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

Example 11 with Voxel3D

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

the class Segment3DSpots method getLocalMaximum.

public Voxel3D getLocalMaximum(int x, int y, int z, float radx, float rady, float radz) {
    Voxel3D v = null;
    int sizex = rawImage.sizeX;
    int sizey = rawImage.sizeY;
    int sizez = rawImage.sizeZ;
    double vmax = Double.NEGATIVE_INFINITY;
    double pix;
    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);
    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) {
                        pix = rawImage.getPixel(i, j, k);
                        if (pix > vmax) {
                            v = new Voxel3D(i, j, k, pix);
                            vmax = pix;
                        }
                    }
                }
            }
        }
    }
    return v;
}

Example 12 with Voxel3D

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

the class Segment3DSpots method segmentAll.

/**
 */
public void segmentAll() {
    segmentedObjects = new ArrayList<Object3D>();
    ArrayList<Voxel3D> obj;
    int o = 1;
    int localThreshold = localValue;
    if (labelImage == null) {
        this.createLabelImage();
    }
    // locate seeds
    for (int z = 0; z < seedsImage.sizeZ; z++) {
        IJ.showStatus("Segmenting slice " + (z + 1));
        // IJ.log("Segmenting slice " + (z + 1));
        for (int y = 0; y < seedsImage.sizeY; y++) {
            for (int x = 0; x < seedsImage.sizeX; x++) {
                if (seedsImage.getPixel(x, y, z) > seedsThreshold) {
                    // LOCAL THRESHOLD
                    if (localMethod == LOCAL_MEAN) {
                        localThreshold = (int) localMean(x, y, z);
                    } else if (localMethod == LOCAL_GAUSS) {
                        double[] gauss;
                        gauss = this.gaussianFit(x, y, z, false);
                        if (gauss != null) {
                            double thresh = CurveFitter.f(CurveFitter.GAUSSIAN, gauss, GAUSS_PC * gauss[3]);
                            // IJ.log("gauss sigma : " + gauss[3] + " thresh=" + thresh);
                            localThreshold = (int) thresh;
                        }
                    } else if (localMethod == LOCAL_DIFF) {
                        localThreshold = (int) Math.max(1, seedsImage.getPixel(x, y, z) - diff);
                    }
                    if (localThreshold > 0) {
                        if (show) {
                            IJ.log("segmenting spot at : " + x + " " + y + " " + " " + z + " lc=" + localThreshold);
                        }
                    }
                    switch(methodSeg) {
                        case SEG_CLASSICAL:
                            obj = this.segmentSpotClassical(x, y, z, localThreshold, o);
                            break;
                        case SEG_MAX:
                            obj = this.segmentSpotMax(x, y, z, localThreshold, o);
                            break;
                        case SEG_BLOCK:
                            obj = this.segmentSpotBlock(x, y, z, localThreshold, o);
                            break;
                        default:
                            obj = this.segmentSpotClassical(x, y, z, localThreshold, o);
                            break;
                    }
                    if ((obj != null) && (obj.size() >= volMin) && (obj.size() <= volMax)) {
                        segmentedObjects.add(new Object3DVoxels(obj));
                        // IJ.log("obj size: "+obj.size());
                        o++;
                    } else if (obj != null) {
                        // erase from label image
                        for (Voxel3D vo : obj) {
                            labelImage.setPixel(vo.getRoundX(), vo.getRoundY(), vo.getRoundZ(), 0);
                        }
                        if (show) {
                            IJ.log("object volume outside range : " + obj.size());
                        }
                    }
                }
            }
        }
    }
}

Example 13 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
 * @return The translation value
 */
public static Voxel3D getTranslation(FHTImage3D xcorr) {
    Voxel3D max = xcorr.getMaxPixel();
    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) {
        if (max.getX() >= sizex - centerx) {
            max.setX(max.getX() - sizex);
        }
        if (max.getY() >= sizey - centery) {
            max.setY(max.getY() - sizey);
        }
        if (max.getZ() >= sizez - centerz) {
            max.setZ(max.getZ() - sizez);
        }
    }
    return max;
}

Example 14 with Voxel3D

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

the class Image3D method computeMinMax.

/**
 * compute the min and max pixels
 */
protected void computeMinMax() {
    minPixel = new Voxel3D(0, 0, 0, getPix(0, 0, 0));
    maxPixel = new Voxel3D(0, 0, 0, getPix(0, 0, 0));
    for (int k = 0; k < sizez; k++) {
        for (int j = 0; j < sizey; j++) {
            for (int i = 0; i < sizex; i++) {
                double val = getPix(i, j, k);
                if (val < minPixel.getValue()) {
                    minPixel.setVoxel(i, j, k, val);
                } else if (val > maxPixel.getValue()) {
                    maxPixel.setVoxel(i, j, k, val);
                }
            }
        }
    }
}

Example 15 with Voxel3D

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

the class RegionGrowing method getBordersMerge.

public ArrayList<Voxel3D> getBordersMerge(int[] oldLabels, boolean outsideBorders) {
    ArrayList<Voxel3D> drawBorders = new ArrayList();
    int nb = oldLabels.length;
    ArrayList allowedValues = new ArrayList();
    allowedValues.add(BORDER);
    if (outsideBorders) {
        allowedValues.add(NO_LABEL);
    }
    for (int o : oldLabels) {
        allowedValues.add(o);
    }
    int maxLabel = 0;
    for (int z = 0; z < watershedImage.sizeZ; z++) {
        for (int y = 0; y < watershedImage.sizeY; y++) {
            for (int x = 0; x < watershedImage.sizeX; x++) {
                int pix = watershedImage.getPixelInt(x, y, z);
                if (pix > maxLabel) {
                    maxLabel = pix;
                }
                if (pix == BORDER) {
                    ArrayUtil neigh = watershedImage.getNeighborhood3x3x3(x, y, z);
                    // IJ.log("" + neigh + " " + neigh.hasOnlyValuesInt(allowedValues));
                    if (neigh.hasOnlyValuesInt(allowedValues)) {
                        drawBorders.add(new Voxel3D(x, y, z, pix));
                    // IJ.log("border " + x + " " + y + " " + z);
                    }
                }
            }
        }
    }
    return drawBorders;
}