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tbepler / topaz

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.
GNU General Public License v3.0
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RuntimeWarning: overflow encountered in exp in training #64

Open huwjenkins opened 3 years ago

huwjenkins commented 3 years ago

Hi,

I see the following message printed to stderr when training. RuntimeWarning: overflow encountered in exp. This is reproducible with Topaz 0.2.4 on the test dataset.

Using numpy.seterr identifies this occurs here for scores < -88.7228 as then np.exp(-score) overflows float32.

https://github.com/tbepler/topaz/blob/11f7ecbdfedfd4820199d43571059de61748c17d/topaz/commands/train.py#L539

Is this an issue? Thanks.

tbepler commented 3 years ago

Thanks for pointing this out. It should be fixed, but won't cause any problems other than the annoying warning.

huwjenkins commented 3 years ago

Thanks for confirming it doesn't cause any problems! Fortunately the warning is only printed the first time it happens.