def test_proxies(self):
mzs = np.array([ 0.0, 1.0, 2.0, 3.0, 4.0, 5.0 ]).reshape(-1,1)
ones = np.ones_like(mzs)
peaks = np.hstack((mzs, ones))
spec = Spectrum(peaks, 0.0, 1, "0")
spec.peaks[:, 0] += 1.0
assert np.linalg.norm(spec.peaks[:, 0] - mzs.flatten(), 1) == 6.0
def check(fun, spec=spec):
before = spec.uniqueId()
exec(fun, dict(spec=spec))
assert "unique_id" not in spec.meta
after = spec.uniqueId()
assert before != after
check("spec.peaks[:, 0] += 1")
check("spec.peaks += 1")
check("spec.peaks -= 1")
check("spec.peaks /= 2.1")
check("spec.peaks //= 2.1")
check("spec.peaks *= 2")
check("spec.peaks %= 1.1")
check("spec.peaks **= 2")
check("spec.rt += 1")
check("spec.msLevel += 1")
check("spec.precursors = [(1, 1, 0)]")
check("spec.polarity = '+'")
pm = PeakMap([spec])
before = pm.uniqueId()
pm.spectra[0].rt += 2
after = spec.uniqueId()
assert before != after
from cPickle import loads, dumps
back = loads(dumps(pm))
back.meta.pop("unique_id", None)
pm.meta.pop("unique_id", None)
assert back.uniqueId() == pm.uniqueId()
# this was broken after pickling, the callback was not pickled and calling
# it whein operatin on peaks rose an excepion
for s in back:
s.peaks += 1
# this was broken because it creates a view which is not continous:
s.peaks = s.peaks[1:-1:2]
assert s.uniqueId()
spec_new = loads(dumps(spec))
assert spec_new.scan_number == spec.scan_number
assert spec_new.rt == spec.rt
assert spec_new.msLevel == spec.msLevel
assert spec_new.precursors == spec.precursors
assert spec_new.polarity == spec.polarity
assert np.linalg.norm(spec_new.peaks - spec.peaks) == 0.0
def test_proxies(self):
mzs = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0]).reshape(-1, 1)
ones = np.ones_like(mzs)
peaks = np.hstack((mzs, ones))
spec = Spectrum(peaks, 0.0, 1, "0")
spec.peaks[:, 0] += 1.0
assert np.linalg.norm(spec.peaks[:, 0] - mzs.flatten(), 1) == 6.0
def check(fun, spec=spec):
before = spec.uniqueId()
exec(fun, dict(spec=spec))
assert "unique_id" not in spec.meta
after = spec.uniqueId()
assert before != after
check("spec.peaks[:, 0] += 1")
check("spec.peaks += 1")
check("spec.peaks -= 1")
check("spec.peaks /= 2.1")
check("spec.peaks //= 2.1")
check("spec.peaks *= 2")
check("spec.peaks %= 1.1")
check("spec.peaks **= 2")
check("spec.rt += 1")
check("spec.msLevel += 1")
check("spec.precursors = [(1, 1, 0)]")
check("spec.polarity = '+'")
pm = PeakMap([spec])
before = pm.uniqueId()
pm.spectra[0].rt += 2
after = spec.uniqueId()
assert before != after
from cPickle import loads, dumps
back = loads(dumps(pm))
back.meta.pop("unique_id", None)
pm.meta.pop("unique_id", None)
assert back.uniqueId() == pm.uniqueId()
# this was broken after pickling, the callback was not pickled and calling
# it whein operatin on peaks rose an excepion
for s in back:
s.peaks += 1
# this was broken because it creates a view which is not continous:
s.peaks = s.peaks[1:-1:2]
assert s.uniqueId()
spec_new = loads(dumps(spec))
assert spec_new.scan_number == spec.scan_number
