[SciPy-User] Bottleneck 0.3 - some tests Fail
Keith Goodman
kwgoodman at gmail.com
Fri Jan 21 10:56:43 EST 2011
On Fri, Jan 21, 2011 at 7:22 AM, Hanno Klemm <klemm at phys.ethz.ch> wrote:
>
> Keith,
>
> thanks for the new release. When I build bottleneck 0.3.0 two of the tests
> fail. Are you aware of that,or is that a problem with my build?
>
> I attached a text file of the session.
Thank you for the report!
I don't see any failures. Anyone else?
Some background on the failing unit test:
Currently only 1d, 2d, and 3d input arrays with data type (dtype)
int32, int64, float32, and float64 are accelerated. All other
ndim/dtype combinations result in calls to slower, unaccelerated
functions. The tests that are failing on your system use a 4d input
array so it calls the slow version of moving_nanmax and moving_max,
which uses scipy.ndimage.maximum_filter1d.
So my first thought is to blame scipy ;) What version of scipy are you
using? I see you are using numpy 1.4.0 so you are probably using scipy
0.7. Would using scipy 0.8 solve it?
Here's the function (bottleneck/slow/move.py):
def move_max_filter(arr, window, axis=-1):
"Moving window maximium implemented with a filter."
if axis == None:
raise ValueError, "An `axis` value of None is not supported."
if window < 1:
raise ValueError, "`window` must be at least 1."
if window > arr.shape[axis]:
raise ValueError, "`window` is too long."
y = arr.astype(float)
x0 = (window - 1) // 2
maximum_filter1d(y, window, axis=axis, mode='constant', cval=np.nan,
origin=x0, output=y)
> Regards,
> Hanno
>
>
>
> On Thu, Jan 20, 2011, Keith Goodman <kwgoodman at gmail.com> said:
>
>> Bottleneck is a collection of fast NumPy array functions written in
>> Cython. It contains functions like median, nanmedian, nanargmax,
>> move_mean.
>>
>> The third release of Bottleneck is twice as fast for small input
>> arrays and contains 10 new functions.
>>
>> Faster:
>> - All functions are faster (less overhead in selector functions)
>>
>> New functions:
>> - nansum()
>> - move_sum()
>> - move_nansum()
>> - move_mean()
>> - move_std()
>> - move_nanstd()
>> - move_min()
>> - move_nanmin()
>> - move_max()
>> - move_nanmax()
>>
>> Enhancements:
>> - You can now specify the dtype and axis to use in the benchmark timings
>> - Improved documentation and more unit tests
>>
>> Breaks from 0.2.0:
>> - Moving window functions now default to axis=-1 instead of axis=0
>> - Low-level moving window selector functions no longer take window as input
>>
>> Bug fix:
>> - int input array resulted in call to slow, non-cython version of move_nanmean
>>
>> 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
>> _______________________________________________
>> SciPy-User mailing list
>> SciPy-User at scipy.org
>> http://mail.scipy.org/mailman/listinfo/scipy-user
>>
>>
>
> --
> Hanno Klemm
> klemm at phys.ethz.ch
>
>
>
> Python 2.6.6 |EPD 6.3-1 (64-bit)| (r266:84292, Sep 18 2010, 08:39:12)
> [GCC 3.4.6] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import bottleneck as bn
>>>> bn.__version__
> '0.3.0'
>>>> import numpy as np
>>>> bn.test()
> Running unit tests for bottleneck
> NumPy version 1.4.0
> NumPy is installed in /scratch/epd-6.3/lib/python2.6/site-packages/numpy
> Python version 2.6.6 |EPD 6.3-1 (64-bit)| (r266:84292, Sep 18 2010,
> 08:39:12) [GCC 3.4.6]
> nose version 0.11.4
> .........................................F.F
> ======================================================================
> FAIL: Test move_max.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/scratch/epd-6.3/lib/python2.6/site-packages/nose/case.py", line
> 186, in runTest
> self.test(*self.arg)
> File
> "/scratch/epd-6.3/lib/python2.6/site-packages/bottleneck/tests/move_test.py",
> line 58, in unit_maker
> err_msg)
> File
> "/scratch/epd-6.3/lib/python2.6/site-packages/numpy/testing/utils.py",
> line 765, in assert_array_almost_equal
> header='Arrays are not almost equal')
> File
> "/scratch/epd-6.3/lib/python2.6/site-packages/numpy/testing/utils.py",
> line 587, in assert_array_compare
> raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal
>
> func move_max | window 2 | input a96 (int32) | shape (1, 2, 3, 4) | axis
> -2
>
> Input array:
> [[[[ 0 1 2 3]
> [ 4 5 6 7]
> [ 8 9 10 11]]
>
> [[12 13 14 15]
> [16 17 18 19]
> [20 21 22 23]]]]
>
> (x and y nan location mismatch [[[[False False False False]
> [False False False False]
> [False False False False]]
>
> [[False False False False]
> [False False False False]
> [False False False False]]]], [[[[ True True True True]
> [False False False False]
> [False False False False]]
>
> [[ True True True True]
> [False False False False]
> [False False False False]]]] mismatch)
> x: array([[[[ 0., 1., 2., 3.],
> [ 4., 5., 6., 7.],
> [ 8., 9., 10., 11.]],...
> y: array([[[[ NaN, NaN, NaN, NaN],
> [ 4., 5., 6., 7.],
> [ 8., 9., 10., 11.]],...
>
> ======================================================================
> FAIL: Test move_nanmax.
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/scratch/epd-6.3/lib/python2.6/site-packages/nose/case.py", line
> 186, in runTest
> self.test(*self.arg)
> File
> "/scratch/epd-6.3/lib/python2.6/site-packages/bottleneck/tests/move_test.py",
> line 58, in unit_maker
> err_msg)
> File
> "/scratch/epd-6.3/lib/python2.6/site-packages/numpy/testing/utils.py",
> line 765, in assert_array_almost_equal
> header='Arrays are not almost equal')
> File
> "/scratch/epd-6.3/lib/python2.6/site-packages/numpy/testing/utils.py",
> line 587, in assert_array_compare
> raise AssertionError(msg)
> AssertionError:
> Arrays are not almost equal
>
> func move_nanmax | window 2 | input a96 (int32) | shape (1, 2, 3, 4) |
> axis -2
>
> Input array:
> [[[[ 0 1 2 3]
> [ 4 5 6 7]
> [ 8 9 10 11]]
>
> [[12 13 14 15]
> [16 17 18 19]
> [20 21 22 23]]]]
>
> (x and y nan location mismatch [[[[False False False False]
> [False False False False]
> [False False False False]]
>
> [[False False False False]
> [False False False False]
> [False False False False]]]], [[[[ True True True True]
> [False False False False]
> [False False False False]]
>
> [[ True True True True]
> [False False False False]
> [False False False False]]]] mismatch)
> x: array([[[[ 0., 1., 2., 3.],
> [ 4., 5., 6., 7.],
> [ 8., 9., 10., 11.]],...
> y: array([[[[ NaN, NaN, NaN, NaN],
> [ 4., 5., 6., 7.],
> [ 8., 9., 10., 11.]],...
>
> ----------------------------------------------------------------------
> Ran 44 tests in 31.774s
>
> FAILED (failures=2)
> <nose.result.TextTestResult run=44 errors=0 failures=2>
>>>>
>
>
>
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