Examples with AbstractLog mcib3d.utils.Logger.AbstractLog used on opensource projects

Example 1 with AbstractLog

use of mcib3d.utils.Logger.AbstractLog in project mcib3d-core by mcib3d.

the class ImageInt method adaptiveFilter.

/**
 * Adaptive Filter in 3D (expermimental) Take 7 neighborhood, compute mean
 * and std dev Assign mean of neighborhood with lowest std dev
 *
 * @param radx
 * @param radz
 * @param rady
 * @return 3D filtered image
 */
@Deprecated
public ImageInt adaptiveFilter(float radx, float rady, float radz, int nbcpus) {
    final ImageInt adaptimg2 = (ImageInt) this.createSameDimensions();
    int nbToProcess = this.sizeZ;
    // Timer
    final Chrono time = new Chrono(nbToProcess);
    time.start();
    final AbstractLog show = new IJStatus();
    // create kernel
    final int[] ker = FastFilters3D.createKernelEllipsoid(radx, rady, radz);
    int nb = 0;
    for (int i = 0; i < ker.length; i++) {
        nb += ker[i];
    }
    final int nb2 = nb;
    final float radX2 = radx;
    final float radY2 = rady;
    final float radZ2 = radz;
    // PARALLEL (Thomas Boudier)
    final AtomicInteger ai = new AtomicInteger(0);
    Thread[] threads = ThreadUtil.createThreadArray(nbcpus);
    for (int ithread = 0; ithread < threads.length; ithread++) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                ArrayUtil[] tab = new ArrayUtil[7];
                // displacement to take neighborhoods
                int dep = 1;
                double mes;
                double mins;
                double si;
                double me;
                for (int k = ai.getAndIncrement(); k < sizeZ; k = ai.getAndIncrement()) {
                    for (int j = 0; j < sizeY; j++) {
                        for (int i = 0; i < sizeX; i++) {
                            tab[0] = getNeighborhoodKernel(ker, nb2, i, j, k, radX2, radY2, radZ2);
                            tab[1] = getNeighborhoodKernel(ker, nb2, i + dep, j, k, radX2, radY2, radZ2);
                            tab[2] = getNeighborhoodKernel(ker, nb2, i - dep, j, k, radX2, radY2, radZ2);
                            tab[3] = getNeighborhoodKernel(ker, nb2, i, j + dep, k, radX2, radY2, radZ2);
                            tab[4] = getNeighborhoodKernel(ker, nb2, i, j - dep, k, radX2, radY2, radZ2);
                            tab[5] = getNeighborhoodKernel(ker, nb2, i, j, k + dep, radX2, radY2, radZ2);
                            tab[6] = getNeighborhoodKernel(ker, nb2, i, j, k - dep, radX2, radY2, radZ2);
                            mes = 0;
                            mins = Float.MAX_VALUE;
                            for (int c = 0; c < 7; c++) {
                                // me = tab[c].median();
                                me = tab[c].getMean();
                                si = tab[c].getStdDev();
                                if (si < mins) {
                                    mins = si;
                                    mes = me;
                                }
                            }
                            adaptimg2.setPixel(i, j, k, (int) mes);
                        }
                    }
                    if (time != null) {
                        String ti = time.getFullInfo(1);
                        if (ti != null)
                            show.log("3D adaptive : " + ti);
                    }
                }
            }
        };
    }
    ThreadUtil.startAndJoin(threads);
    return adaptimg2;
}

Example 2 with AbstractLog

use of mcib3d.utils.Logger.AbstractLog in project mcib3d-core by mcib3d.

the class FastFilters3D method getListMaximaFloat.

public static ArrayList<Voxel3DComparable> getListMaximaFloat(ImageFloat stackorig, float vx, float vy, float vz, int nbcpus, boolean showstatus) {
    int nbToProcess = stackorig.sizeZ;
    // Timer
    final Chrono time = new Chrono(nbToProcess);
    time.start();
    final AbstractLog show = new IJStatus();
    // get stack info
    final float voisx = vx;
    final float voisy = vy;
    final float voisz = vz;
    final ImageFloat ima = stackorig;
    // PARALLEL
    final AtomicInteger ai = new AtomicInteger(0);
    final int n_cpus = nbcpus == 0 ? ThreadUtil.getNbCpus() : nbcpus;
    final int dec = (int) Math.ceil((double) ima.sizeZ / (double) n_cpus);
    Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
    final ArrayList<Voxel3DComparable>[] listes = new ArrayList[n_cpus];
    for (int ithread = 0; ithread < threads.length; ithread++) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                    listes[k] = ima.getListMaxima(voisx, voisy, voisz, dec * k, dec * (k + 1), time, show);
                }
            }
        };
    }
    ThreadUtil.startAndJoin(threads);
    final ArrayList<Voxel3DComparable> liste = new ArrayList<Voxel3DComparable>();
    for (ArrayList<Voxel3DComparable> li : listes) {
        liste.addAll(li);
    }
    return liste;
}

