/// <summary>
/// generates a fake deconvolution solution for the given test spectrum
/// in order to make sure that the deconvolution results are being applied
/// correctly to scale peaks in the test spectrum
/// </summary>
private static void TestPeakIntensityCorrection(MsDataSpectrum testSpectrum,
AbstractIsoWindowMapper isoMapper,
AbstractDemultiplexer demultiplexer)
{
// Store a reference to the old spectrum processor
var oldProcessor = demultiplexer.SpectrumProcessor;
MsxDeconvSolverHandler db = new MsxDeconvSolverHandler(100, 120, 35);
int[] isoIndices;
int[] deconvIndices;
double[] mask = new double[100];
isoMapper.GetWindowMask(testSpectrum, out isoIndices, out deconvIndices, ref mask);
db.SetDeconvIndices(deconvIndices);
Assert.IsTrue(deconvIndices.Contains(50));
Assert.IsTrue(deconvIndices.Contains(47));
Assert.IsTrue(deconvIndices.Contains(15));
Assert.IsTrue(deconvIndices.Contains(17));
Assert.IsTrue(deconvIndices.Contains(74));
Assert.AreEqual(5, deconvIndices.Length);
// Prepare the transition binner with a precursor containing transitions overlapping
// peaks in the test spectrum
List <double> precursors = new List <double>();
List <KeyValuePair <double, double> > transitions = new List <KeyValuePair <double, double> >();
var precVals = new[] { 710.57 };
var transMzs = new[] { 372.18, 373.1588, 373.1794, 375.2, 379.23, 387.19 };
var transWidths = new[] { 0.3, 0.04, 0.02, 1.0, 1.0, 1.0 };
foreach (var precMz in precVals)
{
for (int i = 0; i < isoIndices.Length; ++i)
{
var transMz = transMzs[i];
var transWidth = transWidths[i];
precursors.Add(precMz);
transitions.Add(new KeyValuePair <double, double>(transMz, transWidth));
}
}
var transBinner = new TransitionBinner(precursors, transitions, isoMapper);
var binIndicesSet = new HashSet <int>(transBinner.BinsForDeconvWindows(deconvIndices));
double[][] deconvIntensities = new double[deconvIndices.Length][];
double[][] deconvMzs = new double[deconvIndices.Length][];
for (int i = 0; i < deconvIndices.Length; ++i)
{
deconvIntensities[i] = new double[testSpectrum.Mzs.Length];
deconvMzs[i] = new double[testSpectrum.Mzs.Length];
}
List <int> binIndicesList = binIndicesSet.ToList();
binIndicesList.Sort();
// Use each transition bin index to test a different possible
// type of demultiplexed solution
int numDeMultiplexedTrans = binIndicesSet.Count;
double[] peakSums = new double[numDeMultiplexedTrans];
// Initialize the deconvBlock
db.Solution.Resize(100, binIndicesList.Count);
db.Solution.Clear();
// Transition index 0, each row is a precursor
// the values for each precursor are the relative contribution
// of that precursor to the observed (convolved) intensity of the peak
db.Solution.Matrix[2, 0] = 0.0;
db.Solution.Matrix[1, 0] = 0.0;
db.Solution.Matrix[0, 0] = 0.0;
db.Solution.Matrix[3, 0] = 0.0;
db.Solution.Matrix[4, 0] = 0.0;
peakSums[0] = 0.0;
// Transition index 1, each row is a precursor
db.Solution.Matrix[2, 1] = 1.0;
db.Solution.Matrix[1, 1] = 1.0;
db.Solution.Matrix[0, 1] = 2.0;
db.Solution.Matrix[3, 1] = 1.0;
db.Solution.Matrix[4, 1] = 1.0;
peakSums[1] = 6.0;
// Transition index 2, each row is a precursor
db.Solution.Matrix[2, 2] = 2.0;
db.Solution.Matrix[1, 2] = 1.0;
db.Solution.Matrix[0, 2] = 3.0;
db.Solution.Matrix[3, 2] = 3.0;
db.Solution.Matrix[4, 2] = 1.0;
peakSums[2] = 10.0;
// Transition index 3, each row is a precursor
db.Solution.Matrix[2, 3] = 0.0;
db.Solution.Matrix[1, 3] = 0.0;
db.Solution.Matrix[0, 3] = 1.0;
db.Solution.Matrix[3, 3] = 0.0;
db.Solution.Matrix[4, 3] = 0.0;
peakSums[3] = 1.0;
// Transition index 4, each row is a precursor
