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

Example 1 with FinalInterval

use of net.imglib2.FinalInterval 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 2 with FinalInterval

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

the class DefaultCreateKernelGabor method calculate.

@Override
public RandomAccessibleInterval<T> calculate(final double[] sigmas, final double[] period) {
    // both input arrays must be of the same length
    if (sigmas.length != period.length)
        throw new IllegalArgumentException("Params length mismatch: The number " + "of sigmas must match the dimensionality of the period vector.");
    // NB: sigma==0 indicates no filtering along its axis
    for (final double s : sigmas) if (s < 0.0)
        throw new IllegalArgumentException("Input sigma must be non-negative.");
    // the size and center of the output image
    final long[] dims = new long[sigmas.length];
    final long[] centre = new long[sigmas.length];
    for (int d = 0; d < dims.length; d++) {
        dims[d] = Math.max(3, (2 * (int) (3 * sigmas[d] + 0.5) + 1));
        centre[d] = (int) (dims[d] / 2);
    }
    // prepare the output image
    final RandomAccessibleInterval<T> out = createImgOp.calculate(new FinalInterval(dims));
    // calculate the squared length of the period vector
    double perLengthSq = 0.0;
    for (int d = 0; d < period.length; d++) perLengthSq += period[d] * period[d];
    // fill the output image
    final Cursor<T> cursor = Views.iterable(out).cursor();
    while (cursor.hasNext()) {
        cursor.fwd();
        // obtain the current coordinate (use dims to store it)
        cursor.localize(dims);
        // to calculate current Gabor kernel value
        double GaussExp = 0.0;
        double freqPart = 0.0;
        // but produce no Gaussian envelope for axes for which sigma==0
        // no blocking by default
        double blockingExp = 1.0;
        // sweep over all dimensions to determine voxel value
        for (int d = 0; d < dims.length; d++) {
            final double dx = dims[d] - centre[d];
            if (sigmas[d] > 0.)
                // normal case: cummulate exp's argument
                GaussExp += (dx * dx) / (sigmas[d] * sigmas[d]);
            else if (dx != 0.)
                // sigmas[d] == 0 && we are off the blocking axis
                blockingExp = 0.f;
            // cummulates scalar product...
            freqPart += dx * period[d];
        }
        GaussExp = Math.exp(-0.5 * GaussExp) * blockingExp;
        freqPart = 6.28318 * freqPart / perLengthSq;
        // compose the real value finally
        cursor.get().setReal(GaussExp * Math.cos(freqPart));
        // TODO NB: is it faster to determine type or calculate the math (possible uselessly)
        if (!(typeVar instanceof RealType<?>))
            // set then the imaginary part of the kernel too
            cursor.get().setImaginary(GaussExp * Math.sin(freqPart));
    }
    return out;
}

Example 3 with FinalInterval

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

the class DefaultCreateKernelGauss method calculate.

@Override
public RandomAccessibleInterval<T> calculate(double[] input) {
    final double[] sigmaPixels = new double[input.length];
    final long[] dims = new long[input.length];
    final double[][] kernelArrays = new double[input.length][];
    for (int d = 0; d < input.length; d++) {
        sigmaPixels[d] = input[d];
        dims[d] = Math.max(3, (2 * (int) (3 * sigmaPixels[d] + 0.5) + 1));
        kernelArrays[d] = Util.createGaussianKernel1DDouble(sigmaPixels[d], true);
    }
    final RandomAccessibleInterval<T> out = createOp.calculate(new FinalInterval(dims));
    final Cursor<T> cursor = Views.iterable(out).cursor();
    while (cursor.hasNext()) {
        cursor.fwd();
        double result = 1.0f;
        for (int d = 0; d < input.length; d++) {
            result *= kernelArrays[d][cursor.getIntPosition(d)];
        }
        cursor.get().setReal(result);
    }
    return out;
}

Example 4 with FinalInterval

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

the class CreateKernelSobel method calculate.

