public FeatureSet GetFeatures(double mz, Tolerance tolerance, DataReader.FrameType frameType)
{
var intensityBlock = _uimfUtil.GetXic(mz, tolerance.GetValue(), frameType,
tolerance.GetUnit() == ToleranceUnit.Ppm ? DataReader.ToleranceType.PPM : DataReader.ToleranceType.Thomson);
var features = new FeatureSet(intensityBlock);
return(features);
}
public void TestDoWaterShedAlgorithmByBin()
{
var fileLocation = @"\\proto-2\UnitTest_Files\MultidimensionalFeatureFinding\BSA_10ugml_IMS6_TOF03_CID_27Aug12_Frodo_Collision_Energy_Collapsed.UIMF";
var uimfUtil = new UimfUtil(fileLocation);
var smoother = new SavitzkyGolaySmoother(5, 2);
var bin = 73009;
var intensityPointList = uimfUtil.GetXic(bin, UIMFData.FrameType.MS1);
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityPointList).ToList();
var preSmoothedFeatureList = FeatureDetection.DoWatershedAlgorithm(pointList).ToList();
Console.WriteLine(DateTime.Now + "\tBefore Smoothing:\tNumPoints = " + pointList.Count + "\tNumFeatures = " + preSmoothedFeatureList.Count);
foreach (var featureBlob in preSmoothedFeatureList)
{
var mostIntensePoint = featureBlob.PointList.First();
Console.WriteLine("Num Points = " + featureBlob.PointList.Count + "\tLC = " + mostIntensePoint.ScanLc + "\tIMS = " + mostIntensePoint.ScanIms + "\tIntensity = " + mostIntensePoint.Intensity);
}
Console.WriteLine("******************************************************");
var newPointList = WaterShedMapUtil.BuildWatershedMap(intensityPointList);
smoother.Smooth(ref newPointList);
var smoothedFeatureList = FeatureDetection.DoWatershedAlgorithm(newPointList).ToList();
Console.WriteLine(DateTime.Now + "\tAfter Smoothing:\tNumPoints = " + newPointList.Count() + "\tNumFeatures = " + smoothedFeatureList.Count);
foreach (var featureBlob in smoothedFeatureList)
{
var mostIntensePoint = featureBlob.PointList.First();
Console.WriteLine("Num Points = " + featureBlob.PointList.Count + "\tLC = " + mostIntensePoint.ScanLc + "\tIMS = " + mostIntensePoint.ScanIms + "\tIntensity = " + mostIntensePoint.Intensity);
}
}
public void TestDoWaterShedAlgorithmAllBins()
{
var fileLocation = @"\\proto-2\UnitTest_Files\MultidimensionalFeatureFinding\BSA_10ugml_IMS6_TOF03_CID_27Aug12_Frodo_Collision_Energy_Collapsed.UIMF";
var uimfUtil = new UimfUtil(fileLocation);
// ReSharper disable once UnusedVariable
var numberOfBins = uimfUtil.GetNumberOfBins();
var smoother = new SavitzkyGolaySmoother(5, 2);
for (var i = 73009; i <= 84000; i++)
{
var mz = uimfUtil.GetMzFromBin(i);
var intensityPointList = uimfUtil.GetXic(mz, 25, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
//List<IntensityPoint> intensityPointList = uimfUtil.GetXic(i, DataReader.FrameType.MS1);
//SavitzkyGolaySmoother smoother = new SavitzkyGolaySmoother(9, 2);
//smoother.Smooth(ref intensityBlock);
//int boundX = intensityBlock.GetUpperBound(0);
//int boundY = intensityBlock.GetUpperBound(1);
//TextWriter smoothedWriter = new StreamWriter("smoothedRaw.csv");
//for (int j = 0; j < boundX; j++)
//{
// StringBuilder row = new StringBuilder();
// for (int k = 0; k < boundY; k++)
// {
// row.Append(intensityBlock[j, k] + ",");
// }
// smoothedWriter.WriteLine(row.ToString());
//}
//smoothedWriter.Close();
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityPointList);
smoother.Smooth(ref pointList);
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList);
Console.WriteLine(DateTime.Now + "\tBin = " + i + "\tNumPoints = " + pointList.Count() + "\tNumFeatures = " + featureList.Count());
}
}
public void TestDoWaterShedAlgorithm()
{
var fileLocation = @"\\proto-2\UnitTest_Files\MultidimensionalFeatureFinding\BSA_10ugml_IMS6_TOF03_CID_27Aug12_Frodo_Collision_Energy_Collapsed.UIMF";
var uimfUtil = new UimfUtil(fileLocation);
var targetMz = 582.32181703760114;
double ppmTolerance = 25;
var intensityBlock = uimfUtil.GetXicAsArray(targetMz, ppmTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var smoother = new SavitzkyGolaySmoother(11, 2);
smoother.Smooth(ref intensityBlock);
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock, 0, 0);
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList);
foreach (var featureBlob in featureList)
{
var mostIntensePoint = featureBlob.PointList.First();
Console.WriteLine("Num Points = " + featureBlob.PointList.Count + "\tLC = " + mostIntensePoint.ScanLc + "\tIMS = " + mostIntensePoint.ScanIms + "\tIntensity = " + mostIntensePoint.Intensity);
}
Console.WriteLine("******************************************************");
