private static int GetMSLevel(IXRawfile5 rawFile, int scanNo)
{
int msLevel = 1;
rawFile.GetMSOrderForScanNum(scanNo, ref msLevel);
return(msLevel);
}
/// <summary>
///
/// </summary>
/// <param name="argFullPath"></param>
/// <param name="argFileType">ThermoRawFile</param>
public ThermoRawReader(string argFullPath)
{
_fullFilePath = argFullPath;
_rawConnection = (IXRawfile5) new MSFileReader_XRawfile();
_rawConnection.Open(argFullPath);
_rawConnection.SetCurrentController(0, 1); // first 0 is for mass spectrometer
}
private static double GetRetentionTime(IXRawfile5 rawFile, int scanNo)
{
double rt = 0;
rawFile.RTFromScanNum(scanNo, ref rt);
return(rt);
}
private static double GetIsolationWindowWidth(IXRawfile5 rawFile, int scanNo, int msLevel)
{
double width = 0;
rawFile.GetIsolationWidthForScanNum(scanNo, msLevel - 1, ref width);
return(width);
}
private static double GetCollisionEnergy(IXRawfile5 rawFile, int scanNo, int msLevel)
{
double e = 0;
rawFile.GetCollisionEnergyForScanNum(scanNo, msLevel - 1, ref e);
return(e);
}
private static double GetPrecursorMz(IXRawfile5 rawFile, int scanNo, int msLevel)
{
double mz = 0;
rawFile.GetPrecursorMassForScanNum(scanNo, msLevel, ref mz);
return(mz);
}
public RawFileConverter(string rawFile, string outFolder, string[] outFileTypes, ExperimentType expType, bool exportChargeState)
{
_rawReader = (IXRawfile5) new MSFileReader_XRawfile();
Console.WriteLine("_rawReader created successfully.");
int pnMajorVersion = -1, pnMinorVersion = -1, pnSubMinorVersion = -1, nBuilderNumber = -1;
_rawReader.Version(ref pnMajorVersion, ref pnMinorVersion, ref pnSubMinorVersion, ref nBuilderNumber);
Console.WriteLine("pnMajorVersion = " + pnMajorVersion);
Console.WriteLine("pnMinorVersion = " + pnMinorVersion);
Console.WriteLine("pnSubMinorVersion = " + pnSubMinorVersion);
Console.WriteLine("nBuilderNumber = " + nBuilderNumber);
_rawReader.Open(rawFile);
Console.WriteLine("_rawReader open file successfully.");
_rawReader.SetCurrentController(0, 1);
rawFileName = rawFile;
// get the numbers of the first and the last scans used in MSn file headers;
_rawReader.GetFirstSpectrumNumber(ref FirstScanNum);
_rawReader.GetLastSpectrumNumber(ref LastScanNum);
outFolder = Path.GetDirectoryName(rawFile);
InitWriters(Path.GetFileName(rawFile), outFolder, outFileTypes, expType, exportChargeState);
this.expType = expType;
}
private static int GetChargeState(IXRawfile5 rawFile, int scanNo)
{
object pChargeValue = null;
rawFile.GetTrailerExtraValueForScanNum(scanNo, "Charge State:", ref pChargeValue);
return(Convert.ToInt32(pChargeValue));
}
private static bool IsCentroidSpectrum(IXRawfile5 rawFile, int scanNo)
{
int isCentroidScan = 0;
rawFile.IsCentroidScanForScanNum(scanNo, ref isCentroidScan);
return(isCentroidScan != 0);
}
public ThermoRawFileReader(string rawFilePath)
{
this.rawFilePath = rawFilePath;
if (string.IsNullOrWhiteSpace(rawFilePath))
{
throw new ArgumentNullException("rawFilePath");
}
if (!File.Exists(rawFilePath))
{
throw new FileNotFoundException("Raw file not exists.");
}
try
{
rawFile = new MSFileReader_XRawfile() as IXRawfile5;
rawFile.Open(rawFilePath);
rawFile.SetCurrentController(0, 1);
startScanNo = GetFirstSpectrumNumber(rawFile);
endScanNo = GetLastSpectrumNumber(rawFile);
model = MzLiteJson.HandleExternalModelFile(this, GetModelFilePath());
}
catch (Exception ex)
{
throw new MzLiteIOException(ex.Message, ex);
}
}
private static int GetFirstSpectrumNumber(IXRawfile5 rawFile)
{
int firstScanNumber = 0;
rawFile.GetFirstSpectrumNumber(ref firstScanNumber);
return(firstScanNumber);
}
private static string GetFilterString(IXRawfile5 rawFile, int scanNo)
{
string filter = null;
rawFile.GetFilterForScanNum(scanNo, ref filter);
return(filter);
}
private static int GetLastSpectrumNumber(IXRawfile5 rawFile)
{
int lastScanNumber = 0;
rawFile.GetLastSpectrumNumber(ref lastScanNumber);
return(lastScanNumber);
}
/// <summary>
/// Reads raw data. Puts spectra into a thread safe queue. Closes queue when done. Parses the rawfile-log into the statusLog object
