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

Example 11 with ImageInt

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

the class BinaryMorpho method binaryOpenMultilabel.

public static ImageInt binaryOpenMultilabel(ImageInt in, float radius, float radiusZ, int nbCPUs) {
    ImageByte[] ihs = in.crop3DBinary();
    if (ihs != null) {
        for (int idx = 0; idx < ihs.length; idx++) {
            /*if (radius <= 1 && radiusZ <= 1) {
                 ihs[idx] = BinaryMorpho.binaryOpenRad1(ihs[idx], 1, nbCPUs);
                 } else {
                 ihs[idx] = binaryOpen(ihs[idx], radius, radiusZ, nbCPUs);
                 }*/
            ihs[idx] = binaryOpen(ihs[idx], radius, radiusZ, nbCPUs);
        }
        ImageInt temp = ImageShort.merge3DBinary(ihs, in.sizeX, in.sizeY, in.sizeZ);
        temp.setScale(in);
        temp.setOffset(in);
        return temp;
    }
    return in;
}

Example 12 with ImageInt

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

the class BinaryMorpho method binaryDilateMultilabel.

public static ImageInt binaryDilateMultilabel(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++) {
            ihs[idx] = binaryDilate(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 13 with ImageInt

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

the class BinaryMorpho method binaryCloseRad1.

private static ImageByte binaryCloseRad1(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 (maxRad1(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() {

            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 (minRad1(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 14 with ImageInt

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

the class Watershed3D_old method createArrayList.

private void createArrayList() {
    voxels = new ArrayList();
    int sx = rawImage.sizeX;
    int sy = rawImage.sizeY;
    int sz = rawImage.sizeZ;
    // watershedImage
    this.watershedImage = new ImageShort("watershed", sx, sy, sz);
    okseeds = false;
    float pix;
    float se;
    // compute the labelled image (in case seeds are clustered)
    ImageLabeller labeller = new ImageLabeller();
    ImageInt seedsLabel = labeller.getLabels(seedsImage.thresholdAboveExclusive(seedsThreshold));
    // IJ.log("MAX SEEDS " + seedsLabel.getImageStats(null).getMax());
    // since seedsLabel starts at 1 and watershed at 2, replace values
    seedsLabel.replacePixelsValue(BORDER, (int) seedsLabel.getMax() + 1);
    seedsLabel.resetStats(null);
    // IJ.log("MAX SEEDS " + seedsLabel.getImageStats(null).getMax());
    if (computeVolumes) {
        for (int i = 0; i <= seedsLabel.getMax(); i++) {
            volumeLabels.add(0.0);
        }
    }
    for (int z = 0; z < sz; z++) {
        IJ.showStatus("Processing watershed " + (z + 1));
        for (int y = 0; y < sy; y++) {
            for (int x = 0; x < sx; x++) {
                pix = rawImage.getPixel(x, y, z);
                se = seedsLabel.getPixel(x, y, z);
                if (pix > rawThreshold) {
                    // IJ.log("seed found " + x + " " + y + " " + z+" : "+se);
                    if (se > 0) {
                        // IJ.log("seed found " + x + " " + y + " " + z);
                        watershedImage.setPixel(x, y, z, se);
                        voxels.add(new Voxel3DComparable(x, y, z, pix, se));
                        okseeds = true;
                    } else {
                        voxels.add(new Voxel3DComparable(x, y, z, pix, NO_LABEL));
                        watershedImage.setPixel(x, y, z, NO_LABEL);
                    }
                } else {
                    watershedImage.setPixel(x, y, z, NO_LABEL);
                }
                // compute volumes (warning if seeds are float values)
                if (computeVolumes) {
                    // volumeLabels.get((int) se)[1]++;
                    volumeLabels.set((int) se, volumeLabels.get((int) se) + 1);
                }
            }
        }
    }
}

Example 15 with ImageInt

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

the class IntImage3D method binaryReconstructByObjects.

public ImageInt binaryReconstructByObjects(ImageInt base) {
    // System.out.println("max "+this.getMaximum());
    Segment3DImage seg = new Segment3DImage(new ImageShort(this.getStack()), 1, 65535);
    seg.segment();
    ImageInt label = seg.getLabelledObjectsImage3D();
    boolean[] ok = new boolean[(int) label.getMax() + 1];
    for (int i = 0; i < ok.length; i++) {
        ok[i] = false;
    }
    if (label.getMax() > 0) {
        for (int k = 0; k < sizez; k++) {
            for (int j = 0; j < sizey; j++) {
                for (int i = 0; i < sizex; i++) {
                    if (base.getPixel(i, j, k) != 0) {
                        ok[label.getPixelInt(i, j, k)] = true;
                    }
                }
            }
        }
        for (int k = 0; k < sizez; k++) {
            for (int j = 0; j < sizey; j++) {
                for (int i = 0; i < sizex; i++) {
                    int pix = label.getPixelInt(i, j, k);
                    if (pix > 0) {
                        if (ok[pix]) {
                            label.setPixel(i, j, k, 255);
                        } else {
                            label.setPixel(i, j, k, 0);
                        }
                    }
                }
            }
        }
    }
    return label;
}