Examples with ArrayUtil mcib3d.utils.ArrayUtil used on opensource projects

Example 41 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class IntImage3D method morpho3Dbin.

/**
 * 3D binary morphology - dilatation of objects
 *
 * @param fond Value of background
 * @param obj Value of objects
 * @param rx Radius in x
 * @param ry Radius in x
 * @param rz Radius in x
 * @return Dilated image
 */
private IntImage3D morpho3Dbin(int obj, int fond, float rx, float ry, float rz) {
    int p;
    IntImage3D morphoimg = new IntImage3D(sizex, sizey, sizez, type);
    // create kernel
    int[] ker = createKernelEllipsoid(rx, ry, rz);
    int nb = 0;
    for (int i = 0; i < ker.length; i++) {
        nb += ker[i];
    }
    ArrayUtil tab;
    for (int k = 0; k < sizez; k++) {
        if (this.showStatus) {
            IJ.showStatus("3D Binary Morphology : " + (int) (100 * k / sizez) + "%");
        }
        for (int j = 0; j < sizey; j++) {
            for (int i = 0; i < sizex; i++) {
                p = getPixel(i, j, k);
                if (p == obj) {
                    morphoimg.putPixel(i, j, k, p);
                } else {
                    tab = this.getNeighborhoodKernel(ker, nb, i, j, k, rx, ry, rz);
                    if (!tab.hasOnlyValue(fond)) {
                        morphoimg.putPixel(i, j, k, obj);
                    } else {
                        morphoimg.putPixel(i, j, k, fond);
                    }
                }
            }
        }
    }
    return morphoimg;
}

Example 42 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class IntImage3D method createLocalMaximaImage.

/**
 * Création d'une image des maxima locaux dans un voisiange donne
 *
 * @param voisx taille voisinage en x
 * @param voisy taille voisinage en y
 * @param voisz taille voisinage en z
 * @param th threshold image (255)
 * @param keep
 * @return Image des maxima locaux
 */
public IntImage3D createLocalMaximaImage(float voisx, float voisy, float voisz, int th, boolean keep) {
    // create kernel
    int[] ker = createKernelEllipsoid(voisx, voisy, voisz);
    int nb = 0;
    for (int i = 0; i < ker.length; i++) {
        nb += ker[i];
    }
    int pix;
    int vx = (int) Math.ceil(voisx);
    int vy = (int) Math.ceil(voisy);
    int vz = (int) Math.ceil(voisz);
    IntImage3D maxima = new IntImage3D(sizex, sizey, sizez, type);
    // parcours de l'image3D
    ArrayUtil tab;
    for (int k = vz; k < sizez - vz; k++) {
        if (this.showStatus) {
            IJ.showStatus("3D Max Local : " + (int) (100 * k / sizez) + "%");
        }
        for (int j = vy; j < sizey - vy; j++) {
            for (int i = vx; i < sizex - vx; i++) {
                pix = getPixel(i, j, k);
                if (pix > th) {
                    tab = getNeighborhoodKernel(ker, nb, i, j, k, voisx, voisy, voisz);
                    if (tab.getMaximum() == pix) {
                        // IJ.log(""+i+" "+j+" "+k+" "+pix);
                        if (!keep) {
                            maxima.putPixel(i, j, k, 255);
                        } else {
                            maxima.putPixel(i, j, k, pix);
                        }
                    }
                }
            }
        }
    }
    return maxima;
}

Example 43 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class IntImage3D method grayErosion.

/**
 * @param ker
 * @return
 */
public IntImage3D grayErosion(final IntImage3D ker) {
    final IntImage3D erode = new IntImage3D(sizex, sizey, sizez, type);
    final IntImage3D ker2 = new IntImage3D(ker);
    final int vx = ker.getSizex();
    final int vy = ker.getSizey();
    final int vz = ker.getSizez();
    // PARALLEL
    final AtomicInteger ai = new AtomicInteger(0);
    Thread[] threads = ThreadUtil.createThreadArray(0);
    for (int ithread = 0; ithread < threads.length; ithread++) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                ArrayUtil tab;
                int res = 0;
                int val = 0;
                int x0;
                int x1;
                int y0;
                int y1;
                int z0;
                int z1;
                for (int z = ai.getAndIncrement(); z < sizez; z = ai.getAndIncrement()) {
                    if (showStatus) {
                        IJ.showStatus("3D Gray Erosion : " + (int) (100 * z / sizez) + "%");
                    }
                    for (int y = 0; y < sizey; y++) {
                        for (int x = 0; x < sizex; x++) {
                            res = Integer.MAX_VALUE;
                            x0 = x - vx;
                            x1 = x + vx;
                            y0 = y - vy;
                            y1 = y + vy;
                            z0 = z - vz;
                            z1 = z + vz;
                            for (int k = z0; k <= z1; k++) {
                                for (int j = y0; j <= y1; j++) {
                                    for (int i = x0; i <= x1; i++) {
                                        if (i >= 0 && j >= 0 && k >= 0 && i < sizex && j < sizey && k < sizez) {
                                            val = getPixel(i, j, k) - ker.getPixel(i - x0, j - y0, k - z0);
                                            if (val < res) {
                                                res = val;
                                            }
                                        }
                                    }
                                }
                            }
                            erode.putPixel(x, y, z, res);
                        }
                    }
                }
            }
        };
    }
    ThreadUtil.startAndJoin(threads);
    return erode;
}

