Examples with ImageShort mcib3d.image3d.ImageShort used on opensource projects

Example 6 with ImageShort

use of mcib3d.image3d.ImageShort in project mcib3d-core by mcib3d.

the class Watershed3D method createNeigList.

private void createNeigList() {
    voxels = new LinkedList<Voxel3DComparable>();
    int sx = rawImage.sizeX;
    int sy = rawImage.sizeY;
    int sz = rawImage.sizeZ;
    // watershed images
    watershedImage = new ImageShort("watershed", sx, sy, sz);
    labelQueueImage = new ImageShort("labelQ", sx, sy, sz);
    // okseeds = false;
    float pix;
    float se;
    // compute the seeds image
    // threshold, // TODO 32-bits seeds ?
    ImageHandler seedsLabel = seedsImage.duplicate();
    seedsLabel.thresholdCut(seedsThreshold, false, true);
    if ((labelSeeds)) {
        log.log("Labelling ");
        ImageLabeller labeller = new ImageLabeller();
        seedsLabel = labeller.getLabels(seedsLabel);
    }
    // since seeds Label starts at 1 and watershed at 2, replace values
    int max = (int) seedsLabel.getMax();
    if (seedsLabel.hasOneValue(QUEUE)) {
        seedsLabel.replacePixelsValue(QUEUE, max + 1);
        seedsValue.put(max + 1, QUEUE);
    }
    if (seedsLabel.hasOneValue(DAM)) {
        seedsLabel.replacePixelsValue(DAM, max + 2);
        seedsValue.put(max + 2, DAM);
    }
    if (!seedsValue.isEmpty())
        seedsLabel.resetStats(null);
    for (int z = sz - 1; z >= 0; z--) {
        IJ.showStatus("Processing watershed " + (z + 1));
        for (int y = sy - 1; y >= 0; y--) {
            for (int x = sx - 1; x >= 0; x--) {
                pix = rawImage.getPixel(x, y, z);
                se = seedsLabel.getPixel(x, y, z);
                if (pix > rawThreshold) {
                    if (se > 0) {
                        watershedImage.setPixel(x, y, z, se);
                        // okseeds = true;
                        ArrayList<Voxel3D> list = watershedImage.getNeighborhood3x3x3ListNoCenter(x, y, z);
                        Collections.shuffle(list);
                        for (Voxel3D N : list) {
                            int vx = (int) N.getX();
                            int vy = (int) N.getY();
                            int vz = (int) N.getZ();
                            float raw = rawImage.getPixel(vx, vy, vz);
                            if ((raw > rawThreshold) && (seedsLabel.getPixel(vx, vy, vz) == 0) && (watershedImage.getPixel(vx, vy, vz) != QUEUE)) {
                                voxels.add(new Voxel3DComparable(vx, vy, vz, raw, se));
                                watershedImage.setPixel(vx, vy, vz, QUEUE);
                                labelQueueImage.setPixel(vx, vy, vz, se);
                            }
                        }
                    }
                }
            }
        }
    }
    log.log("Watershed...");
}

Example 7 with ImageShort

use of mcib3d.image3d.ImageShort in project mcib3d-core by mcib3d.

the class Watershed3D_old method createArrayList.

