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

Example 6 with Voxel3D

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

the class Align2DData method computeRotation2ImagesFHT.

/**
 *  compute the rotation between 2 images using the Fourier Transform.<BR>
 *  use the power spectrum to be free of translation<BR>
 *  then convert to polar coordinate to compute rotation with cross-correlation
 *
 * @param  image1          reference image
 * @param  image2          image to rotate
 * @param  range           the rotation computed will be between [-range,+range[
 * @param  angleprecision  the precision wanted (1 for degrees precision, 0.1
 *      for decidegrees precision)
 * @return                 angle in degrees to rotate the second image for it to
 *      coincide with the first
 */
public static double computeRotation2ImagesFHT(ImageProcessor image1, ImageProcessor image2, double range, double angleprecision) {
    // System.out.println("FHT " + image1.getWidth());
    ImageProcessor img1 = toPolar(new FHTImage3D(image1).center().getPowerSpectrum(true).getProcessor(1), range, angleprecision);
    ImageProcessor img2 = toPolar(new FHTImage3D(image2).center().getPowerSpectrum(true).getProcessor(1), range, angleprecision);
    Voxel3D corr = FHTImage3D.getMaxCorrelation(img1, img2);
    // IJ.write("max (" + corr.getX() + ", " + corr.getY() + ", " + corr.getZ() + ") =" + corr.getValue());
    return -corr.getX() * angleprecision;
// ImageProcessor img1 = new FHTImage3D(image1).center().getPowerSpectrum(true).getProcessor(1);
// ImageProcessor img2 = new FHTImage3D(image2).center().getPowerSpectrum(true).getProcessor(1);
// return computeRotation2Images(img1, img2, range, angleprecision);
}

Example 7 with Voxel3D

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

the class Segment3DSpots method segmentSpotMax.

/**
 * Segment an object from a seed, keep only max local
 *
 * @param lcThreshold Threshold to connect pixels
 * @param val value of the object
 * @param xdep x coordinate of the seed
 * @param ydep y coordinate of the seed
 * @param zdep z coordinate of the seed
 * @return true if object cold be segmented
 */
public ArrayList<Voxel3D> segmentSpotMax(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);
    // volume++;
    ArrayList<Voxel3D> object = new ArrayList<Voxel3D>();
    object.add(new Voxel3D(xdep, ydep, zdep, val));
    int i;
    int j;
    int k;
    int l;
    int m;
    int n;
    ImageHandler original = rawImage;
    float pixelCenter;
    int waterCenter = 0;
    int water = 0;
    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.contains(i, j, k) && labelImage.getPixel(i, j, k) == val) {
                        if (WATERSHED) {
                            waterCenter = watershedImage.getPixelInt(i, j, k);
                        }
                        pixelCenter = original.getPixel(i, j, k);
                        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.contains(l, m, n)) {
                                        if (WATERSHED) {
                                            water = watershedImage.getPixelInt(l, m, n);
                                        }
                                        if ((labelImage.getPixel(l, m, n) == 0) && (original.getPixel(l, m, n) >= lcThreshold) && (original.getPixel(l, m, n) <= pixelCenter) && (water == waterCenter)) {
                                            labelImage.setPixel(l, m, n, val);
                                            // original.putPixel(l, m, n, 0);
                                            // add voxel to object
                                            object.add(new Voxel3D(l, m, n, val));
                                            // 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 8 with Voxel3D

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

the class Segment3DSpots method segmentSpotBlock.

