public void TestPWiz(
string fileOrDirectoryName,
bool isDirectory,
int expectedSpectraInFile,
int expectedSpectraLoaded,
int expectedTotalDataPoints,
double expectedMedianTIC,
double expectedMedianBPI)
{
try
{
if (!InstrumentDataUtilities.FindInstrumentData(fileOrDirectoryName, isDirectory, out var instrumentDataFileOrDirectory))
{
Assert.Fail("File or directory not found");
return;
}
using (var reader = new MSDataFileReader(instrumentDataFileOrDirectory.FullName))
{
Console.WriteLine("Chromatogram count: " + reader.ChromatogramCount);
Console.WriteLine();
var ticIntensities = new Dictionary <int, float>();
for (var chromatogramIndex = 0; chromatogramIndex < reader.ChromatogramCount; chromatogramIndex++)
{
// Note that even for a small .Wiff file (1.5 MB), obtaining the Chromatogram list will take some time (20 to 60 seconds)
// The chromatogram at index 0 should be the TIC
// The chromatogram at index >=1 will be each SRM
reader.GetChromatogram(chromatogramIndex, out var chromatogramID, out var timeArray, out var intensityArray);
// Determine the chromatogram type
if (chromatogramID == null)
{
chromatogramID = string.Empty;
}
var cvParams = reader.GetChromatogramCVParams(chromatogramIndex);
if (MSDataFileReader.TryGetCVParamDouble(cvParams, pwiz.CLI.cv.CVID.MS_TIC_chromatogram, out _))
{
// This chromatogram is the TIC
Console.WriteLine("TIC has id {0} and {1} data points", chromatogramID, timeArray.Length);
for (var i = 0; i < intensityArray.Length; i++)
{
ticIntensities.Add(i, intensityArray[i]);
}
}
if (MSDataFileReader.TryGetCVParamDouble(cvParams, pwiz.CLI.cv.CVID.MS_selected_reaction_monitoring_chromatogram, out _))
{
// This chromatogram is an SRM scan
Console.WriteLine("SRM scan has id {0} and {1} data points", chromatogramID, timeArray.Length);
}
}
Console.WriteLine("Spectrum count: " + reader.SpectrumCount);
var spectraLoaded = 0;
long totalPointsRead = 0;
double ticSumAllSpectra = 0;
double bpiSumAllSpectra = 0;
var spectrumIndex = 0;
while (spectrumIndex < reader.SpectrumCount)
{
var spectrum = reader.GetSpectrum(spectrumIndex, getBinaryData: true);
spectraLoaded += 1;
Console.WriteLine();
Console.WriteLine("ScanIndex {0}, NativeId {1}, Elution Time {2:F2} minutes, MS Level {3}",
spectrumIndex, spectrum.NativeId, spectrum.RetentionTime, spectrum.Level);
// Use the following to get the MZs and Intensities
var mzList = spectrum.Mzs.ToList();
var intensities = spectrum.Intensities.ToList();
if (mzList.Count > 0)
{
Console.WriteLine(" Data count: " + mzList.Count);
totalPointsRead += mzList.Count;
double tic = 0;
double bpi = 0;
for (var index = 0; index <= mzList.Count - 1; index++)
{
tic += intensities[index];
if (intensities[index] > bpi)
{
bpi = intensities[index];
}
}
ticSumAllSpectra += tic;
bpiSumAllSpectra += bpi;
if (!ticIntensities.TryGetValue(spectrumIndex, out var ticFromChromatogram))
{
ticFromChromatogram = -1;
}
var spectrumInfo = reader.GetSpectrumObject(spectrumIndex);
if (MSDataFileReader.TryGetCVParamDouble(spectrumInfo.cvParams, pwiz.CLI.cv.CVID.MS_total_ion_current,
out var ticFromSpectrumObject))
{
if (ticFromChromatogram < 0)
{
// ticIntensities did not have an entry for spectrumIndex
// This could be the case on a Waters Synapt instrument, where ticIntensities has one TIC per frame,
// while pWiz.GetSpectrum() returns individual mass spectra, of which there could be hundreds of spectra per frame
Console.WriteLine(" TIC from actual data is {0:E2} vs. {1:E2} from the spectrum object",
tic, ticFromSpectrumObject);
}
else
{
// Note: the TIC value from the CvParams has been seen to be drastically off from the manually computed value
Console.WriteLine(
" TIC from actual data is {0:E2} vs. {1:E2} from the chromatogram and {2:E2} from the spectrum object",
tic, ticFromChromatogram, ticFromSpectrumObject);
}
}
if (MSDataFileReader.TryGetCVParamDouble(spectrumInfo.cvParams, pwiz.CLI.cv.CVID.MS_base_peak_intensity,
out var bpiFromSpectrumObject))
{
if (MSDataFileReader.TryGetCVParamDouble(spectrumInfo.cvParams, pwiz.CLI.cv.CVID.MS_base_peak_m_z,
out var bpiMzFromSpectrumObject))
{
// Note: the BPI intensity from the CvParams has been seen to be drastically off from the manually computed value
Console.WriteLine(" BPI from spectrum object is {0:E2} at {1:F3} m/z",
bpiFromSpectrumObject, bpiMzFromSpectrumObject);
}
}
}
if (spectrumIndex < 25)
{
spectrumIndex += 1;
}
else if (spectrumIndex < 1250)
{
spectrumIndex += 50;
