Performance of NumPy for algorithms concerning individual elements of an array

Question

I'm interested in the performance of NumPy, when it comes to algorithms that check whether a condition is True for an element and its affiliations (e.g. neighbouring elements) and assign a value according to the condition.

An example may be: (I make this up now)

I generate a 2d array of 1's and 0's, randomly.
- Then I check whether the first element of the array is the same with its neighbors.
- If the similar ones are the majority, I switch (0 -> 1 or 1 -> 0) that particular element.
And I proceed to the next element.

I guess that this kind of element wise conditions and element-wise operations are pretty slow with NumPy, is there a way that I can make the performance better?

For example, would creating the array with type dbool and adjusting the code, would it help?

Thanks in advance.

rocksportrocker · Accepted Answer · 2011-08-12 11:42:53Z

1

Maybe http://www.scipy.org/Cookbook/GameOfLifeStrides helps you.

answered Aug 12, 2011 at 11:42

rocksportrocker

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HYRY · Accepted Answer · 2011-08-12 21:21:22Z

1

It looks like your are doing some kind of image processing, you can try scipy.ndimage.

from scipy.ndimage import convolve
import numpy as np
np.random.seed(0)
x = np.random.randint(0,2,(5,5))

print x

w = np.ones((3,3), dtype=np.int8)
w[1,1] = 0
y = convolve(x, w, mode="constant")

print y

the outputs are:

[[0 1 1 0 1]
 [1 1 1 1 1]
 [1 0 0 1 0]
 [0 0 0 0 1]
 [0 1 1 0 0]]

[[3 4 4 5 2]
 [3 5 5 5 3]
 [2 4 4 4 4]
 [2 3 3 3 1]
 [1 1 1 2 1]]

y is the sum of the neighbors of every element. Do the same convolve with all ones, you get the number of neighbors number of every element:

>>> n = convolve(np.ones((5,5),np.int8), w, mode="constant")
>>> n
[[3 5 5 5 3]
 [5 8 8 8 5]
 [5 8 8 8 5]
 [5 8 8 8 5]
 [3 5 5 5 3]]

then you can do element-wise operations with x, y, n, and get your result.

answered Aug 12, 2011 at 21:21

HYRY

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2 Comments

mehmet.ali.anil Over a year ago

Yes, that is a slick answer to my made-up case. But it was rather a general question, I didn't know that this could have been done with a method convolve. My question is more or less about an arbitrary condition and an arbitrary elementwise operation.

HYRY Over a year ago

It isn't a common solution, if you want do some operation that can only be calculated by element-wise for loop, you can build an extention module by cython, SWIG, or embed c code directly into you python code by weave. But before doing that, try image processing methods first, such as convolve, morphology image process.

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