[SciPy-user] Very slow comparison of arrays of integers
Robert Kern
rkern at ucsd.edu
Mon Jul 18 03:15:47 CDT 2005
Brian Granger wrote:
> Hello all,
>
> I have some code that is using scipy/numeric and one bottleneck in the
> code consists of comparing arrays or lists of integers. To my dismay,
> I am finding that using Python lists is 15-20 times _faster_ than using
> numeric array's for this. The problem is that it seems that there is
> no efficient way to compare arrays of integers.
>
> Here is code that clearly demonstrates this problem:
>
> from scipy import *
>
> def test_list(n):
> a = range(100)
> for i in range(n):
> r = (a == a)
>
> def test_array(n):
> a = array(range(100),Int)
> for i in range(n):
> r = allclose(a,a)
>
> The test_list code runs about 20 times as fast as the test_array code
> that uses allclose().
>
> Is there any way of comparing to arrays of integers that would be as
> fast or faster than using lists? Any hints would be greatly appreciated.
allclose() is for floating point arrays. Use alltrue(x == y) for integer
arrays.
Also, use numbers > 100. Small integer objects are cached and object
identity is checked first, I believe.
In [28]: tlist = timeit.Timer("a == a", setup="a = range(1000, 2000)")
In [29]: tarray = timeit.Timer("alltrue(a == a)", setup="from scipy
import alltrue,arange; a = arange(1000, 2000)")
In [30]: tarray.repeat(3, 1000)
Out[30]: [0.097441911697387695, 0.049738168716430664, 0.051641941070556641]
In [31]: tlist.repeat(3, 1000)
Out[31]: [0.1062159538269043, 0.062600851058959961, 0.063454866409301758]
--
Robert Kern
rkern at ucsd.edu
"In the fields of hell where the grass grows high
Are the graves of dreams allowed to die."
-- Richard Harter
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