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

Example 36 with ArrayUtil

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

the class Image3D method getNeighborhoodCross3D.

/**
 * @param x
 * @param y
 * @param z
 * @return
 */
public ArrayUtil getNeighborhoodCross3D(int x, int y, int z) {
    ArrayUtil res = new ArrayUtil(7);
    res.putValue(0, getPix(x, y, z));
    int idx = 1;
    if ((x + 1) < sizex) {
        res.putValue(idx, getPix(x + 1, y, z));
        idx++;
    }
    if ((x - 1) >= 0) {
        res.putValue(idx, getPix(x - 1, y, z));
        idx++;
    }
    if ((y + 1) < sizey) {
        res.putValue(idx, getPix(x, y + 1, z));
        idx++;
    }
    if ((y - 1) >= 0) {
        res.putValue(idx, getPix(x, y - 1, z));
        idx++;
    }
    if ((z + 1) < sizez) {
        res.putValue(idx, getPix(x, y, z + 1));
        idx++;
    }
    if ((z - 1) >= 0) {
        res.putValue(idx, getPix(x, y, z - 1));
        idx++;
    }
    res.setSize(idx);
    return res;
}

Example 37 with ArrayUtil

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

the class Image3D method getNeighborhoodGrayKernelMinus.

/**
 * @param ker
 * @param x
 * @param y
 * @param z
 * @return
 */
public ArrayUtil getNeighborhoodGrayKernelMinus(IntImage3D ker, int x, int y, int z) {
    ArrayUtil pix = new ArrayUtil(ker.getNbPixel());
    int vx = ker.getSizex();
    int vy = ker.getSizey();
    int vz = ker.getSizez();
    int index = 0;
    int x0 = x - vx;
    int x1 = x + vx;
    int y0 = y - vy;
    int y1 = y + vy;
    int z0 = z - vz;
    int z1 = z + vz;
    float val;
    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 = (float) getPix(i, j, k) - (float) ker.getPixel(i - x0, j - y0, k - z0);
                    if (val < 0) {
                        val = 0;
                    }
                    pix.putValue(index, val);
                    index++;
                }
            }
        }
    }
    pix.setSize(index);
    return pix;
}

Example 38 with ArrayUtil

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

the class Image3D method getNeighborhoodSphere.

/**
 * Gets the neighboring of a pixel (sphere)
 *
 * @param x Coordinate x of the pixel
 * @param y Coordinate y of the pixel
 * @param z Coordinate z of the pixel
 * @param radx Radius x of the neighboring
 * @param rady Radius y of the neighboring
 * @param radz Radius z of the neighboring
 * @return The neigbor values in a array
 */
public ArrayUtil getNeighborhoodSphere(int x, int y, int z, float radx, float rady, float radz) {
    int index = 0;
    double rx2;
    if (radx != 0) {
        rx2 = radx * radx;
    } else {
        rx2 = 1;
    }
    double ry2;
    if (rady != 0) {
        ry2 = rady * rady;
    } else {
        ry2 = 1;
    }
    double rz2;
    if (radz != 0) {
        rz2 = radz * radz;
    } else {
        rz2 = 1;
    }
    double dist;
    int vx = (int) Math.ceil(radx);
    int vy = (int) Math.ceil(rady);
    int vz = (int) Math.ceil(radz);
    double[] pix = new double[(2 * vx + 1) * (2 * vy + 1) * (2 * vz + 1)];
    for (int k = z - vz; k <= z + vz; k++) {
        for (int j = y - vy; j <= y + vy; j++) {
            for (int i = x - vx; i <= x + vx; i++) {
                if (i >= 0 && j >= 0 && k >= 0 && i < sizex && j < sizey && k < sizez) {
                    dist = ((x - i) * (x - i)) / rx2 + ((y - j) * (y - j)) / ry2 + ((z - k) * (z - k)) / rz2;
                    if (dist <= 1.0) {
                        // t.putValue(index, );
                        pix[index] = getPix(i, j, k);
                        index++;
                    }
                }
            }
        }
    }
    ArrayUtil t = new ArrayUtil(pix);
    t.setSize(index);
    return t;
}

Example 39 with ArrayUtil

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

the class Image3D method getNeighborhoodSphere.

/**
 * Gets the neighboring of a pixel (sphere)
 *
 * @param x Coordinate x of the pixel
 * @param y Coordinate y of the pixel
 * @param z Coordinate z of the pixel
 * @param radx Radius x of the neighboring
 * @param rady Radius y of the neighboring
 * @param radz Radius z of the neighboring
 * @param edm
 * @return The neigbor values in a array
 */
public ArrayUtil getNeighborhoodSphere(int x, int y, int z, float radx, float rady, float radz, RealImage3D edm) {
    int index = 0;
    double rx2;
    if (radx != 0) {
        rx2 = radx * radx;
    } else {
        rx2 = 1;
    }
    double ry2;
    if (rady != 0) {
        ry2 = rady * rady;
    } else {
        ry2 = 1;
    }
    double rz2;
    if (radz != 0) {
        rz2 = radz * radz;
    } else {
        rz2 = 1;
    }
    double dist;
    double edmvalue, edmtmp;
    int vx = (int) Math.ceil(radx);
    int vy = (int) Math.ceil(rady);
    int vz = (int) Math.ceil(radz);
    double[] pix = new double[(2 * vx + 1) * (2 * vy + 1) * (2 * vz + 1)];
    edmvalue = edm.getPixel(x, y, z);
    for (int k = z - vz; k <= z + vz; k++) {
        for (int j = y - vy; j <= y + vy; j++) {
            for (int i = x - vx; i <= x + vx; i++) {
                if (i >= 0 && j >= 0 && k >= 0 && i < sizex && j < sizey && k < sizez) {
                    dist = ((x - i) * (x - i)) / rx2 + ((y - j) * (y - j)) / ry2 + ((z - k) * (z - k)) / rz2;
                    edmtmp = edm.getPixel(i, j, k);
                    if ((dist <= 1.0) && (edmtmp > edmvalue)) {
                        // t.putValue(index, );
                        pix[index] = getPix(i, j, k);
                        index++;
                    }
                }
            }
        }
    }
    ArrayUtil t = new ArrayUtil(pix);
    t.setSize(index);
    return t;
}

Example 40 with ArrayUtil

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

the class Image3D method getNeighborhoodGrayKernelAdd.

/**
 * @param ker
 * @param x
 * @param y
 * @param z
 * @return
 */
public ArrayUtil getNeighborhoodGrayKernelAdd(IntImage3D ker, int x, int y, int z) {
    ArrayUtil pix = new ArrayUtil(ker.getNbPixel());
    int vx = ker.getSizex();
    int vy = ker.getSizey();
    int vz = ker.getSizez();
    int index = 0;
    int x0 = x - vx;
    int x1 = x + vx;
    int y0 = y - vy;
    int y1 = y + vy;
    int z0 = z - vz;
    int 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) {
                    pix.putValue(index, (float) getPix(i, j, k) + (float) ker.getPixel(i - x0, j - y0, k - z0));
                    index++;
                }
            }
        }
    }
    pix.setSize(index);
    return pix;
}