Examples with Voxel bacmman.data_structure.Voxel used on opensource projects

Example 1 with Voxel

use of bacmman.data_structure.Voxel in project bacmman by jeanollion.

the class SubPixelLocalizator method getPeaks.

public static List<Point> getPeaks(Image img, List<Region> objects) {
    List<Point> peaks = new ArrayList<>(objects.size());
    for (Region o : objects) {
        // get max value within map
        double max = Double.NEGATIVE_INFINITY;
        Voxel maxV = null;
        for (Voxel v : o.getVoxels()) {
            double value = img.getPixel(v.x, v.y, v.z);
            if (value > max) {
                max = value;
                maxV = v;
            }
        }
        if (img.sizeZ() > 1)
            peaks.add(new Point(maxV.x, maxV.y, maxV.z));
        else
            peaks.add(new Point(maxV.x, maxV.y));
    }
    return peaks;
}

Example 2 with Voxel

use of bacmman.data_structure.Voxel in project bacmman by jeanollion.

the class RegionCluster method getInteface.

public static <I extends InterfaceRegion<I>> I getInteface(Region o1, Region o2, ImageInteger labelImage, InterfaceFactory<Region, I> interfaceFactory) {
    EllipsoidalNeighborhood neigh = labelImage.sizeZ() > 1 ? new EllipsoidalNeighborhood(1, 1, true) : new EllipsoidalNeighborhood(1, true);
    Region min;
    int otherLabel;
    I inter = interfaceFactory.create(o1, o2);
    if (o1.getVoxels().size() <= o2.getVoxels().size()) {
        min = o1;
        otherLabel = o2.getLabel();
    } else {
        min = o2;
        otherLabel = o1.getLabel();
    }
    int xx, yy, zz;
    for (Voxel v : min.getVoxels()) {
        for (int i = 0; i < neigh.dx.length; ++i) {
            xx = v.x + neigh.dx[i];
            yy = v.y + neigh.dy[i];
            zz = v.z + neigh.dz[i];
            if (labelImage.contains(xx, yy, zz) && labelImage.getPixelInt(xx, yy, zz) == otherLabel)
                inter.addPair(v, new Voxel(xx, yy, zz));
        }
    }
    return inter;
}

Example 3 with Voxel

use of bacmman.data_structure.Voxel in project bacmman by jeanollion.

the class RegionCluster method setInterfaces.

protected void setInterfaces(boolean background, boolean lowConnectivity) {
    Map<Integer, Region> objects = new HashMap<>();
    for (Region o : population.getRegions()) objects.put(o.getLabel(), o);
    if (background) {
        backgroundRegion = new Region(new HashSet<>(), 0, population.getImageProperties(), population.getImageProperties().sizeZ() == 1, population.getImageProperties().getScaleXY(), population.getImageProperties().getScaleZ());
        objects.put(0, backgroundRegion);
    }
    ImageInteger inputLabels = population.getLabelMap();
    Voxel n = new Voxel(0, 0, 0);
    int otherLabel;
    int[][] neigh = inputLabels.sizeZ() > 1 ? (lowConnectivity ? ImageLabeller.neigh3DLowHalf : ImageLabeller.neigh3DHalf) : (lowConnectivity ? ImageLabeller.neigh2D4Half : ImageLabeller.neigh2D8Half);
    for (Region o : population.getRegions()) {
        for (Voxel vox : o.getVoxels()) {
            for (int i = 0; i < neigh.length; ++i) {
                // only forward for interaction with other spots & background
                n.x = vox.x + neigh[i][0];
                n.y = vox.y + neigh[i][1];
                n.z = vox.z + neigh[i][2];
                if (inputLabels.contains(n.x, n.y, n.z) && foregroundMask.insideMask(n.x, n.y, n.z)) {
                    otherLabel = inputLabels.getPixelInt(n.x, n.y, n.z);
                    if (otherLabel != o.getLabel()) {
                        if (background || otherLabel != 0) {
                            // to avoid having the same instance of voxel as in the region, because voxel can overlap & voxel can be used to store values interface-wise
                            InterfaceRegion inter = getInterface(o, objects.get(otherLabel), true);
                            if (otherLabel > o.getLabel())
                                inter.addPair(vox.duplicate(), n.duplicate());
                            else
                                inter.addPair(n.duplicate(), vox.duplicate());
                        }
                    }
                } else if (background) {
                    InterfaceRegion inter = getInterface(o, objects.get(0), true);
                    inter.addPair(n.duplicate(), vox.duplicate());
                }
                if (background) {
                    // backward for background only
                    n.x = vox.x - neigh[i][0];
                    n.y = vox.y - neigh[i][1];
                    n.z = vox.z - neigh[i][2];
                    if (inputLabels.contains(n.x, n.y, n.z)) {
                        otherLabel = inputLabels.getPixelInt(n.x, n.y, n.z);
                        if (background && otherLabel == 0) {
                            InterfaceRegion inter = getInterface(o, objects.get(otherLabel), true);
                            inter.addPair(n.duplicate(), vox.duplicate());
                        }
                    } else {
                        InterfaceRegion inter = getInterface(o, objects.get(0), true);
                        inter.addPair(n.duplicate(), vox.duplicate());
                    }
                }
            }
        }
    }
    if (verbose)
        logger.debug("Interface collection: nb of interfaces:" + interfaces.size());
}

