Re: [Numpy-discussion] Creating a bool array with Cython

2012-02-26 Thread Neal Becker
Keith Goodman wrote: Is this a reasonable (and fast) way to create a bool array in cython? def makebool(): cdef: int n = 2 np.npy_intp *dims = [n] np.ndarray[np.uint8_t, ndim=1] a a = PyArray_EMPTY(1, dims, NPY_UINT8, 0)

Re: [Numpy-discussion] Problem Building Numpy with Python 2.7.1 and OS X 10.7.3

2012-02-26 Thread Samuel John
Hi The plain gcc (non-llvm) is no longer there, if you install Lion and directly Xcode 4.3. Only, if you have the old Xcode 4.2 or lower, then you may have a non-llvm gcc. For Xcode 4.3, I recommend installing the Command Line Tools for Xcode from the preferences of Xcode. Then you'll have the

Re: [Numpy-discussion] Creating a bool array with Cython

2012-02-26 Thread Keith Goodman
On Sat, Feb 25, 2012 at 7:04 PM, Dag Sverre Seljebotn d.s.seljeb...@astro.uio.no wrote: On 02/25/2012 03:26 PM, Keith Goodman wrote: Is this a reasonable (and fast) way to create a bool array in cython?      def makebool():          cdef:              int n = 2              np.npy_intp

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Warren Weckesser
On Thu, Feb 23, 2012 at 2:19 PM, Warren Weckesser warren.weckes...@enthought.com wrote: On Thu, Feb 23, 2012 at 2:08 PM, Travis Oliphant tra...@continuum.iowrote: This is actually on my short-list as well --- it just didn't make it to the list. In fact, we have someone starting work on it

[Numpy-discussion] log relative error

2012-02-26 Thread josef . pktd
(I got distracted by some numerical accuracy checks. np.polyfit looks good in NIST test.) Does numpy have something like this? def lre(actual, desired): '''calculate log relative error, number of correct significant digits not an informative function name Parameters --

Re: [Numpy-discussion] Migrating issues to GitHub

2012-02-26 Thread Wes McKinney
On Thu, Feb 16, 2012 at 4:32 PM, Ralf Gommers ralf.gomm...@googlemail.com wrote: On Thu, Feb 16, 2012 at 10:20 PM, Thouis (Ray) Jones tho...@gmail.com wrote: On Thu, Feb 16, 2012 at 19:25, Ralf Gommers ralf.gomm...@googlemail.com wrote: In another thread Jira was proposed as an

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Nathaniel Smith
On Sun, Feb 26, 2012 at 5:23 PM, Warren Weckesser warren.weckes...@enthought.com wrote: I haven't pushed it to the extreme, but the big example (in the examples/ directory) is a 1 gig text file with 2 million rows and 50 fields in each row.  This is read in less than 30 seconds (but that's with

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Warren Weckesser
On Sun, Feb 26, 2012 at 1:00 PM, Nathaniel Smith n...@pobox.com wrote: On Sun, Feb 26, 2012 at 5:23 PM, Warren Weckesser warren.weckes...@enthought.com wrote: I haven't pushed it to the extreme, but the big example (in the examples/ directory) is a 1 gig text file with 2 million rows and

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Francesc Alted
On Feb 26, 2012, at 1:16 PM, Warren Weckesser wrote: For anyone benchmarking software like this, be sure to clear the disk cache before each run. In linux: $ sync $ sudo sh -c echo 3 /proc/sys/vm/drop_caches It is also a good idea to run a disk-cache enabled test too, just to better

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Nathaniel Smith
On Sun, Feb 26, 2012 at 7:16 PM, Warren Weckesser warren.weckes...@enthought.com wrote: On Sun, Feb 26, 2012 at 1:00 PM, Nathaniel Smith n...@pobox.com wrote: For this kind of benchmarking, you'd really rather be measuring the CPU time, or reading byte streams that are already in memory. If you

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Warren Weckesser
On Sun, Feb 26, 2012 at 1:49 PM, Nathaniel Smith n...@pobox.com wrote: On Sun, Feb 26, 2012 at 7:16 PM, Warren Weckesser warren.weckes...@enthought.com wrote: On Sun, Feb 26, 2012 at 1:00 PM, Nathaniel Smith n...@pobox.com wrote: For this kind of benchmarking, you'd really rather be

