public FeatureSet(List <IntensityPoint> intensityPointList)
{
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityPointList);
Smoother.Smooth(ref pointList);
FindFeatures(pointList);
}
public void TestBuildWaterShedMap()
{
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 = 643.27094937;
double ppmTolerance = 50;
var intensityBlock = uimfUtil.GetXicAsArray(targetMz, ppmTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var smoother = new SavitzkyGolaySmoother(5, 2);
smoother.Smooth(ref intensityBlock);
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock, 0, 0).ToList();
Console.WriteLine(intensityBlock.Length);
Assert.AreEqual(270000, intensityBlock.Length);
Assert.AreEqual(12969, pointList.Count);
Assert.AreEqual(pointList[1000].Intensity, 14.844082, 0.0001);
Assert.AreEqual(pointList[5000].Intensity, 5.760, 0.0001);
}
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 IDictionary <int, IEnumerable <FeatureBlob> > GetFeatures(IEnumerable <int> targetBinList, double tolerance, UIMFData.FrameType frameType, DataReader.ToleranceType toleranceType)
{
var resultDictionary = new Dictionary <int, IEnumerable <FeatureBlob> >();
Parallel.ForEach(targetBinList, m_parallelOptions, targetBin =>
{
// Grab a UIMF Util object from the stack
m_uimfUtilStack.TryPop(out var uimfUtil);
var targetMz = uimfUtil.GetMzFromBin(targetBin);
// Do Feature Finding
var intensityBlock = uimfUtil.GetXic(targetMz, tolerance, frameType, toleranceType);
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock);
m_smoother.Smooth(ref pointList);
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList);
// Add result to dictionary
resultDictionary.Add(targetBin, featureList);
// Push the UIMF Util object back onto the stack when we are done with it
m_uimfUtilStack.Push(uimfUtil);
});
return(resultDictionary);
}
public IDictionary <double, IEnumerable <FeatureBlobStatistics> > GetFeatureStatistics(IEnumerable <double> targetMzList, double tolerance, DataReader.FrameType frameType, DataReader.ToleranceType toleranceType)
{
var resultDictionary = new Dictionary <double, IEnumerable <FeatureBlobStatistics> >();
Parallel.ForEach(targetMzList, m_parallelOptions, targetMz =>
{
// Grab a UIMF Util object from the stack
UimfUtil uimfUtil;
m_uimfUtilStack.TryPop(out uimfUtil);
// Do Feature Finding
var intensityBlock = uimfUtil.GetXic(targetMz, tolerance, frameType, toleranceType);
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock);
m_smoother.Smooth(ref pointList);
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList);
// Add result to dictionary
resultDictionary.Add(targetMz, featureList.Select(featureBlob => featureBlob.CalculateStatistics()).ToArray());
// Push the UIMF Util object back onto the stack when we are done with it
m_uimfUtilStack.Push(uimfUtil);
});
return(resultDictionary);
}
private void FindFeatures(double[,] intensityBlock)
{
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock);
var featureBlobList = FeatureDetection.DoWatershedAlgorithm(pointList);
var featureBlobStatList = featureBlobList.Select(featureBlob => featureBlob.Statistics).ToList();
_featureList = featureBlobStatList.Select(featureBlobStatistics => new Feature(featureBlobStatistics)).ToList();
}
public void TestBuildWaterShedMap()
{
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 = 643.27094937;
double ppmTolerance = 50;
var intensityBlock = uimfUtil.GetXicAsArray(targetMz, ppmTolerance, DataReader.FrameType.MS1, DataReader.ToleranceType.PPM);
var smoother = new SavitzkyGolaySmoother(5, 2);
smoother.Smooth(ref intensityBlock);
WaterShedMapUtil.BuildWatershedMap(intensityBlock, 0, 0);
Console.WriteLine(intensityBlock.Length);
}
