unidec.UniDecImporter.Thermo package

Submodules

unidec.UniDecImporter.Thermo.RawFileReader module

unidec.UniDecImporter.Thermo.RawFileReader.DotNetArrayToNPArray(arr, dtype=<class 'float'>)
class unidec.UniDecImporter.Thermo.RawFileReader.RawFileReader(filename, **kwargs)

Bases: object

CalculateMassPrecision(scanNumber=1)

Calculates the mass precision for a spectrum.

Parameters:

scanNumber (int) – the scan to process.

Close()

Closes a raw file and frees the associated memory.

GetAverageSpectrum(scanrange=None, outputData=False, filter='FTMS')

Gets the average spectrum from the RAW file.

Parameters:

  • chromatogram (scanrange = [ start scan for the)

  • chromatogram.] (end scan for the)

  • outputData (bool) – the output data flag.

GetCentroidArray(scanNumber=1)
GetCentroidSpectrum(scanNumber=1)
GetChromatogram(scanrange=None, trace_number=0)

Reads the base peak chromatogram for the RAW file. :param scanrange = [ start scan for the chromatogram: :param end scan for the chromatogram.]:

GetFilters()

Returns the list of unique scan filters for the raw file. This function is only supported for MS device controllers.

GetMSOrder(s)
GetScanFilter(s)
GetSeqInfo()

Returns the sequence row number for this sample in an acquired sequence. The numbering starts at 1. NOTE : XCALIBUR INTERFACE “View/Report/Sample Information” part

GetSpectrum(scanNumber, scanFilter=None, outputData=False)

Gets the spectrum from the RAW file.

Parameters:

  • scanNumber (int) – the scan number being read.

  • scanFilter (str) – the scan filter for that scan.

  • outputData (bool) – the output data flag.

Get_EIC(massrange=None, scanrange=None, trace_number=0)

Reads the base peak chromatogram for the RAW file. :param scanrange = [ start scan for the chromatogram: :param end scan for the chromatogram.]:

Get_Header_Item(item)
ListTrailerExtraFields(scanrange=None)

Reads and reports the trailer extra data fields present in the RAW file.

PrintInfo()
ReadScanInformation(scanrange=None, outputData=True)

Reads the general scan information for each scan in the RAW file using the scan filter object and also the trailer extra data section for that same scan. :param scanrange = [ start scan for the chromatogram: :param end scan for the chromatogram.]: :param outputData: the output data flag. :type outputData: bool

get_scan_header(scannumber=1)
get_status_log(scannumber=1)
get_tune_data(scannumber=1)
scan_range()
scan_time_from_scan_name(scan)
time_range()

unidec.UniDecImporter.Thermo.Thermo module

class unidec.UniDecImporter.Thermo.Thermo.ThermoImporter(path, silent=False, **kwargs)

Bases: Importer

Imports Thermo data files.

Note: Thermo scans are 1 indexed, so the first scan is scan 1, not scan 0.

close()
get_all_scans(threshold=-1)
get_analog_voltage1()
get_analog_voltage2()
get_avg_scan(scan_range=None, time_range=None)

Returns merged 1D MS data from mzML import :return: merged data

get_cdms_data(scan_range=None)
get_eic(mass_range=None, scan_range=None)
get_inj_time_array()
get_isolation_mz_width(s)
get_ms_order(scan=1)
get_polarity(scan=1)
get_single_scan(s)
get_tic()
grab_centroid_data(s)
init_scans()

Module contents