public override XYData GetMassSpectrum(ScanSet scanset, double minMZ, double maxMZ)
{
Check.Require(scanset != null, "Can't get mass spectrum; inputted set of scans is null");
Check.Require(scanset.IndexValues.Count > 0, "Can't get mass spectrum; no scan numbers inputted");
var totScans = this.GetNumMSScans();
var xvals = new double[0];
var yvals = new double[0];
if (scanset.IndexValues.Count == 1) //this is the case of only wanting one MS spectrum
{
//TODO: Old DeconTools reference!!
this.RawData.GetSpectrum(scanset.IndexValues[0], ref xvals, ref yvals, false);
}
else
{
throw new NotImplementedException("Summing is not yet supported for ICR2LS_MS Data files.");
//this.rawData.GetSummedSpectra(scanset.getLowestScanNumber(), scanset.getHighestScanNumber(), minMZ, maxMZ, ref xvals, ref yvals);
}
var xydata = new XYData();
xydata.Xvalues = xvals;
xydata.Yvalues = yvals;
xydata = xydata.TrimData(minMZ, maxMZ);
return(xydata);
}
/// <summary>
/// Returns the mass spectrum for a specified LC ScanSet and a IMS ScanSet.
/// </summary>
/// <param name="lcScanSet"></param>
/// <param name="imsScanSet"></param>
/// <param name="minMZ"></param>
/// <param name="maxMZ"></param>
public override XYData GetMassSpectrum(ScanSet lcScanSet, ScanSet imsScanSet, double minMZ, double maxMZ)
{
Check.Require(imsScanSet.GetScanCount() > 0, string.Format(
"Cannot get spectrum. Number of scans in ScanSet ({0}) is 0", nameof(imsScanSet)));
Check.Require(lcScanSet.GetScanCount() > 0, string.Format(
"Cannot get spectrum. Number of frames in FrameSet ({0}) is 0", nameof(lcScanSet)));
var startFrameNumber = lcScanSet.GetLowestScanNumber();
var endFrameNumber = lcScanSet.GetHighestScanNumber();
var startScanNumber = imsScanSet.GetLowestScanNumber();
var endScanNumber = imsScanSet.GetHighestScanNumber();
// TODO: If lowest and highest scan numbers are both 0, should we be summing the mass spectrum?
var frameType = (UIMFData.FrameType)GetMSLevel(lcScanSet.PrimaryScanNumber);
try
{
// Prior to January 2015 the SpectrumCache class in the UIMFReader used Dictionary<int, int> for ListOfIntensityDictionaries
// This caused some datasets, e.g. EXP-Mix5_1um_pos_19Jan15_Columbia_DI, to run out of memory when caching 10 spectra
// The UIMFLibrary now uses List<int, int>, which takes up less memory (at the expense having slower lookups by BinNumber, though this does not affect DeconTools' use of the UIMFLibrary)
mReader.SpectraToCache = 10;
mReader.MaxSpectrumCacheMemoryMB = 750;
mReader.GetSpectrum(
startFrameNumber, endFrameNumber, frameType,
startScanNumber, endScanNumber,
minMZ, maxMZ,
out var xVals, out var yVals);
var xyData = new XYData();
if (xVals == null || xVals.Length == 0)
{
xyData.Xvalues = null;
xyData.Yvalues = null;
return(xyData);
}
xyData.Xvalues = xVals;
xyData.Yvalues = yVals.Select <int, double>(i => i).ToArray();
if (xyData.Xvalues[0] < minMZ || xyData.Xvalues[xyData.Xvalues.Length - 1] > maxMZ)
{
xyData = xyData.TrimData(minMZ, maxMZ);
}
return(xyData);
}
catch (Exception ex)
{
Console.WriteLine("Error in UIMF GetMassSpectrum: " + ex.Message);
throw;
}
}
//NOTE: code duplication here... see BrukerRun too
