[SciPy-dev] scipy.distance

Charles R Harris charlesr.harris@gmail....
Mon Nov 3 11:30:57 CST 2008


On Mon, Nov 3, 2008 at 1:36 AM, Anne Archibald
<aarchiba@physics.mcgill.ca>wrote:

> 2008/11/3 Charles R Harris <charlesr.harris@gmail.com>:
>
> > I usually want a complete list of points in some neighborhood. I looked
> > through your cython code and I think the loops can be improved a bit to
> make
> > better use of low level C code.
>
> The C implementation doesn't currently do this at all. It'd be a good
> addition, though I think you'd have to use object arrays of lists,
> which have always made me faintly queasy. You'd want a whole separate
> tree-traversal routine here, with short-circuit branches for both
> all-in-the-neighborhood and all-outside-the-neighborhood. Since kdtree
> construction is rather fast, does it perhaps make sense to write a
> two-tree version?
>

Looks like the BioPython folks have been busy. The KDTree code has been
updated to use numpy and converted to C from C++. You can view the code in
CVS here<http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/KDTree/?cvsroot=biopython>
.

Chuck
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