def test_select_by_intensity(peaks, intensity_from, intensity_to, expected):
spectrum_in = SpectrumBuilder().with_mz(peaks[0]).with_intensities(
peaks[1]).build()
spectrum = select_by_intensity(spectrum_in,
intensity_from=intensity_from,
intensity_to=intensity_to)
assert spectrum.peaks.mz.size == len(expected[0])
assert spectrum.peaks.mz.size == spectrum.peaks.intensities.size
assert numpy.array_equal(spectrum.peaks.mz, expected[0])
assert numpy.array_equal(spectrum.peaks.intensities, expected[1])
def test_select_by_intensity_with_to_parameter():
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([1, 10, 100, 1000], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum = select_by_intensity(spectrum_in, intensity_to=35.0)
assert spectrum.peaks.mz.size == 1
assert spectrum.peaks.mz.size == spectrum.peaks.intensities.size
assert numpy.array_equal(spectrum.peaks.mz, numpy.array([20],
dtype="float"))
assert numpy.array_equal(spectrum.peaks.intensities,
numpy.array([10], dtype="float"))
def test_select_by_intensity_no_parameters_2():
mz = numpy.array([998, 999, 1000, 1001, 1002], dtype="float")
intensities = numpy.array([198, 199, 200, 201, 202], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum = select_by_intensity(spectrum_in)
assert spectrum.peaks.mz.size == 3
assert spectrum.peaks.mz.size == spectrum.peaks.intensities.size
assert numpy.array_equal(spectrum.peaks.mz,
numpy.array([998, 999, 1000], dtype="float"))
assert numpy.array_equal(spectrum.peaks.intensities,
numpy.array([198, 199, 200], dtype="float"))
def spectrum_processing_minimal(
spectrum: SpectrumType,
**settings: Union[int, float]) -> Union[SpectrumType, None]:
"""Minimal necessary spectrum processing that is required by MS2Query.
This mostly includes intensity normalization and setting spectra to None
when they do not meet the minimum requirements.
Args:
----------
spectrum:
Spectrum to process
mz_from
Set lower threshold for m/z peak positions. Default is 10.0.
n_required_below_mz
Number of minimal required peaks with m/z below 1000.0Da for a spectrum
to be considered.
Spectra not meeting this criteria will be set to None.
intensity_from
Set lower threshold for peak intensity. Default is 0.001.
max_mz_required
Only peaks <= max_mz_required will be counted to check if spectrum
contains sufficient peaks to be considered.
"""
settings = set_minimal_processing_defaults(**settings)
spectrum = normalize_intensities(spectrum)
spectrum = select_by_intensity(spectrum,
intensity_from=settings["intensity_from"])
spectrum = select_by_mz(spectrum,
mz_from=settings["mz_from"],
mz_to=np.inf)
spectrum = require_peaks_below_mz(
spectrum,
n_required=settings["n_required_below_mz"],
max_mz=settings["max_mz_required"])
spectrum = require_precursor_mz(spectrum)
return spectrum