assert spec_new.rt == spec.rt
assert spec_new.msLevel == spec.msLevel
assert spec_new.precursors == spec.precursors
assert spec_new.polarity == spec.polarity
assert np.linalg.norm(spec_new.peaks - spec.peaks) == 0.0
def testFilterIntensity(self, regtest):
data = np.array([ 0.0, 1.0, 2.0, 3.0, 4.0, 5.0 ]).reshape(-1,1)
intensities = np.array([ 10.0, 11.0, 12.0, 13.0, 14.0, 15.0 ]).reshape(-1,1)
peaks = np.hstack((data, intensities))
assert peaks.shape == (6,2)
spec1 = Spectrum(peaks, 0.0, 1, "0")
spec2 = Spectrum(peaks, 0.0, 2, "0")
assert spec1.maxIntensity() == 15.0
pm = PeakMap([spec1, spec2])
pm_x = pm.extract(mslevelmin=1)
assert len(pm_x) == 2
pm_x = pm.extract(mslevelmin=2)
assert len(pm_x) == 1
pm_x = pm.extract(mslevelmin=3)
assert len(pm_x) == 0
pm_x = pm.extract(mslevelmax=1, imin=10.0, imax=15.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (6, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imin=10.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (6, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imax=15.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (6, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imin=10.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (6, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imin=11.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (5, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imin=11.0, imax = 13.5)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (3, 2)
for spec in pm_x:
print >> regtest, spec.peaks
def test_uniuqe_id():
ti = emzed.utils.toTable("id", [1, 1, 2])
t = emzed.utils.toTable("t", (ti, ti, None))
# peakmap unique id already tested by compression of peakmap:
t.addColumn("pm", PeakMap([]))
t.addColumn("blob", Blob("data"))
assert t.uniqueId() == "a03470ffc2876f1c12becb55e5f82f4fd59d9f906afe6f07484755755c4807e0"
def test_remove(self):
mzs = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0]).reshape(-1, 1)
ones = np.ones_like(mzs)
peaks = np.hstack((mzs, ones))
spectra = [
Spectrum(peaks, 0.0, 1, "0"),
Spectrum(peaks, 1.0, 1, "0"),
Spectrum(peaks, 1.5, 2, "0"),
Spectrum(peaks, 2.0, 1, "0")
]
pm = PeakMap(spectra)
pmt = copy.deepcopy(pm)
pmt.remove(0.0, 10.0, 0.0, 2.0)
assert len(pmt) == 1
assert pmt.spectra[0] == Spectrum(peaks, 1.5, 2, "0")
pmt = copy.deepcopy(pm)
pmt.remove(1.0, 3.2, 1.0, 2.0)
assert len(pmt) == 4
assert np.all(pmt.spectra[0].peaks == peaks)
assert np.all(
pmt.spectra[1].peaks.flatten() == [0., 1.0, 4.0, 1.0, 5.0, 1.0])
assert np.all(pmt.spectra[2].peaks == peaks)
assert np.all(
pmt.spectra[3].peaks.flatten() == [0., 1.0, 4.0, 1.0, 5.0, 1.0])
def testCompress(self):
t = toTable("a", [])
import numpy
t.compressPeakMaps()
s = Spectrum(
numpy.arange(12, dtype="float64").reshape(-1, 2), 1.0, 1, "+")
pm = PeakMap([s])
s = Spectrum(
numpy.arange(12, dtype="float64").reshape(-1, 2), 1.0, 1, "+")
pm2 = PeakMap([s])
t = toTable("pm", [pm, pm2])
assert len(set(map(id, t.pm.values))) == 2
