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

Example 11 with ImageFloat

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

the class BinaryMorpho method binaryErode.

public static ImageByte binaryErode(ImageInt in, float radius, float radiusZ, int nbCPUs) {
    try {
        if (nbCPUs == 0) {
            nbCPUs = ThreadUtil.getNbCpus();
        }
        // test rad <=1
        /*if ((radius <= 1) && (radiusZ <= 1)) {
             return binaryErodeRad1(in, 1, nbCPUs);
             }*/
        ImageFloat edm = EDT.run(in, 0, 1, radius / radiusZ, false, nbCPUs);
        ImageByte temp = edm.threshold(radius, false, true);
        edm.flush();
        edm = null;
        temp.setOffset(in);
        temp.setScale(in);
        return temp;
    } catch (Exception e) {
        exceptionPrinter.print(e, null, true);
    }
    return null;
}

Example 12 with ImageFloat

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

the class BinaryMorpho method binaryOpen.

public static ImageByte binaryOpen(ImageInt in, float radius, float radiusZ, int nbCPUs) {
    try {
        if (nbCPUs == 0) {
            nbCPUs = ThreadUtil.getNbCpus();
        }
        // test rad <=1
        /*if ((radius <= 1) && (radiusZ <= 1)) {
             return binaryOpenRad1(in, 1, nbCPUs);
             }*/
        ImageFloat edm = EDT.run(in, 0, 1, radius / radiusZ, false, nbCPUs);
        ImageByte temp = edm.threshold(radius, false, true);
        edm.closeImagePlus();
        edm = EDT.run(temp, 0, 1, radius / radiusZ, true, nbCPUs);
        temp.closeImagePlus();
        temp = edm.threshold(radius, true, false);
        edm.closeImagePlus();
        edm = null;
        System.gc();
        temp.setOffset(in);
        temp.setScale(in);
        return temp;
    } catch (Exception e) {
        exceptionPrinter.print(e, null, true);
    }
    return null;
}

Example 13 with ImageFloat

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

the class SymmetryFilter method computeBins.

private void computeBins() {
    ImageHandler img = edges[0];
    bin1 = new ImageFloat("bin1", img.sizeX, img.sizeY, img.sizeZ);
    bin2 = new ImageFloat("bin2", img.sizeX, img.sizeY, img.sizeZ);
    for (int z = 0; z < img.sizeZ; z++) {
        IJ.showStatus("Symmetry " + z + "/" + img.sizeZ);
        for (int x = 0; x < img.sizeX; x++) {
            for (int y = 0; y < img.sizeY; y++) {
                double ex = edges[0].getPixel(x, y, z);
                double ey = edges[1].getPixel(x, y, z);
                double ez = edges[2].getPixel(x, y, z);
                double ee = Math.sqrt(ex * ex + ey * ey + ez * ez);
                // bin
                Vector3D grad = new Vector3D(ex, ey, ez);
                grad.normalize();
                if (grad.getLength() == 0) {
                    continue;
                }
                Point3D pos = new Vector3D(x, y, z);
                for (int d = 0; d < radius; d++) {
                    pos.translate(grad);
                    if ((d > 0) && (img.contains(pos.getRoundX(), pos.getRoundY(), pos.getRoundZ()))) {
                        bin1.setPixelIncrement(pos, 1);
                        if (improved) {
                            bin2.setPixelIncrement(pos, (float) (d * ee));
                        } else {
                            bin2.setPixelIncrement(pos, (float) (ee));
                        }
                    }
                }
            }
        }
    }
}

Example 14 with ImageFloat

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

the class Density3D method computeDensity.

