MSFileReader.py

#!/bin/env python2.7
# encoding: utf-8
#
# The MIT License (MIT)
#
# Copyright (c) 2016 François ALLAIN
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.

# Standard library imports
from __future__ import print_function
import sys
import os
import time
import logging
from collections import namedtuple
from ctypes import *
import copy

__version__ = "3.1.5.0"
# XRawfile2(_x64).dll 3.0.29.0
# fregistry(_x64).dll 3.0.0.0
# Fileio(_x64).dll 3.0.0.0

# Related third party imports
if sys.version_info.major == 2 and sys.version_info.minor < 7:
    OrderedDict = dict
else:
    from collections import OrderedDict

try:
    import comtypes
    from comtypes.client import GetModule, CreateObject
except (ImportError, NameError) as e:
    sys.exit('Please install comtypes >= 0.6.2 : http://pypi.python.org/pypi/comtypes/')

log = logging.getLogger(os.path.basename(__file__))

try:
    from comtypes.gen import MSFileReaderLib
except ImportError:
    XRawfile2_dll_loaded = False
    XRawfile2_dll_path = [u'C:\\Program Files\\Thermo\\MSFileReader\\XRawfile2_x64.dll',
                          os.path.dirname(os.path.abspath(__file__)) + os.sep + 'XRawfile2.dll',
                          u'C:\\Program Files (x86)\\Thermo\\MSFileReader\\XRawfile2.dll',
                          u'C:\\Program Files\\Thermo\\MSFileReader\\XRawfile2.dll']
    # 64bits msFileReader with 64bits system
    # 32bits msFileReader aside raw.py
    # 32bits msFileReader with 64bits system
    # 32bits msFileReader with 32bits system
    XRawfile2_dll_path_0 = copy.deepcopy(XRawfile2_dll_path)
    while not XRawfile2_dll_loaded:
        try:
            # TODO ? version with XRawfile2.dll integrated
            # = no need to install MSFileReader, dll not registered to the COM server
            # problem : IXRawfile4 not found
            # http://osdir.com/ml/python.comtypes.user/2008-07/msg00045.html messages 42-46 talk about it
            XRawfile2_dll_filename = XRawfile2_dll_path.pop(0)
            log.debug("Trying comtypes.client.GetModule " + XRawfile2_dll_filename + " ...")
            # generation
            GetModule(XRawfile2_dll_filename)
        except IndexError:
            msg = '1) The msFileReader DLL (XRawfile2.dll or XRawfile2_x64.dll) ' \
                  'may not be installed and therefore not registered to the COM server' \
                  '2) the msFileReader DLL may not be a these paths :\n' + '\n'.join(XRawfile2_dll_path_0)
            sys.exit(msg)
        except Exception as e:
            log.debug(e)
        else:
            log.debug('DLL path : ' + XRawfile2_dll_filename)
            XRawfile2_dll_loaded = True


def _to_float(x):
    try:
        out = float(x)
    except ValueError:
        out = str(x)
    return out


try:
    basestring
except NameError:
    basestring = str


# noinspection PyPep8Naming
class ThermoRawfile(object):
    # static class members

    sampleType = {0: 'Unknown',
                  1: 'Blank',
                  2: 'QC',
                  3: 'Standard Clear (None)',
                  4: 'Standard Update (None)',
                  5: 'Standard Bracket (Open)',
                  6: 'Standard Bracket Start (multiple brackets)',
                  7: 'Standard Bracket End (multiple brackets)'}

    controllerType = {-1: 'No device',
                      0: 'MS',
                      1: 'Analog',
                      2: 'A/D card',
                      3: 'PDA',
                      4: 'UV',
                      'No device': -1,
                      'MS': 0,
                      'Analog': 1,
                      'A/D card': 2,
                      'PDA': 3,
                      'UV': 4}

    massAnalyzerType = {'ITMS': 0,
                        'TQMS': 1,
                        'SQMS': 2,
                        'TOFMS': 3,
                        'FTMS': 4,
                        'Sector': 5,
                        0: 'ITMS',
                        1: 'TQMS',
                        2: 'SQMS',
                        3: 'TOFMS',
                        4: 'FTMS',
                        5: 'Sector'}
    activationType = {'CID': 0,
                      'MPD': 1,
                      'ECD': 2,
                      'PQD': 3,
                      'ETD': 4,
                      'HCD': 5,
                      'Any activation type': 6,
                      'SA': 7,
                      'PTR': 8,
                      'NETD': 9,
                      'NPTR': 10,
                      0: 'CID',
                      1: 'MPD',
                      2: 'ECD',
                      3: 'PQD',
                      4: 'ETD',
                      5: 'HCD',
                      6: 'Any activation type',
                      7: 'SA',
                      8: 'PTR',
                      9: 'NETD',
                      10: 'NPTR'}

    detectorType = {'CID': 0,
                    'PQD': 1,
                    'ETD': 2,
                    'HCD': 3,
                    0: 'CID',
                    1: 'PQD',
                    2: 'ETD',
                    3: 'HCD'}

    scanType = {'ScanTypeFull': 0,
                'ScanTypeSIM': 1,
                'ScanTypeZoom': 2,
                'ScanTypeSRM': 3,
                0: 'ScanTypeFull',
                1: 'ScanTypeSIM',
                2: 'ScanTypeZoom',
                3: 'ScanTypeSRM'}

    GetLabelData_Labels = namedtuple('LabelData_Labels', 'mass intensity resolution baseline noise charge')

    GetLabelData_Flags = namedtuple('LabelData_Flags', 'saturated fragmented merged exception reference modified')

    GetAllMSOrderData_Labels = namedtuple('AllMSOrderData_Labels', 'mass intensity resolution baseline noise charge')

    GetAllMSOrderData_Flags = namedtuple('AllMSOrderData_Flags', 'activation_type is_precursor_range_valid')

    FullMSOrderPrecursorData = namedtuple('FullMSOrderPrecursorData',
                                          ['precursorMass', 'isolationWidth', 'collisionEnergy', 'collisionEnergyValid',
                                           'rangeIsValid',
                                           'firstPrecursorMass', 'lastPrecursorMass', 'isolationWidthOffset'])

    GetPrecursorInfoFromScanNum_PrecursorInfo = namedtuple('PrecursorInfo',
                                                           'isolationMass monoIsoMass chargeState scanNumber')

    def __init__(self, filename):
        self.filename = os.path.abspath(filename)
        self.filename = os.path.normpath(self.filename)
        self.source = None

        try:
            log.debug("obj = CreateObject('MSFileReader.XRawfile')")
            obj = CreateObject('MSFileReader.XRawfile')
        except Exception as exc:
            log.debug(exc)
            try:
                log.debug("obj = CreateObject('XRawfile.XRawfile')")
                obj = CreateObject('XRawfile.XRawfile')
            except Exception as exc:
                log.debug(exc)
                sys.exit('Please install the appropriate Thermo MSFileReader version '
                         'depending of your Python version (32bits or 64bits)')

        self.source = obj

        try:
            error = obj.Open(filename)
        except WindowsError:
            raise WindowsError("RAWfile {0} could not be opened, "
                               "is the file accessible and not opened in Xcalibur/QualBrowser ?".format(self.filename))
        if error:
            raise IOError("RAWfile {0} could not be opened, is the file accessible ?".format(self.filename))

        error = obj.SetCurrentController(c_long(0), c_long(1))
        if error:
            obj.Close()
            raise IOError("Open error {} : {}".format(self.filename, error))

        self.StartTime = self.GetStartTime()
        self.EndTime = self.GetEndTime()
        self.FirstSpectrumNumber = self.GetFirstSpectrumNumber()
        self.LastSpectrumNumber = self.GetLastSpectrumNumber()
        self.LowMass = self.GetLowMass()
        self.HighMass = self.GetHighMass()
        self.MassResolution = self.GetMassResolution()
        self.NumSpectra = self.GetNumSpectra()
        try:
            self.InstMethodNames = self.GetInstMethodNames()
            self.NumInstMethods = self.GetNumInstMethods()
        except IOError:
            self.InstMethodNames = None
            self.NumInstMethods = None
        self.NumStatusLog = self.GetNumStatusLog()
        self.NumErrorLog = self.GetNumErrorLog()
        self.NumTuneData = self.GetNumTuneData()
        self.NumTrailerExtra = self.GetNumTrailerExtra()
        self.dll_version = self.Version()
        self.FileName = self.GetFileName()
        self.InstrumentDescription = self.GetInstrumentDescription()
        self.AcquisitionDate = self.GetAcquisitionDate()
        self.InstName = self.GetInstName()
        self.InstModel = self.GetInstModel()
        self.InstSoftwareVersion = self.GetInstSoftwareVersion()
        self.InstHardwareVersion = self.GetInstHardwareVersion()

    def Close(self):
        """Closes a raw file and frees the associated memory."""
        self.source.Close()

    def Version(self):
        """This function returns the version number of the MSFileReader DLL version."""
        MajorVersion, MinorVersion, SubMinorVersion, BuildNumber = c_long(), c_long(), c_long(), c_long()
        error = self.source.Version(byref(MajorVersion), byref(MinorVersion),
                                    byref(SubMinorVersion), byref(BuildNumber))
        if error:
            raise IOError("Version error :", error)
        return '{}.{}.{}.{}'.format(MajorVersion.value, MinorVersion.value, SubMinorVersion.value, BuildNumber.value)

    def GetFileName(self):
        """Returns the fully qualified path name of an open raw file."""
        pbstrFileName = comtypes.automation.BSTR()
        error = self.source.GetFileName(byref(pbstrFileName))
        if error:
            raise IOError("GetFileName error :", error)
        return pbstrFileName.value

    def GetCreatorID(self):
        """Returns the creator ID. The creator ID is the logon name of the user when the raw file was acquired."""
        pbstrCreatorID = comtypes.automation.BSTR()
        error = self.source.GetCreatorID(byref(pbstrCreatorID))
        if error:
            raise IOError("GetCreatorID error :", error)
        return pbstrCreatorID.value

    def GetVersionNumber(self):
        """Returns the file format version number"""
        versionNumber = c_long()
        error = self.source.GetVersionNumber(byref(versionNumber))
        if error:
            raise IOError("GetVersionNumber error :", error)
        return versionNumber.value

    def GetCreationDate(self):
        """Returns the file creation date in DATE format."""
        # https://msdn.microsoft.com/en-us/library/82ab7w69.aspx
        # The DATE type is implemented using an 8-byte floating-point number
        pCreationDate = c_double()
        error = self.source.GetCreationDate(byref(pCreationDate))
        if error:
            raise IOError("GetCreationDate error :", error)
        return time.gmtime(pCreationDate.value)

    def IsError(self):
        """Returns the error state flag of the raw file. A return value of TRUE indicates that an error has
        occurred. For information about the error, call the GetErrorCode or GetErrorMessage
        functions."""
        pbIsError = c_long()
        error = self.source.IsError(byref(pbIsError))
        if error:
            raise IOError("IsError error :", error)
        return bool(pbIsError.value)

    def IsNewFile(self):
        """Returns the creation state flag of the raw file. A return value of TRUE indicates that the file
        has not previously been saved."""
        bNewFile = c_long()
        error = self.source.IsNewFile(byref(bNewFile))
        if error:
            raise IOError("IsNewFile error :", error)
        return bool(bNewFile.value)

    def IsThereMSData(self):
        """This function checks to see if there is MS data in the raw file. A return value of TRUE means
        that the raw file contains MS data. You must open the raw file before performing this check."""
        pbMSData = c_long()
        error = self.source.IsThereMSData(byref(pbMSData))
        if error:
            raise IOError("IsThereMSData error :", error)
        return bool(pbMSData.value)

    def HasExpMethod(self):
        """This function checks to see if the raw file contains an experimental method. A return value of
        TRUE indicates that the raw file contains the method. You must open the raw file before
        performing this check."""
        bHasMethod = c_long()
        error = self.source.HasExpMethod(byref(bHasMethod))
        if error:
            raise IOError("HasExpMethod error :", error)
        return bool(bHasMethod.value)

    def InAcquisition(self):
        """Returns the acquisition state flag of the raw file. A return value of TRUE indicates that the
        raw file is being acquired or that all open handles to the file during acquisition have not been
        closed."""
        pbInAcquisition = c_long()
        error = self.source.InAcquisition(byref(pbInAcquisition))
        if error:
            raise IOError("InAcquisition error :", error)
        return bool(pbInAcquisition.value)

    def GetErrorCode(self):
        """Returns the error code of the raw file. A return value of 0 indicates that there is no error."""
        nErrorCode = c_long()
        error = self.source.GetErrorCode(byref(nErrorCode))
        if error:
            raise IOError("GetErrorCode error :", error)
        return nErrorCode.value

    def GetErrorMessage(self):
        """Returns error information for the raw file as a descriptive string. If there is no error, the
        returned string is empty."""
        pbstrErrorMessage = comtypes.automation.BSTR()
        error = self.source.GetErrorMessage(byref(pbstrErrorMessage))
        if error:
            raise IOError("GetErrorMessage error :", error)
        return pbstrErrorMessage.value

    def GetWarningMessage(self):
        """Returns warning information for the raw file as a descriptive string. If there is no warning, the
        returned string is empty."""
        pbstrWarningMessage = comtypes.automation.BSTR()
        error = self.source.GetWarningMessage(byref(pbstrWarningMessage))
        if error:
            raise IOError("GetWarningMessage error :", error)
        return pbstrWarningMessage.value

    def RefreshViewOfFile(self):
        """Refreshes the view of a file currently being acquired. This function provides a more efficient
        mechanism for gaining access to new data in a raw file during acquisition without closing and
        reopening the raw file. This function has no effect with files that are not being acquired."""
        error = self.source.RefreshViewOfFile()
        if error:
            raise IOError("RefreshViewOfFile error :", error)
        return

