Re: [Numpy-discussion] how to compile Fortran using setup.py

2011-03-11 Thread Dag Sverre Seljebotn
On 03/11/2011 07:57 AM, Ondrej Certik wrote: On Thu, Mar 10, 2011 at 8:25 PM, Robert Kernrobert.k...@gmail.com wrote: On Thu, Mar 10, 2011 at 19:58, Ondrej Certikond...@certik.cz wrote: Hi, I spent about an hour googling and didn't figure this out. Here is my setup.py: setup( name

Re: [Numpy-discussion] how to compile Fortran using setup.py

2011-03-11 Thread Dag Sverre Seljebotn
On 03/11/2011 09:13 AM, Dag Sverre Seljebotn wrote: On 03/11/2011 07:57 AM, Ondrej Certik wrote: On Thu, Mar 10, 2011 at 8:25 PM, Robert Kernrobert.k...@gmail.com wrote: On Thu, Mar 10, 2011 at 19:58, Ondrej Certikond...@certik.cz wrote: Hi, I spent about an hour googling and didn't

[Numpy-discussion] broadcasting behavior for 1.6 (was: Numpy 1.6 schedule)

2011-03-11 Thread Ralf Gommers
I'm just going through the very long 1.6 schedule thread to see what is still on the TODO list before a 1.6.x branch can be made. So I'll send a few separate mails, one for each topic. On Mon, Mar 7, 2011 at 8:30 PM, Francesc Alted fal...@pytables.org wrote: A Sunday 06 March 2011 06:47:34 Mark

[Numpy-discussion] Structured array copying by field name (was: Numpy 1.6 schedule)

2011-03-11 Thread Ralf Gommers
On Tue, Mar 8, 2011 at 1:35 AM, Pauli Virtanen p...@iki.fi wrote: Structured array copying copies by field name. Commit 22d96096bf7d5fb199ca80f2fcd04e8d27815476 Before: x = np.array([(0, 1)], dtype=[('a', int), ('b', int)]) y = np.array([(2, 3)], dtype=[('a', int), ('b', int)]) y =

[Numpy-discussion] memory layout, K vs C order (was: Numpy 1.6 schedule)

2011-03-11 Thread Ralf Gommers
On Tue, Mar 8, 2011 at 1:35 AM, Pauli Virtanen p...@iki.fi wrote: Ufuncs don't necessarily return arrays in C-order, but instead try to keep the memory layout of the original if it seems advantageous vs. memory access. Before: np.sin(np.zeros((5,5,5)).transpose(1,2,0)).strides (200, 40,

Re: [Numpy-discussion] broadcasting behavior for 1.6 (was: Numpy 1.6 schedule)

2011-03-11 Thread Charles R Harris
On Fri, Mar 11, 2011 at 2:01 AM, Ralf Gommers ralf.gomm...@googlemail.comwrote: I'm just going through the very long 1.6 schedule thread to see what is still on the TODO list before a 1.6.x branch can be made. So I'll send a few separate mails, one for each topic. On Mon, Mar 7, 2011 at 8:30

Re: [Numpy-discussion] broadcasting behavior for 1.6 (was: Numpy 1.6 schedule)

2011-03-11 Thread Charles R Harris
On Fri, Mar 11, 2011 at 7:42 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Fri, Mar 11, 2011 at 2:01 AM, Ralf Gommers ralf.gomm...@googlemail.com wrote: I'm just going through the very long 1.6 schedule thread to see what is still on the TODO list before a 1.6.x branch can be

Re: [Numpy-discussion] broadcasting behavior for 1.6 (was: Numpy 1.6 schedule)

2011-03-11 Thread Wes McKinney
On Fri, Mar 11, 2011 at 9:57 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Fri, Mar 11, 2011 at 7:42 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Fri, Mar 11, 2011 at 2:01 AM, Ralf Gommers ralf.gomm...@googlemail.com wrote: I'm just going through the very long 1.6

Re: [Numpy-discussion] broadcasting behavior for 1.6 (was: Numpy 1.6 schedule)

2011-03-11 Thread Charles R Harris
On Fri, Mar 11, 2011 at 8:06 AM, Wes McKinney wesmck...@gmail.com wrote: On Fri, Mar 11, 2011 at 9:57 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Fri, Mar 11, 2011 at 7:42 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Fri, Mar 11, 2011 at 2:01 AM, Ralf

[Numpy-discussion] assert_almost_equal bug?

2011-03-11 Thread Keith Goodman
assert_almost_equal() and assert_array_almost_equal() raise a ValueError instead of an AssertionError when the array contains np.inf: a = np.array([[1., 2.], [3., 4.]]) b = a.copy() np.testing.assert_almost_equal(a, b) b[0,0] = np.inf np.testing.assert_almost_equal(a, b) snip ValueError:

Re: [Numpy-discussion] Anybody going to PyCon?

