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Best way to assert for numpy.array equality?

I want to make some unit-tests for my app, and I need to compare two arrays. Since array.__eq__ returns a new array (so TestCase.assertEqual fails), what is the best way to assert for equality?

Currently I'm using

self.assertTrue((arr1 == arr2).all())

but I don't really like it

note that your example can yield True unexpectedly, e.g. (np.array([1, 1]) == np.array([1])).all() will yield True
self.assertTrue(np.array_equal(array1, array2))

g
ggorlen

check out the assert functions in numpy.testing, e.g.

assert_array_equal

for floating point arrays equality test might fail and assert_almost_equal is more reliable.

update

A few versions ago numpy obtained assert_allclose which is now my favorite since it allows us to specify both absolute and relative error and doesn't require decimal rounding as the closeness criterion.


How does this interact with unittest? I think that some words on the matter would be useful.
I never use unittest. However, it works very well with nosetests which are used by numpy, scipy and statsmodels. Just use the asserts inside a test function or method.
This doesn't verify that the two arguments are both numpy arrays. For example, it would succeed on an array and a list. For testing, it might be useful to verify that these are actually arrays, but I guess it would require manually checking the type?
@RamonMartinez assert_allclose seems to play nicely with unittest :)
@RamonMartinez if you use Python's unittest you can use self.assertIsNone(np.testing.assert_array_equal(a, b)) as it returns None if the arrays are equal.
S
SiggyF

I think (arr1 == arr2).all() looks pretty nice. But you could use:

numpy.allclose(arr1, arr2)

but it's not quite the same.

An alternative, almost the same as your example is:

numpy.alltrue(arr1 == arr2)

Note that scipy.array is actually a reference numpy.array. That makes it easier to find the documentation.


a
asimoneau

I find that using self.assertEqual(arr1.tolist(), arr2.tolist()) is the easiest way of comparing arrays with unittest.

I agree it's not the prettiest solution and it's probably not the fastest but it's probably more uniform with the rest of your test cases, you get all the unittest error description and it's really simple to implement.


Note this won't work well with np.nan, since np.nan != np.nan and the self.assertEqual attempt won't be able to account for that.
H
HagaiH

Since Python 3.2 you can use assertSequenceEqual(array1.tolist(), array2.tolist()).

This has the added value of showing you the exact items in which the arrays differ.


Unfortunately, it doesn't work well when arrays are of float type. We really need assertSequenceAlmostEqual
M
Marseille
self.assertTrue(np.array_equal(x, y, equal_nan=True))

equal_nan = True if you want to np.nan == np.nan returns True

or you can use numpy.allclose to compare with torelance.


E
Edo user1419293

In my tests I use this:

numpy.testing.assert_array_equal(arr1, arr2)

This is best, because it gives an error message pointing to where the error is
a
a_b

Use numpy

numpy.array_equal(a, b)

s
schiebermc

np.linalg.norm(arr1 - arr2) < 1e-6


Please add some context