/// <summary>
/// Creates the corresponding grouping strategy out of the CrossPRESSCalculation enumeration in plsOptions.
/// </summary>
/// <param name="plsOptions">The options for PLS analysis</param>
/// <returns>The used grouping strategy. Returns null if no cross validation is choosen.</returns>
public static ICrossValidationGroupingStrategy GetGroupingStrategy(MultivariateAnalysisOptions plsOptions)
{
return GetGroupingStrategy(plsOptions.CrossPRESSCalculation);
}
/// <summary>
/// Asks the user for the maximum number of factors and the cross validation calculation.
/// </summary>
/// <param name="options">The PLS options to ask for. On return, this is the user's choice.</param>
/// <param name="preprocessOptions">The spectral preprocessing options to ask for (output).</param>
/// <returns>True if the user has made his choice, false if the user pressed the Cancel button.</returns>
public static bool QuestPLSAnalysisOptions(out MultivariateAnalysisOptions options, out SpectralPreprocessingOptions preprocessOptions)
{
options = new MultivariateAnalysisOptions();
options.MaxNumberOfFactors =20;
options.CrossPRESSCalculation = CrossPRESSCalculationType.ExcludeGroupsOfSimilarMeasurements;
PLSStartAnalysisController ctrlAA = new PLSStartAnalysisController(options);
PLSStartAnalysisControl viewAA = new PLSStartAnalysisControl();
ctrlAA.View = viewAA;
preprocessOptions = new SpectralPreprocessingOptions();
SpectralPreprocessingController ctrlBB = new SpectralPreprocessingController(preprocessOptions);
SpectralPreprocessingControl viewBB = new SpectralPreprocessingControl();
ctrlBB.View = viewBB;
TabbedElementController tabController = new TabbedElementController();
tabController.AddTab("Factors",ctrlAA,viewAA);
tabController.AddTab("Preprocessing", ctrlBB, viewBB);
if (Current.Gui.ShowDialog(tabController, "Enter analysis parameters", false))
{
options = ctrlAA.Doc;
return true;
}
/*
TabbedDialogController dialogctrl = new TabbedDialogController("PLS Analysis",false);
dialogctrl.AddTab("Factors",ctrlAA,viewAA);
dialogctrl.AddTab("Preprocessing",ctrlBB,viewBB);
TabbedDialogView dialogview = new TabbedDialogView();
dialogctrl.View = dialogview;
if(dialogctrl.ShowDialog(Current.MainWindow))
{
options = ctrlAA.Doc;
return true;
}
*/
return false;
}
/// <summary>
/// Calculate the cross PRESS values and stores the results in the provided table.
/// </summary>
/// <param name="xOfX">Vector of spectral wavelengths. Necessary to divide the spectras in different regions.</param>
/// <param name="matrixX">Matrix of spectra (horizontal oriented).</param>
/// <param name="matrixY">Matrix of concentrations.</param>
/// <param name="plsOptions">Analysis options.</param>
/// <param name="plsContent">Information about this analysis.</param>
/// <param name="table">Table to store the results.</param>
public virtual void CalculateCrossPRESS(
IROVector xOfX,
IMatrix matrixX,
IMatrix matrixY,
MultivariateAnalysisOptions plsOptions,
MultivariateContentMemento plsContent,
DataTable table
)
{
IROVector crossPRESSMatrix;
Altaxo.Data.DoubleColumn crosspresscol = new Altaxo.Data.DoubleColumn();
double meanNumberOfExcludedSpectra = 0;
if (plsOptions.CrossPRESSCalculation != CrossPRESSCalculationType.None)
{
// now a cross validation - this can take a long time for bigger matrices
MultivariateRegression.GetCrossPRESS(
xOfX, matrixX, matrixY, plsOptions.MaxNumberOfFactors, GetGroupingStrategy(plsOptions),
plsContent.SpectralPreprocessing,
this.CreateNewRegressionObject(),
out crossPRESSMatrix);
VectorMath.Copy(crossPRESSMatrix, DataColumnWrapper.ToVector(crosspresscol, crossPRESSMatrix.Length));
table.DataColumns.Add(crosspresscol, GetCrossPRESSValue_ColumnName(), Altaxo.Data.ColumnKind.V, 4);
plsContent.MeanNumberOfMeasurementsInCrossPRESSCalculation = plsContent.NumberOfMeasurements - meanNumberOfExcludedSpectra;
}
else
{
table.DataColumns.Add(crosspresscol, GetCrossPRESSValue_ColumnName(), Altaxo.Data.ColumnKind.V, 4);
}
}
/// <summary>
/// Execute an analysis and stores the result in the provided table.
/// </summary>
/// <param name="matrixX">The matrix of spectra (horizontal oriented), centered and preprocessed.</param>
/// <param name="matrixY">The matrix of concentrations, centered.</param>
/// <param name="plsOptions">Information how to perform the analysis.</param>
/// <param name="plsContent">A structure to store information about the results of the analysis.</param>
/// <param name="table">The table where to store the results to.</param>
/// <param name="press">On return, gives a vector holding the PRESS values of the analysis.</param>
public virtual void ExecuteAnalysis(
IMatrix matrixX,
IMatrix matrixY,
MultivariateAnalysisOptions plsOptions,
MultivariateContentMemento plsContent,
DataTable table,
out IROVector press
)
{
int numFactors = Math.Min(matrixX.Columns, plsOptions.MaxNumberOfFactors);
MultivariateRegression regress = this.CreateNewRegressionObject();
regress.AnalyzeFromPreprocessed(matrixX, matrixY, numFactors);
plsContent.NumberOfFactors = regress.NumberOfFactors;
plsContent.CrossValidationType = plsOptions.CrossPRESSCalculation;
press = regress.GetPRESSFromPreprocessed(matrixX);
Import(regress.CalibrationModel, table);
}
/// <summary>
/// Makes a PLS (a partial least squares) analysis of the table or the selected columns / rows and stores the results in a newly created table.