t.compressPeakMaps()
assert len(set(map(id, t.pm.values))) == 1
def test_proxies(self):
mzs = np.array([ 0.0, 1.0, 2.0, 3.0, 4.0, 5.0 ]).reshape(-1,1)
ones = np.ones_like(mzs)
peaks = np.hstack((mzs, ones))
spec = Spectrum(peaks, 0.0, 1, "0")
spec.peaks[:, 0] += 1.0
assert np.linalg.norm(spec.peaks[:, 0] - mzs.flatten(), 1) == 6.0
def check(fun, spec=spec):
before = spec.uniqueId()
exec(fun, dict(spec=spec))
assert "unique_id" not in spec.meta
after = spec.uniqueId()
assert before != after
check("spec.peaks[:, 0] += 1")
check("spec.peaks += 1")
check("spec.peaks -= 1")
check("spec.peaks /= 2.1")
check("spec.peaks //= 2.1")
check("spec.peaks *= 2")
check("spec.peaks %= 1.1")
check("spec.peaks **= 2")
check("spec.rt += 1")
check("spec.msLevel += 1")
check("spec.precursors = [(1, 1)]")
check("spec.polarity = '+'")
pm = PeakMap([spec])
before = pm.uniqueId()
pm.spectra[0].rt += 2
after = spec.uniqueId()
assert before != after
from cPickle import loads, dumps
back = loads(dumps(pm))
back.meta.pop("unique_id", None)
pm.meta.pop("unique_id", None)
assert back.uniqueId() == pm.uniqueId()
def testTrapezIntegrationSimple():
p0 = np.array((1.0, 1.0, 2.0, 2.0)).reshape(-1,2)
p1 = np.array((2.0, 2.0, 3.0, 3.0)).reshape(-1,2)
p2 = np.array((1.0, 1.0, 2.0, 2.0, 3.0, 3.0)).reshape(-1,2)
p3 = np.array((3.0, 3.0)).reshape(-1,2)
s0 = Spectrum(p0, 0.0, 1, '0')
s1 = Spectrum(p1, 1.0, 1, '0')
s2 = Spectrum(p2, 2.0, 1, '0')
s3 = Spectrum(p3, 3.0, 1, '0')
pm = PeakMap([s0,s1,s2,s3])
integrator = dict(emzed._algorithm_configs.peakIntegrators)["trapez"]
integrator.setPeakMap(pm)
assert integrator.integrate(1.4, 2.5, 0, 3)["area"] == 5.0
assert integrator.integrate(1.4, 2.5, 0, 2)["area"] == 4.0
assert integrator.integrate(0.4, 2.5, 0, 3)["area"] == 6.5
assert integrator.integrate(0.4, 2.5, 0, 2)["area"] == 5.0
assert integrator.integrate(0.4, 3.0, 0, 3)["area"] == 14
# one level 2 spec:
s1 = Spectrum(p1, 1.0, 2, '0')
pm = PeakMap([s0,s1,s2,s3])
integrator.setPeakMap(pm)
assert integrator.integrate(1.4, 2.5, 0, 3, msLevel=1)["area"] == 5.0
assert integrator.integrate(1.4, 2.5, 0, 2, msLevel=1)["area"] == 4.0
assert integrator.integrate(0.4, 2.5, 0, 3, msLevel=1)["area"] == 7.5
assert integrator.integrate(0.4, 2.5, 0, 2, msLevel=1)["area"] == 6.0
assert integrator.integrate(0.4, 3.0, 0, 3, msLevel=1)["area"] == 13.5
# multiple levels shall rise exception:
ex(lambda: integrator.integrate(0.4, 3.0, 0, 3))
def test_proxies(self):
mzs = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0]).reshape(-1, 1)
ones = np.ones_like(mzs)
peaks = np.hstack((mzs, ones))
spec = Spectrum(peaks, 0.0, 1, "0")
spec.peaks[:, 0] += 1.0
assert np.linalg.norm(spec.peaks[:, 0] - mzs.flatten(), 1) == 6.0
def check(fun, spec=spec):
before = spec.uniqueId()
exec(fun, dict(spec=spec))
assert "unique_id" not in spec.meta
after = spec.uniqueId()
assert before != after
check("spec.peaks[:, 0] += 1")
check("spec.peaks += 1")
check("spec.peaks -= 1")
check("spec.peaks /= 2.1")
