Setting values on Pandas DataFrame subset (copy) is slow

Question

import timeit
import pandas as pd
import numpy as np

df = pd.DataFrame(np.random.rand(10, 10))

dft = df[[True, False] * 5]
# df = dft
dft2 = dft.copy()

new_data = np.random.rand(5, 10)

print(timeit.timeit('dft.loc[:, :] = new_data', setup='from __main__ import dft, new_data', number=100))
print(timeit.timeit('dft2.loc[:, :] = new_data', setup='from __main__ import dft2, new_data', number=100))

On my laptop setting values in dft (the original subset) is about 160 times slower than setting values in dft2 (a deep copy of dft ).

Why is this the case?

Edit : Removed speculation about proxy objects.

As c. leather suggests, this is likely because of a different codepath when setting values on a copy ( dft ) vs an original dataframe ( dft2 ).

Bonus question: removing the reference to the original DataFrame df (by uncommenting the df = dft line), cuts the speed factor to roughly 2 on my laptop. Any idea why this is the case?

Answer 1

This is not exactly a new question on SO. This , and this are related posts. This is the link to the current docs that explains it.

The comments from @c.leather are on the right track. The problem is that dft is a view, not a copy of the dataframe df , as explained in the linked articles. But pandas cannot know whether it really is or not a copy and if the operation is safe or not, and as such there are a lot of checks going on to ensure that it is safe to perform the assignment, and that could be avoided by simply making a copy.

This is a pertinent issue and there is a whole discussion at Github . I've seen a lot of suggestions, the one I like the most is that the docs should encourage the df[[True,False] * 5].copy() idiom, one may call it the slice & copy idiom.

I could not find the exact checks, and on the github issue this performance nuance is only mentioned through some tweets a few developers posted noting the behavior. Maybe someone more involved in the pandas development can add some more input.