Examples with Voxel3D mcib3d.geom.Voxel3D used on opensource projects

Example 1 with Voxel3D

use of mcib3d.geom.Voxel3D in project mcib3d-core by mcib3d.

the class ImageHandler method getNeighborhoodLayerList.

/**
 * Get the neighborhood as a layer of pixels
 *
 * @param x     Coordinate x of the pixel
 * @param y     Coordinate y of the pixel
 * @param z     Coordinate z of the pixel
 * @param r0    Minimu radius value
 * @param r1    Maximum radius value
 * @param water Watershed image, can be null
 * @return arrayList ogf voxels3D
 */
public ArrayList<Voxel3D> getNeighborhoodLayerList(int x, int y, int z, float r0, float r1, ImageInt water) {
    int index = 0;
    double r02 = r0 * r0;
    double r12 = r1 * r1;
    ArrayList<Voxel3D> voxel3DS = new ArrayList<Voxel3D>();
    double dist;
    double ratio = getScaleZ() / getScaleXY();
    double ratio2 = ratio * ratio;
    int vx = (int) Math.ceil(r1);
    int vy = (int) Math.ceil(r1);
    int vz = (int) (Math.ceil(r1 / ratio));
    // double[] pix = new double[(2 * vx + 1) * (2 * vy + 1) * (2 * vz + 1)];
    int wat = 0;
    if (water != null) {
        wat = water.getPixelInt(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) {
                    if (((water != null) && (water.getPixel(i, j, k) == wat)) || (water == null)) {
                        dist = ((x - i) * (x - i)) + ((y - j) * (y - j)) + ((z - k) * (z - k) * ratio2);
                        if ((dist >= r02) && (dist < r12)) {
                            voxel3DS.add(new Voxel3D(i, j, k, getPixel(i, j, k)));
                        }
                    }
                }
            }
        }
    }
    // check if some values are set
    return voxel3DS;
}

Example 2 with Voxel3D

use of mcib3d.geom.Voxel3D in project mcib3d-core by mcib3d.

the class ImageHandler method createListVoxels.

public ArrayList<Voxel3D> createListVoxels(int thresh) {
    ArrayList<Voxel3D> voxelList = new ArrayList<Voxel3D>();
    for (int z = 0; z < sizeZ; z++) {
        for (int x = 0; x < sizeX; x++) {
            for (int y = 0; y < sizeY; y++) {
                if (getPixel(x, y, z) > thresh) {
                    Voxel3D v = new Voxel3D(x, y, z, getPixel(x, y, z));
                    voxelList.add(v);
                }
            }
        }
    }
    return voxelList;
}

Example 3 with Voxel3D

use of mcib3d.geom.Voxel3D in project mcib3d-core by mcib3d.

the class ImageLabeller method getObjects.

// classical default neighborhood for segmentation is 26
public ArrayList<Object3DVoxels> getObjects(ImageHandler mask, boolean connex6) {
    if ((spots == null) || (mask != currentMask)) {
        if (connex6) {
            this.labelSpots6(mask);
        } else {
            this.labelSpots26(mask);
        }
    }
    ArrayList<Object3DVoxels> objects = new ArrayList<Object3DVoxels>();
    int sizeX = mask.sizeX;
    short label = 1;
    for (Spot s : spots.values()) {
        ArrayList<Vox3D> a = s.voxels;
        // check size
        if ((a.size() >= minSize) && (a.size() <= maxsize)) {
            ArrayList voxels3D = new ArrayList();
            for (Vox3D vox : a) {
                voxels3D.add(new Voxel3D(vox.xy % sizeX, vox.xy / sizeX, vox.z, label));
            }
            ArrayList noDuplicate = new ArrayList(new HashSet(voxels3D));
            // set calibration
            Object3DVoxels object3DVoxels = new Object3DVoxels(noDuplicate);
            // Object3D_IJUtils.setCalibration(object3DVoxels, mask.getCalibration());
            object3DVoxels.setCalibration(mask.getScaleXY(), mask.getScaleZ(), mask.getUnit());
            objects.add(object3DVoxels);
            label++;
        }
    }
    return objects;
}

Example 4 with Voxel3D

use of mcib3d.geom.Voxel3D in project mcib3d-core by mcib3d.

the class ImageShort method draw.

@Override
public void draw(Object3D o, int value) {
    Object3DVoxels ov;
    if (!(o instanceof Object3DVoxels)) {
        ov = o.getObject3DVoxels();
    } else {
        ov = (Object3DVoxels) o;
    }
    if (value > 65535) {
        value = 255;
    }
    if (value < 0) {
        value = 0;
    }
    short val = (short) value;
    for (Voxel3D v : ov.getVoxels()) {
        if (contains(v.getX(), v.getY(), v.getZ())) {
            pixels[v.getRoundZ()][v.getRoundX() + v.getRoundY() * sizeX] = val;
        }
    }
}

Example 5 with Voxel3D

use of mcib3d.geom.Voxel3D in project mcib3d-core by mcib3d.

the class Align2DData method align2D.

/**
 *  Description of the Method
 *
 * @param  img1            Description of the Parameter
 * @param  index2          Description of the Parameter
 * @param  rangeangle      Description of the Parameter
 * @param  incrementangle  Description of the Parameter
 */
public void align2D(ImageProcessor img1, int index2, double rangeangle, double incrementangle) {
    double score = correlation(img1, getImage(index2, true), sizex, sizey);
    Voxel3D max = FHTImage3D.getMaxCorrelation(img1, getImage(index2, true));
    serie[index2].addTranslation(max.getX(), max.getY());
}