def _retrieve_masslist_centroids(self, scan_number, polarity):
"""Retrieves centroids from centroided data."""
# read masslist
scan_number_l = ctypes.c_long(scan_number)
mass_list_v = comtypes.automation.VARIANT()
flags_v = comtypes.automation.VARIANT()
size_l = ctypes.c_long()
error = self._raw_reader.GetMassListFromScanNum(
scan_number_l,
comtypes.BSTR(''), # filter
ctypes.c_long(0), # intensity cut-off mode
ctypes.c_long(0), # intensity cut-off value
ctypes.c_long(0), # max num of peaks
ctypes.c_long(0), # centroided result
ctypes.c_double(0), # centroid peak width
mass_list_v,
flags_v,
size_l)
if error:
return None
# get arrays
mz_array = numpy.array(mass_list_v.value[0])
ai_array = numpy.array(mass_list_v.value[1])
# create centroids
centroids = []
for i in range(len(mz_array)):
if ai_array[i] > 0:
centroids.append(Centroid(mz_array[i], ai_array[i]))
return centroids
def _retrieve_profile(self, scan_number):
"""Retrieves profile data."""
# read masslist
scan_number_l = ctypes.c_long(scan_number)
mass_list_v = comtypes.automation.VARIANT()
flags_v = comtypes.automation.VARIANT()
size_l = ctypes.c_long()
error = self._raw_reader.GetMassListFromScanNum(
scan_number_l,
comtypes.BSTR(''), # filter
ctypes.c_long(0), # intensity cut-off mode
ctypes.c_long(0), # intensity cut-off value
ctypes.c_long(0), # max num of peaks
ctypes.c_long(0), # centroid result
ctypes.c_double(0), # centroid peak width
mass_list_v,
flags_v,
size_l)
if error:
return None
# get arrays
mz_array = numpy.array(mass_list_v.value[0])
ai_array = numpy.array(mass_list_v.value[1])
# make profile
profile = numpy.dstack((mz_array, ai_array))[0].copy()
return profile
def _retrieve_scan_filter(self, scan_number):
"""Retrieves scan filter string."""
# get filter string
filter_string_s = comtypes.BSTR()
if self._raw_reader.GetFilterForScanNum(scan_number, filter_string_s):
return None
return filter_string_s.value
def _retrieve_instrument_model(self):
"""Retrieves instrument model value."""
# get instrument model
instrument_model_s = comtypes.BSTR()
if not self._raw_reader.GetInstModel(instrument_model_s):
return instrument_model_s.value
return None
def _retrieve_instrument_name(self):
"""Retrieves instrument name value."""
# get instrument name
instrument_name_s = comtypes.BSTR()
if not self._raw_reader.GetInstName(instrument_name_s):
return instrument_name_s.value
return None
def scan_lists(self):
'''
Returns the mass and intensity scan lists from a given scan
:
GetMassListFromScanNum(long FAR* pnScanNumber, LPCTSTR szFilter,
long nIntensityCutoffType,
long nIntensityCutoffValue,
long nMaxNumberOfPeaks,
BOOL bCentroidResult,
VARIANT FAR* pvarMassList,
VARIANT FAR* pvarPeakFlags,
long FAR* pnArraySize)
-> np.array([401.66, ...]), np.array([4131.76, ...])
'''
num = ctypes.c_long(self.scan_num)
null_filter = comtypes.BSTR()
cutoff_none = ctypes.c_long(0)
cutoff_value = ctypes.c_long()
max_peaks = ctypes.c_long()
centroided = self._centroided
peak_width = ctypes.c_double(0)
mass_list = comtypes.automation.VARIANT()
peak_flags = comtypes.automation.VARIANT()
size = ctypes.c_long()
self.rawfile.GetMassListFromScanNum(
num,
null_filter,
cutoff_none,
cutoff_value,
max_peaks,
centroided,
peak_width,
mass_list,
peak_flags,
size
)
with comtypes.safearray.safearray_as_ndarray:
mzs, intensity = mass_list.value
return mzs, intensity
def _retrieve_activation_energy(self, scan_number, method):
""""Retrieves activation energy value."""
# get value from trailer
label = "%s Energy eV:" % method
activation_energy_v = comtypes.automation.VARIANT()
if not self._raw_reader.GetTrailerExtraValueForScanNum(
scan_number, label, activation_energy_v):
if activation_energy_v.value:
return float(activation_energy_v.value)
# get filter string
filter_string_s = comtypes.BSTR()
if self._raw_reader.GetFilterForScanNum(scan_number, filter_string_s):
return None
# parse filter string
matches = SCAN_FILTER_DISSOCIATION_PATTERN.findall(
filter_string_s.value)
if matches:
return float(matches[-1][3])
return None