check("spec.peaks //= 2.1")
check("spec.peaks *= 2")
check("spec.peaks %= 1.1")
check("spec.peaks **= 2")
check("spec.rt += 1")
check("spec.msLevel += 1")
check("spec.precursors = [(1, 1)]")
check("spec.polarity = '+'")
pm = PeakMap([spec])
before = pm.uniqueId()
pm.spectra[0].rt += 2
after = spec.uniqueId()
assert before != after
from cPickle import loads, dumps
back = loads(dumps(pm))
back.meta.pop("unique_id", None)
pm.meta.pop("unique_id", None)
assert back.uniqueId() == pm.uniqueId()
def test_unique_id(regtest):
ti = emzed.utils.toTable("id", [1, 1, 2])
t = emzed.utils.toTable("t", (ti, ti, None))
# peakmap unique id already tested by compression of peakmap:
t.addColumn("pm", PeakMap([]), type_=object)
t.addColumn("blob", Blob("data"))
print(t.uniqueId(), file=regtest)
ti = emzed.utils.toTable("id", [1, 1, 2])
t = emzed.utils.toTable("t", (ti, ti, None))
# peakmap unique id already tested by compression of peakmap:
t.addColumn("pm", PeakMap([]), type_=PeakMap)
t.addColumn("blob", Blob("data"))
print(t.uniqueId(), file=regtest)
ti = emzed.utils.toTable("id", [1, 1, 2])
t = emzed.utils.toTable("t", (ti, ti, None))
# peakmap unique id already tested by compression of peakmap:
t.addColumn("pm", PeakMap([]))
t.addColumn("blob", Blob("data"))
print(t.uniqueId(), file=regtest)
def testNoIntegration():
integrator = dict(emzed._algorithm_configs.peakIntegrators)["no_integration"]
integrator.setPeakMap(PeakMap([]))
result = integrator.integrate(0.0, 100.0, 0, 300, 1)
assert result.get("area") is None
assert result.get("rmse") is None
assert result.get("params") is None
# assert result.get("eic") is None
assert result.get("baseline") is None
rts = range(0, 600)
x, y = integrator.getSmoothed(rts, result.get("params"))
assert x == []
assert y == []
def _testIntegration(path, n_cpus, integrator_id, check_values=True):
# test with and without unicode:
ft = io.loadTable(path("data/features.table"))
# an invalid row should not stop integration, but result
# in None values for emzed.utils.integrate generated columns
ftr = utils.integrate(ft, integrator_id, n_cpus=n_cpus, min_size_for_parallel_execution=1)
assert len(ftr) == len(ft)
assert "area" in ftr.getColNames()
assert "rmse" in ftr.getColNames()
if check_values:
assert ftr.area.values[0] >= 0, ftr.area.values[0]
assert ftr.rmse.values[0] >= 0, ftr.rmse.values[0]
assert ftr.params.values[0] is not None
assert ftr.method.values[0] is not None
ft.setValue(ft.rows[0], "mzmin", None)
ft._addColumnWithoutNameCheck("mzmin__0", ft.mzmin)
ft._addColumnWithoutNameCheck("mzmax__0", ft.mzmax)
ft._addColumnWithoutNameCheck("rtmin__0", ft.rtmin)
ft._addColumnWithoutNameCheck("rtmax__0", ft.rtmax)
ft._addColumnWithoutNameCheck("peakmap__0", ft.peakmap)
ft.addColumn("mzminX", ft.mzmin)
ft.addColumn("mzmaxX", ft.mzmax)
ft.addColumn("rtminX", ft.rtmin)
ft.addColumn("rtmaxX", ft.rtmax)
ft.addColumn("peakmapX", ft.peakmap)
ftr = utils.integrate(ft, integrator_id, n_cpus=n_cpus, min_size_for_parallel_execution=1)
