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

Example 1 with ComparatorVoxel

use of mcib3d.geom.ComparatorVoxel 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));
    }
}