Examples with RandomAccessible net.imglib2.RandomAccessible used on opensource projects

Example 11 with RandomAccessible

use of net.imglib2.RandomAccessible in project imagej-ops by imagej.

the class AddDimensionViewTest method addDimensionTest.

@Test
public void addDimensionTest() {
    Img<DoubleType> img = new ArrayImgFactory<DoubleType>().create(new int[] { 10, 10 }, new DoubleType());
    MixedTransformView<DoubleType> il2 = Views.addDimension((RandomAccessible<DoubleType>) img);
    MixedTransformView<DoubleType> opr = ops.transform().addDimensionView((RandomAccessible<DoubleType>) img);
    assertEquals(il2.numDimensions(), opr.numDimensions());
    boolean[] il2Transform = new boolean[3];
    boolean[] oprTransform = new boolean[3];
    il2.getTransformToSource().getComponentZero(il2Transform);
    opr.getTransformToSource().getComponentZero(oprTransform);
    for (int i = 0; i < il2Transform.length; i++) {
        assertEquals(il2Transform[i], oprTransform[i]);
    }
}

Example 12 with RandomAccessible

use of net.imglib2.RandomAccessible in project imagej-ops by imagej.

the class CollapseNumericViewTest method defaultCollapseNumericTest.

@Test
public void defaultCollapseNumericTest() {
    Img<NativeARGBDoubleType> img = new ArrayImgFactory<NativeARGBDoubleType>().create(new int[] { 10, 10 }, new NativeARGBDoubleType());
    CompositeIntervalView<NativeARGBDoubleType, NumericComposite<NativeARGBDoubleType>> il2 = Views.collapseNumeric((RandomAccessibleInterval<NativeARGBDoubleType>) img);
    CompositeIntervalView<NativeARGBDoubleType, NumericComposite<NativeARGBDoubleType>> opr = ops.transform().collapseNumericView((RandomAccessibleInterval<NativeARGBDoubleType>) img);
    assertEquals(il2.numDimensions(), opr.numDimensions());
    CompositeView<NativeARGBDoubleType, NumericComposite<NativeARGBDoubleType>> il2_2 = Views.collapseNumeric((RandomAccessible<NativeARGBDoubleType>) img, 1);
    CompositeView<NativeARGBDoubleType, NumericComposite<NativeARGBDoubleType>> opr_2 = ops.transform().collapseNumericView((RandomAccessible<NativeARGBDoubleType>) img, 1);
    assertEquals(il2_2.numDimensions(), opr_2.numDimensions());
}

Example 13 with RandomAccessible

use of net.imglib2.RandomAccessible in project imagej-ops by imagej.

the class CollapseRealViewTest method defaultCollapseRealTest.

@Test
public void defaultCollapseRealTest() {
    Img<DoubleType> img = new ArrayImgFactory<DoubleType>().create(new int[] { 10, 10 }, new DoubleType());
    CompositeIntervalView<DoubleType, RealComposite<DoubleType>> il2 = Views.collapseReal((RandomAccessibleInterval<DoubleType>) img);
    CompositeIntervalView<DoubleType, RealComposite<DoubleType>> opr = ops.transform().collapseRealView((RandomAccessibleInterval<DoubleType>) img);
    assertEquals(il2.numDimensions(), opr.numDimensions());
    CompositeView<DoubleType, RealComposite<DoubleType>> il2_2 = Views.collapseReal((RandomAccessible<DoubleType>) img, 1);
    CompositeView<DoubleType, RealComposite<DoubleType>> opr_2 = ops.transform().collapseRealView((RandomAccessible<DoubleType>) img, 1);
    assertEquals(il2_2.numDimensions(), opr_2.numDimensions());
}

Example 14 with RandomAccessible

use of net.imglib2.RandomAccessible in project imagej-ops by imagej.

the class CollapseViewTest method collapseRATest.

@Test
public void collapseRATest() {
    Img<DoubleType> img = new ArrayImgFactory<DoubleType>().create(new int[] { 10, 10, 10 }, new DoubleType());
    CompositeView<DoubleType, ? extends GenericComposite<DoubleType>> il2 = Views.collapse((RandomAccessible<DoubleType>) img);
    CompositeView<DoubleType, ? extends GenericComposite<DoubleType>> opr = ops.transform().collapseView((RandomAccessible<DoubleType>) img);
    assertEquals(il2.numDimensions(), opr.numDimensions());
}

Example 15 with RandomAccessible

use of net.imglib2.RandomAccessible in project imagej-ops by imagej.

the class Watershed method compute.

