Examples with Point com.geophile.z.spatialobject.d2.Point used on opensource projects

Example 66 with Point

use of com.geophile.z.spatialobject.d2.Point in project imagej-ops by imagej.

the class DefaultDetectRidges method getNextPoint.

/**
 * Recursively determines the next line point and adds it to the running list
 * of line points.
 *
 * @param gradientRA - the {@link RandomAccess} of the gradient image.
 * @param pRA - the {@link RandomAccess} of the eigenvector image.
 * @param nRA - the {@link RandomAccess} of the subpixel line location image.
 * @param points - the {@link ArrayList} containing the line points.
 * @param octant - integer denoting the octant of the last gradient vector,
 *          oriented with 1 being 0 degrees and increasing in the
 *          counterclockwise direction.
 * @param lastnx - the x component of the gradient vector of the last line
 *          point.
 * @param lastny - the y component of the gradient vector of the last line
 *          point.
 * @param lastpx - the x component of the subpixel line location of the last
 *          line point.
 * @param lastpy - the y component of the subpixel line location of the last
 *          line point.
 */
private void getNextPoint(RandomAccess<DoubleType> gradientRA, RandomAccess<DoubleType> pRA, RandomAccess<DoubleType> nRA, List<RealPoint> points, int octant, double lastnx, double lastny, double lastpx, double lastpy) {
    Point currentPos = new Point(gradientRA);
    // variables for the best line point of the three.
    Point salientPoint = new Point(gradientRA);
    double salientnx = 0;
    double salientny = 0;
    double salientpx = 0;
    double salientpy = 0;
    double bestSalience = Double.MAX_VALUE;
    boolean lastPointInLine = true;
    // check the three possible points that could continue the line, starting at
    // the octant after the given octant and rotating clockwise around the
    // current pixel.
    double lastAngle = RidgeDetectionUtils.getAngle(lastnx, lastny);
    for (int i = 1; i < 4; i++) {
        int[] modifier = RidgeDetectionUtils.getOctantCoords(octant + i);
        gradientRA.move(modifier[0], 0);
        gradientRA.move(modifier[1], 1);
        // there.
        if (gradientRA.get().get() > lowerThreshold) /*&& isMaxRA.get().get() > 0*/
        {
            long[] vectorArr = { gradientRA.getLongPosition(0), gradientRA.getLongPosition(1), 0 };
            nRA.setPosition(vectorArr);
            double nx = nRA.get().get();
            nRA.fwd(2);
            double ny = nRA.get().get();
            pRA.setPosition(vectorArr);
            double px = pRA.get().get();
            pRA.fwd(2);
            double py = pRA.get().get();
            double currentAngle = RidgeDetectionUtils.getAngle(nx, ny);
            double subpixelDiff = Math.sqrt(Math.pow(px - lastpx, 2) + Math.pow(py - lastpy, 2));
            double angleDiff = Math.abs(currentAngle - lastAngle);
            lastPointInLine = false;
            // numbers relative to other potential line points.
            if (subpixelDiff + angleDiff < bestSalience) {
                // record the values of the new most salient pixel
                salientPoint = new Point(gradientRA);
                salientnx = nx;
                salientny = ny;
                salientpx = px;
                salientpy = py;
                bestSalience = subpixelDiff + angleDiff;
            }
            // set the values to zero so that they are not added to another line.
            gradientRA.get().set(0);
        }
        // reset our randomAccess for the next check
        gradientRA.setPosition(currentPos);
    }
    // set the current pixel to 0 in the first slice of eigenRA!
    gradientRA.get().setReal(0);
    // find the next line point as long as there is one to find
    if (!lastPointInLine) {
        // take the most salient point
        gradientRA.setPosition(salientPoint);
        points.add(RidgeDetectionUtils.get2DRealPoint(gradientRA.getDoublePosition(0) + salientpx, gradientRA.getDoublePosition(1) + salientpy));
        // the gradient vector itself refers to the greatest change in intensity,
        // and for a pixel on a line this vector will be perpendicular to the
        // direction of the line. But this vector can point to either the left or
        // the right of the line from the perspective of the detector, and there
        // is no guarantee that the vectors at line point will point off the same
        // side of the line. So if they point off different sides, set the current
        // vector by 180 degrees for the purposes of this detector. We set the
        // threshold for angle fixing just above 90 degrees since any lower would
        // prevent ridges curving.
        double potentialGradient = RidgeDetectionUtils.getAngle(salientnx, salientny);
        // even though they are close enough to satisfy.
        if (lastAngle < angleThreshold)
            lastAngle += 360;
        if (potentialGradient < angleThreshold)
            potentialGradient += 360;
        if (Math.abs(potentialGradient - lastAngle) > angleThreshold) {
            salientnx = -salientnx;
            salientny = -salientny;
        }
        // perform the operation again on the new end of the line being formed.
        getNextPoint(gradientRA, pRA, nRA, points, RidgeDetectionUtils.getOctant(salientnx, salientny), salientnx, salientny, salientpx, salientpy);
    }
}

