[Numpy-discussion] faster way for calculating distance matrix...
Kasper.Souren at ircam.fr
Wed May 21 12:56:05 EDT 2003
I was happy to see solutions coming up for Cliff's problems and it made me
think: maybe I can mention my problem here as well.
From an array of feature vectors I want to calculate it's distance matrix.
Something like . Currently it can take quite a while to calculate the
stuff for a long array.
1) Is there a smart speed up possible? Like, a way to avoid the double loop?
It's no problem if this would lead to less generality (like the choice for a
distance function). I know there is a little speed up to be gained by leaving
out the array(f) thing, but that's not what I'm looking for.
2) Is it possible (in Numeric or numarray) to define a class DiagonalMatrix
that at least saves half of the memory?
3) If 1) is not possible, what would be the way to go for speeding it up by
writing it in C? weave because of its availability in scipy or would pyrex be
more interesting, or are there even more options..?
 Example program:
def euclidean_dist(a, b):
diff = a - b
return Numeric.dot(diff, diff)
def calc_dist_matrix(f, distance_function):
W = Numeric.array(f)
length = W.shape
S = Numeric.zeros((length, length)) * 1.0
for i in range(length):
for j in range(i):
S[j, i] = S[i, j] = distance_function(W[i], W[j])
print calc_dist_matrix(Numeric.sin(Numeric.arange(30)), euclidean_dist)
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