[SciPy-User] scipy.ndimage.filters.median_filter with NAN values

[Warren Weckesser]

On Fri, Oct 10, 2014 at 2:43 PM, Shahar Barak <shaharb at stanford.edu> wrote:

> I have a 3D array, in which some values are Nan (masked).
> I am using scipy.ndimage.filters.median_filter to smooth the data.
> Is there a way to have scipy.ndimage.filters.median_filter not include the
> NAN values in its median calculation?
>
>

You could use scipy.ndimage.filters.generic_filter, with np.nanmedian as
the 'function' argument, but it will be painfully slow compared to
median_filter.  E.g.

In [97]: x = np.random.randn(50, 50, 50)

In [98]: %timeit median_filter(x, size=3)
10 loops, best of 3: 47.9 ms per loop

In [99]: %timeit generic_filter(x, np.nanmedian, size=3)
1 loops, best of 3: 2.21 s per loop


That's about 46 times slower for an array with shape (50, 50, 50).

Warren


Thanks,
>
> Shahar
>
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