org.jcamp.spectrum.NMRSpectrum Maven / Gradle / Ivy

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package org.jcamp.spectrum;

import org.jcamp.math.LinearAxisMap;
import org.jcamp.math.Range1D;
import org.jcamp.math.Range2D;
import org.jcamp.math.ReversedLinearAxisMap;
import org.jcamp.units.CommonUnit;
import org.jcamp.units.Unit;
/**
 * 1D NMR spectrum
 * @author Thomas Weber
 */
public class NMRSpectrum extends Spectrum1D {
    private final static Range1D.Double DEFAULT_YRANGE = new Range1D.Double(0., 20.);
    private final static Range1D.Double[] DEFAULT_XRANGE =
        new Range1D.Double[] { new Range1D.Double(-2., 14.), new Range1D.Double(0., 200.)};
    public final static Unit DEFAULT_YUNIT = CommonUnit.intensity;
    public final static Unit DEFAULT_XUNIT = CommonUnit.hertz;
    protected String nucleus;
    protected double frequency = 400.0;
    protected double reference = 0;
    protected double solventReference = 0; // solvent reference in ppm
    protected boolean fid = false;
    protected String solvent = "TMS";

    /**
     */
    protected NMRSpectrum() {
        super();
    }
    /**
     * standard ctor.
     * 
     * @param x org.jcamp.spectrum.IOrderedDataArray1D
     * @param y org.jcamp.spectrum.IDataArray1D
     * @param nucleus String
     * @param freq double observe frequency
     * @param ref double reference frequency
     */
    public NMRSpectrum(IOrderedDataArray1D x, IDataArray1D y, String nucleus, double freq, double ref) {
        super(x, y);
        this.frequency = freq;
        this.reference = ref;
        this.nucleus = nucleus;
    }
    /**
     * standard ctor.
     * 
     * @param x org.jcamp.spectrum.IOrderedDataArray1D
     * @param y org.jcamp.spectrum.IDataArray1D
     * @param nucleus String
     * @param freq double observe frequency
     * @param ref double reference frequency
     * @param fullSpectrum boolean
     */
    public NMRSpectrum(
        IOrderedDataArray1D x,
        IDataArray1D y,
        String nucleus,
        double freq,
        double ref,
        boolean fullSpectrum) {
        super(x, y, fullSpectrum);
        this.frequency = freq;
        this.reference = ref;
        this.nucleus = nucleus;
        convertToPPM();
        convertToPercent();
        this.xAxisMap = new ReversedLinearAxisMap(xData);
        this.yAxisMap = new LinearAxisMap(yData);
        adjustFullViewRange();
    }
    /**
     * cloning.
     * 
     * @return java.lang.Object
     */
    public Object clone() {
        NMRSpectrum spectrum = (NMRSpectrum) super.clone();

        spectrum.xAxisMap = new ReversedLinearAxisMap(spectrum.xData);
        spectrum.yAxisMap = new LinearAxisMap(spectrum.yData);
        return spectrum;
    }
    /**
     * convert x data to Hz
     * 
     */
    protected void convertToHertz() {
        if (frequency != frequency) // safety check
            return;

