[SciPy-User] zscore axis functionality is borked

josef.pktd@gmai... josef.pktd@gmai...
Wed Nov 30 15:25:19 CST 2011


On Wed, Nov 30, 2011 at 4:10 PM, Warren Weckesser
<warren.weckesser@enthought.com> wrote:
>
>
> On Wed, Nov 30, 2011 at 3:05 PM, <josef.pktd@gmail.com> wrote:
>>
>> On Wed, Nov 30, 2011 at 4:02 PM, Warren Weckesser
>> <warren.weckesser@enthought.com> wrote:
>> >
>> >
>> > On Wed, Nov 30, 2011 at 2:54 PM, <josef.pktd@gmail.com> wrote:
>> >>
>> >> On Wed, Nov 30, 2011 at 3:45 PM,  <josef.pktd@gmail.com> wrote:
>> >> > On Wed, Nov 30, 2011 at 3:25 PM, Alacast <alacast@gmail.com> wrote:
>> >> >> axis=0 (the default) works fine. axis=1, etc, is clearly wrong. Am I
>> >> >> misunderstanding how to use this, or is this a bug?
>> >> >>
>> >> >> In [16]: i = rand(4,4)
>> >> >>
>> >> >> In [17]: i
>> >> >> Out[17]:
>> >> >> array([[ 0.85367762,  0.25348857,  0.23572615,  0.50403358],
>> >> >>        [ 0.70199066,  0.81872151,  0.47357357,  0.20425537],
>> >> >>        [ 0.31042673,  0.25837984,  0.73550134,  0.57970176],
>> >> >>        [ 0.42828877,  0.60988596,  0.04059321,  0.73944219]])
>> >> >>
>> >> >> In [18]: zscore(i, axis=0)
>> >> >> Out[18]:
>> >> >> array([[ 1.30128758, -0.96195723, -0.52119142, -0.01453907],
>> >> >>        [ 0.59653471,  1.38544585,  0.39284654, -1.55756529],
>> >> >>        [-1.22271057, -0.94164388,  1.39942427,  0.37494213],
>> >> >>        [-0.67511172,  0.51815526, -1.27107939,  1.19716222]])
>> >> >>
>> >> >> In [19]: zscore(i[:,0])
>> >> >> Out[19]: array([ 1.30128758,  0.59653471, -1.22271057, -0.67511172])
>> >> >>
>> >> >> In [20]: zscore(i[:,0])==zscore(i,axis=0)[:,0]
>> >> >> Out[20]: array([ True,  True,  True,  True], dtype=bool)
>> >> >>
>> >> >> In [21]: zscore(i, axis=1)
>> >> >> Out[21]:
>> >> >> array([[-0.99378502, -1.59397407, -1.61173649, -1.34342906],
>> >> >>        [-1.6379836 , -1.52125275, -1.86640069, -2.13571889],
>> >> >>        [-2.09968257, -2.15172946, -1.67460796, -1.83040754],
>> >> >>        [-1.29796925, -1.11637205, -1.68566481, -0.98681582]])
>> >> >> #The above is obviously wrong, as everything has a negative z score
>> >> >>
>> >> >> In [22]: zscore(i[0,:])
>> >> >> Out[22]: array([ 1.56824016, -0.83321371, -0.90428403,  0.16925757])
>> >> >>
>> >> >> In [23]: zscore(i[0,:])==zscore(i,axis=1)[0,:]
>> >> >> Out[23]: array([False, False, False, False], dtype=bool)
>> >> >> #Using axis=1 produces different results from taking a row directly.
>> >> >>
>> >> >> In [24]: zscore(i, axis=-1)
>> >> >> Out[24]:
>> >> >> array([[-0.99378502, -1.59397407, -1.61173649, -1.34342906],
>> >> >>        [-1.6379836 , -1.52125275, -1.86640069, -2.13571889],
>> >> >>        [-2.09968257, -2.15172946, -1.67460796, -1.83040754],
>> >> >>        [-1.29796925, -1.11637205, -1.68566481, -0.98681582]])
>> >> >> #Getting rows by using axis=-1 is no better (this is the same result
>> >> >> as
>> >> >> axis=1
>> >> >
>> >> > This looks like a serious bug to me. I don't know what happened here
>> >> > (.
>> >> >
>> >> > The docstring example also has negative numbers only.
>> >> >
>> >> > ???
>> >> >
>> >> > I'm looking into it
>> >> >
>> >> > Thanks for reporting
>> >>
>> >> a misplaced axis: if axis>0
>> >> then it calculates   x - mean/std instead of (x - mean) / std
>> >>
>> >> now, how did this go through the testing ?
>> >
>> >
>> >
>> >
>> > There is only one test for zscore, on a 1-d sample without the axis
>> > keyword.
>>
>> which just show that we shouldn't trust changesets that say
>>
>> "stats: rewrite of zscore functions, ticket:1083 regression tests
>> pass, still need tests for enhancements"
>>
>> http://projects.scipy.org/scipy/changeset/6169
>>
>> my mistake  (maybe January 2nd wasn't a good day.)
>>
>> Josef
>>
>
>
> Thanks for the link.  Looks like zmap has the same bug. :(

copy paste errors?

I just don't know why I didn't do basic checks like this in the final version

>>> assert_equal(zscore(x.T, axis=0).T, zscore(x, axis=1))
>>> a = zscore(x, axis=1)
>>> a.var(1)
array([ 1.,  1.,  1.,  1.])
>>> a.mean(1)
array([  0.00000000e+00,  -1.11022302e-16,   0.00000000e+00,
         1.94289029e-16])

Josef

>
> Warren
>
>
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