/// </summary>
/// <param name="raw">Raw file</param>
/// <param name="rawScanQueue">Thread safe queue</param>
private void ReadRawFile(IXRawfile5 raw, BlockingCollection <RawScan> rawScanQueue)
{
int firstScanNumber = -1;
raw.GetFirstSpectrumNumber(ref firstScanNumber);
int lastScanNumber = -1;
raw.GetLastSpectrumNumber(ref lastScanNumber);
for (int scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
{
string scanFilter = null;
raw.GetFilterForScanNum(scanNumber, ref scanFilter);
//read scan header into key/value arrays
object keyRef = null;
object valueRef = null;
int indexRef = 0;
raw.GetTrailerExtraForScanNum(scanNumber, ref keyRef, ref valueRef, ref indexRef);
string[] trailerKeys = (string[])keyRef;
string[] trailerValues = (string[])valueRef;
//read tic and base peak mass using dummy variables
double tic = 0.0;
int int1 = 0;
int int2 = 0;
int int3 = 0;
double double1 = 0.0;
double double2 = 0.0;
double double3 = 0.0;
double basePeakMass = 0.0;
double double5 = 0.0;
double double6 = 0.0;
raw.GetScanHeaderInfoForScanNum(scanNumber, ref int1, ref double1, ref double2, ref double3, ref tic, ref basePeakMass, ref double5, ref int2, ref int3, ref double6);
//read data (mz,int,...) using dummy variables
object labels_obj = null;
object flags_obj = null;
raw.GetLabelData(ref labels_obj, ref flags_obj, ref scanNumber);
double[,] data = (double[, ])labels_obj;
//read precursorMz
double precursorMz = 0.0;
raw.GetPrecursorMassForScanNum(scanNumber, 2, ref precursorMz);
RawScan rawScan = new RawScan(scanNumber, scanFilter, tic, trailerKeys, trailerValues, data, precursorMz, basePeakMass);
rawScanQueue.Add(rawScan);
//read status log
double rtLog = 0.0;
object statuslogKeys = null;
object statuslogValues = null;
int statuslogN = 0;
raw.GetStatusLogForScanNum(scanNumber, ref rtLog, ref statuslogKeys, ref statuslogValues, ref statuslogN);
statusLog.Add(rtLog, (string[])statuslogKeys, (string[])statuslogValues);
}
rawScanQueue.CompleteAdding();
Log.Information("Read all spectra in base module");
}
public void Init()
{
_rawConnect = new MSFileReader_XRawfile() as IXRawfile5;
_rawReader = new RawReader();
fullSpecGetter = new FullMSSpectrumGetter();
nSpecGetter = new MSnSpectrumGetter();
specParamGetter = new GeneralSpectrumGetter();
}
public override void Dispose()
{
if (_rawConnection != null)
{
_rawConnection.Close();
_rawConnection = null;
}
base.Dispose();
}
public static ThermoDynamicData InitiateDynamicConnection(string filePath, IFilteringParams filterParams = null)
{
if (!File.Exists(filePath))
{
throw new FileNotFoundException();
}
if (!ThermoStaticData.CheckForMsFileReader())
{
throw new MzLibException("MsFileReader Not Installed");
}
IXRawfile5 _rawConnection = (IXRawfile5) new MSFileReader_XRawfile();
_rawConnection.Open(filePath);
_rawConnection.SetCurrentController(0, 1);
int lastspectrumNumber = -1;
_rawConnection.GetLastSpectrumNumber(ref lastspectrumNumber);
int firstspectrumNumber = -1;
_rawConnection.GetFirstSpectrumNumber(ref firstspectrumNumber);
var precursorInfoArray = new ManagedThermoHelperLayer.PrecursorInfo[lastspectrumNumber - firstspectrumNumber + 1];
string sendCheckSum;
using (FileStream stream = File.OpenRead(filePath))
{
using (SHA1Managed sha = new SHA1Managed())
{
byte[] checksum = sha.ComputeHash(stream);
sendCheckSum = BitConverter.ToString(checksum)
.Replace("-", string.Empty);
}
}
SourceFile sourceFile = new SourceFile(
@"Thermo nativeID format",
@"Thermo RAW format",
sendCheckSum,
@"SHA-1",
filePath,
Path.GetFileNameWithoutExtension(filePath));
var thermoGlobalParams = ThermoStaticData.GetAllGlobalStuff(_rawConnection, precursorInfoArray, filePath);
// if the spectra file only contains 1 scan and its MS order is 0, this indicates an errored read result
if (thermoGlobalParams.MsOrderByScan.Length == 1 && thermoGlobalParams.MsOrderByScan[0] == 0)
{
throw new MzLibException("Could not read data from file " + Path.GetFileName(filePath));
}
