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Replace all elements of NumPy array that are greater than some value

python
numpy
performance
optimizations
Alex KataevbyAlex Kataev·Sep 17, 2024
TLDR

Efficiently change values exceeding a limit in a numpy array using boolean indexing:

import numpy as np arr = np.array([1, 2, 5, 7, 4]) arr[arr > 3] = 0 # "Zap!" goes the array. Elements >3 are zeroed now.

Your numpy array now looks like this arr: [1 2 0 0 0]. Elements above 3 are all 0s now.

Maximizing efficiency: optimized operations and performance wins

In-place operations and clip

You like speed, and NumPy loves giving it to you. Use clip to keep all values within a range, right in-place:

arr.clip(max=3, out=arr) # 3, playing the role of the caped superhero, swoops in to save the day!

Now, anything that tries to go beyond 3 is firmly told, "Nope, you stay at 3."

Conditional replacements with np.where

np.where is more than just a question. It plays hide 'n' seek with array elements:

arr = np.where(arr > 3, 0, arr) # "Old man 3 called. He wants his >3 grandkids replaced with 0s."

This does give you a new array though. For Hulk-sized arrays, heap space might flex its muscles.

Check your engine: performance profiling

How do you know you've won the race? You time it! Here's how you can use timeit with large matrices:

import timeit # Assume 'large_arr' is a big, fat 2D array timeit.timeit('large_arr[large_arr > 255] = 0', globals=globals(), number=1000)

Put that stopwatch to work!

Keep it at bay: np.minimum/maximum

You don't want values running around like headless chickens. Use np.minimum and np.maximum to keep them within limits:

arr = np.minimum(arr, 3) # "Everyone in the pool! But you can only go as far as 3m."

Now everyone's in the pool, but no one's drowning. Isn't safety beautiful?

Optimizations you didn't know existed

np.putmask: the in-place savior

np.putmask gets rid of any pretense and replaces values right in-place:

np.putmask(arr, arr > 3, 0) # "Arr matey, all ye greater than 3 be 0 now."

Fast as a fox, np.putmask delivers. Especially handy when your arrays start resembling the cosmos.

Mastering np.clip's in-place modifications

You want your data in-place, top of the tables & within limits? np.clip has your back:

np.clip(arr, None, 3, out=arr) # "Conga line, humans! And remember, no one's taller than 3."

It's in-place, maintains array structure, and scores +1 on efficiency!

Boolean indexing power play

What's faster than an F1 car and operates directly on arrays? Boolean indexing:

arr[arr > 3] = np.minimum(arr, 3) # "Faster than a supercar. And well within speed limits."

Runs directly on arrays and gives speed demons a run for their money. What's not to love?