assert len(ftr) == len(ft)
assert "area" in ftr.getColNames()
assert "rmse" in ftr.getColNames()
# assert "eic" in ftr.getColNames()
assert "area__0" in ftr.getColNames()
assert "rmse__0" in ftr.getColNames()
# assert "eic__0" in ftr.getColNames()
assert "areaX" in ftr.getColNames()
assert "rmseX" in ftr.getColNames()
assert "rmseX" in ftr.getColNames()
# assert "eicX" in ftr.getColNames()
if check_values:
assert ftr.area.values[0] is None
assert ftr.rmse.values[0] is None
assert ftr.params.values[0] is None
assert ftr.method.values[0] is not None
# assert ftr.eic.values[0] is None
assert ftr.area.values[1] is not None
assert ftr.rmse.values[1] is not None
assert ftr.params.values[1] is not None
assert ftr.method.values[1] is not None
# assert len(ftr.eic.values[1]) == 2
assert ftr.area__0.values[0] is None
assert ftr.rmse__0.values[0] is None
assert ftr.params__0.values[0] is None
assert ftr.method__0.values[0] is not None
# assert ftr.eic__0.values[0] is None
assert ftr.area__0.values[1] is not None
assert ftr.rmse__0.values[1] is not None
assert ftr.params__0.values[1] is not None
assert ftr.method__0.values[1] is not None
# assert len(ftr.eic__0.values[1]) == 2
assert ftr.areaX.values[0] is None
assert ftr.rmseX.values[0] is None
assert ftr.paramsX.values[0] is None
assert ftr.methodX.values[0] is not None
# assert ftr.eicX.values[0] is None
assert ftr.areaX.values[1] is not None
assert ftr.rmseX.values[1] is not None
assert ftr.paramsX.values[1] is not None
assert ftr.methodX.values[1] is not None
# assert len(ftr.eicX.values[1]) == 2
# test with empty chromatograms
s0 = ft.peakmap.values[0].spectra[0]
rt0 = s0.rt
pm = PeakMap([s0])
rts, iis = pm.chromatogram(0, 10000, rt0 + 20, rt0 + 30)
assert len(rts) == 0
assert len(iis) == 0
ft.replaceColumn("peakmap", pm)
ft.replaceColumn("rtmin", rt0 + 10)
ft.replaceColumn("rtmax", rt0 + 20)
ftr2 = utils.integrate(ft, integrator_id, n_cpus=n_cpus, min_size_for_parallel_execution=1)
# assert set(ftr2.eic.values) == {None}
return ftr
def testEmptyPeakMap(self):
pm = PeakMap([])
assert pm.extract(0, 9999, 0, 10000).spectra == ()
assert pm.filter(lambda t: True).spectra == ()
assert pm.specsInRange(0, 10e6) == []
assert pm.levelNSpecsInRange(1, 0, 10e6) == []
assert pm.chromatogram(0, 10e6, 0, 10e6) == ([], [])
assert pm.chromatogram(0, 10e6) == ([], [])
assert pm.msNPeaks(1, 0, 10e6).tolist() == []
assert pm.allRts() == []
assert pm.levelOneRts() == []
assert pm.levelNSpecs(1,2) == []
def testActions():
t = buildTable()
n = len(t)
recorder = RecordingObject()
model = TableModel(t, recorder)
t_orig = t.copy()
action = DeleteRowsAction(model, [0], [0])
action.do()
assert len(model.table) == len(t_orig) - 1
assert model.table.rows[0] == t_orig.rows[1]
action.undo()
assert len(model.table) == len(t_orig)
assert model.table.rows[0] == t_orig.rows[0]
action = CloneRowAction(model, 0, 0)
action.do()
assert model.table.rows[0] == t_orig.rows[0]
