Example usage for org.apache.commons.math3.analysis.interpolation LoessInterpolator LoessInterpolator

Introduction

In this page you can find the example usage for org.apache.commons.math3.analysis.interpolation LoessInterpolator LoessInterpolator.

Prototype

public LoessInterpolator(double bandwidth, int robustnessIters, double accuracy)
        throws OutOfRangeException, NotPositiveException 

Source Link

Document

Construct a new LoessInterpolator with given bandwidth, number of robustness iterations and accuracy.

Usage

From source file:jp.ac.tohoku.ecei.sb.metabolomeqc.basiccorrector.LoessIntensityCorrector.java

@Override
public IntensityMatrix doCorrection(IntensityMatrix original) {
    updateBadInjections(original);/*from   www. j a va2s .  c om*/
    List<Injection> normalSamples = original.getNormalInjections();

    List<Sample> globalQCSamples = original.getGlobalQCSamples();
    if (globalQCSamples.size() == 0)
        throw new UnsupportedOperationException("No global QC");
    Sample selectedGlobalQC = globalQCSamples.get(0);

    // Calculate SQC median
    Map<Compound, Double> compoundIntensityBase = GlobalQCMedianCalculator.calcGlobalQCMedian(original,
            badInjections);

    // Main Correction
    IntensityMatrix corrected = new IntensityMatrixImpl(original.getSize()[0], normalSamples.size());
    corrected.setRowKeys(original.getRowKeys());
    corrected.setColumnKeys(normalSamples);
    //corrected.getAttributes().putAll(original.getAttributes());

    LoessInterpolator loessInterpolator = new LoessInterpolator(bandwidth, robustnessIters, accuracy);

    for (Compound oneCompound : corrected.getRowKeys()) {
        double base = compoundIntensityBase.get(oneCompound);
        for (Map.Entry<Plate, List<Injection>> plateInjection : original.getInjectionsByPlate().entrySet()) {
            List<Double> xlist = new ArrayList<>();
            List<Double> ylist = new ArrayList<>();
            for (Injection injection : plateInjection.getValue()) {
                //log.info("injection: {}", injection);
                if (!injection.getSample().equals(selectedGlobalQC))
                    continue;
                if (injection.isIgnored())
                    continue;
                if (badInjections != null && badInjections.contains(injection))
                    continue;

                xlist.add((double) injection.getRunIndex());
                ylist.add(original.get(oneCompound, injection));
            }

            //log.info("X : {}", xlist.size());

            PolynomialSplineFunction fn = loessInterpolator.interpolate(
                    xlist.stream().mapToDouble(x -> x).toArray(), ylist.stream().mapToDouble(x -> x).toArray());

            for (Injection injection : plateInjection.getValue()) {
                if (!normalSamples.contains(injection))
                    continue;
                corrected.put(oneCompound, injection,
                        original.get(oneCompound, injection) - base + fn.value(injection.getRunIndex()));
            }
        }
    }

    return corrected;
}

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