return(new ThermoDynamicData(_rawConnection, filterParams, lastspectrumNumber - firstspectrumNumber + 1, sourceFile, thermoGlobalParams));
}
public ThermoRawReader(string argFullPath)
{
//Check if XRawfle2.dll exist
CheckDLL();
_fullFilePath = argFullPath;
//Open
_rawConnection = (IXRawfile5)new MSFileReader_XRawfile();
_rawConnection.Open(_fullFilePath);
_rawConnection.SetCurrentController(0, 1); // first 0 is for mass spectrometer
}
protected override void Dispose(bool disposing)
{
if (disposing)
{
if (_rawConnection != null)
{
_rawConnection.Close();
_rawConnection = null;
}
}
base.Dispose(disposing);
}
public RawFileImpl()
{
try
{
this.rawFile = new MSFileReader_XRawfile() as IXRawfile5;
}
catch (Exception)
{
throw new Exception("Reading Thermo RAW files requires MSFileReader to be installed. It is available for download at: http://sjsupport.thermofinnigan.com/public/detail.asp?id=703");
}
this.valid = false;
this.FileName = string.Empty;
}
public ThermoRawReader(string argFullPath)
{
//Check if XRawfle2.dll exist
CheckDLL();
_fullFilePath = argFullPath;
//Open
_rawConnection = (IXRawfile5) new MSFileReader_XRawfile();
_rawConnection.Open(_fullFilePath);
_rawConnection.SetCurrentController(0, 1); // first 0 is for mass spectrometer
}
public override void Open()
{
if (_rawConnection != null)
{
return;
}
if (!File.Exists(FilePath) && !Directory.Exists(FilePath))
{
throw new IOException(string.Format("The MS data file {0} does not currently exist", FilePath));
}
_rawConnection = (IXRawfile5) new MSFileReader_XRawfile();
_rawConnection.Open(FilePath);
_rawConnection.SetCurrentController(0, 1); // first 0 is for mass spectrometer
}
public RawFileProcessing(IXRawfile5 raw, string rawFileName, SettingsForAnalysis settingName)
{
//open rawfile (add error check)
raw.Open(rawFileName);
raw.SetCurrentController(0, 1);
raw.GetCreationDate(ref _msStart);
double endtime = 0.0;
raw.GetEndTime(ref endtime);
_msEnd = _msStart.AddMinutes(endtime);
_filecreation = File.GetCreationTime(rawFileName);
raw.GetWarningMessage(ref WarningMessage);
ProcessScans(raw, settingName);
raw.Close();
ReduceToMetaVariables(settingName);
}
public static ThermoDynamicData InitiateDynamicConnection(string filePath, IFilteringParams filterParams = null)
{
if (CheckForMsFileReader() == false)
{
throw new MzLibException("MsFileReader Not Installed");
}
IXRawfile5 _rawConnection = (IXRawfile5) new MSFileReader_XRawfile();
_rawConnection.Open(filePath);
_rawConnection.SetCurrentController(0, 1);
int lastspectrumNumber = -1;
_rawConnection.GetLastSpectrumNumber(ref lastspectrumNumber);
int firstspectrumNumber = -1;
_rawConnection.GetFirstSpectrumNumber(ref firstspectrumNumber);
var precursorInfoArray = new ManagedThermoHelperLayer.PrecursorInfo[lastspectrumNumber - firstspectrumNumber + 1];
string sendCheckSum;
using (FileStream stream = File.OpenRead(filePath))
{
using (SHA1Managed sha = new SHA1Managed())
{
byte[] checksum = sha.ComputeHash(stream);
sendCheckSum = BitConverter.ToString(checksum)
.Replace("-", string.Empty);
}
}
SourceFile sourceFile = new SourceFile(
@"Thermo nativeID format",
@"Thermo RAW format",
sendCheckSum,
@"SHA-1",
filePath,
Path.GetFileNameWithoutExtension(filePath));
var thermoGlobalParams = GetAllGlobalStuff(_rawConnection, precursorInfoArray, filePath);
return(new ThermoDynamicData(_rawConnection, filterParams, lastspectrumNumber - firstspectrumNumber + 1, precursorInfoArray, sourceFile, thermoGlobalParams));
}
/// <summary>
/// Read and parse all spectra, spawns a task.
/// </summary>
/// <param name="raw">Raw file</param>
/// <param name="msScanParameters">Parameters</param>
private void ProcessScans(IXRawfile5 raw, SettingsForAnalysis msScanParameters)
{
BlockingCollection <RawScan> rawScanQueue = new BlockingCollection <RawScan>();
List <Task <Tuple <List <MsScan>, List <Ms2Scan> > > > parseTaskList = new List <Task <Tuple <List <MsScan>, List <Ms2Scan> > > >();
for (int i = 0; i < 1; i++)//option here to increase threading if computations get more complicated - note possible problem with unsorted spectra?