2011-03-11 Thread Charles R Harris
On Mon, Mar 7, 2011 at 7:11 AM, David Cournapeau courn...@gmail.com wrote: On Mon, Mar 7, 2011 at 5:53 PM, Gökhan Sever gokhanse...@gmail.com wrote: Hello, I am going to the PyCon this week. I am presenting a poster about an atmospheric sciences related project -- the most active

Re: [Numpy-discussion] broadcasting behavior for 1.6 (was: Numpy 1.6 schedule)

2011-03-11 Thread Charles R Harris
On Fri, Mar 11, 2011 at 9:19 AM, Travis Oliphant oliph...@enthought.comwrote: This discussion is interesting and useful for NumPy 2.0, but the subtle change is not acceptable for NumPy 1.6. The rules were consistent, even if seen as unintuitive by some. The fact that two libraries we know

Re: [Numpy-discussion] ragged array implimentation

2011-03-11 Thread Francesc Alted
A Thursday 10 March 2011 22:25:27 Christopher Barker escrigué: On 3/10/11 12:01 PM, Francesc Alted wrote: 3) when the extra space is used up, it re-allocates the entire array, with some more extra room again, carray works exactly the same: the extra room is just a new chunk does it

Re: [Numpy-discussion] how to compile Fortran using setup.py

2011-03-11 Thread Ondrej Certik
On Fri, Mar 11, 2011 at 12:24 AM, Dag Sverre Seljebotn d.s.seljeb...@astro.uio.no wrote: On 03/11/2011 09:13 AM, Dag Sverre Seljebotn wrote: On 03/11/2011 07:57 AM, Ondrej Certik wrote: On Thu, Mar 10, 2011 at 8:25 PM, Robert Kernrobert.k...@gmail.com   wrote: On Thu, Mar 10, 2011 at 19:58,

[Numpy-discussion] loop vectorization

2011-03-11 Thread Thomas K Gamble
I have the followin loop in my code: for i in range(0, nFrames): data += dot(transpose(bipData[:,i,:]), bipData[:,i,:]) bipData is a 1024x258x256 double precision float array. The loop takes all of 15 seconds to run on my computer and, with several hundred files to process... Is

[Numpy-discussion] Using ndpointer with ctypes argtypes

2011-03-11 Thread Josh Mayer
I am trying to call a C function that takes a double array as one of its parameters. I am using ndpointer to define the argtypes so that I can pass a numpy array directly. The issue I'm having is that this parameter need not always be set, and when it is not set, the C functions expects a null

[Numpy-discussion] RFC: Detecting array changes (NumPy 2.0?)

2011-03-11 Thread Dag Sverre Seljebotn
There's a few libraries out there that needs to know whether or not an array changed since the last time it was used: joblib and pymc comes to mind. I believe joblib computes a SHA1 or md5 hash of array contents, while pymc simply assume you never change an array and uses the id(). The pymc

Re: [Numpy-discussion] RFC: Detecting array changes (NumPy 2.0?)

2011-03-11 Thread Charles R Harris
On Fri, Mar 11, 2011 at 11:41 AM, Dag Sverre Seljebotn d.s.seljeb...@astro.uio.no wrote: There's a few libraries out there that needs to know whether or not an array changed since the last time it was used: joblib and pymc comes to mind. I believe joblib computes a SHA1 or md5 hash of array

Re: [Numpy-discussion] loop vectorization

2011-03-11 Thread Josh Hykes
I think you can use tensordot here. Maybe something like the following: from numpy.random import random import numpy as np ni, nj, nk = 4, 5, 6 bipData = random((ni,nj,nk)) data1 = np.zeros((nk,nk)) # loop for i in range(nj): data1 += np.dot(np.transpose(bipData[:,i,:]), bipData[:,i,:])

Re: [Numpy-discussion] loop vectorization

2011-03-11 Thread qubax
we have had that discussion about ... two days ago. please look up 'How to sum weighted matrices' with at least two efficient solutions. On Fri, Mar 11, 2011 at 02:00:09PM -0500, Josh Hykes wrote: I think you can use tensordot here. Maybe something like the following: from

Re: [Numpy-discussion] RFC: Detecting array changes (NumPy 2.0?)

2011-03-11 Thread Pauli Virtanen
On Fri, 11 Mar 2011 11:47:58 -0700, Charles R Harris wrote: [clip] What about views? Wouldn't it be easier to write another object wrapping an ndarray? I think the buffer interfaces and all other various ways Numpy provides exports for arrays make keeping tabs on modification impossible to do

Re: [Numpy-discussion] RFC: Detecting array changes (NumPy 2.0?)

