Java Code Examples for org.apache.commons.math3.util.MathArrays#sortInPlace()

/**
 * Evaluate the Lagrange polynomial using
 * <a href="http://mathworld.wolfram.com/NevillesAlgorithm.html">
 * Neville's Algorithm</a>. It takes O(n^2) time.
 *
 * @param x Interpolating points array.
 * @param y Interpolating values array.
 * @param z Point at which the function value is to be computed.
 * @return the function value.
 * @throws DimensionMismatchException if {@code x} and {@code y} have
 * different lengths.
 * @throws NonMonotonicSequenceException
 * if {@code x} is not sorted in strictly increasing order.
 * @throws NumberIsTooSmallException if the size of {@code x} is less
 * than 2.
 */
public static double evaluate(double x[], double y[], double z)
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    if (verifyInterpolationArray(x, y, false)) {
        return evaluateInternal(x, y, z);
    }

    // Array is not sorted.
    final double[] xNew = new double[x.length];
    final double[] yNew = new double[y.length];
    System.arraycopy(x, 0, xNew, 0, x.length);
    System.arraycopy(y, 0, yNew, 0, y.length);

    MathArrays.sortInPlace(xNew, yNew);
    // Second check in case some abscissa is duplicated.
    verifyInterpolationArray(xNew, yNew, true);
    return evaluateInternal(xNew, yNew, z);
}
 

/**
 * Evaluate the Lagrange polynomial using
 * <a href="http://mathworld.wolfram.com/NevillesAlgorithm.html">
 * Neville's Algorithm</a>. It takes O(n^2) time.
 *
 * @param x Interpolating points array.
 * @param y Interpolating values array.
 * @param z Point at which the function value is to be computed.
 * @return the function value.
 * @throws DimensionMismatchException if {@code x} and {@code y} have
 * different lengths.
 * @throws NonMonotonicSequenceException
 * if {@code x} is not sorted in strictly increasing order.
 * @throws NumberIsTooSmallException if the size of {@code x} is less
 * than 2.
 */
public static double evaluate(double x[], double y[], double z)
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    if (verifyInterpolationArray(x, y, false)) {
        return evaluateInternal(x, y, z);
    }

    // Array is not sorted.
    final double[] xNew = new double[x.length];
    final double[] yNew = new double[y.length];
    System.arraycopy(x, 0, xNew, 0, x.length);
    System.arraycopy(y, 0, yNew, 0, y.length);

    MathArrays.sortInPlace(xNew, yNew);
    // Second check in case some abscissa is duplicated.
    verifyInterpolationArray(xNew, yNew, true);
    return evaluateInternal(xNew, yNew, z);
}
 

/**
 * Evaluate the Lagrange polynomial using
 * <a href="http://mathworld.wolfram.com/NevillesAlgorithm.html">
 * Neville's Algorithm</a>. It takes O(n^2) time.
 *
 * @param x Interpolating points array.
 * @param y Interpolating values array.
 * @param z Point at which the function value is to be computed.
 * @return the function value.
 * @throws DimensionMismatchException if {@code x} and {@code y} have
 * different lengths.
 * @throws NonMonotonicSequenceException
 * if {@code x} is not sorted in strictly increasing order.
 * @throws NumberIsTooSmallException if the size of {@code x} is less
 * than 2.
 */
public static double evaluate(double x[], double y[], double z)
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    if (verifyInterpolationArray(x, y, false)) {
        return evaluateInternal(x, y, z);
    }

    // Array is not sorted.
    final double[] xNew = new double[x.length];
    final double[] yNew = new double[y.length];
    System.arraycopy(x, 0, xNew, 0, x.length);
    System.arraycopy(y, 0, yNew, 0, y.length);

    MathArrays.sortInPlace(xNew, yNew);
    // Second check in case some abscissa is duplicated.
    verifyInterpolationArray(xNew, yNew, true);
    return evaluateInternal(xNew, yNew, z);
}
 

