private void InitMzXMLFile()
{
int scanCount = LastScanNum - FirstScanNum + 1;
double startTime = 0, endTime = 0;
_rawReader.GetStartTime(ref startTime);
_rawReader.GetEndTime(ref endTime);
// get the instrument model
String msModel = null;
_rawReader.GetInstModel(ref msModel);
// get acquisition software version
String softwareVersion = null;
_rawReader.GetInstSoftwareVersion(ref softwareVersion);
String filter = null;
_rawReader.GetFilterForScanNum(FirstScanNum, ref filter);
String rawConverterVersion = "1.0.0.x";
_mzXMLWriter.WriteHeader(scanCount, startTime * 60, endTime * 60, rawFileName, "Thermo Scientific",
msModel, "nanoelectrospray", msModel, msModel, "acquisition", "Xcalibur", softwareVersion, rawConverterVersion);
}
public bool IsCIDScan(int argScanNum)
{
string filter = null;
_rawConnection.GetFilterForScanNum(argScanNum, ref filter);
if (filter.ToLower().Contains("cid"))
{
return(true);
}
return(false);
}
private static string GetFilterString(IXRawfile5 rawFile, int scanNo)
{
string filter = null;
rawFile.GetFilterForScanNum(scanNo, ref filter);
return(filter);
}
public string GetScanFilter(int spectrumNumber)
{
string filter = null;
_rawConnection.GetFilterForScanNum(spectrumNumber, ref filter);
return(filter);
}
/// <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");
}
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();
}
}
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));
}
}
