MAINT: Use np.ix_ to extract submatrix

[oyamad]

Replace matrix[indices, :][:, indices] with matrix[np.ix_(indices, indices)].

I happened to find this fact.

[coveralls]

Coverage increased (+0.001%) to 94.91% when pulling d1d48f8 on submatrix into 2aa53f7 on master.

[mmcky]

reference to docs: https://docs.scipy.org/doc/numpy-1.13.0/reference/generated/numpy.ix_.html