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

Example 1 with ImageShort

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

the class MereoAnalysis method computeFastRelationships.

public void computeFastRelationships() {
    int[] size = popB.getMaxSizeAllObjects();
    ImageHandler segB = new ImageShort("popB", size[0] + 1, size[1] + 1, size[2] + 1);
    // segB.show();
    popB.draw(segB);
    boolean[] checkedObject = new boolean[popB.getNbObjects()];
    int nbA = popA.getNbObjects();
    for (int a = 0; a < nbA; a++) {
        log.log("Processing object A" + a);
        for (int o = 0; o < popB.getNbObjects(); o++) {
            checkedObject[o] = false;
            relationships[a][o] = MereoObject3D.DC;
        }
        Object3D A = popA.getObject(a);
        Object3D Adil = A.getDilatedObject(RadX, RadY, RadZ);
        // TEST
        // Adil.getLabelImage().show("dilated "+Adil);
        ArrayList<Voxel3D> al = Adil.listVoxels(segB);
        for (Voxel3D vox : al) {
            int pix = (int) vox.getValue();
            if (pix != 0) {
                int idx = popB.getIndexFromValue(pix);
                if (!checkedObject[idx]) {
                    checkedObject[idx] = true;
                    Object3D B = popB.getObject(idx);
                    MereoObject3D mereo = new MereoObject3D(A, B, RadX, RadY, RadZ);
                    relationships[a][idx] = mereo.getRCC8Relationship();
                }
            }
        }
    }
}

Example 2 with ImageShort

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

the class SpatialRandom method getSampleImage.

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

Example 3 with ImageShort

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

the class SpatialRandomHardCore method getSampleImage.

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

Example 4 with ImageShort

use of mcib3d.image3d.ImageShort 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 5 with ImageShort

use of mcib3d.image3d.ImageShort 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.");
    }
}