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 TestFakeSaturatedPoints()
{
var intensityPointList = new List <IntensityPoint>();
for (var i = 0; i < 5; i++)
{
for (var j = 0; j < 5; j++)
{
var point = new IntensityPoint(i, j, 8925);
intensityPointList.Add(point);
}
}
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityPointList).ToList();
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList).ToList();
Console.WriteLine(DateTime.Now + "\tNumPoints = " + pointList.Count + "\tNumFeatures = " + featureList.Count);
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);
}
}
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");
}
public void TestFragmentCorrelation()
{
var fileLocation = @"\\proto-2\UnitTest_Files\MultidimensionalFeatureFinding\BSA_10ugml_IMS6_TOF03_CID_27Aug12_Frodo_Collision_Energy_Collapsed.UIMF";
var uimfUtil = new UimfUtil(fileLocation);
var parentMz = 643.27094937;
double ppmTolerance = 50;
var parentIntensityBlock = uimfUtil.GetXicAsArray(parentMz, ppmTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var smoother = new SavitzkyGolaySmoother(5, 2);
smoother.Smooth(ref parentIntensityBlock);
// ReSharper disable RedundantArgumentDefaultValue
var parentPointList = WaterShedMapUtil.BuildWatershedMap(parentIntensityBlock, 0, 0);
// ReSharper restore RedundantArgumentDefaultValue
var parentFeature = FeatureDetection.DoWatershedAlgorithm(parentPointList).First();
using (var fragmentReader = new StreamReader(@"\\proto-2\UnitTest_Files\MultidimensionalFeatureFinding\testFiles\fragments.csv"))
{
while (!fragmentReader.EndOfStream)
{
var dataLine = fragmentReader.ReadLine();
if (string.IsNullOrWhiteSpace(dataLine))
{
continue;
}
var mzString = dataLine.Trim();
var targetMz = double.Parse(mzString);
TextWriter unsmoothedWriter = new StreamWriter("unsmoothedRaw" + targetMz + ".csv");
var intensityBlock = uimfUtil.GetXicAsArray(targetMz, ppmTolerance, UIMFData.FrameType.MS2, DataReader.ToleranceType.PPM);
var boundX = intensityBlock.GetUpperBound(0);
var boundY = intensityBlock.GetUpperBound(1);
for (var i = 0; i < boundX; i++)
{
var row = new StringBuilder();
for (var j = 0; j < boundY; j++)
{
row.Append(intensityBlock[i, j] + ",");
}
unsmoothedWriter.WriteLine(row.ToString());
}
unsmoothedWriter.Close();
smoother.Smooth(ref intensityBlock);
TextWriter smoothedWriter = new StreamWriter("smoothedRaw" + targetMz + ".csv");
for (var i = 0; i < boundX; i++)
{
var row = new StringBuilder();
for (var j = 0; j < boundY; j++)
{
row.Append(intensityBlock[i, j] + ",");
}
smoothedWriter.WriteLine(row.ToString());
}
smoothedWriter.Close();
// ReSharper disable RedundantArgumentDefaultValue
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock, 0, 0);
// ReSharper restore RedundantArgumentDefaultValue
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList);
featureList = featureList.Where(x => x.PointList.Count > 50).OrderByDescending(x => x.PointList.Count);
Console.WriteLine("******************************************************");
Console.WriteLine("targetMz = " + targetMz);
foreach (var featureBlob in featureList)
{
// ReSharper disable once UnusedVariable
var rSquared = FeatureCorrelator.CorrelateFeatures(parentFeature, featureBlob);
//Point mostIntensePoint = featureBlob.PointList.OrderByDescending(x => x.Intensity).First();
//Console.WriteLine("Num Points = " + featureBlob.PointList.Count + "\tLC = " + mostIntensePoint.ScanLc + "\tIMS = " + mostIntensePoint.ScanIms + "\tIntensity = " + mostIntensePoint.Intensity + "\tRSquared = " + rSquared);
}
}
}
}
public void TestDoWaterShedAlgorithmPrecursorAndFragments()
{
var fileLocation = @"\\proto-2\UnitTest_Files\MultidimensionalFeatureFinding\BSA_10ugml_IMS6_TOF03_CID_27Aug12_Frodo_Collision_Energy_Collapsed.UIMF";
