Eric Firing wrote:
> David,
>
> I think my earlier post got lost in the exchange between you and Stefan,
> so I will reiterate the central point: numpy.clip *is* slow, in that an
> implementation using putmask is substantially faster:
>
> def fastclip(a, vmin, vmax):
> a = a.copy()
> putmask(a, a<=vmin, vmin)
> putmask(a, a>=vmax, vmax)
> return a
>
> Using the equivalent of this in a modification of your benchmark, the
> time using the native clip on *or* your alternative on my machine was
> about 2.3 s, versus 1.5 s for the putmask-based equivalent. It seems
> that putmask is quite a bit faster than boolean indexing.
>
> Obviously, the function above could be implemented as a method, and a
> copy kwarg could be used to make the copy optional--often one does not
> need a copy.
>
> It is also clear that it should be possible to make a much faster native
> clip function that does everything in one pass with no intermediate
> arrays at all. Whether this is something numpy devels would want to do,
> and how much effort it would take, are entirely different questions. I
> looked at the present code in clip (and part of the way through the
> chain of functions it invokes) and was quite baffled.
Well, this is something I would be willing to try *if* this is the main
bottleneck of imshow/show. I am still unsure about the problem, because
if I change numpy.clip to my function, including a copy, I really get a
big difference myself:
val = ma.array(nx.clip(val.filled(vmax), vmin, vmax),
mask=mask)
vs
def myclip(b, m, M):
a = b.copy()
a[a<m] = m
a[a>M] = M
return a
val = ma.array(myclip(val.filled(vmax), vmin, vmax), mask=mask)
By trying the best result, I get 0.888 ms vs 0.784 for a show() call,
which is already a 10 % improvement, and I get almost a 15 % if I remove
the copy. I am updating numpy/scipy/mpl on my laptop to see if this is
specific to the CPU of my workstation (big cache, high frequency clock,
bi CPU with HT enabled).
I would really like to see the imshow/show calls goes in the range of a
few hundred ms; for interactive plotting, this really change a lot in my
opinion.
cheers,
David
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