    def GetNumberOfControllers(self):
        """Returns the number of registered device controllers in the raw file. A device controller
        represents an acquisition stream such as MS data, UV data, and so on. Devices that do not
        acquire data, such as autosamplers, are not registered with the raw file during acquisition."""
        pnNumControllers = c_long()
        error = self.source.GetNumberOfControllers(byref(pnNumControllers))
        if error:
            raise IOError("GetNumberOfControllers error :", error)
        return pnNumControllers.value

    def GetNumberOfControllersOfType(self, controllerType='MS'):
        """Returns the number of registered device controllers of a particular type in the raw file. See
        Controller Type in the Enumerated Types section for a list of the available controller types
        and their respective values."""
        if isinstance(controllerType, basestring):
            controllerType = ThermoRawfile.controllerType[controllerType]
        pnNumControllersOfType = c_long()
        error = self.source.GetNumberOfControllersOfType(c_long(controllerType), byref(pnNumControllersOfType))
        if error:
            raise IOError("GetNumberOfControllersOfType error :", error)
        return pnNumControllersOfType.value

    def GetControllerType(self, index):
        """Returns the type of the device controller registered at the specified index position in the raw
        file. Index values start at 0. See Controller Type in the Enumerated Types section for a list of
        the available controller types and their respective values."""
        controllerType = c_long()
        error = self.source.GetControllerType(index, byref(controllerType))
        if error:
            raise IOError("GetControllerType error :", error)
        return ThermoRawfile.controllerType[controllerType.value]

    def SetCurrentController(self, controllerType, controllerNumber):
        """Sets the current controller in the raw file. This function must be called before subsequent calls
        to access data specific to a device controller (for example, MS or UV data) may be made. All
        requests for data specific to a device controller are forwarded to the current controller until the
        current controller is changed. The controller number is used to indicate which device
        controller to use if there is more than one registered device controller of the same type (for
        example, multiple UV detectors). Controller numbers for each type are numbered starting
        at 1. See Controller Type in the Enumerated Types section for a list of the available controller
        types and their respective values."""
        if isinstance(controllerType, basestring):
            controllerType = ThermoRawfile.controllerType[controllerType]
        error = self.source.SetCurrentController(c_long(controllerType), c_long(controllerNumber))
        if error:
            raise IOError("SetCurrentController error :", error)
        return

    def GetCurrentController(self):
        """Gets the current controller type and number for the raw file. The controller number is used to
        indicate which device controller to use if there is more than one registered device controller of
        the same type (for example, multiple UV detectors). Controller numbers for each type are
        numbered starting at 1. See Controller Type in the Enumerated Types section for a list of the
        available controller types and their respective values."""
        pnControllerType = c_long()
        pnControllerNumber = c_long()
        error = self.source.GetCurrentController(byref(pnControllerType), byref(pnControllerNumber))
        if error:
            raise IOError("GetCurrentController error :", error)
        return pnControllerType.value, pnControllerNumber.value

    def GetExpectedRunTime(self):
        """Gets the expected acquisition run time for the current controller. The actual acquisition may
        be longer or shorter than this value. This value is intended to allow displays to show the
        expected run time on chromatograms. To obtain an accurate run time value during or after
        acquisition, use the GetEndTime function."""
        pdExpectedRunTime = c_double()
        error = self.source.GetExpectedRunTime(byref(pdExpectedRunTime))
        if error:
            raise IOError("GetExpectedRunTime error :", error)
        return pdExpectedRunTime.value

    def GetNumTrailerExtra(self):
        """Gets the trailer extra entries recorded for the current controller. Trailer extra entries are only
        supported for MS device controllers and are used to store instrument specific information for
        each scan if used."""
        pnNumberOfTrailerExtraEntries = c_long()
        error = self.source.GetNumTrailerExtra(byref(pnNumberOfTrailerExtraEntries))
        if error:
            raise IOError("GetNumTrailerExtra error :", error)
        return pnNumberOfTrailerExtraEntries.value

    def GetMaxIntegratedIntensity(self):
        """Gets the highest integrated intensity of all the scans for the current controller. This value is
        only relevant to MS device controllers."""
        pdMaxIntegIntensity = c_double()
        error = self.source.GetMaxIntegratedIntensity(byref(pdMaxIntegIntensity))
        if error:
            raise IOError("GetMaxIntegratedIntensity error :", error)
        return pdMaxIntegIntensity.value

    def GetMaxIntensity(self):
        """Gets the highest base peak of all the scans for the current controller. This value is only relevant
        to MS device controllers."""
        dMaxInt = c_long()
        error = self.source.GetMaxIntensity(byref(dMaxInt))
        if error:
            raise IOError("GetMaxIntensity error :", error)
        return dMaxInt.value

    def GetInletID(self):
        """Gets the inlet ID number for the current controller. This value is typically only set for raw
        files converted from other file formats."""
        nInletID = c_long()
        error = self.source.GetInletID(byref(nInletID))
        if error:
            raise IOError("GetInletID error :", error)
        return nInletID.value

    def GetErrorFlag(self):
        """Gets the error flag value for the current controller. This value is typically only set for raw files
        converted from other file formats."""
        pnErrorFlag = c_long()
        error = self.source.GetErrorFlag(byref(pnErrorFlag))
        if error:
            raise IOError("GetErrorFlag error :", error)
        return pnErrorFlag.value

    def GetFlags(self):
        """Returns the acquisition flags field for the current controller. This value is typically only set for
        raw files converted from other file formats."""
        pbstrFlags = comtypes.automation.BSTR(None)
        error = self.source.GetFlags(byref(pbstrFlags))
        if error:
            raise IOError("GetFlags error :", error)
        return pbstrFlags.value

    def GetAcquisitionFileName(self):
        """Returns the acquisition file name for the current controller. This value is typically only set for
        raw files converted from other file formats."""
        pbstrFileName = comtypes.automation.BSTR(None)
        error = self.source.GetAcquisitionFileName(byref(pbstrFileName))
        if error:
            raise IOError("GetAcquisitionFileName error :", error)
        return pbstrFileName.value

    def GetAcquisitionDate(self):
        """Returns the acquisition date for the current controller. This value is typically only set for raw
        files converted from other file formats."""
        pbstrAcquisitionDate = comtypes.automation.BSTR(None)
        error = self.source.GetAcquisitionDate(byref(pbstrAcquisitionDate))
        if error:
            raise IOError("GetAcquisitionDate error :", error)
        return pbstrAcquisitionDate.value

    def GetOperator(self):
        """Returns the operator name for the current controller. This value is typically only set for raw
        files converted from other file formats."""
        pbstrOperator = comtypes.automation.BSTR(None)
        error = self.source.GetOperator(byref(pbstrOperator))
        if error:
            raise IOError("GetOperator error :", error)
        return pbstrOperator.value

    def GetComment1(self):
        """Returns the first comment for the current controller. This value is typically only set for raw
        files converted from other file formats."""
        pbstrComment1 = comtypes.automation.BSTR(None)
        error = self.source.GetComment1(byref(pbstrComment1))
        if error:
            raise IOError("GetComment1 error :", error)
        return pbstrComment1.value

    def GetComment2(self):
        """Returns the second comment for the current controller. This value is typically only set for raw
        files converted from other file formats."""
        pbstrComment2 = comtypes.automation.BSTR(None)
        error = self.source.GetComment2(byref(pbstrComment2))
        if error:
            raise IOError("GetComment2 error :", error)
        return pbstrComment2.value

    def GetFilters(self):
        """Returns the list of unique scan filters for the raw file. This function is only supported for MS
        device controllers. If the function succeeds, pvarFilterArray points to an array of BSTR fields,
        each containing a unique scan filter, and pnArraySize contains the number of scan filters in the
        pvarFilterArray."""
        pvarFilterArray = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetFilters(byref(pvarFilterArray), byref(pnArraySize))
        if error:
            raise IOError("GetFilters error :", error)
        return pvarFilterArray.value

    def SetMassTolerance(self, userDefined=True, massTolerance=500.0, units=0):
        """This function sets the mass tolerance that will be used with the raw file.

        userDefined        A boolean indicating whether the mass tolerance is user-defined (True) or
                            based on the values in the raw file (False).
        massTolerance      The mass tolerance value.
        units              The type of tolerance value (amu = 2, mmu = 0, or ppm = 1).
        """
        error = self.source.SetMassTolerance(userDefined, c_double(massTolerance), c_long(units))
        if error:
            raise IOError("SetMassTolerance error :", error)
        return

    def GetMassTolerance(self):
        """This function gets the mass tolerance that is being used with the raw file. To set these values,
        use the SetMassTolerance() function.

        bUserDefined        A flag indicating whether the mass tolerance is user-defined (TRUE) or
                            based on the values in the raw file (FALSE).
        dMassTolerance      The mass tolerance value.
        nUnits              The type of tolerance value (amu = 2, mmu = 0, or ppm = 1).
        """
        bUserDefined = c_long()
        dMassTolerance = c_double()
        nUnits = c_long()
        error = self.source.GetMassTolerance(byref(bUserDefined), byref(dMassTolerance), byref(nUnits))
        if error:
            raise IOError("GetMassTolerance error :", error)
        return bool(bUserDefined.value), dMassTolerance.value, nUnits.value

    # INSTRUMENT BEGIN
    def GetInstrumentDescription(self):
        """Returns the instrument description field for the current controller. This value is typically only
        set for raw files converted from other file formats."""
        pbstrInstrumentDescription = comtypes.automation.BSTR(None)
        error = self.source.GetInstrumentDescription(byref(pbstrInstrumentDescription))
        if error:
            raise IOError("GetInstrumentDescription error :", error)
        return pbstrInstrumentDescription.value

    def GetInstrumentID(self):
        """Gets the instrument ID number for the current controller. This value is typically only set for
        raw files converted from other file formats."""
        pnInstrumentID = c_long()
        error = self.source.GetInstrumentID(byref(pnInstrumentID))
        if error:
            raise IOError("GetInstrumentID error :", error)
        return pnInstrumentID.value

    def GetInstName(self):
        """Returns the instrument name, if available, for the current controller."""
        pbstrInstName = comtypes.automation.BSTR(None)
        error = self.source.GetInstName(byref(pbstrInstName))
        if error:
            raise IOError("GetInstName error :", error)
        return pbstrInstName.value

    def GetInstModel(self):
        """Returns the instrument model, if available, for the current controller."""
        pbstrInstModel = comtypes.automation.BSTR(None)
        error = self.source.GetInstModel(byref(pbstrInstModel))
        if error:
            raise IOError("GetInstModel error :", error)
        return pbstrInstModel.value

    def GetInstSerialNumber(self):
        """Returns the serial number, if available, for the current controller."""
        pbstrInstSerialNumber = comtypes.automation.BSTR(None)
        error = self.source.GetInstSerialNumber(byref(pbstrInstSerialNumber))
        if error:
            raise IOError("GetInstSerialNumber error :", error)
        return pbstrInstSerialNumber.value

    def GetInstSoftwareVersion(self):
        """Returns revision information for the current controller software, if available."""
        InstSoftwareVersion = comtypes.automation.BSTR()
        error = self.source.GetInstSoftwareVersion(byref(InstSoftwareVersion))
        if error:
            raise IOError("GetInstSoftwareVersion error :", error)
        return InstSoftwareVersion.value

    def GetInstHardwareVersion(self):
        """Returns revision information for the current controller software, if available."""
        InstHardwareVersion = comtypes.automation.BSTR()
        error = self.source.GetInstHardwareVersion(byref(InstHardwareVersion))
        if error:
            raise IOError("GetInstHardwareVersion error :", error)
        return InstHardwareVersion.value

    def GetInstFlags(self):
        """Returns the experiment flags, if available, for the current controller. The returned string may
        contain one or more fields denoting information about the type of experiment performed.
        These are the currently defined experiment fields:
        TIM - total ion map
        NLM - neutral loss map
        PIM - parent ion map
        DDZMap - data-dependent ZoomScan map"""
        pbstrInstFlags = comtypes.automation.BSTR()
        error = self.source.GetInstFlags(byref(pbstrInstFlags))
        if error:
            raise IOError("GetInstFlags error :", error)
        return pbstrInstFlags.value

    def GetInstNumChannelLabels(self):
        """Returns the number of channel labels specified for the current controller. This field is only
        relevant to channel devices such as UV detectors, A/D cards, and Analog inputs. Typically, the
        number of channel labels, if labels are available, is the same as the number of configured
        channels for the current controller."""
        pnInstNumChannelLabels = c_long()
        error = self.source.GetInstNumChannelLabels(byref(pnInstNumChannelLabels))
        if error:
            raise IOError("GetInstNumChannelLabels error :", error)
        return pnInstNumChannelLabels.value

    def GetInstChannelLabel(self, channelLabelNumber=0):
        """Returns the channel label, if available, at the specified index for the current controller. This
        field is only relevant to channel devices such as UV detectors, A/D cards, and Analog inputs.
        Channel label indices are numbered starting at 0."""
        pbstrFlags = comtypes.automation.BSTR()
        error = self.source.GetInstChannelLabel(c_long(channelLabelNumber), byref(pbstrFlags))
        if error:
            raise IOError("GetInstChannelLabel error :", error)
        return pbstrFlags.value

