python计算n维欧几里得距离,在Python中计算numpy的欧几里得距离

I am new to Python so this question might look trivia. However, I did not find a similar case to mine. I have a matrix of coordinates for 20 nodes. I want to compute the euclidean distance between all pairs of nodes from this set and store them in a pairwise matrix. For example, If I have 20 nodes, I want the end result to be a matrix of (20,20) with values of euclidean distance between each pairs of nodes. I tried to used a for loop to go through each element of the coordinate set and compute euclidean distance as follows:

ncoord=numpy.matrix('3225 318;2387 989;1228 2335;57 1569;2288 8138;3514 2350;7936 314;9888 4683;6901 1834;7515 8231;709 3701;1321 8881;2290 2350;5687 5034;760 9868;2378 7521;9025 5385;4819 5943;2917 9418;3928 9770')

n=20

c=numpy.zeros((n,n))

for i in range(0,n):

for j in range(i+1,n):

c[i][j]=math.sqrt((ncoord[i][0]-ncoord[j][0])**2+(ncoord[i][1]-ncoord[j][1])**2)

How ever, I am getting an error of "input must be a square array

". I wonder if anybody knows what is happening here.

Thanks

解决方案

There are much, much faster alternatives to using nested for loops for this. I'll show you two different approaches - the first will be a more general method that will introduce you to broadcasting and vectorization, and the second uses a more convenient scipy library function.

1. The general way, using broadcasting & vectorization

One of the first things I'd suggest doing is switching to using np.array rather than np.matrix. Arrays are preferred for a number of reasons, most importantly because they can have >2 dimensions, and they make element-wise multiplication much less awkward.

import numpy as np

ncoord = np.array(ncoord)

With an array, we can eliminate the nested for loops by inserting a new singleton dimension and broadcasting the subtraction over it:

# indexing with None (or np.newaxis) inserts a new dimension of size 1

print(ncoord[:, :, None].shape)

# (20, 2, 1)

# by making the 'inner' dimensions equal to 1, i.e. (20, 2, 1) - (1, 2, 20),

# the subtraction is 'broadcast' over every pair of rows in ncoord

xydiff = ncoord[:, :, None] - ncoord[:, :, None].T

print(xydiff.shape)

# (20, 2, 20)

This is equivalent to looping over every pair of rows using nested for loops, but much, much faster!

xydiff2 = np.zeros((20, 2, 20), dtype=xydiff.dtype)

for ii in range(20):

for jj in range(20):

for kk in range(2):

xydiff[ii, kk, jj] = ncoords[ii, kk] - ncoords[jj, kk]

# check that these give the same result

print(np.all(xydiff == xydiff2))

# True

The rest we can also do using vectorized operations:

# we square the differences and sum over the 'middle' axis, equivalent to

# computing (x_i - x_j) ** 2 + (y_i - y_j) ** 2

ssdiff = (xydiff * xydiff).sum(1)

# finally we take the square root

D = np.sqrt(ssdiff)

The whole thing could be done in one line like this:

D = np.sqrt(((ncoord[:, :, None] - ncoord[:, :, None].T) ** 2).sum(1))

2. The lazy way, using pdist

It turns out that there's already a fast and convenient function for computing all pairwise distances: scipy.spatial.distance.pdist.

from scipy.spatial.distance import pdist, squareform

d = pdist(ncoord)

# pdist just returns the upper triangle of the pairwise distance matrix. to get

# the whole (20, 20) array we can use squareform:

print(d.shape)

# (190,)

D2 = squareform(d)

print(D2.shape)

# (20, 20)

# check that the two methods are equivalent

print np.all(D == D2)

# True