assert model.table.rows[1] == t_orig.rows[0]
assert model.table.rows[2] == t_orig.rows[1]
assert len(model.table) == n + 1
action.undo()
assert len(model.table) == n
assert model.table.rows[0] == t_orig.rows[0]
assert model.table.rows[1] == t_orig.rows[1]
action = SortTableAction(model, [("mz", True)])
action.do()
assert model.table.mz.values == (None, 1.0, 2.0)
action.undo()
assert model.table.mz.values == t_orig.mz.values
action = SortTableAction(model, [("mz", False)])
action.do()
assert model.table.mz.values == (2.0, 1.0, None)
action.undo()
assert model.table.mz.values == t_orig.mz.values
class Index(object):
def row(self):
return 0
def column(self):
return 0
action = ChangeValueAction(model, Index(), 0, 0, 3.0)
action.do()
assert model.table.rows[0][0] == 3.0
action.undo()
assert model.table.rows[0][0] == 1.0
t = buildTable()
import numpy
peak = numpy.array(((1.0, 100.0), ))
specs = [Spectrum(peak, rt, 1, "+") for rt in range(9, 15)]
pm = PeakMap(specs)
t.replaceColumn("peakmap", pm)
model.table = emzed.utils.integrate(t, "no_integration")
action = IntegrateAction(model, 0, "", "trapez", 0, 100, {0: 0})
action.do()
assert model.table.area.values[0] == 500.0
action.undo()
assert model.table.area.values[0] == None
def testFilterIntensity(self, regtest):
data = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0]).reshape(-1, 1)
intensities = np.array([10.0, 11.0, 12.0, 13.0, 14.0,
15.0]).reshape(-1, 1)
peaks = np.hstack((data, intensities))
assert peaks.shape == (6, 2)
spec1 = Spectrum(peaks, 0.0, 1, "0")
spec2 = Spectrum(peaks, 0.0, 2, "0")
assert spec1.maxIntensity() == 15.0
pm = PeakMap([spec1, spec2])
pm_x = pm.extract(mslevelmin=1)
assert len(pm_x) == 2
pm_x = pm.extract(mslevelmin=2)
assert len(pm_x) == 1
pm_x = pm.extract(mslevelmin=3)
assert len(pm_x) == 0
pm_x = pm.extract(mslevelmax=1, imin=10.0, imax=15.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (6, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imin=10.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (6, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imax=15.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (6, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imin=10.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (6, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imin=11.0)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (5, 2)
for spec in pm_x:
print >> regtest, spec.peaks
pm_x = pm.extract(mslevelmax=1, imin=11.0, imax=13.5)
assert len(pm_x) == 1
assert pm_x[0].peaks.shape == (3, 2)
for spec in pm_x:
print >> regtest, spec.peaks
def testEmptyPeakMap(self):
pm = PeakMap([])
assert pm.extract(0, 9999, 0, 10000).spectra == ()
assert pm.filter(lambda t: True).spectra == ()
assert pm.specsInRange(0, 10e6) == []
assert pm.levelNSpecsInRange(1, 0, 10e6) == []
assert pm.chromatogram(0, 10e6, 0, 10e6) == ([], [])
assert pm.chromatogram(0, 10e6) == ([], [])
assert pm.msNPeaks(1, 0, 10e6).tolist() == []
assert pm.allRts() == []