Example 4 with Voxel

use of bacmman.data_structure.Voxel in project bacmman by jeanollion.

the class BacteriaSpineFactory method getSpineInSkeletonDirection.

private static <T extends Localizable> List<PointContainer2<Vector, Double>> getSpineInSkeletonDirection(ImageMask mask, CircularNode<T> s1, CircularNode<T> s2, List<PointContainer2<Vector, Double>> skeleton, int persistanceRadius, boolean firstNext, Offset logOff) {
    List<PointContainer2<Vector, Double>> sp = new ArrayList<>();
    Vector skDir = SlidingVector.getMeanVector2D(skeleton.stream().skip(firstNext ? 0 : skeleton.size() - persistanceRadius).limit(persistanceRadius).map(p -> p.getContent1()));
    Vector spineDir = skDir.duplicate().normalize().rotateXY90();
    if (!firstNext)
        spineDir.reverseOffset();
    Point lastPoint = skeleton.get(firstNext ? 0 : skeleton.size() - 1);
    List<CircularNode<T>> bucketFirst = new ArrayList<>();
    while (true) {
        // within loop there is a condition of inclusion of point in bacteria
        Point nextPoint = lastPoint.duplicate().translate(spineDir);
        // get direction of current point according to contour
        Point c1 = getIntersectionWithContour(mask, nextPoint, skDir.duplicate().multiply(-1), s1, bucketFirst, logOff);
        // push
        s1 = bucketFirst.get(0);
        Point c2 = getIntersectionWithContour(mask, nextPoint, skDir.duplicate(), s2, bucketFirst, logOff);
        // push
        s2 = bucketFirst.get(0);
        PointContainer2<Vector, Double> next = PointContainer2.fromPoint(nextPoint, Vector.vector2D(c1, c2), 0d);
        if (imageDisp != null)
            logger.debug("extend skeleton {}: [{};{}] -> {}", firstNext ? "up" : "down", c1.duplicate().translate(logOff), c2.duplicate().translate(logOff), next.duplicate().translate(logOff));
        sp.add(next);
        // stop condition
        Point nextPoint2 = next.duplicate().translate(spineDir);
        Voxel nextVox2 = nextPoint2.asVoxel();
        if (!mask.containsWithOffset(nextVox2.x, nextVox2.y, mask.zMin()) || !mask.insideMaskWithOffset(nextVox2.x, nextVox2.y, mask.zMin())) {
            // adjust to contour. First search is middle point between the 2 sides points
            adjustPointToContour(next, spineDir, CircularNode.getMiddlePoint(s1, s2, firstNext), bucketFirst);
            if (sp.size() > 2) {
                // check that adjusted point is after previous point AND not too close to previous point (if too close may cause projection issues)
                Point ref = sp.get(sp.size() - 3);
                if (// adjusted before previous
                sp.get(sp.size() - 2).distSqXY(ref) > next.distSqXY(ref))
                    // adjusted before previous
                    sp.remove(sp.size() - 2);
                else // adjusted too close to previous
                if (sp.get(sp.size() - 2).dist(sp.get(sp.size() - 1)) < 0.25)
                    sp.remove(sp.size() - 2);
            }
            break;
        }
        lastPoint = next;
    }
    // check direction of last point: if the norm is too small direction is not precise -> take direction of previous one keeping the norm
    if (sp.size() > 1) {
        double norm = sp.get(sp.size() - 1).getContent1().norm();
        if (norm < 3) {
            // minimal norm
            if (norm < 2)
                norm = 2;
            sp.get(sp.size() - 1).setContent1(sp.get(sp.size() - 2).getContent1().duplicate().normalize().multiply(norm));
        }
    }
    return sp;
}

Example 5 with Voxel

use of bacmman.data_structure.Voxel in project bacmman by jeanollion.

the class BacteriaSpineFactory method getEdtCenter.

private Voxel getEdtCenter(ImageMask mask) {
    Image edt = EDT.transform(mask, true, 1, 1, false);
    Voxel[] max = new Voxel[1];
    ImageMask.loopWithOffset(mask, (x, y, z) -> {
        float edtV = edt.getPixelWithOffset(x, y, z);
        if (max[0] == null || edtV > max[0].value)
            max[0] = new Voxel(x, y, z, edtV);
    });
    return max[0];
}