public static void TestReadRaw()
{
try
{
var dataFilePath = @"..\..\Data\Angiotensin_AllScans.raw";
var reader = new pwiz.ProteowizardWrapper.MSDataFileReader(dataFilePath);
var isABSciexFile = reader.IsABFile;
var isThermoFile = reader.IsThermoFile;
Console.WriteLine();
Console.WriteLine(System.IO.Path.GetFileName(dataFilePath) + " IsABSciexFile: " + isABSciexFile);
Console.WriteLine(System.IO.Path.GetFileName(dataFilePath) + " IsThermoFile: " + isThermoFile);
for (var targetIndex = 1; targetIndex < reader.SpectrumCount; targetIndex *= 2)
{
var spectrum = reader.GetSpectrum(targetIndex);
Console.WriteLine("Spectrum at index {0,-4} is scan {1,-45} with {2,4} points", targetIndex, spectrum.NativeId, spectrum.Mzs.Length);
}
}
catch (Exception ex)
{
Console.WriteLine("Error: " + ex.Message);
}
}
public MzRun(string datasetFilePath)
: this()
{
var fileInfo = new FileInfo(datasetFilePath);
if (!fileInfo.Exists)
{
throw new FileNotFoundException("Cannot initialize Run. File not found: " + datasetFilePath);
}
var fileExtension = Path.GetExtension(datasetFilePath).ToLower();
switch (fileExtension)
{
case ".mzxml":
MSFileType = Globals.MSFileType.MZXML_Rawdata;
break;
case ".mzml":
MSFileType = Globals.MSFileType.MZML;
break;
case ".mz5":
MSFileType = Globals.MSFileType.MZ5;
break;
default:
throw new IOException("Cannot initialize Run. File extension " + fileExtension + " isn't supported. The following file extensions are supported: mzXML, mzML, and mz5");
}
DatasetFileOrDirectoryPath = datasetFilePath;
var baseFilename = Path.GetFileName(DatasetFileOrDirectoryPath);
DatasetName = baseFilename.Substring(0, baseFilename.LastIndexOf('.'));
DatasetDirectoryPath = Path.GetDirectoryName(DatasetFileOrDirectoryPath);
_reader = new pwiz.ProteowizardWrapper.MSDataFileReader(datasetFilePath);
MinLCScan = GetMinPossibleLCScanNum();
MaxLCScan = GetMaxPossibleLCScanNum();
}
public static void TestReadBruker()
{
try
{
var dataFilePath = @"\\proto-6\12T_FTICR_B\2014_4\2014_09_30_Stegen_ALK-3_ACN_Core05-org-1_000001\2014_09_30_Stegen_ALK-3_ACN_Core05-org-1_000001.d";
var reader = new pwiz.ProteowizardWrapper.MSDataFileReader(dataFilePath);
var isABSciexFile = reader.IsABFile;
var isThermoFile = reader.IsThermoFile;
Console.WriteLine();
Console.WriteLine(System.IO.Path.GetFileName(dataFilePath) + " IsABSciexFile: " + isABSciexFile);
Console.WriteLine(System.IO.Path.GetFileName(dataFilePath) + " IsThermoFile: " + isThermoFile);
const int targetIndex = 0;
var spectrum = reader.GetSpectrum(targetIndex);
Console.WriteLine("Spectrum at index {0} is scan {1} with {2} points", targetIndex, spectrum.NativeId, spectrum.Mzs.Length);
}
catch (Exception ex)
{
Console.WriteLine("Error: " + ex.Message);
}
}
private void ProcessWiffFile(FileSystemInfo fiDatasetFile, clsDatasetFileInfo datasetFileInfo)
{
try
{
// Open the .Wiff file using the ProteoWizardWrapper
var objPWiz = new pwiz.ProteowizardWrapper.MSDataFileReader(fiDatasetFile.FullName);
try
{
var dtRunStartTime = Convert.ToDateTime(objPWiz.RunStartTime);
// Update AcqTimeEnd if possible
// Found out by trial and error that we need to use .ToUniversalTime() to adjust the time reported by ProteoWizard
dtRunStartTime = dtRunStartTime.ToUniversalTime();
if (dtRunStartTime < datasetFileInfo.AcqTimeEnd)
{
if (datasetFileInfo.AcqTimeEnd.Subtract(dtRunStartTime).TotalDays < 1)
{
datasetFileInfo.AcqTimeStart = dtRunStartTime;
}
}
}
catch (Exception)
{
datasetFileInfo.AcqTimeStart = datasetFileInfo.AcqTimeEnd;
}
// Instantiate the Proteowizard Data Parser class
var pWizParser = new clsProteowizardDataParser(objPWiz, mDatasetStatsSummarizer, mTICandBPIPlot,
mLCMS2DPlot, mSaveLCMS2DPlots, mSaveTICAndBPI,
mCheckCentroidingStatus)
{
HighResMS1 = true,
HighResMS2 = true
};
RegisterEvents(pWizParser);
var blnTICStored = false;
var blnSRMDataCached = false;
double dblRuntimeMinutes = 0;
// Note that SRM .Wiff files will only have chromatograms, and no spectra
if (objPWiz.ChromatogramCount > 0)
{
// Process the chromatograms