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Francesc Alted
On Feb 26, 2012, at 1:49 PM, Nathaniel Smith wrote: On Sun, Feb 26, 2012 at 7:16 PM, Warren Weckesser warren.weckes...@enthought.com wrote: On Sun, Feb 26, 2012 at 1:00 PM, Nathaniel Smith n...@pobox.com wrote: For this kind of benchmarking, you'd really rather be measuring the CPU time, or

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Nathaniel Smith
On Sun, Feb 26, 2012 at 7:58 PM, Warren Weckesser warren.weckes...@enthought.com wrote: Right, I got that.  Sorry if the placement of the notes about how to clear the cache seemed to imply otherwise. OK, cool, np. Clearing the disk cache is very important for getting meaningful, repeatable

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Warren Weckesser
On Sun, Feb 26, 2012 at 3:00 PM, Nathaniel Smith n...@pobox.com wrote: On Sun, Feb 26, 2012 at 7:58 PM, Warren Weckesser warren.weckes...@enthought.com wrote: Right, I got that. Sorry if the placement of the notes about how to clear the cache seemed to imply otherwise. OK, cool, np.

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Erin Sheldon
Excerpts from Warren Weckesser's message of Sun Feb 26 16:22:35 -0500 2012: Yes, thanks! I'm working on a mmap version now. I'm very curious to see just how much of an improvement it can give. FYI, memmap is generally an incomplete solution for numpy arrays; it only understands rows, not

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Erin Sheldon
Excerpts from Erin Sheldon's message of Sun Feb 26 17:35:00 -0500 2012: Excerpts from Warren Weckesser's message of Sun Feb 26 16:22:35 -0500 2012: Yes, thanks! I'm working on a mmap version now. I'm very curious to see just how much of an improvement it can give. FYI, memmap is

Re: [Numpy-discussion] Problem Building Numpy with Python 2.7.1 and OS X 10.7.3

2012-02-26 Thread Patrick Armstrong
Hi, On 2012-02-25, at 5:14 AM, Ralf Gommers wrote: Since you're using pip, I assume that gcc-4.2 is llvm-gcc. As a first step, I suggest using plain gcc and not using pip (so just python setup.py install). Also make sure you follow the recommendations in version specific notes at

[Numpy-discussion] How to modify an array

2012-02-26 Thread tetsuro_kikuchi
Dear sirs, Please allow me to ask you a beginner's question. I have an nparray whose shape is (144, 91, 1). The elements of this array are integer 0, 1 or 2, but I don't know which of the three integers is assigned to each element. I would like to make a copy of this array, and then replace

Re: [Numpy-discussion] How to modify an array

2012-02-26 Thread Olivier Delalleau
This should do what you want: array_copy = my_array.copy() array_copy[array_copy == 2] = 0 -=- Olivier Le 26 février 2012 19:53, tetsuro_kiku...@jesc.or.jp a écrit : Dear sirs, Please allow me to ask you a beginner's question. I have an nparray whose shape is (144, 91, 1). The elements

Re: [Numpy-discussion] How to modify an array

2012-02-26 Thread tetsuro_kikuchi
Dear Olivier, Thank you very much for your help. It worked fine! Tetsuro Kikuchi Olivier Delalleau

[Numpy-discussion] numpy ndenumerate

2012-02-26 Thread Nathan Faggian
Hi, Is there a good reason for ndenumerate in numpy being slower than standard indexing? For example: --- import numpy as np def fast_itt(a): for index, value in np.ndenumerate(a): a[index] += 1 def slow_itt(a): for r in range(0, a.shape[0]): for c in range(0,

Re: [Numpy-discussion] Possible roadmap addendum: building better text file readers

2012-02-26 Thread Jay Bourque
Erin Sheldon erin.sheldon at gmail.com writes: Excerpts from Wes McKinney's message of Sat Feb 25 15:49:37 -0500 2012: That may work-- I haven't taken a look at the code but it is probably a good starting point. We could create a new repo on the pydata GitHub org