{
parseTaskList.Add(Task.Run(() =>
{
return(ParseSpectra(rawScanQueue, msScanParameters));
}));
}
ReadRawFile(raw, rawScanQueue);
Task.WaitAll(parseTaskList.ToArray());
foreach (Task <Tuple <List <MsScan>, List <Ms2Scan> > > resultTask in parseTaskList)
{
this.msScanList.AddRange(resultTask.Result.Item1);
this.ms2ScanList.AddRange(resultTask.Result.Item2);
}
}
public static ThermoGlobalParams GetAllGlobalStuff(IXRawfile5 _rawConnection, ManagedThermoHelperLayer.PrecursorInfo[] couldBePrecursor, string filePath)
{
int pnNumInstMethods = 0;
_rawConnection.GetNumInstMethods(ref pnNumInstMethods);
string[] instrumentMethods = new string[pnNumInstMethods];
for (int nInstMethodItem = 0; nInstMethodItem < pnNumInstMethods; nInstMethodItem++)
{
string pbstrInstMethod = null;
_rawConnection.GetInstMethod(nInstMethodItem, ref pbstrInstMethod);
instrumentMethods[nInstMethodItem] = pbstrInstMethod;
}
string pbstrInstSoftwareVersion = null;
_rawConnection.GetInstSoftwareVersion(ref pbstrInstSoftwareVersion);
string pbstrInstName = null;
_rawConnection.GetInstName(ref pbstrInstName);
string pbstrInstModel = null;
_rawConnection.GetInstModel(ref pbstrInstModel);
int pnControllerNumber = 0;
int pnControllerType = 0;
_rawConnection.GetCurrentController(ref pnControllerType, ref pnControllerNumber);
int[] msOrderByScan = new int[couldBePrecursor.Length];
for (int i = 0; i < couldBePrecursor.Length; i++)
{
_rawConnection.GetMSOrderForScanNum((i + 1), ref msOrderByScan[i]);
}
return(new ThermoGlobalParams(pnNumInstMethods, instrumentMethods, pbstrInstSoftwareVersion, pbstrInstName, pbstrInstModel, pnControllerType, pnControllerNumber, couldBePrecursor, filePath, msOrderByScan));
}
public static ThermoStaticData LoadAllStaticData(string filePath, IFilteringParams filterParams = null)
{
if (!File.Exists(filePath))
{
throw new FileNotFoundException();
}
if (CheckForMsFileReader() == false)
{
throw new MzLibException("MsFileReader Not Installed");
}
var ok = new ManagedThermoHelperLayer.HelperClass();
IXRawfile5 theConnection = (IXRawfile5) new MSFileReader_XRawfile();
theConnection.Open(filePath);
int pbSMData = 0;
theConnection.IsThereMSData(ref pbSMData);
if (pbSMData == 0)
{
throw new MzLibException("Could not read data from file " + Path.GetFileName(filePath));
}
theConnection.SetCurrentController(0, 1);
var precursorInfosArray = ok.GetAllPrecursorInfos(filePath);
for (int i = 0; i < precursorInfosArray.Length; i++)
{
if (precursorInfosArray[i].nScanNumber == 0)
{
precursorInfosArray[i].nScanNumber = -1;
}
}
int pnFirstSpectrum = 0;
theConnection.GetFirstSpectrumNumber(ref pnFirstSpectrum);
int pnLastSpectrum = 0;
theConnection.GetLastSpectrumNumber(ref pnLastSpectrum);
ThermoGlobalParams p = GetAllGlobalStuff(theConnection, precursorInfosArray, filePath);
MsDataScan[] scans = new MsDataScan[pnLastSpectrum - pnFirstSpectrum + 1];
for (int nScanNumber = pnFirstSpectrum; nScanNumber <= pnLastSpectrum; nScanNumber++)
{
scans[nScanNumber - pnFirstSpectrum] = GetMsDataOneBasedScanFromThermoFile(theConnection, nScanNumber, p, filterParams);
}
theConnection.Close();
string sendCheckSum;
using (FileStream stream = File.OpenRead(filePath))
{
using (SHA1Managed sha = new SHA1Managed())
{
byte[] checksum = sha.ComputeHash(stream);
sendCheckSum = BitConverter.ToString(checksum)
.Replace("-", string.Empty);
}
}
SourceFile sourceFile = new SourceFile(
@"Thermo nativeID format",
@"Thermo RAW format",
sendCheckSum,
@"SHA-1",
filePath,
Path.GetFileNameWithoutExtension(filePath));
return(new ThermoStaticData(scans, p, sourceFile));
}
/// <summary>
/// Opens the connection to the underlying data
/// </summary>
public override void Open()
{
if (IsOpen && _rawConnection != null)
return;
if (!File.Exists(FilePath) && !Directory.Exists(FilePath))
{
throw new IOException(string.Format("The MS data file {0} does not currently exist", FilePath));
}
_rawConnection = (IXRawfile5)new MSFileReader_XRawfile();
_rawConnection.Open(FilePath);
_rawConnection.SetCurrentController(0, 1); // first 0 is for mass spectrometer
base.Open();
}
/// <summary>
///
/// </summary>
/// <param name="argFullPath"></param>
/// <param name="argFileType">ThermoRawFile</param>
public ThermoRawReader(string argFullPath)
