/// <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>
/// Reduces the model filtering by height of the component.
/// </summary>
/// <param name="model">The reduced model.</param>
/// <returns>Reduced model</returns>
/// <exception cref="System.ObjectDisposedException">thrown if this object has been disposed.</exception>
/// <exception cref="NotImplementedException">in any other case, as status of filtering threshold specification is unknown</exception>
public GmmModel ReduceModelByComponentHeight(GmmModel model)
{
ValidateDispose();
throw new NotImplementedException(message: nameof(GmmModelling.ReduceModelByComponentHeight)
+ " is not implemented.");
// var matlabModel = model.MatlabStruct;
//// @gmrukwa: this has an issue with opts.thr -> it must be defined, but no one knows how
// var reduced = _gmm.reduce_gmm_by_component_height(matlabModel, model.OriginalMz, model.OriginalMeanSpectrum);
// return new GmmModel(reduced, model) { IsNoiseReduced = 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)));
}
/// <summary>
/// Merges the components supposed to correspond to the same compound.
/// </summary>
/// <param name="model">The merged model.</param>
/// <param name="mzThreshold">The mz threshold used for components matching.</param>
/// <returns>Merged model</returns>
/// <exception cref="System.InvalidOperationException">Applying merging on merged model.</exception>
/// <exception cref="System.ObjectDisposedException">thrown if this object has been disposed.</exception>
public GmmModel MergeComponents(GmmModel model, double mzThreshold = 0.3)
{
ValidateDispose();
if (model.IsMerged)
{
throw new InvalidOperationException(message: "Applying merging on merged model.");
}
var matlabModel = model.MatlabStruct;
var merged = _gmm.merge_gmm_model_components(
matlabModel,
model.OriginalMz,
model.OriginalMeanSpectrum,
mzThreshold);
return(new GmmModel(merged, model)
{
IsMerged = true, MzMergingThreshold = mzThreshold
});
}