private void createArrayList() {
    voxels = new ArrayList();
    int sx = rawImage.sizeX;
    int sy = rawImage.sizeY;
    int sz = rawImage.sizeZ;
    // watershedImage
    this.watershedImage = new ImageShort("watershed", sx, sy, sz);
    okseeds = false;
    float pix;
    float se;
    // compute the labelled image (in case seeds are clustered)
    ImageLabeller labeller = new ImageLabeller();
    ImageInt seedsLabel = labeller.getLabels(seedsImage.thresholdAboveExclusive(seedsThreshold));
    // IJ.log("MAX SEEDS " + seedsLabel.getImageStats(null).getMax());
    // since seedsLabel starts at 1 and watershed at 2, replace values
    seedsLabel.replacePixelsValue(BORDER, (int) seedsLabel.getMax() + 1);
    seedsLabel.resetStats(null);
    // IJ.log("MAX SEEDS " + seedsLabel.getImageStats(null).getMax());
    if (computeVolumes) {
        for (int i = 0; i <= seedsLabel.getMax(); i++) {
            volumeLabels.add(0.0);
        }
    }
    for (int z = 0; z < sz; z++) {
        IJ.showStatus("Processing watershed " + (z + 1));
        for (int y = 0; y < sy; y++) {
            for (int x = 0; x < sx; x++) {
                pix = rawImage.getPixel(x, y, z);
                se = seedsLabel.getPixel(x, y, z);
                if (pix > rawThreshold) {
                    // IJ.log("seed found " + x + " " + y + " " + z+" : "+se);
                    if (se > 0) {
                        // IJ.log("seed found " + x + " " + y + " " + z);
                        watershedImage.setPixel(x, y, z, se);
                        voxels.add(new Voxel3DComparable(x, y, z, pix, se));
                        okseeds = true;
                    } else {
                        voxels.add(new Voxel3DComparable(x, y, z, pix, NO_LABEL));
                        watershedImage.setPixel(x, y, z, NO_LABEL);
                    }
                } else {
                    watershedImage.setPixel(x, y, z, NO_LABEL);
                }
                // compute volumes (warning if seeds are float values)
                if (computeVolumes) {
                    // volumeLabels.get((int) se)[1]++;
                    volumeLabels.set((int) se, volumeLabels.get((int) se) + 1);
                }
            }
        }
    }
}

Example 8 with ImageShort

use of mcib3d.image3d.ImageShort in project mcib3d-core by mcib3d.

the class SpatialShuffle method getSampleImage.

@Override
public ImageHandler getSampleImage() {
    Object3D mask = population.getMask();
    ImageHandler tmp = new ImageShort(getName(), mask.getXmax() + 1, mask.getYmax() + 1, mask.getZmax() + 1);
    getSample().draw(tmp);
    return tmp;
}

Example 9 with ImageShort

use of mcib3d.image3d.ImageShort in project mcib3d-core by mcib3d.

the class IntImage3D method binaryReconstructByObjects.

public ImageInt binaryReconstructByObjects(ImageInt base) {
    // System.out.println("max "+this.getMaximum());
    Segment3DImage seg = new Segment3DImage(new ImageShort(this.getStack()), 1, 65535);
    seg.segment();
    ImageInt label = seg.getLabelledObjectsImage3D();
    boolean[] ok = new boolean[(int) label.getMax() + 1];
    for (int i = 0; i < ok.length; i++) {
        ok[i] = false;
    }
    if (label.getMax() > 0) {
        for (int k = 0; k < sizez; k++) {
            for (int j = 0; j < sizey; j++) {
                for (int i = 0; i < sizex; i++) {
                    if (base.getPixel(i, j, k) != 0) {
                        ok[label.getPixelInt(i, j, k)] = true;
                    }
                }
            }
        }
        for (int k = 0; k < sizez; k++) {
            for (int j = 0; j < sizey; j++) {
                for (int i = 0; i < sizex; i++) {
                    int pix = label.getPixelInt(i, j, k);
                    if (pix > 0) {
                        if (ok[pix]) {
                            label.setPixel(i, j, k, 255);
                        } else {
                            label.setPixel(i, j, k, 0);
                        }
                    }
                }
            }
        }
    }
    return label;
}

Example 10 with ImageShort

use of mcib3d.image3d.ImageShort in project mcib3d-core by mcib3d.

the class Objects3DPopulation method drawPopulation.

public ImageInt drawPopulation() {
    int[] sizes = this.getMaxSizeAllObjects();
    ImageInt drawImage = new ImageShort("population", sizes[0], sizes[1], sizes[2]);
    for (Object3D object3DVoxels : getObjectsList()) {
        object3DVoxels.draw(drawImage);
    }
    return drawImage;
}