public override XYData GetMassSpectrum(DeconTools.Backend.Core.ScanSet scanSet, double minMZ, double maxMZ)
{
Check.Require(scanSet != null, "Can't get mass spectrum; inputted set of scans is null");
Check.Require(scanSet.IndexValues.Count > 0, "Can't get mass spectrum; no scan numbers inputted");
var totScans = this.GetNumMSScans();
var xvals = new double[0];
var yvals = new double[0];
if (scanSet.IndexValues.Count == 1) //this is the case of only wanting one MS spectrum
{
this.RawData.GetSpectrum(scanSet.IndexValues[0], ref xvals, ref yvals, false);
}
else // need to sum spectra
{
//assume: each scan has exactly same x values
//get first spectrum
this.RawData.GetSpectrum(scanSet.IndexValues[0], ref xvals, ref yvals, false);
//
var summedYvals = new double[xvals.Length];
yvals.CopyTo(summedYvals, 0);
for (var i = 1; i < scanSet.IndexValues.Count; i++)
{
this.RawData.GetSpectrum(scanSet.IndexValues[i], ref xvals, ref yvals, false);
for (var n = 0; n < xvals.Length; n++)
{
summedYvals[n] += yvals[n];
}
}
yvals = summedYvals;
}
var xydata = new XYData();
xydata.Xvalues = xvals;
xydata.Yvalues = yvals;
xydata = xydata.TrimData(minMZ, maxMZ);
return(xydata);
}
public override XYData GetMassSpectrum(DeconTools.Backend.Core.ScanSet scanset, double minMZ, double maxMZ)
{
var xydata = new XYData();
try
{
xydata = loadDataFromFile(this.Filename);
}
catch (Exception ex)
{
throw new System.IO.IOException("There was an error reading file " + Utilities.DiagnosticUtilities.GetFullPathSafe(this.Filename) + "\n\n" + ex.Message);
}
xydata = xydata.TrimData(minMZ, maxMZ);
return(xydata);
}
protected virtual XYData TrimData(XYData xyData, double targetVal, double leftTrimAmount, double rightTrimAmount)
{
if (xyData == null)
{
return(xyData);
}
if (xyData.Xvalues == null || xyData.Xvalues.Length == 0)
{
return(xyData);
}
var leftTrimValue = targetVal - leftTrimAmount;
var rightTrimValue = targetVal + rightTrimAmount;
return(xyData.TrimData(leftTrimValue, rightTrimValue, 0.1));
}
private void CreateObservedIsotopicProfilePlot()
{
XYData xydata = new XYData();
if (Workflow.MassSpectrumXYData == null)
{
xydata.Xvalues = Workflow.MassSpectrumXYData == null ? new double[] { 400, 1500 } : Workflow.MassSpectrumXYData.Xvalues;
xydata.Yvalues = Workflow.MassSpectrumXYData == null ? new double[] { 0, 0 } : Workflow.MassSpectrumXYData.Yvalues;
}
else
{
xydata.Xvalues = Workflow.MassSpectrumXYData.Xvalues;
xydata.Yvalues = Workflow.MassSpectrumXYData.Yvalues;
xydata = xydata.TrimData(Workflow.Result.Target.MZ - 100, Workflow.Result.Target.MZ + 100);
}
if (Workflow.Result.IsotopicProfile != null)
{
MsGraphMaxY = Workflow.Result.IsotopicProfile.getMostIntensePeak().Height;
}
else
{
MsGraphMaxY = (float)xydata.getMaxY();
}
string msGraphTitle = Workflow.Result.Target.Code + "; m/z " +
Workflow.Result.Target.MZ.ToString("0.0000") + "; z=" +
Workflow.Result.Target.ChargeState;
PlotModel plotModel = new PlotModel(msGraphTitle);
plotModel.TitleFontSize = 11;
plotModel.Padding = new OxyThickness(0);
plotModel.PlotMargins = new OxyThickness(0);
plotModel.PlotAreaBorderThickness = 0;
var series = new OxyPlot.Series.LineSeries();
series.MarkerSize = 1;
series.Color = OxyColors.Black;
for (int i = 0; i < xydata.Xvalues.Length; i++)
