Examples with Voxel3DComparable mcib3d.geom.Voxel3DComparable used on opensource projects

Example 1 with Voxel3DComparable

use of mcib3d.geom.Voxel3DComparable in project mcib3d-core by mcib3d.

the class FastFilters3D method getListMaximaFloat.

public static ArrayList<Voxel3DComparable> getListMaximaFloat(ImageFloat stackorig, float vx, float vy, float vz, int nbcpus, boolean showstatus) {
    int nbToProcess = stackorig.sizeZ;
    // Timer
    final Chrono time = new Chrono(nbToProcess);
    time.start();
    final AbstractLog show = new IJStatus();
    // get stack info
    final float voisx = vx;
    final float voisy = vy;
    final float voisz = vz;
    final ImageFloat ima = stackorig;
    // PARALLEL
    final AtomicInteger ai = new AtomicInteger(0);
    final int n_cpus = nbcpus == 0 ? ThreadUtil.getNbCpus() : nbcpus;
    final int dec = (int) Math.ceil((double) ima.sizeZ / (double) n_cpus);
    Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
    final ArrayList<Voxel3DComparable>[] listes = new ArrayList[n_cpus];
    for (int ithread = 0; ithread < threads.length; ithread++) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                    listes[k] = ima.getListMaxima(voisx, voisy, voisz, dec * k, dec * (k + 1), time, show);
                }
            }
        };
    }
    ThreadUtil.startAndJoin(threads);
    final ArrayList<Voxel3DComparable> liste = new ArrayList<Voxel3DComparable>();
    for (ArrayList<Voxel3DComparable> li : listes) {
        liste.addAll(li);
    }
    return liste;
}

Example 2 with Voxel3DComparable

use of mcib3d.geom.Voxel3DComparable in project mcib3d-core by mcib3d.

the class FastFilters3D method getListMaximaInt.

public static ArrayList<Voxel3DComparable> getListMaximaInt(ImageInt stackorig, float vx, float vy, float vz, int nbcpus, boolean showstatus) {
    int nbToProcess = stackorig.sizeZ;
    // Timer
    final Chrono time = new Chrono(nbToProcess);
    time.start();
    final AbstractLog show = new IJStatus();
    // get stack info
    final float voisx = vx;
    final float voisy = vy;
    final float voisz = vz;
    final ImageInt ima = stackorig;
    // PARALLEL
    final AtomicInteger ai = new AtomicInteger(0);
    final int n_cpus = nbcpus == 0 ? ThreadUtil.getNbCpus() : nbcpus;
    final int dec = (int) Math.ceil((double) ima.sizeZ / (double) n_cpus);
    Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
    final ArrayList<Voxel3DComparable>[] listes = new ArrayList[n_cpus];
    for (int ithread = 0; ithread < threads.length; ithread++) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                    listes[k] = ima.getListMaxima(voisx, voisy, voisz, dec * k, dec * (k + 1), time, show);
                }
            }
        };
    }
    ThreadUtil.startAndJoin(threads);
    final ArrayList<Voxel3DComparable> liste = new ArrayList<Voxel3DComparable>();
    for (ArrayList<Voxel3DComparable> li : listes) {
        liste.addAll(li);
    }
    return liste;
}

Example 3 with Voxel3DComparable

use of mcib3d.geom.Voxel3DComparable 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 4 with Voxel3DComparable

use of mcib3d.geom.Voxel3DComparable in project mcib3d-core by mcib3d.

the class Watershed3D_old method assignWatershedAccurate.

