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

Example 6 with KDTreeC

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

the class Object3DVoxels method computeContours.

/**
 * Compute the contours of the object rad=0.5
 */
private void computeContours(ImageInt segImage, int x0, int y0, int z0) {
    // IJ.log("computing contours for "+this+"  "+x0+" "+y0+" "+z0+" "+xmin+" "+ymin+" "+zmin);
    // segImage.show(""+this);
    // init kdtree
    kdtreeContours = new KDTreeC(3);
    kdtreeContours.setScale3(this.resXY, this.resXY, this.resZ);
    areaNbVoxels = 0;
    areaContactUnit = 0;
    areaContactVoxels = 0;
    contours = new ArrayList<Voxel3D>();
    boolean cont;
    double XZ = resXY * resZ;
    double XX = resXY * resXY;
    int pix0, pix1, pix2, pix3, pix4, pix5, pix6;
    int sx = segImage.sizeX;
    int sy = segImage.sizeY;
    int sz = segImage.sizeZ;
    int face;
    int class3or4;
    int class1 = 0, class2 = 0, class3 = 0, class4 = 0, class5 = 0, class6 = 0;
    int val = value;
    // special case value=0
    if (val == 0) {
        val = (int) segImage.getMinAboveValue(0);
    }
    // int k = vox.getRoundZ() - z0;
    for (int k = zmin - z0; k <= zmax - z0; k++) {
        if (showStatus) {
        // IJ.showStatus("Contours " + (100 * (k - zmin) / (zmax - zmin + 1)) + " % ");
        }
        for (int j = ymin - y0; j <= ymax - y0; j++) {
            for (int i = xmin - x0; i <= xmax - x0; i++) {
                cont = false;
                if (segImage.contains(i, j, k)) {
                    pix0 = segImage.getPixelInt(i, j, k);
                    if (pix0 == val) {
                        face = 0;
                        class3or4 = 0;
                        if (i + 1 < sx) {
                            pix1 = segImage.getPixelInt(i + 1, j, k);
                        } else {
                            pix1 = 0;
                        }
                        if (i - 1 >= 0) {
                            pix2 = segImage.getPixelInt(i - 1, j, k);
                        } else {
                            pix2 = 0;
                        }
                        if (j + 1 < sy) {
                            pix3 = segImage.getPixelInt(i, j + 1, k);
                        } else {
                            pix3 = 0;
                        }
                        if (j - 1 >= 0) {
                            pix4 = segImage.getPixelInt(i, j - 1, k);
                        } else {
                            pix4 = 0;
                        }
                        if (k + 1 < sz) {
                            pix5 = segImage.getPixelInt(i, j, k + 1);
                        } else {
                            pix5 = 0;
                        }
                        if (k - 1 >= 0) {
                            pix6 = segImage.getPixelInt(i, j, k - 1);
                        } else {
                            pix6 = 0;
                        }
                        if (pix1 != val) {
                            cont = true;
                            areaContactUnit += XZ;
                            areaContactVoxels++;
                            face++;
                            if (pix2 != val) {
                                class3or4 = 1;
                            }
                        }
                        if (pix2 != val) {
                            cont = true;
                            areaContactUnit += XZ;
                            areaContactVoxels++;
                            face++;
                        }
                        if (pix3 != val) {
                            cont = true;
                            areaContactUnit += XZ;
                            areaContactVoxels++;
                            face++;
                            if (pix4 != val) {
                                class3or4 = 1;
                            }
                        }
                        if (pix4 != val) {
                            cont = true;
                            areaContactUnit += XZ;
                            areaContactVoxels++;
                            face++;
                        }
                        if (pix5 != val) {
                            cont = true;
                            areaContactUnit += XX;
                            areaContactVoxels++;
                            face++;
                            if (pix6 != val) {
                                class3or4 = 1;
                            }
                        }
                        if (pix6 != val) {
                            cont = true;
                            areaContactUnit += XX;
                            areaContactVoxels++;
                            face++;
                        }
                        if (cont) {
                            areaNbVoxels++;
                            Voxel3D voxC = new Voxel3D(i + x0, j + y0, k + z0, val);
                            contours.add(voxC);
                            kdtreeContours.add(voxC.getArray(), voxC);
                            // Surface area estimation of digitized 3D objects using weighted local configurations
                            if (face == 1) {
                                class1++;
                            }
                            if (face == 2) {
                                class2++;
                            }
                            if (face == 3 && class3or4 == 0) {
                                class3++;
                            }
                            if (face == 3 && class3or4 == 1) {
                                class4++;
                            }
                            if (face == 4) {
                                class5++;
                            }
                            if (face == 5) {
                                class6++;
                            }
                        }
                    }
                }
            }
        }
    }
    // IJ.log("contours "+contours.size());
    // METHOD LAURENT GOLE FROM Lindblad2005 TO COMPUTE SURFACE
    // Surface area estimation of digitized 3D objects using weighted local configurations
    double w1 = 0.894, w2 = 1.3409, w3 = 1.5879, w4 = 2.0, w5 = 8.0 / 3.0, w6 = 10.0 / 3.0;
    correctedSurfaceArea = (class1 * w1 + class2 * w2 + class3 * w3 + class4 * w4 + class5 * w5 + class6 * w6);
// if (areaNbVoxels == 0) {
// new ImagePlus("MiniSeg 0", segImage.getImageStack()).show();
// IJ.log(" " + x0 + " " + y0 + " " + z0 + " " + xmin + " " + ymin + " " + zmin);
// }
}