/// </summary>
/// <param name="mainDocument">The main document of the application.</param>
/// <param name="srctable">The table where the data come from.</param>
/// <param name="selectedColumns">The selected columns.</param>
/// <param name="selectedRows">The selected rows.</param>
/// <param name="selectedPropertyColumns">The selected property column(s).</param>
/// <param name="bHorizontalOrientedSpectrum">True if a spectrum is a single row, False if a spectrum is a single column.</param>
/// <param name="plsOptions">Provides information about the max number of factors and the calculation of cross PRESS value.</param>
/// <param name="preprocessOptions">Provides information about how to preprocess the spectra.</param>
/// <returns></returns>
public virtual string ExecuteAnalysis(
Altaxo.AltaxoDocument mainDocument,
Altaxo.Data.DataTable srctable,
IAscendingIntegerCollection selectedColumns,
IAscendingIntegerCollection selectedRows,
IAscendingIntegerCollection selectedPropertyColumns,
bool bHorizontalOrientedSpectrum,
MultivariateAnalysisOptions plsOptions,
SpectralPreprocessingOptions preprocessOptions
)
{
IMatrix matrixX, matrixY;
IROVector xOfX;
var plsContent = new MultivariateContentMemento();
plsContent.Analysis = this;
// now we have to create a new table where to place the calculated factors and loads
// we will do that in a vertical oriented manner, i.e. even if the loads are
// here in horizontal vectors: in our table they are stored in (vertical) columns
string newName = this.AnalysisName + " of " + Main.ProjectFolder.GetNamePart(srctable.Name);
newName = Main.ProjectFolder.CreateFullName(srctable.Name, newName);
Altaxo.Data.DataTable table = new Altaxo.Data.DataTable(newName);
// Fill the Table
using (var suspendToken = table.SuspendGetToken())
{
table.SetTableProperty("Content", plsContent);
plsContent.OriginalDataTableName = srctable.Name;
// Get matrices
GetXYMatrices(
srctable,
selectedColumns,
selectedRows,
selectedPropertyColumns,
bHorizontalOrientedSpectrum,
plsContent,
out matrixX, out matrixY, out xOfX);
StoreXOfX(xOfX, table);
// Preprocess
plsContent.SpectralPreprocessing = preprocessOptions;
IVector meanX, scaleX, meanY, scaleY;
MultivariateRegression.PreprocessForAnalysis(preprocessOptions, xOfX, matrixX, matrixY,
out meanX, out scaleX, out meanY, out scaleY);
StorePreprocessedData(meanX, scaleX, meanY, scaleY, table);
// Analyze and Store
IROVector press;
ExecuteAnalysis(
matrixX,
matrixY,
plsOptions,
plsContent,
table, out press);
this.StorePRESSData(press, table);
if (plsOptions.CrossPRESSCalculation != CrossPRESSCalculationType.None)
CalculateCrossPRESS(xOfX, matrixX, matrixY, plsOptions, plsContent, table);
StoreFRatioData(table, plsContent);
StoreOriginalY(table, plsContent);
suspendToken.Dispose();
}
Current.Project.DataTableCollection.Add(table);
// create a new worksheet without any columns
Current.ProjectService.CreateNewWorksheet(table);
return null;
}
public PLSStartAnalysisController(MultivariateAnalysisOptions options)
{
_doc = options;
}
/// <summary>
/// Asks the user for the maximum number of factors and the cross validation calculation.
/// </summary>
/// <param name="options">The PLS options to ask for. On return, this is the user's choice.</param>
/// <param name="preprocessOptions">The spectral preprocessing options to ask for (output).</param>
/// <returns>True if the user has made his choice, false if the user pressed the Cancel button.</returns>
public static bool QuestPLSAnalysisOptions(out MultivariateAnalysisOptions options, out SpectralPreprocessingOptions preprocessOptions)
{
options = new MultivariateAnalysisOptions();
options.MaxNumberOfFactors = 20;
options.CrossPRESSCalculation = CrossPRESSCalculationType.ExcludeGroupsOfSimilarMeasurements;
PLSStartAnalysisController ctrlAA = new PLSStartAnalysisController(options);
Current.Gui.FindAndAttachControlTo(ctrlAA);
preprocessOptions = new SpectralPreprocessingOptions();
SpectralPreprocessingController ctrlBB = new SpectralPreprocessingController(preprocessOptions);
Current.Gui.FindAndAttachControlTo(ctrlBB);
TabbedElementController tabController = new TabbedElementController();
tabController.AddTab("Factors", ctrlAA, ctrlAA.ViewObject);
tabController.AddTab("Preprocessing", ctrlBB, ctrlBB.ViewObject);
if (Current.Gui.ShowDialog(tabController, "Enter analysis parameters", false))
{
options = ctrlAA.Doc;
return true;
}
return false;
}
