Examples with Object3DVoxels mcib3d.geom.Object3DVoxels used on opensource projects

Example 1 with Object3DVoxels

use of mcib3d.geom.Object3DVoxels in project mcib3d-core by mcib3d.

the class ImageLabeller method getObjects.

// classical default neighborhood for segmentation is 26
public ArrayList<Object3DVoxels> getObjects(ImageHandler mask, boolean connex6) {
    if ((spots == null) || (mask != currentMask)) {
        if (connex6) {
            this.labelSpots6(mask);
        } else {
            this.labelSpots26(mask);
        }
    }
    ArrayList<Object3DVoxels> objects = new ArrayList<Object3DVoxels>();
    int sizeX = mask.sizeX;
    short label = 1;
    for (Spot s : spots.values()) {
        ArrayList<Vox3D> a = s.voxels;
        // check size
        if ((a.size() >= minSize) && (a.size() <= maxsize)) {
            ArrayList voxels3D = new ArrayList();
            for (Vox3D vox : a) {
                voxels3D.add(new Voxel3D(vox.xy % sizeX, vox.xy / sizeX, vox.z, label));
            }
            ArrayList noDuplicate = new ArrayList(new HashSet(voxels3D));
            // set calibration
            Object3DVoxels object3DVoxels = new Object3DVoxels(noDuplicate);
            // Object3D_IJUtils.setCalibration(object3DVoxels, mask.getCalibration());
            object3DVoxels.setCalibration(mask.getScaleXY(), mask.getScaleZ(), mask.getUnit());
            objects.add(object3DVoxels);
            label++;
        }
    }
    return objects;
}

Example 2 with Object3DVoxels

use of mcib3d.geom.Object3DVoxels in project mcib3d-core by mcib3d.

the class ImageShort method draw.

@Override
public void draw(Object3D o, int value) {
    Object3DVoxels ov;
    if (!(o instanceof Object3DVoxels)) {
        ov = o.getObject3DVoxels();
    } else {
        ov = (Object3DVoxels) o;
    }
    if (value > 65535) {
        value = 255;
    }
    if (value < 0) {
        value = 0;
    }
    short val = (short) value;
    for (Voxel3D v : ov.getVoxels()) {
        if (contains(v.getX(), v.getY(), v.getZ())) {
            pixels[v.getRoundZ()][v.getRoundX() + v.getRoundY() * sizeX] = val;
        }
    }
}

Example 3 with Object3DVoxels

use of mcib3d.geom.Object3DVoxels in project mcib3d-core by mcib3d.

the class Segment3DSpots method splitSpotWatershed.

