/// <summary>
/// Constructor
/// </summary>
protected clsMSFileInfoProcessorBaseClass()
{
mTICandBPIPlot = new clsTICandBPIPlotter("TICandBPIPlot", true);
RegisterEvents(mTICandBPIPlot);
mInstrumentSpecificPlots = new clsTICandBPIPlotter("InstrumentSpecificPlots", true);
RegisterEvents(mInstrumentSpecificPlots);
mDatasetStatsSummarizer = new clsDatasetStatsSummarizer();
RegisterEvents(mDatasetStatsSummarizer);
mLCMS2DPlot = new clsLCMSDataPlotter();
RegisterEvents(mLCMS2DPlot);
mLCMS2DPlotOverview = new clsLCMSDataPlotter();
RegisterEvents(mLCMS2DPlotOverview);
InitializeLocalVariables();
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="pWiz"></param>
/// <param name="datasetStatsSummarizer"></param>
/// <param name="ticAndBPIPlot"></param>
/// <param name="lcms2DPlot"></param>
/// <param name="saveLCMS2DPlots"></param>
/// <param name="saveTICAndBPI"></param>
/// <param name="checkCentroidingStatus"></param>
public clsProteoWizardDataParser(
MSDataFileReader pWiz,
DatasetStatsSummarizer datasetStatsSummarizer,
clsTICandBPIPlotter ticAndBPIPlot,
clsLCMSDataPlotter lcms2DPlot,
bool saveLCMS2DPlots,
bool saveTICAndBPI,
bool checkCentroidingStatus)
{
mPWiz = pWiz;
mDatasetStatsSummarizer = datasetStatsSummarizer;
mTICAndBPIPlot = ticAndBPIPlot;
mLCMS2DPlot = lcms2DPlot;
mSaveLCMS2DPlots = saveLCMS2DPlots;
mSaveTICAndBPI = saveTICAndBPI;
mCheckCentroidingStatus = checkCentroidingStatus;
mGetQ1MZ = new Regex("Q[0-9]=([0-9.]+)", RegexOptions.Compiled);
mGetQ3MZ = new Regex("Q1=[0-9.]+ Q3=([0-9.]+)", RegexOptions.Compiled);
mWarnedAccessViolationException = false;
}
private void LoadFrameDetails(
DataReader uimfReader,
IReadOnlyDictionary <int, UIMFData.FrameType> dctMasterFrameList,
IReadOnlyList <int> masterFrameNumList)
{
const int BAD_TIC_OR_BPI = int.MinValue;
// The StartTime value for each frame is the number of minutes since 12:00 am
// If acquiring data from 11:59 pm through 12:00 am, the StartTime will reset to zero
clsTICandBPIPlotter pressurePlot;
if (mSaveTICAndBPI)
{
// Initialize the TIC and BPI arrays
InitializeTICAndBPI();
mTICAndBPIPlot.BPIXAxisLabel = "Frame number";
mTICAndBPIPlot.TICXAxisLabel = "Frame number";
if (mInstrumentSpecificPlots.Count == 0)
{
AddInstrumentSpecificPlot("Drift tube Pressure");
}
// Track drift tube pressures using mTIC in pressurePlot
pressurePlot = mInstrumentSpecificPlots.First();
pressurePlot.DeviceType = Device.Analog;
pressurePlot.BPIXAxisLabel = "Frame number";
pressurePlot.TICXAxisLabel = "Frame number";
pressurePlot.TICYAxisLabel = "Pressure";
pressurePlot.TICYAxisExponentialNotation = false;
pressurePlot.TICPlotAbbrev = "Pressure";
pressurePlot.TICAutoMinMaxY = true;
pressurePlot.RemoveZeroesFromEnds = true;
}
else
{
pressurePlot = new clsTICandBPIPlotter();
}
if (mSaveLCMS2DPlots)
{
InitializeLCMS2DPlot();
}
var lastProgressTime = DateTime.UtcNow;
// Note that this starts at 2 seconds, but is extended after each progress message is shown (maxing out at 30 seconds)
var progressThresholdSeconds = 2;
var globalParams = uimfReader.GetGlobalParams();
var globalMaxBins = globalParams.Bins;
var mzList = new double[globalMaxBins + 1];
var intensityList = new int[globalMaxBins + 1];
var ionsIntensity = new double[globalMaxBins + 1];
// Call .GetStartAndEndScans to get the start and end Frames
GetStartAndEndScans(globalParams.NumFrames, out var frameStart, out var frameEnd);
