[SciPy-User] Bottleneck 0.4.1

Wes McKinney wesmckinn@gmail....
Tue Mar 8 20:06:05 CST 2011


On Tue, Mar 8, 2011 at 6:07 PM, Keith Goodman <kwgoodman@gmail.com> wrote:
> On Tue, Mar 8, 2011 at 1:19 PM, Keith Goodman <kwgoodman@gmail.com> wrote:
>> Bottleneck is a collection of fast NumPy array functions written in
>> Cython. It contains functions like median, nanmedian, nanargmax,
>> move_mean.
>>
>> This is a bug fix release.
>>
>> The low-level functions nanstd_3d_int32_axis1 and
>> nanstd_3d_int64_axis1, called by bottleneck.nanstd(), wrote beyond the
>> memory owned by the output array if both arr.shape[1] == 0 and
>> arr.shape[0] > arr.shape[2], where arr is the input array.
>>
>> Thanks to Christoph Gohlke for finding an example to demonstrate the bug.
>
> How embarrassing! The same bug in nanstd() that was fixed in 0.4.1
> exists in nanvar(). Thank you, Christoph, for pointing that out. Fixed
> in Bottleneck 0.4.2.
>
>> download
>>   http://pypi.python.org/pypi/Bottleneck
>> docs
>>   http://berkeleyanalytics.com/bottleneck
>> code
>>   http://github.com/kwgoodman/bottleneck
>> mailing list
>>   http://groups.google.com/group/bottle-neck
>> mailing list 2
>>   http://mail.scipy.org/mailman/listinfo/scipy-user
>>
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Keith,

Any interest adding a "min_periods" argument to the moving window
functions in bottleneck?

cf. http://pandas.sourceforge.net/stats_moments.html

It would introduce some additional CPU cycles into the existing
functions of course, but there are many practical applications (e.g.
smoothing slightly patchy data) where you want it.

One random question. Any idea on the long import time:

$ time python -c "import bottleneck"

real	0m0.712s
user	0m0.546s
sys	0m0.114s
$ time python -c "import numpy"

real	0m0.142s
user	0m0.090s
sys	0m0.049s
$ time python -c "import scipy"

real	0m0.201s
user	0m0.132s
sys	0m0.066s

Best,
Wes


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