    # INSTRUMENT END

    def GetScanEventForScanNum(self, scanNumber):
        """This function returns scan event information as a string for the specified scan number."""
        pbstrScanEvent = comtypes.automation.BSTR()
        error = self.source.GetScanEventForScanNum(c_long(scanNumber), byref(pbstrScanEvent))
        if error:
            raise IOError("GetScanEventForScanNum error :", error)
        return pbstrScanEvent.value

    def GetSegmentAndEventForScanNum(self, scanNumber):  # NOT GetSegmentAndScanEventForScanNum
        """Returns the segment and scan event indexes for the specified scan."""
        pbstrScanEvent = comtypes.automation.BSTR()
        pnSegment = c_long(0)
        pnScanEvent = c_long(0)
        error = self.source.GetSegmentAndEventForScanNum(c_long(scanNumber), byref(pnSegment), byref(pnScanEvent))
        if error:
            raise IOError("GetSegmentAndEventForScanNum error :", error)
        return pbstrScanEvent.value

    def GetSegmentAndScanEventForScanNum(self, scanNumber):
        return self.GetSegmentAndEventForScanNum(scanNumber)

    def GetCycleNumberFromScanNumber(self, scanNumber):
        """This function returns the cycle number for the scan specified by scanNumber from the scan
        index structure in the raw file."""
        pnCycleNumber = c_long()
        error = self.source.GetCycleNumberFromScanNumber(c_long(scanNumber), byref(pnCycleNumber))
        if error:
            raise IOError("GetCycleNumberFromScanNumber error :", error)
        return pnCycleNumber.value

    def GetAValueFromScanNum(self, scanNumber):
        """This function gets the A parameter value in the scan event. The value returned is either 0, 1,
        or 2 for parameter A off, parameter A on, or accept any parameter A, respectively."""
        pnXValue = c_long()
        error = self.source.GetAValueFromScanNum(c_long(scanNumber), byref(pnXValue))
        if error:
            raise IOError("GetAValueFromScanNum error :", error)
        return pnXValue.value

    def GetBValueFromScanNum(self, scanNumber):
        """This function gets the B parameter value in the scan event. The value returned will be either
        0, 1, or 2 for parameter B off, parameter B on, or accept any parameter B, respectively."""
        pnXValue = c_long()
        error = self.source.GetBValueFromScanNum(c_long(scanNumber), byref(pnXValue))
        if error:
            raise IOError("GetBValueFromScanNum error :", error)
        return pnXValue.value

    def GetFValueFromScanNum(self, scanNumber):
        """This function gets the F parameter value in the scan event. The value returned is either 0, 1,
        or 2 for parameter F off, parameter F on, or accept any parameter F, respectively."""
        pnXValue = c_long()
        error = self.source.GetFValueFromScanNum(c_long(scanNumber), byref(pnXValue))
        if error:
            raise IOError("GetFValueFromScanNum error :", error)
        return pnXValue.value

    def GetKValueFromScanNum(self, scanNumber):
        """This function gets the K parameter value in the scan event. The value returned is either 0, 1,
        or 2 for parameter K off, parameter K on, or accept any parameter K, respectively."""
        pnXValue = c_long()
        error = self.source.GetKValueFromScanNum(c_long(scanNumber), byref(pnXValue))
        if error:
            raise IOError("GetKValueFromScanNum error :", error)
        return pnXValue.value

    def GetRValueFromScanNum(self, scanNumber):
        """This function gets the R parameter value in the scan event. The value returned is either 0, 1,
        or 2 for parameter R off, parameter R on, or accept any parameter R, respectively."""
        pnXValue = c_long()
        error = self.source.GetRValueFromScanNum(c_long(scanNumber), byref(pnXValue))
        if error:
            raise IOError("GetRValueFromScanNum error :", error)
        return pnXValue.value

    def GetVValueFromScanNum(self, scanNumber):
        """This function gets the V parameter value in the scan event. The value returned is either 0, 1,
        or 2 for parameter V off, parameter V on, or accept any parameter V, respectively."""
        pnXValue = c_long()
        error = self.source.GetVValueFromScanNum(c_long(scanNumber), byref(pnXValue))
        if error:
            raise IOError("GetVValueFromScanNum error :", error)
        return pnXValue.value

    def GetMSXMultiplexValueFromScanNum(self, scanNumber):
        """This function gets the msx-multiplex parameter value in the scan event. The value returned is
        either 0, 1, or 2 for multiplex off, multiplex on, or accept any multiplex, respectively."""
        pnMSXValue = c_long()
        error = self.source.GetMSXMultiplexValueFromScanNum(c_long(scanNumber), byref(pnMSXValue))
        if error:
            raise IOError("GetMSXMultiplexValueFromScanNum error :", error)
        return pnMSXValue.value

    def GetNumberOfMassRangesFromScanNum(self, scanNumber):
        """This function gets the number of MassRange data items in the scan."""
        result = c_long()
        error = self.source.GetNumberOfMassRangesFromScanNum(c_long(scanNumber), byref(result))
        if error:
            raise IOError("GetNumberOfMassRangesFromScanNum error :", error)
        return result.value

    def GetMassRangeFromScanNum(self, scanNumber, massRangeIndex):
        """This function retrieves information about the mass range data of a scan (high and low
        masses). You can find the count of mass ranges for the scan by calling
        GetNumberOfMassRangesFromScanNum()."""
        pdMassRangeLowValue = c_double()
        pdMassRangeHighValue = c_double()
        error = self.source.GetMassRangeFromScanNum(c_long(scanNumber), c_long(massRangeIndex),
                                                    byref(pdMassRangeLowValue), byref(pdMassRangeHighValue))
        if error:
            raise IOError("GetMassRangeFromScanNum error :", error)
        return pdMassRangeLowValue.value, pdMassRangeHighValue.value

    def GetNumberOfSourceFragmentsFromScanNum(self, scanNumber):
        """This function gets the number of source fragments (or compensation voltages) in the scan."""
        result = c_long()
        error = self.source.GetNumberOfSourceFragmentsFromScanNum(c_long(scanNumber), byref(result))
        if error:
            raise IOError("GetNumberOfSourceFragmentsFromScanNum error :", error)
        return result.value

    def GetSourceFragmentValueFromScanNum(self, scanNumber, sourceFragmentIndex):
        """This function retrieves information about one of the source fragment values of a scan. It is
        also the same value as the compensation voltage. You can find the count of source fragments
        for the scan by calling GetNumberOfSourceFragmentsFromScanNum ()."""
        pdSourceFragmentValue = c_double()
        error = self.source.GetSourceFragmentValueFromScanNum(c_long(scanNumber), c_long(sourceFragmentIndex),
                                                              byref(pdSourceFragmentValue))
        if error:
            raise IOError("GetSourceFragmentValueFromScanNum error :", error)
        return pdSourceFragmentValue.value

    def GetNumberOfSourceFragmentationMassRangesFromScanNum(self, scanNumber):
        """This function gets the number of source fragmentation mass ranges in the scan."""
        result = c_long()
        error = self.source.GetNumberOfSourceFragmentationMassRangesFromScanNum(c_long(scanNumber), byref(result))
        if error:
            raise IOError("GetNumberOfSourceFragmentationMassRangesFromScanNum error :", error)
        return result.value

    def GetSourceFragmentationMassRangeFromScanNum(self, scanNumber, sourceFragmentIndex):
        """This function retrieves information about the source fragment mass range data of a scan (high
        and low source fragment masses). You can find the count of mass ranges for the scan by calling
        GetNumberOfSourceFragmentationMassRangesFromScanNum ()."""
        pdSourceFragmentRangeLowValue = c_double()
        pdSourceFragmentRangeHighValue = c_double()
        error = self.source.GetSourceFragmentationMassRangeFromScanNum(c_long(scanNumber), c_long(sourceFragmentIndex),
                                                                       byref(pdSourceFragmentRangeLowValue),
                                                                       byref(pdSourceFragmentRangeHighValue))
        if error:
            raise IOError("GetSourceFragmentationMassRangeFromScanNum error :", error)
        return pdSourceFragmentRangeLowValue.value, pdSourceFragmentRangeHighValue.value

    def GetIsolationWidthForScanNum(self, scanNumber, MSOrder):
        """This function returns the isolation width for the scan specified by scanNumber and the
        transition specified by MSOrder from the scan event structure in the raw file."""
        result = c_double()
        error = self.source.GetIsolationWidthForScanNum(c_long(scanNumber), c_long(MSOrder), byref(result))
        if error:
            raise IOError("GetIsolationWidthForScanNum error :", error)
        return result.value

    def GetCollisionEnergyForScanNum(self, scanNumber, MSOrder):
        """This function returns the collision energy for the scan specified by scanNumber and the
        transition specified by MSOrder from the scan event structure in the raw file. """
        result = c_double()
        error = self.source.GetCollisionEnergyForScanNum(c_long(scanNumber), c_long(MSOrder), byref(result))
        if error:
            raise IOError("GetCollisionEnergyForScanNum error :", error)
        return result.value

    def GetActivationTypeForScanNum(self, scanNumber, MSOrder):
        """This function returns the activation type for the scan specified by scanNumber and the
        transition specified by MSOrder from the scan event structure in the RAW file.
        The value returned in the pnActivationType variable is one of the following:
        CID  0
        MPD 1
        ECD  2
        PQD 3
        ETD 4
        HCD 5
        Any activation type 6
        SA 7
        PTR 8
        NETD 9
        NPTR 10"""
        result = c_long()
        error = self.source.GetActivationTypeForScanNum(c_long(scanNumber), c_long(MSOrder), byref(result))
        if error:
            raise IOError("GetActivationTypeForScanNum error :", error)
        return ThermoRawfile.activationType[result.value]

    def GetMassAnalyzerTypeForScanNum(self, scanNumber):
        """This function returns the mass analyzer type for the scan specified by scanNumber from the
        scan event structure in the RAW file. The value of scanNumber must be within the range of
        scans or readings for the current controller. The range of scans or readings for the current
        controller may be obtained by calling GetFirstSpectrumNumber and
        GetLastSpectrumNumber.
        The value returned in the pnMassAnalyzerType variable is one of the following:
        ITMS  0
        TQMS 1
        SQMS  2
        TOFMS 3
        FTMS 4
        Sector 5"""
        result = c_long()
        error = self.source.GetMassAnalyzerTypeForScanNum(c_long(scanNumber), byref(result))
        if error:
            raise IOError("GetMassAnalyzerTypeForScanNum error :", error)
        try:
            massAnalyzerType = ThermoRawfile.massAnalyzerType[result.value]
        except KeyError:
            massAnalyzerType = "Unknown"
        return massAnalyzerType

    def GetDetectorTypeForScanNum(self, scanNumber):
        """This function returns the detector type for the scan specified by scanNumber from the scan
        event structure in the RAW file.
        The value returned in the pnDetectorType variable is one of the following:
        CID  0
        PQD  1
        ETD  2
        HCD  3"""
        result = c_long()
        error = self.source.GetDetectorTypeForScanNum(c_long(scanNumber), byref(result))
        if error:
            raise IOError("GetDetectorTypeForScanNum error :", error)
        return ThermoRawfile.detectorType[result.value]

    def GetScanTypeForScanNum(self, scanNumber):
        """This function returns the scan type for the scan specified by scanNumber from the scan
        event structure in the RAW file.
        The value returned in the pnScanType variable is one of the following:
        ScanTypeFull  0
        ScanTypeSIM  1
        ScanTypeZoom  2
        ScanTypeSRM  3"""
        result = c_long()
        error = self.source.GetScanTypeForScanNum(c_long(scanNumber), byref(result))
        if error:
            raise IOError("GetScanTypeForScanNum error :", error)
        return ThermoRawfile.scanType[result.value]

    def GetNumberOfMassCalibratorsFromScanNum(self, scanNumber):
        """This function gets the number of mass calibrators (each of which is a double) in the scan."""
        result = c_long()
        error = self.source.GetNumberOfMassCalibratorsFromScanNum(c_long(scanNumber), byref(result))
        if error:
            raise IOError("GetNumberOfMassCalibratorsFromScanNum error :", error)
        return result.value

    def GetMassCalibrationValueFromScanNum(self, scanNumber, massCalibrationIndex):
        """This function retrieves information about one of the mass calibration data values of a scan.
        You can find the count of mass calibrations for the scan by calling
        GetNumberOfMassCalibratorsFromScanNum()."""
        result = c_double()
        error = self.source.GetMassCalibrationValueFromScanNum(c_long(scanNumber), c_long(massCalibrationIndex),
                                                               byref(result))
        if error:
            raise IOError("GetMassCalibrationValueFromScanNum error :", error)
        return result.value

    def GetFilterMassPrecision(self):
        """This function gets the mass precision for the filter associated with an MS scan."""
        result = c_long()
        error = self.source.GetFilterMassPrecision(byref(result))
        if error:
            raise IOError("GetFilterMassPrecision error :", error)
        return result.value

    def GetMassPrecisionEstimate(self, scanNumber):
        """This function is only applicable to scanning devices such as MS. It gets the mass precision
        information for an accurate mass spectrum (that is, acquired on an FTMS- or Orbitrap-class
        instrument).

        If no scan filter is supplied, the scan corresponding to pnScanNumber is returned. If a scan
        filter is provided, the closest matching scan to pnScanNumber that matches the scan filter is
        returned.

        The format of the mass list returned is an array of double-precision
        values in the order of intensity, mass, accuracy in MMU, accuracy in PPM, and resolution."""
        pnArraySize = c_long()
        result = comtypes.automation.VARIANT()
        error = self.source.GetMassPrecisionEstimate(c_long(scanNumber), byref(result), byref(pnArraySize))
        if error:
            raise IOError("GetMassPrecisionEstimate error :", error)
        return result.value

    def IsQExactive(self):
        """Checks the instrument name by calling GetInstName() and comparing the result to Q
        Exactive Orbitrap. If it matches, IsQExactive pVal is set to TRUE. Otherwise, pVal is set to
        FALSE.

