def labelscan(
self,
pickingHeight=0.75,
absThreshold=0.0,
relThreshold=0.0,
snThreshold=0.0,
baselineWindow=0.1,
baselineOffset=0.0,
smoothMethod=None,
smoothWindow=0.2,
smoothCycles=1,
):
"""Label centroides in current scan.
pickingHeight (float) - peak picking height for centroiding
absThreshold (float) - absolute intensity threshold
relThreshold (float) - relative intensity threshold
snThreshold (float) - signal to noise threshold
baselineWindow (float) - noise calculation window (in %/100)
baselineOffset (float) - baseline offset, relative to noise width (in %/100)
smoothMethod (None, MA, GA or SG) - smoothing method
smoothWindow (float) - m/z window size for smoothing
smoothCycles (int) - number of smoothing cycles
"""
# get baseline
baseline = self.baseline(window=baselineWindow, offset=baselineOffset)
# pre-smooth profile
profile = self.profile
if smoothMethod:
profile = mod_signal.smooth(signal=profile, method=smoothMethod, window=smoothWindow, cycles=smoothCycles)
# label peaks
peaklist = mod_peakpicking.labelscan(
signal=profile,
pickingHeight=pickingHeight,
absThreshold=absThreshold,
relThreshold=relThreshold,
snThreshold=snThreshold,
baseline=baseline,
)
# check peaklist
if peaklist == None:
return False
# update peaklist
self.peaklist = peaklist
return True
def labelscan(self,
pickingHeight=0.75,
absThreshold=0.,
relThreshold=0.,
snThreshold=0.,
baselineWindow=0.1,
baselineOffset=0.,
smoothMethod=None,
smoothWindow=0.2,
smoothCycles=1):
"""Label centroides in current scan.
pickingHeight (float) - peak picking height for centroiding
absThreshold (float) - absolute intensity threshold
relThreshold (float) - relative intensity threshold
snThreshold (float) - signal to noise threshold
baselineWindow (float) - noise calculation window (in %/100)
baselineOffset (float) - baseline offset, relative to noise width (in %/100)
smoothMethod (None, MA, GA or SG) - smoothing method
smoothWindow (float) - m/z window size for smoothing
smoothCycles (int) - number of smoothing cycles
"""
# get baseline
baseline = self.baseline(window=baselineWindow, offset=baselineOffset)
# pre-smooth profile
profile = self.profile
if smoothMethod:
profile = mod_signal.smooth(signal=profile,
method=smoothMethod,
window=smoothWindow,
cycles=smoothCycles)
# label peaks
peaklist = mod_peakpicking.labelscan(signal=profile,
pickingHeight=pickingHeight,
absThreshold=absThreshold,
relThreshold=relThreshold,
snThreshold=snThreshold,
baseline=baseline)
# check peaklist
if peaklist == None:
return False
# update peaklist
self.peaklist = peaklist
return True
def smooth(self, method, window, cycles=1):
"""Smooth profile.
method (MA GA SG) - smoothing method
window (float) - m/z window size for smoothing
cycles (int) - number of repeating cycles
"""
# smooth data
profile = mod_signal.smooth(signal=self.profile, method=method, window=window, cycles=cycles)
# store data
self.profile = profile
self.peaklist.empty()
# clear buffers
self.reset()
def smooth(self, method, window, cycles=1):
"""Smooth profile.
method (MA GA SG) - smoothing method
window (float) - m/z window size for smoothing
cycles (int) - number of repeating cycles
"""
# smooth data
profile = mod_signal.smooth(signal=self.profile,
method=method,
window=window,
cycles=cycles)
# store data
self.profile = profile
self.peaklist.empty()
# clear buffers
self.reset()