assert pm.levelOneRts() == []
assert pm.levelNSpecs(1, 2) == []
def test001(self):
exp = MSExperiment()
basename = "SHORT_MS2_FILE.mzData"
here = os.path.dirname(os.path.abspath(__file__))
FileHandler().loadExperiment(os.path.join(here, "data", basename), exp)
assert exp.size() > 0
pc = Precursor()
pc.setMZ(1.0)
pc.setIntensity(100)
s0 = exp[0]
s0.setPrecursors([pc])
s0.setMSLevel(2)
spec = Spectrum.fromMSSpectrum(s0)
settings = InstrumentSettings()
settings.setPolarity(IonSource.Polarity.POSITIVE)
s0.setInstrumentSettings(settings)
self.compare_specs(spec, s0)
specneu = Spectrum.fromMSSpectrum(spec.toMSSpectrum())
self.compare_specs(specneu, s0)
pm = PeakMap.fromMSExperiment(exp)
assert os.path.basename(pm.meta["source"]) == basename
rtmin, rtmax = pm.rtRange(None)
ms1s = pm.msNPeaks(1, rtmin, rtmax)
assert ms1s.shape == (1797, 2), ms1s.shape
ms1s2 = pm.msNPeaks(1, rtmax=rtmax)
assert np.all(ms1s == ms1s2)
ms1s3 = pm.msNPeaks(1, rtmin=0)
assert np.all(ms1s == ms1s3)
spec = pm.spectra[0]
assert len(list(spec)) == len(spec) # calls iter
allrts = pm.allRts()
assert allrts[0] <= pm.rtRange()[0]
assert allrts[-1] >= pm.rtRange()[1]
assert len(allrts) == 41, len(allrts)
level1 = pm.levelNSpecs(1, 1)
level2 = pm.levelNSpecs(2, 2)
level12 = pm.levelNSpecs(1, 2)
assert len(level1) > 0
assert len(level2) > 0
assert len(level1) + len(level2) == len(level12) == len(pm)
assert level1[0].msLevel == 1
assert level2[0].msLevel == 2
# use default arg: nmax = nmin if not provided:
level1 = pm.levelNSpecs(1)
level2 = pm.levelNSpecs(2)
assert len(level1) > 0
assert len(level2) > 0
assert len(level1) + len(level2) == len(level12) == len(pm)
assert level1[0].msLevel == 1
assert level2[0].msLevel == 2
lone = pm.levelOneRts()
assert len(lone) == len(level1)
self.compare_exp(pm, exp, basename)
pm2 = PeakMap.fromMSExperiment(pm.toMSExperiment())
self.compare_exp(pm2, exp, basename)
pm2 = pm.extract(rtmin=rtmin + .000001)
assert len(pm2) == len(pm) - 1
pm2 = pm2.extract(rtmax=rtmax - 0.000001)
assert len(pm2) == len(pm) - 2
mzmin, mzmax = pm.mzRange(2)
assert mzmin < 250
assert mzmax > 860
mzmin, mzmax = pm.mzRange(1)
assert mzmin >= 700
assert mzmax <= 1050
pm2 = pm.extract(rtmin + 0.00001, mzmin=300)
mzmin2, mzmax2 = pm2.mzRange()
assert mzmin2 >= 300
assert mzmax2 == mzmax
pm2 = pm.extract(rtmin=rtmin + 0.000001, mzmin=300, mzmax=1000)
mzmin2, mzmax2 = pm2.mzRange()
assert mzmin2 >= 300
assert mzmax2 <= 1000
with pytest.raises(Exception):
pm.spectra[0].peaksInRange()
pp1 = pm.spectra[0].peaksInRange(mzmax=10000)
pp2 = pm.spectra[0].peaksInRange(mzmin=0)
assert np.all(pp1 == pp2)
specs0 = list(pm.spectra)
specs1 = pm.specsInRange(0, 99999)
specs2 = pm.specsInRange(0, specs0[0].rt)
specs3 = pm.specsInRange(specs0[-1].rt, 999999)
assert specs0 == specs1
assert specs2 == [specs0[0]]
assert specs3 == [specs0[-1]]
pm.spectra[0].polarity = "+"
pm.spectra[1].polarity = "-"
pm = PeakMap(pm.spectra)
mz = pm.representingMzPeak(0, 99999, 0, 99999)
