[Numpy-discussion] fast_any_all , a trivial but fast/useful helper function for numpy
Julian Taylor
jtaylor.debian at googlemail.com
Wed Sep 4 13:38:58 EDT 2013
On 04.09.2013 12:05, Graeme B. Bell wrote:
> In my current GIS raster work I often have a situation where I generate code something like this:
>
> np.any([A>4, A==2, B==5, ...])
>
> However, np.any() is quite slow.
>
> It's possible to use np.logical_or to solve the problem, but then you get nested logical_or's, since logical_or combines only two parameters.
> It's also possible to use integer maths e.g. (A>4)+(A==2)+(B==5)>0.
>
> The question is: which is best (syntactically, in terms of performance, etc)?
>
> I've written a little helper function to provide a faster version of any() and all(). It's embarrassingly simple - just a for loop. However, I think there's a syntactic advantage to using a helper function for this situation rather than writing it idiomatically each time; and it reduces the chance of a bug in idiomatic implementation. However, the code does not cover all the use cases currently addressed by np.any() and np.all().
>
> I benchmarked to pick the fastest underlying implementation (logical_or rather than integer maths).
>
> The result is 14 to 17x faster than np.any() for this use case.*
any/all and boolean operations have been significantly speed up by
vectorization in numpy 1.8 [0].
They are now around 10 times faster than before, especially if the
boolean array fits into one of the cpu caching layers.
If they don't I recommend using a blocking utility function, something like:
for i in range(0, n, blocksize):
view = d[i:i+blocksize]
#dostuff on view
with this method and the new vectorizations in numpy you are almost as
fast as numexpr for floats and probably a lot faster with bools.
[0]
http://www.onerussian.com/tmp/numpy-vbench/vb_vb_ufunc.html#numpy-and-bool
http://www.onerussian.com/tmp/numpy-vbench/vb_vb_reduce.html#numpy-any-slow
(the dip before 1.7 was part of the NA branch and never released, 1.8
adds some of its optimizations back)
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