Re: [Numpy-discussion] huge array calculation speed

[ Sorry I never sent this, I just found it in my drafts folder. Just in case it's useful to the OP, here it is. ] On Thu, Jul 10, 2008 at 9:38 AM, Dan Lussier <[EMAIL PROTECTED]> wrote: > r2 = numpy.power(r2,2).sum(axis=1) > > r2 = numpy.extract(r2

Re: [Numpy-discussion] huge array calculation speed

On Fri, Jul 11, 2008 at 11:04 AM, Lou Pecora <[EMAIL PROTECTED]> wrote: > If your positions are static (I'm not clear on that from your message), > then you might want to check the technique of "slice searching". It only > requires one sort of the data for each dimension initially, then uses a >

Re: [Numpy-discussion] huge array calculation speed

CHINE INTELLIGENCE 19 (9), 989 (1997). -- Lou Pecora, my views are my own. --- On Thu, 7/10/08, Dan Lussier <[EMAIL PROTECTED]> wrote: > From: Dan Lussier <[EMAIL PROTECTED]> > Subject: [Numpy-discussion] huge array calculation speed > To: numpy-discussion@scipy.org >

Re: [Numpy-discussion] huge array calculation speed

Hi, scikits.learn.machine/manifold_learning.regression.neighbor contains a kd-tree for neighbors search as well (implemented in C++). Matthieu 2008/7/11 Charles R Harris <[EMAIL PROTECTED]>: > > > On Thu, Jul 10, 2008 at 5:48 PM, Andrew Dalke <[EMAIL PROTECTED]> > wrote: > > > >> >> You can als

Re: [Numpy-discussion] huge array calculation speed

On Thu, Jul 10, 2008 at 5:48 PM, Andrew Dalke <[EMAIL PROTECTED]> wrote: > You can also grab the KDTree from Biopython, which is implemented in C. > > > http://www.biopython.org/DIST/docs/api/Bio.KDTree.KDTree'-module.html

Re: [Numpy-discussion] huge array calculation speed

On Jul 10, 2008, at 6:38 PM, Dan Lussier wrote: > What I'm trying to do is to calculate the total total potential > energy and coordination number of each atom within a relatively large > simulation. Anne Archibald already responded: > you could try a three-dimensional grid (if your atoms aren't >

Re: [Numpy-discussion] huge array calculation speed

Anne Archibald wrote: > Unfortunately, implementing most of the algorithms in the literature > within numpy is going to be fairly cumbersome. Maybe this rtree implementation would help: http://pypi.python.org/pypi/Rtree -Chris -- Christopher Barker, Ph.D. Oceanographer Emergency Response Divi

Re: [Numpy-discussion] huge array calculation speed

2008/7/10 Anne Archibald <[EMAIL PROTECTED]>: > Unfortunately, implementing most of the algorithms in the literature > within numpy is going to be fairly cumbersome. But I think there are > better algorithms you could try: There's also http://pypi.python.org/pypi/scikits.ann Regards Stéfan _

Re: [Numpy-discussion] huge array calculation speed

On Fri, Jul 11, 2008 at 5:55 AM, Anne Archibald <[EMAIL PROTECTED]> wrote: > 2008/7/10 Dan Lussier <[EMAIL PROTECTED]>: > > We seem to get quite a few posts from people wanting some kind of > spatial data structure (whether they know it or not). Would it make > sense to come up with some kind of c

Re: [Numpy-discussion] huge array calculation speed

On Thu, Jul 10, 2008 at 2:55 PM, Anne Archibald <[EMAIL PROTECTED]> wrote: > 2008/7/10 Dan Lussier <[EMAIL PROTECTED]>: > > > I am relatively new to numpy and am having trouble with the speed of > > a specific array based calculation that I'm trying to do. > > > > What I'm trying to do is to calcu

Re: [Numpy-discussion] huge array calculation speed

2008/7/10 Dan Lussier <[EMAIL PROTECTED]>: > I am relatively new to numpy and am having trouble with the speed of > a specific array based calculation that I'm trying to do. > > What I'm trying to do is to calculate the total total potential > energy and coordination number of each atom within a r

Re: [Numpy-discussion] huge array calculation speed

Charles R Harris wrote: > > > On Thu, Jul 10, 2008 at 10:38 AM, Dan Lussier <[EMAIL PROTECTED] > > wrote: > > Hello, > > I am relatively new to numpy and am having trouble with the speed of > a specific array based calculation that I'm trying to do. > > Wh

Re: [Numpy-discussion] huge array calculation speed

On Thu, Jul 10, 2008 at 10:38 AM, Dan Lussier <[EMAIL PROTECTED]> wrote: > Hello, > > I am relatively new to numpy and am having trouble with the speed of > a specific array based calculation that I'm trying to do. > > What I'm trying to do is to calculate the total total potential > energy and co

[Numpy-discussion] huge array calculation speed

Hello, I am relatively new to numpy and am having trouble with the speed of a specific array based calculation that I'm trying to do. What I'm trying to do is to calculate the total total potential energy and coordination number of each atom within a relatively large simulation. Each atom