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

Search in sources :

Example 6 with AbstractLog

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

the class Object3DSurface method computeVoxelsMultithread.

// private void computeVoxelsFill() {
// voxels = new ArrayList<Voxel3D>();
// // start at 1 1 1 to let 0 0 0 as background for fill holes
// int w = getXmax() - getXmin() + 2;
// int h = getYmax() - getYmin() + 2;
// int d = getZmax() - getZmin() + 2;
// ImageByte mask = new ImageByte("mask",w, h, d);
// 
// Point3f vox;
// int x, y, z;
// int val = 1;
// 
// Iterator it = unique_vertices.iterator();
// while (it.hasNext()) {
// vox = (Point3f) it.next();
// x = (int) (vox.getX() - getXmin() + 1);
// y = (int) (vox.getY() - getYmin() + 1);
// z = (int) (vox.getZ() - getZmin() + 1);
// mask.putPixel(x, y, z, val);
// }
// // fill holes 3D
// mask.fillHoles3D(0, val);
// 
// // create voxels lists
// double xx, yy, zz;
// for (z = 0; z < mask.getSizez(); z++) {
// for (y = 0; y < mask.getSizey(); y++) {
// for (x = 0; x < mask.getSizex(); x++) {
// if (mask.getPixel(x, y, z) == val) {
// xx = x + getXmin() - 1;
// yy = y + getYmin() - 1;
// zz = z + getZmin() - 1;
// voxels.add(new Voxel3D(xx, yy, zz, val));
// }
// }
// }
// }
// 
// }
// Voxellisation ; coordinates should be backed to pixels coordinates
private ArrayList<Voxel3D> computeVoxelsMultithread() {
    final int zminv = (int) Math.floor(getZmin()) - 1;
    final int yminv = (int) Math.floor(getYmin()) - 1;
    final int xminv = (int) Math.floor(getXmin()) - 1;
    final int zmaxv = (int) Math.ceil(getZmax()) + 1;
    final int ymaxv = (int) Math.ceil(getYmax()) + 1;
    final int xmaxv = (int) Math.ceil(getXmax()) + 1;
    final int n_cpus = ThreadUtil.getNbCpus();
    final int val = this.getValue();
    final ArrayList[] voxelss = new ArrayList[n_cpus];
    for (int i = 0; i < voxelss.length; i++) {
        voxelss[i] = new ArrayList();
    }
    final Vector3D dir0 = new Vector3D(1, 0, 0);
    final Vector3D dir1 = new Vector3D(-1, 0, 0);
    final int dec = (int) Math.ceil((double) (zmaxv - zminv + 1) / (double) n_cpus);
    // IJ.log("dec " + dec + " " + zminv + " " + zmaxv + " " + n_cpus);
    // Timer
    final Chrono time = new Chrono(zmaxv - zminv + 1);
    time.start();
    final AbstractLog show = new IJStatus();
    final AtomicInteger ai = new AtomicInteger(0);
    Thread[] threads = ThreadUtil.createThreadArray(n_cpus);
    for (int ithread = 0; ithread < threads.length; ithread++) {
        threads[ithread] = new Thread() {

            @Override
            public void run() {
                boolean in;
                Point3D origin;
                for (int k = ai.getAndIncrement(); k < n_cpus; k = ai.getAndIncrement()) {
                    int zmaxx = Math.min(zminv + (k + 1) * dec, zmaxv);
                    for (float zi = zminv + dec * k; zi < zmaxx; zi += 1) {
                        // IJ.showStatus(k + " : Voxellisation " + zi + "/" + (zmaxx - 1));
                        for (float yi = yminv; yi <= ymaxv; yi += 1) {
                            in = false;
                            float xi = xminv;
                            while (xi <= xmaxv) {
                                if (!in) {
                                    origin = new Point3D(xi, yi + 0.5, zi + 0.5);
                                    double distMin = minDistSquareTriangles(origin, dir0, 1.0);
                                    if (distMin <= 1) {
                                        in = true;
                                    } else if ((distMin >= 9.0) && (distMin < Double.MAX_VALUE)) {
                                        // IJ.log(" " + distMin + " " + (Math.floor(Math.sqrt(distMin)) - 1));
                                        xi += Math.floor(Math.sqrt(distMin)) - 1;
                                    } else if (distMin == Double.MAX_VALUE) {
                                        xi += xmaxv;
                                    }
                                } else {
                                    // voxels are in pixels not calibrated units
                                    voxelss[k].add(new Voxel3D(xi, yi, zi, val));
                                    origin = new Point3D(xi, yi + 0.5, zi + 0.5);
                                    double distMin = minDistSquareTriangles(origin, dir1, 1);
                                    if (distMin <= 1) {
                                        in = false;
                                    } else if ((distMin >= 9.0) && (distMin < Double.MAX_VALUE)) {
                                        // IJ.log(" " + distMin + " " + (Math.floor(Math.sqrt(distMin)) - 1));
                                        int nb = (int) Math.floor(Math.sqrt(distMin));
                                        if (xi + nb < xmaxv) {
                                            addLineXVoxels(voxelss[k], val, xi + 1, yi, zi, nb);
                                            xi += nb;
                                            in = false;
                                        }
                                    }
                                }
                                xi += 1;
                            }
                        }
                        String ti = time.getFullInfo(1);
                        if (ti != null)
                            show.log("3D voxellisation : " + ti);
                    }
                }
            }
        };
    }
    ThreadUtil.startAndJoin(threads);
    // put all arrays in one
    ArrayList<Voxel3D> newVox = new ArrayList<Voxel3D>();
    for (ArrayList voxels1 : voxelss) {
        newVox.addAll(voxels1);
    }
    return newVox;
}
Also used : Chrono(mcib3d.utils.Chrono) IJStatus(mcib3d.utils.Logger.IJStatus) AbstractLog(mcib3d.utils.Logger.AbstractLog) AtomicInteger(java.util.concurrent.atomic.AtomicInteger)