Example 67 with Point

use of com.geophile.z.spatialobject.d2.Point in project imagej-ops by imagej.

the class WatershedSeeded method compute.

@SuppressWarnings("unchecked")
@Override
public void compute(final RandomAccessibleInterval<T> in, final ImgLabeling<Integer, IntType> out) {
    // extend border to be able to do a quick check, if a voxel is inside
    final LabelingType<Integer> oustide = out.firstElement().copy();
    oustide.clear();
    oustide.add(OUTSIDE);
    final ExtendedRandomAccessibleInterval<LabelingType<Integer>, ImgLabeling<Integer, IntType>> outExt = Views.extendValue(out, oustide);
    final OutOfBounds<LabelingType<Integer>> raOut = outExt.randomAccess();
    // if no mask provided, set the mask to the whole image
    if (mask == null) {
        mask = (RandomAccessibleInterval<B>) ops().create().img(in, new BitType());
        for (B b : Views.flatIterable(mask)) {
            b.set(true);
        }
    }
    // initialize output labels
    final Cursor<B> maskCursor = Views.flatIterable(mask).cursor();
    while (maskCursor.hasNext()) {
        maskCursor.fwd();
        if (maskCursor.get().get()) {
            raOut.setPosition(maskCursor);
            raOut.get().clear();
            raOut.get().add(INIT);
        }
    }
    // RandomAccess for Mask, Seeds and Neighborhoods
    final RandomAccess<B> raMask = mask.randomAccess();
    final RandomAccess<LabelingType<Integer>> raSeeds = seeds.randomAccess();
    final Shape shape;
    if (useEightConnectivity) {
        shape = new RectangleShape(1, true);
    } else {
        shape = new DiamondShape(1);
    }
    final RandomAccessible<Neighborhood<T>> neighborhoods = shape.neighborhoodsRandomAccessible(in);
    final RandomAccess<Neighborhood<T>> raNeigh = neighborhoods.randomAccess();
    /*
		 * Carry over the seeding points to the new label and adds them to a
		 * voxel priority queue
		 */
    final PriorityQueue<WatershedVoxel> pq = new PriorityQueue<>();
    // Only iterate seeds that are not excluded by the mask
    final IterableRegion<B> maskRegions = Regions.iterable(mask);
    final IterableInterval<LabelingType<Integer>> seedsMasked = Regions.sample(maskRegions, seeds);
    final Cursor<LabelingType<Integer>> cursorSeeds = seedsMasked.localizingCursor();
    while (cursorSeeds.hasNext()) {
        final Set<Integer> l = cursorSeeds.next();
        if (l.isEmpty()) {
            continue;
        }
        if (l.size() > 1) {
            throw new IllegalArgumentException("Seeds must have exactly one label!");
        }
        final Integer label = l.iterator().next();
        if (label < 0) {
            throw new IllegalArgumentException("Seeds must have positive integers as labels!");
        }
        raNeigh.setPosition(cursorSeeds);
        final Cursor<T> neighborhood = raNeigh.get().cursor();
        // Add unlabeled neighbors to priority queue
        while (neighborhood.hasNext()) {
            neighborhood.fwd();
            raSeeds.setPosition(neighborhood);
            raMask.setPosition(neighborhood);
            raOut.setPosition(neighborhood);
            if (raOut.isOutOfBounds() || !raMask.get().get() || !raSeeds.get().isEmpty())
                continue;
            final Integer labelNeigh = raOut.get().iterator().next();
            if (labelNeigh != INQUEUE && labelNeigh != OUTSIDE) {
                raOut.setPosition(neighborhood);
                pq.add(new WatershedVoxel(IntervalIndexer.positionToIndex(neighborhood, in), neighborhood.get().getRealDouble()));
                raOut.get().clear();
                raOut.get().add(INQUEUE);
            }
        }
        // Overwrite label in output with the seed label
        raOut.setPosition(cursorSeeds);
        raOut.get().clear();
        raOut.get().add(label);
    }
    /*
		 * Pop the head of the priority queue, label and push all unlabeled
