[Numpy-discussion] moving window product
Keith Goodman
kwgoodman@gmail....
Mon Mar 21 12:57:26 CDT 2011
On Mon, Mar 21, 2011 at 10:34 AM, Brent Pedersen <bpederse@gmail.com> wrote:
> On Mon, Mar 21, 2011 at 11:19 AM, Keith Goodman <kwgoodman@gmail.com> wrote:
>> On Mon, Mar 21, 2011 at 10:10 AM, Brent Pedersen <bpederse@gmail.com> wrote:
>>> hi, is there a way to take the product along a 1-d array in a moving
>>> window? -- similar to convolve, with product in place of sum?
>>> currently, i'm column_stacking the array with offsets of itself into
>>> window_size columns and then taking the product at axis 1.
>>> like::
>>>
>>> w = np.column_stack(a[i:-window_size+i] for i in range(0, window_size))
>>> window_product = np.product(w, axis=1)
>>>
>>> but then there are the edge effects/array size issues--like those
>>> handled in np.convolve.
>>> it there something in numpy/scipy that addresses this. or that does
>>> the column_stacking with an offset?
>>
>> The Bottleneck package has a fast moving window sum (bn.move_sum and
>> bn.move_nansum). You could use that along with
>>
>>>> a = np.random.rand(5)
>>>> a.prod()
>> 0.015877866878931741
>>>> np.exp(np.log(a).sum())
>> 0.015877866878931751
>>
>> Or you could use strides or scipy.ndimage as in
>> https://github.com/kwgoodman/bottleneck/blob/master/bottleneck/slow/move.py
>>
>
> ah yes, of course. thank you.
>
> def moving_product(a, window_size, mode="same"):
> return np.exp(np.convolve(np.log(a), np.ones(window_size), mode))
>
> i'll have a closer look at your strided version in bottleneck as well.
I don't know what size problem you are working on or if speed is an
issue, but here are some timings:
>> a = np.random.rand(1000000)
>> window_size = 1000
>> timeit np.exp(np.convolve(np.log(a), np.ones(window_size), 'same'))
1 loops, best of 3: 889 ms per loop
>> timeit np.exp(bn.move_sum(np.log(a), window_size))
10 loops, best of 3: 82.5 ms per loop
Most all that time is spent in np.exp(np.log(a)):
>> timeit bn.move_sum(a, window_size)
100 loops, best of 3: 3.72 ms per loop
So I assume if I made a bn.move_prod the time would be around 200x
compared to convolve.
BTW, you could do the exp inplace:
>> timeit b = bn.move_sum(np.log(a), window_size); np.exp(b, b)
10 loops, best of 3: 76.3 ms per loop
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