        NOTE : implemented in version 3.0 SP3 / 3.0.31.0 (2015-04-30)
        """
        result = c_long()
        error = self.source.IsQExactive(byref(result))
        if error:
            raise IOError("IsQExactive error :", error)
        return bool(result.value)

    def GetMassResolution(self):
        """Gets the mass resolution value recorded for the current controller. The value is returned as one
        half of the mass resolution. For example, a unit resolution controller returns a value of 0.5.
        This value is only relevant to scanning controllers such as MS."""
        result = c_double()
        error = self.source.GetMassResolution(byref(result))
        if error:
            raise IOError("GetMassResolution error :", error)
        return result.value

    def GetLowMass(self):
        """Gets the lowest mass or wavelength recorded for the current controller. This value is only
        relevant to scanning devices such as MS or PDA."""
        pdLowMass = c_double()
        error = self.source.GetLowMass(byref(pdLowMass))
        if error:
            raise IOError("GetLowMass error :", error)
        return pdLowMass.value

    def GetHighMass(self):
        """Gets the highest mass or wavelength recorded for the current controller. This value is only
        relevant to scanning devices such as MS or PDA."""
        pdHighMass = c_double()
        error = self.source.GetHighMass(byref(pdHighMass))
        if error:
            raise IOError("GetHighMass error :", error)
        return pdHighMass.value

    def GetStartTime(self):
        """Gets the start time of the first scan or reading for the current controller. This value is typically
        close to zero unless the device method contains a start delay."""
        pdStartTime = c_double()
        error = self.source.GetStartTime(byref(pdStartTime))
        if error:
            raise IOError("GetStartTime error :", error)
        return pdStartTime.value

    def GetEndTime(self):
        pdEndTime = c_double()
        error = self.source.GetEndTime(byref(pdEndTime))
        if error:
            raise IOError("GetEndTime error :", error)
        return pdEndTime.value

    def GetNumSpectra(self):
        """Gets the number of spectra acquired by the current controller. For non-scanning devices like
        UV detectors, the number of readings per channel is returned."""
        numSpectra = c_long()
        error = self.source.GetNumSpectra(byref(numSpectra))
        if error:
            raise IOError("GetNumSpectra error :", error)
        return numSpectra.value

    def GetFirstSpectrumNumber(self):
        """Gets the first scan or reading number for the current controller. If data has been acquired, this
        value is always one."""
        pnFirstSpectrum = c_long()
        error = self.source.GetFirstSpectrumNumber(byref(pnFirstSpectrum))
        if error:
            raise IOError("GetFirstSpectrumNumber error :", error)
        return pnFirstSpectrum.value

    def GetLastSpectrumNumber(self):
        """Gets the last scan or reading number for the current controller."""
        pnLastSpectrum = c_long()
        error = self.source.GetLastSpectrumNumber(byref(pnLastSpectrum))
        if error:
            raise IOError("GetLastSpectrumNumber error :", error)
        return pnLastSpectrum.value

    def ScanNumFromRT(self, RT):
        """Returns the closest matching scan number that corresponds to RT for the current controller.
        For non-scanning devices, such as UV, the closest reading number is returned. The value of
        RT must be within the acquisition run time for the current controller. The acquisition run
        time for the current controller may be obtained by calling GetStartTime and GetEndTime."""
        pnScanNumber = c_long()
        error = self.source.ScanNumFromRT(c_double(RT), byref(pnScanNumber))
        if error:
            raise IOError("scan {}, ScanNumFromRT error : {}".format(pnScanNumber, error))
        else:
            return pnScanNumber.value

    def RTFromScanNum(self, scanNumber):
        """Returns the closest matching run time or retention time that corresponds to scanNumber for
        the current controller. For non-scanning devices, such as UV, the scanNumber is the reading
        number."""
        pdRT = c_double()
        error = self.source.RTFromScanNum(c_long(scanNumber), byref(pdRT))
        if error:
            raise IOError("scan {}, RTFromScanNum error : {}".format(scanNumber, str(error)))
        else:
            return pdRT.value

    def IsProfileScanForScanNum(self, scanNumber):
        """Returns TRUE if the scan specified by scanNumber is a profile scan, FALSE if the scan is a
        centroid scan."""
        pbIsProfileScan = c_long()
        error = self.source.IsProfileScanForScanNum(c_long(scanNumber), byref(pbIsProfileScan))
        if error:
            raise IOError("IsProfileScanForScanNum error :", error)
        return bool(pbIsProfileScan.value)

    def IsCentroidScanForScanNum(self, scanNumber):
        """Returns TRUE if the scan specified by scanNumber is a centroid scan, FALSE if the scan is a
        profile scan."""
        pbIsCentroidScan = c_long()
        error = self.source.IsCentroidScanForScanNum(c_long(scanNumber), byref(pbIsCentroidScan))
        if error:
            raise IOError("IsCentroidScanForScanNum error :", error)
        return bool(pbIsCentroidScan.value)

    def GetFilterForScanNum(self, scanNumber):
        """Returns the closest matching run time that corresponds to scanNumber for the current
        controller. This function is only supported for MS device controllers.
        e.g. "FTMS + c NSI Full ms [300.00-1800.00]"
        """
        pbstrFilter = comtypes.automation.BSTR(None)
        error = self.source.GetFilterForScanNum(scanNumber, byref(pbstrFilter))
        if error:
            raise IOError("scan {}, GetFilterForScanNum error : {}".format(scanNumber, str(error)))
        else:
            return pbstrFilter.value

    def GetMassListFromScanNum(self, scanNumber,
                               scanFilter="",
                               intensityCutoffType=0,
                               intensityCutoffValue=0,
                               maxNumberOfPeaks=0,
                               centroidResult=False,
                               centroidPeakWidth=0.0):
        """This function is only applicable to scanning devices such as MS and PDA.

        If no scanFilter is supplied, the scan corresponding to pnScanNumber is returned. If a
        scanFilter is provided, the closest matching scan to pnScanNumber that matches the scanFilter is
        returned.
        scanFilter must match the Xcalibur scanFilter format (e.g. "FTMS + c NSI Full ms [300.00-1800.00]").

        To reduce the number of low intensity data peaks returned, an intensity cutoff,
        nIntensityCutoffType, may be applied. The available types of cutoff are
        0   None (all values returned)
        1   Absolute (in intensity units)
        2   Relative (to base peak)

        To limit the total number of data peaks that are returned in the mass list, set
        nMaxNumberOfPeaks to a value greater than zero. To have all data peaks returned, set
        nMaxNumberOfPeaks to zero.

        To have profile scans centroided, set bCentroidResult to TRUE. This parameter is ignored for
        centroid scans.

        The pvarPeakFlags variable is currently not used. This variable is reserved for future use to
        return flag information, such as saturation, about each mass intensity pair.
        """
        peakList = comtypes.automation.VARIANT()
        peakFlags = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetMassListFromScanNum(c_long(scanNumber), scanFilter, intensityCutoffType,
                                                   intensityCutoffValue, maxNumberOfPeaks, centroidResult,
                                                   c_double(centroidPeakWidth), peakList, peakFlags, byref(pnArraySize))
        if error:
            raise IOError("GetMassListFromScanNum error : ", error)
        return peakList.value, peakFlags.value

    def GetMassListRangeFromScanNum(self, scanNumber,
                                    massRange="",
                                    scanFilter="",
                                    intensityCutoffType=0,
                                    intensityCutoffValue=0,
                                    maxNumberOfPeaks=0,
                                    centroidResult=False,
                                    centroidPeakWidth=0.0):
        """This function is only applicable to scanning devices such as MS and PDA.

        If no scanFilter is supplied, the scan corresponding to pnScanNumber is returned. If a
        scanFilter is provided, the closest matching scan to pnScanNumber that matches the scanFilter is
        returned.
        scanFilters must match the Xcalibur scanFilter format (e.g. "FTMS + c NSI Full ms [300.00-1800.00]").

        To reduce the number of low intensity data peaks returned, an intensity cutoff,
        nIntensityCutoffType, may be applied. The available types of cutoff are
        0   None (all values returned)
        1   Absolute (in intensity units)
        2   Relative (to base peak)

        To limit the total number of data peaks that are returned in the mass list, set
        nMaxNumberOfPeaks to a value greater than zero. To have all data peaks returned, set
        nMaxNumberOfPeaks to zero.

        To have profile scans centroided, set bCentroidResult to True. This parameter is ignored for
        centroid scans.

        To get a range of masses between two points that are returned in the mass list, set the string of
        szMassRange1 to a valid range (e.g. "450.00-640.00").

        The pvarPeakFlags variable is currently not used. This variable is reserved for future use to
        return flag information, such as saturation, about each mass intensity pair.

        NOTE: same as GetMassListFromScanNum but is able to filter on a m/z range."""
        if not massRange:
            massRange = "{}-{}".format(self.LowMass, self.HighMass)
        peakList = comtypes.automation.VARIANT()
        peakFlags = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetMassListRangeFromScanNum(c_long(scanNumber), scanFilter, intensityCutoffType,
                                                        intensityCutoffValue, maxNumberOfPeaks, centroidResult,
                                                        c_double(centroidPeakWidth), peakList, peakFlags, massRange,
                                                        byref(pnArraySize))
        if error:
            raise IOError("GetMassListRangeFromScanNum error :", error)
        return peakList.value, peakFlags.value

    def GetSegmentedMassListFromScanNum(self, scanNumber,
                                        scanFilter="",
                                        intensityCutoffType=0,
                                        intensityCutoffValue=0,
                                        maxNumberOfPeaks=0,
                                        centroidResult=False,
                                        centroidPeakWidth=0.0):
        """This function is only applicable to scanning devices such as MS.

        If no scanFilter is supplied, the scan corresponding to pnScanNumber is returned. If a
        scanFilter is provided, the closest matching scan to pnScanNumber that matches the scanFilter is
        returned.
        scanFilters must match the Xcalibur scan scanFilter format (e.g. "FTMS + c NSI Full ms [300.00-1800.00]").

        To reduce the number of low intensity data peaks returned, an intensity cutoff,
        nIntensityCutoffType, may be applied. The available types of cutoff are
        0   None (all values returned)
        1   Absolute (in intensity units)
        2   Relative (to base peak)

        To limit the total number of data peaks that are returned in the mass list, set
        nMaxNumberOfPeaks to a value greater than zero. To have all data peaks returned, set
        nMaxNumberOfPeaks to zero.

        To have profile scans centroided, set bCentroidResult to True. This parameter is ignored for
        centroid scans.

        The pvarPeakFlags variable is currently not used. This variable is reserved for future use to
        return flag information, such as saturation, about each mass intensity pair.

        The varSegments array contains information about the segments, and the varMassRange array
        contains the mass range for each segment. The nSegments variable contains the number of
        segments.

        NOTE: same as GetMassListFromScanNum but is able to filter on a m/z range."""
        peakList = comtypes.automation.VARIANT()
        peakFlags = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        pvarSegments = comtypes.automation.VARIANT()
        pnNumSegments = c_long()
        massRange = comtypes.automation.VARIANT()
        error = self.source.GetSegmentedMassListFromScanNum(byref(c_long(scanNumber)),
                                                            scanFilter,
                                                            intensityCutoffType,
                                                            intensityCutoffValue,
                                                            maxNumberOfPeaks,
                                                            centroidResult,
                                                            c_double(centroidPeakWidth),
                                                            peakList,
                                                            peakFlags,
                                                            byref(pnArraySize),
                                                            byref(pvarSegments),
                                                            byref(pnNumSegments),
                                                            byref(massRange))
        if error:
            raise IOError("GetSegmentedMassListFromScanNum error :", error)
        return peakList.value, peakFlags.value, pvarSegments.value, pnNumSegments.value

    def GetAverageMassList(self, firstAvgScanNumber,
                           lastAvgScanNumber,
                           firstBkg1ScanNumber=0,
                           lastBkg1ScanNumber=0,
                           firstBkg2ScanNumber=0,
                           lastBkg2ScanNumber=0,
                           scanFilter="",
                           intensityCutoffType=0,
                           intensityCutoffValue=0,
                           maxNumberOfPeaks=0,
                           centroidResult=False,
                           centroidPeakWidth=0.0):
        """
        This function is only applicable to scanning devices such as MS and PDA.

        If no scanFilter is supplied, the scans between firstAvgScanNumber and
        lastAvgScanNumber that match the scanFilter of the firstAvgScanNumber, inclusive, are
        returned. Likewise, all the scans between firstBkg1ScanNumber and
        lastBkg1ScanNumber and firstBkg2ScanNumber and lastBkg2ScanNumber, inclusive,
        are averaged and subtracted from the firstAvgScanNumber to lastAvgScanNumber
        averaged scans.
        If a scanFilter is provided, the scans in the preceding scan number ranges that
        match the scanFilter are utilized in obtaining the background subtracted mass list. The
        specified scan numbers must be valid for the current controller. If no background subtraction
        is performed, the background scan numbers should be set to zero. On return, the scan
        number variables contain the actual first and last scan numbers, respectively, for the scans
        used.

        scanFilters must match the Xcalibur scanFilter format (e.g. "FTMS + c NSI Full ms [300.00-1800.00]").

        To reduce the number of low intensity data peaks returned, an intensity cutoff,
        nIntensityCutoffType, may be applied. The available types of cutoff are
        0   None (all values returned)
        1   Absolute (in intensity units)
        2   Relative (to base peak)

        To limit the total number of data peaks that are returned in the mass list, set
        nMaxNumberOfPeaks to a value greater than zero. To have all data peaks returned, set
        nMaxNumberOfPeaks to zero.

        To have profile scans centroided, set bCentroidResult to True. This parameter is ignored for
        centroid scans.

        The format of the mass list returned is an array of double precision values in
        mass intensity pairs in ascending mass order,
        for example, mass 1, intensity 1, mass 2, intensity 2, mass 3, intensity 3.

        The pvarPeakFlags variable is currently not used. This variable is reserved for future use to
        return flag information, such as saturation, about each mass intensity pair.
        """
        peakList = comtypes.automation.VARIANT()
        peakFlags = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetAverageMassList(byref(c_long(firstAvgScanNumber)),
                                               byref(c_long(lastAvgScanNumber)),
                                               byref(c_long(firstBkg1ScanNumber)),
                                               byref(c_long(lastBkg1ScanNumber)),
                                               byref(c_long(firstBkg2ScanNumber)),
                                               byref(c_long(lastBkg2ScanNumber)),
                                               scanFilter,
                                               intensityCutoffType,
                                               intensityCutoffValue,
                                               maxNumberOfPeaks,
                                               centroidResult,
                                               c_double(centroidPeakWidth),
                                               byref(peakList),
                                               byref(peakFlags),
                                               byref(pnArraySize))
        if error:
            raise IOError("GetAverageMassList error :", error)
        return peakList.value, peakFlags.value

    def GetAveragedMassSpectrum(self, listOfScanNumbers, centroidResult=False):
        """
        This function is only applicable to scanning devices such as MS.