{
_fullFilePath = argFullPath;
_rawConnection = (IXRawfile5)new MSFileReader_XRawfile();
_rawConnection.Open(argFullPath);
_rawConnection.SetCurrentController(0, 1); // first 0 is for mass spectrometer
}
public void CloseRawFile()
{
try
{
if ((mXRawFile != null))
{
mXRawFile.Close();
}
mCorruptMemoryEncountered = false;
}
catch (AccessViolationException)
{
// Ignore this error
}
catch (Exception)
{
// Ignore any errors
}
finally
{
mXRawFile = null;
mCachedFileName = string.Empty;
mFileInfo.Clear();
}
}
/// <summary>
/// Open the .raw file
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
public bool OpenRawFile(string filePath)
{
var intResult = 0;
var success = false;
try
{
// Make sure any existing open files are closed
CloseRawFile();
mCachedScanInfo.Clear();
if (mXRawFile == null)
{
// ReSharper disable once SuspiciousTypeConversion.Global
mXRawFile = new MSFileReader_XRawfile() as IXRawfile5;
}
if (mXRawFile == null)
{
throw new Exception("Could not instantiate an instance of MSFileReader_XRawfile");
}
mXRawFile.Open(filePath);
mXRawFile.IsError(ref intResult);
// Unfortunately, .IsError() always returns 0, even if an error occurred
if (intResult == 0)
{
mCachedFileName = filePath;
if (FillFileInfo())
{
if (mFileInfo.ScanStart == 0 && mFileInfo.ScanEnd == 0 && mFileInfo.VersionNumber == 0 && Math.Abs(mFileInfo.MassResolution - 0) < double.Epsilon && mFileInfo.InstModel == null)
{
// File actually didn't load correctly, since these shouldn't all be blank
success = false;
mFileInfo.CorruptFile = true;
}
else
{
success = true;
}
}
else
{
success = false;
}
}
else
{
success = false;
}
}
catch (Exception)
{
success = false;
}
finally
{
if (!success)
{
mCachedFileName = string.Empty;
}
}
return success;
}
protected ThermoFile(IXRawfile5 _rawConnection, int numSpectra, ManagedThermoHelperLayer.PrecursorInfo[] couldBePrecursor, SourceFile sourceFile, ThermoGlobalParams thermoGlobalParams) : base(numSpectra, sourceFile)
{
this.ThermoGlobalParams = thermoGlobalParams;
}
public ThermoRawSpectrumReader()
{
rawConnect = new MSFileReader_XRawfile() as IXRawfile5;
}
public static MsDataScan GetMsDataOneBasedScanFromThermoFile(IXRawfile5 theConnection, int nScanNumber, ThermoGlobalParams globalParams, IFilteringParams filterParams = null)
{
int pnNumPackets = 0;
double pdLowMass = 0;
double pdHighMass = 0;
double pdTIC = 0;
double pdBasePeakMass = 0;
double pdBasePeakIntensity = 0;
int pnNumChannels = 0;
int pbUniformTime = 0;
double pdFrequency = 0;
double pdStartTime = 0;
theConnection.GetScanHeaderInfoForScanNum(nScanNumber, ref pnNumPackets, ref pdStartTime, ref pdLowMass, ref pdHighMass, ref pdTIC, ref pdBasePeakMass, ref pdBasePeakIntensity, ref pnNumChannels, ref pbUniformTime, ref pdFrequency);
double?ms2isolationWidthFromTrailerExtra = null;
double?injectionTimeFromTrailerExtra = null;
double?precursorMonoisotopicMZfromTrailierExtra = null;
int? chargeStatefromTrailierExtra = null;
int? masterScanfromTrailierExtra = null;
object pvarValues = null;
object pvarLables = null;
int pnArraySize = 0;
theConnection.GetTrailerExtraForScanNum(nScanNumber, ref pvarLables, ref pvarValues, ref pnArraySize);
string[] labels = (string[])pvarLables;
string[] values = (string[])pvarValues;
for (int i = labels.GetLowerBound(0); i <= labels.GetUpperBound(0); i++)
{
if (labels[i].StartsWith("MS2 Isolation Width", StringComparison.Ordinal))
{
ms2isolationWidthFromTrailerExtra = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Ion Injection Time (ms)", StringComparison.Ordinal))
{
injectionTimeFromTrailerExtra = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Monoisotopic M/Z", StringComparison.Ordinal))
{
precursorMonoisotopicMZfromTrailierExtra = double.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(double?)null :
double.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Charge State", StringComparison.Ordinal))
{
chargeStatefromTrailierExtra = int.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(int?)null :
int.Parse(values[i], CultureInfo.InvariantCulture);
}
if (labels[i].StartsWith("Master Scan Number", StringComparison.Ordinal))
{
masterScanfromTrailierExtra = int.Parse(values[i], CultureInfo.InvariantCulture) == 0 ?