db.Solution.Matrix[2, 4] = 1.0;
db.Solution.Matrix[1, 4] = 1.0;
db.Solution.Matrix[0, 4] = 1.0;
db.Solution.Matrix[3, 4] = 1.0;
db.Solution.Matrix[4, 4] = 1.0;
peakSums[4] = 5.0;
// Transition bin index (in transBinner) -> solution transition index (0-4 above), needed for
// CorrectPeakIntensities call
Dictionary <int, int> binToDeconvIndex = new Dictionary <int, int>(numDeMultiplexedTrans);
int numBinIndices = binIndicesList.Count;
for (int i = 0; i < numBinIndices; ++i)
{
binToDeconvIndex[binIndicesList[i]] = i;
}
var queryBinEnumerator = transBinner.BinsFromValues(testSpectrum.Mzs, true);
demultiplexer.SpectrumProcessor = new SpectrumProcessor(165, isoMapper, transBinner);
// Apply the peak intensity correction
demultiplexer.CorrectPeakIntensitiesTest(testSpectrum, binIndicesSet, peakSums,
queryBinEnumerator, db, ref deconvIntensities,
ref deconvMzs);
// Check that the five solutions defined above were applied correctly
// by CorrectPeakIntensities
// If all precursors contribute 0 intensity, the peak should be zero for every
// deconvolved spectrum
for (int i = 0; i < deconvIndices.Length; ++i)
{
Assert.AreEqual(deconvIntensities[i][binToDeconvIndex[0]], 0.0);
}
// Find the index of the demultiplexed spectrum corresponding to the precursor
// at 710.57 m/z for which we generated the dummy demultiplexing solution for
int windowIndex;
isoMapper.TryGetDeconvFromMz(710.57, out windowIndex);
Assert.AreEqual(50, windowIndex);
int isoIndex = deconvIndices.IndexOf(i => i == windowIndex);
Assert.AreNotEqual(-1, isoIndex);
// This peak falls in one transition bin (transition index 1)
// 47 is the index of a peak in the test spectrum
var originalIntensity = testSpectrum.Intensities[47];
var expectedIntensity = originalIntensity * (2.0 / 6.0);
Assert.AreEqual(deconvIntensities[isoIndex][47], expectedIntensity, 0.00001);
// This peak falls in one transitions bin (transition index 2)
originalIntensity = testSpectrum.Intensities[50];
expectedIntensity = originalIntensity * (3.0 / 10.0);
Assert.AreEqual(deconvIntensities[isoIndex][50], expectedIntensity, 0.00001);
// This peak falls in both transition indices 1 and 2, the expected adjusted
// intensity should be the average of the solution from each transition bin
originalIntensity = testSpectrum.Intensities[49];
expectedIntensity = originalIntensity * (19.0 / 60.0);
Assert.AreEqual(deconvIntensities[isoIndex][49], expectedIntensity, 0.00001);
// This peak falls in transition index 3, and the demultiplexing spectra
// indicates that all of the intensity of teh original peak comes from
// the precursor window at isoIndex that's being queried. The peak intensity
// should not change
originalIntensity = testSpectrum.Intensities[108];
expectedIntensity = originalIntensity;
Assert.AreEqual(deconvIntensities[isoIndex][108], expectedIntensity, 0.00001);
// This peak falls in one transition bin (transition index 5)
originalIntensity = testSpectrum.Intensities[149];
expectedIntensity = originalIntensity * (1.0 / 5.0);
Assert.AreEqual(deconvIntensities[isoIndex][149], expectedIntensity, 0.00001);
// Undo changes to the spectrum processor in case this demultiplexer object is
// reused
demultiplexer.SpectrumProcessor = oldProcessor;
}
/// <summary>
/// generates a fake deconvolution solution for the given test spectrum
/// in order to make sure that the deconvolution results are being applied
/// correctly to scale peaks in the test spectrum
/// </summary>
private static void TestPeakIntensityCorrection(MsDataSpectrum testSpectrum,
AbstractIsoWindowMapper isoMapper,
AbstractDemultiplexer demultiplexer)
{