/**
 * Evaluate the Lagrange polynomial using
 * <a href="http://mathworld.wolfram.com/NevillesAlgorithm.html">
 * Neville's Algorithm</a>. It takes O(n^2) time.
 *
 * @param x Interpolating points array.
 * @param y Interpolating values array.
 * @param z Point at which the function value is to be computed.
 * @return the function value.
 * @throws DimensionMismatchException if {@code x} and {@code y} have
 * different lengths.
 * @throws NonMonotonicSequenceException
 * if {@code x} is not sorted in strictly increasing order.
 * @throws NumberIsTooSmallException if the size of {@code x} is less
 * than 2.
 */
public static double evaluate(double x[], double y[], double z)
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    if (verifyInterpolationArray(x, y, false)) {
        return evaluateInternal(x, y, z);
    }

    // Array is not sorted.
    final double[] xNew = new double[x.length];
    final double[] yNew = new double[y.length];
    System.arraycopy(x, 0, xNew, 0, x.length);
    System.arraycopy(y, 0, yNew, 0, y.length);

    MathArrays.sortInPlace(xNew, yNew);
    // Second check in case some abscissa is duplicated.
    verifyInterpolationArray(xNew, yNew, true);
    return evaluateInternal(xNew, yNew, z);
}
 

/**
 * Evaluate the Lagrange polynomial using
 * <a href="http://mathworld.wolfram.com/NevillesAlgorithm.html">
 * Neville's Algorithm</a>. It takes O(n^2) time.
 *
 * @param x Interpolating points array.
 * @param y Interpolating values array.
 * @param z Point at which the function value is to be computed.
 * @return the function value.
 * @throws DimensionMismatchException if {@code x} and {@code y} have
 * different lengths.
 * @throws org.apache.commons.math3.exception.NonMonotonicSequenceException
 * if {@code x} is not sorted in strictly increasing order.
 * @throws NumberIsTooSmallException if the size of {@code x} is less
 * than 2.
 */
public static double evaluate(double x[], double y[], double z) {
    if (verifyInterpolationArray(x, y, false)) {
        return evaluateInternal(x, y, z);
    }

    // Array is not sorted.
    final double[] xNew = new double[x.length];
    final double[] yNew = new double[y.length];
    System.arraycopy(x, 0, xNew, 0, x.length);
    System.arraycopy(y, 0, yNew, 0, y.length);

    MathArrays.sortInPlace(xNew, yNew);
    // Second check in case some abscissa is duplicated.
    verifyInterpolationArray(xNew, yNew, true);
    return evaluateInternal(xNew, yNew, z);
}
 

/**
 * Evaluate the Lagrange polynomial using
 * <a href="http://mathworld.wolfram.com/NevillesAlgorithm.html">
 * Neville's Algorithm</a>. It takes O(n^2) time.
 *
 * @param x Interpolating points array.
 * @param y Interpolating values array.
 * @param z Point at which the function value is to be computed.
 * @return the function value.
 * @throws DimensionMismatchException if {@code x} and {@code y} have
 * different lengths.
 * @throws org.apache.commons.math3.exception.NonMonotonicSequenceException
 * if {@code x} is not sorted in strictly increasing order.
 * @throws NumberIsTooSmallException if the size of {@code x} is less
 * than 2.
 */
public static double evaluate(double x[], double y[], double z) {
    if (verifyInterpolationArray(x, y, false)) {
        return evaluateInternal(x, y, z);
    }

    // Array is not sorted.
    final double[] xNew = new double[x.length];
    final double[] yNew = new double[y.length];
    System.arraycopy(x, 0, xNew, 0, x.length);
    System.arraycopy(y, 0, yNew, 0, y.length);

    MathArrays.sortInPlace(xNew, yNew);
    // Second check in case some abscissa is duplicated.
    verifyInterpolationArray(xNew, yNew, true);
    return evaluateInternal(xNew, yNew, z);
}
 

/**
 * Evaluate the Lagrange polynomial using
 * <a href="http://mathworld.wolfram.com/NevillesAlgorithm.html">
 * Neville's Algorithm</a>. It takes O(n^2) time.
 *
 * @param x Interpolating points array.
 * @param y Interpolating values array.
 * @param z Point at which the function value is to be computed.
 * @return the function value.
 * @throws DimensionMismatchException if {@code x} and {@code y} have
 * different lengths.
 * @throws org.apache.commons.math3.exception.NonMonotonicSequenceException
 * if {@code x} is not sorted in strictly increasing order.
 * @throws NumberIsTooSmallException if the size of {@code x} is less
 * than 2.
 */
public static double evaluate(double x[], double y[], double z) {
    if (verifyInterpolationArray(x, y, false)) {
        return evaluateInternal(x, y, z);
    }