(int?)null :
int.Parse(values[i], CultureInfo.InvariantCulture);
}
}
string pbstrFilter = null;
theConnection.GetFilterForScanNum(nScanNumber, ref pbstrFilter);
int pnMSOrder = 0;
theConnection.GetMSOrderForScanNum(nScanNumber, ref pnMSOrder);
int pnMassAnalyzerType = 0;
theConnection.GetMassAnalyzerTypeForScanNum(nScanNumber, ref pnMassAnalyzerType);
object pvarNoisePacket = null;
try //if there is no noise data
{
theConnection.GetNoiseData(ref pvarNoisePacket, nScanNumber);
}
catch
{
//pvarNoisePAcket is already null
}
double[,] noiseData = pvarNoisePacket as double[, ];
double[,] data;
try
{
object pvarFlags = null;
object pvarLabels = null;
theConnection.GetLabelData(ref pvarLabels, ref pvarFlags, ref nScanNumber);
data = pvarLabels as double[, ];
if (data == null || data.Length == 0)
{
throw new MzLibException("For spectrum number " + nScanNumber + " the data is null!");
}
}
catch (MzLibException)
{
// Warning: the masses reported by GetMassListFromScanNum when centroiding are not properly calibrated and thus could be off by 0.3 m/z or more
double pdCentroidPeakWidth = 0;
object pvarnMassList = null;
object pvarPeakFlags = null;
theConnection.GetMassListFromScanNum(ref nScanNumber, null, 0, 0, 0, 1, ref pdCentroidPeakWidth, ref pvarnMassList, ref pvarPeakFlags, ref pnArraySize);
data = (double[, ])pvarnMassList;
}
MzSpectrum thermoSpectrum;
if (filterParams != null && data.GetLength(1) > 0 && (filterParams.MinimumAllowedIntensityRatioToBasePeakM.HasValue || filterParams.NumberOfPeaksToKeepPerWindow.HasValue) && ((filterParams.ApplyTrimmingToMs1 && pnMSOrder == 1) || (filterParams.ApplyTrimmingToMsMs && pnMSOrder > 1)))
{
var count = data.GetLength(1);
var mzArray = new double[count];
var intensityArray = new double[count];
Buffer.BlockCopy(data, 0, mzArray, 0, sizeof(double) * count);
Buffer.BlockCopy(data, sizeof(double) * count, intensityArray, 0, sizeof(double) * count);
if (filterParams.NumberOfWindows == null)
{
int numPeaks = TopNpeakHelper(ref intensityArray, ref mzArray, filterParams);
//the following arrays are modified after TopN helper
Array.Resize(ref intensityArray, numPeaks);
Array.Resize(ref mzArray, numPeaks);
}
//Array reference passed by value, array calues will be modified after calling
else
{
WindowModeHelper(ref intensityArray, ref mzArray, filterParams);
}
Array.Sort(mzArray, intensityArray);
thermoSpectrum = new MzSpectrum(mzArray, intensityArray, false);
}
else
{
thermoSpectrum = new MzSpectrum(data);
}
MZAnalyzerType mzAnalyzerType;
if ((ThermoMzAnalyzer)pnMassAnalyzerType == ThermoMzAnalyzer.FTMS)
{
mzAnalyzerType = MZAnalyzerType.Orbitrap;
}
else
{
mzAnalyzerType = MZAnalyzerType.Unknown;
}
string nativeId = "controllerType=0 controllerNumber=1 scan=" + nScanNumber;
if (pnMSOrder > 1)
{
int pnActivationType = 0;
theConnection.GetActivationTypeForScanNum(nScanNumber, pnMSOrder, ref pnActivationType);
// INITIALIZE globalParams.couldBePrecursor[nScanNumber - 1] (for dynamic connections that don't have it initialized yet)
if (globalParams.CouldBePrecursor[nScanNumber - 1].Equals(default(ManagedThermoHelperLayer.PrecursorInfo)))
{
var ok = new ManagedThermoHelperLayer.HelperClass();
globalParams.CouldBePrecursor[nScanNumber - 1] = ok.GetSingleScanPrecursorInfo(nScanNumber, globalParams.FilePath);
}
var precursorInfo = globalParams.CouldBePrecursor[nScanNumber - 1];
// THIS METHOD IS BUGGY!!! DO NOT USE
//theConnection.FindPrecursorMassInFullScan(nScanNumber, ref pnMasterScan, ref pdFoundMass, ref pdHeaderMass, ref pnChargeState);
int oneBasedPrecursorScanNumber = -1;
if (precursorInfo.nScanNumber > 0)
{
oneBasedPrecursorScanNumber = precursorInfo.nScanNumber;
}
else if (masterScanfromTrailierExtra.HasValue && masterScanfromTrailierExtra > 0)
{
oneBasedPrecursorScanNumber = masterScanfromTrailierExtra.Value;
}
else
{
// we weren't able to get the precursor scan number, so we'll have to guess;
