def test_chromatogram():
pm = _load()
rtmin = pm.spectra[0].rt
rtmax = pm.spectra[-1].rt
mzmin = min(min(s.peaks[:, 0]) for s in pm.spectra)
mzmax = max(max(s.peaks[:, 0]) for s in pm.spectra)
rts, chromo = chromatogram(pm, 0, 0, 0, 0, 1)
assert len(rts) == 0
assert len(chromo) == 0
rts, chromo = chromatogram(pm, 0, 10000, 0, 10000, 2)
assert len(rts) == 0
assert len(chromo) == 0
rts, chromo = chromatogram(pm, 0, 1000, rtmin, rtmin, 1)
assert len(rts) == 1
assert len(chromo) == 1
rts, chromo = chromatogram(pm, 0, 1000, rtmax, rtmax, 1)
assert len(rts) == 1
assert len(chromo) == 1
rts, chromo = chromatogram(pm, mzmin - 1e-5, mzmin - 1e-5, rtmin, rtmax, 1)
assert len(rts) == 2540
assert len(chromo) == 2540
assert sum(chromo) == 0.0
rts, chromo = chromatogram(pm, mzmax + 1e-5, mzmax + 1e-5, rtmin, rtmax, 1)
assert len(rts) == 2540
assert len(chromo) == 2540
assert sum(chromo) == 0.0
rts, chromo = chromatogram(pm, 0, 1000, 41, 41.5, 1)
assert len(rts) == 34
assert len(chromo) == 34
assert abs(rts[0] - 41.00279998779) < 1e-4, rts[0]
assert abs(chromo[0] - 33628524.55078125) < 1e-2, chromo[0]
rts, chromo = chromatogram(pm, 0, 1000, 41, 3000, 1)
assert len(rts) == 216
assert len(chromo) == 216
assert abs(rts[215] - 44.89799880) < 1e-5, rts[215]
assert abs(chromo[215] - 309048.935241) < 1e-2, chromo[215]
rts, chromo = chromatogram(pm, 0, 1000, rtmax + 10, rtmax + 20, 1)
assert len(rts) == 0
assert len(chromo) == 0
def chromatogram(self, mzmin, mzmax, rtmin=None, rtmax=None, msLevel=None):
"""
extracts chromatogram in given rt- and mz-window.
returns a tuple ``(rts, intensities)`` where ``rts`` is a list of
rt values (in seconds, as always) and ``intensities`` is a
list of same length containing the summed up peaks for each
rt value.
"""
if not self.spectra:
return [], []
if rtmin is None:
rtmin = self.spectra[0].rt
if rtmax is None:
rtmax = self.spectra[-1].rt
if msLevel is None:
msLevel = min(self.getMsLevels())
if OPTIMIZATIONS_INSTALLED:
rts, iis = emzed_optimizations.chromatogram(
self, mzmin, mzmax, rtmin, rtmax, msLevel)
# fix bug in old version of emzed_optimizations:
# fails if rtmin and rtmax are beyond max rt in peakmap !
f = (rts >= rtmin) * (rts <= rtmax)
return rts[f], iis[f]
specs = self.levelNSpecsInRange(msLevel, rtmin, rtmax)
rts = [s.rt for s in specs]
intensities = [s.intensityInRange(mzmin, mzmax) for s in specs]
return rts, intensities
def chromatogram(self, mzmin, mzmax, rtmin=None, rtmax=None, msLevel=None):
"""
extracts chromatogram in given rt- and mz-window.
returns a tuple ``(rts, intensities)`` where ``rts`` is a list of
rt values (in seconds, as always) and ``intensities`` is a
list of same length containing the summed up peaks for each
rt value.
"""
if not self.spectra:
return [], []
if rtmin is None:
rtmin = self.spectra[0].rt
if rtmax is None:
rtmax = self.spectra[-1].rt
if msLevel is None:
msLevel = min(self.getMsLevels())
if OPTIMIZATIONS_INSTALLED:
rts, iis = emzed_optimizations.chromatogram(self, mzmin, mzmax, rtmin, rtmax, msLevel)
# fix bug in old version of emzed_optimizations:
# fails if rtmin and rtmax are beyond max rt in peakmap !
f = (rts >= rtmin) * (rts <= rtmax)
return rts[f], iis[f]
specs = self.levelNSpecsInRange(msLevel, rtmin, rtmax)
rts = [s.rt for s in specs]
intensities = [s.intensityInRange(mzmin, mzmax) for s in specs]
return rts, intensities
def test_chromatogram():
pm = _load()
rtmin = pm.spectra[0].rt
rtmax = pm.spectra[-1].rt
mzmin = min(min(s.peaks[:, 0]) for s in pm.spectra)
mzmax = max(max(s.peaks[:, 0]) for s in pm.spectra)
rts, chromo = chromatogram(pm, 0, 0, 0, 0, 1)
assert len(rts) == 0
assert len(chromo) == 0
rts, chromo = chromatogram(pm, 0, 10000, 0, 10000, 2)
assert len(rts) == 0
assert len(chromo) == 0
rts, chromo = chromatogram(pm, 0, 1000, rtmin, rtmin, 1)
assert len(rts) == 1
assert len(chromo) == 1
rts, chromo = chromatogram(pm, 0, 1000, rtmax, rtmax, 1)
assert len(rts) == 1
assert len(chromo) == 1
rts, chromo = chromatogram(pm, mzmin - 1e-5, mzmin - 1e-5, rtmin, rtmax, 1)
assert len(rts) == 2540
assert len(chromo) == 2540
assert sum(chromo) == 0.0
rts, chromo = chromatogram(pm, mzmax + 1e-5, mzmax + 1e-5, rtmin, rtmax, 1)
assert len(rts) == 2540
assert len(chromo) == 2540
assert sum(chromo) == 0.0
rts, chromo = chromatogram(pm, 0, 1000, 41, 41.5, 1)
assert len(rts) == 34
assert len(chromo) == 34
assert abs(rts[0] - 41.00279998779) < 1e-4, rts[0]
assert abs(chromo[0] - 33628524.55078125) < 1e-2, chromo[0]
rts, chromo = chromatogram(pm, 0, 1000, 41, 3000, 1)
assert len(rts) == 216
assert len(chromo) == 216
assert abs(rts[215] - 44.89799880) < 1e-5, rts[215]
assert abs(chromo[215] - 309048.935241) < 1e-2, chromo[215]
rts, chromo = chromatogram(pm, 0, 1000, rtmax + 10, rtmax + 20, 1)
assert len(rts) == 0
assert len(chromo) == 0