2011-03-11 Thread Dag Sverre Seljebotn
On Fri, 11 Mar 2011 19:37:42 + (UTC), Pauli Virtanen p...@iki.fi wrote: On Fri, 11 Mar 2011 11:47:58 -0700, Charles R Harris wrote: [clip] What about views? Wouldn't it be easier to write another object wrapping an ndarray? I think the buffer interfaces and all other various ways

Re: [Numpy-discussion] broadcasting behavior for 1.6 (was: Numpy 1.6 schedule)

2011-03-11 Thread Mark Wiebe
On Fri, Mar 11, 2011 at 8:19 AM, Travis Oliphant oliph...@enthought.comwrote: This discussion is interesting and useful for NumPy 2.0, but the subtle change is not acceptable for NumPy 1.6. The rules were consistent, even if seen as unintuitive by some. The fact that two libraries we know

Re: [Numpy-discussion] Structured array copying by field name (was: Numpy 1.6 schedule)

2011-03-11 Thread Mark Wiebe
On Fri, Mar 11, 2011 at 1:07 AM, Ralf Gommers ralf.gomm...@googlemail.comwrote: On Tue, Mar 8, 2011 at 1:35 AM, Pauli Virtanen p...@iki.fi wrote: Structured array copying copies by field name. Commit 22d96096bf7d5fb199ca80f2fcd04e8d27815476 Before: x = np.array([(0, 1)],

Re: [Numpy-discussion] memory layout, K vs C order (was: Numpy 1.6 schedule)

2011-03-11 Thread Mark Wiebe
On Fri, Mar 11, 2011 at 1:13 AM, Ralf Gommers ralf.gomm...@googlemail.comwrote: On Tue, Mar 8, 2011 at 1:35 AM, Pauli Virtanen p...@iki.fi wrote: Ufuncs don't necessarily return arrays in C-order, but instead try to keep the memory layout of the original if it seems advantageous vs.

Re: [Numpy-discussion] RFC: Detecting array changes (NumPy 2.0?)

2011-03-11 Thread Charles R Harris
On Fri, Mar 11, 2011 at 1:06 PM, Dag Sverre Seljebotn d.s.seljeb...@astro.uio.no wrote: On Fri, 11 Mar 2011 19:37:42 + (UTC), Pauli Virtanen p...@iki.fi wrote: On Fri, 11 Mar 2011 11:47:58 -0700, Charles R Harris wrote: [clip] What about views? Wouldn't it be easier to write

Re: [Numpy-discussion] RFC: Detecting array changes (NumPy 2.0?)

2011-03-11 Thread Anne Archibald
On 11 March 2011 15:34, Charles R Harris charlesr.har...@gmail.com wrote: On Fri, Mar 11, 2011 at 1:06 PM, Dag Sverre Seljebotn d.s.seljeb...@astro.uio.no wrote: On Fri, 11 Mar 2011 19:37:42 + (UTC), Pauli Virtanen p...@iki.fi wrote: On Fri, 11 Mar 2011 11:47:58 -0700, Charles R

Re: [Numpy-discussion] RFC: Detecting array changes (NumPy 2.0?)

2011-03-11 Thread Dag Sverre Seljebotn
On 03/11/2011 10:04 PM, Anne Archibald wrote: On 11 March 2011 15:34, Charles R Harrischarlesr.har...@gmail.com wrote: On Fri, Mar 11, 2011 at 1:06 PM, Dag Sverre Seljebotn d.s.seljeb...@astro.uio.no wrote: On Fri, 11 Mar 2011 19:37:42 + (UTC), Pauli Virtanenp...@iki.fi wrote: On

Re: [Numpy-discussion] broadcasting behavior for 1.6 (was: Numpy 1.6 schedule)

2011-03-11 Thread Benjamin Root
On Fri, Mar 11, 2011 at 4:33 PM, Charles R Harris charlesr.har...@gmail.com wrote: On Fri, Mar 11, 2011 at 1:10 PM, Mark Wiebe mwwi...@gmail.com wrote: On Fri, Mar 11, 2011 at 8:19 AM, Travis Oliphant oliph...@enthought.comwrote: This discussion is interesting and useful for NumPy 2.0,

Re: [Numpy-discussion] Structured array copying by field name (was: Numpy 1.6 schedule)

2011-03-11 Thread Benjamin Root
On Fri, Mar 11, 2011 at 2:20 PM, Mark Wiebe mwwi...@gmail.com wrote: On Fri, Mar 11, 2011 at 1:07 AM, Ralf Gommers ralf.gomm...@googlemail.com wrote: On Tue, Mar 8, 2011 at 1:35 AM, Pauli Virtanen p...@iki.fi wrote: Structured array copying copies by field name. Commit

Re: [Numpy-discussion] RFC: Detecting array changes (NumPy 2.0?)

2011-03-11 Thread Charles R Harris
On Fri, Mar 11, 2011 at 12:37 PM, Pauli Virtanen p...@iki.fi wrote: On Fri, 11 Mar 2011 11:47:58 -0700, Charles R Harris wrote: [clip] What about views? Wouldn't it be easier to write another object wrapping an ndarray? I think the buffer interfaces and all other various ways Numpy

Re: [Numpy-discussion] Inaccuracy in documentation of np.linalg.pinv

2011-03-11 Thread Hao Xiong
Hi Ralf, I am happy to edit it, although I will have to do it later as I won't have much free time recently. I have registered as haoxiong on docs.scipy.org and would like to request edit rights to the pinv page. Thanks, Hao On 03/09/11 04:16, Ralf Gommers wrote: Hi Hao, On Wed, Mar 9,