@Override
public RandomAccessibleInterval<T> calculate() {
    long[] dim = new long[4];
    dim[0] = 3;
    dim[1] = 1;
    for (int k = 2; k < dim.length; k++) {
        dim[k] = 1;
    }
    dim[dim.length - 1] = 2;
    RandomAccessibleInterval<T> output = createOp.calculate(new FinalInterval(dim));
    final Cursor<T> cursor = Views.iterable(output).cursor();
    int i = 0;
    while (cursor.hasNext()) {
        cursor.fwd();
        cursor.get().setReal(values[i]);
        i++;
    }
    return output;
}

Example 5 with FinalInterval

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

the class DefaultCreateKernelBiGauss method calculate.

@Override
public RandomAccessibleInterval<T> calculate(final double[] sigmas, final Integer dimensionality) {
    // both sigmas must be available
    if (sigmas.length < 2)
        throw new IllegalArgumentException("Two sigmas (for inner and outer Gauss)" + " must be supplied.");
    // both sigmas must be reasonable
    if (sigmas[0] <= 0 || sigmas[1] <= 0)
        throw new IllegalArgumentException("Input sigmas must be both positive.");
    // dimension as well...
    if (dimensionality <= 0)
        throw new IllegalArgumentException("Input dimensionality must both positive.");
    // the size and center of the output image
    final long[] dims = new long[dimensionality];
    final long[] centre = new long[dimensionality];
    // time-saver... (must hold now: dimensionality > 0)
    dims[0] = Math.max(3, (2 * (int) (sigmas[0] + 2 * sigmas[1] + 0.5) + 1));
    centre[0] = (int) (dims[0] / 2);
    // fill the size and center arrays
    for (int d = 1; d < dims.length; d++) {
        dims[d] = dims[0];
        centre[d] = centre[0];
    }
    // prepare some scaling constants
    // eq. (6)
    final double k = (sigmas[1] / sigmas[0]) * (sigmas[1] / sigmas[0]);
    // eq. (9)
    final double c0 = 0.24197 * ((sigmas[1] / sigmas[0]) - 1.0) / sigmas[0];
    // 0.24197 = 1/sqrt(2*PI*e) = 1/sqrt(2*PI) * exp(-0.5)
    final double[] C = { 1.0 / (2.50663 * sigmas[0]), 1.0 / (2.50663 * sigmas[1]) };
    // 2.50663 = sqrt(2*PI)
    // prepare squared input sigmas
    final double[] sigmasSq = { sigmas[0] * sigmas[0], sigmas[1] * sigmas[1] };
    // prepare the output image
    final RandomAccessibleInterval<T> out = createImgOp.calculate(new FinalInterval(dims));
    // fill the output image
    final Cursor<T> cursor = Views.iterable(out).cursor();
    while (cursor.hasNext()) {
        cursor.fwd();
        // obtain the current coordinate (use dims to store it)
        cursor.localize(dims);
        // calculate distance from the image centre
        // TODO: can JVM reuse this var or is it allocated again and again (and multipling in the memory)?
        double dist = 0.;
        for (int d = 0; d < dims.length; d++) {
            final double dx = dims[d] - centre[d];
            dist += dx * dx;
        }
        // dist = Math.sqrt(dist); -- gonna work with squared distance
        // which of the two Gaussians should we use?
        double val = 0.;
        if (dist < sigmasSq[0]) {
            // the inner one
            val = C[0] * Math.exp(-0.5 * dist / sigmasSq[0]) + c0;
        } else {
            // the outer one, get new distance first:
            dist = Math.sqrt(dist) - (sigmas[0] - sigmas[1]);
            dist *= dist;
            val = k * C[1] * Math.exp(-0.5 * dist / sigmasSq[1]);
        }
        // compose the real value finally
        cursor.get().setReal(val);
    }
    return out;
}