def extract_peaks(file,time_range):
peak_data = {}
run = pymzml.run.Reader(file)
peak_data[file] = {}
print(file)
for spec in run:
if spec.get('filter string')!= None and spec.get('total ion current') != None and spec.get('scan time') >= time_range[0] and spec.get('scan time') <= time_range[1]:
if spec.get('filter string') in peak_data[file]:
peak_data[file][spec.get('filter string')]['scan_count'] += 1
peak_data[file][spec.get('filter string')]['scan'] = mspy.combine(peak_data[file][spec.get('filter string')]['scan'], np.array(spec.peaks))
else:
peak_data[file][spec.get('filter string')] = {}
peak_data[file][spec.get('filter string')]['scan_count'] = 1
peak_data[file][spec.get('filter string')]['scan'] = np.array(spec.peaks)
for scan in peak_data[file].keys():
peak_data[file][scan]['scan'] = mspy.reduce(peak_data[file][scan]['scan'])
peak_data[file][scan]['scan'] = mspy.multiply(peak_data[file][scan]['scan'],y=1.0/peak_data[file][scan]['scan_count'])
with open(file+scan+'.np', 'wb') as f:
np.save(f,peak_data[file][scan]['scan'])
def makeProfile(self):
"""Generate pattern profile."""
self.currentPatternProfile = None
self.currentPatternPeaks = None
self.currentPatternScan = None
# check pattern
if self.currentPattern == None:
return
# get selected charge
charge = 0
if self.currentIon != None:
charge = self.currentIon[3]
# make profile
self.currentPatternProfile = mspy.profile(
peaklist=self.currentPattern,
fwhm=config.massCalculator['patternFwhm'],
points=20,
model=config.massCalculator['patternPeakShape'],
)
# get scale and shift for specified intensity and baseline
basepeak = mspy.basepeak(self.currentPatternProfile)
scale = (config.massCalculator['patternIntensity'] -
config.massCalculator['patternBaseline']
) / self.currentPatternProfile[basepeak][1]
shift = config.massCalculator['patternBaseline']
# rescale profile
self.currentPatternProfile = mspy.multiply(self.currentPatternProfile,
y=scale)
self.currentPatternProfile = mspy.offset(self.currentPatternProfile,
y=shift)
# make real peaklist from profile
peaklist = []
for isotope in mspy.maxima(self.currentPatternProfile):
mz = isotope[0]
centroid = mspy.centroid(self.currentPatternProfile, isotope[0],
isotope[1] * 0.99)
if abs(mz - centroid) < config.massCalculator['patternFwhm'] / 20:
mz = centroid
peak = mspy.peak(mz=mz, ai=isotope[1], base=shift, charge=charge)
peaklist.append(peak)
peaklist = mspy.peaklist(peaklist)
# make individual peak shapes
self.currentPatternPeaks = []
if config.massCalculator['patternShowPeaks']:
# gaussian shape
if config.massCalculator['patternPeakShape'] == 'gaussian':
for isotope in self.currentPattern:
peak = mspy.gaussian(
x=isotope[0],
minY=shift,
maxY=isotope[1] * scale + shift,
fwhm=config.massCalculator['patternFwhm'])
self.currentPatternPeaks.append(peak)
# lorentzian shape
elif config.massCalculator['patternPeakShape'] == 'lorentzian':
for isotope in self.currentPattern:
peak = mspy.lorentzian(
x=isotope[0],
minY=shift,
maxY=isotope[1] * scale + shift,
fwhm=config.massCalculator['patternFwhm'])
self.currentPatternPeaks.append(peak)
# gauss-lorentzian shape
elif config.massCalculator[
'patternPeakShape'] == 'gausslorentzian':
for isotope in self.currentPattern:
peak = mspy.gausslorentzian(
x=isotope[0],
minY=shift,
maxY=isotope[1] * scale + shift,
fwhm=config.massCalculator['patternFwhm'])
self.currentPatternPeaks.append(peak)
# make scan object
self.currentPatternScan = mspy.scan(profile=self.currentPatternProfile,
peaklist=peaklist)
def makeProfile(self):
"""Generate pattern profile."""
self.currentPatternProfile = None
self.currentPatternPeaks = None
self.currentPatternScan = None
# check pattern
if self.currentPattern == None:
return
# get selected charge
charge = 0
if self.currentIon != None:
charge = self.currentIon[3]
# make profile
self.currentPatternProfile = mspy.profile(
peaklist = self.currentPattern,
fwhm = config.massCalculator['patternFwhm'],
points = 20,
model = config.massCalculator['patternPeakShape'],
)
# get scale and shift for specified intensity and baseline
basepeak = mspy.basepeak(self.currentPatternProfile)
scale = (config.massCalculator['patternIntensity'] - config.massCalculator['patternBaseline']) / self.currentPatternProfile[basepeak][1]
shift = config.massCalculator['patternBaseline']
# rescale profile
self.currentPatternProfile = mspy.multiply(self.currentPatternProfile, y=scale)
self.currentPatternProfile = mspy.offset(self.currentPatternProfile, y=shift)
# make real peaklist from profile
peaklist = []
for isotope in mspy.maxima(self.currentPatternProfile):
mz = isotope[0]
centroid = mspy.centroid(self.currentPatternProfile, isotope[0], isotope[1]*0.99)
if abs(mz-centroid) < config.massCalculator['patternFwhm']/20:
mz = centroid
peak = mspy.peak(
mz = mz,
ai = isotope[1],
base = shift,
charge = charge
)
peaklist.append(peak)
peaklist = mspy.peaklist(peaklist)
# make individual peak shapes
self.currentPatternPeaks = []
if config.massCalculator['patternShowPeaks']:
# gaussian shape
if config.massCalculator['patternPeakShape'] == 'gaussian':
for isotope in self.currentPattern:
peak = mspy.gaussian(
x = isotope[0],
minY = shift,
maxY = isotope[1]*scale+shift,
fwhm = config.massCalculator['patternFwhm']
)
self.currentPatternPeaks.append(peak)
# lorentzian shape
elif config.massCalculator['patternPeakShape'] == 'lorentzian':
for isotope in self.currentPattern:
peak = mspy.lorentzian(
x = isotope[0],
minY = shift,
maxY = isotope[1]*scale+shift,
fwhm = config.massCalculator['patternFwhm']
)
self.currentPatternPeaks.append(peak)
# gauss-lorentzian shape
elif config.massCalculator['patternPeakShape'] == 'gausslorentzian':
for isotope in self.currentPattern:
peak = mspy.gausslorentzian(
x = isotope[0],
minY = shift,
maxY = isotope[1]*scale+shift,
fwhm = config.massCalculator['patternFwhm']
)
self.currentPatternPeaks.append(peak)
# make scan object
self.currentPatternScan = mspy.scan(profile=self.currentPatternProfile, peaklist=peaklist)