var uimfUtil = new UimfUtil(fileLocation);
var parentMz = 643.27094937;
double ppmTolerance = 50;
var parentIntensityBlock = uimfUtil.GetXicAsArray(parentMz, ppmTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var smoother = new SavitzkyGolaySmoother(5, 2);
smoother.Smooth(ref parentIntensityBlock);
// ReSharper disable RedundantArgumentDefaultValue
var parentPointList = WaterShedMapUtil.BuildWatershedMap(parentIntensityBlock, 0, 0);
// ReSharper restore RedundantArgumentDefaultValue
var parentFeature = FeatureDetection.DoWatershedAlgorithm(parentPointList).First();
var statistics = parentFeature.Statistics;
var scanLcMin = statistics.ScanLcMin;
var scanLcMax = statistics.ScanLcMax;
var scanImsMin = statistics.ScanImsMin;
var scanImsMax = statistics.ScanImsMax;
using (var fragmentReader = new StreamReader(@"\\proto-2\UnitTest_Files\MultidimensionalFeatureFinding\testFiles\OneFragment.csv"))
{
while (!fragmentReader.EndOfStream)
{
var dataLine = fragmentReader.ReadLine();
if (string.IsNullOrWhiteSpace(dataLine))
{
continue;
}
var mzString = dataLine.Trim();
var targetMz = double.Parse(mzString);
TextWriter unsmoothedWriter = new StreamWriter("unsmoothedRaw" + targetMz + ".csv");
var intensityBlock = uimfUtil.GetXicAsArray(targetMz, ppmTolerance, UIMFData.FrameType.MS2, scanLcMin, scanLcMax, scanImsMin, scanImsMax, DataReader.ToleranceType.PPM);
var boundX = intensityBlock.GetUpperBound(0);
var boundY = intensityBlock.GetUpperBound(1);
for (var i = 0; i < boundX; i++)
{
var row = new StringBuilder();
for (var j = 0; j < boundY; j++)
{
row.Append(intensityBlock[i, j] + ",");
}
unsmoothedWriter.WriteLine(row.ToString());
}
unsmoothedWriter.Close();
smoother.Smooth(ref intensityBlock);
TextWriter smoothedWriter = new StreamWriter("smoothedRaw" + targetMz + ".csv");
for (var i = 0; i < boundX; i++)
{
var row = new StringBuilder();
for (var j = 0; j < boundY; j++)
{
row.Append(intensityBlock[i, j] + ",");
}
smoothedWriter.WriteLine(row.ToString());
}
smoothedWriter.Close();
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock, scanLcMin, scanImsMin).ToList();
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList).ToList();
Assert.AreEqual(430, pointList.Count);
Assert.AreEqual(37, featureList.Count);
Console.WriteLine("******************************************************");
Console.WriteLine("targetMz = " + targetMz);
for (var i = 0; i < featureList.Count; i++)
{
var featureBlob = featureList[i];
var mostIntensePoint = featureBlob.PointList.OrderByDescending(x => x.Intensity).First();
Console.WriteLine("Num Points = " + featureBlob.PointList.Count + "\tLC = " + mostIntensePoint.ScanLc + "\tIMS = " + mostIntensePoint.ScanIms + "\tIntensity = " + mostIntensePoint.Intensity);
if (i != 1)
{
continue;
}
// Num Points = 34 LC = 138 IMS = 122 Intensity = 79.5697959183673
Assert.AreEqual(34, featureBlob.PointList.Count);
Assert.AreEqual(138, mostIntensePoint.ScanLc);
Assert.AreEqual(122, mostIntensePoint.ScanIms);
Assert.AreEqual(79.569796, mostIntensePoint.Intensity, 0.0001);
}
}
}
}
public void TestDoWaterShedAlgorithmOutput()
{
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 = 643.27094937;
double ppmTolerance = 50;
TextWriter unsmoothedWriter = new StreamWriter("unsmoothedRaw.csv");
var intensityBlock = uimfUtil.GetXicAsArray(targetMz, ppmTolerance, UIMFData.FrameType.MS1, DataReader.ToleranceType.PPM);
var boundX = intensityBlock.GetUpperBound(0);
var boundY = intensityBlock.GetUpperBound(1);
for (var i = 0; i < boundX; i++)
{
var row = new StringBuilder();
for (var j = 0; j < boundY; j++)
{
row.Append(intensityBlock[i, j] + ",");
}
unsmoothedWriter.WriteLine(row.ToString());
}
unsmoothedWriter.Close();