		 * neighbored pixels.
		 */
    // list to store neighbor labels
    final ArrayList<Integer> neighborLabels = new ArrayList<>();
    // list to store neighbor voxels
    final ArrayList<WatershedVoxel> neighborVoxels = new ArrayList<>();
    // iterate the queue
    final Point pos = new Point(in.numDimensions());
    while (!pq.isEmpty()) {
        IntervalIndexer.indexToPosition(pq.poll().getPos(), out, pos);
        // reset list of neighbor labels
        neighborLabels.clear();
        // reset list of neighbor voxels
        neighborVoxels.clear();
        // iterate the neighborhood of the pixel
        raNeigh.setPosition(pos);
        final Cursor<T> neighborhood = raNeigh.get().cursor();
        while (neighborhood.hasNext()) {
            neighborhood.fwd();
            // Unlabeled neighbors go into the queue if they are not there
            // yet
            raOut.setPosition(neighborhood);
            raMask.setPosition(raOut);
            if (!raOut.get().isEmpty()) {
                final Integer label = raOut.get().iterator().next();
                if (label == INIT && raMask.get().get()) {
                    neighborVoxels.add(new WatershedVoxel(IntervalIndexer.positionToIndex(neighborhood, out), neighborhood.get().getRealDouble()));
                } else {
                    if (label > WSHED && (!drawWatersheds || !neighborLabels.contains(label))) {
                        // store labels of neighbors in a list
                        neighborLabels.add(label);
                    }
                }
            }
        }
        if (drawWatersheds) {
            // if the neighbors of the extracted voxel that have already
            // been labeled
            // all have the same label, then the voxel is labeled with their
            // label.
            raOut.setPosition(pos);
            raOut.get().clear();
            if (neighborLabels.size() == 1) {
                raOut.get().add(neighborLabels.get(0));
                // list
                for (final WatershedVoxel v : neighborVoxels) {
                    IntervalIndexer.indexToPosition(v.getPos(), out, raOut);
                    raOut.get().clear();
                    raOut.get().add(INQUEUE);
                    pq.add(v);
                }
            } else if (neighborLabels.size() > 1)
                raOut.get().add(WSHED);
        } else {
            if (neighborLabels.size() > 0) {
                raOut.setPosition(pos);
                raOut.get().clear();
                // take the label which most of the neighbors have
                if (neighborLabels.size() > 2) {
                    final Map<Integer, Long> countLabels = neighborLabels.stream().collect(Collectors.groupingBy(e -> e, Collectors.counting()));
                    final Integer keyMax = Collections.max(countLabels.entrySet(), Comparator.comparingLong(Map.Entry::getValue)).getKey();
                    raOut.get().add(keyMax);
                } else {
                    raOut.get().add(neighborLabels.get(0));
                }
                // list
                for (final WatershedVoxel v : neighborVoxels) {
                    IntervalIndexer.indexToPosition(v.getPos(), out, raOut);
                    raOut.get().clear();
                    raOut.get().add(INQUEUE);
                    pq.add(v);
                }
            }
        }
    }
    /*
		 * Merge already present labels before calculation of watershed
		 */
    if (out() != null) {
        final Cursor<LabelingType<Integer>> cursor = out().cursor();
        while (cursor.hasNext()) {
            cursor.fwd();
            raOut.setPosition(cursor);
            final List<Integer> labels = new ArrayList<>();
            cursor.get().iterator().forEachRemaining(labels::add);
            raOut.get().addAll(labels);
        }
    }
}

