def test_peaks(self):
assert Spectrum().peaks == []
assert Spectrum(peaks=[]).peaks == []
assert Spectrum(peaks=()).peaks == []
spectrum = Spectrum(
peaks=[Peak(170.0965, 172.1028, 890559.25, 1, "M+H")])
assert spectrum.peaks == [
Peak(170.0965, 172.1028, 890559.25, 1, "M+H")
]
def spectrum(): return Spectrum( spectrum_type="FbF", algorithm="FindByFormula", saturation_limit=10000, scans=1, scan_type="Scan", ionisation="Esi", polarity='+', peaks=[Peak(170.0965, 172.1028, 890559.25, 1, "M+H")], rt_ranges=[RTRange(12, 34)], )
def fbf_spectrum(): return Spectrum( spectrum_type="FbF", algorithm="FindByFormula", scan_type="Scan", ionisation="Esi", polarity='+', device=Device(device_type="QuadrupoleTimeOfFlight", number=1), peaks=[ Peak(170.0965, 170.0964, 890559.25, charge=1, label="M+H"), Peak(171.0998, 171.0996, 114286.09, charge=1, label="M+H+1"), Peak(172.1033, 172.1028, 7151.12, charge=1, label="M+H+2"), Peak(192.0831, 192.0784, 490.62, charge=1, label="M+Na"), ], )
def tof_spectrum(): return Spectrum( spectrum_type="TOF-MS1", algorithm="FindByFormula", saturation_limit=16742400, scans=12, scan_type="Scan", ionisation="Esi", polarity='+', voltage="380V", device=Device(device_type="QuadrupoleTimeOfFlight", number=1), peaks=[ Peak(170.0965, 170.0964, 890559.25, charge=1, label="M+H"), Peak(171.0998, 171.0996, 114286.09, charge=1, label="M+H+1"), Peak(172.1033, 172.1028, 7151.12, charge=1, label="M+H+2"), Peak(192.0831, 192.0784, 490.62, charge=1, label="M+Na"), ], rt_ranges=[RTRange(13.561, 13.808)], )
def test_voltage(self, voltage, expected):
assert Spectrum(voltage=voltage).voltage == expected
def test_rt_ranges(self):
assert Spectrum().rt_ranges == []
assert Spectrum(rt_ranges=[]).rt_ranges == []
assert Spectrum(rt_ranges=()).rt_ranges == []
assert Spectrum(rt_ranges=[RTRange(12, 34)
], ).rt_ranges == [RTRange(12, 34)]
def test_ionisation(self):
assert Spectrum(ionisation="Esi").ionisation == "Esi"
def test_polarity(self, polarity, expected):
assert Spectrum(polarity=polarity).polarity == expected
def test_scans(self):
assert Spectrum(scans=1).scans == 1
assert Spectrum(scans='1').scans == 1 # type: ignore
def test_scan_type(self):
assert Spectrum(scan_type="Scan").scan_type == "Scan"
def test_from_xml(raw_xml, expects):
tree = lxml.objectify.fromstring(raw_xml)
spec = Spectrum.from_xml(tree)
assert spec == expects
def test_saturation_limit(self):
assert Spectrum(saturation_limit=10000).saturation_limit == 10000
assert Spectrum(
saturation_limit="10000").saturation_limit == 10000 # type: ignore
def test_algorithm(self):
assert Spectrum(algorithm="FindByFormula").algorithm == "FindByFormula"
def test_spectrum_type(self):
assert Spectrum(spectrum_type="FbF").spectrum_type == "FbF"
<p x="195.0612" rx="195.0652" y="690.56" z="1" s="M+H" />
<p x="196.0679" rx="196.0686" y="22.97" z="1" s="M+H+1" />
<p x="217.0466" rx="217.0471" y="1286.60" z="1" s="M+Na" />
<p x="219.0532" rx="219.0524" y="44.93" z="1" s="M+Na+1" />
</MSPeaks>
</Spectrum>
"""
fbf_expects = Spectrum(
spectrum_type="FbF",
algorithm="FindByFormula",
scans=0,
scan_type="Scan",
ionisation="Esi",
polarity='+',
peaks=[
Peak(x=195.0612, rx=195.0652, y=690.56, charge=1, label="M+H"),
Peak(x=196.0679, rx=196.0686, y=22.97, charge=1, label="M+H+1"),
Peak(x=217.0466, rx=217.0471, y=1286.60, charge=1, label="M+Na"),
Peak(x=219.0532, rx=219.0524, y=44.93, charge=1, label="M+Na+1"),
],
device=Device("QuadrupoleTimeOfFlight", 1),
)
raw_xml_tof = """
<Spectrum type="TOF-MS1" satLimit="16742400" scans="28" cpdAlgo="FindByFormula">
<MSDetails scanType="Scan" is="Esi" p="+" fv="380.0V" />
<RTRanges>
<RTRange min="12.158" max="12.461" />
</RTRanges>
<Device type="QuadrupoleTimeOfFlight" num="1" />