        Returns the average spectrum for the list of scans that are supplied
        to the function in listOfScanNumbers. If no scans are provided in listOfScanNumbers,
        then the function returns an error code.

        If the bCentroidData value is true, profile data is centroided before it is returned by this
        routine.

        The format of the mass list returned is an array of double precision values in
        mass intensity pairs in ascending mass order,
        for example, mass 1, intensity 1, mass 2, intensity 2, mass 3, intensity 3.

        The pvarPeakFlags variable is currently not used. This variable is reserved for future use to
        return flag information, such as saturation, about each mass intensity pair
        """
        # http://stackoverflow.com/questions/1363163/pointers-and-arrays-in-python-ctypes
        x = (c_long * len(listOfScanNumbers))()
        cast(x, POINTER(c_long))
        for i_scanNumber, scanNumber in enumerate(listOfScanNumbers):
            x[i_scanNumber] = scanNumber

        peakList = comtypes.automation.VARIANT()
        peakFlags = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetAveragedMassSpectrum(x,
                                                    len(x),
                                                    centroidResult,
                                                    byref(peakList),
                                                    byref(peakFlags),
                                                    byref(pnArraySize))
        if error:
            raise IOError("GetAveragedMassSpectrum error :", error)
        return peakList.value, peakFlags.value

    def GetSummedMassSpectrum(self, listOfScanNumbers, centroidResult=False):
        """
        This function is only applicable to scanning devices such as MS.

        Returns the summed spectrum for the list of scans that are supplied
        to the function in listOfScanNumbers. If no scans are provided in listOfScanNumbers,
        then the function returns an error code.

        If the bCentroidData value is true, profile data is centroided before it is returned by this
        routine.

        The format of the mass list returned is an array of double precision values in
        mass intensity pairs in ascending mass order,
        for example, mass 1, intensity 1, mass 2, intensity 2, mass 3, intensity 3.

        The pvarPeakFlags variable is currently not used. This variable is reserved for future use to
        return flag information, such as saturation, about each mass intensity pair

        NOTE: seems to return same output that GetAveragedMassSpectrum...
        """
        # http://stackoverflow.com/questions/1363163/pointers-and-arrays-in-python-ctypes
        x = (c_long * len(listOfScanNumbers))()
        cast(x, POINTER(c_long))
        for i_scanNumber, scanNumber in enumerate(listOfScanNumbers):
            x[i_scanNumber] = scanNumber

        peakList = comtypes.automation.VARIANT()
        peakFlags = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetSummedMassSpectrum(x,
                                                  len(x),
                                                  centroidResult,
                                                  byref(peakList),
                                                  byref(peakFlags),
                                                  byref(pnArraySize))
        if error:
            raise IOError("GetSummedMassSpectrum error :", error)
        return peakList.value, peakFlags.value

    def IncludeReferenceAndExceptionData(self, boolean):
        """Controls whether the reference and exception data is included in the spectral data when using
        the GetLabelData method. Reference and exception peaks are only present on instruments
        that can collect FTMS data. A value of TRUE causes the reference and exception data to be
        included in the spectrum, and a value of FALSE excludes this data.
        """
        error = self.source.IncludeReferenceAndExceptionData(c_bool(boolean))
        if error:
            raise IOError("IncludeReferenceAndExceptionData error :", error)
        return

    def GetLabelData(self, scanNumber):
        """This is a higher level function than GetMassListRangeFromScanNum, only for profile data (MS1).

        This method enables you to read the FT-PROFILE labels of a scan represented by the scanNumber.
        The label data contains values of :
        mass (double),
        intensity (double),
        resolution (float),
        baseline (float),
        noise (float)
        and charge (int).

        The flags are returned as unsigned char values. The flags are :
        saturated,
        fragmented,
        merged,
        exception,
        reference,
        and modified.

        NOTE : This is a higher level function than GetMassListRangeFromScanNum, only for profile data (MS1).
        """
        pvarLabels = comtypes.automation.VARIANT()
        pvarFlags = comtypes.automation.VARIANT()
        error = self.source.GetLabelData(pvarLabels, pvarFlags, c_long(scanNumber))
        if error:
            raise IOError("GetLabelData error :", error)
        return ThermoRawfile.GetLabelData_Labels(*pvarLabels.value), ThermoRawfile.GetLabelData_Flags(*pvarFlags.value)

    def GetAveragedLabelData(self, listOfScanNumbers):
        """This method enables you to read the averaged FT-PROFILE labels for the list of scans
        represented by the listOfScanNumbers. If no scans are provided in listOfScanNumbers,
        the function returns an error code.

        The format of the mass list returned is an array of double precision values in
        mass intensity pairs in ascending mass order,
        for example, mass 1, intensity 1, mass 2, intensity 2, mass 3, intensity 3.

        The flags are returned as unsigned char values.
        These flags are saturated, fragmented, merged, exception, reference, and modified.
        """
        x = (c_long * len(listOfScanNumbers))()
        cast(x, POINTER(c_long))
        for i_scanNumber, scanNumber in enumerate(listOfScanNumbers):
            x[i_scanNumber] = scanNumber

        peakList = comtypes.automation.VARIANT()
        peakFlags = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetAveragedLabelData(x,
                                                 len(x),
                                                 byref(peakList),
                                                 byref(peakFlags),
                                                 byref(pnArraySize))
        if error:
            raise IOError("GetAveragedLabelData error :", error)
        return peakList.value, ThermoRawfile.GetLabelData_Flags(*peakFlags.value)

    def GetNoiseData(self, scanNumber):  # already included in GetLabelData ?
        """This method enables you to read the FT-PROFILE noise packets of a scan represented by the scanNumber.
        The noise packets contain values of mass (double), noise (float) and baseline (float).
        NOTE: already included in GetLabelData ?
        """
        NoisePacket = comtypes.automation.VARIANT()
        error = self.source.GetNoiseData(NoisePacket, c_long(scanNumber))
        if error:
            raise IOError("GetNoiseData error :", error)
        return NoisePacket.value

    def GetAllMSOrderData(self, scanNumber):  # same as GetLabelData ?
        """This method enables you to obtain all of the precursor information from the scan (event).

        The FT-PROFILE labels of a scan are represented by scanNumber. PvarFlags can be NULL
        if you do not want to receive the flags. The label data contains values of mass (double),
        intensity (double), resolution (float), baseline (float), noise (float), and charge (int).
        The flags are returned as unsigned character values. The flags are saturated, fragmented,
        merged, exception, reference, and modified."""
        pvarLabels = comtypes.automation.VARIANT()
        pvarFlags = comtypes.automation.VARIANT()
        pnNumberOfMSOrders = c_long()
        error = self.source.GetAllMSOrderData(scanNumber, pvarLabels, pvarFlags, byref(pnNumberOfMSOrders))
        if error:
            raise IOError("GetNoiseData error :", error)
        return (ThermoRawfile.GetAllMSOrderData_Labels(*pvarLabels.value),
                ThermoRawfile.GetAllMSOrderData_Flags(*pvarFlags.value),
                pnNumberOfMSOrders.value)

    def GetFullMSOrderPrecursorDataFromScanNum(self, scanNumber, MSOrder):
        """This function retrieves information about the reaction data of a data-dependent MSn for the
        scan specified by scanNumber and the transition specified by MSOrder from the scan event
        structure in the raw file.

        - Reaction data refers to precursor mass, isolation width, collision energy, whether the
        collision energy is valid, whether the precursor mass is valid, the first precursor mass, the
        last precursor mass, and the isolation width offset.

        - Specify the data-dependent MSn through the MSOrder input. You can find the count of
        MS orders by calling GetNumberOfMSOrdersFromScanNum.

        - Specify the scan through the scanNumber input. The value of scanNumber must be
        within the range of scans or readings for the current controller. You can obtain the range
        of scans or readings for the current controller by calling GetFirstSpectrumNumber and
        GetLastSpectrumNumber.
        """
        pvarFullMSOrderPrecursorInfo = comtypes.automation.VARIANT()
        error = self.source.GetFullMSOrderPrecursorDataFromScanNum(scanNumber, MSOrder,
                                                                   byref(pvarFullMSOrderPrecursorInfo))
        if error:
            raise IOError("GetFullMSOrderPrecursorDataFromScanNum error :", error)
        return ThermoRawfile.FullMSOrderPrecursorData(*pvarFullMSOrderPrecursorInfo.value[:8])

    def GetMSOrderForScanNum(self, scanNumber):
        """This function returns the MS order for the scan specified by scanNumber from the scan
        event structure in the raw file.
        The value returned in the pnScanType variable is one of the following:
        Neutral gain -3
        Neutral loss -2
        Parent scan -1
        Any scan order 0
        MS  1
        MS2  2
        MS3  3
        MS4  4
        MS5  5
        MS6  6
        MS7  7
        MS8  8
        MS9  9
        """
        MSOrder = c_long()
        error = self.source.GetMSOrderForScanNum(c_long(scanNumber), byref(MSOrder))
        if error:
            raise IOError("scan {} : GetMSOrderForScanNum error : {}".format(scanNumber, error))
        return MSOrder.value

    def GetNumberOfMSOrdersFromScanNum(self, scanNumber):
        """This function gets the number of MS reaction data items in the scan event for the scan
        specified by scanNumber and the transition specified by MSOrder from the scan event
        structure in the raw file."""
        result = c_long()
        error = self.source.GetNumberOfMSOrdersFromScanNum(c_long(scanNumber), byref(result))
        if error:
            raise IOError("GetNumberOfMSOrdersFromScanNum error :", error)
        return result.value

    # PRECURSOR BEGIN
    def GetPrecursorInfoFromScanNum(self, scanNumber):
        """This function is used to retrieve information about the parent scans of a data-dependent MS n
        scan.
        You retrieve the scan number of the parent scan, the isolation mass used, the charge state, and
        the monoisotopic mass as determined by the instrument firmware. You will obtain access to
        the scan data of the parent scan in the form of a XSpectrumRead object.
        Further refine the charge state and the monoisotopic mass values from the actual parent scan
        data.
        NOTE : !!! VARIANT conversion to struct does not work : we only retrieve dIsolationMass and dMonoIsoMass AND
        this does not work with Qexactive files...
        """
        # struct PrecursorInfo
        # {
        #       double dIsolationMass;
        #       double dMonoIsoMass;
        #       long nChargeState;
        #       long scanNumber;
        # }
        # http://www.codeproject.com/Articles/6462/A-simple-class-to-encapsulate-VARIANTs
        # http://digital.ni.com/public.nsf/3efedde4322fef19862567740067f3cc/c5834a84795dfa86862565fc0079baf5/$FILE/Information%20on%20Variants%20and%20SafeArrays.doc
        # http://www.roblocher.com/whitepapers/oletypes.html
        variant = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetPrecursorInfoFromScanNum(scanNumber, variant, byref(pnArraySize))
        if error:
            raise IOError("GetPrecursorInfoFromScanNum error :", error)
        if variant.value:
            variant.vt = comtypes.automation.VT_ARRAY | comtypes.automation.VT_R8  # SAFEARRAY of double
            dMonoIsoMass, dIsolationMass = variant.value[:2]
            variant.vt = comtypes.automation.VT_ARRAY | comtypes.automation.VT_I4  # SAFEARRAY of long
            nChargeState, nScanNumber = variant.value[4:6]
            return ThermoRawfile.GetPrecursorInfoFromScanNum_PrecursorInfo(isolationMass=dIsolationMass,
                                                                           monoIsoMass=dMonoIsoMass,
                                                                           chargeState=nChargeState,
                                                                           scanNumber=nScanNumber)
        else:
            return

    def GetPrecursorMassForScanNum(self, scanNumber, MSOrder):
        """This function returns the precursor mass for the scan specified by scanNumber and the
        transition specified by MSOrder from the scan event structure in the RAW file."""
        precursorMass = c_double()
        error = self.source.GetPrecursorMassForScanNum(scanNumber, MSOrder, byref(precursorMass))
        if error:
            raise IOError("scan {} : GetPrecursorMassForScanNum error : {}".format(scanNumber, error))
        return precursorMass.value

    def GetPrecursorRangeForScanNum(self, scanNumber, MSOrder):
        """This function returns the first and last precursor mass values of the range and
        whether they are valid for the scan specified by scanNumber and
        the transition specified by MSOrder from the scan event structure in the raw file."""
        pdFirstPrecursorMass = c_double()
        pdLastPrecursorMass = c_double()
        pbIsValid = c_long()
        error = self.source.GetPrecursorRangeForScanNum(c_long(scanNumber), c_long(MSOrder),
                                                        byref(pdFirstPrecursorMass), byref(pdLastPrecursorMass),
                                                        byref(pbIsValid))
        if error:
            raise IOError("GetPrecursorRangeForScanNum error :", error)
        return pdFirstPrecursorMass.value, pdLastPrecursorMass.value, bool(pbIsValid.value)

    # PRECURSOR END

    # XCALIBUR INTERFACE BEGIN
    def GetScanHeaderInfoForScanNum(self, scanNumber):  # "View/Scan header", upper part
        """For a given scan number, this function returns information from the scan header for the
        current controller.

        The validity of these parameters depends on the current controller. For example, pdLowMass,
        pdHighMass, pdTIC, pdBasePeakMass, and pdBasePeakIntensity are only likely to be set on
        return for MS or PDA controllers. PnNumChannels is only likely to be set on return for
        Analog, UV, and A/D Card controllers. PdUniformTime, and pdFrequency are only likely to be
        set on return for UV, and A/D Card controllers and may be valid for Analog controllers. In
        cases where the value is not set, a value of zero is returned.