    // Array is not sorted.
    final double[] xNew = new double[x.length];
    final double[] yNew = new double[y.length];
    System.arraycopy(x, 0, xNew, 0, x.length);
    System.arraycopy(y, 0, yNew, 0, y.length);

    MathArrays.sortInPlace(xNew, yNew);
    // Second check in case some abscissa is duplicated.
    verifyInterpolationArray(xNew, yNew, true);
    return evaluateInternal(xNew, yNew, z);
}
 

/**
 * Evaluate the Lagrange polynomial using
 * <a href="http://mathworld.wolfram.com/NevillesAlgorithm.html">
 * Neville's Algorithm</a>. It takes O(n^2) time.
 *
 * @param x Interpolating points array.
 * @param y Interpolating values array.
 * @param z Point at which the function value is to be computed.
 * @return the function value.
 * @throws DimensionMismatchException if {@code x} and {@code y} have
 * different lengths.
 * @throws NonMonotonicSequenceException
 * if {@code x} is not sorted in strictly increasing order.
 * @throws NumberIsTooSmallException if the size of {@code x} is less
 * than 2.
 */
public static double evaluate(double x[], double y[], double z)
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    if (verifyInterpolationArray(x, y, false)) {
        return evaluateInternal(x, y, z);
    }

    // Array is not sorted.
    final double[] xNew = new double[x.length];
    final double[] yNew = new double[y.length];
    System.arraycopy(x, 0, xNew, 0, x.length);
    System.arraycopy(y, 0, yNew, 0, y.length);

    MathArrays.sortInPlace(xNew, yNew);
    // Second check in case some abscissa is duplicated.
    verifyInterpolationArray(xNew, yNew, true);
    return evaluateInternal(xNew, yNew, z);
}
 

/**
 * Construct a Lagrange polynomial with the given abscissas and function
 * values. The order of interpolating points are not important.
 * <p>
 * The constructor makes copy of the input arrays and assigns them.</p>
 *
 * @param x interpolating points
 * @param y function values at interpolating points
 * @throws DimensionMismatchException if the array lengths are different.
 * @throws NumberIsTooSmallException if the number of points is less than 2.
 * @throws org.apache.commons.math3.exception.NonMonotonicSequenceException
 * if two abscissae have the same value.
 */
public PolynomialFunctionLagrangeForm(double x[], double y[]) {
    this.x = new double[x.length];
    this.y = new double[y.length];
    System.arraycopy(x, 0, this.x, 0, x.length);
    System.arraycopy(y, 0, this.y, 0, y.length);
    coefficientsComputed = false;

    if (!verifyInterpolationArray(x, y, false)) {
        MathArrays.sortInPlace(this.x, this.y);
        // Second check in case some abscissa is duplicated.
        verifyInterpolationArray(this.x, this.y, true);
    }
}
 

/**
 * Construct a Lagrange polynomial with the given abscissas and function
 * values. The order of interpolating points are not important.
 * <p>
 * The constructor makes copy of the input arrays and assigns them.</p>
 *
 * @param x interpolating points
 * @param y function values at interpolating points
 * @throws DimensionMismatchException if the array lengths are different.
 * @throws NumberIsTooSmallException if the number of points is less than 2.
 * @throws org.apache.commons.math3.exception.NonMonotonicSequenceException
 * if two abscissae have the same value.
 */
public PolynomialFunctionLagrangeForm(double x[], double y[]) {
    this.x = new double[x.length];
    this.y = new double[y.length];
    System.arraycopy(x, 0, this.x, 0, x.length);
    System.arraycopy(y, 0, this.y, 0, y.length);
    coefficientsComputed = false;

    if (!verifyInterpolationArray(x, y, false)) {
        MathArrays.sortInPlace(this.x, this.y);
        // Second check in case some abscissa is duplicated.
        verifyInterpolationArray(this.x, this.y, true);
    }
}
 