pWizParser.StoreChromatogramInfo(datasetFileInfo, out blnTICStored, out blnSRMDataCached, out dblRuntimeMinutes);
pWizParser.PossiblyUpdateAcqTimeStart(datasetFileInfo, dblRuntimeMinutes);
}
if (objPWiz.SpectrumCount > 0 & !blnSRMDataCached)
{
// Process the spectral data (though only if we did not process SRM data)
pWizParser.StoreMSSpectraInfo(datasetFileInfo, blnTICStored, ref dblRuntimeMinutes);
pWizParser.PossiblyUpdateAcqTimeStart(datasetFileInfo, dblRuntimeMinutes);
}
objPWiz.Dispose();
clsProgRunner.GarbageCollectNow();
}
catch (Exception ex)
{
OnErrorEvent("Error using ProteoWizard reader: " + ex.Message, ex);
}
}
private void ReadBinaryData(string dataDirectoryPath, DatasetFileInfo datasetFileInfo, double acquisitionLengthMinutes)
{
try
{
// Open the data directory using the ProteoWizardWrapper
var pWiz = new pwiz.ProteowizardWrapper.MSDataFileReader(dataDirectoryPath);
try
{
var runStartTime = Convert.ToDateTime(pWiz.RunStartTime);
// Update AcqTimeEnd if possible
if (runStartTime < datasetFileInfo.AcqTimeEnd)
{
if (datasetFileInfo.AcqTimeEnd.Subtract(runStartTime).TotalDays < 1)
{
datasetFileInfo.AcqTimeStart = runStartTime;
if (acquisitionLengthMinutes > 0)
{
datasetFileInfo.AcqTimeEnd = datasetFileInfo.AcqTimeStart.AddMinutes(acquisitionLengthMinutes);
}
}
}
}
catch (Exception)
{
// Leave the times unchanged
}
// Instantiate the ProteoWizard Data Parser class
var pWizParser = new clsProteoWizardDataParser(pWiz, mDatasetStatsSummarizer, mTICAndBPIPlot,
mLCMS2DPlot, mSaveLCMS2DPlots, mSaveTICAndBPI,
mCheckCentroidingStatus)
{
HighResMS1 = true,
HighResMS2 = true
};
RegisterEvents(pWizParser);
var ticStored = false;
double runtimeMinutes = 0;
if (pWiz.ChromatogramCount > 0)
{
// Process the chromatograms
pWizParser.StoreChromatogramInfo(datasetFileInfo, out ticStored, out _, out runtimeMinutes);
pWizParser.PossiblyUpdateAcqTimeStart(datasetFileInfo, runtimeMinutes);
}
if (pWiz.SpectrumCount > 0)
{
// Process the spectral data
var skipExistingScans = (pWiz.ChromatogramCount > 0);
pWizParser.StoreMSSpectraInfo(ticStored, ref runtimeMinutes,
skipExistingScans,
skipScansWithNoIons: true,
maxScansToTrackInDetail: MAX_SCANS_TO_TRACK_IN_DETAIL,
maxScansForTicAndBpi: MAX_SCANS_FOR_TIC_AND_BPI);
pWizParser.PossiblyUpdateAcqTimeStart(datasetFileInfo, runtimeMinutes);
}
pWiz.Dispose();
ProgRunner.GarbageCollectNow();
}
catch (Exception ex)
{
OnErrorEvent("Exception reading the Binary Data in the Agilent TOF .D directory using ProteoWizard: " + ex.Message, ex);
}
}
private void ReadBinaryData(string strDataFolderPath, clsDatasetFileInfo datasetFileInfo)
{
try
{
// Open the data folder using the ProteoWizardWrapper
var objPWiz = new pwiz.ProteowizardWrapper.MSDataFileReader(strDataFolderPath);
try
{
var dtRunStartTime = Convert.ToDateTime(objPWiz.RunStartTime);
// Update AcqTimeEnd if possible
if (dtRunStartTime < datasetFileInfo.AcqTimeEnd)
{
if (datasetFileInfo.AcqTimeEnd.Subtract(dtRunStartTime).TotalDays < 1)
{
datasetFileInfo.AcqTimeStart = dtRunStartTime;
}
}
}
catch (Exception)
{
// Leave the times unchanged
}
// Instantiate the Proteowizard Data Parser class
var pWizParser = new clsProteowizardDataParser(objPWiz, mDatasetStatsSummarizer, mTICandBPIPlot,
mLCMS2DPlot, mSaveLCMS2DPlots, mSaveTICAndBPI,
mCheckCentroidingStatus)
{
HighResMS1 = true,
HighResMS2 = true
};
RegisterEvents(pWizParser);
var blnTICStored = false;
double dblRuntimeMinutes = 0;
if (objPWiz.ChromatogramCount > 0)
{
// Process the chromatograms
pWizParser.StoreChromatogramInfo(datasetFileInfo, out blnTICStored, out _, out dblRuntimeMinutes);
pWizParser.PossiblyUpdateAcqTimeStart(datasetFileInfo, dblRuntimeMinutes);
}
if (objPWiz.SpectrumCount > 0)
{
// Process the spectral data
pWizParser.StoreMSSpectraInfo(datasetFileInfo, blnTICStored, ref dblRuntimeMinutes);
pWizParser.PossiblyUpdateAcqTimeStart(datasetFileInfo, dblRuntimeMinutes);
}
objPWiz.Dispose();
clsProgRunner.GarbageCollectNow();
}
catch (Exception ex)
{
OnErrorEvent("Exception reading the Binary Data in the Agilent TOF .D folder using Proteowizard: " + ex.Message, ex);
}
}
