CODEWITHSUNDEEP
pythonscipyruntime-error
Tendero
Tendero

Reputation: 1166

"SystemError: <class 'int'> returned a result with an error set" in Python

I wanted to apply a very simple function using ndimage.generic_filter() from scipy. This is the code:

import numpy as np
import scipy.ndimage as ndimage

data = np.random.rand(400,128)
dimx = int(np.sqrt(np.size(data,0)))
dimy = dimx    
coord = np.random.randint(np.size(data,0), size=(dimx,dimy))

def test_func(values):
    idx_center = int(values[4])
    weight_center = data[idx_center]
    weights_around = data[values]
    differences = weights_around - weight_center
    distances = np.linalg.norm(differences, axis=1)
    return np.max(distances)

results = ndimage.generic_filter(coord,
                                 test_func,
                                 footprint = np.ones((3,3)))

When I execute it though, the following error shows up:

SystemError: <class 'int'> returned a result with an error set

when trying to coerce values[4] to an int. If I run the function test_func() without using ndimage.generic_filter() for a random array values, the function works alright.

Why is this error occurring? Is there a way to make it work?

Upvotes: 4

Views: 25338

Answers (2)

Toenex
Toenex

Reputation: 233

I was having a very similar experience with Python 3.8.1 and SciPy 1.4.1 on Linux. A workaround was to introduce np.floor so that:

centre = int(window.size / 2) becomes centre = int(np.floor(window.size/2))

which seems to have resolved the issue.

Upvotes: 0

Kevin
Kevin

Reputation: 30151

For your case:

This must be a bug in either Python or SciPy. Please file a bug at https://bugs.python.org and/or https://www.scipy.org/bug-report.html. Include the version numbers of Python and NumPy/SciPy, the full code that you have here, and the entire traceback.

(Also, if you can find a way to trigger this bug that doesn't require the use of randomness, they will likely appreciate it. But if you can't find such a method, then please do file it as-is.)

In general:

"[R]eturned a result with an error set" is something that can only be done at the C level. In general, the Python/C API expects most C functions to do one of two things:

  1. Set an exception using one of these functions and return NULL (corresponds to throwing an exception).
  2. Don't set an exception and return a "real" value, usually a PyObject* (corresponds to returning a value, including returning None).

These two cases are normally incorrect:

  1. Set an exception (or fail to clear one that already exists), but then return some value other than NULL.
  2. Don't set an exception, but then return NULL.

Python is raising a SystemError because the implementation of int, in the Python standard library, tried to do (3), possibly as a result of SciPy doing it first. This is always wrong, so there must be a bug in either Python or the SciPy code that it called into.

Upvotes: 19

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