/**
 * Construct a Lagrange polynomial with the given abscissas and function
 * values. The order of interpolating points are not important.
 * <p>
 * The constructor makes copy of the input arrays and assigns them.</p>
 *
 * @param x interpolating points
 * @param y function values at interpolating points
 * @throws DimensionMismatchException if the array lengths are different.
 * @throws NumberIsTooSmallException if the number of points is less than 2.
 * @throws NonMonotonicSequenceException
 * if two abscissae have the same value.
 */
public PolynomialFunctionLagrangeForm(double x[], double y[])
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    this.x = new double[x.length];
    this.y = new double[y.length];
    System.arraycopy(x, 0, this.x, 0, x.length);
    System.arraycopy(y, 0, this.y, 0, y.length);
    coefficientsComputed = false;

    if (!verifyInterpolationArray(x, y, false)) {
        MathArrays.sortInPlace(this.x, this.y);
        // Second check in case some abscissa is duplicated.
        verifyInterpolationArray(this.x, this.y, true);
    }
}
 

/**
 * Sort in place given dataset and reorder ancillary datasets too
 * @param a dataset to be sorted
 * @param b ancillary datasets
 */
public static void sort(Dataset a, Dataset... b) {
	if (!InterfaceUtils.isNumerical(a.getClass())) {
		throw new UnsupportedOperationException("Sorting non-numerical datasets not supported yet");
	}

	// gather all datasets as double dataset copies
	DoubleDataset s = copy(DoubleDataset.class, a);
	int l = b == null ? 0 : b.length;
	DoubleDataset[] t = new DoubleDataset[l];
	int n = 0;
	for (int i = 0; i < l; i++) {
		if (b[i] != null) {
			if (!InterfaceUtils.isNumerical(b[i].getClass())) {
				throw new UnsupportedOperationException("Sorting non-numerical datasets not supported yet");
			}
			t[i] = copy(DoubleDataset.class, b[i]);
			n++;
		}
	}

	double[][] y = new double[n][];
	for (int i = 0, j = 0; i < l; i++) {
		if (t[i] != null) {
			y[j++] = t[i].getData();
		}
	}

	MathArrays.sortInPlace(s.getData(), y);

	a.setSlice(s);
	for (int i = 0; i < l; i++) {
		if (b[i] != null) {
			b[i].setSlice(t[i]);
		}
	}
}
 

/**
 * Construct a Lagrange polynomial with the given abscissas and function
 * values. The order of interpolating points are not important.
 * <p>
 * The constructor makes copy of the input arrays and assigns them.</p>
 *
 * @param x interpolating points
 * @param y function values at interpolating points
 * @throws DimensionMismatchException if the array lengths are different.
 * @throws NumberIsTooSmallException if the number of points is less than 2.
 * @throws org.apache.commons.math3.exception.NonMonotonicSequenceException
 * if two abscissae have the same value.
 */
public PolynomialFunctionLagrangeForm(double x[], double y[]) {
    this.x = new double[x.length];
    this.y = new double[y.length];
    System.arraycopy(x, 0, this.x, 0, x.length);
    System.arraycopy(y, 0, this.y, 0, y.length);
    coefficientsComputed = false;

    if (!verifyInterpolationArray(x, y, false)) {
        MathArrays.sortInPlace(this.x, this.y);
        // Second check in case some abscissa is duplicated.
        verifyInterpolationArray(this.x, this.y, true);
    }
}
 

/**
 * Construct a Lagrange polynomial with the given abscissas and function
 * values. The order of interpolating points are not important.
 * <p>
 * The constructor makes copy of the input arrays and assigns them.</p>
 *
 * @param x interpolating points
 * @param y function values at interpolating points
 * @throws DimensionMismatchException if the array lengths are different.
 * @throws NumberIsTooSmallException if the number of points is less than 2.
 * @throws NonMonotonicSequenceException
 * if two abscissae have the same value.
 */
public PolynomialFunctionLagrangeForm(double x[], double y[])
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    this.x = new double[x.length];
    this.y = new double[y.length];
    System.arraycopy(x, 0, this.x, 0, x.length);
    System.arraycopy(y, 0, this.y, 0, y.length);
    coefficientsComputed = false;

    if (!verifyInterpolationArray(x, y, false)) {
        MathArrays.sortInPlace(this.x, this.y);
        // Second check in case some abscissa is duplicated.
        verifyInterpolationArray(this.x, this.y, true);
    }
}
 