/**
 * @param xdep
 * @param ydep
 * @param zdep
 * @param lcThreshold
 * @param val
 * @return
 */
public ArrayList<Voxel3D> segmentSpotBlock(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;
    int sx = rawImage.sizeX;
    int sy = rawImage.sizeY;
    int sz = rawImage.sizeZ;
    ImageHandler original = rawImage;
    ArrayList<Voxel3D> neigh;
    Iterator it;
    Voxel3D tmpneigh;
    float pixelCenter;
    int waterne = 0, water = 0;
    boolean ok;
    // int ite = 0;
    while (changement) {
        // IJ.log("Ite " + ite + " " + xdep + " " + xfin);
        // ite++;
        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.contains(i, j, k) && labelImage.getPixel(i, j, k) == val) {
                        pixelCenter = original.getPixel(i, j, k);
                        if (WATERSHED) {
                            water = watershedImage.getPixelInt(i, j, k);
                        }
                        // 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 ((l >= 0) && (l < sx) && (m >= 0) && (m < sy) && (n >= 0) && (n < sz)) {
                                        if (WATERSHED) {
                                            waterne = watershedImage.getPixelInt(l, m, n);
                                        }
                                        if ((labelImage.getPixel(l, m, n) == 0) && (original.getPixel(l, m, n) >= lcThreshold) && (waterne == water)) {
                                            neigh.add(new Voxel3D(l, m, n, original.getPixel(l, m, n)));
                                        }
                                    }
                                }
                            // l
                            }
                        // m
                        }
                        // n
                        // analyse list
                        ok = true;
                        // empty
                        if (neigh.isEmpty()) {
                            ok = false;
                        }
                        // test 1 neighbor
                        if (neigh.size() == 1) {
                            ok = false;
                        }
                        // test all neighbors
                        it = neigh.iterator();
                        while (it.hasNext() && ok) {
                            tmpneigh = (Voxel3D) it.next();
                            // BLOCK
                            if (tmpneigh.getValue() > pixelCenter) {
                                ok = false;
                                break;
                            }
                        }
                        if (ok) {
                            changement = true;
                            if (neigh.size() > volMax) {
                                return null;
                            }
                            it = neigh.iterator();
                            while (it.hasNext()) {
                                tmpneigh = (Voxel3D) it.next();
                                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++;
                                }
                            }
                        }
                    // BLOCKING
                    // else {
                    // it = neigh.iterator();
                    // while ((it != null) && (it.hasNext())) {
                    // tmpneigh = (Voxel3D) it.next();
                    // l = (int) tmpneigh.getX();
                    // m = (int) tmpneigh.getY();
                    // n = (int) tmpneigh.getZ();
                    // 0 do not change 1 exclude from future seg
                    // labelImage.putPixel(l, m, n, 0);
                    // }
                    // }
                    }
                // labelimage==value
                }
            // i
            }
        // j
        }
        // k
        sens *= -1;
    }
    // IJ.log("obj size: ");
    return object;
}

Example 9 with Voxel3D

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

the class Segment3DSpots method splitSpotWatershed.

