def test_make_chromatograms_end(simulated_experiment):
n_sp = simulated_experiment.getNrSpectra()
end = 90
rt, chromatograms = lcms.make_chromatograms(simulated_experiment, mz_list,
end=end)
assert rt.size == end
assert rt[-1] == simulated_experiment.getSpectrum(end - 1).getRT()
def test_make_chromatograms_end(simulated_experiment):
end = 90
chromatograms = lcms.make_chromatograms(simulated_experiment, mz_list,
end=end)
for c in chromatograms:
assert c.rt.size == end
assert c.rt[-1] == simulated_experiment.getSpectrum(end - 1).getRT()
def test_make_chromatograms_start(simulated_experiment):
n_sp = simulated_experiment.getNrSpectra()
start = 10
chromatogram_length = n_sp - start
rt, chromatograms = lcms.make_chromatograms(simulated_experiment, mz_list,
start=start)
assert rt.size == chromatogram_length
assert rt[0] == simulated_experiment.getSpectrum(start).getRT()
def test_make_chromatograms(simulated_experiment):
# test that the chromatograms generated are valid
# create chromatograms
n_sp = simulated_experiment.getNrSpectra()
n_mz = simulated_experiment.mz_params.shape[0]
rt = np.zeros(n_sp)
chromatogram = np.zeros((n_mz, n_sp))
for scan in range(n_sp):
sp = simulated_experiment.getSpectrum(scan)
rt[scan] = sp.getRT()
_, spint = sp.get_peaks()
chromatogram[:, scan] = spint
expected_chromatograms = [lcms.Chromatogram(rt, x) for x in chromatogram]
test_chromatograms = lcms.make_chromatograms(simulated_experiment, mz_list)
assert len(test_chromatograms) == len(expected_chromatograms)
for ec, tc in zip(expected_chromatograms, test_chromatograms):
assert np.array_equal(ec.rt, tc.rt)
assert np.array_equal(ec.spint, tc.spint)
def test_make_chromatograms_outside_range_mz(simulated_experiment):
# the total intensity of the chromatogram should be equal to zero
_, chromatograms = lcms.make_chromatograms(simulated_experiment, [550])
assert np.isclose(chromatograms.sum(), 0)
def test_make_chromatograms_accumulator_mean(simulated_experiment):
lcms.make_chromatograms(simulated_experiment, mz_list, accumulator="mean")
assert True
def test_make_chromatograms(simulated_experiment):
lcms.make_chromatograms(simulated_experiment, mz_list)
assert True
