Thresholds input file specification needs fix

[kimdn]

• membrain-seg version: commit 0a87963b798ee2652bdbe07f467e04e87d951a54 Author: LorenzLamm 34575029+LorenzLamm@users.noreply.github.com Date: Tue Jul 16 15:36:42 2024 +0200

• Python version: Python 3.9.5

• Operating System: linux

Description

According to

membrain thresholds --scoremap-path <path-to-scoremap>
        --thresholds -1.5

I did

membrain thresholds --scoremap-path outputs/2024_06_06-MED4_10p4_Apix_MED4_TS_11_SIRT_CTF_no_Au_rec/2024_06_06-MED4_10p4_Apix_MED4_TS_11_SIRT_CTF_no_Au_rec_scores.mrc --thresholds -1.5

but MemBrain-seg seeks /predictions (hardcoded?)

[LorenzLamm]

Hey @kimdn, Thanks a lot for raising this.

You can control the output folder in the command line via the flag --out-folder /path/to/your/output If no argument is provided here, it will default to ./predictions, i.e. also the default output folder for segmentations.

E.g. for your case, you could do membrain thresholds --scoremap-path outputs/2024_06_06-MED4_10p4_Apix_MED4_TS_11_SIRT_CTF_no_Au_rec/2024_06_06-MED4_10p4_Apix_MED4_TS_11_SIRT_CTF_no_Au_rec_scores.mrc --thresholds -1.5 --out-folder outputs/2024_06_06-MED4_10p4_Apix_MED4_TS_11_SIRT_CTF_no_Au_rec/ and it should work just fine.

To avoid the error, maybe we should automatically create the output folder? I should definitely add the out_folder argument to the documentation.

Let me know if this helps. :)

[kimdn]

@LorenzLamm

Adding --out-folder outputs/2024_06_06-MED4_10p4_Apix_MED4_TS_11_SIRT_CTF_no_Au_rec/ works.

Yes, either adding document or adding exception handling like 'MemBrain-seg can't find score file in default "predictions" folder. Specify --out-folder as you did for "membrain segment"' might be nice.

Thank you for making MemBrain-seg. Just using your latest pre-trained model segmented our target membrane well (even when our input tomogram is not denoised yet) !