def extract_peaks(file,time_range):
peak_data = {}
run = pymzml.run.Reader(file+'.mzML')
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'] = mod_signal.combine(peak_data[file][spec.get('filter string')]['scan'], np.array(spec.peaks))
calculations.signal_filter(peak_data[file][spec.get('filter string')]['scan'],0.005)
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'] = mod_signal.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 combine(self, other):
"""Add data from given scan.
other (mspy.scan) - scan to combine with
"""
# check scan
if not isinstance(other, scan):
raise TypeError, "Cannot combine with non-scan object!"
# use profiles only
if len(self.profile) or len(other.profile):
# combine profiles
self.profile = mod_signal.combine(self.profile, other.profile)
# empty peaklist
self.peaklist.empty()
# use peaklists only
elif len(self.peaklist) or len(other.peaklist):
self.peaklist.combine(other.peaklist)
# clear buffers
self.reset()
def combine(self, other):
"""Add data from given scan.
other (mspy.scan) - scan to combine with
"""
# check scan
if not isinstance(other, scan):
raise TypeError, "Cannot combine with non-scan object!"
# use profiles only
if len(self.profile) or len(other.profile):
# combine profiles
self.profile = mod_signal.combine(self.profile, other.profile)
# empty peaklist
self.peaklist.empty()
# use peaklists only
elif len(self.peaklist) or len(other.peaklist):
self.peaklist.combine(other.peaklist)
# clear buffers
self.reset()
