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if word == 'P':
values['peak_mode'] = 'profile'
else:
values['peak_mode'] = 'centroid'
word = words[i]
i += 1
ionization_info = ionization_pat.search(word)
if ionization_info is not None:
values['ionization'] = ionization_info.group(0)
word = words[i]
i += 1
cv_info = compensation_voltage_pat.search(word)
if cv_info is not None:
values['compensation_voltage'] = unitfloat(cv_info.group(1), None)
word = words[i]
i += 1
return values
except IndexError:
return values
def _acquisition_information(self, scan):
fline = self._filter_string(scan)
event = self._get_scan_event(scan)
trailer_extras = self._trailer_values(scan)
traits = {
'preset scan configuration': event,
'filter string': fline,
}
cv = fline.get("compensation_voltage")
if cv is not None:
traits[FAIMS_compensation_voltage] = cv
event = ScanEventInformation(
self._scan_time(scan),
injection_time=unitfloat(trailer_extras.get(
'Ion Injection Time (ms)', 0.0), 'millisecond'),
window_list=[ScanWindow(
fline.get("scan_window")[0], fline.get("scan_window")[1])],
traits=traits)
return ScanAcquisitionInformation("no combination", [event])
combination = "no combination"
elif "sum of spectra" in scan_list_struct:
combination = "sum of spectra"
elif "median of spectra" in scan_list_struct:
combination = "median of spectra"
elif "mean of spectra" in scan_list_struct:
combination = "mean of spectra"
scan_info['combination'] = combination
scan_info_scan_list = []
misplaced_FAIMS_value = scan.get(FAIMS_compensation_voltage.name, None)
for i, scan_ in enumerate(scan_list_struct.get("scan", [])):
scan_ = scan_.copy()
if misplaced_FAIMS_value is not None and i == 0:
scan[FAIMS_compensation_voltage.name] = misplaced_FAIMS_value
struct = {}
struct['start_time'] = scan_.pop('scan start time', unitfloat(0, 'minute'))
struct['injection_time'] = scan_.pop("ion injection time", unitfloat(0, 'millisecond'))
windows = []
for window in scan_.pop("scanWindowList", {}).get("scanWindow", []):
windows.append(ScanWindow(
window['scan window lower limit'],
window['scan window upper limit']))
struct['window_list'] = windows
scan_.pop("instrumentConfigurationRef", None)
struct['traits'] = scan_
scan_info_scan_list.append(ScanEventInformation(**struct))
scan_info['scan_list'] = scan_info_scan_list
return ScanAcquisitionInformation(**scan_info)
elif "sum of spectra" in scan_list_struct:
combination = "sum of spectra"
elif "median of spectra" in scan_list_struct:
combination = "median of spectra"
elif "mean of spectra" in scan_list_struct:
combination = "mean of spectra"
scan_info['combination'] = combination
scan_info_scan_list = []
misplaced_FAIMS_value = scan.get(FAIMS_compensation_voltage.name, None)
for i, scan_ in enumerate(scan_list_struct.get("scan", [])):
scan_ = scan_.copy()
if misplaced_FAIMS_value is not None and i == 0:
scan[FAIMS_compensation_voltage.name] = misplaced_FAIMS_value
struct = {}
struct['start_time'] = scan_.pop('scan start time', unitfloat(0, 'minute'))
struct['injection_time'] = scan_.pop("ion injection time", unitfloat(0, 'millisecond'))
windows = []
for window in scan_.pop("scanWindowList", {}).get("scanWindow", []):
windows.append(ScanWindow(
window['scan window lower limit'],
window['scan window upper limit']))
struct['window_list'] = windows
scan_.pop("instrumentConfigurationRef", None)
struct['traits'] = scan_
scan_info_scan_list.append(ScanEventInformation(**struct))
scan_info['scan_list'] = scan_info_scan_list
return ScanAcquisitionInformation(**scan_info)
def _acquisition_information(self, scan):
fline = self._filter_string(scan)
event = self._get_scan_event(scan)
trailer_extras = self._trailer_values(scan)
traits = {
'preset scan configuration': event,
'filter string': fline,
}
cv = fline.get("compensation_voltage")
if cv is not None:
traits[FAIMS_compensation_voltage] = cv
event = ScanEventInformation(
self._scan_time(scan),
injection_time=unitfloat(trailer_extras.get('Ion Injection Time (ms)', 0.0), 'millisecond'),
window_list=[ScanWindow(
fline.get("scan_window")[0], fline.get("scan_window")[1])], traits=traits)
return ScanAcquisitionInformation("no combination", [event])