memview_bench_v6.pyx

# memview_bench_v6.pyx
import numpy as np

cimport numpy as np
from libc.math cimport sqrt
cimport cython

@cython.boundscheck(False)
@cython.wraparound(False)
def pairwise(np.ndarray[double, ndim=2, mode='c'] X not None):

    cdef np.intp_t i, j, k, n_samples, n_dim
    cdef double tmp, d
    n_samples = X.shape[0]
    n_dim = X.shape[1]

    cdef np.ndarray[double, ndim=2, mode='c'] D = np.empty((n_samples,
                                                            n_samples))
                                                            
    for i in xrange(n_samples):
        for j in xrange(n_samples):
            d = 0.0
            for k in xrange(n_dim):
                tmp = X[i, k] - X[j, k]
                d += tmp*tmp
            D[i, j] = sqrt(d)

    return D