Example 7 with AbstractLog

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

the class FastArithmetic3D method mathIntImage.

public static ImageInt mathIntImage(ImageInt stackorig, final ImageInt stackother, int operation, final float par1, final float par2, int nbcpus, boolean showstatus, final AbstractLog log) {
    int nbToProcess = stackorig.sizeZ;
    // Timer
    final Chrono time = new Chrono(nbToProcess);
    time.start();
    final AbstractLog show = log;
    // get stack info
    final ImageInt ima = stackorig;
    final ImageInt res = (ImageInt) ima.createSameDimensions();
    final ImageInt out = res;
    final AtomicInteger ai = new AtomicInteger(0);
    final int n_cpus = nbcpus == 0 ? ThreadUtil.getNbCpus() : nbcpus;
    final int fi = operation;
    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.mathGeneric(stackother, res, dec * k, dec * (k + 1), fi, par1, par2, time, log);
                }
            }
        };
    }
    ThreadUtil.startAndJoin(threads);
    show.log("Finished");
    return res;
}
Also used : Chrono(mcib3d.utils.Chrono) AtomicInteger(java.util.concurrent.atomic.AtomicInteger) AbstractLog(mcib3d.utils.Logger.AbstractLog)

Example 8 with AbstractLog

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

the class FastFilters3D method filterIntImage.

public static ImageInt filterIntImage(ImageInt stackorig, int filter, float vx, float vy, float vz, int nbcpus, boolean showstatus, AbstractLog log) {
    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 = log;
    // get stack info
    final float voisx = vx;
    final float voisy = vy;
    final float voisz = vz;
    final ImageInt ima = stackorig;
    ImageInt res = (ImageInt) ima.createSameDimensions();
    if ((filter == MEAN) || (filter == MEDIAN) || (filter == MIN) || (filter == MAX) || (filter == MAXLOCAL) || (filter == TOPHAT) || (filter == VARIANCE) || (filter == CLOSEGRAY) || (filter == OPENGRAY)) {
        // PARALLEL
        final ImageInt 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);
        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.filterGeneric(out, voisx, voisy, voisz, dec * k, dec * (k + 1), f, time, show);
                    }
                }
            };
        }
        ThreadUtil.startAndJoin(threads);
        show.log("Finished");
        // TOPHAT MAX
        if ((filter == TOPHAT) || (filter == OPENGRAY)) {
            final int f2 = MAX;
            final ImageInt res2 = (ImageInt) 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.subtractImageInt(res2);
            } else {
                res = res2;
            }
        }
        // CLOSING 2nd Step
        if (filter == CLOSEGRAY) {
            final int f2 = MIN;
            final ImageInt res2 = (ImageInt) 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 ImageInt 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;
}
Also used : Chrono(mcib3d.utils.Chrono) AtomicInteger(java.util.concurrent.atomic.AtomicInteger) AbstractLog(mcib3d.utils.Logger.AbstractLog)

Example 9 with AbstractLog

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

the class FastFilters3D method filterIntImage.

public static ImageInt filterIntImage(ImageInt 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 ImageInt ima = stackorig;
    ImageInt res = (ImageInt) ima.createSameDimensions();
    if ((filter == MEAN) || (filter == MEDIAN) || (filter == MIN) || (filter == MAX) || (filter == MAXLOCAL) || (filter == TOPHAT) || (filter == VARIANCE) || (filter == CLOSEGRAY) || (filter == OPENGRAY)) {
        // PARALLEL
        final ImageInt 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 ImageInt res2 = (ImageInt) 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.substractImage(res2);
            } else {
                res = res2;
            }
        }
        // CLOSING 2nd Step
        if (filter == CLOSEGRAY) {
            final int f2 = MIN;
            final ImageInt res2 = (ImageInt) 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;
}
Also used : Chrono(mcib3d.utils.Chrono) AtomicInteger(java.util.concurrent.atomic.AtomicInteger) IJStatus(mcib3d.utils.Logger.IJStatus) AbstractLog(mcib3d.utils.Logger.AbstractLog) Object3DVoxels(mcib3d.geom.Object3DVoxels)

Aggregations

AtomicInteger (java.util.concurrent.atomic.AtomicInteger)9 Chrono (mcib3d.utils.Chrono)9 AbstractLog (mcib3d.utils.Logger.AbstractLog)9 IJStatus (mcib3d.utils.Logger.IJStatus)7 ArrayList (java.util.ArrayList)2 Object3DVoxels (mcib3d.geom.Object3DVoxels)2 Voxel3DComparable (mcib3d.geom.Voxel3DComparable)2
About Me
UseOf

Java Tutorials :

Simple Java RabbitMQ Example with Spring
Simple Springboot JPA Eclipeslink Example
Simple SpringBoot JPA Hibernate Example
Jackson JSON @JsonIgnore and @JsonIgnoreProperties Examples
Java Infinite recursion (StackOverflowError) Jackson solutions
Simple Java Jackson Serialize Objects to JSON and convert them back To Object
ElasticSearch 5 - Upload files using Java API in binary field Example
Java JAXB marshall unmarshall Examples from String and Stream
Java 8 forEach List and Map examples
ElasticSearch 5 Java API SearchRequestBuilder examples
Java ElasticSearch 5 examples with node index and mapping - running local
Convert String to int or Integer Java 8
Java 9 in action - JShell - Ubuntu
Java - removing invalid characters from a file name
Hello world!? or Hello Tutorial