/**
 * Construct a Lagrange polynomial with the given abscissas and function
 * values. The order of interpolating points are not important.
 * <p>
 * The constructor makes copy of the input arrays and assigns them.</p>
 *
 * @param x interpolating points
 * @param y function values at interpolating points
 * @throws DimensionMismatchException if the array lengths are different.
 * @throws NumberIsTooSmallException if the number of points is less than 2.
 * @throws NonMonotonicSequenceException
 * if two abscissae have the same value.
 */
public PolynomialFunctionLagrangeForm(double x[], double y[])
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    this.x = new double[x.length];
    this.y = new double[y.length];
    System.arraycopy(x, 0, this.x, 0, x.length);
    System.arraycopy(y, 0, this.y, 0, y.length);
    coefficientsComputed = false;

    if (!verifyInterpolationArray(x, y, false)) {
        MathArrays.sortInPlace(this.x, this.y);
        // Second check in case some abscissa is duplicated.
        verifyInterpolationArray(this.x, this.y, true);
    }
}
 

/**
 * Construct a Lagrange polynomial with the given abscissas and function
 * values. The order of interpolating points are not important.
 * <p>
 * The constructor makes copy of the input arrays and assigns them.</p>
 *
 * @param x interpolating points
 * @param y function values at interpolating points
 * @throws DimensionMismatchException if the array lengths are different.
 * @throws NumberIsTooSmallException if the number of points is less than 2.
 * @throws NonMonotonicSequenceException
 * if two abscissae have the same value.
 */
public PolynomialFunctionLagrangeForm(double x[], double y[])
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    this.x = new double[x.length];
    this.y = new double[y.length];
    System.arraycopy(x, 0, this.x, 0, x.length);
    System.arraycopy(y, 0, this.y, 0, y.length);
    coefficientsComputed = false;

    if (!verifyInterpolationArray(x, y, false)) {
        MathArrays.sortInPlace(this.x, this.y);
        // Second check in case some abscissa is duplicated.
        verifyInterpolationArray(this.x, this.y, true);
    }
}
 

/**
 * Estimate the quantile for the current marker.
 *
 * @return estimated quantile
 */
private double estimate() {
    final double di = difference();
    final boolean isNextHigher =
            next.intMarkerPosition - intMarkerPosition > 1;
    final boolean isPreviousLower =
            previous.intMarkerPosition - intMarkerPosition < -1;

    if (di >= 1 && isNextHigher || di <= -1 && isPreviousLower) {
        final int d = di >= 0 ? 1 : -1;
        final double[] xval =
                new double[] { previous.intMarkerPosition,
                        intMarkerPosition, next.intMarkerPosition };
        final double[] yval =
                new double[] { previous.markerHeight, markerHeight,
                        next.markerHeight };
        final double xD = intMarkerPosition + d;

        UnivariateFunction univariateFunction =
                nonLinear.interpolate(xval, yval);
        markerHeight = univariateFunction.value(xD);

        // If parabolic estimate is bad then turn linear
        if (isEstimateBad(yval, markerHeight)) {
            int delta = xD - xval[1] > 0 ? 1 : -1;
            final double[] xBad =
                    new double[] { xval[1], xval[1 + delta] };
            final double[] yBad =
                    new double[] { yval[1], yval[1 + delta] };
            MathArrays.sortInPlace(xBad, yBad);// since d can be +/- 1
            univariateFunction = linear.interpolate(xBad, yBad);
            markerHeight = univariateFunction.value(xD);
        }
        incrementPosition(d);
    }
    return markerHeight;
}
 

