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

Example 1 with ImageInt

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

the class BinaryMorpho method binaryDilate.

// if no resize of the image, object at the border may be truncated
public static ImageByte binaryDilate(ImageInt in, float radius, float radiusZ, int nbCPUs, boolean enlarge) {
    try {
        if (nbCPUs == 0) {
            nbCPUs = ThreadUtil.getNbCpus();
        }
        ImageInt resize = in;
        // resize
        int reX = (int) (radius + 1);
        int reY = (int) (radius + 1);
        int reZ = (int) (radiusZ + 1);
        if (enlarge)
            resize = (ImageInt) in.enlarge(reX, reY, reZ);
        ImageFloat edm = EDT.run(resize, 0, 1, radius / radiusZ, true, nbCPUs);
        // edm.duplicate().show("edm");
        ImageByte temp = edm.threshold(radius, true, false);
        // temp.show("thres");
        edm.flush();
        edm = null;
        if (enlarge)
            temp.setOffset(in.offsetX - reX, in.offsetY - reY, in.offsetZ - reZ);
        else
            temp.setOffset(in);
        temp.setScale(in);
        return temp;
    } catch (Exception e) {
        exceptionPrinter.print(e, null, true);
    }
    return null;
}

Example 2 with ImageInt

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

the class BinaryMorpho method binaryCloseMultilabel.

public static ImageInt binaryCloseMultilabel(ImageInt in, float[] radiusXY, float[] radiusZ, int nbCPUs) {
    ImageByte[] ihs = in.crop3DBinary();
    if ((radiusXY.length != ihs.length) || (radiusZ.length != ihs.length)) {
        return null;
    }
    if (ihs != null) {
        // ij.IJ.log("BinaryClose multilabel nb :"+ihs.length);
        for (int idx = 0; idx < ihs.length; idx++) {
            if (radiusXY[idx] <= 1 && radiusZ[idx] <= 1) {
                ihs[idx] = BinaryMorpho.binaryCloseRad1(ihs[idx], 1, nbCPUs);
            } else {
                ihs[idx] = binaryClose(ihs[idx], radiusXY[idx], radiusZ[idx], nbCPUs);
            }
            ihs[idx] = binaryClose(ihs[idx], radiusXY[idx], radiusZ[idx], nbCPUs);
        }
        ImageInt temp = ImageShort.merge3DBinary(ihs, in.sizeX, in.sizeY, in.sizeZ);
        temp.setScale(in);
        temp.setOffset(in);
        return temp;
    }
    return in;
}

Example 3 with ImageInt

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

the class BinaryMorpho method binaryDilate2D.

public static ImageByte binaryDilate2D(ImageByte in, float radius, boolean enlarge) {
    ImageInt resize = in;
    // resize
    int reX = (int) (radius + 1);
    int reY = (int) (radius + 1);
    int reZ = 0;
    if (enlarge)
        resize = (ImageInt) in.enlarge(reX, reY, reZ);
    ImageByte temp = (ImageByte) FastFilters3D.filterIntImage(resize, FastFilters3D.MAX, radius, radius, 0, 1, false);
    temp.setScale(in);
    if (enlarge)
        temp.setOffset(in.offsetX - reX, in.offsetY - reY, in.offsetZ - reZ);
    else
        temp.setOffset(in);
    return temp;
}

Example 4 with ImageInt

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

the class BinaryMorpho method binaryCloseRad1diag.

private static ImageByte binaryCloseRad1diag(final ImageInt in_, final float thld, int nbCPUs) {
    if (nbCPUs == 0) {
        nbCPUs = ThreadUtil.getNbCpus();
    }
    // TODO: faire sans resize avec un simple décalage des indices
    final ImageInt in = (ImageInt) in_.resize(1, 1, 1);
    final ImageByte max = new ImageByte("max", in.sizeX, in.sizeY, in.sizeZ);
    final ThreadRunner tr = new ThreadRunner(0, max.sizeZ, nbCPUs);
    for (int i = 0; i < tr.threads.length; i++) {
        tr.threads[i] = new Thread(new Runnable() {

            @Override
            public void run() {
                for (int z = tr.ai.getAndIncrement(); z < tr.end; z = tr.ai.getAndIncrement()) {
                    for (int y = 0; y < max.sizeY; y++) {
                        for (int x = 0; x < max.sizeX; x++) {
                            if (maxRad15(in, thld, x, y, z)) {
                                max.pixels[z][x + y * in.sizeX] = (byte) 255;
                            }
                        }
                    }
                }
            }
        });
    }
    tr.startAndJoin();
    final ThreadRunner tr2 = new ThreadRunner(0, in.sizeZ, nbCPUs);
    final ImageByte close = new ImageByte(in.getTitle() + "::close", in.sizeX, in.sizeY, in.sizeZ);
    for (int i = 0; i < tr2.threads.length; i++) {
        tr2.threads[i] = new Thread(new Runnable() {

            @Override
            public void run() {
                for (int z = tr2.ai.getAndIncrement(); z < tr2.end; z = tr2.ai.getAndIncrement()) {
                    for (int y = 0; y < in.sizeY; y++) {
                        for (int x = 0; x < in.sizeX; x++) {
                            if (minRad15(max, 1, x, y, z)) {
                                close.pixels[z][x + y * in.sizeX] = (byte) 255;
                            }
                        }
                    }
                }
            }
        });
    }
    tr2.startAndJoin();
    max.closeImagePlus();
    close.setOffset(in);
    close.setScale(in);
    return close;
}

Example 5 with ImageInt

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

the class SpatialRandom method getSample.

@Override
public Objects3DPopulation getSample() {
    Point3D[] points = new Point3D[nbObjects];
    Objects3DPopulation pop = new Objects3DPopulation();
    pop.setMask(mask);
    ImageInt maskimgTmp = maskimg.duplicate();
    Random ra = new Random();
    for (int i = 0; i < nbObjects; i++) {
        Voxel3D vox = maskVox.getRandomvoxel(ra);
        while (maskimgTmp.getPixel(vox) == 0) {
            vox = maskVox.getRandomvoxel(ra);
        }
        points[i] = vox;
        maskimgTmp.setPixel(vox, 0);
    }
    pop.addPoints(points);
    return pop;
}