def get_scans_labels_for_scan_number(self, scan_number):
scan_label = BSTR()
scan_number = c_long(scan_number)
self.thermo_Library.GetFilterForScanNum(scan_number, scan_label)
return scan_label
def get_bruker_tics(self):
strAnalysisData = BSTR("SumIntensity")
if self.Bruker_Library.HasAnalysisData(strAnalysisData):
tics_array = self.Bruker_Library.GetAnalysisData(strAnalysisData)
tics_array = array(tics_array)
return tics_array
def get_bruker_retention_time(self):
strAnalysisData = BSTR("RetentionTime")
if self.Bruker_Library.HasAnalysisData(strAnalysisData):
tics_array = self.Bruker_Library.GetAnalysisData(strAnalysisData)
tics_array = array(tics_array)
else:
tics_array = [0]
return tics_array
def get_filter_for_scan_num(self, scan_number):
"""Returns the closest matching run time that corresponds to scan_number for the current
controller. This function is only supported for MS device controllers.
e.g. ['FTMS', '-', 'p', 'NSI', 'Full', 'ms', '[200.00-1000.00]']
"""
str_filter = BSTR(None)
error = self.thermo_Library.GetFilterForScanNum(scan_number, byref(str_filter))
if error:
raise IOError(
"scan %i GetFilterForScanNum error : %s" % (scan_number, str(error))
)
else:
return str(str_filter.value).split()
def QueryPathOfRegTypeLib(libid, wVerMajor, wVerMinor, lcid=0):
"Return the path of a registered type library"
pathname = BSTR()
_oleaut32.QueryPathOfRegTypeLib(byref(GUID(libid)), wVerMajor, wVerMinor,
lcid, byref(pathname))
return pathname.value.split("\0")[0]
def RetrieveData(hRaw):
MatPyLib = {
'InstrumentName': '',
'InstrumentModel': '',
'Reply': 0,
'DetectorCount': 0,
'ScanList': [],
'Filters': [],
'FiltersCount': 0,
'ScanInfo': OrderedDict()
}
pnNumControllers = c_long()
hRaw.GetNumberOfControllers(pnNumControllers)
MatPyLib['DetectorCount'] = pnNumControllers.value
if pnNumControllers.value == 0 or pnNumControllers.value > 1:
print "Warning: Number of Controlers is 0 or larger than 1"
nControllerType = 0 #MS
pnNumControllers = c_long()
hRaw.GetNumberOfControllersOfType(nControllerType, pnNumControllers)
if pnNumControllers.value > 1:
print "Warning: Multipe ControllersOfType of MS"
reply = 0
hRaw.SetCurrentController(0, 1)
pbstrInstName = BSTR()
hRaw.GetInstName(pbstrInstName)
MatPyLib['InstrumentName'] = pbstrInstName.value
pvarFilterArray = VARIANT()
pnArraySize = c_long()
hRaw.GetFilters(pvarFilterArray, pnArraySize)
MatPyLib['FiltersCount'] = pnArraySize.value
MatPyLib["Filters"] = zeros((pnArraySize.value,), dtype = nobj)
MatPyLib["Filters"][:] = pvarFilterArray.value
MatPyLib["Filters"] = []
pnFirstSpectrum = c_long()
pnLastSpectrum = c_long()
hRaw.GetFirstSpectrumNumber(pnFirstSpectrum)
hRaw.GetLastSpectrumNumber(pnLastSpectrum)
MatPyLib['ScanList'] = range(pnFirstSpectrum.value, pnLastSpectrum.value + 1)
for i in MatPyLib['ScanList']:
ScanNumber = "Scan" + str(int(i))
