Comparing numpy arrays containing NaN

python numpy nan equality-operator
saroele picture saroele · May 22, 2012 · Viewed 37.4k times · Source

For my unittest, I want to check if two arrays are identical. Reduced example:

a = np.array([1, 2, np.NaN])
b = np.array([1, 2, np.NaN])

if np.all(a==b):
    print 'arrays are equal'

This does not work because nan != nan. What is the best way to proceed?

Answer

senderle picture senderle · May 22, 2012

For versions of numpy prior to 1.19, this is probably the best approach in situations that don't specifically involve unit tests:

>>> ((a == b) | (numpy.isnan(a) & numpy.isnan(b))).all()
True

However, modern versions provide the array_equal function with a new keyword argument, equal_nan, which fits the bill exactly.

This was first pointed out by flyingdutchman; see his answer below for details.

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