[Numpy-discussion] finding close together points.
Tue Nov 10 23:51:16 CST 2009
Anne Archibald wrote:
> 2009/11/10 Christopher Barker <Chris.Barker@noaa.gov>:
>> I have a bunch of points in 2-d space, and I need to find out which
>> pairs of points are within a certain distance of one-another (regular
>> old Euclidean norm).
> This is an eminently reasonable thing to want, and KDTree should
> support it. Unfortunately it doesn't.
> It's slow both because you're using the python implementation rather
> than the C,
I noticed that.
> The one good thing about using the python implementation rather than
> the Cython one is that you can subclass it, providing a new method.
> There's still a certain amount of boilerplate code to write, but it
> shouldn't be too bad.
Can you give me a hint as to where to start? I have no idea how kd
> If this is still too slow, I have no problem incorporating additional
> code into cKDTree; the only reason none of the ball queries are in
> there is because ball queries must return variable-size results, so
> you lose a certain amount of speed because you're forced to manipulate
> python objects. But if there are relatively few result points, this
> need not be much of a slowdown.
And certainly in this case, there would not be very many results, and
lists are pretty fast.
However, this does bring up the need for a growable numpy array. I've
been working on one in Python, but it would be really nice to have one
that could be accessed by C (or cython) code.
It wouldn't be that hard to do (for someone familiar with the numpy
code, anyway), I don't think. It is mostly boiler plate in Python. I'm
imagining it would only support contiguous arrays, and could only grow
is the first dimension.
Christopher Barker, Ph.D.
Emergency Response Division
NOAA/NOS/OR&R (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
More information about the NumPy-Discussion