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Fix spectra skipping and add min_n_peaks option #265

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@melihyilmaz melihyilmaz commented Nov 10, 2023

Skips spectra with fewer than min_n_peaks (min_n_peaks=20 by default) and adds the corresponding config option. Fixes #264

This solution is a bit hacky and discards spectra at the batching stage but I think the existing functionality for skipping spectra was buggy to begin with: it only replaces the spectra to be skipped with dummy spectra and runs the model on those dummies so that we still get predictions for them. Am I missing something, @bittremieux @wfondrie?

TODOs:

  • Find a way to skip spectra before batching, e.g. inside the dataset
  • Log how many spectra are skipped
  • Unit tests

@melihyilmaz melihyilmaz marked this pull request as draft November 10, 2023 21:54
@bittremieux bittremieux added this to the Depthcharge v0.4 milestone May 15, 2024
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