// Store a reference to the old spectrum processor
var oldProcessor = demultiplexer.SpectrumProcessor;
MsxDeconvSolverHandler db = new MsxDeconvSolverHandler(100, 120, 35);
int[] isoIndices;
int[] deconvIndices;
double[] mask = new double[100];
isoMapper.GetWindowMask(testSpectrum, out isoIndices, out deconvIndices, ref mask);
db.SetDeconvIndices(deconvIndices);
Assert.IsTrue(deconvIndices.Contains(50));
Assert.IsTrue(deconvIndices.Contains(47));
Assert.IsTrue(deconvIndices.Contains(15));
Assert.IsTrue(deconvIndices.Contains(17));
Assert.IsTrue(deconvIndices.Contains(74));
Assert.AreEqual(5, deconvIndices.Length);
// Prepare the transition binner with a precursor containing transitions overlapping
// peaks in the test spectrum
List<double> precursors = new List<double>();
List<KeyValuePair<double, double>> transitions = new List<KeyValuePair<double, double>>();
var precVals = new[] {710.57};
var transMzs = new[] {372.18, 373.1588, 373.1794, 375.2, 379.23, 387.19};
var transWidths = new[] {0.3, 0.04, 0.02, 1.0, 1.0, 1.0};
foreach (var precMz in precVals)
{
for (int i = 0; i < isoIndices.Length; ++i)
{
var transMz = transMzs[i];
var transWidth = transWidths[i];
precursors.Add(precMz);
transitions.Add(new KeyValuePair<double, double>(transMz, transWidth));
}
}
var transBinner = new TransitionBinner(precursors, transitions, isoMapper);
var binIndicesSet = new HashSet<int>(transBinner.BinsForDeconvWindows(deconvIndices));
double[][] deconvIntensities = new double[deconvIndices.Length][];
double[][] deconvMzs = new double[deconvIndices.Length][];
for (int i = 0; i < deconvIndices.Length; ++i)
{
deconvIntensities[i] = new double[testSpectrum.Mzs.Length];
deconvMzs[i] = new double[testSpectrum.Mzs.Length];
}
List<int> binIndicesList = binIndicesSet.ToList();
binIndicesList.Sort();
// Use each transition bin index to test a different possible
// type of demultiplexed solution
int numDeMultiplexedTrans = binIndicesSet.Count;
double[] peakSums = new double[numDeMultiplexedTrans];
// Initialize the deconvBlock
db.Solution.Resize(100, binIndicesList.Count);
db.Solution.Clear();
// Transition index 0, each row is a precursor
// the values for each precursor are the relative contribution
// of that precursor to the observed (convolved) intensity of the peak
db.Solution.Matrix[2, 0] = 0.0;
db.Solution.Matrix[1, 0] = 0.0;
db.Solution.Matrix[0, 0] = 0.0;
db.Solution.Matrix[3, 0] = 0.0;
db.Solution.Matrix[4, 0] = 0.0;
peakSums[0] = 0.0;
// Transition index 1, each row is a precursor
db.Solution.Matrix[2, 1] = 1.0;
db.Solution.Matrix[1, 1] = 1.0;
db.Solution.Matrix[0, 1] = 2.0;
db.Solution.Matrix[3, 1] = 1.0;
db.Solution.Matrix[4, 1] = 1.0;
peakSums[1] = 6.0;
// Transition index 2, each row is a precursor
db.Solution.Matrix[2, 2] = 2.0;
db.Solution.Matrix[1, 2] = 1.0;
db.Solution.Matrix[0, 2] = 3.0;
db.Solution.Matrix[3, 2] = 3.0;
db.Solution.Matrix[4, 2] = 1.0;
peakSums[2] = 10.0;
// Transition index 3, each row is a precursor
db.Solution.Matrix[2, 3] = 0.0;
db.Solution.Matrix[1, 3] = 0.0;
db.Solution.Matrix[0, 3] = 1.0;
db.Solution.Matrix[3, 3] = 0.0;
db.Solution.Matrix[4, 3] = 0.0;
peakSums[3] = 1.0;
// Transition index 4, each row is a precursor
db.Solution.Matrix[2, 4] = 1.0;
db.Solution.Matrix[1, 4] = 1.0;
db.Solution.Matrix[0, 4] = 1.0;
db.Solution.Matrix[3, 4] = 1.0;
db.Solution.Matrix[4, 4] = 1.0;
peakSums[4] = 5.0;
// Transition bin index (in transBinner) -> solution transition index (0-4 above), needed for
// CorrectPeakIntensities call
Dictionary<int, int> binToDeconvIndex = new Dictionary<int, int>(numDeMultiplexedTrans);
int numBinIndices = binIndicesList.Count;