public static Object3DVoxels[] splitSpotWatershed(Object3D obj, float rad, float dist) {
    ImageInt seg = obj.createSegImage(0, 0, 0, obj.getXmax(), obj.getYmax(), obj.getZmax(), 255);
    // seg.show();
    ImagePlus segplus = seg.getImagePlus();
    segplus.setCalibration(obj.getCalibration());
    // return
    Object3DVoxels[] res = null;
    try {
        int cpus = ThreadUtil.getNbCpus();
        // FIXME variable multithread
        ImageFloat edt3d = EDT.run(seg, 1f, false, cpus);
        // 3D filtering of the edt to remove small local maxima
        ImageFloat edt3dseeds = FastFilters3D.filterFloatImage(edt3d, FastFilters3D.MEAN, 1, 1, 1, cpus, false);
        // edt3d.showDuplicate("edt");
        // ImageStack localMax = FastFilters3D.filterFloatImageStack(edt3d.getImageStack(), FastFilters3D.MAXLOCAL, rad, rad, rad, cpus, false);
        ImageFloat maxlocal3d = FastFilters3D.filterFloatImage(edt3dseeds, FastFilters3D.MAXLOCAL, rad, rad, rad, cpus, false);
        // maxlocal3d.show("max local");
        ArrayList<Voxel3D> locals = obj.listVoxels(maxlocal3d, 0);
        int nb = locals.size();
        // IJ.log("nb=" + nb);
        if (nb < 2) {
            return null;
        }
        // look for most far apart local maxima
        int i1 = 0;
        int i2 = 0;
        double dmax = 0.0;
        double d;
        for (int i = 0; i < nb; i++) {
            for (int j = i + 1; j < nb; j++) {
                d = locals.get(i).distance(locals.get(j));
                if (d > dmax) {
                    dmax = d;
                    i1 = i;
                    i2 = j;
                }
            }
        }
        // perform a 2-means clustering
        double cx1 = 0;
        double cy1 = 0;
        double cz1 = 0;
        double cx2 = 0;
        double cy2 = 0;
        double cz2 = 0;
        double d1;
        double d2;
        Voxel3D PP1 = new Voxel3D(locals.get(i1).getX(), locals.get(i1).getY(), locals.get(i1).getZ(), 1);
        Voxel3D PP2 = new Voxel3D(locals.get(i2).getX(), locals.get(i2).getY(), locals.get(i2).getZ(), 2);
        Voxel3D P1 = new Voxel3D(cx1, cy1, cz1, 0);
        Voxel3D P2 = new Voxel3D(cx2, cy2, cz2, 0);
        int nb1, nb2;
        int nbite = 0;
        while ((nb > 2) && ((P1.distance(PP1) > 1) || (P2.distance(PP2) > 1)) && (nbite < 100)) {
            nbite++;
            cx1 = 0;
            cy1 = 0;
            cx2 = 0;
            cy2 = 0;
            cz1 = 0;
            cz2 = 0;
            nb1 = 0;
            nb2 = 0;
            P1.setX(PP1.getX());
            P1.setY(PP1.getY());
            P1.setZ(PP1.getZ());
            P2.setX(PP2.getX());
            P2.setY(PP2.getY());
            P2.setZ(PP2.getZ());
            for (Voxel3D local : locals) {
                d1 = P1.distance(local);
                d2 = P2.distance(local);
                if (d1 < d2) {
                    cx1 += local.getX();
                    cy1 += local.getY();
                    cz1 += local.getZ();
                    nb1++;
                } else {
                    cx2 += local.getX();
                    cy2 += local.getY();
                    cz2 += local.getZ();
                    nb2++;
                }
            }
            cx1 /= nb1;
            cy1 /= nb1;
            cx2 /= nb2;
            cy2 /= nb2;
            cz1 /= nb1;
            cz2 /= nb2;
            PP1.setX(cx1);
            PP1.setY(cy1);
            PP1.setZ(cz1);
            PP2.setX(cx2);
            PP2.setY(cy2);
            PP2.setZ(cz2);
        }
        // check minimal distances
        double distPP = PP1.distance(PP2);
        IJ.log("Centers found for split PP1=" + PP1 + " PP2=" + PP2 + " distance " + distPP);
        if (distPP < dist) {
            return null;
        }
        // find closest max local to two barycenters, in case barycenters outside object
        Voxel3D PP1closest = new Voxel3D(locals.get(0));
        Voxel3D PP2closest = new Voxel3D(locals.get(0));
        double dist1 = PP1.distanceSquare(PP1closest);
        double dist2 = PP2.distanceSquare(PP2closest);
        for (Voxel3D local : locals) {
            double dd1 = PP1.distanceSquare(local);
            double dd2 = PP2.distanceSquare(local);
            if (dd1 < dist1) {
                dist1 = dd1;
                PP1closest = local;
            }
            if (dd2 < dist2) {
                dist2 = dd2;
                PP2closest = local;
            }
        }
        ImageInt seeds = new ImageShort("seeds", seg.sizeX, seg.sizeY, seg.sizeZ);
        seeds.setPixel(PP1closest.getRoundX(), PP1closest.getRoundY(), PP1closest.getRoundZ(), 255);
        seeds.setPixel(PP2closest.getRoundX(), PP2closest.getRoundY(), PP2closest.getRoundZ(), 255);
        // seeds.show();
        // Watershed3D_old wat = new Watershed3D_old(edt3d, seeds, 0, 0);
        // ImageInt wat2 = wat.getWatershedImage3D();
        // ImageHandler edt16 = edt3d.convertToShort(true);
        Watershed3D wat = new Watershed3D(edt3d, seeds, 0, 0);
        ImageInt wat2 = wat.getWatershedImage3D();
        // wat2.show();
        // in watershed label starts at 1
        Object3DVoxels ob1 = new Object3DVoxels(wat2, 1);
        Object3DVoxels ob2 = new Object3DVoxels(wat2, 2);
        // IJ.log("split1="+ob1+" split2="+ob2);
        // translate objects if needed by miniseg
        // ob1.translate(seg.offsetX, seg.offsetY, seg.offsetZ);
        // new ImagePlus("wat", wat2.getStack()).show();
        res = new Object3DVoxels[2];
        res[0] = ob1;
        res[1] = ob2;
    } catch (Exception e) {
        IJ.log("Exception EDT " + e);
    }
    return res;
}

