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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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TypeError using Topaz denoise #119

Closed bencreekm closed 3 years ago

bencreekm commented 3 years ago

I am using topaz denoise on my own dataset following the denoising tutorial. I keep getting an error that I am not sure how to fix. Do you know what may be going wrong? Thanks!

version: Topaz 0.2.4

My command is: topaz denoise -a denoised/training_data/partA/ -b denoised/training_data/partB/

The error is: Traceback (most recent call last): File "/usr/local/EMAN2/eman2-sphire-sparx/envs/topaz/bin/topaz", line 11, in load_entry_point('topaz-em==0.2.4', 'console_scripts', 'topaz')() File "/usr/local/EMAN2/eman2-sphire-sparx/envs/topaz/lib/python3.6/site-packages/topaz/main.py", line 148, in main args.func(args) File "/usr/local/EMAN2/eman2-sphire-sparx/envs/topaz/lib/python3.6/site-packages/topaz/commands/denoise.py", line 535, in main if not os.path.exists(args.output): File "/usr/local/EMAN2/eman2-sphire-sparx/envs/topaz/lib/python3.6/genericpath.py", line 19, in exists os.stat(path) TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

bencreekm commented 3 years ago

Update: This issue does go away if you include the -o flag