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 GetFirstSpectrumNumber(IXRawfile5 rawFile) { int firstScanNumber = 0; rawFile.GetFirstSpectrumNumber(ref firstScanNumber); return(firstScanNumber); }
protected override int GetFirstSpectrumNumber() { int spectrumNumber = 0; _rawConnection.GetFirstSpectrumNumber(ref spectrumNumber); return(spectrumNumber); }
/// <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 int GetFirstScan() { int startScanNum = 0; rawConnect.GetFirstSpectrumNumber(ref startScanNum); return(startScanNum); }
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 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)); }
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 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)); }