Example 3 with AbstractLog

use of mcib3d.utils.Logger.AbstractLog in project mcib3d-core by mcib3d.

the class FastFilters3D method filterFloatImage.

public static ImageFloat filterFloatImage(ImageFloat stackorig, int filter, Object3DVoxels obj, int nbcpus, boolean showstatus) {
    int nbToProcess = stackorig.sizeZ;
    if ((filter == TOPHAT) || (filter == CLOSEGRAY) || (filter == OPENGRAY))
        nbToProcess *= 2;
    // Timer
    final Chrono time = new Chrono(nbToProcess);
    time.start();
    final AbstractLog show = new IJStatus();
    final Object3DVoxels object = obj;
    // IJ.log("Using java filtering " + voisx + " " + voisy + " " + voisz + " " + filter + " " + nbcpus);
    final ImageFloat ima = stackorig;
    ImageFloat res = (ImageFloat) ima.createSameDimensions();
    if ((filter == MEAN) || (filter == MEDIAN) || (filter == MIN) || (filter == MAX) || (filter == MAXLOCAL) || (filter == TOPHAT) || (filter == VARIANCE) || (filter == CLOSEGRAY) || (filter == OPENGRAY)) {
        // PARALLEL
        final ImageFloat out = res;
        final AtomicInteger ai = new AtomicInteger(0);
        final int n_cpus = nbcpus == 0 ? ThreadUtil.getNbCpus() : nbcpus;
        int fi = filter;
        if ((fi == TOPHAT) || (fi == OPENGRAY)) {
            fi = MIN;
        }
        if (fi == CLOSEGRAY) {
            fi = MAX;
        }
        final int f = fi;
        final int dec = (int) Math.ceil((double) ima.sizeZ / (double) n_cpus);
        Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
        for (int ithread = 0; ithread < threads.length; ithread++) {
            threads[ithread] = new Thread() {

                @Override
                public void run() {
                    for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                        ima.filterGeneric(out, object, dec * k, dec * (k + 1), f, time, show);
                    }
                }
            };
        }
        ThreadUtil.startAndJoin(threads);
        // TOPHAT MAX
        if ((filter == TOPHAT) || (filter == OPENGRAY)) {
            final int f2 = MAX;
            final ImageFloat res2 = (ImageFloat) ima.createSameDimensions();
            ai.set(0);
            for (int ithread = 0; ithread < threads.length; ithread++) {
                threads[ithread] = new Thread() {

                    @Override
                    public void run() {
                        for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                            out.filterGeneric(res2, object, dec * k, dec * (k + 1), f2, time, show);
                        }
                    }
                };
            }
            ThreadUtil.startAndJoin(threads);
            // TOPHAT DIFFERENCE
            if (filter == TOPHAT) {
                res = ima.subtractImage(res2);
            } else {
                res = res2;
            }
        }
        // CLOSING 2nd Step
        if (filter == CLOSEGRAY) {
            final int f2 = MIN;
            final ImageFloat res2 = (ImageFloat) ima.createSameDimensions();
            ai.set(0);
            for (int ithread = 0; ithread < threads.length; ithread++) {
                threads[ithread] = new Thread() {

                    @Override
                    public void run() {
                        for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                            out.filterGeneric(res2, object, dec * k, dec * (k + 1), f2, time, show);
                        }
                    }
                };
            }
            ThreadUtil.startAndJoin(threads);
            res = res2;
        }
    } else if (filter == SOBEL) {
        res = ima.sobelFilter();
    } else if (filter == ADAPTIVE) {
    // res = ima.adaptiveFilter(voisx, voisy, voisz, nbcpus);
    }
    return res;
}

Example 4 with AbstractLog

use of mcib3d.utils.Logger.AbstractLog in project mcib3d-core by mcib3d.

the class FastFilters3D method filterFloatImage.

public static ImageFloat filterFloatImage(ImageFloat stackorig, int filter, float vx, float vy, float vz, int nbcpus, boolean showstatus) {
    int nbToProcess = stackorig.sizeZ;
    if ((filter == TOPHAT) || (filter == CLOSEGRAY) || (filter == OPENGRAY))
        nbToProcess *= 2;
    // Timer
    final Chrono time = new Chrono(nbToProcess);
    time.start();
    final AbstractLog show = new IJStatus();
    // get stack info
    final float voisx = vx;
    final float voisy = vy;
    final float voisz = vz;
    final ImageFloat ima = stackorig;
    ImageFloat res = (ImageFloat) ima.createSameDimensions();
    if ((filter == MEAN) || (filter == MEDIAN) || (filter == MIN) || (filter == MAX) || (filter == MAXLOCAL) || (filter == TOPHAT) || (filter == VARIANCE) || (filter == CLOSEGRAY) || (filter == OPENGRAY)) {
        // PARALLEL
        final ImageFloat out = res;
        final AtomicInteger ai = new AtomicInteger(0);
        final int n_cpus = nbcpus == 0 ? ThreadUtil.getNbCpus() : nbcpus;
        int fi = filter;
        if ((fi == TOPHAT) || (fi == OPENGRAY)) {
            fi = MIN;
        }
        if (fi == CLOSEGRAY) {
            fi = MAX;
        }
        final int f = fi;
        final int dec = (int) Math.ceil((double) ima.sizeZ / (double) n_cpus);
        Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
        for (int ithread = 0; ithread < threads.length; ithread++) {
            threads[ithread] = new Thread() {