        NOTE : XCALIBUR INTERFACE "View/Scan header", upper part
        """
        header = OrderedDict()
        header['numPackets'] = c_long()
        header['StartTime'] = c_double()
        header['LowMass'] = c_double()
        header['HighMass'] = c_double()
        header['TIC'] = c_double()
        header['BasePeakMass'] = c_double()
        header['BasePeakIntensity'] = c_double()
        header['numChannels'] = c_long()
        header['uniformTime'] = c_long()
        header['Frequency'] = c_double()
        error = self.source.GetScanHeaderInfoForScanNum(c_long(scanNumber), header['numPackets'], header['StartTime'],
                                                        header['LowMass'], header['HighMass'],
                                                        header['TIC'], header['BasePeakMass'],
                                                        header['BasePeakIntensity'], header['numChannels'],
                                                        header['uniformTime'], header['Frequency'])
        if error:
            raise IOError("GetScanHeaderInfoForScanNum error :", error)
        for k in header:
            header[k] = header[k].value
        return header

    def GetTrailerExtraForScanNum(self, scanNumber):  # "View/Scan header", lower part
        """Returns the recorded trailer extra entry labels and values for the current controller. This
        function is only valid for MS controllers.

        NOTE : XCALIBUR INTERFACE "View/Scan header", lower part
        """
        labels = comtypes.automation.VARIANT()
        values = comtypes.automation.VARIANT()
        val_num = c_long()
        error = self.source.GetTrailerExtraForScanNum(c_long(scanNumber), labels, values, val_num)
        if error:
            raise IOError("GetTrailerExtraForScanNum error :", error)
        return OrderedDict(zip(map(lambda x: str(x[:-1]), labels.value), map(_to_float, values.value)))

    def GetNumTuneData(self):
        """Gets the number of tune data entries recorded for the current controller. Tune Data is only
        supported by MS controllers. Typically, if there is more than one tune data entry, each tune
        data entry corresponds to a particular acquisition segment."""
        pnNumTuneData = c_long()
        error = self.source.GetNumTuneData(byref(pnNumTuneData))
        if error:
            raise IOError("GetNumTuneData error :", error)
        return pnNumTuneData.value

    def GetTuneData(self, segmentNumber=1):  # "View/Report/Tune Method"
        """Returns the recorded tune parameter labels and values for the current controller. This
        function is only valid for MS controllers. The value of segmentNumber must be within the
        range of one to the number of tune data items recorded for the current controller. The
        number of tune data items for the current controller may be obtained by calling
        GetNumTuneData.

        NOTE : XCALIBUR INTERFACE "View/Report/Tune Method"
        """
        pvarLabels = comtypes.automation.VARIANT()
        pvarValues = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetTuneData(c_long(segmentNumber), pvarLabels, pvarValues, byref(pnArraySize))
        if error:
            raise IOError("GetTuneData error :", error)
        # return dict(zip(pvarLabels.value,pvarValues.value))
        # return dict(zip([label.rstrip(':') for label in pvarLabels.value],pvarValues.value))
        result = []
        for label, value in zip(pvarLabels.value, pvarValues.value):
            result.append(label)
            result.append(value)
            result.append('\n')
        return ''.join(result)

    def GetNumInstMethods(self):
        """Returns the number of instrument methods contained in the raw file. Each instrument used
        in the acquisition with a method that was created in Instrument Setup (for example,
        autosampler, LC, MS, PDA) has its instrument method contained in the raw file."""
        pnNumInstMethods = c_long()
        error = self.source.GetNumInstMethods(byref(pnNumInstMethods))
        if error:
            raise IOError("GetNumInstMethods error : ", error)
        return pnNumInstMethods.value

    def GetInstMethod(self, instMethodItem=0):  # "View/Report/Instrument Method"
        """Returns the channel label, if available, at the specified index for the current controller. This
        field is only relevant to channel devices such as UV detectors, A/D cards, and Analog inputs.
        Channel labels indices are numbered starting at 0.
        Returns the instrument method, if available, at the index specified in instMethodItem. The
        instrument method indices are numbered starting at 0. The number of instrument methods
        are obtained by calling GetNumInstMethods.

        instMethodItem     A long variable containing the index value of the instrument method to
                            be returned.

        NOTE : XCALIBUR INTERFACE "View/Report/Instrument Method"
        """
        strInstMethod = comtypes.automation.BSTR()
        error = self.source.GetInstMethod(c_long(instMethodItem), byref(strInstMethod))
        if error:
            raise IOError("GetInstMethod error :", error)
        if sys.version_info.major == 2:
            return strInstMethod.value.encode('utf-8').replace('\r\n', '\n')
        elif sys.version_info.major == 3:
            return strInstMethod.value.replace('\r\n', '\n')

    def GetInstMethodNames(self):
        """This function returns the recorded names of the instrument methods for the current
        controller."""
        pnArraySize = c_long(0)
        pvarNames = comtypes.automation.VARIANT()
        error = self.source.GetInstMethodNames(byref(pnArraySize), byref(pvarNames))
        if error:
            raise IOError("GetInstMethodNames error :", error)
        return pvarNames.value

    def ExtractInstMethodFromRaw(self, instMethodFileName):
        """This function enables you to save the embedded instrument method in the raw file in a
        separated method (.meth)) file. It overwrites any pre-existing method file in the same path
        with the same name."""
        error = self.source.ExtractInstMethodFromRaw(comtypes.automation.BSTR(instMethodFileName))
        if error:
            raise IOError("ExtractInstMethodFromRaw error :", error)
        return

    # # # # # # # "View/Report/Sample Information" BEGIN
    def GetVialNumber(self):
        """Gets the vial number for the current controller. This value is typically only set for raw files
        converted from other file formats.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_long()
        error = self.source.GetVialNumber(byref(result))
        if error:
            raise IOError("GetVialNumber error : ", error)
        return result.value

    def GetInjectionVolume(self):
        """Gets the injection volume for the current controller. This value is typically only set for raw
        files converted from other file formats.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_double()
        error = self.source.GetInjectionVolume(byref(result))
        if error:
            raise IOError("GetInjectionVolume error : ", error)
        return result.value

    def GetInjectionAmountUnits(self):
        """Returns the injection amount units for the current controller. This value is typically only set
        for raw files converted from other file formats.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetInjectionAmountUnits(byref(result))
        if error:
            raise IOError("GetInjectionAmountUnits error : ", error)
        return result.value

    def GetSampleVolume(self):
        """Gets the sample volume value for the current controller.
        This value is typically only set for raw files converted from other file formats.

        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_double()
        error = self.source.GetSampleVolume(byref(result))
        if error:
            raise IOError("GetSampleVolume error : ", error)
        return result.value

    def GetSampleVolumeUnits(self):
        """Returns the sample volume units for the current controller.
        This value is typically only set for raw files converted from other file formats.

        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSampleVolumeUnits(byref(result))
        if error:
            raise IOError("GetSampleVolumeUnits error : ", error)
        return result.value

    def GetSampleWeight(self):
        """Gets the sample weight value for the current controller.
        This value is typically only set for raw files converted from other file formats.

        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_double()
        error = self.source.GetSampleWeight(byref(result))
        if error:
            raise IOError("GetSampleWeight error : ", error)
        return result.value

    def GetSampleAmountUnits(self):
        """Returns the sample amount units for the current controller.
        This value is typically only set for raw files converted from other file formats.

        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSampleAmountUnits(byref(result))
        if error:
            raise IOError("GetSampleAmountUnits error : ", error)
        return result.value

    def GetSeqRowNumber(self):
        """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
        """
        result = c_long()
        error = self.source.GetSeqRowNumber(byref(result))
        if error:
            raise IOError("GetSeqRowNumber error : ", error)
        return result.value

    def GetSeqRowSampleType(self):
        """Returns the sequence row sample type for this sample. See Sample Type in the Enumerated
        Types section for the possible sample type values.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_long()
        error = self.source.GetSeqRowSampleType(byref(result))
        if error:
            raise IOError("GetSeqRowSampleType error : ", error)
        return ThermoRawfile.sampleType[result.value]

    def GetSeqRowDataPath(self):
        """Returns the path of the directory where this raw file was acquired.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSampleAmountUnits(byref(result))
        if error:
            raise IOError("GetSampleAmountUnits error : ", error)
        return result.value

    def GetSeqRowRawFileName(self):
        """Returns the file name of the raw file when the raw file was acquired. This value is typically
        used in conjunction with GetSeqRowDataPath to obtain the fully qualified path name of the
        raw file when it was acquired.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowRawFileName(byref(result))
        if error:
            raise IOError("GetSeqRowRawFileName error : ", error)
        return result.value

    def GetSeqRowSampleName(self):
        """Returns the sample name value from the sequence row of the raw file.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowSampleName(byref(result))
        if error:
            raise IOError("GetSeqRowSampleName error : ", error)
        return result.value

    def GetSeqRowSampleID(self):
        """Returns the sample ID value from the sequence row of the raw file.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowSampleID(byref(result))
        if error:
            raise IOError("GetSeqRowSampleID error : ", error)
        return result.value

    def GetSeqRowComment(self):
        """Returns the comment field from the sequence row of the raw file.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowComment(byref(result))
        if error:
            raise IOError("GetSeqRowComment error : ", error)
        return result.value

    def GetSeqRowLevelName(self):
        """Returns the level name from the sequence row of the raw file. This field is empty except for
        standard and QC sample types, which may contain a value if a processing method was
        specified in the sequence at the time of acquisition.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowLevelName(byref(result))
        if error:
            raise IOError("GetSeqRowLevelName error : ", error)
        return result.value

    def GetSeqRowUserText(self, index=0):
        """Returns a user text field from the sequence row of the raw file. There are five user text fields in
        the sequence row that are indexed 0 through 4.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowUserText(c_long(index), byref(result))
        if error:
            raise IOError("GetSeqRowUserText error : ", error)
        return result.value

    def GetSeqRowInstrumentMethod(self):
        """Returns the fully qualified path name of the instrument method used to acquire the raw file.
        If the raw file is created by file format conversion or acquired from a tuning program, this
        field is empty.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowInstrumentMethod(byref(result))
        if error:
            raise IOError("GetSeqRowInstrumentMethod error : ", error)
        return result.value

    def GetSeqRowProcessingMethod(self):
        """Returns the fully qualified path name of the processing method specified in the sequence used
        to acquire the raw file. If no processing method is specified at the time of acquisition, this field is empty.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowProcessingMethod(byref(result))
        if error:
            raise IOError("GetSeqRowProcessingMethod error : ", error)
        return result.value

    def GetSeqRowCalibrationFile(self):
        """Returns the fully qualified path name of the calibration file specified in the sequence used to
        acquire the raw file. If no calibration file is specified at the time of acquisition, this field is empty.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowCalibrationFile(byref(result))
        if error:
            raise IOError("GetSeqRowCalibrationFile error : ", error)
        return result.value

    def GetSeqRowVial(self):
        """Returns the vial or well number of the sample when it was acquired. If the raw file is not
        acquired using an autosampler, this value should be ignored.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowVial(byref(result))
        if error:
            raise IOError("GetSeqRowVial error : ", error)
        return result.value

    def GetSeqRowInjectionVolume(self):
        """Returns the autosampler injection volume from the sequence row for this sample.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_double()
        error = self.source.GetSeqRowInjectionVolume(byref(result))
        if error:
            raise IOError("GetSeqRowInjectionVolume error : ", error)
        return result.value

    def GetSeqRowSampleWeight(self):
        """Returns the sample weight from the sequence row for this sample.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_double()
        error = self.source.GetSeqRowSampleWeight(byref(result))
        if error:
            raise IOError("GetSeqRowSampleWeight error : ", error)
        return result.value

    def GetSeqRowSampleVolume(self):
        """Returns the sample volume from the sequence row for this sample.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_double()
        error = self.source.GetSeqRowSampleVolume(byref(result))
        if error:
            raise IOError("GetSeqRowSampleVolume error : ", error)
        return result.value

    def GetSeqRowISTDAmount(self):
        """Returns the bulk ISTD correction amount from the sequence row for this sample.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_double()
        error = self.source.GetSeqRowISTDAmount(byref(result))
        if error:
            raise IOError("GetSeqRowISTDAmount error : ", error)
        return result.value

    def GetSeqRowDilutionFactor(self):
        """Returns the bulk dilution factor (volume correction) from the sequence row for this sample.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_double()
        error = self.source.GetSeqRowDilutionFactor(byref(result))
        if error:
            raise IOError("GetSeqRowDilutionFactor error : ", error)
        return result.value

    def GetSeqRowUserLabel(self, index=0):
        """Returns a user label field from the sequence row of the raw file.
        There are five user label fields in the sequence row that are indexed 0 through 4.
        The user label fields correspond one-to-one with the user text fields.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowUserLabel(c_long(index), byref(result))
        if error:
            raise IOError("GetSeqRowUserLabel error : ", error)
        return result.value

    def GetSeqRowUserTextEx(self, index=0):
        """This function returns a user text field from the sequence row of the raw file.
        There are five user text fields in the sequence row that are indexed 0 through 4.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowUserTextEx(c_long(index), byref(result))
        if error:
            raise IOError("GetSeqRowUserTextEx error : ", error)
        return result.value

    def GetSeqRowBarcode(self):
        """This function returns the barcode used to acquire the raw file.
        This field is empty if the raw file was created by file format
        conversion or acquired from a tuning program.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = comtypes.automation.BSTR()
        error = self.source.GetSeqRowBarcode(byref(result))
        if error:
            raise IOError("GetSeqRowBarcode error : ", error)
        return result.value

    def GetSeqRowBarcodeStatus(self):
        """This function returns the barcode status from the raw file.
        This field is empty if the raw file was created by file format
        conversion or acquired from a tuning program.
        NOTE : XCALIBUR INTERFACE "View/Report/Sample Information" part
        """
        result = c_long()
        error = self.source.GetSeqRowBarcodeStatus(byref(result))
        if error:
            raise IOError("GetSeqRowBarcodeStatus error : ", error)
        return result.value

