Examples with BitType mpicbg.imglib.type.logic.BitType used on opensource projects

Example 1 with BitType

use of mpicbg.imglib.type.logic.BitType in project TrakEM2 by trakem2.

the class BinaryInterpolation2D method process.

/**
 * The first time, it will prepare the distance transform images, which are computed only once.
 */
public Image<BitType> process(final float weight) {
    synchronized (this) {
        if (null == idt1 || null == idt2) {
            ExecutorService exec = Executors.newFixedThreadPool(Math.min(2, Runtime.getRuntime().availableProcessors()));
            Future<IDT2D> fu1 = exec.submit(new NewITD2D(img1));
            Future<IDT2D> fu2 = exec.submit(new NewITD2D(img2));
            exec.shutdown();
            try {
                this.idt1 = fu1.get();
                this.idt2 = fu2.get();
            } catch (InterruptedException ie) {
                throw new RuntimeException(ie);
            } catch (ExecutionException e) {
                throw new RuntimeException(e);
            }
        }
    }
    // Cannot just img1.createNewImage() because the container may not be able to receive data,
    // such as the ShapeList container.
    final ImageFactory<BitType> f = new ImageFactory<BitType>(new BitType(), new ArrayContainerFactory());
    final Image<BitType> interpolated = f.createImage(new int[] { img1.getDimension(0), img1.getDimension(1) });
    if (img1.getContainer().compareStorageContainerCompatibility(img2.getContainer())) {
        final Cursor<IntType> c1 = idt1.result.createCursor();
        final Cursor<IntType> c2 = idt2.result.createCursor();
        final Cursor<BitType> ci = interpolated.createCursor();
        while (ci.hasNext()) {
            c1.fwd();
            c2.fwd();
            ci.fwd();
            if ((c1.getType().get() * weight) + (c2.getType().get() * (1 - weight)) > 0) {
                ci.getType().set(true);
            }
        }
        c1.close();
        c2.close();
        ci.close();
    } else {
        System.out.println("using option 2");
        final LocalizableByDimCursor<IntType> c1 = idt1.result.createLocalizableByDimCursor();
        final LocalizableByDimCursor<IntType> c2 = idt2.result.createLocalizableByDimCursor();
        final LocalizableByDimCursor<BitType> ci = interpolated.createLocalizableByDimCursor();
        while (ci.hasNext()) {
            ci.fwd();
            c1.setPosition(ci);
            c2.setPosition(ci);
            if (0 <= c1.getType().get() * weight + c2.getType().get() * (1 - weight)) {
                ci.getType().set(true);
            }
        }
        c1.close();
        c2.close();
        ci.close();
    }
    return interpolated;
}

Example 2 with BitType

use of mpicbg.imglib.type.logic.BitType 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;
}