[SciPy-Dev] warnings in scipy.stats.entropy

[Skipper Seabold]

On Mon, May 21, 2012 at 7:11 PM,  <josef.pktd at gmail.com> wrote:
> On Mon, May 21, 2012 at 6:43 PM, Nathaniel Smith <njs at pobox.com> wrote:
>> On Mon, May 21, 2012 at 11:39 PM, Skipper Seabold <jsseabold at gmail.com> wrote:
>>> Currently in scipy.stats.entropy if you are not ignoring them you will
>>> see warnings when the function is given a probability of zero even
>>> though the case of zero is specifically handled in the function.
>>> Rightly or wrongly this makes me cringe. What do people think about
>>> fixing this by using seterr explicitly in the function or masking the
>>> zeros. Eg.,
>>>
>>> import numpy as np
>>> from scipy.stats import entropy
>>>
>>> prob = np.random.uniform(0,20, size=10)
>>> prob[5] = 0
>>> prob = prob/prob.sum()
>>>
>>> np.seterr(all = 'warn')
>>> entropy(prob) # too loud
>>>
>>> Instead we could do (within entropy)
>>>
>>> oldstate = np.geterr()
>>> np.seterr(divide='ignore', invalid='ignore')
>>> entropy(prob)
>>> np.seterr(**oldstate)
>>>
>>> or just mask the zeros in the first place if this is too much
>>>
>>> idx = prob > 0
>>> -np.sum(prob[idx] * np.log(prob[idx]))
>>>
>>> Thoughts?
>>
>> I like the mask version better.
>
> +1,

https://github.com/scipy/scipy/pull/226

>
> buggy: if qk is given, then the function isn't vectorized.
>
> Josef
>
>>
>> - N
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