// loop back to find precursor scan
// (assumed to be the first scan before this scan with an MS order of this scan's MS order - 1)
// e.g., if this is an MS2 scan, find the first MS1 scan before this and assume that's the precursor scan
int scanOrder = globalParams.MsOrderByScan[nScanNumber - 1];
int precursorScanOrder = scanOrder - 1;
for (int i = nScanNumber - 1; i >= 0; i--)
{
int msOrder = globalParams.MsOrderByScan[i];
if (msOrder == precursorScanOrder)
{
oneBasedPrecursorScanNumber = i + 1;
break;
}
}
}
if (oneBasedPrecursorScanNumber == -1)
{
throw new MzLibException("Could not find precursor info for scan #" + nScanNumber);
}
int?selectedIonGuessChargeStateGuess = null;
if (precursorInfo.nChargeState > 0)
{
selectedIonGuessChargeStateGuess = precursorInfo.nChargeState;
}
else if (chargeStatefromTrailierExtra.HasValue)
{
selectedIonGuessChargeStateGuess = chargeStatefromTrailierExtra;
}
double?selectedIonGuessMonoisotopicMz = null;
if (precursorMonoisotopicMZfromTrailierExtra.HasValue && precursorMonoisotopicMZfromTrailierExtra.Value > 0)
{
selectedIonGuessMonoisotopicMz = precursorMonoisotopicMZfromTrailierExtra;
}
if (precursorInfo.dMonoIsoMass > 0 && !selectedIonGuessMonoisotopicMz.HasValue)
{
selectedIonGuessMonoisotopicMz = precursorInfo.dMonoIsoMass;
}
Regex matcher;
if (pbstrFilter.ToLower().Contains("msx"))
{
matcher = mFindParentIonOnlyMsx;
}
else
{
matcher = mFindParentIonOnlyNonMsx;
}
double selectedIonGuessMZ = double.Parse(matcher.Match(pbstrFilter).Groups["ParentMZ"].Value);
// int? selectedIonChargeStateGuess, double? selectedIonIntensity, double? isolationMZ, double? isolationWidth, DissociationType dissociationType, int? oneBasedPrecursorScanNumber, double? selectedIonMonoisotopicGuessMz, double? injectionTime, double[,] noiseData, string nativeId)
// double TotalIonCurrent, double selectedIonMZ, int? selectedIonChargeStateGuess, double? selectedIonIntensity, double? isolationMZ, double? isolationWidth, DissociationType dissociationType, int? oneBasedPrecursorScanNumber, double? selectedIonMonoisotopicGuessMz, double? injectionTime, double[,] noiseData, string nativeId)
return(new MsDataScan(
thermoSpectrum,
nScanNumber,
pnMSOrder,
true,
PolarityRegex.IsMatch(pbstrFilter) ? Polarity.Positive : Polarity.Negative,
pdStartTime,
new MzRange(pdLowMass, pdHighMass),
pbstrFilter,
mzAnalyzerType,
pdTIC,
injectionTimeFromTrailerExtra,
noiseData,
nativeId,
selectedIonGuessMZ,
selectedIonGuessChargeStateGuess,
null,
selectedIonGuessMZ,
ms2isolationWidthFromTrailerExtra,
(DissociationType)pnActivationType,
oneBasedPrecursorScanNumber,
selectedIonGuessMonoisotopicMz
));
}
else
{
return(new MsDataScan(
thermoSpectrum,
nScanNumber,
1,
true,
PolarityRegex.IsMatch(pbstrFilter) ? Polarity.Positive : Polarity.Negative,
pdStartTime,
new MzRange(pdLowMass, pdHighMass),
pbstrFilter,
mzAnalyzerType,
pdTIC,
injectionTimeFromTrailerExtra,
noiseData,
nativeId));
}
}
private void SaveDataToCdf(MsSpectrum spec, string fpath)
{
DataSetFactory.SearchFolder("Microsoft.Research.Science.Data.NetCDF4.dll");
DataSetFactory.SearchFolder("Microsoft.Research.Science.Data.dll");
DataSetFactory.SearchFolder("Microsoft.Research.Science.Data.Imperative.dll");
int nControllerType = 0; // 0 == mass spec device
int nContorllerNumber = 1; // first MS device
int totalNumScans = 0; // Number of scans
int firstScanNumber = 0, lastScanNumber = -1; // Number of first and last scan
string scanFilter = null; // Scan filter line
int numDataPoints = -1; // points in both the m/z and intensity arrays
double retentionTimeInMinutes = -1;
double minObservedMZ = -1;
double maxObservedMZ = -1;
double totalIonCurrent = -1;
double basePeakMZ = -1;
double basePeakIntensity = -1;
int channel = 0; // unused
int uniformTime = 0; // unused
double frequency = 0; // unused
int arraySize = -1;