public static Object3DVoxels[] splitSpotWatershed(Object3D obj, float rad, float dist) {
    ImageInt seg = obj.createSegImage(0, 0, 0, obj.getXmax(), obj.getYmax(), obj.getZmax(), 255);
    // seg.show();
    ImagePlus segplus = seg.getImagePlus();
    segplus.setCalibration(obj.getCalibration());
    // return
    Object3DVoxels[] res = null;
    try {
        int cpus = ThreadUtil.getNbCpus();
        // FIXME variable multithread
        ImageFloat edt3d = EDT.run(seg, 1f, false, cpus);
        // 3D filtering of the edt to remove small local maxima
        ImageFloat edt3dseeds = FastFilters3D.filterFloatImage(edt3d, FastFilters3D.MEAN, 1, 1, 1, cpus, false);
        // edt3d.showDuplicate("edt");
        // ImageStack localMax = FastFilters3D.filterFloatImageStack(edt3d.getImageStack(), FastFilters3D.MAXLOCAL, rad, rad, rad, cpus, false);
        ImageFloat maxlocal3d = FastFilters3D.filterFloatImage(edt3dseeds, FastFilters3D.MAXLOCAL, rad, rad, rad, cpus, false);
        // maxlocal3d.show("max local");
        ArrayList<Voxel3D> locals = obj.listVoxels(maxlocal3d, 0);
        int nb = locals.size();
        // IJ.log("nb=" + nb);
        if (nb < 2) {
            return null;
        }
        // look for most far apart local maxima
        int i1 = 0;
        int i2 = 0;
        double dmax = 0.0;
        double d;
        for (int i = 0; i < nb; i++) {
            for (int j = i + 1; j < nb; j++) {
                d = locals.get(i).distance(locals.get(j));
                if (d > dmax) {
                    dmax = d;
                    i1 = i;
                    i2 = j;
                }
            }
        }
        // perform a 2-means clustering
        double cx1 = 0;
        double cy1 = 0;
        double cz1 = 0;
        double cx2 = 0;
        double cy2 = 0;
        double cz2 = 0;
        double d1;
        double d2;
        Voxel3D PP1 = new Voxel3D(locals.get(i1).getX(), locals.get(i1).getY(), locals.get(i1).getZ(), 1);
        Voxel3D PP2 = new Voxel3D(locals.get(i2).getX(), locals.get(i2).getY(), locals.get(i2).getZ(), 2);
        Voxel3D P1 = new Voxel3D(cx1, cy1, cz1, 0);
        Voxel3D P2 = new Voxel3D(cx2, cy2, cz2, 0);
        int nb1, nb2;
        int nbite = 0;
        while ((nb > 2) && ((P1.distance(PP1) > 1) || (P2.distance(PP2) > 1)) && (nbite < 100)) {
            nbite++;
            cx1 = 0;
            cy1 = 0;
            cx2 = 0;
            cy2 = 0;
            cz1 = 0;
            cz2 = 0;
            nb1 = 0;
            nb2 = 0;
            P1.setX(PP1.getX());
            P1.setY(PP1.getY());
            P1.setZ(PP1.getZ());
            P2.setX(PP2.getX());
            P2.setY(PP2.getY());
            P2.setZ(PP2.getZ());
            for (Voxel3D local : locals) {
                d1 = P1.distance(local);
                d2 = P2.distance(local);
                if (d1 < d2) {
                    cx1 += local.getX();
                    cy1 += local.getY();
                    cz1 += local.getZ();
                    nb1++;
                } else {
                    cx2 += local.getX();
                    cy2 += local.getY();
                    cz2 += local.getZ();
                    nb2++;
                }
            }
            cx1 /= nb1;
            cy1 /= nb1;
            cx2 /= nb2;
            cy2 /= nb2;
            cz1 /= nb1;
            cz2 /= nb2;
            PP1.setX(cx1);
            PP1.setY(cy1);
            PP1.setZ(cz1);
            PP2.setX(cx2);
            PP2.setY(cy2);
            PP2.setZ(cz2);
        }
        // check minimal distances
        double distPP = PP1.distance(PP2);
        IJ.log("Centers found for split PP1=" + PP1 + " PP2=" + PP2 + " distance " + distPP);
        if (distPP < dist) {
            return null;
        }
        // find closest max local to two barycenters, in case barycenters outside object
        Voxel3D PP1closest = new Voxel3D(locals.get(0));
        Voxel3D PP2closest = new Voxel3D(locals.get(0));
        double dist1 = PP1.distanceSquare(PP1closest);
        double dist2 = PP2.distanceSquare(PP2closest);
        for (Voxel3D local : locals) {
            double dd1 = PP1.distanceSquare(local);
            double dd2 = PP2.distanceSquare(local);
            if (dd1 < dist1) {
                dist1 = dd1;
                PP1closest = local;
            }
            if (dd2 < dist2) {
                dist2 = dd2;
                PP2closest = local;
            }
        }
        ImageInt seeds = new ImageShort("seeds", seg.sizeX, seg.sizeY, seg.sizeZ);
        seeds.setPixel(PP1closest.getRoundX(), PP1closest.getRoundY(), PP1closest.getRoundZ(), 255);
        seeds.setPixel(PP2closest.getRoundX(), PP2closest.getRoundY(), PP2closest.getRoundZ(), 255);
        // seeds.show();
        // Watershed3D_old wat = new Watershed3D_old(edt3d, seeds, 0, 0);
        // ImageInt wat2 = wat.getWatershedImage3D();
        // ImageHandler edt16 = edt3d.convertToShort(true);
        Watershed3D wat = new Watershed3D(edt3d, seeds, 0, 0);
        ImageInt wat2 = wat.getWatershedImage3D();
        // wat2.show();
        // in watershed label starts at 1
        Object3DVoxels ob1 = new Object3DVoxels(wat2, 1);
        Object3DVoxels ob2 = new Object3DVoxels(wat2, 2);
        // IJ.log("split1="+ob1+" split2="+ob2);
        // translate objects if needed by miniseg
        // ob1.translate(seg.offsetX, seg.offsetY, seg.offsetZ);
        // new ImagePlus("wat", wat2.getStack()).show();
        res = new Object3DVoxels[2];
        res[0] = ob1;
        res[1] = ob2;
    } catch (Exception e) {
        IJ.log("Exception EDT " + e);
    }
    return res;
}