// Construct the TIC and BPI (of all frames)
ConstructTICAndBPI(uimfReader, frameStart, frameEnd, out var dctTIC, out var dctBPI);
Console.Write(" Loading frame details");
// Initialize the frame StartTime variables
double frameStartTimeInitial = -1;
double frameStartTimeAddon = 0;
double frameStartTimePrevious = -1;
double frameStartTimeCurrent = 0;
for (var masterFrameNumIndex = 0; masterFrameNumIndex <= masterFrameNumList.Count - 1; masterFrameNumIndex++)
{
var frameNumber = masterFrameNumList[masterFrameNumIndex];
if (!dctMasterFrameList.TryGetValue(frameNumber, out var eFrameType))
{
OnWarningEvent(string.Format(
"Frametype {0} not found in dictionary dctMasterFrameList; ignoring frame {1} in LoadFrameDetails",
eFrameType, frameNumber));
continue;
}
// Check whether the frame number is within the desired range
if (frameNumber < frameStart || frameNumber > frameEnd)
{
continue;
}
try
{
FrameParams frameParams;
try
{
frameParams = uimfReader.GetFrameParams(frameNumber);
}
catch (Exception)
{
Console.WriteLine("Exception obtaining frame parameters for frame " + frameNumber + "; will skip this frame");
frameParams = null;
}
if (frameParams == null || eFrameType == UIMFData.FrameType.Calibration)
{
continue;
}
var nonZeroPointsInFrame = uimfReader.GetCountPerFrame(frameNumber);
int msLevel;
if (frameParams.FrameType == UIMFData.FrameType.MS2)
{
msLevel = 2;
}
else
{
msLevel = 1;
}
// Read the frame StartTime
// This will be zero in older .UIMF files, or in files converted from Agilent .D directories
// In newer files, it is the number of minutes since 12:00 am
frameStartTimeCurrent = frameParams.GetValueDouble(FrameParamKeyType.StartTimeMinutes);
if (masterFrameNumIndex == 0 || frameStartTimeInitial < -0.9)
{
frameStartTimeInitial = frameStartTimeCurrent;
}
if (frameStartTimePrevious > 1400 && frameStartTimePrevious > frameStartTimeCurrent)
{
// We likely rolled over midnight; bump up frameStartTimeAddon by 1440 minutes
frameStartTimeAddon += 60 * 24;
}
// Compute the elution time (in minutes) of this frame
var elutionTime = frameStartTimeCurrent + frameStartTimeAddon - frameStartTimeInitial;
if (!dctBPI.TryGetValue(frameNumber, out var bpi))
{
bpi = BAD_TIC_OR_BPI;
}
if (!dctTIC.TryGetValue(frameNumber, out var tic))
{
tic = BAD_TIC_OR_BPI;
}
if (mSaveTICAndBPI)
{
if (bpi > BAD_TIC_OR_BPI && tic > BAD_TIC_OR_BPI)
{
mTICAndBPIPlot.AddData(frameNumber, msLevel, (float)elutionTime, bpi, tic);
}
var pressure = frameParams.GetValueDouble(FrameParamKeyType.PressureBack);
if (Math.Abs(pressure) < float.Epsilon)
{
pressure = frameParams.GetValueDouble(FrameParamKeyType.RearIonFunnelPressure);
}
if (Math.Abs(pressure) < float.Epsilon)
{
pressure = frameParams.GetValueDouble(FrameParamKeyType.IonFunnelTrapPressure);
}
if (Math.Abs(pressure) < float.Epsilon)
{
pressure = frameParams.GetValueDouble(FrameParamKeyType.PressureFront);
}
pressurePlot.AddDataTICOnly(frameNumber, msLevel, (float)elutionTime, pressure);
}
var scanStatsEntry = new ScanStatsEntry
{
ScanNumber = frameNumber,
ScanType = msLevel
};
if (msLevel <= 1)
{
scanStatsEntry.ScanTypeName = "HMS";
}
else
{
scanStatsEntry.ScanTypeName = "HMSn";
}
scanStatsEntry.ScanFilterText = "IMS";
scanStatsEntry.ExtendedScanInfo.ScanFilterText = scanStatsEntry.ScanFilterText;
scanStatsEntry.ElutionTime = elutionTime.ToString("0.0###");
if (tic > BAD_TIC_OR_BPI)
{
scanStatsEntry.TotalIonIntensity = StringUtilities.ValueToString(tic, 5);