{
series.Points.Add(new DataPoint(xydata.Xvalues[i], xydata.Yvalues[i]));
}
var xAxis = new LinearAxis(AxisPosition.Bottom, "m/z");
xAxis.Minimum = MsGraphMinX;
xAxis.Maximum = MsGraphMaxX;
var yAxis = new LinearAxis(AxisPosition.Left, "Intensity");
yAxis.Minimum = 0;
yAxis.AbsoluteMinimum = 0;
yAxis.Maximum = MsGraphMaxY + MsGraphMaxY * 0.05;
yAxis.StringFormat = "0.0E0";
//yAxis.Maximum = maxIntensity + (maxIntensity * .05);
//yAxis.AbsoluteMaximum = maxIntensity + (maxIntensity * .05);
yAxis.AxisChanged += OnYAxisChange;
xAxis.AxislineStyle = LineStyle.Solid;
xAxis.AxislineThickness = 1;
yAxis.AxislineStyle = LineStyle.Solid;
yAxis.AxislineThickness = 1;
plotModel.Series.Add(series);
plotModel.Axes.Add(xAxis);
plotModel.Axes.Add(yAxis);
ObservedIsoPlot = plotModel;
}
public double GetFit(XYData theorXYData, XYData observedXYData, double minIntensityForScore, out int ionCountUsed, double offset = 0)
{
Check.Require(theorXYData != null && theorXYData.Xvalues != null && theorXYData.Yvalues != null,
"AreaFitter failed. Theoretical XY data is null");
Check.Require(observedXYData != null & observedXYData.Xvalues != null && observedXYData.Yvalues != null,
"AreaFitter failed. Observed XY data is null");
//Check.Require(minIntensityForScore >= 0 && minIntensityForScore <= 100, "MinIntensityForScore should be between 0 and 100");
ionCountUsed = 0;
double sumOfSquaredDiff = 0;
double sumOfSquaredTheorIntens = 0;
var xmin = theorXYData.Xvalues[0] + offset;
var xmax = theorXYData.Xvalues.Max() + offset;
var trimmedObservedXYData = observedXYData.TrimData(xmin, xmax);
//XYData trimmedObservedXYData = observedXYData;
//trimmedObservedXYData.Display();
//theorXYData.Display();
var interpolatedValues = new List <double>();
var theoreticalValues = new List <double>();
for (var i = 0; i < theorXYData.Xvalues.Length; i++)
{
if (theorXYData.Yvalues[i] >= minIntensityForScore)
{
var currentTheorMZ = theorXYData.Xvalues[i] + offset;
var indexOfClosest = MathUtils.GetClosest(trimmedObservedXYData.Xvalues, currentTheorMZ, 0.1);
if (indexOfClosest == -1)
{
//Console.WriteLine(i + "\t" + currentTheorMZ);
return(1);
}
//findout if closest is above or below
var closestIsBelow = (trimmedObservedXYData.Xvalues[indexOfClosest] < currentTheorMZ);
double mz1 = 0;
double mz2 = 0;
double intensity1 = 0;
double intensity2 = 0;
if (closestIsBelow)
{
mz1 = trimmedObservedXYData.Xvalues[indexOfClosest];
intensity1 = trimmedObservedXYData.Yvalues[indexOfClosest];
if (indexOfClosest == trimmedObservedXYData.Xvalues.Length - 1) //if at the end of the XY array; this should be very rare
{
mz2 = mz1;
intensity2 = intensity1;
}
else
{
mz2 = trimmedObservedXYData.Xvalues[indexOfClosest + 1];
intensity2 = trimmedObservedXYData.Yvalues[indexOfClosest + 1];
}
}
else // closest point is above the targetMZ; so get the mz of the point below
{
mz2 = trimmedObservedXYData.Xvalues[indexOfClosest];
intensity2 = trimmedObservedXYData.Yvalues[indexOfClosest];
if (indexOfClosest == 0) //if at the beginning of the XY array (rare)
{
mz1 = mz2;
intensity1 = intensity2;
}
else
{
mz1 = trimmedObservedXYData.Xvalues[indexOfClosest - 1];