public ImageHandler computeDensity(ImageHandler handler, boolean multi) {
    final ImageHandler img = handler;
    ImageHandler res = new ImageFloat("density", img.sizeX, img.sizeY, img.sizeZ);
    Objects3DPopulation population = new Objects3DPopulation(img);
    population.createKDTreeCenters();
    // non parallel version
    if (!multi) {
        densityProcess(img, population, res, 0, handler.sizeZ, neighbours, sigma);
    } else {
        // parallel version
        // PARALLEL, need to duplicate populations
        int neighbours2 = Math.min(neighbours, population.getNbObjects());
        final AtomicInteger ai = new AtomicInteger(0);
        final int n_cpus = ThreadUtil.getNbCpus();
        final int dec = (int) Math.ceil((double) handler.sizeZ / (double) n_cpus);
        Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
        int bound = threads.length;
        for (int iThread = 0; iThread < bound; iThread++) {
            threads[iThread] = new Thread(() -> {
                for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                    Objects3DPopulation pop = new Objects3DPopulation(img);
                    densityProcess(img, pop, res, dec * k, dec * (k + 1), neighbours2, sigma);
                }
            });
        }
        ThreadUtil.startAndJoin(threads);
    }
    res.setScale(img);
    return res;
}

Example 15 with ImageFloat

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

the class EdtShort method run.

/**
 * @param imp
 * @param thresh
 * @param scaleXY
 * @param scaleZ
 * @return
 * @throws Exception
 */
public ImageFloat run(ImageShort imp, int thresh, float scaleXY, float scaleZ, int nbCPUs) throws Exception {
    int w = imp.sizeX;
    int h = imp.sizeY;
    int d = imp.sizeZ;
    float scale = scaleZ / scaleXY;
    short[][] data = imp.pixels;
    // Create 32 bit floating point stack for output, s.  Will also use it for g in Transformation 1.
    ImageStack sStack = new ImageStack(w, h);
    float[][] s = new float[d][];
    for (int k = 0; k < d; k++) {
        ImageProcessor ipk = new FloatProcessor(w, h);
        sStack.addSlice(null, ipk);
        s[k] = (float[]) ipk.getPixels();
    }
    float[] sk;
    // Transformation 1.  Use s to store g.
    Step1Thread[] s1t = new Step1Thread[nbCPUs];
    for (int thread = 0; thread < nbCPUs; thread++) {
        s1t[thread] = new Step1Thread(thread, nbCPUs, w, h, d, thresh, s, data, scale);
        s1t[thread].start();
    }
    try {
        for (int thread = 0; thread < nbCPUs; thread++) {
            s1t[thread].join();
        }
    } catch (InterruptedException ie) {
        IJ.error("A thread was interrupted in step 1 .");
    }
    // Transformation 2.  g (in s) -> h (in s)
    Step2Thread[] s2t = new Step2Thread[nbCPUs];
    for (int thread = 0; thread < nbCPUs; thread++) {
        s2t[thread] = new Step2Thread(thread, nbCPUs, w, h, d, s);
        s2t[thread].start();
    }
    try {
        for (int thread = 0; thread < nbCPUs; thread++) {
            s2t[thread].join();
        }
    } catch (InterruptedException ie) {
        IJ.error("A thread was interrupted in step 2 .");
    }
    // check image size, if sizeZ==1 do not perform Z distance processing
    if (imp.sizeZ > 1) {
        Step3Thread[] s3t = new Step3Thread[nbCPUs];
        for (int thread = 0; thread < nbCPUs; thread++) {
            s3t[thread] = new Step3Thread(thread, nbCPUs, w, h, d, s, data, thresh, scale);
            s3t[thread].start();
        }
        try {
            for (int thread = 0; thread < nbCPUs; thread++) {
                s3t[thread].join();
            }
        } catch (InterruptedException ie) {
            IJ.error("A thread was interrupted in step 3 .");
        }
    }
    // Find the largest distance for scaling
    // Also fill in the background values.
    float distMax = 0;
    int wh = w * h;
    float dist;
    for (int k = 0; k < d; k++) {
        sk = s[k];
        for (int ind = 0; ind < wh; ind++) {
            if (((data[k][ind] & 0xffff) <= thresh)) {
                sk[ind] = 0;
            } else {
                dist = (float) Math.sqrt(sk[ind]) * scaleXY;
                sk[ind] = dist;
                distMax = (dist > distMax) ? dist : distMax;
            }
        }
    }
    ImageFloat res = (ImageFloat) ImageFloat.wrap(sStack);
    res.setScale(imp);
    res.setOffset(imp);
    res.setMinAndMax(0, distMax);
    return res;
}