Example 68 with Point

use of com.geophile.z.spatialobject.d2.Point in project imagej-ops by imagej.

the class ConvolveTest method testCreateAndConvolvePoints.

/**
 * tests fft based convolve
 */
@Test
public void testCreateAndConvolvePoints() {
    final int xSize = 128;
    final int ySize = 128;
    final int zSize = 128;
    int[] size = new int[] { xSize, ySize, zSize };
    Img<DoubleType> phantom = ops.create().img(size);
    RandomAccess<DoubleType> randomAccess = phantom.randomAccess();
    randomAccess.setPosition(new long[] { xSize / 2, ySize / 2, zSize / 2 });
    randomAccess.get().setReal(255.0);
    randomAccess.setPosition(new long[] { xSize / 4, ySize / 4, zSize / 4 });
    randomAccess.get().setReal(255.0);
    Point location = new Point(phantom.numDimensions());
    location.setPosition(new long[] { 3 * xSize / 4, 3 * ySize / 4, 3 * zSize / 4 });
    HyperSphere<DoubleType> hyperSphere = new HyperSphere<>(phantom, location, 5);
    for (DoubleType value : hyperSphere) {
        value.setReal(16);
    }
    // create psf using the gaussian kernel op (alternatively PSF could be an
    // input to the script)
    RandomAccessibleInterval<DoubleType> psf = ops.create().kernelGauss(new double[] { 5, 5, 5 }, new DoubleType());
    RandomAccessibleInterval<DoubleType> convolved = ops.create().img(size);
    // convolve psf with phantom
    convolved = ops.filter().convolve(convolved, phantom, psf);
    DoubleType sum = new DoubleType();
    DoubleType max = new DoubleType();
    DoubleType min = new DoubleType();
    ops.stats().sum(sum, Views.iterable(convolved));
    ops.stats().max(max, Views.iterable(convolved));
    ops.stats().min(min, Views.iterable(convolved));
    assertEquals(sum.getRealDouble(), 8750.000184601617, 0.0);
    assertEquals(max.getRealDouble(), 3.154534101486206, 0.0);
    assertEquals(min.getRealDouble(), -2.9776862220387557E-7, 0.0);
}

Example 69 with Point

use of com.geophile.z.spatialobject.d2.Point in project imagej-ops by imagej.

the class FFTTest method placeSphereInCenter.

/**
 * utility that places a sphere in the center of the image
 *
 * @param img
 */
private void placeSphereInCenter(final Img<FloatType> img) {
    final Point center = new Point(img.numDimensions());
    for (int d = 0; d < img.numDimensions(); d++) center.setPosition(img.dimension(d) / 2, d);
    final HyperSphere<FloatType> hyperSphere = new HyperSphere<>(img, center, 2);
    for (final FloatType value : hyperSphere) {
        value.setReal(1);
    }
}

Example 70 with Point

use of com.geophile.z.spatialobject.d2.Point in project imagej-ops by imagej.

the class DeconvolveTest method placeSphereInCenter.

// utility to place a small sphere at the center of the image
private void placeSphereInCenter(Img<FloatType> img) {
    final Point center = new Point(img.numDimensions());
    for (int d = 0; d < img.numDimensions(); d++) center.setPosition(img.dimension(d) / 2, d);
    HyperSphere<FloatType> hyperSphere = new HyperSphere<>(img, center, 30);
    for (final FloatType value : hyperSphere) {
        value.setReal(1);
    }
}