Remove losses #321
Remove losses #321
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Kudos, SonarCloud Quality Gate passed! |
| def losses(self, loss_mz_from, loss_mz_to) -> Optional[Fragments]: | ||
| precursor_mz = self.get("precursor_mz", None) | ||
| if precursor_mz: | ||
| assert isinstance(precursor_mz, (float, int)), ("Expected 'precursor_mz' to be a scalar number.", | ||
| "Consider applying 'add_precursor_mz' filter first.") | ||
| peaks_mz, peaks_intensities = self.peaks.mz, self.peaks.intensities | ||
| losses_mz = (precursor_mz - peaks_mz)[::-1] | ||
| losses_intensities = peaks_intensities[::-1] | ||
| # Add losses which are within given boundaries | ||
| mask = np.where((losses_mz >= loss_mz_from) | ||
| & (losses_mz <= loss_mz_to)) | ||
| losses = Fragments(mz=losses_mz[mask], | ||
| intensities=losses_intensities[mask]) | ||
| return losses | ||
| logger.warning("No precursor_mz found. Consider applying 'add_precursor_mz' filter first.") | ||
| return None |
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Is it possible in python to have a property that is in fact a proper function? This way, the compatibility with the spectrum.losses pipelines would be retained.
I'm not sure on how to incorporate the filtering here though.
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That seems like a nice solution
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@niekdejonge maybe you could give some input on this? This has been open for a while but I think it is still relevant. |
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@hechth @florian-huber I agree with both points, it makes sense to remove this and make this a function. But it will indeed also break functionality of Spec2Vec and MS2Query. For MS2Query this is not directly a problem, since it is set to Matchms 0.13.0 anyway, so we can make this switch when upgrading to matchms >0.18.0. |
spectrum.losses