def get_matching_pairs():
"""Get pairs of peaks that match within the given tolerance."""
zero_pairs = collect_peak_pairs(spec1, spec2, tolerance, shift=0.0)
if modified_cosine:
message = "Precursor_mz missing. Apply 'add_precursor_mz' filter first."
assert spectrum1.get("precursor_mz") and spectrum2.get("precursor_mz"), message
mass_shift = spectrum1.get("precursor_mz") - spectrum2.get("precursor_mz")
nonzero_pairs = collect_peak_pairs(spec1, spec2, tolerance, shift=mass_shift)
unsorted_matching_pairs = zero_pairs + nonzero_pairs
else:
unsorted_matching_pairs = zero_pairs
return sorted(unsorted_matching_pairs, key=lambda x: x[2], reverse=True)
def get_matching_pairs():
"""Get pairs of peaks that match within the given tolerance."""
matching_pairs = collect_peak_pairs(spec1,
spec2,
self.tolerance,
shift=0.0)
return sorted(matching_pairs, key=lambda x: x[2], reverse=True)
def test_collect_peak_pairs_compiled(shift, expected_pairs, expected_matches):
"""Test finding expected peak matches for given tolerance."""
spec1 = numpy.array([[100, 200, 300, 500],
[0.1, 0.1, 1.0, 1.0]], dtype="float").T
spec2 = numpy.array([[105, 205.1, 300, 500.1],
[0.1, 0.1, 1.0, 1.0]], dtype="float").T
matching_pairs = numpy.array(collect_peak_pairs(spec1, spec2, tolerance=0.2, shift=shift))
assert matching_pairs.shape == expected_matches, "Expected different number of matching peaks"
assert numpy.allclose(matching_pairs, numpy.array(expected_pairs), atol=1e-8), "Expected different values."
def test_collect_peak_pairs_no_matches(numba_compiled):
"""Test function for no matching peaks."""
shift = -20.0
spec1 = numpy.array([[100, 200, 300, 500],
[0.1, 0.1, 1.0, 1.0]], dtype="float").T
spec2 = numpy.array([[105, 205.1, 300, 500.1],
[0.1, 0.1, 1.0, 1.0]], dtype="float").T
if numba_compiled:
matching_pairs = collect_peak_pairs(spec1, spec2, tolerance=0.2, shift=shift)
else:
matching_pairs = collect_peak_pairs.py_func(spec1, spec2, tolerance=0.2, shift=shift)
assert matching_pairs is None, "Expected pairs to be None."
def get_matching_pairs():
"""Get pairs of peaks that match within the given tolerance."""
matching_pairs = collect_peak_pairs(
spec1,
spec2,
self.tolerance,
shift=0.0,
mz_power=self.mz_power,
intensity_power=self.intensity_power)
if matching_pairs is None:
return None
matching_pairs = matching_pairs[
numpy.argsort(matching_pairs[:, 2])[::-1], :]
return matching_pairs
def test_collect_peak_pairs_compiled(shift, expected_pairs):
"""Test finding expected peak matches for given tolerance."""
spec1 = numpy.array([[100, 200, 300, 500], [0.1, 0.1, 1.0, 1.0]],
dtype="float").T
spec2 = numpy.array([[105, 205.1, 300, 500.1], [0.1, 0.1, 1.0, 1.0]],
dtype="float").T
matching_pairs = collect_peak_pairs(spec1,
spec2,
tolerance=0.2,
shift=shift)
assert len(
matching_pairs) == 2, "Expected different number of matching peaks"
assert matching_pairs == [pytest.approx(x, 1e-9) for x in expected_pairs
], "Expected different pairs."