Suggestions on how to speed up a distance calculation

Question

Consider the following class:

class SquareErrorDistance(object):
    def __init__(self, dataSample):
        variance = var(list(dataSample))
        if variance == 0:
            self._norm = 1.0
        else:
            self._norm = 1.0 / (2 * variance)

    def __call__(self, u, v): # u and v are floats
        return (u - v) ** 2 * self._norm

I use it to calculate the distance between two elements of a vector. I basically create one instance of that class for every dimension of the vector that uses this distance measure (there are dimensions that use other distance measures). Profiling reveals that the __call__ function of this class accounts for 90% of the running-time of my knn-implementation (who would have thought). I do not think there is any pure-Python way to speed this up, but maybe if I implement it in C?

If I run a simple C program that just calculates distances for random values using the formula above, it is orders of magnitude faster than Python. So I tried using ctypes and call a C function that does the computation, but apparently the conversion of the parameters and return-values is far to expensive, because the resulting code is much slower.

I could of course implement the entire knn in C and just call that, but the problem is that, like I described, I use different distance functions for some dimension of the vectors, and translating these to C would be too much work.

So what are my alternatives? Will writing the C-function using the Python C-API get rid of the overhead? Are there any other ways to speed this calculation up?

Answer 1

The following cython code (I realize the first line of __init__ is different, I replaced it with random stuff because I don't know var and because it doesn't matter anyway - you stated __call__ is the bottleneck):

cdef class SquareErrorDistance:
    cdef double _norm

    def __init__(self, dataSample):
        variance = round(sum(dataSample)/len(dataSample))
        if variance == 0:
            self._norm = 1.0
        else:
            self._norm = 1.0 / (2 * variance)

    def __call__(self, double u, double v): # u and v are floats
        return (u - v) ** 2 * self._norm

Compiled via a simple setup.py (just the example from the docs with the file name altered), it performs nearly 20 times better than the equivalent pure python in a simple contrieved timeit benchmark. Note that the only changed were cdefs for the _norm field and the __call__ parameters. I consider this pretty impressive.