nScanNumber = c_long(int(i))
MatPyLib['ScanInfo'][ScanNumber] = {}
pbstrFilter = BSTR()
hRaw.GetFilterForScanNum(nScanNumber, pbstrFilter)
MatPyLib['ScanInfo'][ScanNumber]["Filter"] = pbstrFilter.value
if pbstrFilter.value not in MatPyLib["Filters"]:
MatPyLib["Filters"].append(pbstrFilter.value)
pnNumPackets = c_long()
pdStartTime = c_double()
pdLowMass = c_double()
pdHighMass = c_double()
pdTIC = c_double()
pdBasePeakMass = c_double()
pdBasePeakIntensity = c_double()
pnNumChannels = c_long()
pbUniformTime = c_long()
pdFrequency = c_double()
hRaw.GetScanHeaderInfoForScanNum(nScanNumber,
pnNumPackets,
pdStartTime,
pdLowMass,
pdHighMass,
pdTIC,
pdBasePeakMass,
pdBasePeakIntensity,
pnNumChannels,
pbUniformTime,
pdFrequency
)
MatPyLib['ScanInfo'][ScanNumber]["TIC"] = float(pdTIC.value)
MatPyLib['ScanInfo'][ScanNumber]["LowMass"] = float(pdLowMass.value)
MatPyLib['ScanInfo'][ScanNumber]["HighMass"] = float(pdHighMass.value)
pvarNoisePackets = VARIANT()
pnScanNumber = c_long(int(i))
hRaw.GetNoiseData(pvarNoisePackets, pnScanNumber);
MatPyLib['ScanInfo'][ScanNumber]["NoisePackets"] = {"Mass":pvarNoisePackets.value[0]}
MatPyLib['ScanInfo'][ScanNumber]["NoisePackets"]["Noise"] = pvarNoisePackets.value[1]
MatPyLib['ScanInfo'][ScanNumber]["NoisePackets"]["Base"] = pvarNoisePackets.value[2]
pvarLabels = VARIANT()
pvarValues = VARIANT()
pnArraySize = c_long()
hRaw.GetTrailerExtraForScanNum(nScanNumber, pvarLabels, pvarValues, pnArraySize)
MatPyLib['ScanInfo'][ScanNumber]["IT"] = float(pvarValues.value[pvarLabels.value.index('Ion Injection Time (ms):')])
if "Q Exactive" in MatPyLib['InstrumentName'] or "Orbitrap" in MatPyLib['InstrumentName']:
MatPyLib['ScanInfo'][ScanNumber]["B"] = float(
pvarValues.value[pvarLabels.value.index('Conversion Parameter B:')])
MatPyLib['ScanInfo'][ScanNumber]["C"] = float(
pvarValues.value[pvarLabels.value.index('Conversion Parameter C:')])
elif "LTQ FT" in MatPyLib['InstrumentName']:
MatPyLib['ScanInfo'][ScanNumber]["A"] = float(
pvarValues.value[pvarLabels.value.index('Conversion Parameter A:')])
MatPyLib['ScanInfo'][ScanNumber]["B"] = float(
pvarValues.value[pvarLabels.value.index('Conversion Parameter B:')])
else:
print "Instrument name not available"
return
szFilter = BSTR()
nIntensityCutoffType = c_long(0)
nIntensityCutoffValue = c_long(0)
nMaxNumberOfPeaks = c_long(0)
bCentroidResult = c_long(0)
pdCentroidPeakWidth = c_double(0)
pvarMassList = VARIANT()
pvarPeakFlags = VARIANT()
pnArraySize = c_long()
hRaw.GetMassListFromScanNum(nScanNumber,
szFilter,
nIntensityCutoffType,
nIntensityCutoffValue,
nMaxNumberOfPeaks,
bCentroidResult,
pdCentroidPeakWidth,
pvarMassList,
pvarPeakFlags, pnArraySize
)
MatPyLib['ScanInfo'][ScanNumber]["scanmz"] = array(pvarMassList.value[0])
MatPyLib['ScanInfo'][ScanNumber]["scand"] = array(pvarMassList.value[1])
return MatPyLib