t0 = time() pairs = [] truedists = [] for i in range(N1): pt1 = x1[i,:] d2s = np.sum((x2 - pt1)**2, axis=1) good = np.where(d2s <= r**2)[0] for j in good: pairs.append((i, j)) truedists.append(d2s[j]) dt = time() - t0 pairs = np.array(pairs) truedists = np.sqrt(np.array(truedists)) print 'naive : found', len(pairs), 'pairs in', int(dt*1000.), 'ms' order = np.argsort(pairs[:,0]*N2 + pairs[:,1]) pairs = pairs[order] ok = np.array_equal(pairs, inds) print 'Indices equal:', ok ok = np.array_equal(truedists[order], dists.ravel()) print 'Dists equal:', ok t0 = time() (inds,dists) = spherematch.nearest(x1, x2, r) dt = time() - t0
dists = dists[order]
t0 = time()
pairs = []
truedists = []
for i in range(N1):
pt1 = x1[i, :]
d2s = np.sum((x2 - pt1)**2, axis=1)
good = np.where(d2s <= r**2)[0]
for j in good:
pairs.append((i, j))
truedists.append(d2s[j])
dt = time() - t0
pairs = np.array(pairs)
truedists = np.sqrt(np.array(truedists))
print 'naive : found', len(pairs), 'pairs in', int(dt * 1000.), 'ms'
order = np.argsort(pairs[:, 0] * N2 + pairs[:, 1])
pairs = pairs[order]
ok = np.array_equal(pairs, inds)
print 'Indices equal:', ok
ok = np.array_equal(truedists[order], dists.ravel())
print 'Dists equal:', ok
t0 = time()
(inds, dists) = spherematch.nearest(x1, x2, r)
dt = time() - t0