var intensityPointList = uimfUtil.GetXic(targetMz, ppmTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var newPointList = WaterShedMapUtil.BuildWatershedMap(intensityPointList);
smoother.Smooth(ref newPointList);
var newFeatureList = FeatureDetection.DoWatershedAlgorithm(newPointList);
foreach (var featureBlob in newFeatureList)
{
var mostIntensePoint = featureBlob.PointList.First();
Console.WriteLine("Num Points = " + featureBlob.PointList.Count + "\tLC = " + mostIntensePoint.ScanLc + "\tIMS = " + mostIntensePoint.ScanIms + "\tIntensity = " + mostIntensePoint.Intensity);
}
}
public void TestComputingApexProfiles()
{
var fileLocation = @"\\proto-2\UnitTest_Files\MultidimensionalFeatureFinding\BSA_10ugml_IMS6_TOF03_CID_27Aug12_Frodo_Collision_Energy_Collapsed.UIMF";
var uimfUtil = new UimfUtil(fileLocation);
var smoother = new SavitzkyGolaySmoother(5, 2);
var targetMz = 964.40334;
double tolerance = 20;
var intensityPointList = uimfUtil.GetXic(targetMz, tolerance, UIMFData.FrameType.MS1,
DataReader.ToleranceType.PPM);
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityPointList);
smoother.Smooth(ref pointList);
var featureBlobs = FeatureDetection.DoWatershedAlgorithm(pointList);
IEnumerable <FeatureBlobStatistics> featureBlobStatList = featureBlobs.Select(featureBlob => featureBlob.Statistics).ToList();
foreach (var f in featureBlobStatList)
{
Console.WriteLine(
"LC: [{0},{1}], IMS: [{2},{3}], Apex: [{4},{5}] SumIntensities: {6}, NumPoints: {7}",
f.ScanLcMin,
f.ScanLcMax,
f.ScanImsMin,
f.ScanImsMax,
f.ScanLcRep,
f.ScanImsRep,
f.SumIntensities,
f.NumPoints
);
Console.WriteLine("LC Apex profile");
Console.WriteLine(string.Join(",", f.LcApexPeakProfile));
Console.WriteLine("IMS Apex profile");
Console.WriteLine(string.Join(",", f.ImsApexPeakProfile));
}
}
private void FindFeatures()
{
m_FeatureFinderBackgroundWorker.ReportProgress(0, "Finding 3-D Features for Precursor and Fragments");
var seqGraph = SequenceGraph.CreateGraph(m_aminoAcidSet, CurrentPeptide);
// var scoringGraph = seqGraph.GetScoringGraph(0);
// var precursorIon = scoringGraph.GetPrecursorIon(this.CurrentChargeState);
// var monoMz = precursorIon.GetMz();
var sequence = new Sequence(CurrentPeptide, m_aminoAcidSet);
var precursorIon = sequence.GetPrecursorIon(CurrentChargeState);
var monoMz = precursorIon.GetMonoIsotopicMz();
var uimfPointList = UimfUtil.GetXic(monoMz, CurrentTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var watershedPointList = WaterShedMapUtil.BuildWatershedMap(uimfPointList);
var smoother = new SavitzkyGolaySmoother(11, 2);
smoother.Smooth(ref watershedPointList);
FeatureList = FeatureDetection.DoWatershedAlgorithm(watershedPointList).ToList();
IsotopeFeaturesDictionary.Clear();
var precursorTargetList = CurrentChargeState == 2 ? new List <string> {
"-1", "0.5", "1", "1.5", "2", "3"
} : new List <string> {
"-1", "1", "2", "3"
};
foreach (var precursorTarget in precursorTargetList)
{
var targetMz = precursorIon.GetIsotopeMz(double.Parse(precursorTarget));
var isotopeUimfPointList = UimfUtil.GetXic(targetMz, CurrentTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var isotopeWatershedPointList = WaterShedMapUtil.BuildWatershedMap(isotopeUimfPointList);
var isotopeFeatures = FeatureDetection.DoWatershedAlgorithm(isotopeWatershedPointList).ToList();
IsotopeFeaturesDictionary.Add(precursorTarget, isotopeFeatures);
}
LcSlicePlot = new PlotModel();
ImsSlicePlot = new PlotModel();
FragmentFeaturesDictionary.Clear();
// var sequence = new Sequence(this.CurrentPeptide, m_aminoAcidSet);
var ionTypeDictionary = sequence.GetProductIons(m_ionTypeFactory.GetAllKnownIonTypes());
double fragmentCount = ionTypeDictionary.Count;
var index = 0;
foreach (var ionTypeKvp in ionTypeDictionary)
{
var ionTypeTuple = ionTypeKvp.Key;
var ion = ionTypeKvp.Value;
var fragmentMz = ion.GetMonoIsotopicMz();
uimfPointList = UimfUtil.GetXic(fragmentMz, CurrentTolerance, UIMFData.FrameType.MS2, DataReader.ToleranceType.PPM);
watershedPointList = WaterShedMapUtil.BuildWatershedMap(uimfPointList);
smoother.Smooth(ref watershedPointList);
var fragmentFeatureBlobList = FeatureDetection.DoWatershedAlgorithm(watershedPointList).ToList();
FragmentFeaturesDictionary.Add(ionTypeTuple, fragmentFeatureBlobList);
index++;
var progress = (int)((index / fragmentCount) * 100);
m_FeatureFinderBackgroundWorker.ReportProgress(progress);
}
OnPropertyChanged("FeatureList");
OnPropertyChanged("LcSlicePlot");
OnPropertyChanged("ImsSlicePlot");
}