for (int i = 0; i < numBinIndices; ++i)
binToDeconvIndex[binIndicesList[i]] = i;
var queryBinEnumerator = transBinner.BinsFromValues(testSpectrum.Mzs, true);
demultiplexer.SpectrumProcessor = new SpectrumProcessor(165, isoMapper, transBinner);
// Apply the peak intensity correction
demultiplexer.CorrectPeakIntensitiesTest(testSpectrum, binIndicesSet, peakSums,
queryBinEnumerator, db, ref deconvIntensities,
ref deconvMzs);
// Check that the five solutions defined above were applied correctly
// by CorrectPeakIntensities
// If all precursors contribute 0 intensity, the peak should be zero for every
// deconvolved spectrum
for (int i = 0; i < deconvIndices.Length; ++i)
{
Assert.AreEqual(deconvIntensities[i][binToDeconvIndex[0]], 0.0);
}
// Find the index of the demultiplexed spectrum corresponding to the precursor
// at 710.57 m/z for which we generated the dummy demultiplexing solution for
int windowIndex;
isoMapper.TryGetDeconvFromMz(710.57, out windowIndex);
Assert.AreEqual(50, windowIndex);
int isoIndex = deconvIndices.IndexOf(i => i == windowIndex);
Assert.AreNotEqual(-1 , isoIndex);
// This peak falls in one transition bin (transition index 1)
// 47 is the index of a peak in the test spectrum
var originalIntensity = testSpectrum.Intensities[47];
var expectedIntensity = originalIntensity*(2.0/6.0);
Assert.AreEqual(deconvIntensities[isoIndex][47], expectedIntensity, 0.00001);
// This peak falls in one transitions bin (transition index 2)
originalIntensity = testSpectrum.Intensities[50];
expectedIntensity = originalIntensity*(3.0/10.0);
Assert.AreEqual(deconvIntensities[isoIndex][50], expectedIntensity, 0.00001);
// This peak falls in both transition indices 1 and 2, the expected adjusted
// intensity should be the average of the solution from each transition bin
originalIntensity = testSpectrum.Intensities[49];
expectedIntensity = originalIntensity*(19.0/60.0);
Assert.AreEqual(deconvIntensities[isoIndex][49], expectedIntensity, 0.00001);
// This peak falls in transition index 3, and the demultiplexing spectra
// indicates that all of the intensity of teh original peak comes from
// the precursor window at isoIndex that's being queried. The peak intensity
// should not change
originalIntensity = testSpectrum.Intensities[108];
expectedIntensity = originalIntensity;
Assert.AreEqual(deconvIntensities[isoIndex][108], expectedIntensity, 0.00001);
// This peak falls in one transition bin (transition index 5)
originalIntensity = testSpectrum.Intensities[149];
expectedIntensity = originalIntensity * (1.0/5.0);
Assert.AreEqual(deconvIntensities[isoIndex][149], expectedIntensity, 0.00001);
// Undo changes to the spectrum processor in case this demultiplexer object is
// reused
demultiplexer.SpectrumProcessor = oldProcessor;
}
private static void TestIsolationWindowMapper(AbstractIsoWindowMapper isoMapper, MsDataFileImpl file, double width)
{
// Check the first five spectra in the file
for (int checkIndex = 0; checkIndex < 5; ++checkIndex)
{
var spectrum = file.GetSpectrum(checkIndex);
var precursors = spectrum.Precursors;
List <int> isoIndices = new List <int>();
// Make sure that each precursor read from the file is included in the isolation
// window mapper
foreach (var precursor in precursors)
{
int index;
Assert.IsTrue(precursor.IsolationMz.HasValue);
Assert.IsTrue(isoMapper.TryGetWindowIndex(precursor.IsolationMz.Value, out index));
isoIndices.Add(index);
}
int[] isoIndicesFromMapper;
int[] overlapIndicesFromMapper;
double[] mask = new double[isoMapper.NumWindows];
// Make sure the isolation windows called from GetWindowMask match those
