[SciPy-dev] Ball Tree class

Yaroslav Halchenko lists@onerussian....
Thu Dec 3 10:53:21 CST 2009

Hi Jake and SciPy,

I wonder what is the status of this endeavor?

For our little project we need fast search for a spherical neighborhood
in a cloud of points.  Only now I discovered that scipy has KDTree and
cKDTree which could be  used, BUT both interfaces are somewhat
misfit for this simple goal one way or another.

Also I've ran into libkdtree++ library with Python bindings which seems
to do close what I need (just does range search, not sphere but it could
be more or less efficiently computed post-hoc) and do it very
efficiently upon my simple tests: http://libkdtree.alioth.debian.org/
but it is under Artistic License 2.0...  but may be it might be of use
to inspire modification of scipy's ways to interface with the user

And Jake, how are you going along with your project since there were no
follow ups on this thread I wonder if there was any progress?

On Thu, 29 Oct 2009, Jake VanderPlas wrote:

> Hello,
> I've been using scipy.spatial.KDTree for my research, and found it
> very useful.  Recently, though, my datasets have been getting larger -
> upwards of 10,000 points in 1000-2000 dimensions.
> The KDTree starts getting slow with such a
> large dimensionality.  I've addressed this by writing a C++ Ball Tree
> code, and wrapping it using swig and numpy.i.  I've been wanting to
> begin contributing to the scipy project, and I think this would be a
> great place to start.  I'd like to begin the process of adding
> this to the scipy.spatial package.

> A few questions: Is it preferable to have an
> implementation in C rather than C++?  Cython, swig, or hand-wrapped code?
> cKDTree is written in Cython, with C.  Should I stick to that
> convention to maintain uniformity in the scipy.spatial package?
> Please let me know what you think
>   -Jake
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> Scipy-dev@scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev

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