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 TestGetXic()
{
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, DataReader.FrameType.MS1, DataReader.ToleranceType.PPM);
Console.WriteLine(intensityBlock.Length);
}
public void Test3DSmooth()
{
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);
Console.WriteLine(intensityBlock.Length);
}
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 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);
}
}
}
}