IsoNet-cryoET / IsoNet

Self-supervised learning for isotropic cryoET reconstruction
https://www.nature.com/articles/s41467-022-33957-8
MIT License
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No compatibility with NumPy > 1.23 #51

Open Pfirsichriegel opened 11 months ago

Pfirsichriegel commented 11 months ago

I just wanted to let everyone know that we ran into an error regarding a deprecation from NumPy:

 File IsoNet/util/noise_generator.py", line 110, in simulate_noise
    res = p.map(part_iradon_nofilter,sinograms)
 File "lib/python3.9/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
 File "lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
AttributeError: module 'numpy' has no attribute 'int'.
`np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

The deprecation warning finally became an error in v1.24, which is why we had to downgrade numpy to 1.23.*. This solved the issue 👍

procyontao commented 9 months ago

Thank you for reporting. I did find numpy.int used in our code. I think this can also be resolved by upgrade scikit-image