Examples with BinaryInterpolation2D ini.trakem2.imaging.BinaryInterpolation2D used on opensource projects

Example 1 with BinaryInterpolation2D

use of ini.trakem2.imaging.BinaryInterpolation2D in project TrakEM2 by trakem2.

the class AreaUtils method manyToManyInterpolation.

public static final Area[] manyToManyInterpolation(final Area a1, final Area a2, final int nInterpolates) throws InterruptedException, ExecutionException {
    final Rectangle b = a1.getBounds();
    b.add(a2.getBounds());
    final AffineTransform translate = new AffineTransform(1, 0, 0, 1, -b.x, -b.y);
    final ShapeList<BitType> shapeList1 = new ShapeListCached<BitType>(new int[] { b.width, b.height }, new BitType(false), 32);
    shapeList1.addShape(a1.createTransformedArea(translate), new BitType(true), new int[] { 0 });
    final Image<BitType> img1 = new Image<BitType>(shapeList1, shapeList1.getBackground(), "ShapeListContainer");
    final ShapeList<BitType> shapeList2 = new ShapeListCached<BitType>(new int[] { b.width, b.height }, new BitType(false), 32);
    shapeList2.addShape(a2.createTransformedArea(translate), new BitType(true), new int[] { 0 });
    final Image<BitType> img2 = new Image<BitType>(shapeList2, shapeList2.getBackground(), "ShapeListContainer");
    final float inc = 1.0f / (nInterpolates + 1);
    final BinaryInterpolation2D interpol = new BinaryInterpolation2D(img1, img2, inc);
    if (!interpol.checkInput()) {
        System.out.println("Error: " + interpol.getErrorMessage());
        return null;
    }
    final Area[] as = new Area[nInterpolates];
    final AffineTransform back = new AffineTransform(1, 0, 0, 1, b.x, b.y);
    // TODO parallelize, which needs the means to call process() in parallel too--currently it cannot,
    // the result would get overwritten.
    final ExecutorService exec = Executors.newFixedThreadPool(Math.min(nInterpolates, Runtime.getRuntime().availableProcessors()));
    final ArrayList<Future<Area>> fus = new ArrayList<Future<Area>>();
    try {
        for (int i = 1; i <= nInterpolates; i++) {
            final float weight = 1 - inc * i;
            fus.add(exec.submit(new Callable<Area>() {

                @Override
                public Area call() throws Exception {
                    final Image<BitType> imb = interpol.process(weight);
                    final ImagePlus imp = ImageJFunctions.copyToImagePlus(imb, ImagePlus.GRAY8);
                    // BitType gets copied to 0 and 255 in 8-bit ByteProcessor
                    final ThresholdToSelection ts = new ThresholdToSelection();
                    ts.setup("", imp);
                    final ImageProcessor ip = imp.getProcessor();
                    ip.setThreshold(1, 255, ImageProcessor.NO_LUT_UPDATE);
                    ts.run(ip);
                    final Roi roi = imp.getRoi();
                    return null == roi ? new Area() : M.getArea(roi).createTransformedArea(back);
                }
            }));
        }
        int i = 0;
        for (final Future<Area> fu : fus) {
            as[i++] = fu.get();
        }
    } catch (final Throwable t) {
        IJError.print(t);
    } finally {
        exec.shutdown();
    }
    return as;
}

Example 2 with BinaryInterpolation2D

use of ini.trakem2.imaging.BinaryInterpolation2D in project TrakEM2 by trakem2.

the class AreaList method interpolate.

/**
 * Interpolate areas between the given first and last layers,
 * both of which must contain an area.
 *
 * @return false if the interpolation could not be done.
 * @throws Exception
 */
public boolean interpolate(final Layer first, final Layer last, final boolean always_use_distance_map) throws Exception {
    int i1 = layer_set.indexOf(first);
    int i2 = layer_set.indexOf(last);
    if (i1 > i2) {
        final int tmp = i1;
        i1 = i2;
        i2 = tmp;
    }
    final List<Layer> range = layer_set.getLayers().subList(i1, i2 + 1);
    Area start = null;
    int istart = 0;
    int inext = -1;
    final HashSet<Layer> touched = new HashSet<Layer>();
    for (final Layer la : range) {
        inext++;
        final Area next = getArea(la);
        if (null == next || next.isEmpty())
            continue;
        if (null == start || 0 == inext - istart - 1) {
            // skip for first area or for no space in between
            start = next;
            istart = inext;
            continue;
        }
        // Interpolate from start to next
        Area[] as = always_use_distance_map ? null : AreaUtils.singularInterpolation(start, next, inext - istart - 1);
        if (null == as) {
            // NOT SINGULAR: must use BinaryInterpolation2D
            as = AreaUtils.manyToManyInterpolation(start, next, inext - istart - 1);
        }
        if (null != as) {
            for (int k = 0; k < as.length; k++) {
                final Layer la2 = range.get(k + istart + 1);
                addArea(la2.getId(), as[k]);
                touched.add(la2);
            }
        }
        // Prepare next interval
        start = next;
        istart = inext;
    }
    for (final Layer la : touched) calculateBoundingBox(la);
    return true;
}