def pack(self):
d = {
"scan start time": unitfloat(self.start_time, 'minute'),
"ion injection time": unitfloat(self.injection_time,
'millisecond'),
}
d.update(self.traits)
window_list = [{
'scan window lower limit': unitfloat(sw.lower, 'm/z'),
'scan window upper limit': unitfloat(sw.upper, 'm/z')
} for sw in self.window_list]
d['scanWindowList'] = {
"count": len(window_list),
"scanWindow": window_list
}
return d
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,
}
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])
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,
}
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])
def _acquisition_information(self, scan):
scan_info = {}
scan_list_struct = scan['scanList']
combination = "unknown"
if "no combination" in scan_list_struct:
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)
def filter_string_parser(line):
"""Parses instrument information from Thermo's filter string
Parameters
----------
line : str
The filter string associated with a scan
Returns
-------
dict
Fields extracted from the filter string
"""
words = line.upper().split(" ")
values = dict()
i = 0
values['supplemental_activation'] = " sa " in line
ms_level_info = ms_level_pat.search(line)
if ms_level_info is not None:
ms_level_data = ms_level_info.groupdict()
level = ms_level_data.get("level")
if level != "":
parts = line[ms_level_info.end():].split(" ")
tandem_sequence = []
for part in parts:
activation_info = activation_pat.search(part)
if activation_info is not None:
activation_info = activation_info.groupdict()
activation_event = dict()
activation_event["isolation_mz"] = float(activation_info['isolation_mz'])
activation_event["activation_type"] = [activation_info['activation_type']]
activation_event["activation_energy"] = [float(activation_info['activation_energy'])]
if part.count("@") > 1:
act_events = activation_mode_pat.finditer(part)
# discard the first match which we already recorded
next(act_events)
for match in act_events:
act_type, act_energy = match.groups()
act_energy = float(act_energy)
activation_event["activation_type"].append(act_type)
activation_event['activation_energy'].append(act_energy)
tandem_sequence.append(activation_event)
values['ms_level'] = int(level)
values['tandem_sequence'] = tandem_sequence
scan_window_info = scan_window_pat.search(line)
if scan_window_info is not None:
values['scan_window'] = (float(scan_window_info.group(1)), float(scan_window_info.group(2)))
try:
word = words[i]
i += 1
analyzer_info = analyzer_pat.search(word)
if analyzer_info is not None:
values['analyzer'] = analyzer_info.group(0)
word = words[i]
i += 1
polarity_info = polarity_pat.search(word)
if polarity_info is not None:
polarity_sigil = polarity_info.group(0)
if polarity_sigil == "+":
polarity = 1
elif polarity_sigil == "-":
polarity = -1
else:
polarity = 0
values["polarity"] = polarity
word = words[i]
i += 1
if word in "PC":
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
