Examples with ValuePair net.imglib2.util.ValuePair used on opensource projects

Example 6 with ValuePair

use of net.imglib2.util.ValuePair in project vcell by virtualcell.

the class ImageStatsForPlotting method computeMean.

/**
 * Computes the mean of each XY slice along the 3rd dimension
 * TODO: Currently assumes only 3 dimensions, must handle time series of z stacks and multiple channels
 * @param data
 * @return Pair containing A) the 3rd dimension index, and B) the mean value of the XY slice
 */
private Pair<double[], double[]> computeMean(RandomAccessibleInterval<T> data, IterableInterval<BitType> mask) {
    double[] indices = new double[(int) data.dimension(2)];
    double[] means = new double[indices.length];
    for (int z = 0; z < indices.length; z++) {
        FinalInterval interval = Intervals.createMinMax(0, 0, z, data.dimension(0) - 1, data.dimension(1) - 1, z);
        double mean = 0.0;
        RandomAccessibleInterval<T> cropped = ops.transform().crop(data, interval);
        if (mask == null) {
            mean = ops.stats().mean(Views.iterable(cropped)).getRealDouble();
        } else {
            Cursor<BitType> maskCursor = mask.localizingCursor();
            RandomAccess<T> dataRA = cropped.randomAccess();
            RealSum sum = new RealSum();
            int size = 0;
            maskCursor.reset();
            while (maskCursor.hasNext()) {
                maskCursor.fwd();
                if (maskCursor.get().get()) {
                    dataRA.setPosition(maskCursor);
                    sum.add(dataRA.get().getRealDouble());
                    size++;
                }
            }
            mean = sum.getSum() / size;
        }
        indices[z] = z;
        means[z] = mean;
    }
    return new ValuePair<double[], double[]>(indices, means);
}

Example 7 with ValuePair

use of net.imglib2.util.ValuePair in project imagej-ops by imagej.

the class DefaultMinimumFeret method calculate.

@Override
public Pair<RealLocalizable, RealLocalizable> calculate(Polygon2D input) {
    final List<? extends RealLocalizable> points = GeomUtils.vertices(function.calculate(input));
    double distance = Double.POSITIVE_INFINITY;
    RealLocalizable p0 = points.get(0);
    RealLocalizable p1 = points.get(0);
    double tmpDist = 0;
    RealLocalizable tmpP0 = p0;
    RealLocalizable tmpP1 = p1;
    for (int i = 0; i < points.size() - 2; i++) {
        final RealLocalizable lineStart = points.get(i);
        final RealLocalizable lineEnd = points.get(i + 1);
        tmpDist = 0;
        final Line l = new Line(new Vector2D(lineStart.getDoublePosition(0), lineStart.getDoublePosition(1)), new Vector2D(lineEnd.getDoublePosition(0), lineEnd.getDoublePosition(1)), 10e-12);
        for (int j = 0; j < points.size(); j++) {
            if (j != i && j != i + 1) {
                final RealLocalizable ttmpP0 = points.get(j);
                final double tmp = l.distance(new Vector2D(ttmpP0.getDoublePosition(0), ttmpP0.getDoublePosition(1)));
                if (tmp > tmpDist) {
                    tmpDist = tmp;
                    final Vector2D vp = (Vector2D) l.project(new Vector2D(ttmpP0.getDoublePosition(0), ttmpP0.getDoublePosition(1)));
                    tmpP0 = new RealPoint(vp.getX(), vp.getY());
                    tmpP1 = ttmpP0;
                }
            }
        }
        if (tmpDist < distance) {
            distance = tmpDist;
            p0 = tmpP0;
            p1 = tmpP1;
        }
    }
    final RealLocalizable lineStart = points.get(points.size() - 1);
    final RealLocalizable lineEnd = points.get(0);
    final Line l = new Line(new Vector2D(lineStart.getDoublePosition(0), lineStart.getDoublePosition(1)), new Vector2D(lineEnd.getDoublePosition(0), lineEnd.getDoublePosition(1)), 10e-12);
    tmpDist = 0;
    for (int j = 0; j < points.size(); j++) {
        if (j != points.size() - 1 && j != 0 + 1) {
            final RealLocalizable ttmpP0 = points.get(j);
            final double tmp = l.distance(new Vector2D(ttmpP0.getDoublePosition(0), ttmpP0.getDoublePosition(1)));
            if (tmp > tmpDist) {
                tmpDist = tmp;
                final Vector2D vp = (Vector2D) l.project(new Vector2D(ttmpP0.getDoublePosition(0), ttmpP0.getDoublePosition(1)));
                tmpP0 = new RealPoint(vp.getX(), vp.getY());
                tmpP1 = ttmpP0;
            }
        }
    }
    if (tmpDist < distance) {
        distance = tmpDist;
        p0 = tmpP0;
        p1 = tmpP1;
    }
    return new ValuePair<>(p0, p1);
}