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

Example 6 with ImageInt

use of mcib3d.image3d.ImageInt 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 7 with ImageInt

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

the class Object3D_IJUtils method drawIntersectionLabel.

public static void drawIntersectionLabel(Object3DLabel object3DLabel, Object3DLabel other, ImageStack mask, int red, int green, int blue) {
    ImageProcessor tmp;
    ImageHandler otherSeg = other.getLabelImage();
    int otherValue = other.getValue();
    Color col = new Color(red, green, blue);
    int zmin = object3DLabel.getZmin();
    int zmax = object3DLabel.getZmax();
    int ymin = object3DLabel.getYmin();
    int ymax = object3DLabel.getYmax();
    int xmin = object3DLabel.getXmin();
    int xmax = object3DLabel.getXmax();
    ImageInt labelImage = object3DLabel.getLabelImage();
    int value = object3DLabel.getValue();
    for (int z = zmin; z <= zmax; z++) {
        tmp = mask.getProcessor(z + 1);
        tmp.setColor(col);
        for (int x = xmin; x <= xmax; x++) {
            for (int y = ymin; y <= ymax; y++) {
                if ((labelImage.getPixel(x, y, z) == value) && (otherSeg.getPixel(x, y, z) == otherValue)) {
                    tmp.drawPixel(x, y);
                }
            }
        }
    }
}

Example 8 with ImageInt

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

the class Objects3DPopulation method addImage.

/**
 * @param plus
 */
@Deprecated
public void addImage(ImagePlus plus) {
    Calibration calplus = plus.getCalibration();
    if (calplus == null) {
        calplus = new Calibration();
        calplus.pixelWidth = 1;
        calplus.pixelHeight = 1;
        calplus.pixelDepth = 1;
        calplus.setUnit("pix");
    }
    this.setCalibration(calplus);
    ImageInt seg = ImageInt.wrap(plus);
    addImage(seg, calplus);
}

Example 9 with ImageInt

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

the class Viewer3D_Utils method computeMeshSurface.

public static List computeMeshSurface(Object3D object3D, boolean calibrated) {
    // IJ.showStatus("computing mesh");
    // use miniseg
    ImageInt miniseg = object3D.getLabelImage();
    ImageByte miniseg8 = ((ImageShort) (miniseg)).convertToByte(false);
    ImagePlus objectImage = miniseg8.getImagePlus();
    if (calibrated) {
        objectImage.setCalibration(getCalibration(object3D));
    }
    boolean[] bl = { true, true, true };
    Volume vol = new Volume(objectImage, bl);
    vol.setAverage(true);
    List l = MCCube.getTriangles(vol, 0);
    // needs to invert surface
    l = Object3DSurface.invertNormals(l);
    // translate object with units coordinates
    float tx, ty, tz;
    if (calibrated) {
        tx = (float) (miniseg.offsetX * object3D.getResXY());
        ty = (float) (miniseg.offsetY * object3D.getResXY());
        tz = (float) (miniseg.offsetZ * object3D.getResZ());
    } else {
        tx = (float) (miniseg.offsetX);
        ty = (float) (miniseg.offsetY);
        tz = (float) (miniseg.offsetZ);
    }
    l = Object3DSurface.translateTool(l, tx, ty, tz);
    return l;
}

Example 10 with ImageInt

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

the class Object3DLabel method hasOneVoxelColoc.

@Override
public boolean hasOneVoxelColoc(Object3D obj) {
    if (this.disjointBox(obj)) {
        return false;
    }
    if ((labelImage == null) || (obj.getMaxLabelImage(obj.getValue()) == null)) {
        return false;
    }
    // taken from object3DLabel
    int xmin0;
    int ymin0;
    int zmin0;
    int xmax0;
    int ymax0;
    int zmax0;
    int val = obj.getValue();
    ImageInt otherseg = obj.getLabelImage();
    xmin0 = getXmin();
    ymin0 = getYmin();
    zmin0 = getZmin();
    xmax0 = getXmax();
    ymax0 = getYmax();
    zmax0 = getZmax();
    xmin0 = Math.max(xmin0, obj.getXmin());
    ymin0 = Math.max(ymin0, obj.getYmin());
    zmin0 = Math.max(zmin0, obj.getZmin());
    xmax0 = Math.min(xmax0, obj.getXmax());
    ymax0 = Math.min(ymax0, obj.getYmax());
    zmax0 = Math.min(zmax0, obj.getZmax());
    // IJ.log(""+xmin0+"-"+xmax0+" "+ymin0+"-"+ymax0+" "+zmin0+"-"+zmax0+" "+otherseg);
    // labelImage.show("this");
    // otherseg.show("other");
    int offX1 = otherseg.offsetX;
    int offY1 = otherseg.offsetY;
    int offZ1 = otherseg.offsetZ;
    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 - offX1, j - offY1, k - offZ1) == val)) {
                    return true;
                }
            }
        }
    }
    return false;
}