Example 44 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class IntImage3D method gradient.

/**
 * The gradient of the image in a given direction (sobel)
 *
 * @param axis x,y, or z
 * @return the gradient image
 */
public IntImage3D gradient(int axis) {
    IntImage3D res = new IntImage3D(sizex, sizey, sizez);
    ArrayUtil nei;
    double[] edgeX = { -1, 0, 1, -2, 0, 2, -1, 0, 1, -2, 0, 2, -4, 0, 4, -2, 0, 2, -1, 0, 1, -2, 0, 2, -1, 0, 1 };
    double[] edgeY = { -1, -2, -1, 0, 0, 0, 1, 2, 1, -2, -4, -2, 0, 0, 0, 2, 4, 2, -1, -2, -1, 0, 0, 0, 1, 2, 1 };
    double[] edgeZ = { -1, -2, -1, -2, -4, -2, -1, -2, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 1, 2, 4, 2, 1, 2, 1 };
    double ex;
    double ey;
    double ez;
    double edge;
    for (int k = 0; k < sizez; k++) {
        if (this.showStatus) {
            IJ.showStatus("3D Sobel : " + (int) (100 * k / sizez) + "%");
        }
        for (int j = 0; j < sizey; j++) {
            for (int i = 0; i < sizex; i++) {
                nei = getNeighborhood3x3x3(i, j, k);
                ex = nei.convolve(edgeX, 1.0f);
                ey = nei.convolve(edgeY, 1.0f);
                ez = nei.convolve(edgeZ, 1.0f);
                if (axis == XAXIS) {
                    edge = ex;
                } else if (axis == YAXIS) {
                    edge = ey;
                } else if (axis == ZAXIS) {
                    edge = ez;
                } else {
                    edge = 0;
                }
                if (edge > 65535) {
                    edge = 65535;
                }
                res.putPixel(i, j, k, (int) edge);
            }
        }
    }
    return res;
}

Example 45 with ArrayUtil

use of mcib3d.utils.ArrayUtil in project mcib3d-core by mcib3d.

the class IntImage3D method varianceFilter.

/**
 * Variance Filter in 3D
 *
 * @param radx radius in x
 * @param rady radius in y
 * @param radz radius in z
 * @return 3D variance image
 */
public RealImage3D varianceFilter(float radx, float rady, float radz) {
    RealImage3D varimg = null;
    varimg = new RealImage3D(sizex, sizey, sizez);
    final RealImage3D varimg2 = varimg;
    // create kernel
    final int[] ker = createKernelEllipsoid(radx, rady, radz);
    int nb = 0;
    for (int i = 0; i < ker.length; i++) {
        nb += ker[i];
    }
    final int nb2 = nb;
    final float radx2 = radx;
    final float rady2 = rady;
    final float radz2 = radz;
    // PARALLEL
    final AtomicInteger ai = new AtomicInteger(0);
    Thread[] threads = ThreadUtil.createThreadArray(0);
    for (int ithread = 0; ithread < threads.length; ithread++) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                // median filter
                ArrayUtil tab;
                for (int k = ai.getAndIncrement(); k < sizez; k = ai.getAndIncrement()) {
                    if (showStatus) {
                        IJ.showStatus("3D Variance : " + (int) (100 * k / sizez) + "%");
                    }
                    for (int j = 0; j < sizey; j++) {
                        for (int i = 0; i < sizex; i++) {
                            tab = getNeighborhoodKernel(ker, nb2, i, j, k, radx2, rady2, radz2);
                            varimg2.putPixel(i, j, k, (int) tab.getVariance2());
                        }
                    }
                }
            }
        };
    }
    ThreadUtil.startAndJoin(threads);
    return varimg2;
}