Examples with Dimensions net.imglib2.Dimensions used on opensource projects

Example 16 with Dimensions

use of net.imglib2.Dimensions in project imagej-ops by imagej.

the class CreateLabelingTest method testImageDimensions.

@Test
public void testImageDimensions() {
    final Random randomGenerator = new Random();
    for (int i = 0; i < TEST_SIZE; i++) {
        // between 2 and 5 dimensions
        final long[] dim = new long[randomGenerator.nextInt(4) + 2];
        // between 2 and 10 pixels per dimensions
        for (int j = 0; j < dim.length; j++) {
            dim[j] = randomGenerator.nextInt(9) + 2;
        }
        // create imglabeling
        @SuppressWarnings("unchecked") final ImgLabeling<String, ?> img = (ImgLabeling<String, ?>) ops.run(DefaultCreateImgLabeling.class, dim);
        assertArrayEquals("Labeling Dimensions:", dim, Intervals.dimensionsAsLongArray(img));
    }
}

Example 17 with Dimensions

use of net.imglib2.Dimensions in project imagej-ops by imagej.

the class CreateKernelDiffractionTest method testKernelDiffraction.

@Test
public void testKernelDiffraction() {
    final Dimensions dims = new FinalDimensions(10, 10);
    // numerical aperture
    final double NA = 1.4;
    // wavelength
    final double lambda = 610E-09;
    // specimen refractive index
    final double ns = 1.33;
    // immersion refractive index, experimental
    final double ni = 1.5;
    // lateral pixel size
    final double resLateral = 100E-9;
    // axial pixel size
    final double resAxial = 250E-9;
    // position of particle
    final double pZ = 2000E-9D;
    // pixel type of created kernel
    final DoubleType type = new DoubleType();
    final // 
    Img<DoubleType> kernel = ops.create().kernelDiffraction(dims, NA, lambda, ns, ni, resLateral, resAxial, pZ, type);
    final double[] expected = { 0.03298495871588273, 0.04246786111102021, 0.0543588031627261, 0.06650574371357207, 0.07370280610722534, 0.07370280610722534, 0.06650574371357207, 0.0543588031627261, 0.04246786111102021, 0.03298495871588273, 0.04246786111102021, 0.05962205221267819, 0.08320071670150801, 0.10800022978800021, 0.1247473245002288, 0.1247473245002288, 0.10800022978800021, 0.08320071670150801, 0.05962205221267819, 0.04246786111102021, 0.0543588031627261, 0.08320071670150801, 0.1247473245002288, 0.1971468112729564, 0.2691722397359577, 0.2691722397359577, 0.1971468112729564, 0.1247473245002288, 0.08320071670150801, 0.0543588031627261, 0.06650574371357207, 0.10800022978800021, 0.1971468112729564, 0.40090474481128285, 0.6227157103102976, 0.6227157103102976, 0.40090474481128285, 0.1971468112729564, 0.10800022978800021, 0.06650574371357207, 0.07370280610722534, 0.1247473245002288, 0.2691722397359577, 0.6227157103102976, 1.0, 1.0, 0.6227157103102976, 0.2691722397359577, 0.1247473245002288, 0.07370280610722534, 0.07370280610722534, 0.1247473245002288, 0.2691722397359577, 0.6227157103102976, 1.0, 1.0, 0.6227157103102976, 0.2691722397359577, 0.1247473245002288, 0.07370280610722534, 0.06650574371357207, 0.10800022978800021, 0.1971468112729564, 0.40090474481128285, 0.6227157103102976, 0.6227157103102976, 0.40090474481128285, 0.1971468112729564, 0.10800022978800021, 0.06650574371357207, 0.0543588031627261, 0.08320071670150801, 0.1247473245002288, 0.1971468112729564, 0.2691722397359577, 0.2691722397359577, 0.1971468112729564, 0.1247473245002288, 0.08320071670150801, 0.0543588031627261, 0.04246786111102021, 0.05962205221267819, 0.08320071670150801, 0.10800022978800021, 0.1247473245002288, 0.1247473245002288, 0.10800022978800021, 0.08320071670150801, 0.05962205221267819, 0.04246786111102021, 0.03298495871588273, 0.04246786111102021, 0.0543588031627261, 0.06650574371357207, 0.07370280610722534, 0.07370280610722534, 0.06650574371357207, 0.0543588031627261, 0.04246786111102021, 0.03298495871588273 };
    assertArrayEquals(expected, asArray(kernel), 0.0);
}

Example 18 with Dimensions

use of net.imglib2.Dimensions in project imagej-ops by imagej.

the class BoxCount method countTranslatedGrids.

/**
 * Count foreground sections in all grids created from the translations
 *
 * @param input N-dimensional binary interval
 * @param translations Stream of translation coordinates in n-dimensions
 * @param sizes Sizes of the interval's dimensions in pixels
 * @param sectionSize Size of a section in the grids
 * @return Foreground sections counted in each grid
 */
private static <B extends BooleanType<B>> LongStream countTranslatedGrids(final RandomAccessibleInterval<B> input, final Stream<long[]> translations, final long[] sizes, final long sectionSize) {
    final int lastDimension = sizes.length - 1;
    final LongType foreground = new LongType();
    final long[] sectionPosition = new long[sizes.length];
    return translations.mapToLong(gridOffset -> {
        foreground.setZero();
        Arrays.fill(sectionPosition, 0);
        countGrid(input, lastDimension, sizes, gridOffset, sectionPosition, sectionSize, foreground);
        return foreground.get();
    });
}

Example 19 with Dimensions

use of net.imglib2.Dimensions 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 20 with Dimensions

use of net.imglib2.Dimensions in project imagej-ops by imagej.

the class BoxCount method calculate.

/**
 * Counts the number of foreground sections in the interval repeatedly with
 * different size sections
 *
 * @param input an n-dimensional binary interval
 * @return A list of (log(foreground count), -log(section size))
 *         {@link ValuePair} objects for curve fitting
 */
@Override
public List<ValuePair<DoubleType, DoubleType>> calculate(final RandomAccessibleInterval<B> input) {
    final List<ValuePair<DoubleType, DoubleType>> points = new ArrayList<>();
    final int dimensions = input.numDimensions();
    final long[] sizes = new long[dimensions];
    final long numTranslations = 1 + gridMoves;
    input.dimensions(sizes);
    for (long sectionSize = maxSize; sectionSize >= minSize; sectionSize /= scaling) {
        final long translationAmount = Math.max(1, sectionSize / numTranslations);
        final Stream<long[]> translations = translationStream(numTranslations, translationAmount, dimensions - 1, new long[dimensions]);
        final LongStream foregroundCounts = countTranslatedGrids(input, translations, sizes, sectionSize);
        final long foreground = foregroundCounts.min().orElse(0);
        final double logSize = -Math.log(sectionSize);
        final double logCount = Math.log(foreground);
        final ValuePair<DoubleType, DoubleType> point = new ValuePair<>(new DoubleType(logSize), new DoubleType(logCount));
        points.add(point);
    }
    return points;
}