[SciPy-User] Bottleneck 0.3 - some tests Fail
Hanno Klemm
klemm at phys.ethz.ch
Mon Jan 24 10:42:09 EST 2011
I was indeed using scipy 0.8.0. However, upgrading to the most recent EPD
distribution made the error go away. Apparently there are some minute
changes between EPD-6.3-1 and EPD-6.3-2 that solved the problem.
On Fri, Jan 21, 2011, Keith Goodman <kwgoodman at gmail.com> said:
> 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>
>>>>>
>>
>>
>>
>
>
--
Hanno Klemm
klemm at phys.ethz.ch
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