def safe_read_key(spectrum: Spectrum, key: str) -> Optional[float]:
""" Read key from spectrum and convert to float or return 'None'.
Tries to read the given key from the spectrum metadata and convert it to a float.
In case an exception is thrown or the key is not present, returns 'None'.
Parameters
----------
spectrum:
Spectrum from which to read the key.
key:
Key to be read from the spectrum metadata.
Returns
-------
Either the key's value converted to float or 'None'.
"""
value = spectrum.get(key, default=None)
if value is not None:
try:
value = float(value)
except ValueError:
# RT is in format that can't be converted to float -> set rt to None
value = None
return value
def test_derive_formula_from_name_remove_formula_false():
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"compound_name": "peptideXYZ [M+H+K] C5H12NO2"})
spectrum = derive_formula_from_name(spectrum_in, remove_formula_from_name=False)
assert spectrum.get("formula") == "C5H12NO2", "Expected different formula."
assert spectrum.get("compound_name") == spectrum_in.get("compound_name"), "Expected no name change."
def test_spectrum_getters_return_copies():
"""Test if getters return (deep)copies so that edits won't change the original entries."""
spectrum = Spectrum(mz=numpy.array([100.0, 101.0], dtype="float"),
intensities=numpy.array([0.4, 0.5], dtype="float"),
metadata={"testdata": 1})
# Get entries and modify
testdata = spectrum.get("testdata")
testdata += 1
assert spectrum.get("testdata") == 1, "Expected different entry"
peaks_mz = spectrum.peaks.mz
peaks_mz += 100.0
assert numpy.all(spectrum.peaks.mz == numpy.array(
[100.0, 101.0])), "Expected different peaks.mz"
metadata = spectrum.metadata
metadata["added_info"] = "this"
assert spectrum.metadata == {
'testdata': 1
}, "Expected metadata to remain unchanged"
def test_derive_adduct_from_name_dont_remove_from_name():
spectrum_in = Spectrum(mz=numpy.array([], dtype="float"),
intensities=numpy.array([], dtype="float"),
metadata={"compound_name": "peptideXYZ [M+H+K]"})
spectrum = derive_adduct_from_name(spectrum_in,
remove_adduct_from_name=False)
assert spectrum.get("adduct") == "[M+H+K]", "Expected different adduct."
assert spectrum.get("compound_name") == spectrum_in.get(
"compound_name"), "Expected no change to name."
def test_if_spectrum_is_cloned():
"""Test if filter is correctly cloning the input spectrum."""
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum = require_minimum_of_high_peaks(spectrum_in, no_peaks=2)
spectrum.set("testfield", "test")
assert not spectrum_in.get(
"testfield"), "Expected input spectrum to remain unchanged."
def test_if_spectrum_is_cloned():
"""Test if filter is correctly cloning the input spectrum."""
mz = numpy.array([], dtype="float")
intensities = numpy.array([], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum = remove_peaks_outside_top_k(spectrum_in)
spectrum.set("testfield", "test")
assert not spectrum_in.get(
"testfield"), "Expected input spectrum to remain unchanged."
def test_if_spectrum_is_cloned():
"""Test if filter is correctly cloning the input spectrum."""
mz = numpy.array([10, 20, 30, 40], dtype="float")
intensities = numpy.array([0, 1, 10, 100], dtype="float")
spectrum_in = Spectrum(mz=mz, intensities=intensities)
spectrum_in.set("precursor_mz", 1.)
spectrum = require_precursor_mz(spectrum_in)
spectrum.set("testfield", "test")
assert not spectrum_in.get("testfield"), \
"Expected input spectrum to remain unchanged."