var smoother = new SavitzkyGolaySmoother(5, 2);
smoother.Smooth(ref intensityBlock);
TextWriter smoothedWriter = new StreamWriter("smoothedRaw.csv");
for (var i = 0; i < boundX; i++)
{
var row = new StringBuilder();
for (var j = 0; j < boundY; j++)
{
row.Append(intensityBlock[i, j] + ",");
}
smoothedWriter.WriteLine(row.ToString());
}
smoothedWriter.Close();
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock, 0, 0);
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList).ToList();
Console.WriteLine(featureList.Count);
var sortedFeatureList = featureList.OrderByDescending(x => x.PointList.Count);
TextWriter intensityWriter = new StreamWriter("intensities.csv");
foreach (var featureBlob in sortedFeatureList)
{
var mostIntensePoint = featureBlob.PointList.First();
Console.WriteLine("Num Points = " + featureBlob.PointList.Count + "\tLC = " + mostIntensePoint.ScanLc + "\tIMS = " + mostIntensePoint.ScanIms + "\tIntensity = " + mostIntensePoint.Intensity);
intensityWriter.WriteLine(mostIntensePoint.Intensity.ToString(CultureInfo.InvariantCulture));
}
}
public void TestDoWaterShedAlgorithmPrecursorAndFragments()
{
var fileLocation = @"\\proto-2\UnitTest_Files\MultidimensionalFeatureFinding\BSA_10ugml_IMS6_TOF03_CID_27Aug12_Frodo_Collision_Energy_Collapsed.UIMF";
var uimfUtil = new UimfUtil(fileLocation);
var parentMz = 643.27094937;
double ppmTolerance = 50;
var parentIntensityBlock = uimfUtil.GetXicAsArray(parentMz, ppmTolerance, DataReader.FrameType.MS1, DataReader.ToleranceType.PPM);
var smoother = new SavitzkyGolaySmoother(5, 2);
smoother.Smooth(ref parentIntensityBlock);
var parentPointList = WaterShedMapUtil.BuildWatershedMap(parentIntensityBlock, 0, 0);
var parentFeature = FeatureDetection.DoWatershedAlgorithm(parentPointList).First();
var statistics = parentFeature.Statistics;
var scanLcMin = statistics.ScanLcMin;
var scanLcMax = statistics.ScanLcMax;
var scanImsMin = statistics.ScanImsMin;
var scanImsMax = statistics.ScanImsMax;
using (TextReader fragmentReader = new StreamReader(@"..\..\..\testFiles\OneFragment.csv"))
{
var line = "";
while ((line = fragmentReader.ReadLine()) != null)
{
var mzString = line.Trim();
var targetMz = double.Parse(mzString);
TextWriter unsmoothedWriter = new StreamWriter("unsmoothedRaw" + targetMz + ".csv");
var intensityBlock = uimfUtil.GetXicAsArray(targetMz, ppmTolerance, DataReader.FrameType.MS2, scanLcMin, scanLcMax, scanImsMin, scanImsMax, DataReader.ToleranceType.PPM);
var boundX = intensityBlock.GetUpperBound(0);
var boundY = intensityBlock.GetUpperBound(1);
for (var i = 0; i < boundX; i++)
{
var row = new StringBuilder();
for (var j = 0; j < boundY; j++)
{
row.Append(intensityBlock[i, j] + ",");
}
unsmoothedWriter.WriteLine(row.ToString());
}
unsmoothedWriter.Close();
smoother.Smooth(ref intensityBlock);
TextWriter smoothedWriter = new StreamWriter("smoothedRaw" + targetMz + ".csv");
for (var i = 0; i < boundX; i++)
{
var row = new StringBuilder();
for (var j = 0; j < boundY; j++)
{
row.Append(intensityBlock[i, j] + ",");
}
smoothedWriter.WriteLine(row.ToString());
}
smoothedWriter.Close();
var pointList = WaterShedMapUtil.BuildWatershedMap(intensityBlock, scanLcMin, scanImsMin);
var featureList = FeatureDetection.DoWatershedAlgorithm(pointList);
Console.WriteLine("******************************************************");
Console.WriteLine("targetMz = " + targetMz);
foreach (var featureBlob in featureList)
{
var mostIntensePoint = featureBlob.PointList.OrderByDescending(x => x.Intensity).First();
Console.WriteLine("Num Points = " + featureBlob.PointList.Count + "\tLC = " + mostIntensePoint.ScanLc + "\tIMS = " + mostIntensePoint.ScanIms + "\tIntensity = " + mostIntensePoint.Intensity);
}
}
}
}
