Assert array almost equal zero

Question

I'm writing unit tests for my simulation and want to check that for specific parameters the result, a numpy array, is zero. Due to calculation inaccuracies, small values are also accepted (1e-7). What is the best way to assert this array is close to 0 in all places?

np.testing.assert_array_almost_equal(a, np.zeros(a.shape)) and assert_allclose fail as the relative tolerance is inf (or 1 if you switch the arguments) Docu
I feel like np.testing.assert_array_almost_equal_nulp(a, np.zeros(a.shape)) is not precise enough as it compares the difference to the spacing, therefore it's always true for nulps >= 1 and false otherways but does not say anything about the amplitude of a Docu
Use of np.testing.assert_(np.all(np.absolute(a) < 1e-7)) based on this question does not give any of the detailed output, I am used to by other np.testing methods

Is there another way to test this? Maybe another testing package?

Why can't you use the absolute tolerance argument in assert_allclose for this? — MrBean Bremen
– MrBean Bremen, Commented Aug 7, 2020 at 8:55
Thanks, @MrBeanBremen, you are totally right. Can you post it as answer, so I can accept it? I'm sorry, I did not think about this easy solution. — Caah Arch
– Caah Arch, Commented Aug 8, 2020 at 18:50
Also, the contruction with np.zeros does not work, it's probably better to use np.zeros_like. — Caah Arch
– Caah Arch, Commented Aug 8, 2020 at 19:10

MrBean Bremen · Accepted Answer · 2021-10-16 10:09:26Z

6

If you compare a numpy array with all zeros, you can use the absolute tolerance, as the relative tolerance does not make sense here:

from numpy.testing import assert_allclose

def test_zero_array():
    a = np.array([0, 1e-07, 1e-08])
    assert_allclose(a, 0, atol=1e-07)

The rtol value does not matter in this case, as it is multiplied with 0 if calculating the tolerance:

atol + rtol * abs(desired)

Update: Replaced np.zeros_like(a) with the simpler scalar 0. As pointed out by @hintze, np array comparisons also work against scalars.

edited Oct 16, 2021 at 10:09

answered Aug 8, 2020 at 19:22

MrBean Bremen

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2 Comments

hintze Over a year ago

minor thing, but still: assert_allclose can compare ND arrays and scalars, so no need to use np.zeros_like() ;)

MrBean Bremen Over a year ago

@hintze - Thanks, good catch! I adapted the answer accordingly.

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