/**
 * Estimate the quantile for the current marker.
 *
 * @return estimated quantile
 */
private double estimate() {
    final double di = difference();
    final boolean isNextHigher =
            next.intMarkerPosition - intMarkerPosition > 1;
    final boolean isPreviousLower =
            previous.intMarkerPosition - intMarkerPosition < -1;

    if (di >= 1 && isNextHigher || di <= -1 && isPreviousLower) {
        final int d = di >= 0 ? 1 : -1;
        final double[] xval =
                new double[] { previous.intMarkerPosition,
                        intMarkerPosition, next.intMarkerPosition };
        final double[] yval =
                new double[] { previous.markerHeight, markerHeight,
                        next.markerHeight };
        final double xD = intMarkerPosition + d;

        UnivariateFunction univariateFunction =
                nonLinear.interpolate(xval, yval);
        markerHeight = univariateFunction.value(xD);

        // If parabolic estimate is bad then turn linear
        if (isEstimateBad(yval, markerHeight)) {
            int delta = xD - xval[1] > 0 ? 1 : -1;
            final double[] xBad =
                    new double[] { xval[1], xval[1 + delta] };
            final double[] yBad =
                    new double[] { yval[1], yval[1 + delta] };
            MathArrays.sortInPlace(xBad, yBad);// since d can be +/- 1
            univariateFunction = linear.interpolate(xBad, yBad);
            markerHeight = univariateFunction.value(xD);
        }
        incrementPosition(d);
    }
    return markerHeight;
}
 

/**
 * Construct a Lagrange polynomial with the given abscissas and function
 * values. The order of interpolating points are not important.
 * <p>
 * The constructor makes copy of the input arrays and assigns them.</p>
 *
 * @param x interpolating points
 * @param y function values at interpolating points
 * @throws DimensionMismatchException if the array lengths are different.
 * @throws NumberIsTooSmallException if the number of points is less than 2.
 * @throws NonMonotonicSequenceException
 * if two abscissae have the same value.
 */
public PolynomialFunctionLagrangeForm(double x[], double y[])
    throws DimensionMismatchException, NumberIsTooSmallException, NonMonotonicSequenceException {
    this.x = new double[x.length];
    this.y = new double[y.length];
    System.arraycopy(x, 0, this.x, 0, x.length);
    System.arraycopy(y, 0, this.y, 0, y.length);
    coefficientsComputed = false;

    if (!verifyInterpolationArray(x, y, false)) {
        MathArrays.sortInPlace(this.x, this.y);
        // Second check in case some abscissa is duplicated.
        verifyInterpolationArray(this.x, this.y, true);
    }
}
 

private static BinningResults binResultByFrame(double[] x, double[] y, double[] frame, int binCount) {
    double minFrame = findMinFrame(frame);
    double maxFrame = findMaxFrame(frame);

    if(maxFrame == minFrame) {
        throw new RuntimeException("Requires multiple frames.");
    }

    MathArrays.sortInPlace(frame, x, y);
    int detectionsPerBin = frame.length / binCount;

    //alloc space for binned results
    double[][] xBinnedByFrame = new double[binCount][];
    double[][] yBinnedByFrame = new double[binCount][];
    double[] binCenters = new double[binCount];
    int currentPos = 0;
    for(int i = 0; i < binCount; i++) {
        int endPos = currentPos + detectionsPerBin;
        if(endPos >= frame.length || i == binCount - 1) {
            endPos = frame.length;
        } else {
            double frameAtEndPos = frame[endPos - 1];
            while(endPos < frame.length - 1 && frame[endPos] == frameAtEndPos) {
                endPos++;
            }
        }
        if(currentPos > frame.length - 1) {
            xBinnedByFrame[i] = new double[0];
            yBinnedByFrame[i] = new double[0];
            binCenters[i] = maxFrame;
        } else {
            xBinnedByFrame[i] = Arrays.copyOfRange(x, currentPos, endPos);
            yBinnedByFrame[i] = Arrays.copyOfRange(y, currentPos, endPos);
            binCenters[i] = (frame[currentPos] + frame[endPos - 1]) / 2;
        }
        currentPos = endPos;
    }
    return new BinningResults(xBinnedByFrame, yBinnedByFrame, binCenters, (int) minFrame, (int) maxFrame);
}