}
else
{
scanStatsEntry.TotalIonIntensity = "0";
}
if (bpi > BAD_TIC_OR_BPI)
{
scanStatsEntry.BasePeakIntensity = StringUtilities.ValueToString(bpi, 5);
}
else
{
scanStatsEntry.BasePeakIntensity = "0";
}
scanStatsEntry.BasePeakMZ = "0";
// Base peak signal to noise ratio
scanStatsEntry.BasePeakSignalToNoiseRatio = "0";
scanStatsEntry.IonCount = nonZeroPointsInFrame;
scanStatsEntry.IonCountRaw = nonZeroPointsInFrame;
// For UIMF files, we only store one entry per frame
// Use the median drift time as the representative drift time
var medianScanNum = frameParams.Scans / 2;
var driftTimeMsec = uimfReader.GetDriftTime(frameNumber, medianScanNum, true);
scanStatsEntry.DriftTimeMsec = driftTimeMsec.ToString("0.0###");
mDatasetStatsSummarizer.AddDatasetScan(scanStatsEntry);
if (mSaveLCMS2DPlots || mCheckCentroidingStatus)
{
try
{
// Also need to load the raw data
// We have to clear the m/z and intensity arrays before calling GetSpectrum
Array.Clear(mzList, 0, mzList.Length);
Array.Clear(intensityList, 0, intensityList.Length);
// Process all of the IMS scans in this Frame to compute a summed spectrum representative of the frame
// In UIMF files from IMS04, if Frame_Parameters.Scans = 360, Frame_Scans will have scans 0 through 359
// In UIMF files from IMS08, prior to December 1, 2014, if Frame_Parameters.Scans = 374, Frame_Scans will have scans 0 through 373
// in UIMF files from IMS08, after December 1, 2014 if Frame_Parameters.Scans = 374, Frame_Scans will have scans 1 through 374
var ionCount = uimfReader.GetSpectrum(frameNumber, frameNumber, eFrameType, 0, frameParams.Scans, out mzList, out intensityList);
if (ionCount > 0)
{
// The m/z and intensity arrays might contain entries with m/z values of 0;
// need to copy the data in place to get the data in the correct format.
// In addition, we'll copy the intensity values from intensityList() into ionsIntensity()
if (ionCount > mzList.Length)
{
ionCount = mzList.Length;
}
if (ionsIntensity.Length < ionCount)
{
Array.Resize(ref ionsIntensity, ionCount);
}
var targetIndex = 0;
for (var ionIndex = 0; ionIndex <= ionCount - 1; ionIndex++)
{
if (mzList[ionIndex] > 0)
{
mzList[targetIndex] = mzList[ionIndex];
ionsIntensity[targetIndex] = intensityList[ionIndex];
targetIndex += 1;
}
}
ionCount = targetIndex;
if (ionCount > 0)
{
if (ionsIntensity.Length > ionCount)
{
Array.Resize(ref ionsIntensity, ionCount);
}
if (mSaveLCMS2DPlots)
{
mLCMS2DPlot.AddScan(frameNumber, msLevel, (float)elutionTime, ionCount, mzList, ionsIntensity);
}
if (mCheckCentroidingStatus)
{
mDatasetStatsSummarizer.ClassifySpectrum(ionCount, mzList, msLevel, "Frame " + frameNumber);
}
}
}
}
catch (Exception ex)
{
OnWarningEvent("Error loading m/z and intensity values for frame " + frameNumber + ": " + ex.Message);
}
}
}
catch (Exception ex)
{
OnWarningEvent("Error loading header info for frame " + frameNumber + ": " + ex.Message);
}
frameStartTimePrevious = frameStartTimeCurrent;
if (DateTime.UtcNow.Subtract(lastProgressTime).TotalSeconds < progressThresholdSeconds)
{
continue;
}
lastProgressTime = DateTime.UtcNow;
if (progressThresholdSeconds < 30)
{
progressThresholdSeconds += 2;
}
var percentComplete = masterFrameNumIndex / (float)masterFrameNumList.Count * 100;
OnProgressUpdate(string.Format("Frames processed: {0:N0}", masterFrameNumIndex), percentComplete);
}
Console.WriteLine();
}