    # # # # # # # "View/Report/Sample Information" END

    def GetNumStatusLog(self):
        """Gets the number of status log entries recorded for the current controller."""
        pnNumberOfStatusLogEntries = c_long()
        error = self.source.GetNumStatusLog(byref(pnNumberOfStatusLogEntries))
        if error:
            raise IOError("GetNumStatusLog error :", error)
        return pnNumberOfStatusLogEntries.value

    def GetStatusLogForScanNum(self, scanNumber):  # "View/Report/Status Log"
        """Returns the recorded status log entry labels and values for the current controller.
        On return, pdStatusLogRT contains the retention time when the status log entry was recorded.
        This time may not be the same as the retention time corresponding to the specified scan
        number but is the closest status log entry to the scan time.
        NOTE : XCALIBUR INTERFACE "View/Report/Status Log"
        """
        pdStatusLogRT = c_double()
        pvarLabels = comtypes.automation.VARIANT()
        pvarValues = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetStatusLogForScanNum(c_long(scanNumber), byref(pdStatusLogRT), pvarLabels, pvarValues,
                                                   byref(pnArraySize))
        if error:
            raise IOError("GetStatusLogForScanNum error :", error)
        # return pdStatusLogRT.value, pvarLabels.value, pvarValues.value
        return pdStatusLogRT.value, list(zip([label.rstrip(':') for label in pvarLabels.value], pvarValues.value))

    def GetStatusLogForPos(self, position=0):
        """This function returns the recorded status log entry labels and values for the current controller.
        position    The position that the status log information is to be returned for.
        """
        pvarRT = comtypes.automation.VARIANT()
        pvarValues = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetStatusLogForPos(c_long(position), byref(pvarRT), byref(pvarValues), byref(pnArraySize))
        if error:
            raise IOError("GetStatusLogForPos error :", error)
        return pvarRT.value, pvarValues.value

    def GetStatusLogPlottableIndex(self):
        """This function returns the recorded status log entry labels and values for the current controller."""
        pvarIndex = comtypes.automation.VARIANT()
        pvarValues = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetStatusLogPlottableIndex(byref(pvarIndex), byref(pvarValues), byref(pnArraySize))
        if error:
            raise IOError("GetStatusLogPlottableIndex error :", error)
        return pvarIndex.value, pvarValues.value

    def GetNumErrorLog(self):
        """Gets the number of error log entries recorded for the current controller."""
        pnNumberOfErrorLogEntries = c_long()
        error = self.source.GetNumErrorLog(byref(pnNumberOfErrorLogEntries))
        if error:
            raise IOError("GetNumErrorLog error :", error)
        return pnNumberOfErrorLogEntries.value

    def GetErrorLogItem(self, itemNumber=1):  # "View/Report/Error Log"
        """Returns the specified error log item information and the retention time when the error
        occurred. The value of itemNumber must be within the range of one to the number of error
        log items recorded for the current controller. The number of error log items for the current
        controller may be obtained by calling GetNumErrorLog.

        NOTE : XCALIBUR INTERFACE "View/Report/Error Log"
        """
        pdRT = c_double()  # A valid pointer to a variable of type double to receive the retention
        # time when the error occurred. This variable must exist.
        pbstrErrorMessage = comtypes.automation.BSTR()
        error = self.source.GetErrorLogItem(c_long(itemNumber), byref(pdRT), byref(pbstrErrorMessage))
        if error:
            raise IOError("GetErrorLogItem error :", error)
        return pbstrErrorMessage.value, pdRT.value

    # XCALIBUR INTERFACE END

    def GetChroData(self, startTime=0.0,
                    endTime=0.0,
                    massRange1="",
                    massRange2="",
                    scanFilter="",
                    chroType1=0,
                    chroOperator=0,
                    chroType2=0,
                    delay=0.0,
                    smoothingType=0,
                    smoothingValue=0):
        """Returns the requested chromatogram data as an array of double precision time intensity pairs
        in pvarChroData.

        The start and end times, pdStartTime and pdEndTime, may be used to return a portion of the
        chromatogram. The start time and end time must be within the acquisition time range of the
        current controller which may be obtained by calling GetStartTime and GetEndTime,
        respectively. Or, if the entire chromatogram is returned, pdStartTime and pdEndTime may be
        set to zero. On return, pdStartTime and pdEndTime contain the actual time range of the
        returned chromatographic data.

        The mass ranges are only valid for MS or PDA controllers. For all other controller types, these
        fields must be NULL or empty strings. For MS controllers, the mass ranges must be correctly
        formatted mass ranges and are only valid for Mass Range and Base Peak chromatogram trace
        types. For PDA controllers, the mass ranges must be correctly formatted wavelength ranges
        and are only valid for Wavelength Range and Spectrum Maximum chromatogram trace types.
        These values may be left empty for Base Peak or Spectrum Maximum trace types but must be
        specified for Mass Range or Wavelength Range trace types. For information on how to format
        mass ranges, go to the Mass1 (m/z) text box topic in the Xcalibur Help.

        The scanFilter field is only valid for MS controllers (e.g. "Full ms ").

        The chromatogram trace types and operator values of chroType1, chroOperator, and
        chroType2 depend on the current controller. See Chromatogram Type and Chromatogram
        Operator in the Enumerated Types section for a list of the valid values for the different
        controller types.

        The delay value contains the retention time offset to add to the returned chromatogram
        times. The value may be set to 0.0 if no offset is desired. This value must be 0.0 for MS
        controllers. It must be greater than or equal to 0.0 for all other controller types.

        The smoothingType :
          0 None (no smoothing)
          1 Boxcar http://en.wikipedia.org/wiki/Boxcar_function
          2 Gaussian http://homepages.inf.ed.ac.uk/rbf/HIPR2/gsmooth.htm
        The value of smoothingValue must be an odd number in the range of 3-15 if smoothing is desired.

        The pvarPeakFlags variable is currently not used. This variable is reserved for future use to
        return flag information, such as saturation, about each time intensity pair.

        NOTE: Generates Total Ion Chromatogram (TIC) and eXtracted Ion Chromatogram (XIC) for given time range
        and mz range.
        """
        pvarChroData = comtypes.automation.VARIANT()
        pvarPeakFlags = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetChroData(chroType1,
                                        chroOperator,
                                        chroType2,
                                        scanFilter,
                                        massRange1,
                                        massRange2,
                                        c_double(delay),
                                        byref(c_double(startTime)),
                                        byref(c_double(endTime)),
                                        smoothingType,
                                        smoothingValue,
                                        pvarChroData,
                                        pvarPeakFlags,
                                        byref(pnArraySize))
        if error:
            raise IOError("GetChroData error :", error)
        # scan2tic = dict( zip( [self.ScanNumFromRT(rt) for rt in pvarChroData.value[0]], pvarChroData.value[1] ) )
        return pvarChroData.value, pvarPeakFlags.value

    def _GetChros(self):  # REDUNDANT with GetChroData
        pass

    def GetChroByCompoundName(self, compoundNamesList=None,
                              startTime=0.0,
                              endTime=0.0,
                              massRanges1="",
                              massRanges2="",
                              chroType1=0,
                              chroOperator=0,
                              chroType2=0,
                              delay=0.0,
                              smoothingType=0,
                              smoothingValue=0):
        """
        chroType1      A long variable containing the first chromatogram trace type of interest
        chroOperator   A long variable containing the chromatogram trace operator.
        chroType2      A long variable containing the second chromatogram trace type of interest.
        compoundNamesList (Input) An array of strings containing the compounds to filter the chromatogram with.
        massRanges1   A string containing the formatted mass ranges for the first chromatogram trace type.
        massRanges2   A string containing the formatted mass ranges for the second chromatogram trace type.
        delay          A double-precision variable containing the chromatogram delay in minutes.
        startTime     A pointer to a double-precision variable containing the start time of the chromatogram time range
                      to return.
        endTime       A pointer to a double-precision variable containing the end time of the chromatogram time range
                      to return.
        smoothingType  A long variable containing the type of chromatogram smoothing to be performed.
        smoothingValue A long variable containing the chromatogram smoothing value.
        """
        if not compoundNamesList:
            compoundNamesList = []
        pvarChroData = comtypes.automation.VARIANT()
        pvarPeakFlags = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetChroByCompoundName(c_long(chroType1),
                                                  c_long(chroOperator),
                                                  c_long(chroType2),
                                                  comtypes.automation.VARIANT(compoundNamesList),
                                                  massRanges1,
                                                  massRanges2,
                                                  c_double(delay),
                                                  byref(c_double(startTime)),
                                                  byref(c_double(endTime)),
                                                  c_long(smoothingType),
                                                  c_long(smoothingValue),
                                                  pvarChroData,
                                                  pvarPeakFlags,
                                                  byref(pnArraySize))
        if error:
            raise IOError("GetChroByCompoundName error :", error)
        return pvarChroDataArray.value, pvarChroParamsArray.value, pvarPeakFlagsArray.value

    def GetUniqueCompoundNames(self):
        """This function returns the list of unique compound names for the raw file."""
        pvarCompoundNamesArray = comtypes.automation.VARIANT()
        pnArraySize = c_long()
        error = self.source.GetUniqueCompoundNames(byref(pvarCompoundNamesArray), byref(pnArraySize))
        if error:
            raise IOError("GetUniqueCompoundNames error :", error)
        return pvarCompoundNamesArray.value

    def GetCompoundNameFromScanNum(self, scanNumber):
        """This function returns a compound name as a string for the specified scan number."""
        pvarCompoundName = comtypes.automation.BSTR()
        error = self.source.GetCompoundNameFromScanNum(c_long(scanNumber), byref(pvarCompoundName))
        if error:
            raise IOError("GetCompoundNameFromScanNum error :", error)
        return pvarCompoundName.value

    def _GetStatusLogForRT(self):  # REDUNDANT with GetStatusLogForScanNum
        pass

    def _GetStatusLogLabelsForScanNum(self):  # REDUNDANT with GetStatusLogForScanNum
        pass

    def _GetStatusLogLabelsForRT(self):  # REDUNDANT with GetStatusLogForScanNum
        pass

    def _GetStatusLogValueForScanNum(self):  # REDUNDANT with GetStatusLogForScanNum
        pass

    def _GetStatusLogValueForRT(self):  # REDUNDANT with GetStatusLogForScanNum
        pass

    def _GetTrailerExtraForRT(self):  # REDUNDANT with GetTrailerExtraForScanNum
        pass

    def _GetTrailerExtraLabelsForScanNum(self):  # REDUNDANT with GetTrailerExtraForScanNum
        pass

    def _GetTrailerExtraLabelsForRT(self):  # REDUNDANT with GetTrailerExtraForScanNum
        pass

    def _GetTrailerExtraValueForScanNum(self):  # REDUNDANT with GetTrailerExtraForScanNum
        pass

    def _GetTrailerExtraValueForRT(self):  # REDUNDANT with GetTrailerExtraForScanNum
        pass

    def _GetTuneDataValue(self):  # REDUNDANT with GetTuneData
        pass

    def _GetTuneDataLabels(self):  # REDUNDANT with GetTuneData
        pass

    def _GetPrevMassListRangeFromScanNum(self):  # REDUNDANT with GetMassListRangeFromScanNum
        pass

    def _GetMassListRangeFromRT(self):  # REDUNDANT with GetMassListRangeFromScanNum
        pass

    def _GetNextMassListRangeFromScanNum(self):  # REDUNDANT with GetMassListRangeFromScanNum
        pass

    def _GetMassListFromRT(self):  # REDUNDANT with GetMassListFromScanNum
        pass

    def _GetNextMassListFromScanNum(self):  # REDUNDANT with GetMassListFromScanNum
        pass

    def _GetPrevMassListFromScanNum(self):  # REDUNDANT with GetMassListFromScanNum
        pass

    def _GetFilterForScanRT(self):  # REDUNDANT with GetFilterForScanNum
        pass

    def _GetSegmentedMassListFromRT(self):  # REDUNDANT with GetSegmentedMassListFromScanNum
        pass


if __name__ == "__main__":
    if len(sys.argv) == 1:
        print("A filename must be provided")
        raise SystemExit

    from pprint import pprint

    rawfile = ThermoRawfile(" ".join(sys.argv[1:]))
    print('Version', rawfile.Version())
    print('GetFileName', rawfile.GetFileName())
    print('GetCreatorID', rawfile.GetCreatorID())
    print('GetVersionNumber', rawfile.GetVersionNumber())
    print('GetCreationDate', rawfile.GetCreationDate())
    print('IsError', rawfile.IsError())
    print('IsNewFile', rawfile.IsNewFile())
    print('IsThereMSData', rawfile.IsThereMSData())
    print('HasExpMethod', rawfile.HasExpMethod())
    print('InAcquisition', rawfile.InAcquisition())
    print('GetErrorCode', rawfile.GetErrorCode())
    print('GetErrorMessage', rawfile.GetErrorMessage())
    print('GetWarningMessage', rawfile.GetWarningMessage())
    print('RefreshViewOfFile', rawfile.RefreshViewOfFile())
    print('GetNumberOfControllers', rawfile.GetNumberOfControllers())

    print("GetNumberOfControllersOfType('No device')", rawfile.GetNumberOfControllersOfType('No device'))
    print("GetNumberOfControllersOfType('MS')", rawfile.GetNumberOfControllersOfType('MS'))
    print("GetNumberOfControllersOfType('Analog')", rawfile.GetNumberOfControllersOfType('Analog'))
    print("GetNumberOfControllersOfType('A/D card')", rawfile.GetNumberOfControllersOfType('A/D card'))
    print("GetNumberOfControllersOfType('PDA')", rawfile.GetNumberOfControllersOfType('PDA'))
    print("GetNumberOfControllersOfType('UV')", rawfile.GetNumberOfControllersOfType('UV'))
    print("GetControllerType('MS')", rawfile.GetControllerType('MS'))
    # print( 'GetControllerType(1)',  rawfile.GetControllerType(1) )

