Examples with BoundingBox net.imglib2.roi.labeling.BoundingBox used on opensource projects

Example 1 with BoundingBox

use of net.imglib2.roi.labeling.BoundingBox in project imagej-ops by imagej.

the class BoxCount method sectionView.

/**
 * Creates a {@link net.imglib2.View} of the given grid section in the
 * interval
 * <p>
 * Fits the view inside the bounds of the interval.
 * </p>
 *
 * @param interval An n-dimensional interval with binary elements
 * @param sizes Sizes of the interval's dimensions
 * @param coordinates Starting coordinates of the section
 * @param sectionSize Size of the section (n * n * ... n)
 * @return A view of the interval spanning n pixels in each dimension from the
 *         coordinates. Null if view couldn't be set inside the interval
 */
private static <B extends BooleanType<B>> IntervalView<B> sectionView(final RandomAccessibleInterval<B> interval, final long[] sizes, final long[] coordinates, final long sectionSize) {
    final int n = sizes.length;
    final long[] startPosition = IntStream.range(0, n).mapToLong(i -> Math.max(0, coordinates[i])).toArray();
    final long[] endPosition = IntStream.range(0, n).mapToLong(i -> Math.min((sizes[i] - 1), (coordinates[i] + sectionSize - 1))).toArray();
    final boolean badBox = IntStream.range(0, n).anyMatch(d -> (startPosition[d] >= sizes[d]) || (endPosition[d] < 0) || (endPosition[d] < startPosition[d]));
    if (badBox) {
        return null;
    }
    final BoundingBox box = new BoundingBox(n);
    box.update(startPosition);
    box.update(endPosition);
    return Views.offsetInterval(interval, box);
}

Example 2 with BoundingBox

use of net.imglib2.roi.labeling.BoundingBox in project imagej-ops by imagej.

the class Outline method neighbourhoodInterval.

/**
 * Creates a view that spans from (x-1, y-1, ... i-1) to (x+1, y+1, ... i+1)
 * around the given coordinates
 *
 * @param interval the space of the coordinates
 * @param coordinates coordinates (x, y, ... i)
 * @return a view of a neighbourhood in the space
 */
private IntervalView<B> neighbourhoodInterval(final ExtendedRandomAccessibleInterval<B, RandomAccessibleInterval<B>> interval, final long[] coordinates) {
    final int dimensions = interval.numDimensions();
    final BoundingBox box = new BoundingBox(dimensions);
    final long[] minBounds = Arrays.stream(coordinates).map(c -> c - 1).toArray();
    final long[] maxBounds = Arrays.stream(coordinates).map(c -> c + 1).toArray();
    box.update(minBounds);
    box.update(maxBounds);
    return Views.offsetInterval(interval, box);
}

Example 3 with BoundingBox

use of net.imglib2.roi.labeling.BoundingBox in project imagej-ops by imagej.

the class PolygonFeatureTests method boundingBox.

@Test
public void boundingBox() {
    // ground truth verified with matlab
    final List<? extends RealLocalizable> received = GeomUtils.vertices(((Polygon2D) ops.run(DefaultBoundingBox.class, contour)));
    final RealPoint[] expected = new RealPoint[] { new RealPoint(1, 6), new RealPoint(1, 109), new RealPoint(78, 109), new RealPoint(78, 6) };
    assertEquals("Number of polygon points differs.", expected.length, received.size());
    for (int i = 0; i < expected.length; i++) {
        assertEquals("Polygon point " + i + " differs in x-coordinate.", expected[i].getDoublePosition(0), received.get(i).getDoublePosition(0), EPSILON);
        assertEquals("Polygon point " + i + " differs in y-coordinate.", expected[i].getDoublePosition(1), received.get(i).getDoublePosition(1), EPSILON);
    }
}