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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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Bug with Topaz #207

Open win5tan opened 3 days ago

win5tan commented 3 days ago

Hi there, it looks like there's a bug with Topaz. The line where it is erroring is bad. 

It should be:

pd.concat(groups_train, axis=0)

Instead of

pd.concat(groups_train, 0) <--- BAD!

Could the developers please debug/fix it? Thanks a lot.

DarnellGranberry commented 3 days ago

What file and line is it referencing in your error? Also, what branch are you using?

win5tan commented 3 days ago

Hi Darnell,

It was when I execute the Topaz path in cryosparc. IT officer from my institute thinks it's a bug error.

I used the following Topaz path: /stornext/System/data/software/rhel/9/base/structbio/topaz/0.2.5/bin/topaz

Thanks, Winnie

On Wed, Oct 16, 2024 at 12:12 AM Darnell Granberry @.***> wrote:

What file and line is it referencing in your error?

— Reply to this email directly, view it on GitHub https://github.com/tbepler/topaz/issues/207#issuecomment-2413879031, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBBYF6OYMV6JS7Z36KMYORTZ3UICZAVCNFSM6AAAAABP6J6DMSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJTHA3TSMBTGE . You are receiving this because you authored the thread.Message ID: @.***>

DarnellGranberry commented 1 day ago

The only instances of pd.concat I can find all use that keyword argument. Can you try re-installing topaz? It would be helpful if you could paste the full traceback output when your error appears.

vatese commented 22 hours ago

Hey! Hope this helps. Ran into something similar.

I see this was updated on the master branch https://github.com/tbepler/topaz/commit/25cb2cb8de2a0f995da42a472eb86b7011c8535a.

Topaz was installed with pip install topaz-em.

Traceback (most recent call last):
File "/sw/topaz/bin/topaz", line 8, in <module>
sys.exit(main())
File "/sw/topaz/lib64/python3.9/site-packages/topaz/main.py", line 148, in main
args.func(args)
File "/sw/topaz/lib64/python3.9/site-packages/topaz/commands/train_test_split.py", line 108, in main
targets_train = pd.concat(groups_train, 0)
TypeError: concat() takes 1 positional argument but 2 were given

Current version provided by pip:

./topaz --version
TOPAZ 0.2.5a