@Test
public void testIterableIntervalView() {
@SuppressWarnings("unchecked")
final IterableInterval<ByteType> res =
(IterableInterval<ByteType>)
ops.run(MapViewIterableIntervalToIterableInterval.class, in, op, new ByteType());
final Cursor<ByteType> iterable = res.cursor();
while (iterable.hasNext()) {
assertEquals((byte) 10, iterable.next().get());
}
}
public static final <T extends RealType<T>> void addGaussianNoiseToImage(
RandomAccessibleInterval<T> img, double sigma_noise) {
IterableInterval<T> iterImg = Views.iterable(img);
Cursor<T> lc = iterImg.localizingCursor();
double val;
T var = iterImg.firstElement().createVariable();
while (lc.hasNext()) {
lc.fwd();
val = Math.max(0, sigma_noise * ran.nextGaussian());
var.setReal(val);
lc.get().add(var);
}
}
public static final <T extends RealType<T>> void addGaussianSpotToImage(
RandomAccessibleInterval<T> img, double[] params) {
IterableInterval<T> iterImg = Views.iterable(img);
Cursor<T> lc = iterImg.localizingCursor();
int nDims = img.numDimensions();
double[] position = new double[nDims];
double val;
T var = iterImg.firstElement().createVariable();
while (lc.hasNext()) {
lc.fwd();
lc.localize(position);
val = gaussian.val(position, params);
var.setReal(val);
lc.get().add(var);
}
}
@Test
public void testListDilateFull() {
final List<Shape> shapes = new ArrayList<Shape>();
shapes.add(new DiamondShape(1));
shapes.add(new DiamondShape(1));
shapes.add(new RectangleShape(1, false));
shapes.add(new HorizontalLineShape(2, 1, false));
@SuppressWarnings("unchecked")
final IterableInterval<ByteType> out1 =
(IterableInterval<ByteType>)
ops.run(ListDilate.class, IterableInterval.class, in, shapes, true);
final Img<ByteType> out2 = Dilation.dilateFull(in, shapes, 1);
final Cursor<ByteType> c1 = out1.cursor();
final Cursor<ByteType> c2 = out2.cursor();
while (c1.hasNext()) assertEquals(c1.next().get(), c2.next().get());
}
@Override
public RealSum call() throws Exception {
final Cursor<FloatType> psiCursor = psiIterable.localizingCursor();
psiCursor.jumpFwd(portion.getStartPosition());
final int m = iterableImgs.size();
if (compatibleIteration) {
final ArrayList<Cursor<FloatType>> cursorWeights = new ArrayList<Cursor<FloatType>>();
final ArrayList<Cursor<FloatType>> cursorImgs = new ArrayList<Cursor<FloatType>>();
for (final IterableInterval<FloatType> img : iterableImgs) {
final Cursor<FloatType> imgCursor = img.cursor();
imgCursor.jumpFwd(portion.getStartPosition());
cursorImgs.add(imgCursor);
}
for (final IterableInterval<FloatType> weight : iterableWeights) {
final Cursor<FloatType> weightCursor = weight.cursor();
weightCursor.jumpFwd(portion.getStartPosition());
cursorWeights.add(weightCursor);
}
for (int j = 0; j < portion.getLoopSize(); ++j)
compatibleLoop(psiCursor, cursorWeights, cursorImgs, realSum, m);
} else {
final ArrayList<RandomAccess<FloatType>> randomAccessWeights =
new ArrayList<RandomAccess<FloatType>>();
final ArrayList<RandomAccess<FloatType>> randomAccessImgs =
new ArrayList<RandomAccess<FloatType>>();
for (final RandomAccessibleInterval<FloatType> img : imgs)
randomAccessImgs.add(img.randomAccess());
for (final RandomAccessibleInterval<FloatType> weight : weights)
randomAccessWeights.add(weight.randomAccess());
for (int j = 0; j < portion.getLoopSize(); ++j)
incompatibleLoop(psiCursor, randomAccessWeights, randomAccessImgs, realSum, m);
}
return realSum;
}
@Override
