/// <summary>
/// Perform FFT-based peak alignment.
/// </summary>
/// <param name="dataset">Input dataset.</param>
/// <returns>Aligned dataset.</returns>
/// <exception cref="System.ObjectDisposedException">thrown if this object has been disposed.</exception>
public IDataset AlignPeaksFft(IDataset dataset)
{
ValidateDispose();
var pafftResult = _preprocessing.pafft(mz: dataset.GetRawMzArray(), data: dataset.GetRawIntensities());
return(new BasicTextDataset(
mz: dataset.GetRawMzArray(),
data: (double[, ])pafftResult,
coordinates: dataset.GetRawSpacialCoordinates(is2D: true)));
}
/// <summary>
/// Removes the baseline.
/// </summary>
/// <param name="dataset">Input dataset.</param>
/// <returns>Dataset without baseline.</returns>
/// <exception cref="System.ObjectDisposedException">thrown if this object has been disposed.</exception>
public IDataset RemoveBaseline(IDataset dataset)
{
ValidateDispose();
var baselineRemovalResult =
_preprocessing.remove_baseline(mz: dataset.GetRawMzArray(), data: dataset.GetRawIntensities());
return(new BasicTextDataset(
mz: dataset.GetRawMzArray(),
data: (double[, ])baselineRemovalResult,
coordinates: dataset.GetRawSpacialCoordinates(is2D: true)));
}
public void CreateFromFileTest()
{
Assert.DoesNotThrow(code: () => { _dataset = new BasicTextDataset(textFilePath: "small-test.txt"); },
message: "Dataset failed to initialize from file.");
Assert.Throws <IOException>(code: () =>
{
_dataset = new BasicTextDataset(textFilePath: "wrong-filepath.txt");
},
message: "Dataset has been initialized using wrong file path.");
var coordinates = _dataset.SpatialCoordinates;
var enumerator = coordinates.GetEnumerator();
enumerator.MoveNext();
var sc = enumerator.Current;
Assert.AreEqual(expected: 1,
actual: sc.X,
message: "Spatial coordinates differ");
Assert.AreEqual(expected: 1,
actual: sc.Y,
message: "Spatial coordinates differ");
Assert.AreEqual(expected: 0,
actual: sc.Z,
message: "Spatial coordinates differ");
enumerator.MoveNext();
sc = enumerator.Current;
Assert.AreEqual(expected: 2,
actual: sc.X,
message: "Spatial coordinates differ in second spectrum");
Assert.AreEqual(expected: 1,
actual: sc.Y,
message: "Spatial coordinates differ in second spectrum");
Assert.AreEqual(expected: 0,
actual: sc.Z,
message: "Spatial coordinates differ in second spectrum");
Assert.AreEqual(expected: _dataset.GetRawMzArray(),
actual: new[] { 899.99, 902.58, 912.04 },
message: "The m/zs differ");
Assert.AreEqual(expected: _dataset.GetRawIntensityArray(spectrumIdx: 0),
actual: new[] { 12.0, 20.0, 0.0 },
message: "The intensities of first spectrum differs");
}
/// <summary>
/// Estimates the GMM model from the data set.
/// </summary>
/// <param name="dataset">Input dataset.</param>
/// <returns>Estimated model</returns>
/// <exception cref="System.ObjectDisposedException">thrown if this object has been disposed.</exception>
public GmmModel EstimateGmm(IDataset dataset)
{
ValidateDispose();
var originalMz = dataset.GetRawMzArray();
var matlabModel = _gmm.estimate_gmm(originalMz, data: dataset.GetRawIntensities());
var model = new GmmModel(matlabModel, originalMz);
return(model);
}
/// <summary>
/// Normalizes dataset by TIC-based method.
/// </summary>
/// <param name="dataset">Input dataset.</param>
/// <returns>Normalized dataset.</returns>
/// <exception cref="System.ObjectDisposedException">thrown if this object has been disposed.</exception>
public IDataset NormalizeByTic(IDataset dataset)
{
ValidateDispose();
var normalizationResult = _preprocessing.ticnorm(data: dataset.GetRawIntensities());
return(new BasicTextDataset(
mz: dataset.GetRawMzArray(),
data: (double[, ])normalizationResult,
coordinates: dataset.GetRawSpacialCoordinates(is2D: true)));
}
/// <summary>
/// Applies the GMM model onto data.
/// </summary>
/// <param name="model">The model.</param>
/// <param name="dataset">Input dataset.</param>
/// <returns>Convolved data.</returns>
/// <exception cref="System.ObjectDisposedException">thrown if this object has been disposed.</exception>
/// <exception cref="InvalidOperationException">Applying model build on different m/z axis.</exception>
public IDataset ApplyGmm(GmmModel model, IDataset dataset)
{
ValidateDispose();
if (!dataset.GetRawMzArray()
.SequenceEqual(model.OriginalMz))
{
throw new InvalidOperationException(message: "Applying model built on different m/z axis.");
}
var matlabModel = model.MatlabStruct;
var applyResult = _gmm.apply_gmm(matlabModel, data: dataset.GetRawIntensities(), mz: dataset.GetRawMzArray());
var data = (double[, ])((MWStructArray)model.MatlabStruct).GetField(fieldName: "mu");
var mz = new double[data.GetLength(dimension: 0)];
Buffer.BlockCopy(data, srcOffset: 0, dst: mz, dstOffset: 0, count: data.GetLength(dimension: 0));
return(new BasicTextDataset(mz, data: (double[, ])applyResult, coordinates: dataset.GetRawSpacialCoordinates(is2D: true)));
}
