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

Example 21 with ImageInt

use of mcib3d.image3d.ImageInt 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;
}

Example 22 with ImageInt

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

the class Objects3DPopulation method shuffle.

public ArrayList<Object3D> shuffle() {
    ArrayList<Object3D> shuObj = new ArrayList<Object3D>();
    Random ra = new Random();
    ImageInt maskImage = mask.getMaxLabelImage(1);
    Object3DVoxels maskVox = mask.getObject3DVoxels();
    // shuffle indices
    ArrayUtil shuffleIndex = new ArrayUtil(getNbObjects());
    shuffleIndex.fillRange(0, getNbObjects(), 1);
    shuffleIndex.shuffle();
    for (int i = 0; i < getNbObjects(); i++) {
        Object3DVoxels obj = (Object3DVoxels) getObject(shuffleIndex.getValueInt(i));
        Point3D center = obj.getCenterAsPoint();
        boolean ok = false;
        int it = 0;
        int maxIt = 1000000;
        while (!ok) {
            // log.log("Shuffling " + getObject3D(i).getValue());
            Voxel3D vox = maskVox.getRandomvoxel(ra);
            obj.setNewCenter(vox.getX(), vox.getY(), vox.getZ());
            ok = true;
            it++;
            obj.resetQuantifImage();
            if (maskVox.includesBox(obj)) {
                if (obj.getPixMinValue(maskImage) < 1) {
                    ok = false;
                }
            } else {
                ok = false;
            }
            if (it >= maxIt) {
                ok = true;
            }
        }
        if (it == maxIt) {
            if (log != null)
                log.log("Could not shuffle " + obj);
            obj.setNewCenter(center.x, center.y, center.z);
        }
        shuObj.add(obj);
        // update mask
        obj.draw(maskImage, 0);
    }
    return shuObj;
}

Example 23 with ImageInt

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

the class Objects3DPopulationColocalisation method computeColocalisation.

private void computeColocalisation() {
    ImageInt image1 = population1.drawPopulation();
    ImageInt image2 = population2.drawPopulation();
    computeColocalisationImage(image1, image2);
}

Example 24 with ImageInt

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

the class Object3DLabel method getColoc.

@Override
public int getColoc(Object3D other) {
    if (this.disjointBox(other)) {
        return 0;
    }
    int count = 0;
    int xmin0;
    int ymin0;
    int zmin0;
    int xmax0;
    int ymax0;
    int zmax0;
    int val = other.getValue();
    ImageInt otherseg = other.getMaxLabelImage(val);
    xmin0 = getXmin();
    ymin0 = getYmin();
    zmin0 = getZmin();
    xmax0 = getXmax();
    ymax0 = getYmax();
    zmax0 = getZmax();
    if (other != null) {
        xmin0 = Math.max(xmin0, other.getXmin());
        ymin0 = Math.max(ymin0, other.getYmin());
        zmin0 = Math.max(zmin0, other.getZmin());
        xmax0 = Math.min(xmax0, other.getXmax());
        ymax0 = Math.min(ymax0, other.getYmax());
        zmax0 = Math.min(zmax0, other.getZmax());
    }
    for (int k = zmin0; k <= zmax0; k++) {
        for (int j = ymin0; j <= ymax0; j++) {
            for (int i = xmin0; i <= xmax0; i++) {
                if ((labelImage.getPixel(i, j, k) == value) && (otherseg.getPixel(i, j, k) == val)) {
                    count++;
                }
            }
        }
    }
    return count;
}