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 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 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) == []
