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

Example 16 with Voxel3D

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

the class Watershed3D method processWatershed.

private void processWatershed() {
    long step = 100;
    createNeigList();
    long t0 = System.currentTimeMillis();
    if (anim) {
        watershedImage.show();
    }
    if (rawImage.getMin() > rawThreshold) {
        log.log("Setting minimum for raw image to " + rawImage.getMin());
        rawThreshold = rawImage.getMin();
    }
    // tree set
    ComparatorVoxel comp = new ComparatorVoxel();
    TreeSet<Voxel3DComparable> tree = new TreeSet<Voxel3DComparable>(comp);
    int idx = 1;
    for (Voxel3DComparable V : voxels) {
        V.setMax(idx, 0);
        idx++;
        tree.add(V);
    }
    boolean newt = true;
    log.log("");
    if (log instanceof IJLog)
        ((IJLog) (log)).setUpdate(true);
    while (newt) {
        newt = false;
        while (!tree.isEmpty()) {
            Voxel3DComparable V = tree.pollFirst();
            ArrayList<Voxel3D> Nei = watershedImage.getNeighborhood3x3x3ListNoCenter(V.getRoundX(), V.getRoundY(), V.getRoundZ());
            // if in DAM, do not process
            if (watershedImage.getPixel(V) == DAM)
                continue;
            watershedImage.setPixel(V, labelQueueImage.getPixel(V));
            // all free voxels around are put into queue
            for (Voxel3D N : Nei) {
                float rawN = rawImage.getPixel(N);
                if (rawN > rawThreshold) {
                    // neighbor voxel not in queue yet
                    if ((N.getValue() == 0)) {
                        watershedImage.setPixel(N, QUEUE);
                        labelQueueImage.setPixel(N, (int) V.getLabel());
                        Voxel3DComparable Vnew = new Voxel3DComparable(N.getRoundX(), N.getRoundY(), N.getRoundZ(), rawN, V.getLabel());
                        Vnew.setMax(idx, 0);
                        idx++;
                        tree.add(Vnew);
                    } else // neighbor was already in Q by another label --> dam !
                    if ((N.getValue() == QUEUE) && (labelQueueImage.getPixel(V) != labelQueueImage.getPixel(N))) {
                        watershedImage.setPixel(N, DAM);
                    }
                }
            }
            if (System.currentTimeMillis() - t0 > step) {
                log.log("Voxels to process : " + Math.abs(tree.size()));
                if (anim) {
                    watershedImage.updateDisplay();
                }
                t0 = System.currentTimeMillis();
            }
        }
    }
    log.log("Voxels to process : " + Math.abs(tree.size()));
    if (log instanceof IJLog)
        ((IJLog) (log)).setUpdate(false);
    log.log("Watershed completed.");
    damImage = (ImageInt) watershedImage.createSameDimensions();
    watershedImage.transfertPixelValues(damImage, 1, 255);
    // replace dam values with 0
    watershedImage.replacePixelsValue(1, 0);
    // back to original seeds value
    for (int val : seedsValue.keySet()) {
        watershedImage.replacePixelsValue(val, seedsValue.get(val));
    }
}

Example 17 with Voxel3D

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

the class SpatialRandom method getSample.

@Override
public Objects3DPopulation getSample() {
    Point3D[] points = new Point3D[nbObjects];
    Objects3DPopulation pop = new Objects3DPopulation();
    pop.setMask(mask);
    ImageInt maskimgTmp = maskimg.duplicate();
    Random ra = new Random();
    for (int i = 0; i < nbObjects; i++) {
        Voxel3D vox = maskVox.getRandomvoxel(ra);
        while (maskimgTmp.getPixel(vox) == 0) {
            vox = maskVox.getRandomvoxel(ra);
        }
        points[i] = vox;
        maskimgTmp.setPixel(vox, 0);
    }
    pop.addPoints(points);
    return pop;
}

Example 18 with Voxel3D

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

the class SpatialRandomHardCore method getSample.

@Override
public Objects3DPopulation getSample() {
    Point3D[] points = new Point3D[nbObjects];
    Objects3DPopulation pop = new Objects3DPopulation();
    pop.setMask(mask);
    Random ra = new Random();
    ImageInt maskImgTmp = maskimg.duplicate();
    ObjectCreator3D create = new ObjectCreator3D(maskImgTmp);
    for (int i = 0; i < nbObjects; i++) {
        Voxel3D vox = maskVox.getRandomvoxel(ra);
        while (maskImgTmp.getPixel(vox) == 0) {
            vox = maskVox.getRandomvoxel(ra);
        }
        points[i] = vox;
        create.createSphere(vox.getRoundX(), vox.getRoundY(), vox.getRoundZ(), distHardCore, 0, false);
    }
    pop.addPoints(points);
    return pop;
}

Example 19 with Voxel3D

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

the class Deriche method voxelsCounter.

// Pourcentage de voxels noirs/blancs dans une surface
public float voxelsCounter(ArrayList<Voxel3D> voxels, ImageStack s, boolean b) {
    float percent = 0.f;
    int c1, c2;
    double val;
    for (Voxel3D voxel : voxels) {
        val = s.getVoxel(voxel.getRoundX(), voxel.getRoundY(), voxel.getRoundZ());
    }
    return percent;
}

Example 20 with Voxel3D

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

the class Align2DData method XCorr.

/**
 *  crosscorrelation of all images
 */
public void XCorr() {
    int rayon = sizex < sizey ? sizex / 2 : sizey / 2;
    // ImageProcessor tmp = insert2(serie[0].getImage(true), rayon, true);
    int oldtx = serie[0].getTx();
    int oldty = serie[0].getTy();
    ImageProcessor ip = serie[0].getImage(true);
    ip.setRoi(selection);
    FHTImage3D fht1 = new FHTImage3D(ip.crop());
    FHTImage3D fht2;
    int totx = 0;
    int toty = 0;
    System.out.println("Xcorr...");
    Chrono time = new Chrono(sizez - 1);
    time.start();
    for (int i = 1; i < sizez; i++) {
        // if (show) {
        // IJ.showStatus("" + i + "/" + (sizez - 1));
        // }
        // tmp = insert2(serie[i].getImage(true), rayon, true);
        ip = serie[i].getImage(true);
        ip.setRoi(selection);
        fht2 = new FHTImage3D(ip.crop());
        Voxel3D max = FHTImage3D.getMaxCorrelation(fht1, fht2);
        fht1 = fht2;
        int tmpx = oldtx;
        int tmpy = oldty;
        oldtx = serie[i].getTx();
        oldty = serie[i].getTy();
        serie[i].addTranslation(serie[i - 1].getTx() + max.getX() - tmpx, serie[i - 1].getTy() + max.getY() - tmpy);
        totx += serie[i].getTx();
        toty += serie[i].getTy();
        time.stop();
        String strtime = "Xcorr : " + 100 * (i + 1) / sizez + "% remaining " + time.remainString(i);
        System.out.print("\r                                                                 \r" + strtime + " total :" + time.totalTimeEstimateString(i) + "           ");
        if (show) {
            IJ.showStatus(strtime);
        }
    // System.out.print("\r" + 100 * (i + 1) / sizez + "% \t" + time.delayString() + "\t (" + time.remainString(i) + ")                ");
    }
    totx /= sizez;
    toty /= sizez;
    for (int i = 0; i < sizez; i++) {
        serie[i].addTranslation(-totx, -toty);
        IJ.log(" final image " + i + " : tx =" + serie[i].getTx() + ", ty=" + serie[i].getTy());
    }
    System.out.print("\n");
    IJ.freeMemory();
}