will need to maintain the code in the future and
>> that is sometimes problematic, a large portion of portability problems
>> we get are due to some 3rd party C++ codes we put into igraph....
>>
>> We already include many smaller and bigger pieces of software, e.g.
>> the walktrap, the spinglass community finding algorithms, parts of
>> ARPACK, LAPACK and BLAS, the BLISS graph isomorphism library, etc.
>>
>> Maybe I am just frustrated because I have been trying to repair the
>> igraph version of ARPACK for a couple of days now....
>>
>> But actually the MCL code looks pretty good. So we will see. Thanks for
>> the tip.
>>
>> Best,
>> Gabor
>>
>> On Tue, Dec 30, 2008 at 11:20 PM, Chris Wj <address@hidden> wrote:
>> > I have been using MCL lately and before working on a way to export
>> > igraph in
>> > MCL matrix format, I was looking to see if there was any further
>> > thoughts on
>> > including this library in igraph. I searched the archives and found that
>> > Tamas said something about possibly including MCL in igraph.
>> > For now, I will probably just exec it (popen) to test it.
>> >
>> > MCL: http://www.micans.org/mcl/
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > http://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> >
>>
>>
>>
>> --
>> Gabor Csardi <address@hidden>     UNIL DGM
>>
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
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>
>



-- 
Gabor Csardi <address@hidden>     UNIL DGM