                @Override
                public void run() {
                    for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                        ima.filterGeneric(out, voisx, voisy, voisz, dec * k, dec * (k + 1), f, time, show);
                    }
                }
            };
        }
        ThreadUtil.startAndJoin(threads);
        // TOPHAT MAX
        if ((filter == TOPHAT) || (filter == OPENGRAY)) {
            final int f2 = MAX;
            final ImageFloat res2 = (ImageFloat) ima.createSameDimensions();
            ai.set(0);
            for (int ithread = 0; ithread < threads.length; ithread++) {
                threads[ithread] = new Thread() {

                    @Override
                    public void run() {
                        for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                            out.filterGeneric(res2, voisx, voisy, voisz, dec * k, dec * (k + 1), f2, time, show);
                        }
                    }
                };
            }
            ThreadUtil.startAndJoin(threads);
            // TOPHAT DIFFERENCE
            if (filter == TOPHAT) {
                res = ima.subtractImage(res2);
            } else {
                res = res2;
            }
        }
        // CLOSING 2nd Step
        if (filter == CLOSEGRAY) {
            final int f2 = MIN;
            final ImageFloat res2 = (ImageFloat) ima.createSameDimensions();
            ai.set(0);
            for (int ithread = 0; ithread < threads.length; ithread++) {
                threads[ithread] = new Thread() {

                    @Override
                    public void run() {
                        for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                            out.filterGeneric(res2, voisx, voisy, voisz, dec * k, dec * (k + 1), f2, time, show);
                        }
                    }
                };
            }
            ThreadUtil.startAndJoin(threads);
            res = res2;
        }
    } else if (filter == SOBEL) {
        res = ima.sobelFilter();
    } else if (filter == ADAPTIVE) {
        // res = ima.adaptiveFilter(voisx, voisy, voisz, nbcpus);
        // PARALLEL
        final ImageFloat out = res;
        final AtomicInteger ai = new AtomicInteger(0);
        final int n_cpus = nbcpus == 0 ? ThreadUtil.getNbCpus() : nbcpus;
        final int dec = (int) Math.ceil((double) ima.sizeZ / (double) n_cpus);
        Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
        show.log("Starting");
        for (int ithread = 0; ithread < threads.length; ithread++) {
            threads[ithread] = new Thread() {

                @Override
                public void run() {
                    for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                        ima.adaptiveFilter(out, voisx, voisy, voisz, dec * k, dec * (k + 1), time, show);
                    }
                }
            };
        }
        ThreadUtil.startAndJoin(threads);
        show.log("Finished");
    }
    return res;
}

Example 5 with AbstractLog

use of mcib3d.utils.Logger.AbstractLog in project mcib3d-core by mcib3d.

the class FastFilters3D method getListMaximaInt.

public static ArrayList<Voxel3DComparable> getListMaximaInt(ImageInt stackorig, float vx, float vy, float vz, int nbcpus, boolean showstatus) {
    int nbToProcess = stackorig.sizeZ;
    // Timer
    final Chrono time = new Chrono(nbToProcess);
    time.start();
    final AbstractLog show = new IJStatus();
    // get stack info
    final float voisx = vx;
    final float voisy = vy;
    final float voisz = vz;
    final ImageInt ima = stackorig;
    // PARALLEL
    final AtomicInteger ai = new AtomicInteger(0);
    final int n_cpus = nbcpus == 0 ? ThreadUtil.getNbCpus() : nbcpus;
    final int dec = (int) Math.ceil((double) ima.sizeZ / (double) n_cpus);
    Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
    final ArrayList<Voxel3DComparable>[] listes = new ArrayList[n_cpus];
    for (int ithread = 0; ithread < threads.length; ithread++) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                    listes[k] = ima.getListMaxima(voisx, voisy, voisz, dec * k, dec * (k + 1), time, show);
                }
            }
        };
    }
    ThreadUtil.startAndJoin(threads);
    final ArrayList<Voxel3DComparable> liste = new ArrayList<Voxel3DComparable>();
    for (ArrayList<Voxel3DComparable> li : listes) {
        liste.addAll(li);
    }
    return liste;
}