Examples with ShapeList mpicbg.imglib.container.shapelist.ShapeList used on opensource projects

Example 1 with ShapeList

use of mpicbg.imglib.container.shapelist.ShapeList in project TrakEM2 by trakem2.

the class MCCube method getTriangles.

/**
 * Create a list of triangles from the specified image data and the
 * given isovalue.
 * @param volume
 * @param thresh
 * @return
 */
public static final List<Point3f> getTriangles(final Volume volume, final int thresh) {
    final List<Point3f> tri = new ArrayList<Point3f>();
    final Carrier car = new Carrier();
    car.w = volume.xDim;
    car.h = volume.yDim;
    car.d = volume.zDim;
    car.threshold = thresh + 0.5f;
    car.volume = volume;
    if (volume instanceof ImgLibVolume && ((ImgLibVolume) volume).getImage().getContainer() instanceof ShapeList) {
        getShapeListImageTriangles((ImgLibVolume) volume, car, tri);
    } else {
        final MCCube cube = new MCCube();
        for (int z = -1; z < car.d + 1; z += 1) {
            for (int x = -1; x < car.w + 1; x += 1) {
                for (int y = -1; y < car.h + 1; y += 1) {
                    cube.init(x, y, z);
                    cube.computeEdges(car);
                    cube.getTriangles(tri, car);
                }
            }
            IJ.showProgress(z, car.d - 2);
        }
    }
    // convert pixel coordinates
    for (int i = 0; i < tri.size(); i++) {
        final Point3f p = (Point3f) tri.get(i);
        p.x = (float) (p.x * volume.pw + volume.minCoord.x);
        p.y = (float) (p.y * volume.ph + volume.minCoord.y);
        p.z = (float) (p.z * volume.pd + volume.minCoord.z);
    }
    return tri;
}

Example 2 with ShapeList

use of mpicbg.imglib.container.shapelist.ShapeList in project TrakEM2 by trakem2.

the class MCCube method getShapeListImageTriangles.

/**
 * Identical to getTriangles, but iterates only the minimal necessary bounding box, by asking the shapes objects.
 */
private static final void getShapeListImageTriangles(final ImgLibVolume volume, final Carrier car, final List<Point3f> tri) {
    final ShapeList sli = (ShapeList) volume.getImage().getContainer();
    final ArrayList<ArrayList<Shape>> shapeLists = sli.getShapeLists();
    final Area[] sectionAreas = new Area[shapeLists.size()];
    // Create one Area for each section, composed of the addition of all Shape instances
    {
        int next = -1;
        for (final ArrayList<Shape> shapeList : shapeLists) {
            next++;
            if (shapeList.isEmpty()) {
                continue;
            }
            final Area a = new Area(shapeList.get(0));
            for (int i = 1; i < shapeList.size(); i++) {
                a.add(new Area(shapeList.get(i)));
            }
            sectionAreas[next] = a;
        }
    }
    // Fuse Area instances for previous and next sections
    final Area[] scanAreas = new Area[sectionAreas.length];
    for (int i = 0; i < sectionAreas.length; i++) {
        if (null == sectionAreas[i])
            continue;
        final Area a = new Area(sectionAreas[i]);
        if (i - 1 < 0 || null == sectionAreas[i - 1]) {
        } else
            a.add(sectionAreas[i - 1]);
        if (i + 1 > sectionAreas.length - 1 || null == sectionAreas[i + 1]) {
        } else
            a.add(sectionAreas[i + 1]);
        scanAreas[i] = a;
    }
    // Collect the bounds of all subareas in each scanArea:
    final HashMap<Integer, ArrayList<Rectangle>> sectionBounds = new HashMap<Integer, ArrayList<Rectangle>>();
    for (int i = 0; i < scanAreas.length; i++) {
        if (null == scanAreas[i])
            continue;
        final ArrayList<Rectangle> bs = new ArrayList<Rectangle>();
        Polygon pol = new Polygon();
        final float[] coords = new float[6];
        for (final PathIterator pit = scanAreas[i].getPathIterator(null); !pit.isDone(); pit.next()) {
            switch(pit.currentSegment(coords)) {
                case PathIterator.SEG_MOVETO:
                case PathIterator.SEG_LINETO:
                    pol.addPoint((int) coords[0], (int) coords[1]);
                    break;
                case PathIterator.SEG_CLOSE:
                    bs.add(pol.getBounds());
                    pol = new Polygon();
                    break;
                default:
                    System.out.println("WARNING: unhandled seg type.");
                    break;
            }
        }
        sectionBounds.put(i, bs);
    }
    // Add Z paddings on top and bottom
    sectionBounds.put(-1, sectionBounds.get(0));
    sectionBounds.put(car.d, sectionBounds.get(car.d - 1));
    // Scan only relevant areas:
    final MCCube cube = new MCCube();
    for (int z = -1; z < car.d + 1; z += 1) {
        final ArrayList<Rectangle> bs = sectionBounds.get(z);
        if (null == bs || bs.isEmpty())
            continue;
        for (final Rectangle bounds : bs) {
            for (int x = bounds.x - 1; x < bounds.x + bounds.width + 2; x += 1) {
                for (int y = bounds.y - 1; y < bounds.y + bounds.height + 2; y += 1) {
                    cube.init(x, y, z);
                    cube.computeEdges(car);
                    cube.getTriangles(tri, car);
                }
            }
        }
        IJ.showProgress(z, car.d - 2);
    }
}

