Re: [Numpy-discussion] neighborhood iterator speed

2011-10-24 Thread David Cournapeau
On Mon, Oct 24, 2011 at 6:57 AM, Nadav Horesh nad...@visionsense.com wrote: I am trying to replace an old code (biliteral filter) that rely on ndimage.generic_filter with the neighborhood iterator. In the old code, the generic_filter generates a contiguous copy of the neighborhood, thus the

Re: [Numpy-discussion] neighborhood iterator speed

2011-10-24 Thread Nadav Horesh
* Iterator mode: Mirror. Does the mode make a huge difference? * I can not find any reference to PyArrayNeightborhoodIter_Next2d, where can I find it? * I think that making a copy on reset is (maybe in addition to the creation), since there is a reset for every change of the parent iterator, and

Re: [Numpy-discussion] NA masks in the next numpy release?

2011-10-24 Thread Lluís
Nathaniel Smith writes: [...] Is the idea to continue the discussion and rework the API while it is in master, delaying the next release for as long as it takes to achieve consensus? Well, for those who missed it, I think the first thing to do should be to carefully read and discuss the

Re: [Numpy-discussion] neighborhood iterator speed

2011-10-24 Thread David Cournapeau
On Mon, Oct 24, 2011 at 10:48 AM, Nadav Horesh nad...@visionsense.com wrote: * Iterator mode: Mirror. Does the mode make a huge difference? It could, at least in principle. The underlying translate function is called often enough that a slight different can be significant. * I can not find any

Re: [Numpy-discussion] neighborhood iterator speed

2011-10-24 Thread Nadav Horesh
* I'll try to implement the 2D iterator as far as far as my programming expertise goes. It might take few days. * There is a risk in providing a buffer pointer, and for my (and probably most) use cases it is better for the iterator constructor to provide it. I was thinking about the

[Numpy-discussion] ANN: MDP 3.2 released!

2011-10-24 Thread Tiziano Zito
We are glad to announce release 3.2 of the Modular toolkit for Data Processing (MDP). MDP is a Python library of widely used data processing algorithms that can be combined according to a pipeline analogy to build more complex data processing software. The base of available algorithms includes

Re: [Numpy-discussion] neighborhood iterator speed

2011-10-24 Thread David Cournapeau
On Mon, Oct 24, 2011 at 1:23 PM, Nadav Horesh nad...@visionsense.com wrote: * I'll try to implement the 2D iterator as far as far as my programming expertise goes. It might take few days. I am pretty sure the code is in the history, if you are patient enough to look for it in git history. I

Re: [Numpy-discussion] NA masks in the next numpy release?

2011-10-24 Thread Charles R Harris
On Sun, Oct 23, 2011 at 11:23 PM, Wes McKinney wesmck...@gmail.com wrote: On Sun, Oct 23, 2011 at 8:07 PM, Eric Firing efir...@hawaii.edu wrote: On 10/23/2011 12:34 PM, Nathaniel Smith wrote: like. And in this case I do think we can come up with an API that will make everyone happy, but

Re: [Numpy-discussion] NA masks in the next numpy release?

2011-10-24 Thread Charles R Harris
On Mon, Oct 24, 2011 at 8:40 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Sun, Oct 23, 2011 at 11:23 PM, Wes McKinney wesmck...@gmail.comwrote: On Sun, Oct 23, 2011 at 8:07 PM, Eric Firing efir...@hawaii.edu wrote: On 10/23/2011 12:34 PM, Nathaniel Smith wrote: like. And

Re: [Numpy-discussion] NA masks in the next numpy release?

2011-10-24 Thread Pauli Virtanen
24.10.2011 16:40, Charles R Harris kirjoitti: [clip] The missing data functionality looks far more like R than numpy.ma ... and masked arrays must be explicitly requested by the user [1]. The MA stuff can leak through only if the user makes use of a library that returns masked results (or

Re: [Numpy-discussion] neighborhood iterator speed

2011-10-24 Thread Nadav Horesh
My use case is a biliterl filter: It is a convolution-like filter used mainly in image-processing, which may use relatively large convolution kernels (in the order of 50x50). I would like to run the inner loop (iteration over the neighbourhood) with a direct indexing (in a cython code) rather

Re: [Numpy-discussion] NA masks in the next numpy release?

2011-10-24 Thread Wes McKinney
On Mon, Oct 24, 2011 at 10:54 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Mon, Oct 24, 2011 at 8:40 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Sun, Oct 23, 2011 at 11:23 PM, Wes McKinney wesmck...@gmail.com wrote: On Sun, Oct 23, 2011 at 8:07 PM, Eric Firing

Re: [Numpy-discussion] NA masks in the next numpy release?

2011-10-24 Thread Charles R Harris
On Mon, Oct 24, 2011 at 11:12 AM, Wes McKinney wesmck...@gmail.com wrote: On Mon, Oct 24, 2011 at 10:54 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Mon, Oct 24, 2011 at 8:40 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Sun, Oct 23, 2011 at 11:23 PM, Wes

Re: [Numpy-discussion] NA masks in the next numpy release?

2011-10-24 Thread Lluís
Charles R Harris writes: [...] It might useful to have a way of setting global defaults, or something like a with statement. These are the sort of things that can be adjusted based on experience. For instance, I'm thinking skipna=1 is the natural default for the masked arrays. I already

[Numpy-discussion] [ANN] Multifactor analysis tool for experiment planning

2011-10-24 Thread Dmitrey
Hi all, new OpenOpt feature is available: Multifactor analysis tool for experiment planning (in physics, chemistry, biology etc). It is based on numerical optimization solver BOBYQA, released in 2009 by Michael J.D. Powell, and has easy and convenient GUI frontend,

Re: [Numpy-discussion] neighborhood iterator speed

2011-10-24 Thread Nadav Horesh
I found the 2d iterator definition active in numpy 1.6.1. I'll test it. Nadav From: numpy-discussion-boun...@scipy.org [numpy-discussion-boun...@scipy.org] On Behalf Of David Cournapeau [courn...@gmail.com] Sent: 24 October 2011 16:04 To: Discussion of

[Numpy-discussion] numpy.matrix subclassing

2011-10-24 Thread David Voong
Hi guys, I have a question regarding subclassing of the numpy.matrix class. I read through the wiki page, http://docs.scipy.org/doc/numpy/user/basics.subclassing.html and tried to subclass numpy.matrix, I find that if I override the __finalize_array__ method I have problems using the sum method

[Numpy-discussion] Fwd: libmkl_lapack error in numpy

2011-10-24 Thread akshar bhosale
-- Forwarded message -- From: akshar bhosale akshar.bhos...@gmail.com Date: Sun, Oct 23, 2011 at 1:05 PM Subject: Re: libmkl_lapack error in numpy To: numpy-discussion@scipy.org Hi, libmkl_lapack.so is added in site.cfg and now the matrix function is not giving an error, but

[Numpy-discussion] float128 / longdouble on PPC - is it broken?

2011-10-24 Thread Matthew Brett
Hi, I just ran into this on a PPC machine: In [1]: import numpy as np In [2]: np.__version__ Out[2]: '2.0.0.dev-4daf949' In [3]: res = np.longdouble(2)**64 In [4]: res Out[4]: 18446744073709551616.0 In [5]: 2**64 Out[5]: 18446744073709551616L In [6]: res-1 Out[6]: 36893488147419103231.0