Examples with Facet net.imagej.ops.geom.geom3d.mesh.Facet used on opensource projects

Example 1 with Facet

use of net.imagej.ops.geom.geom3d.mesh.Facet in project imagej-ops by imagej.

the class DefaultInertiaTensor3DMesh method calculate.

@Override
public RealMatrix calculate(final Mesh input) {
    final RealLocalizable o = centroid.calculate(input);
    BlockRealMatrix tensor = new BlockRealMatrix(3, 3);
    final Iterator<Facet> c = input.getFacets().iterator();
    while (c.hasNext()) {
        final TriangularFacet tf = (TriangularFacet) c.next();
        tensor = tensor.add(tetrahedronInertiaTensor(tf.getVertex(0), tf.getVertex(1), tf.getVertex(2), o));
    }
    return tensor;
}

Example 2 with Facet

use of net.imagej.ops.geom.geom3d.mesh.Facet in project imagej-ops by imagej.

the class DefaultVoxelization3D method calculate.

@Override
public RandomAccessibleInterval<BitType> calculate(Mesh input) {
    Img<BitType> outImg = ops.create().img(new FinalInterval(width, height, depth), new BitType());
    DefaultMesh dMesh = (DefaultMesh) input;
    Set<RealLocalizable> verts = dMesh.getVertices();
    RealPoint minPoint = new RealPoint(verts.iterator().next());
    RealPoint maxPoint = new RealPoint(verts.iterator().next());
    for (RealLocalizable v : verts) {
        if (v.getDoublePosition(0) < minPoint.getDoublePosition(0))
            minPoint.setPosition(v.getDoublePosition(0), 0);
        if (v.getDoublePosition(1) < minPoint.getDoublePosition(1))
            minPoint.setPosition(v.getDoublePosition(1), 1);
        if (v.getDoublePosition(2) < minPoint.getDoublePosition(2))
            minPoint.setPosition(v.getDoublePosition(2), 2);
        if (v.getDoublePosition(0) > maxPoint.getDoublePosition(0))
            maxPoint.setPosition(v.getDoublePosition(0), 0);
        if (v.getDoublePosition(1) > maxPoint.getDoublePosition(1))
            maxPoint.setPosition(v.getDoublePosition(1), 1);
        if (v.getDoublePosition(2) > maxPoint.getDoublePosition(2))
            maxPoint.setPosition(v.getDoublePosition(2), 2);
    }
    RealPoint dimPoint = new RealPoint((maxPoint.getDoublePosition(0) - minPoint.getDoublePosition(0)), (maxPoint.getDoublePosition(1) - minPoint.getDoublePosition(1)), (maxPoint.getDoublePosition(2) - minPoint.getDoublePosition(2)));
    double[] stepSizes = new double[3];
    stepSizes[0] = dimPoint.getDoublePosition(0) / width;
    stepSizes[1] = dimPoint.getDoublePosition(1) / height;
    stepSizes[2] = dimPoint.getDoublePosition(2) / depth;
    double[] voxelHalfsize = new double[3];
    for (int k = 0; k < stepSizes.length; k++) voxelHalfsize[k] = stepSizes[k] / 2.0;
    for (Facet f : dMesh.getFacets()) {
        TriangularFacet tri = (TriangularFacet) f;
        Vector3D v1 = tri.getP0();
        Vector3D v2 = tri.getP1();
        Vector3D v3 = tri.getP2();
        double[] minSubBoundary = new double[] { Math.min(Math.min(v1.getX(), v2.getX()), v3.getX()) - minPoint.getDoublePosition(0), Math.min(Math.min(v1.getY(), v2.getY()), v3.getY()) - minPoint.getDoublePosition(1), Math.min(Math.min(v1.getZ(), v2.getZ()), v3.getZ()) - minPoint.getDoublePosition(2) };
        double[] maxSubBoundary = new double[] { Math.max(Math.max(v1.getX(), v2.getX()), v3.getX()) - minPoint.getDoublePosition(0), Math.max(Math.max(v1.getY(), v2.getY()), v3.getY()) - minPoint.getDoublePosition(1), Math.max(Math.max(v1.getZ(), v2.getZ()), v3.getZ()) - minPoint.getDoublePosition(2) };
        // Should use the
        RandomAccess<BitType> ra = outImg.randomAccess();
        // interval
        // implementation
        // for speed
        long[] indices = new long[3];
        for (indices[0] = (long) Math.floor(minSubBoundary[0] / stepSizes[0]); indices[0] < Math.floor(maxSubBoundary[0] / stepSizes[0]); indices[0]++) {
            for (indices[1] = (long) Math.floor(minSubBoundary[1] / stepSizes[1]); indices[1] < Math.floor(maxSubBoundary[1] / stepSizes[1]); indices[1]++) {
                for (indices[2] = (long) Math.floor(minSubBoundary[2] / stepSizes[2]); indices[2] < Math.floor(maxSubBoundary[2] / stepSizes[2]); indices[2]++) {
                    ra.setPosition(indices);
                    if (// Don't check if voxel is already
                    !ra.get().get()) // filled
                    {
                        double[] voxelCenter = new double[3];
                        for (int k = 0; k < 3; k++) voxelCenter[k] = indices[k] * stepSizes[k] + voxelHalfsize[k];
                        if (triBoxOverlap(voxelCenter, voxelHalfsize, v1, v2, v3) == 1) {
                            ra.get().set(true);
                        }
                    }
                }
            }
        }
    }
    return outImg;
}

Example 3 with Facet

use of net.imagej.ops.geom.geom3d.mesh.Facet in project imagej-ops by imagej.

the class DefaultVolumeMesh method calculate.

@Override
public DoubleType calculate(final Mesh input) {
    double volume = 0;
    for (Facet f : input.getFacets()) {
        TriangularFacet tf = (TriangularFacet) f;
        volume += signedVolumeOfTriangle(tf.getP0(), tf.getP1(), tf.getP2());
    }
    return new DoubleType(Math.abs(volume));
}

Example 4 with Facet

use of net.imagej.ops.geom.geom3d.mesh.Facet in project imagej-ops by imagej.

the class MeshFeatureTests method marchingCubes.

@Test
public void marchingCubes() {
    final DefaultMesh result = (DefaultMesh) ops.run(DefaultMarchingCubes.class, ROI);
    final List<Facet> expectedFacets = mesh.getFacets();
    final List<Facet> resultFacets = result.getFacets();
    for (int i = 0; i < expectedFacets.size(); i++) {
        final TriangularFacet tmpR = (TriangularFacet) resultFacets.get(i);
        final TriangularFacet tmpE = (TriangularFacet) expectedFacets.get(i);
        for (int j = 0; j < 3; j++) {
            final Vertex resultVertex = tmpR.getVertex(j);
            final Vertex expectedVertex = tmpE.getVertex(j);
            assertEquals("Triangular Facet point " + j + " differes in x- coordinate:", expectedVertex.getDoublePosition(0), resultVertex.getDoublePosition(0), EPSILON);
            assertEquals("Triangular Facet point " + j + " differes in y- coordinate:", expectedVertex.getDoublePosition(1), resultVertex.getDoublePosition(1), EPSILON);
            assertEquals("Triangular Facet point " + j + " differes in z- coordinate:", expectedVertex.getDoublePosition(2), resultVertex.getDoublePosition(2), EPSILON);
        }
    }
}