Example usage for org.apache.commons.math3.analysis.function Identity Identity

Introduction

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

Prototype

Identity

Source Link

Usage

From source file:de.unijena.bioinf.FragmentationTreeConstruction.computation.recalibration.LeastSquare.java

@Override
public UnivariateFunction recalibrate(MutableSpectrum<Peak> spectrum, Spectrum<Peak> referenceSpectrum) {
    spectrum = new SimpleMutableSpectrum(spectrum);
    SimpleMutableSpectrum refSpectrum = new SimpleMutableSpectrum(referenceSpectrum);
    preprocess(spectrum, refSpectrum);//  w w w .j av  a2 s .  c o  m
    final double[] eps = new double[spectrum.size()];
    for (int k = 0; k < eps.length; ++k)
        eps[k] = this.epsilon.absoluteFor(spectrum.getMzAt(k));
    final double[][] values = MzRecalibration.maxIntervalStabbing(spectrum, refSpectrum, eps, threshold);
    if (values[0].length < minNumberOfPeaks)
        return new Identity();

    if (forceParentPeakIn)
        forceParentPeakInRecalibration(spectrum, referenceSpectrum, values);

    final UnivariateFunction recalibration = MzRecalibration.getLinearRecalibration(values[0], values[1]);
    MzRecalibration.recalibrate(spectrum, recalibration);
    return recalibration;
}

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From source file:de.unijena.bioinf.FragmentationTreeConstruction.computation.recalibration.MedianSlope.java

@Override
public UnivariateFunction recalibrate(MutableSpectrum<Peak> spectrum, Spectrum<Peak> referenceSpectrum) {
    spectrum = new SimpleMutableSpectrum(spectrum);
    final SimpleMutableSpectrum ref = new SimpleMutableSpectrum(referenceSpectrum);

    preprocess(spectrum, ref);/*  w  w  w .  ja va  2s.  c om*/
    final double[] eps = new double[spectrum.size()];
    for (int k = 0; k < eps.length; ++k)
        eps[k] = this.epsilon.absoluteFor(spectrum.getMzAt(k));
    final double[][] values = MzRecalibration.maxIntervalStabbing(spectrum, ref, eps, threshold);
    //final double[][] values = getMedianSubset(spectrum, ref);//getMedianSubsetFairDistributed(spectrum, ref);
    // getMedianSubsetFairDistributed(spectrum, ref);
    if (values[0].length < minNumberOfPeaks)
        return new Identity();

    if (forceParentPeakIn)
        forceParentPeakInRecalibration(spectrum, referenceSpectrum, values);

    final UnivariateFunction recalibration = MzRecalibration.getMedianLinearRecalibration(values[0], values[1]);
    MzRecalibration.recalibrate(spectrum, recalibration);
    return recalibration;
}

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From source file:de.unijena.bioinf.FragmentationTreeConstruction.computation.recalibration.ExpRek.java

@Override
public UnivariateFunction recalibrate(MutableSpectrum<Peak> spectrum, Spectrum<Peak> referenceSpectrum) {
    final SimpleMutableSpectrum ref = new SimpleMutableSpectrum(referenceSpectrum);
    final SimpleMutableSpectrum mes = new SimpleMutableSpectrum(spectrum);
    final TDoubleList list = new TDoubleArrayList(spectrum.size());
    // 1. allow only peaks with >2.5% intensity for recalibration
    for (int i = 0; i < mes.size(); ++i) {
        if (mes.getIntensityAt(i) <= 0.025) {
            ref.removePeakAt(i);/*  ww  w  .  jav a  2s . com*/
            mes.removePeakAt(i);
            --i;
        } else if (mes.getIntensityAt(i) > 0.04) {
            list.add(mes.getMzAt(i));
        }
    }
    final Deviation dev = new Deviation(4, 1e-3);
    final double[][] values = MzRecalibration.maxIntervalStabbing(mes, ref, new UnivariateFunction() {
        @Override
        public double value(double x) {
            return dev.absoluteFor(x);
        }
    });
    // 2. there have to be at least 6 peaks with > 4% intensity
    int found = 0;
    for (double x : values[0]) {
        if (list.contains(x))
            ++found;
    }

    if (found < 6)
        return new Identity();
    final UnivariateFunction recalibration = MzRecalibration.getLinearRecalibration(values[0], values[1]);
    MzRecalibration.recalibrate(spectrum, recalibration);
    return recalibration;
}

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From source file:de.unijena.bioinf.FragmentationTreeConstruction.computation.recalibration.AbstractRecalibrationStrategy.java

@Override
public UnivariateFunction recalibrate(MutableSpectrum<Peak> spectrum, Spectrum<Peak> referenceSpectrum) {
    spectrum = new SimpleMutableSpectrum(spectrum);
    final SimpleMutableSpectrum ref = new SimpleMutableSpectrum(referenceSpectrum);

    preprocess(spectrum, ref);/*from  w ww .j av  a2 s.co  m*/
    final double[][] values = MzRecalibration.maxIntervalStabbing(spectrum, referenceSpectrum,
            new UnivariateFunction() {
                @Override
                public double value(double x) {
                    return epsilon.absoluteFor(x);
                }
            }, threshold);
    if (values[0].length < minNumberOfPeaks)
        return new Identity();
    final UnivariateFunction recalibration = MzRecalibration.getMedianLinearRecalibration(values[0], values[1]);
    MzRecalibration.recalibrate(spectrum, recalibration);
    return recalibration;
}

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