intensity1 = trimmedObservedXYData.Yvalues[indexOfClosest - 1];
}
}
var interopolatedIntensity = MathUtils.getInterpolatedValue(mz1, mz2, intensity1, intensity2, currentTheorMZ);
interpolatedValues.Add(interopolatedIntensity);
theoreticalValues.Add(theorXYData.Yvalues[i]);
//double normalizedObservedIntensity = interopolatedIntensity / maxIntensity;
//double normalizedTheorIntensity = theorXYData.Yvalues[i]/maxTheorIntensity;
//double diff = normalizedTheorIntensity - normalizedObservedIntensity;
//sumOfSquaredDiff += diff * diff;
//sumOfSquaredTheorIntens += normalizedTheorIntensity * normalizedTheorIntensity;
}
}
var maxTheoreticalIntens = getMax(theoreticalValues);
var maxObservIntens = getMax(interpolatedValues);
for (var i = 0; i < theoreticalValues.Count; i++)
{
var normalizedObservedIntensity = interpolatedValues[i] / maxObservIntens;
var normalizedTheorIntensity = theoreticalValues[i] / maxTheoreticalIntens;
var diff = normalizedTheorIntensity - normalizedObservedIntensity;
sumOfSquaredDiff += diff * diff;
sumOfSquaredTheorIntens += normalizedTheorIntensity * normalizedTheorIntensity;
}
if (theoreticalValues.Count == 0 || Math.Abs(sumOfSquaredTheorIntens) < double.Epsilon)
{
return(-1);
}
//StringBuilder sb = new StringBuilder();
//TestUtilities.GetXYValuesToStringBuilder(sb, theoreticalValues.ToArray(), interpolatedValues.ToArray());
//Console.Write(sb.ToString());
var fitScore = sumOfSquaredDiff / sumOfSquaredTheorIntens;
ionCountUsed = theoreticalValues.Count;
// Future possibility (considered in January 2014):
// Normalize the fit score by the number of theoretical ions
// fitScore /= ionCountUsed;
return(fitScore);
}
private void GetMassSpectrumForCurrentResult()
{
if (ObservedIsoPlot==null)
{
ObservedIsoPlot= CreateObservedIsoPlot();
}
XYData xydata = new XYData();
if (CurrentResultInfo.MassSpectrumXYData == null)
{
xydata.Xvalues = CurrentResultInfo.MassSpectrumXYData == null ? new double[] { 400, 1500 } : CurrentResultInfo.MassSpectrumXYData.Xvalues;
xydata.Yvalues = CurrentResultInfo.MassSpectrumXYData == null ? new double[] { 0, 0 } : CurrentResultInfo.MassSpectrumXYData.Yvalues;
}
else
{
xydata.Xvalues = CurrentResultInfo.MassSpectrumXYData.Xvalues;
xydata.Yvalues = CurrentResultInfo.MassSpectrumXYData.Yvalues;
xydata = xydata.TrimData(CurrentResultInfo.Result.Target.MZ - 2, CurrentResultInfo.Result.Target.MZ + 8);
}
double msGraphMaxY;
if (CurrentResultInfo.Result.IsotopicProfile != null)
{
msGraphMaxY = CurrentResultInfo.Result.IsotopicProfile.getMostIntensePeak().Height;
}
else
{
msGraphMaxY = (float)xydata.getMaxY();
}
string msGraphTitle = "TargetID= " + CurrentResultInfo.Result.Target.ID + "; m/z " + CurrentResultInfo.Result.Target.MZ.ToString("0.0000") + "; z=" +
CurrentResultInfo.Result.Target.ChargeState + "; Scan= " + CurrentResultInfo.Result.ScanSet??"[No scan selected]";
ObservedIsoPlot.Series.Clear();
var series = new OxyPlot.Series.LineSeries();
series.MarkerSize = 1;
series.Color = OxyColors.Black;
for (int i = 0; i < xydata.Xvalues.Length; i++)
{
series.Points.Add(new DataPoint(xydata.Xvalues[i], xydata.Yvalues[i]));
}
ObservedIsoPlot.Axes[1].Maximum = msGraphMaxY + msGraphMaxY * 0.05;
ObservedIsoPlot.Series.Add(series);
}