@Override
public void compute(final RandomAccessibleInterval<T> in, final ImgLabeling<Integer, IntType> out) {
    final RandomAccess<T> raIn = in.randomAccess();
    RandomAccess<B> raMask = null;
    if (mask != null) {
        raMask = mask.randomAccess();
    }
    // stores the size of each dimension
    final long[] dimensSizes = new long[in.numDimensions()];
    in.dimensions(dimensSizes);
    // calculates the number of points in the n-d space
    long numPixels = Intervals.numElements(in);
    // the pixels indices are stored in an array, which is sorted depending
    // on the pixel values
    final List<Long> imiList = new ArrayList<>();
    if (mask != null) {
        final Cursor<Void> c = Regions.iterable(mask).localizingCursor();
        while (c.hasNext()) {
            c.next();
            imiList.add(IntervalIndexer.positionToIndex(c, in));
        }
    } else {
        for (long i = 0; i < numPixels; i++) {
            imiList.add(i);
        }
    }
    final Long[] imi = imiList.toArray(new Long[imiList.size()]);
    /*
		 * Sort the pixels of imi in the increasing order of their grey value
		 * (only the pixel indices are stored)
		 */
    Arrays.sort(imi, new Comparator<Long>() {

        @Override
        public int compare(final Long o1, final Long o2) {
            IntervalIndexer.indexToPosition(o1, in, raIn);
            final T value = raIn.get().copy();
            IntervalIndexer.indexToPosition(o2, in, raIn);
            return value.compareTo(raIn.get());
        }
    });
    // lab and dist store the values calculated after each phase
    final RandomAccessibleInterval<IntType> lab = ops().create().img(in, new IntType());
    // extend border to be able to do a quick check, if a voxel is inside
    final ExtendedRandomAccessibleInterval<IntType, RandomAccessibleInterval<IntType>> labExt = Views.extendBorder(lab);
    final OutOfBounds<IntType> raLab = labExt.randomAccess();
    final RandomAccessibleInterval<IntType> dist = ops().create().img(in, new IntType());
    final RandomAccess<IntType> raDist = dist.randomAccess();
    // initial values
    for (final IntType pixel : Views.flatIterable(lab)) {
        pixel.set(INIT);
    }
    int current_label = 0;
    int current_dist;
    final ArrayList<Long> fifo = new ArrayList<>();
    // RandomAccess for Neighborhoods
    final Shape shape;
    if (useEightConnectivity) {
        shape = new RectangleShape(1, true);
    } else {
        shape = new DiamondShape(1);
    }
    final RandomAccessible<Neighborhood<T>> neighborhoods = shape.neighborhoodsRandomAccessible(in);
    final RandomAccess<Neighborhood<T>> raNeighbor = neighborhoods.randomAccess();
    /*
		 * Start flooding
		 */
    for (int j = 0; j < imi.length; j++) {
        IntervalIndexer.indexToPosition(imi[j], in, raIn);
        final T actualH = raIn.get().copy();
        int i = j;
        while (actualH.compareTo(raIn.get()) == 0) {
            final long p = imi[i];
            IntervalIndexer.indexToPosition(p, in, raIn);
            raLab.setPosition(raIn);
            raLab.get().set(MASK);
            raNeighbor.setPosition(raIn);
            final Cursor<T> neighborHood = raNeighbor.get().cursor();
            while (neighborHood.hasNext()) {
                neighborHood.fwd();
                raLab.setPosition(neighborHood);
                if (!raLab.isOutOfBounds()) {
                    final int f = raLab.get().get();
                    if ((f > 0) || (f == WSHED)) {
                        raDist.setPosition(raIn);
                        raDist.get().set(1);
                        fifo.add(p);
                        break;
                    }
                }
            }
            i++;
            if (i == imi.length) {
                break;
            }
            IntervalIndexer.indexToPosition(imi[i], in, raIn);
        }
        current_dist = 1;
        // add fictitious pixel
        fifo.add(-1l);
        while (true) {
            long p = fifo.remove(0);
            if (p == -1) {
                if (fifo.isEmpty()) {
                    break;
                }
                fifo.add(-1l);
                current_dist++;
                p = fifo.remove(0);
            }
            IntervalIndexer.indexToPosition(p, in, raNeighbor);
            final Cursor<T> neighborHood = raNeighbor.get().cursor();
            raLab.setPosition(raNeighbor);
            int labp = raLab.get().get();
            final long[] posNeighbor = new long[neighborHood.numDimensions()];
            while (neighborHood.hasNext()) {
                neighborHood.fwd();
                neighborHood.localize(posNeighbor);
                raLab.setPosition(posNeighbor);
                if (!raLab.isOutOfBounds()) {
                    raDist.setPosition(posNeighbor);
                    final int labq = raLab.get().get();
