Source code for matchms.filtering.remove_peaks_outside_top_k

import numpy
from ..Fragments import Fragments
from ..typing import SpectrumType


[docs]def remove_peaks_outside_top_k(spectrum_in: SpectrumType, k: int = 6, mz_window: float = 50) -> SpectrumType: """Remove all peaks which are not within *mz_window* of at least one of the *k* highest intensity peaks of the spectrum. Parameters ---------- spectrum_in: Input spectrum. k: The number of most intense peaks to compare to. Default is 6. mz_window: Window of mz values (in Da) that are allowed to lie within the top k peaks. Default is 50 Da. """ if spectrum_in is None: return None spectrum = spectrum_in.clone() assert k >= 1, "k must be a positive nonzero integer." assert mz_window >= 0, "mz_window must be a positive scalar." mzs, intensities = spectrum.peaks.mz, spectrum.peaks.intensities top_k = intensities.argsort()[::-1][0:k] k_ordered_mzs = mzs[top_k] indices = [i for i in range(len(mzs)) if i not in top_k] keep_idx = top_k.tolist() for i in indices: compare = abs(mzs[i]-k_ordered_mzs) <= mz_window if numpy.any(compare): keep_idx.append(i) keep_idx.sort() new_mzs, new_intensities = mzs[keep_idx], intensities[keep_idx] spectrum.peaks = Fragments(mz=new_mzs, intensities=new_intensities) return spectrum