private boolean assignWatershedAccurate(int threshold) {
    Voxel3DComparable voxel;
    int px, py, pz;
    ArrayUtil neigh;
    int max, max2;
    boolean loop = false;
    ArrayList<Voxel3DComparable> voxelsNextRound = new ArrayList();
    ArrayList<Voxel3DComparable> voxelsToProcess = new ArrayList();
    for (Iterator it = voxels.iterator(); it.hasNext(); ) {
        voxel = (Voxel3DComparable) it.next();
        if (voxel.getValue() < threshold) {
            // voxelsNextRound.addAll(voxels.subList(voxels.indexOf(voxel), voxels.size()));
            break;
        // voxelsNextRound.add(voxel);
        // continue;
        }
        px = voxel.getRoundX();
        py = voxel.getRoundY();
        pz = voxel.getRoundZ();
        if (watershedImage.getPixel(px, py, pz) == NO_LABEL) {
            // 6-neighbor
            // neigh = watershedImage.getNeighborhoodCross3D(px, py, pz);
            // 26-neighbor
            neigh = watershedImage.getNeighborhood3x3x3(px, py, pz);
            max = (int) neigh.getMaximum();
            if ((max == NO_LABEL) || (max == BORDER)) {
                voxelsNextRound.add(voxel);
            } else {
                // has a neighbor already labeled // test if two differents labels around
                voxelsToProcess.add(voxel);
            }
        }
    }
    // process voxels
    for (Voxel3DComparable vox : voxelsToProcess) {
        px = vox.getRoundX();
        py = vox.getRoundY();
        pz = vox.getRoundZ();
        neigh = watershedImage.getNeighborhood3x3x3(px, py, pz);
        max = (int) neigh.getMaximum();
        max2 = (int) neigh.getMaximumBelow(max);
        if ((max2 == NO_LABEL) || (max2 == BORDER)) {
            watershedImage.setPixel(px, py, pz, max);
            loop = true;
            // compute volumes
            if (computeVolumes) {
                // volumeLabels.get(max)[1]++;
                volumeLabels.set(max, volumeLabels.get(max) + 1);
            }
            // get active label
            if (computeUpdatedLabels) {
                String la = "" + max;
                // test if exists already
                boolean ok = true;
                for (String S : updatedLabels) {
                    if ((S.compareTo(la)) == 0) {
                        ok = false;
                        break;
                    }
                }
                if (ok) {
                    updatedLabels.add(la);
                }
            }
            // add the new labels sharing a border
            if ((max2 == BORDER) && (computeAssociation)) {
                updateAssociationBorder(px, py, pz, max);
            }
        // two or more labels around
        } else {
            watershedImage.setPixel(px, py, pz, BORDER);
            // get association
            if (computeAssociation) {
                String asso = max + "_" + max2;
                AssociationRegion assoR = new AssociationRegion();
                assoR.addRegion(max);
                assoR.addRegion(max2);
                max2 = (int) neigh.getMaximumBelow(max2);
                while ((max2 != NO_LABEL) && (max2 != BORDER)) {
                    asso = asso.concat("_" + max2);
                    assoR.addRegion(max2);
                    max2 = (int) neigh.getMaximumBelow(max2);
                }
                // if next to border update
                if ((max2 == BORDER) && (computeAssociation)) {
                    for (String S : asso.split("_")) {
                        updateAssociationBorder(px, py, pz, Integer.parseInt(S));
                    }
                }
                // test if association exists already
                boolean ok = true;
                for (String S : associations) {
                    if ((S.compareTo(asso)) == 0) {
                        ok = false;
                        break;
                    }
                }
                if (ok) {
                    associations.add(asso);
                }
                assoRegions.addAssoRegion(assoR);
            }
        }
    }
    voxels = voxelsNextRound;
    System.gc();
    return loop;
}

Example 5 with Voxel3DComparable

use of mcib3d.geom.Voxel3DComparable in project mcib3d-core by mcib3d.

the class MaximaFinder method computePeaks.

private void computePeaks() {
    imagePeaks = new ImageShort("peaks", img.sizeX, img.sizeY, img.sizeZ);
    if (verbose) {
        IJ.log("Finding all peaks");
    }
    ArrayList<Voxel3DComparable> maximaTmp = FastFilters3D.getListMaxima(img, radXY, radXY, radZ, nbCpus, false);
    Collections.sort(maximaTmp);
    for (Voxel3DComparable V : maximaTmp) {
        imagePeaks.setPixel(V, (float) V.getValue());
    }
    if (verbose) {
        IJ.log(maximaTmp.size() + " peaks found");
    }
    if (verbose) {
        IJ.log("Removing peaks below noise");
    }
    maxima = new ArrayList<Voxel3D>();
    int c = 1;
    int nb = maximaTmp.size();
    Date start = new Date();
    Date temp;
    for (Voxel3DComparable V : maximaTmp) {
        if (img.getPixel(V) > 0) {
            if (V.getValue() > noiseTolerance) {
                maxima.add(V);
                if (verbose) {
                    temp = new Date();
                    if ((temp.getTime() - start.getTime()) > 100) {
                        IJ.showStatus("Processing peak " + c + "/" + nb + " " + V);
                        start = new Date();
                    }
                    c++;
                }
                Flood3D.flood3DNoise26(img, new IntCoord3D(V.getRoundX(), V.getRoundY(), V.getRoundZ()), (int) (Math.max(1, V.getValue() - noiseTolerance)), 0);
            }
        }
    }
    if (verbose) {
        IJ.log(maxima.size() + " peaks found");
    }
    if (verbose) {
        IJ.log("Creating final peaks");
    }
    imagePeaks.fill(0);
    for (Voxel3D V : maxima) {
        imagePeaks.setPixel(V, (float) V.getValue());
    }
    if (verbose) {
        IJ.log("MaximaFinder3D finished.");
    }
}