Example 4 with Object3DVoxels

use of mcib3d.geom.Object3DVoxels in project mcib3d-core by mcib3d.

the class Segment3DSpots method segmentAll.

/**
 */
public void segmentAll() {
    segmentedObjects = new ArrayList<Object3D>();
    ArrayList<Voxel3D> obj;
    int o = 1;
    int localThreshold = localValue;
    if (labelImage == null) {
        this.createLabelImage();
    }
    // locate seeds
    for (int z = 0; z < seedsImage.sizeZ; z++) {
        IJ.showStatus("Segmenting slice " + (z + 1));
        // IJ.log("Segmenting slice " + (z + 1));
        for (int y = 0; y < seedsImage.sizeY; y++) {
            for (int x = 0; x < seedsImage.sizeX; x++) {
                if (seedsImage.getPixel(x, y, z) > seedsThreshold) {
                    // LOCAL THRESHOLD
                    if (localMethod == LOCAL_MEAN) {
                        localThreshold = (int) localMean(x, y, z);
                    } else if (localMethod == LOCAL_GAUSS) {
                        double[] gauss;
                        gauss = this.gaussianFit(x, y, z, false);
                        if (gauss != null) {
                            double thresh = CurveFitter.f(CurveFitter.GAUSSIAN, gauss, GAUSS_PC * gauss[3]);
                            // IJ.log("gauss sigma : " + gauss[3] + " thresh=" + thresh);
                            localThreshold = (int) thresh;
                        }
                    } else if (localMethod == LOCAL_DIFF) {
                        localThreshold = (int) Math.max(1, seedsImage.getPixel(x, y, z) - diff);
                    }
                    if (localThreshold > 0) {
                        if (show) {
                            IJ.log("segmenting spot at : " + x + " " + y + " " + " " + z + " lc=" + localThreshold);
                        }
                    }
                    switch(methodSeg) {
                        case SEG_CLASSICAL:
                            obj = this.segmentSpotClassical(x, y, z, localThreshold, o);
                            break;
                        case SEG_MAX:
                            obj = this.segmentSpotMax(x, y, z, localThreshold, o);
                            break;
                        case SEG_BLOCK:
                            obj = this.segmentSpotBlock(x, y, z, localThreshold, o);
                            break;
                        default:
                            obj = this.segmentSpotClassical(x, y, z, localThreshold, o);
                            break;
                    }
                    if ((obj != null) && (obj.size() >= volMin) && (obj.size() <= volMax)) {
                        segmentedObjects.add(new Object3DVoxels(obj));
                        // IJ.log("obj size: "+obj.size());
                        o++;
                    } else if (obj != null) {
                        // erase from label image
                        for (Voxel3D vo : obj) {
                            labelImage.setPixel(vo.getRoundX(), vo.getRoundY(), vo.getRoundZ(), 0);
                        }
                        if (show) {
                            IJ.log("object volume outside range : " + obj.size());
                        }
                    }
                }
            }
        }
    }
}

Example 5 with Object3DVoxels

use of mcib3d.geom.Object3DVoxels 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;
}