In [227]: x.mask Out[227]: array([[ True, False, False], [False, True, False], [False, False, True]], dtype=bool) In [228]: np.where(x.mask) Out[228]: (array([0, 1, 2]), array([0, 1, 2])) In [229]: yy, xx = np.where(x.mask) In [230]: yy Out[230]: array([0, 1, 2]) In [231]: xx Out[231]: array([0, 1, 2])