object rawData = null; // rawData wil come as Double[,]
object peakFlags = null;
string szFilter = null; // No filter
int intensityCutoffType = 1; // No cutoff
int intensityCutoffValue = 0; // No cutoff
int maxNumberOfPeaks = 0; // 0 : return all data peaks
double centroidPeakWidth = 0; // No centroiding
int centroidThisScan = 0; // No centroiding
DateTime creationDate = DateTime.MinValue;
var scanPath = Path.Combine(fpath, $"{spec.Id}.cdf");
var cdf = DataSet.Open(scanPath);
cdf.IsAutocommitEnabled = false;
AddMetadata(cdf);
IXRawfile5 rawFile = (IXRawfile5) new MSFileReader_XRawfile();
rawFile.Open(spec.RawFilePath);
rawFile.SetCurrentController(nControllerType, nContorllerNumber);
rawFile.GetNumSpectra(ref totalNumScans);
rawFile.GetFirstSpectrumNumber(ref firstScanNumber);
rawFile.GetLastSpectrumNumber(ref lastScanNumber);
rawFile.GetCreationDate(ref creationDate);
var massVar = cdf.Add <double>("mass_values", new[] { "point_number" });
var intensities = cdf.Add <Int32>("intensity_values", new[] { "point_number" });
var acqTimeVar = cdf.Add <double>("scan_acquisition_time", new[] { "scan_number" });
var scIndexVar = cdf.Add <int>("scan_index", new[] { "scan_number" });
var scCountVar = cdf.Add <int>("point_count", new[] { "scan_number" });
var totalIntensityVar = cdf.Add <double>("total_intensity", new[] { "scan_number" });
massVar.Metadata["scale_factor"] = 1.0;
intensities.Metadata["scale_factor"] = 1.0;
try
{
var retTimes = new double[lastScanNumber];
var ticArr = new double[lastScanNumber];
var scanIndex = new Int32[lastScanNumber];
var pointCount = new Int32[lastScanNumber];
for (int curScanNum = firstScanNumber; curScanNum <= lastScanNumber; curScanNum++)
{
rawFile.GetScanHeaderInfoForScanNum(curScanNum,
ref numDataPoints,
ref retentionTimeInMinutes,
ref minObservedMZ,
ref maxObservedMZ,
ref totalIonCurrent,
ref basePeakMZ,
ref basePeakIntensity,
ref channel, // unused
ref uniformTime, // unused
ref frequency // unused
);
scanFilter = null;
rawFile.GetFilterForScanNum(curScanNum, ref scanFilter);
peakFlags = null;
centroidPeakWidth = 0;
arraySize = 0;
intensityCutoffType = 1;
intensityCutoffValue = (int)(0.001 * basePeakIntensity);
rawFile.GetMassListFromScanNum(
ref curScanNum,
szFilter, // filter
intensityCutoffType, // intensityCutoffType
intensityCutoffValue, // intensityCutoffValue
maxNumberOfPeaks, // maxNumberOfPeaks
centroidThisScan, // centroid result?
ref centroidPeakWidth, // centroidingPeakWidth
ref rawData, // daw data
ref peakFlags, // peakFlags
ref arraySize); // array size
;
var datArray = (Array)rawData;
var massArr = new double[arraySize];
var intArr = new int[arraySize];
for (var j = 0; j < arraySize; j++)
{
massArr[j] = (double)datArray.GetValue(0, j);
intArr[j] = Convert.ToInt32(datArray.GetValue(1, j));
}
//Console.Write($"curScan = {curScanNum}\n");
var ind = curScanNum - 1;
pointCount[ind] = arraySize;
if (ind == 0)
{
scanIndex[ind] = 0;
scanIndex[ind + 1] = arraySize;
}
else
{
scanIndex[ind] += scanIndex[ind - 1];
if (ind + 1 < lastScanNumber)
{
scanIndex[ind + 1] = arraySize;
}
}
retTimes[ind] = TimeSpan.FromMinutes(retentionTimeInMinutes).TotalSeconds;
ticArr[ind] = totalIonCurrent;
massVar.Append(massArr);
intensities.Append(intArr);
rawData = null;
}
totalIntensityVar.PutData(ticArr);
scIndexVar.PutData(scanIndex);
acqTimeVar.PutData(retTimes);
scCountVar.PutData(pointCount);
cdf.Commit();
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
finally
{
cdf.Dispose();
rawFile.Close();
}
}
private ThermoDynamicData(IXRawfile5 _rawConnection, IFilteringParams filterParams, int numSpectra, ManagedThermoHelperLayer.PrecursorInfo[] couldBePrecursor, SourceFile sourceFile, ThermoGlobalParams thermoGlobalParams) : base(_rawConnection, numSpectra, couldBePrecursor, sourceFile, thermoGlobalParams)
{
this._rawConnection = _rawConnection;
this.filterParams = filterParams;
}