        if (xData.getUnit().equals(CommonUnit.ppm)) {
            // hz = freq * ppm + ref;
            this.xData.scale(frequency);
            if (reference == reference) // we are notin a peak table
                this.xData.translate(reference);
            this.xData.setUnit(CommonUnit.hertz);
            adjustFullViewRange();
        }
    }
    /**
     * convert an array of ppm values to hertz.
     */
    public static double[] convertToHertz(double[] ppm, double freq, double ref) {
        int n = ppm.length;
        double[] hz = new double[n];
        for (int i = 0; i < n; i++) {
            hz[i] = freq * ppm[i] + ref;
        }
        return hz;
    }
    /**
     * convert a ppm value to hertz.
     */
    public static double convertToHertz(double ppm, double freq, double ref) {
        double hz = freq * ppm + ref;
        return hz;
    }
    /**
     * convert y data to percent
     * 
     */
    protected void convertToPercent() {
        if (!yData.equals(CommonUnit.percentIntensity)) {
            // rescale intensities to percent of maximum
            double imax = yData.getRange1D().getXMax();
            if (imax != 0.0) {
                imax = 100. / imax;
                yData.scale(imax);
                yData.setUnit(CommonUnit.percentIntensity);
            }
        }
    }
    /**
     * converts intensities to percentage.
     * @param intensities double[]
     */
    public static void convertToPercent(double[] intensities) {
        // rescale intensities to percent of maximum
        double imax = Math.abs(intensities[0]);
        for (int i = 1; i < intensities.length; i++) {
            double iabs = Math.abs(intensities[i]);
            if (iabs > imax)
                imax = iabs;
        }
        if (imax != 0.0) {
            imax = 100. / imax;
            for (int i = 0; i < intensities.length; i++)
                intensities[i] *= imax;
        }
    }
    /**
     * convert x data to Hz
     * 
     */
    protected void convertToPPM() {
        if (frequency != frequency)
            return;
        if (xData.getUnit().equals(CommonUnit.hertz)) {
            // ppm = (hz - ref) / freq;
            if (reference == reference)
                xData.translate(-reference);
            xData.scale(1. / frequency);
            xData.setUnit(CommonUnit.ppm);
            adjustFullViewRange();
        }
    }
    /**
     * convert an array of hertz values to ppms.
     */
    public static double[] convertToPPM(double[] hz, double freq, double ref) {
        int n = hz.length;
        double[] ppm = new double[n];
        for (int i = 0; i < n; i++) {
            ppm[i] = (hz[i] - ref) / freq;
        }
        return ppm;
    }
    /**
     * convert a hertz values to ppm.
     */
    public static double convertToPPM(double hz, double freq, double ref) {
        double ppm = (hz - ref) / freq;
        return ppm;
    }
    /**
     * getDataRange method comment.
     */
    public Range2D.Double getDataRange() {
        return new Range2D.Double(xAxisMap.getDataRange(), yAxisMap.getDataRange());
    }
    /**
     * gets observe frequency.
     * @return double
     */
    public double getFrequency() {
        return frequency;
    }
    /**
     * gets spectrum ID.
     * @return int
     */
    public int getIdentifier() {
        return ISpectrumIdentifier.NMR;
    }
    /**
     * gets observe nucleus
     * @return java.lang.String
     */
    public java.lang.String getNucleus() {
        return nucleus;
    }
    /**
     * gets shift reference frequency in Hz.
     * @return double
     */
    public double getReference() {
        return reference;
    }
    /**
     * gets solvent.
     * 
     * @return java.lang.String
     */
    public java.lang.String getSolvent() {
        return solvent;
    }
    /**
     * gets solvent reference in ppm.
     * 
     * @return double
     */
    public double getSolventReference() {
        return solventReference;
    }
    /**
     * gets full view range on x axis.
     */
    public Range1D.Double getXFullViewRange() {
        return new Range1D.Double(this.xAxisMap.getFullViewRange());
    }
    /**
     * gets full view range on y axis.
     */
    public Range1D.Double getYFullViewRange() {
        return new Range1D.Double(this.yAxisMap.getFullViewRange());
    }
    /**
     * indicates a FID.
     * 
     * @return boolean
     */
    public boolean isFID() {
        return false;
    }
    /**
     * isSameType method comment.
     */
    public boolean isSameType(Spectrum otherSpectrum) {
        if (otherSpectrum instanceof NMRSpectrum)
            return true;
        return false;
    }
    /**
     * sets observe frequency.
     * @param newFrequency double
     */
    public void setFrequency(double newFrequency) {
        if (this.frequency != newFrequency) {
            convertToHertz();
            this.frequency = newFrequency;
            convertToPPM();
        }
    }
    /**
     * sets observe nucleus.
     * @param newNucleus java.lang.String
     */
    public void setNucleus(java.lang.String newNucleus) {
        nucleus = newNucleus;
    }
    /**
     * sets shift reference frequency in Hz.
     * @param newReference double
     */
    public void setReference(double newReference) {
        if (this.reference != newReference) {
            convertToHertz();
            this.reference = newReference;
            convertToPPM();
        }
    }
    /**
     * sets solvent.
     * 
     * @param newSolvent java.lang.String
     */
    public void setSolvent(java.lang.String newSolvent) {
        solvent = newSolvent;
    }
    /**
     * sets solvent reference in ppm.
     * 
     * @param newSolventReference double
     */
    public void setSolventReference(double newSolventReference) {
        solventReference = newSolventReference;
    }
    /**
     * sets full view range on x axis.
     */
    public void setXFullViewRange(Range1D.Double dataRange) {
        if (dataRange.getXWidth() > 0)
            this.xAxisMap = new ReversedLinearAxisMap(xData, dataRange);
    }
    /**
     * sets full view range on y axis.
     */
    public void setYFullViewRange(Range1D.Double dataRange) {
        this.yAxisMap = new LinearAxisMap(yData, dataRange);
    }
}