import numpy, mkl_fft from numpy.testing import assert_allclose a = numpy.array([[[5, 7, 6, 5], [4, 6, 4, 8], [9, 3, 7, 5]], [[5, 9, 0, 0], [0, 8, 7, 8], [9, 7, 4, 7]]], dtype=numpy.float32) print(a.shape) # (2, 3, 4) r1 = mkl_fft.irfftn(a, s=(1, 4, 10), axes=None) r2 = numpy.fft.irfftn(a, s=(1, 4, 10), axes=None) print(r1.shape, r2.shape) # (2, 4, 10) (1, 4, 10)