public void ExecuteWithoutXYData()
{
IXYData xyData = new XYData(new List<XYPoint>());
outputEvent.Subscribe(OnPublishWithoutPeaks);
IList<ChromatographicPeak> peaks = chromatographicPeakDetection.Execute(xyData);
Assert.AreEqual(0, peaks.Count);
Assert.AreEqual(2, messageCount);
Assert.AreEqual(true, publishCalled);
}
public void ExecuteWithoutXYData()
{
IXYData xyData = new XYData(new List<XYPoint>());
SetupOutputEvents();
IXYData smoothedXYData = smoothing.Execute(xyData);
Assert.AreEqual(xyData.XValues.Count, smoothedXYData.XValues.Count);
Assert.AreEqual(0, smoothedXYData.XValues.Count);
Assert.AreEqual(true, publishCalled);
Assert.AreEqual(true, clickablePublishCalled);
}
public void ExecuteWithoutPeaks()
{
IXYData xyData = new XYData(new double[] { 1, 2, 3, 4, 5 }, new double[] { 2, 2, 2, 2, 2 });
SetupOutputEvents();
IXYData smoothedXYData = smoothing.Execute(xyData);
Assert.AreEqual(xyData.XValues.Count, smoothedXYData.XValues.Count);
Assert.AreEqual(2, xyData.YValues[3]);
Assert.AreEqual(2.00000, Math.Round(smoothedXYData.YValues[3], 5));
Assert.AreEqual(true, publishCalled);
Assert.AreEqual(true, clickablePublishCalled);
}
public void TestInitialize()
{
IXYData xyData = new XYData(new double[] { 1, 2 }, new double[] { 3, 4 });
mockServiceLocator = new Mock<IServiceLocator>();
mockEventAggregator = new Mock<IEventAggregator>();
mockDataProvider = new Mock<IDataProvider>();
mockDataProvider.Setup(mock => mock.GetTotalIonChromatogram(TimeUnit.Seconds)).Returns(xyData);
mockDataProvider.Setup(mock => mock.GetExtractedIonChromatogram(2, 2, 0.5, TimeUnit.Seconds)).Returns(xyData);
mockDataProvider.Setup(mock => mock.GetSpectrum(2, 3, 3, 6, 0)).Returns(xyData);
experiment = Test.TestHelper.GetTestExperiment(mockServiceLocator);
run = new Run(Path.GetFileName(Properties.Settings.Default.mzXMLTestFile1), Properties.Settings.Default.mzXMLTestFile1, new ProteinState(experiment), new Labeling(experiment), experiment, mockDataProvider.Object);
}
public IXYData Generate(double mass1, double mass2, double mzTolerance, TimeUnit timeUnits)
{
if (mass1 != mass2)
{
throw new ArgumentException("This method only supports getting an XIC for one mass. Mass1 must be equal to Mass2.");
}
pwiz.CLI.msdata.SpectrumList spectrumList = run.spectrumList;
int timePoints = spectrumList.size();
List<double> msLevelXVals = new List<double>();
List<double> msLevelYVals = new List<double>();
for (int i = 0; i < timePoints; i++)
{
IList<double> mzValues = new List<double>();
IList<double> intensityValues = new List<double>();
double rt;
if (spectrumCache.IsInCache(i))
{
SpectrumCacheItem cacheItem = spectrumCache.ReadRawCacheItem(i);
mzValues = cacheItem.Spectrum.XValues;
intensityValues = cacheItem.Spectrum.YValues;
rt = cacheItem.Spectrum.StartRT;
}
else
{
Domain.ISpectrum spectrum = spectrumExtractor.GetSpectrum(i, timeUnits);
mzValues = spectrum.XValues;
intensityValues = spectrum.YValues;
rt = spectrum.StartRT;
}
XicHelper.GetIntensities(mzValues, intensityValues, rt, mass1, mzTolerance, msLevelXVals, msLevelYVals);
}
IXYData xyData = new XYData(msLevelXVals.ToArray(), msLevelYVals.ToArray());
xyData.TimeUnit = TimeUnit.Minutes;
return xyData;
}
public IXYData Execute(IXYData xyData)
{
if (Enabled && !executeDisabled)
{
_output.Publish(" Savitzky Golay Smoothing Started (LeftParam=" + LeftParam + ", RightParam=" + RightParam + ", Order=" + order + ")");
float[] xvals = new float[xyData.XValues.Count];
float[] yvals = new float[xyData.YValues.Count];
xvals = xyData.XValues.Select(item => (float)item).ToArray();
yvals = xyData.YValues.Select(item => (float)item).ToArray();
DeconEngine.Utils.SavitzkyGolaySmooth(this.leftParam, this.rightParam, this.order, ref xvals, ref yvals);
IXYData smoothedXYData = new XYData(xvals.Select(item => (double)item).ToList(), yvals.Select(item => (double)item).ToList());
smoothedXYData.Title = "Smoothed " + xyData.Title;
_clickableOutput.Publish(new ClickableOutputEvent()
{
Parameter = smoothedXYData,
Text = " Smoothing completed",
Click = new DelegateCommand<IXYData>(OnViewXIC)
});
return smoothedXYData;
}
return xyData;
}
public static IXYData Generate(double[] xValues, double[] yValues)
{
IXYData xyData = new XYData(xValues, yValues);
return xyData;
}