                    final int distq = raDist.get().get();
                    if ((distq < current_dist) && ((labq > 0) || (labq == WSHED))) {
                        // the watersheds
                        if (labq > 0) {
                            if ((labp == MASK) || (labp == WSHED)) {
                                labp = labq;
                            } else {
                                if (labp != labq) {
                                    labp = WSHED;
                                }
                            }
                        } else {
                            if (labp == MASK) {
                                labp = WSHED;
                            }
                        }
                        raLab.setPosition(raNeighbor);
                        raLab.get().set(labp);
                    } else {
                        if ((labq == MASK) && (distq == 0)) {
                            raDist.setPosition(posNeighbor);
                            raDist.get().set(current_dist + 1);
                            fifo.add(IntervalIndexer.positionToIndex(posNeighbor, dimensSizes));
                        }
                    }
                }
            }
        }
        // checks if new minima have been discovered
        IntervalIndexer.indexToPosition(imi[j], in, raIn);
        i = j;
        while (actualH.compareTo(raIn.get()) == 0) {
            final long p = imi[i];
            IntervalIndexer.indexToPosition(p, dist, raDist);
            // the distance associated with p is reseted to 0
            raDist.get().set(0);
            raLab.setPosition(raDist);
            if (raLab.get().get() == MASK) {
                current_label++;
                fifo.add(p);
                raLab.get().set(current_label);
                while (!fifo.isEmpty()) {
                    final long q = fifo.remove(0);
                    IntervalIndexer.indexToPosition(q, in, raNeighbor);
                    final Cursor<T> neighborHood = raNeighbor.get().cursor();
                    final long[] posNeighbor = new long[neighborHood.numDimensions()];
                    while (neighborHood.hasNext()) {
                        neighborHood.fwd();
                        neighborHood.localize(posNeighbor);
                        raLab.setPosition(posNeighbor);
                        if (!raLab.isOutOfBounds()) {
                            final long r = IntervalIndexer.positionToIndex(posNeighbor, dimensSizes);
                            if (raLab.get().get() == MASK) {
                                fifo.add(r);
                                raLab.get().set(current_label);
                            }
                        }
                    }
                }
            }
            i++;
            if (i == imi.length) {
                break;
            }
            IntervalIndexer.indexToPosition(imi[i], in, raIn);
        }
        j = i - 1;
    }
    /*
		 * Draw output and remove as the case may be the watersheds
		 */
    final Cursor<LabelingType<Integer>> cursorOut = out.cursor();
    while (cursorOut.hasNext()) {
        cursorOut.fwd();
        boolean maskValue = true;
        if (mask != null) {
            raMask.setPosition(cursorOut);
            if (!raMask.get().get()) {
                maskValue = false;
            }
        }
        raLab.setPosition(cursorOut);
        if (!maskValue) {
            cursorOut.get().clear();
        } else {
            if (!drawWatersheds && raLab.get().get() == WSHED) {
                raNeighbor.setPosition(cursorOut);
                final Cursor<T> neighborHood = raNeighbor.get().cursor();
                int newLab = WSHED;
                while (neighborHood.hasNext()) {
                    neighborHood.fwd();
                    raLab.setPosition(neighborHood);
                    if (!raLab.isOutOfBounds()) {
                        newLab = raLab.get().get();
                        if (newLab > WSHED) {
                            break;
                        }
                    }
                }
                if (newLab == WSHED) {
                    cursorOut.get().clear();
                } else {
                    cursorOut.get().add(newLab);
                }
            } else {
                cursorOut.get().add(raLab.get().get());
            }
        }
    }
    /*
		 * Merge already present labels before calculation of watershed
		 */
    if (out() != null) {
        final Cursor<LabelingType<Integer>> cursor = out().cursor();
        final RandomAccess<LabelingType<Integer>> raOut = out.randomAccess();
        while (cursor.hasNext()) {
            cursor.fwd();
            raOut.setPosition(cursor);
            final List<Integer> labels = new ArrayList<>();
            cursor.get().iterator().forEachRemaining(labels::add);
            raOut.get().addAll(labels);
        }
    }
}