public void map() {
for (int d = 2; d < position.length; ++d) min[d] = max[d] = position[d];
min[0] = target.min(0);
min[1] = target.min(1);
max[0] = target.max(0);
max[1] = target.max(1);
final FinalInterval sourceInterval = new FinalInterval(min, max);
final Cursor<B> targetCursor = target.cursor();
final RandomAccess<A> sourceRandomAccess = source.randomAccess(sourceInterval);
sourceRandomAccess.setPosition(position);
while (targetCursor.hasNext()) {
final B b = targetCursor.next();
sourceRandomAccess.setPosition(targetCursor.getLongPosition(0), 0);
if (numDimensions > 1) sourceRandomAccess.setPosition(targetCursor.getLongPosition(1), 1);
converter.convert(sourceRandomAccess.get(), b);
}
}
public FirstIteration(
final ImagePortion portion,
final RandomAccessibleInterval<FloatType> psi,
final ArrayList<RandomAccessibleInterval<FloatType>> imgs,
final ArrayList<RandomAccessibleInterval<FloatType>> weights) {
this.portion = portion;
this.psi = psi;
this.imgs = imgs;
this.weights = weights;
this.psiIterable = Views.iterable(psi);
this.iterableImgs = new ArrayList<IterableInterval<FloatType>>();
this.iterableWeights = new ArrayList<IterableInterval<FloatType>>();
this.realSum = new RealSum();
if (imgs.size() != weights.size())
throw new RuntimeException("Number of weights and images must be equal.");
compatibleIteration = true;
for (final RandomAccessibleInterval<FloatType> img : imgs) {
final IterableInterval<FloatType> imgIterable = Views.iterable(img);
if (!psiIterable.iterationOrder().equals(imgIterable.iterationOrder()))
compatibleIteration = false;
this.iterableImgs.add(imgIterable);
}
for (final RandomAccessibleInterval<FloatType> weight : weights) {
final IterableInterval<FloatType> weightIterable = Views.iterable(weight);
if (!psiIterable.iterationOrder().equals(weightIterable.iterationOrder()))
compatibleIteration = false;
for (final IterableInterval<FloatType> imgIterable : iterableImgs)
if (!imgIterable.iterationOrder().equals(weightIterable.iterationOrder()))
compatibleIteration = false;
this.iterableWeights.add(weightIterable);
}
}
@Override
public void compute1(final IterableInterval<I> input, final O output) {
double moment10 = 0;
final Cursor<I> cur = input.localizingCursor();
while (cur.hasNext()) {
cur.fwd();
double x = cur.getDoublePosition(0);
double val = cur.get().getRealDouble();
moment10 += x * val;
}
output.setReal(moment10);
}
@Override
public void compute(final RandomAccessibleInterval<T> input, final IterableInterval<V> output) {
final Cursor<V> cursor = output.localizingCursor();
final RandomAccess<T> access = input.randomAccess();
while (cursor.hasNext()) {
cursor.fwd();
for (int d = 0; d < input.numDimensions(); d++) {
if (d != dim) {
access.setPosition(cursor.getIntPosition(d - d > dim ? -1 : 0), d);
}
}
method.compute(new DimensionIterable(input.dimension(dim), access), cursor.get());
}
}
@Override
public void compute(final IterableInterval<I> input, final O output) {
final double moment00 = moment00Func.compute(input).getRealDouble();
final double moment01 = moment01Func.compute(input).getRealDouble();
final double centerY = moment01 / moment00;
double centralmoment02 = 0;
final Cursor<I> it = input.localizingCursor();
while (it.hasNext()) {
it.fwd();
final double y = it.getDoublePosition(1) - centerY;
final double val = it.get().getRealDouble();
centralmoment02 += val * y * y;
}
output.setReal(centralmoment02);
}