// extracted from the spectrum manually above using TryGetWindowIndex
isoMapper.GetWindowMask(spectrum, out isoIndicesFromMapper, out overlapIndicesFromMapper, ref mask);
Assert.AreEqual(isoIndices.Count, isoIndicesFromMapper.Length);
foreach (int index in isoIndicesFromMapper)
{
Assert.IsTrue(isoIndices.Contains(index));
}
// Make sure the overlapIndicesFromMapper matches the mask
for (int i = 0; i < mask.Length; ++i)
{
if (mask[i] < 0.5)
{
Assert.AreEqual(0.0, mask[i]);
}
else
{
Assert.AreEqual(1.0, mask[i]);
Assert.IsTrue(overlapIndicesFromMapper.Contains(i));
}
}
}
var testMzs = new[] { 553.49, 623.7, 859, 658.55, 768.7, 621.52 };
// For each test m/z, get the matching isolation window from isoMapper and
// make sure the m/z does indeed fall within the window
foreach (var checkMz in testMzs)
{
int windowIndex;
Assert.IsTrue(isoMapper.TryGetWindowFromMz(checkMz, out windowIndex));
var matchWindowCenterMz = isoMapper.GetPrecursor(windowIndex);
Assert.IsTrue(matchWindowCenterMz.IsolationMz.HasValue);
// Check that mz is within window (width/2 )
Assert.IsTrue(Math.Abs(matchWindowCenterMz.IsolationMz.Value - checkMz) < width / 2);
}
// Test out of range precursors
int dummyIndex;
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(315.25, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(1005.2, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
}
private static void TestIsolationWindowMapper(AbstractIsoWindowMapper isoMapper, MsDataFileImpl file, double width)
{
// Check the first five spectra in the file
for (int checkIndex = 0 ; checkIndex < 5; ++checkIndex)
{
var spectrum = file.GetSpectrum(checkIndex);
var precursors = spectrum.Precursors;
List<int> isoIndices = new List<int>();
// Make sure that each precursor read from the file is included in the isolation
// window mapper
foreach (var precursor in precursors)
{
int index;
Assert.IsTrue(precursor.IsolationMz.HasValue);
Assert.IsTrue(isoMapper.TryGetWindowIndex(precursor.IsolationMz.Value, out index));
isoIndices.Add(index);
}
int[] isoIndicesFromMapper;
int[] overlapIndicesFromMapper;
double[] mask = new double[isoMapper.NumWindows];
// Make sure the isolation windows called from GetWindowMask match those
// extracted from the spectrum manually above using TryGetWindowIndex
isoMapper.GetWindowMask(spectrum, out isoIndicesFromMapper, out overlapIndicesFromMapper, ref mask);
Assert.AreEqual(isoIndices.Count,isoIndicesFromMapper.Length);
foreach (int index in isoIndicesFromMapper)
{
Assert.IsTrue(isoIndices.Contains(index));
}
// Make sure the overlapIndicesFromMapper matches the mask
for (int i = 0; i < mask.Length; ++i)
{
if (mask[i] < 0.5)
Assert.AreEqual(0.0, mask[i]);
else
{
Assert.AreEqual(1.0, mask[i]);
Assert.IsTrue(overlapIndicesFromMapper.Contains(i));
}
}
}
var testMzs = new[] {553.49, 623.7, 859, 658.55, 768.7, 621.52};
// For each test m/z, get the matching isolation window from isoMapper and
// make sure the m/z does indeed fall within the window
foreach (var checkMz in testMzs)
{
int windowIndex;
Assert.IsTrue(isoMapper.TryGetWindowFromMz(checkMz, out windowIndex));
var matchWindowCenterMz = isoMapper.GetPrecursor(windowIndex);
Assert.IsTrue(matchWindowCenterMz.IsolationMz.HasValue);
// Check that mz is within window (width/2 )
Assert.IsTrue(Math.Abs(matchWindowCenterMz.IsolationMz.Value - checkMz) < width/2);
}
// Test out of range precursors
int dummyIndex;
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(315.25, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(1005.2, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
}
