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

Example 56 with Cursor

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

the class SliceTest method setUp.

@Override
@Before
public void setUp() {
    context = new Context(OpService.class);
    ops = context.service(OpService.class);
    in = ArrayImgs.bytes(20, 20, 21);
    out = ArrayImgs.bytes(20, 20, 21);
    for (final Cursor<ByteType> cur = in.cursor(); cur.hasNext(); ) {
        cur.fwd();
        cur.get().set((byte) cur.getIntPosition(2));
    }
}

Example 57 with Cursor

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

the class MorphologyOpsTest method testFillHoles1.

@Test
public void testFillHoles1() {
    Img<BitType> result = ops.create().img(invertedImgWithFilledHoles);
    Img<BitType> inverted = ops.create().img(invertedImgWithFilledHoles);
    ops.image().invert(inverted, imgWithHoles);
    ops.morphology().fillHoles(result, inverted, new DiamondShape(1));
    Cursor<BitType> resultC = result.localizingCursor();
    RandomAccess<BitType> groundTruthRA = invertedImgWithFilledHoles.randomAccess();
    while (resultC.hasNext()) {
        boolean r = resultC.next().get();
        groundTruthRA.setPosition(resultC);
        assertEquals(groundTruthRA.get().get(), r);
    }
}

Example 58 with Cursor

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

the class JoinTest method testJoinComputerAndInplace.

@Test
public void testJoinComputerAndInplace() {
    final Op op = ops.op(DefaultJoinComputerAndInplace.class, out, in, computerOp, inplaceOp);
    op.run();
    // test
    final Cursor<ByteType> c = out.cursor();
    while (c.hasNext()) {
        assertEquals(2, c.next().get());
    }
}

Example 59 with Cursor

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

the class DefaultMarchingCubes method calculate.

@SuppressWarnings({ "unchecked" })
@Override
public DefaultMesh calculate(final RandomAccessibleInterval<T> input) {
    DefaultMesh output = new DefaultMesh();
    ExtendedRandomAccessibleInterval<T, RandomAccessibleInterval<T>> extended = Views.extendValue(input, (T) new BoolType(false));
    Cursor<T> c = Views.interval(extended, new FinalInterval(new long[] { input.min(0) - 1, input.min(1) - 1, input.min(2) - 1 }, new long[] { input.max(0) + 1, input.max(1) + 1, input.max(2) + 1 })).localizingCursor();
    while (c.hasNext()) {
        c.next();
        int cursorX = c.getIntPosition(0);
        int cursorY = c.getIntPosition(1);
        int cursorZ = c.getIntPosition(2);
        Cursor<T> cu = getCube(extended, cursorX, cursorY, cursorZ);
        int i = 0;
        double[] vertex_values = new double[8];
        while (cu.hasNext()) {
            vertex_values[i++] = (cu.next().get()) ? 1 : 0;
        }
        // 6------7
        // /| /|
        // 2-----3 |
        // | 4---|-5
        // |/ |/
        // 0-----1
        vertex_values = mapFlatIterableToLookUpCube(vertex_values);
        // 4------5
        // /| /|
        // 7-----6 |
        // | 0---|-1
        // |/ |/
        // 3-----2
        int cubeindex = getCubeIndex(vertex_values);
        if (EDGE_TABLE[cubeindex] != 0) {
            int[] p0 = new int[] { 0 + cursorX, 0 + cursorY, 1 + cursorZ };
            int[] p1 = new int[] { 1 + cursorX, 0 + cursorY, 1 + cursorZ };
            int[] p2 = new int[] { 1 + cursorX, 0 + cursorY, 0 + cursorZ };
            int[] p3 = new int[] { 0 + cursorX, 0 + cursorY, 0 + cursorZ };
            int[] p4 = new int[] { 0 + cursorX, 1 + cursorY, 1 + cursorZ };
            int[] p5 = new int[] { 1 + cursorX, 1 + cursorY, 1 + cursorZ };
            int[] p6 = new int[] { 1 + cursorX, 1 + cursorY, 0 + cursorZ };
            int[] p7 = new int[] { 0 + cursorX, 1 + cursorY, 0 + cursorZ };
            double[][] vertlist = new double[12][];
            /* Find the vertices where the surface intersects the cube */
            if (0 != (EDGE_TABLE[cubeindex] & 1)) {
                vertlist[0] = interpolatePoint(p0, p1, vertex_values[0], vertex_values[1]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 2)) {
                vertlist[1] = interpolatePoint(p1, p2, vertex_values[1], vertex_values[2]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 4)) {
                vertlist[2] = interpolatePoint(p2, p3, vertex_values[2], vertex_values[3]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 8)) {
                vertlist[3] = interpolatePoint(p3, p0, vertex_values[3], vertex_values[0]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 16)) {
                vertlist[4] = interpolatePoint(p4, p5, vertex_values[4], vertex_values[5]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 32)) {
                vertlist[5] = interpolatePoint(p5, p6, vertex_values[5], vertex_values[6]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 64)) {
                vertlist[6] = interpolatePoint(p6, p7, vertex_values[6], vertex_values[7]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 128)) {
                vertlist[7] = interpolatePoint(p7, p4, vertex_values[7], vertex_values[4]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 256)) {
                vertlist[8] = interpolatePoint(p0, p4, vertex_values[0], vertex_values[4]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 512)) {
                vertlist[9] = interpolatePoint(p1, p5, vertex_values[1], vertex_values[5]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 1024)) {
                vertlist[10] = interpolatePoint(p2, p6, vertex_values[2], vertex_values[6]);
            }
            if (0 != (EDGE_TABLE[cubeindex] & 2048)) {
                vertlist[11] = interpolatePoint(p3, p7, vertex_values[3], vertex_values[7]);
            }
            /* Create the triangle */
            for (i = 0; TRIANGLE_TABLE[cubeindex][i] != -1; i += 3) {
                TriangularFacet face = new TriangularFacet(new Vertex(vertlist[TRIANGLE_TABLE[cubeindex][i + 2]][0], vertlist[TRIANGLE_TABLE[cubeindex][i + 2]][1], vertlist[TRIANGLE_TABLE[cubeindex][i + 2]][2]), new Vertex(vertlist[TRIANGLE_TABLE[cubeindex][i + 1]][0], vertlist[TRIANGLE_TABLE[cubeindex][i + 1]][1], vertlist[TRIANGLE_TABLE[cubeindex][i + 1]][2]), new Vertex(vertlist[TRIANGLE_TABLE[cubeindex][i]][0], vertlist[TRIANGLE_TABLE[cubeindex][i]][1], vertlist[TRIANGLE_TABLE[cubeindex][i]][2]));
                face.getArea();
                output.addFace(face);
            }
        }
    }
    return output;
}

Example 60 with Cursor

use of net.imglib2.Cursor 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);
        }
    }
}