[SciPy-user] Finding Neighboors

Barry Wark barrywark@gmail....
Wed Aug 1 15:31:58 CDT 2007


Hi all,

Catching this conversation late. As jelle points out, BioPython has a
k-d tree implemetation, but it hasn't been converted to numpy yet (I
think it still uses Numeric). I've written a SWIG (with numpy type
maps) wrapper around the Approximate Nearest Neighbor library
(http://www.cs.umd.edu/~mount/ANN/), which includes both exact and
approximate k-d tree searches. Email me off list if you would like a
copy of the swig definition files. If there's interest, I will send it
on to the ANN writers for inclusion in the library itself.

Barry

On 7/31/07, Emanuele Zattin <emanuelez@gmail.com> wrote:
> Hi, you might want to take a look at kd-trees. No implementation in
> scipy, but it should not be too hard to achieve. As far as i can
> remember its definition in wikipedia includes some python code. Just
> my 2 cents :)
>
> On 8/1/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
> > Hi,
> >
> > I have an implementation, but it depends on my own matrix library... That's
> > a stopper... But it works.
> > I do not know the other templated matrix libraries very well, but I'd say I
> > do not need much to make it work with another library.
> >
> > Matthieu
> >
> > 2007/8/1, Alan G Isaac <aisaac@american.edu>:
> > > On Tue, 17 Apr 2007, Matthieu Brucher apparently wrote:
> > > > I wanted to know if there was a module in scipy that is able to find the
> > > > k-neighboors of a point ?
> > > > If so, is there an optimized one - tree-based search - ?
> > > > If not, I'm doing the optimized version.
> > >
> > > Hi Matthieu,
> > >
> > > Where did you go with this?
> > >
> > > Thanks!
> > > Alan
> > >
> > >
> > >
> > >
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> >
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>
>
> --
> Emanuele Zattin
> ---------------------------------------------------
> -I don't have to know an answer. I don't feel frightened by not
> knowing things; by being lost in a mysterious universe without any
> purpose — which is the way it really is, as far as I can tell,
> possibly. It doesn't frighten me.- Richard Feynman
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