assert abs(mz - 831.86538) < 0.0001
def test001(self):
exp = MSExperiment()
basename = "SHORT_MS2_FILE.mzData"
here = os.path.dirname(os.path.abspath(__file__))
FileHandler().loadExperiment(os.path.join(here, "data", basename), exp)
assert exp.size()>0
pc = Precursor()
pc.setMZ(1.0)
pc.setIntensity(100)
s0 = exp[0]
s0.setPrecursors([pc])
s0.setMSLevel(2)
spec = Spectrum.fromMSSpectrum(s0)
settings = InstrumentSettings()
settings.setPolarity(IonSource.Polarity.POSITIVE)
s0.setInstrumentSettings(settings)
self.compare_specs(spec, s0)
specneu = Spectrum.fromMSSpectrum(spec.toMSSpectrum())
self.compare_specs(specneu, s0)
pm = PeakMap.fromMSExperiment(exp)
assert os.path.basename(pm.meta["source"]) == basename
rtmin, rtmax = pm.rtRange(None)
ms1s = pm.msNPeaks(1, rtmin, rtmax)
assert ms1s.shape == (1797, 2), ms1s.shape
ms1s2 = pm.msNPeaks(1, rtmax=rtmax)
assert np.all(ms1s == ms1s2)
ms1s3 = pm.msNPeaks(1, rtmin=0)
assert np.all(ms1s == ms1s3)
spec = pm.spectra[0]
assert len(list(spec)) == len(spec) # calls iter
allrts = pm.allRts()
assert allrts[0] <= pm.rtRange()[0]
assert allrts[-1] >= pm.rtRange()[1]
assert len(allrts) == 41, len(allrts)
level1 = pm.levelNSpecs(1, 1)
level2 = pm.levelNSpecs(2, 2)
level12 = pm.levelNSpecs(1, 2)
assert len(level1) > 0
assert len(level2) > 0
assert len(level1) + len(level2) == len(level12) == len(pm)
assert level1[0].msLevel == 1
assert level2[0].msLevel == 2
# use default arg: nmax = nmin if not provided:
level1 = pm.levelNSpecs(1)
level2 = pm.levelNSpecs(2)
assert len(level1) > 0
assert len(level2) > 0
assert len(level1) + len(level2) == len(level12) == len(pm)
assert level1[0].msLevel == 1
assert level2[0].msLevel == 2
lone = pm.levelOneRts()
assert len(lone) == len(level1)
self.compare_exp(pm, exp, basename)
pm2 = PeakMap.fromMSExperiment(pm.toMSExperiment())
self.compare_exp(pm2, exp, basename)
pm2 = pm.extract(rtmin=rtmin + .000001)
assert len(pm2) == len(pm) - 1
pm2 = pm2.extract(rtmax=rtmax - 0.000001)
assert len(pm2) == len(pm) - 2
mzmin, mzmax = pm.mzRange(2)
assert mzmin < 250
assert mzmax > 860
mzmin, mzmax = pm.mzRange(1)
assert mzmin >= 700
assert mzmax <= 1050
pm2 = pm.extract(rtmin+0.00001, mzmin=300)
mzmin2, mzmax2 = pm2.mzRange()
assert mzmin2 >= 300
assert mzmax2 == mzmax
pm2 = pm.extract(rtmin = rtmin+0.000001, mzmin=300, mzmax=1000)
mzmin2, mzmax2 = pm2.mzRange()
assert mzmin2 >= 300
assert mzmax2 <= 1000
with pytest.raises(Exception):
pm.spectra[0].peaksInRange()
pp1 = pm.spectra[0].peaksInRange(mzmax = 10000)
pp2 = pm.spectra[0].peaksInRange(mzmin = 0)
assert np.all(pp1 == pp2)
specs0 = list(pm.spectra)
specs1 = pm.specsInRange(0, 99999)
specs2 = pm.specsInRange(0, specs0[0].rt)
specs3 = pm.specsInRange(specs0[-1].rt, 999999)
assert specs0 == specs1
assert specs2 == [ specs0[0] ]
assert specs3 == [ specs0[-1] ]
pm.spectra[0].polarity = "+"
pm.spectra[1].polarity = "-"
pm = PeakMap(pm.spectra)
mz = pm.representingMzPeak(0, 99999, 0, 99999)
assert abs(mz-831.86538) < 0.0001