Example 10 with Voxel3D

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

the class Segment3DSpots method segmentSpotClassical.

// FIXME a revoir, notamment dist ??
/**
 * Segment an object from a seed
 *
 * @param lcThreshold Threshold to connect pixels
 * @param val value of the object
 * @param xdep x coordinate of the seed
 * @param ydep y coordinate of the seed
 * @param zdep z coordinate of the seed
 * @return true if object cold be segmented
 */
public ArrayList<Voxel3D> segmentSpotClassical(int xdep, int ydep, int zdep, int lcThreshold, int val) {
    boolean change = true;
    int xEnd = xdep + 1;
    int yEnd = ydep + 1;
    int zEnd = 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;
    int waterCenter = 0;
    int water = 0;
    while (change) {
        change = false;
        for (k = sens == 1 ? zdep : zEnd; ((sens == 1 && k <= zEnd) || (sens == -1 && k >= zdep)); k += sens) {
            for (j = sens == 1 ? ydep : yEnd; ((sens == 1 && j <= yEnd) || (sens == -1 && j >= ydep)); j += sens) {
                for (i = sens == 1 ? xdep : xEnd; ((sens == 1 && i <= xEnd) || (sens == -1 && i >= xdep)); i += sens) {
                    if (labelImage.contains(i, j, k) && labelImage.getPixel(i, j, k) == val) {
                        if (WATERSHED) {
                            waterCenter = watershedImage.getPixelInt(i, j, k);
                        }
                        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.contains(l, m, n)) {
                                        if (WATERSHED) {
                                            water = watershedImage.getPixelInt(l, m, n);
                                        }
                                        if ((labelImage.getPixel(l, m, n) == 0) && (original.getPixel(l, m, n) >= lcThreshold) && (water == waterCenter)) {
                                            labelImage.setPixel(l, m, n, val);
                                            // original.putPixel(l, m, n, 0);
                                            // add voxel to object
                                            object.add(new Voxel3D(l, m, n, val));
                                            volume++;
                                            if (volume > volMax) {
                                                if (show) {
                                                    IJ.log("VOL TOO BIG STOP SEG :" + volume);
                                                }
                                                return null;
                                            }
                                            // update min-max
                                            if (l < xdep) {
                                                xdep--;
                                            }
                                            if (l > xEnd) {
                                                xEnd++;
                                            }
                                            if (m < ydep) {
                                                ydep--;
                                            }
                                            if (m > yEnd) {
                                                yEnd++;
                                            }
                                            if (n < zdep) {
                                                zdep--;
                                            }
                                            if (n > zEnd) {
                                                zEnd++;
                                            }
                                            change = true;
                                        }
                                    }
                                }
                            }
                        }
                    }
                }
            }
        }
        sens *= -1;
    }
    return object;
}