    # print( 'GetControllerType(2)',  rawfile.GetControllerType(2) )
    # print( 'GetControllerType(3)',  rawfile.GetControllerType(3) )
    # print( 'GetControllerType(4)',  rawfile.GetControllerType(4) )
    print('GetCurrentController()', rawfile.GetCurrentController())
    # print( 'SetCurrentController(4,1)',  rawfile.SetCurrentController(4,1) )

    print('GetCurrentController()', rawfile.GetCurrentController())
    # print( 'SetCurrentController(0,1)',  rawfile.SetCurrentController(0,1) )

    print('GetCurrentController()', rawfile.GetCurrentController())
    print('GetExpectedRunTime()', rawfile.GetExpectedRunTime())
    print('GetMaxIntegratedIntensity()', rawfile.GetMaxIntegratedIntensity())
    print('GetMaxIntensity()', rawfile.GetMaxIntensity())
    print('GetInletID()', rawfile.GetInletID())
    print('GetErrorFlag()', rawfile.GetErrorFlag())
    print('GetFlags()', rawfile.GetFlags())
    print('GetAcquisitionFileName()', rawfile.GetAcquisitionFileName())
    print('GetOperator()', rawfile.GetOperator())
    print('GetComment1()', rawfile.GetComment1())
    print('GetComment2()', rawfile.GetComment2())
    print('GetFilters()', rawfile.GetFilters())
    print('GetMassTolerance()', rawfile.GetMassTolerance())

    print('rawfile.SetMassTolerance(userDefined=True, massTolerance=555.0, units=2)',
          rawfile.SetMassTolerance(userDefined=True, massTolerance=555.0, units=2))
    print('GetMassTolerance()', rawfile.GetMassTolerance())
    print('rawfile.SetMassTolerance(userDefined=False, massTolerance=500.0, units=0)',
          rawfile.SetMassTolerance(userDefined=False, massTolerance=500.0, units=0))
    print('GetMassResolution', rawfile.GetMassResolution())
    print('GetNumTrailerExtra', rawfile.GetNumTrailerExtra())
    print('GetLowMass', rawfile.GetLowMass())
    print('GetHighMass', rawfile.GetHighMass())
    print('GetStartTime', rawfile.GetStartTime())
    print('GetEndTime', rawfile.GetEndTime())
    print('GetNumSpectra', rawfile.GetNumSpectra())
    print('GetFirstSpectrumNumber', rawfile.GetFirstSpectrumNumber())
    print('GetLastSpectrumNumber', rawfile.GetLastSpectrumNumber())
    print('GetAcquisitionDate', rawfile.GetAcquisitionDate())
    print('GetUniqueCompoundNames', rawfile.GetUniqueCompoundNames())

    print('############################################## INSTRUMENT BEGIN')
    print('GetInstrumentDescription', rawfile.GetInstrumentDescription())
    print('GetInstrumentID', rawfile.GetInstrumentID())
    print('GetInstSerialNumber', rawfile.GetInstSerialNumber())
    print('GetInstName', rawfile.GetInstName())
    print('GetInstModel', rawfile.GetInstModel())
    print('GetInstSoftwareVersion', rawfile.GetInstSoftwareVersion())
    print('GetInstHardwareVersion', rawfile.GetInstHardwareVersion())
    print('GetInstFlags', rawfile.GetInstFlags())
    print('GetInstNumChannelLabels', rawfile.GetInstNumChannelLabels())
    # print( 'GetInstChannelLabel(0)', rawfile.GetInstChannelLabel(0) )
    print('IsQExactive', rawfile.IsQExactive())  # Not implemented in MSFileReader 3.0.29.0
    print('############################################## INSTRUMENT END')

    scan_number = 1
    print('############################################## XCALIBUR INTERFACE BEGIN')
    print('GetScanHeaderInfoForScanNum',
          rawfile.GetScanHeaderInfoForScanNum(scan_number))  # "View/Scan header", upper part
    print('GetTrailerExtraForScanNum', rawfile.GetTrailerExtraForScanNum(scan_number))  # "View/Scan header", lower part
    print('GetNumTuneData', rawfile.GetNumTuneData())
    print('GetTuneData(0)', rawfile.GetTuneData(0))  # "View/Report/Tune Method"
    print('GetNumInstMethods', rawfile.GetNumInstMethods())
    print('GetInstMethodNames', rawfile.GetInstMethodNames())
    for i in range(rawfile.GetNumInstMethods()):
        print('-------------------------------------------------------------------------------')
        print(rawfile.GetInstMethod(i))  # "View/Report/Instrument Method"
        print('-------------------------------------------------------------------------------')
    print('rawfile.ExtractInstMethodFromRaw', rawfile.ExtractInstMethodFromRaw(rawfile.filename + '.meth'))

    # # # # # # "View/Report/Sample Information" BEGIN
    print('GetVialNumber', rawfile.GetVialNumber())
    print('GetInjectionVolume', rawfile.GetInjectionVolume())
    print('GetInjectionAmountUnits', rawfile.GetInjectionAmountUnits())
    print('GetSampleVolume', rawfile.GetSampleVolume())
    print('GetSampleVolumeUnits', rawfile.GetSampleVolumeUnits())
    print('GetSampleWeight', rawfile.GetSampleWeight())
    print('GetSampleAmountUnits', rawfile.GetSampleAmountUnits())
    print('GetSeqRowNumber', rawfile.GetSeqRowNumber())
    print('GetSeqRowSampleType', rawfile.GetSeqRowSampleType())
    print('GetSeqRowDataPath', rawfile.GetSeqRowDataPath())
    print('GetSeqRowRawFileName', rawfile.GetSeqRowRawFileName())
    print('GetSeqRowSampleName', rawfile.GetSeqRowSampleName())
    print('GetSeqRowSampleID', rawfile.GetSeqRowSampleID())
    print('GetSeqRowComment', rawfile.GetSeqRowComment())
    print('GetSeqRowLevelName', rawfile.GetSeqRowLevelName())
    print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=0))
    print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=1))
    print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=2))
    print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=3))
    print('GetSeqRowUserText', rawfile.GetSeqRowUserText(index=4))
    print('GetSeqRowInstrumentMethod', rawfile.GetSeqRowInstrumentMethod())
    print('GetSeqRowProcessingMethod', rawfile.GetSeqRowProcessingMethod())
    print('GetSeqRowCalibrationFile', rawfile.GetSeqRowCalibrationFile())
    print('GetSeqRowVial', rawfile.GetSeqRowVial())
    print('GetSeqRowInjectionVolume', rawfile.GetSeqRowInjectionVolume())
    print('GetSeqRowSampleWeight', rawfile.GetSeqRowSampleWeight())
    print('GetSeqRowSampleVolume', rawfile.GetSeqRowSampleVolume())
    print('GetSeqRowISTDAmount', rawfile.GetSeqRowISTDAmount())
    print('GetSeqRowDilutionFactor', rawfile.GetSeqRowDilutionFactor())
    print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=0))
    print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=1))
    print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=2))
    print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=3))
    print('GetSeqRowUserLabel', rawfile.GetSeqRowUserLabel(index=4))
    print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=0))
    print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=1))
    print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=2))
    print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=3))
    print('GetSeqRowUserTextEx', rawfile.GetSeqRowUserTextEx(index=4))
    print('GetSeqRowBarcode', rawfile.GetSeqRowBarcode())
    print('GetSeqRowBarcodeStatus', rawfile.GetSeqRowBarcodeStatus())
    # # # # # # # "View/Report/Sample Information" END
    print('GetNumStatusLog', rawfile.GetNumStatusLog())
    print('GetStatusLogForScanNum')  # "View/Report/Status Log"
    pprint(rawfile.GetStatusLogForScanNum(scan_number))
    print('GetStatusLogForPos(position=0)', rawfile.GetStatusLogForPos(position=0))
    print('GetStatusLogForPos(position=1)', rawfile.GetStatusLogForPos(position=1))
    print('GetStatusLogPlottableIndex()', rawfile.GetStatusLogPlottableIndex())

    print('GetNumErrorLog', rawfile.GetNumErrorLog())
    for i in range(rawfile.GetNumErrorLog()):
        print('GetErrorLogItem', i, rawfile.GetErrorLogItem(i))  # "View/Report/Error Log"
    print('############################################## XCALIBUR INTERFACE END')

    print('GetMassListFromScanNum', rawfile.GetMassListFromScanNum(scan_number))
    print('GetMassListRangeFromScanNum', rawfile.GetMassListRangeFromScanNum(scan_number))
    print('GetSegmentedMassListFromScanNum', rawfile.GetSegmentedMassListFromScanNum(scan_number))
    print('GetAverageMassList', rawfile.GetAverageMassList(scan_number, scan_number + 10))
    print('GetAveragedMassSpectrum', rawfile.GetAveragedMassSpectrum([scan_number, scan_number + 5, scan_number + 10]))
    print('GetSummedMassSpectrum', rawfile.GetSummedMassSpectrum([scan_number, scan_number + 5, scan_number + 10]))
    print('GetLabelData', rawfile.GetLabelData(scan_number))
    print('GetAveragedLabelData', rawfile.GetAveragedLabelData([scan_number, scan_number + 5, scan_number + 10]))
    print('GetAllMSOrderData', rawfile.GetAllMSOrderData(scan_number))
    print('GetChroData', rawfile.GetChroData(startTime=rawfile.StartTime,
                                             endTime=rawfile.EndTime,
                                             massRange1="{}-{}".format(rawfile.LowMass, rawfile.HighMass),
                                             scanFilter="Full ms "))
    # print( 'GetChroByCompoundName', rawfile.GetChroByCompoundName(["methyltestosterone"]) )

    # print( 'GetMassPrecisionEstimate', rawfile.GetMassPrecisionEstimate(scan_number) )

    print('GetFullMSOrderPrecursorDataFromScanNum(scan_number,0)',
          rawfile.GetFullMSOrderPrecursorDataFromScanNum(scan_number, 0))
    print('GetFullMSOrderPrecursorDataFromScanNum(scan_number,1)',
          rawfile.GetFullMSOrderPrecursorDataFromScanNum(scan_number, 1))

    print('GetPrecursorInfoFromScanNum(scan_number,1)', rawfile.GetPrecursorInfoFromScanNum(scan_number))

    with open('test.tsv', 'wt') as f:
        print('\t'.join(map(str, ('scan_number',
                                  'RetentionTime',
                                  'scan_number',
                                  'GetFilterForScanNum(i)',
                                  'GetMSOrderForScanNum(i)',
                                  'GetNumberOfMSOrdersFromScanNum(i)',
                                  'GetScanTypeForScanNum(i)',
                                  'GetDetectorTypeForScanNum(i)',
                                  'GetMassAnalyzerTypeForScanNum(i)',
                                  'GetActivationTypeForScanNum(i,MSOrder=2)',
                                  'IsProfileScanForScanNum(i)',
                                  'IsCentroidScanForScanNum(i)',
                                  'GetIsolationWidthForScanNum(i,MSOrder=1)',
                                  'GetCollisionEnergyForScanNum(i,MSOrder=1)',
                                  'GetPrecursorInfoFromScanNum(i)',
                                  'GetMassCalibrationValueFromScanNum(i,massCalibrationIndex=0)',
                                  'GetScanEventForScanNum(i)',
                                  'GetSegmentAndEventForScanNum(i)',
                                  'GetCycleNumberFromScanNumber(i)',
                                  'GetAValueFromScanNum(i)',
                                  'GetBValueFromScanNum(i)',
                                  'GetKValueFromScanNum(i)',
                                  'GetRValueFromScanNum(i)',
                                  'GetVValueFromScanNum(i)',
                                  'GetMSXMultiplexValueFromScanNum(i)',
                                  'GetCompoundNameFromScanNum(i)',
                                  'GetNumberOfMassRangesFromScanNum(i)',
                                  'GetMassRangeFromScanNum(i,0)',
                                  'GetMassRangeFromScanNum(i,1)',
                                  'GetNumberOfSourceFragmentsFromScanNum(i)',
                                  'GetSourceFragmentValueFromScanNum(i,0)',
                                  'GetNumberOfSourceFragmentationMassRangesFromScanNum(i)'
                                  ))), file=f)

        for i in range(rawfile.FirstSpectrumNumber, rawfile.LastSpectrumNumber + 1):
            print('\t'.join(map(str, (i,
                                      rawfile.RTFromScanNum(i),
                                      rawfile.ScanNumFromRT(rawfile.RTFromScanNum(i)),
                                      rawfile.GetFilterForScanNum(i),
                                      rawfile.GetMSOrderForScanNum(i),
                                      rawfile.GetNumberOfMSOrdersFromScanNum(i),
                                      rawfile.GetScanTypeForScanNum(i),
                                      rawfile.GetDetectorTypeForScanNum(i),
                                      rawfile.GetMassAnalyzerTypeForScanNum(i),
                                      rawfile.GetActivationTypeForScanNum(i, MSOrder=2),
                                      rawfile.IsProfileScanForScanNum(i),
                                      rawfile.IsCentroidScanForScanNum(i),
                                      rawfile.GetIsolationWidthForScanNum(i, MSOrder=1),
                                      rawfile.GetCollisionEnergyForScanNum(i, MSOrder=1),
                                      rawfile.GetPrecursorInfoFromScanNum(i),
                                      rawfile.GetMassCalibrationValueFromScanNum(i, massCalibrationIndex=0),
                                      rawfile.GetScanEventForScanNum(i),
                                      rawfile.GetSegmentAndEventForScanNum(i),
                                      rawfile.GetCycleNumberFromScanNumber(i),
                                      rawfile.GetAValueFromScanNum(i),
                                      rawfile.GetBValueFromScanNum(i),
                                      rawfile.GetKValueFromScanNum(i),
                                      rawfile.GetRValueFromScanNum(i),
                                      rawfile.GetVValueFromScanNum(i),
                                      rawfile.GetMSXMultiplexValueFromScanNum(i),
                                      rawfile.GetCompoundNameFromScanNum(i),
                                      rawfile.GetNumberOfMassRangesFromScanNum(i),
                                      rawfile.GetMassRangeFromScanNum(i, 0),
                                      rawfile.GetMassRangeFromScanNum(i, 1),
                                      rawfile.GetNumberOfSourceFragmentsFromScanNum(i),
                                      rawfile.GetSourceFragmentValueFromScanNum(i, 0),
                                      rawfile.GetNumberOfSourceFragmentationMassRangesFromScanNum(i)
                                      ))), file=f)

    rawfile.Close()