Example 3 with ShapeList

use of mpicbg.imglib.container.shapelist.ShapeList in project TrakEM2 by trakem2.

the class Patch method addAlphaMaskLocal.

/**
 * Add the given area, in local coordinates, to the alpha mask, using the given fill value.
 */
public void addAlphaMaskLocal(final Area aLocal, int value) {
    if (value < 0)
        value = 0;
    if (value > 255)
        value = 255;
    // 
    CoordinateTransform ct = null;
    if (hasCoordinateTransform() && null == (ct = getCT())) {
        return;
    }
    // When the area is larger than the image, sometimes the area fails to be set at all
    // Also, intersection accelerates calls to contains(x,y) for complex polygons
    final Area a = new Area(new Rectangle(0, 0, (int) (width + 1), (int) (height + 1)));
    a.intersect(aLocal);
    if (M.isEmpty(a)) {
        Utils.log("ROI does not intersect the active image!");
        return;
    }
    ByteProcessor mask = getAlphaMask();
    // Use imglib to bypass all the problems with ShapeROI
    // Create a Shape image with background and the Area on it with 'value'
    final int background = (null != mask && 255 == value) ? 0 : 255;
    final ShapeList<UnsignedByteType> shapeList = new ShapeList<UnsignedByteType>(new int[] { (int) width, (int) height, 1 }, new UnsignedByteType(background));
    shapeList.addShape(a, new UnsignedByteType(value), new int[] { 0 });
    final mpicbg.imglib.image.Image<UnsignedByteType> shapeListImage = new mpicbg.imglib.image.Image<UnsignedByteType>(shapeList, shapeList.getBackground(), "mask");
    ByteProcessor rmask = (ByteProcessor) ImageJFunctions.copyToImagePlus(shapeListImage, ImagePlus.GRAY8).getProcessor();
    if (hasCoordinateTransform()) {
        // inverse the coordinate transform
        final TransformMesh mesh = new TransformMesh(ct, meshResolution, o_width, o_height);
        final TransformMeshMapping mapping = new TransformMeshMapping(mesh);
        rmask = (ByteProcessor) mapping.createInverseMappedImageInterpolated(rmask);
    }
    if (null == mask) {
        // There wasn't a mask, hence just set it
        mask = rmask;
    } else {
        final byte[] b1 = (byte[]) mask.getPixels();
        final byte[] b2 = (byte[]) rmask.getPixels();
        // Whatever is not background in the new mask gets set on the old mask
        for (int i = 0; i < b1.length; i++) {
            // background pixel in new mask
            if (background == (b2[i] & 0xff))
                continue;
            // replace old pixel with new pixel
            b1[i] = b2[i];
        }
    }
    setAlphaMask(mask);
}