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

Example 26 with Voxel3D

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

the class Segment3DSpots method segmentSpotTemplate.

/**
 * @param xdep
 * @param ydep
 * @param zdep
 * @param lcThreshold
 * @param val
 * @return
 */
private ArrayList<Voxel3D> segmentSpotTemplate(int xdep, int ydep, int zdep, int lcThreshold, int val) {
    boolean changement = true;
    int xfin = xdep + 1;
    int yfin = ydep + 1;
    int zfin = zdep + 1;
    int sens = 1;
    if (labelImage == null) {
        this.createLabelImage();
    }
    // pixel already segmented ?
    if (labelImage.getPixel(xdep, ydep, zdep) > 0) {
        return null;
    }
    labelImage.setPixel(xdep, ydep, zdep, val);
    ArrayList<Voxel3D> object = new ArrayList<Voxel3D>();
    object.add(new Voxel3D(xdep, ydep, zdep, val));
    int volume = 1;
    int i;
    int j;
    int k;
    int l;
    int m;
    int n;
    ImageHandler original = rawImage;
    ArrayList<Voxel3D> neigh;
    Iterator it;
    Voxel3D tmpneigh;
    while (changement) {
        changement = false;
        for (k = sens == 1 ? zdep : zfin; ((sens == 1 && k <= zfin) || (sens == -1 && k >= zdep)); k += sens) {
            for (j = sens == 1 ? ydep : yfin; ((sens == 1 && j <= yfin) || (sens == -1 && j >= ydep)); j += sens) {
                for (i = sens == 1 ? xdep : xfin; ((sens == 1 && i <= xfin) || (sens == -1 && i >= xdep)); i += sens) {
                    if (labelImage.getPixel(i, j, k) == val) {
                        // create neighbors list
                        neigh = new ArrayList<Voxel3D>();
                        for (n = k - 1; n < k + 2; n++) {
                            for (m = j - 1; m < j + 2; m++) {
                                for (l = i - 1; l < i + 2; l++) {
                                    if (labelImage.getPixel(l, m, n) == 0) {
                                        neigh.add(new Voxel3D(l, m, n, original.getPixel(l, m, n)));
                                    }
                                }
                            }
                        }
                        // analyse list
                        it = neigh.iterator();
                        while (it.hasNext()) {
                            tmpneigh = (Voxel3D) it.next();
                            // CLASSICAL
                            if (tmpneigh.getValue() >= lcThreshold) {
                                l = tmpneigh.getRoundX();
                                m = tmpneigh.getRoundY();
                                n = tmpneigh.getRoundZ();
                                labelImage.setPixel(l, m, n, val);
                                object.add(new Voxel3D(l, m, n, val));
                                volume++;
                                if (volume > volMax) {
                                    if (show) {
                                        IJ.log("VOL :" + volume);
                                    }
                                    return null;
                                }
                                // update min-max
                                if (l < xdep) {
                                    xdep--;
                                }
                                if (l > xfin) {
                                    xfin++;
                                }
                                if (m < ydep) {
                                    ydep--;
                                }
                                if (m > yfin) {
                                    yfin++;
                                }
                                if (n < zdep) {
                                    zdep--;
                                }
                                if (n > zfin) {
                                    zfin++;
                                }
                                changement = true;
                            }
                        }
                    }
                }
            }
        }
        sens *= -1;
    }
    return object;
}

Example 27 with Voxel3D

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

the class FHTImage3D method getTranslation.

/**
 * Gets the translation attribute of the FHTImage3D class
 *
 * @param xcorr Description of the Parameter
 * @param RmaxX Description of the Parameter
 * @param RmaxY Description of the Parameter
 * @param RmaxZ Description of the Parameter
 * @return The translation value
 */
public static Voxel3D getTranslation(FHTImage3D xcorr, int RmaxX, int RmaxY, int RmaxZ) {
    int sizex = xcorr.sizex;
    int sizey = xcorr.sizey;
    int sizez = xcorr.sizez;
    int centerx = (int) ((sizex) / 2.0F);
    int centery = (int) ((sizey) / 2.0F);
    int centerz = (int) ((sizez) / 2.0F);
    if (xcorr.centered) {
        centerx = 0;
        centery = 0;
        centerz = 0;
    }
    Voxel3D max = new Voxel3D(centerx, centery, centerz, xcorr.getPixel(centerx, centery, centerz));
    for (int k = 0; k < sizez; k++) {
        int dz = (k >= sizez - centerz) ? k - sizez : k;
        for (int j = 0; j < sizey; j++) {
            int dy = (j >= sizey - centery) ? j - sizey : j;
            for (int i = 0; i < sizex; i++) {
                int dx = (i >= sizex - centerx) ? i - sizex : i;
                if (Math.abs(dx) <= RmaxX && Math.abs(dy) <= RmaxY && Math.abs(dz) <= RmaxZ) {
                    double val = xcorr.getPixel(i, j, k);
                    if (val > max.getValue()) {
                        max.setVoxel(dx, dy, dz, val);
                    }
                }
            }
        }
    }
    return max;
}

Example 28 with Voxel3D

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

the class Mesh method computeConvexHull3D.

public ArrayList<Point3f> computeConvexHull3D() {
    QuickHull3D hull = new QuickHull3D();
    System.out.println("Computing 3d convex hull...");
    Object3DSurface o = new Object3DSurface(vertices);
    ArrayList<Voxel3D> pointsList = o.getContours();
    Point3d[] points = new Point3d[pointsList.size()];
    for (int ve = 0; ve < points.length; ve++) {
        points[ve] = new Point3d(pointsList.get(ve).getX(), pointsList.get(ve).getY(), pointsList.get(ve).getZ());
    }
    System.out.println("done 1st for");
    hull.build(points);
    hull.triangulate();
    ArrayList<Point3f> convex = new ArrayList<Point3f>();
    int[][] faceIndices = hull.getFaces();
    Point3d[] verticesHull = hull.getVertices();
    for (int k = 0; k < faceIndices.length; k++) {
        for (int ve = 0; ve < 3; ve++) {
            Point3d point = verticesHull[faceIndices[k][ve]];
            convex.add(new Point3f((float) point.x, (float) point.y, (float) point.z));
        }
    }
    return convex;
}