}
else
{
spectrumIndex += 500;
}
}
if (spectraLoaded > 0)
{
var medianTIC = ticSumAllSpectra / spectraLoaded;
var medianBPI = bpiSumAllSpectra / spectraLoaded;
Console.WriteLine();
Console.WriteLine("Read {0:N0} data points from {1} spectra in {2}",
totalPointsRead, spectraLoaded, Path.GetFileName(fileOrDirectoryName));
Console.WriteLine("Median TIC: {0:E4}", medianTIC);
Console.WriteLine("Median BPI: {0:E4}", medianBPI);
Assert.AreEqual(expectedSpectraInFile, reader.SpectrumCount, "Total spectrum count mismatch");
Assert.AreEqual(expectedSpectraLoaded, spectraLoaded, "Spectra loaded mismatch");
Assert.AreEqual(expectedTotalDataPoints, totalPointsRead, "Spectra loaded mismatch");
var ticComparisonTolerance = expectedMedianTIC * 0.01;
var bpiComparisonTolerance = expectedMedianBPI * 0.01;
Assert.AreEqual(expectedMedianTIC, medianTIC, ticComparisonTolerance, "Median TIC mismatch");
Assert.AreEqual(expectedMedianBPI, medianBPI, bpiComparisonTolerance, "Median BPI mismatch");
}
}
}
catch (Exception ex)
{
ConsoleMsgUtils.ShowError("Error using ProteoWizard reader", ex);
}
}
public void StoreChromatogramInfo(DatasetFileInfo datasetFileInfo, out bool ticStored, out bool srmDataCached, out double runtimeMinutes)
{
var ticScanTimes = new List <float>();
var ticScanNumbers = new List <int>();
// This dictionary tracks the m/z and intensity values for parent (Q1) ions of each scan
// Key is ScanNumber; Value is a dictionary holding m/z and intensity values for that scan
var dct2DDataParent = new Dictionary <int, Dictionary <double, double> >();
// This dictionary tracks the m/z and intensity values for product (Q3) ions of each scan
var dct2DDataProduct = new Dictionary <int, Dictionary <double, double> >();
// This dictionary tracks the scan times for each scan number tracked by dct2DDataParent and/or dct2DDataProduct
var dct2DDataScanTimes = new Dictionary <int, float>();
// Note that even for a small .Wiff file (1.5 MB), obtaining the first chromatogram will take some time (20 to 60 seconds)
// The chromatogram at index 0 should be the TIC
// The chromatogram at index >=1 will be each SRM
runtimeMinutes = 0;
ticStored = false;
srmDataCached = false;
for (var chromatogramIndex = 0; chromatogramIndex <= mPWiz.ChromatogramCount - 1; chromatogramIndex++)
{
try
{
if (chromatogramIndex == 0)
{
OnStatusEvent("Obtaining chromatograms (this could take as long as 60 seconds)");
}
mPWiz.GetChromatogram(chromatogramIndex, out var chromatogramID, out var scanTimes, out var intensities);
if (chromatogramID == null)
{
chromatogramID = string.Empty;
}
var cvParams = mPWiz.GetChromatogramCVParams(chromatogramIndex);
if (MSDataFileReader.TryGetCVParam(cvParams, pwiz.CLI.cv.CVID.MS_TIC_chromatogram, out _))
{
// This chromatogram is the TIC
var storeInTICAndBPIPlot = (mSaveTICAndBPI && mPWiz.SpectrumCount == 0);
ProcessTIC(scanTimes, intensities, ticScanTimes, ticScanNumbers, ref runtimeMinutes, storeInTICAndBPIPlot);
ticStored = storeInTICAndBPIPlot;
// This is FrameCount for Bruker timsTOF datasets
datasetFileInfo.ScanCount = scanTimes.Length;
}
if (MSDataFileReader.TryGetCVParam(cvParams, pwiz.CLI.cv.CVID.MS_selected_reaction_monitoring_chromatogram, out _))
{
// This chromatogram is an SRM scan
ProcessSRM(chromatogramID, scanTimes, intensities, ticScanTimes, ticScanNumbers, ref runtimeMinutes, dct2DDataParent,
dct2DDataProduct, dct2DDataScanTimes);
srmDataCached = true;
}
}
catch (AccessViolationException)
{
// Attempted to read or write protected memory. This is often an indication that other memory is corrupt.
if (!mWarnedAccessViolationException)
{
OnWarningEvent("Error loading chromatogram data with ProteoWizard: Attempted to read or write protected memory. " +
"The instrument data file is likely corrupt.");
mWarnedAccessViolationException = true;
}
mDatasetStatsSummarizer.CreateEmptyScanStatsFiles = false;
}
catch (Exception ex)
{
OnErrorEvent("Error processing chromatogram " + chromatogramIndex + " with ProteoWizard: " + ex.Message, ex);
}
}
if (!mSaveLCMS2DPlots)
{
return;
}
if (dct2DDataParent.Count <= 0 && dct2DDataProduct.Count <= 0)
{
return;
}
// Now that all of the chromatograms have been processed, transfer data from dct2DDataParent and dct2DDataProduct into mLCMS2DPlot
mLCMS2DPlot.Options.MS1PlotTitle = "Q1 m/z";
mLCMS2DPlot.Options.MS2PlotTitle = "Q3 m/z";
Store2DPlotData(dct2DDataScanTimes, dct2DDataParent, dct2DDataProduct);
}