Java Code Examples for net.imglib2.IterableInterval#localizingCursor()

@Override
public void compute(final UnaryFunctionOp<long[], N> op,
	final IterableInterval<T> output)
{

	final Cursor<T> c = output.localizingCursor();
	final long[] pos = new long[output.numDimensions()];

	// loop through all pixels, set the current position and call the op
	while (c.hasNext()) {
		c.fwd();
		c.localize(pos);

		for (int i = 0; i < output.numDimensions(); i++) {

			op.calculate(pos);

			c.get().setReal(op.calculate(pos).floatValue());

		}

	}
}
 

@Override
public void compute(final IterableInterval<I> input, final O output) {

	double moment11 = 0;

	final Cursor<I> cur = input.localizingCursor();
	while (cur.hasNext()) {
		cur.fwd();
		double x = cur.getDoublePosition(0);
		double y = cur.getDoublePosition(1);
		double val = cur.get().getRealDouble();
		moment11 += x * y * val;
	}

	output.setReal(moment11);
}
 

public static <I1, I2, O> void map(final IterableInterval<I1> a,
	final RandomAccessibleInterval<I2> b, final IterableInterval<O> c,
	final BinaryComputerOp<I1, I2, O> op, final long startIndex,
	final long stepSize, final long numSteps)
{
	if (numSteps <= 0) return;
	final Cursor<I1> aCursor = a.localizingCursor();
	final RandomAccess<I2> bAccess = b.randomAccess();
	final Cursor<O> cCursor = c.cursor();

	for (long ctr = 0; ctr < numSteps; ctr++) {
		final long m = ctr == 0 ? startIndex + 1 : stepSize;
		aCursor.jumpFwd(m);
		cCursor.jumpFwd(m);
		bAccess.setPosition(aCursor);
		op.compute(aCursor.get(), bAccess.get(), cCursor.get());
	}
}
 

@Override
public void compute(final IterableInterval<I> input, final O output) {
	final double moment00 = moment00Func.calculate(input).getRealDouble();
	final double moment01 = moment01Func.calculate(input).getRealDouble();
	
	final double centerY = moment01 / moment00;

	double centralmoment03 = 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();

		centralmoment03 += val * y * y * y;
	}

	output.setReal(centralmoment03);
}
 

public static <I1, I2, O> void map(final IterableInterval<I1> a,
	final IterableInterval<I2> b, final RandomAccessibleInterval<O> c,
	final BinaryComputerOp<I1, I2, O> op, final long startIndex,
	final long stepSize, final long numSteps)
{
	if (numSteps <= 0) return;
	final Cursor<I1> aCursor = a.localizingCursor();
	final Cursor<I2> bCursor = b.cursor();
	final RandomAccess<O> cAccess = c.randomAccess();

	for (long ctr = 0; ctr < numSteps; ctr++) {
		final long m = ctr == 0 ? startIndex + 1 : stepSize;
		aCursor.jumpFwd(m);
		bCursor.jumpFwd(m);
		cAccess.setPosition(aCursor);
		op.compute(aCursor.get(), bCursor.get(), cAccess.get());
	}
}
 

@Override
public void compute(final IterableInterval<I> input, final O output) {
	final double moment00 = moment00Func.calculate(input).getRealDouble();
	final double moment01 = moment01Func.calculate(input).getRealDouble();
	final double moment10 = moment10Func.calculate(input).getRealDouble();
	final double centerX = moment10 / moment00;
	final double centerY = moment01 / moment00;

	double centralmoment12 = 0;

	final Cursor<I> it = input.localizingCursor();
	while (it.hasNext()) {
		it.fwd();
		final double x = it.getDoublePosition(0) - centerX;
		final double y = it.getDoublePosition(1) - centerY;
		final double val = it.get().getRealDouble();

		centralmoment12 += val * x * y * y;
	}

	output.setReal(centralmoment12);
}
 

public static <A, I> void inplace(final IterableInterval<A> arg,
	final RandomAccessibleInterval<I> in, final BinaryInplace1Op<A, I, A> op,
	final long startIndex, final long stepSize, final long numSteps)
{
	if (numSteps <= 0) return;
	final Cursor<A> argCursor = arg.localizingCursor();
	final RandomAccess<I> inAccess = in.randomAccess();

	for (long ctr = 0; ctr < numSteps; ctr++) {
		argCursor.jumpFwd(ctr == 0 ? startIndex + 1 : stepSize);
		inAccess.setPosition(argCursor);
		op.mutate1(argCursor.get(), inAccess.get());
	}
}
 

public static <T extends RealType<T>> String ascii(
	final IterableInterval<T> image, final T min, final T max)
{
	final long dim0 = image.dimension(0);
	final long dim1 = image.dimension(1);
	// TODO: Check bounds.
	final int w = (int) (dim0 + 1);
	final int h = (int) dim1;

	// span = max - min
	final T span = max.copy();
	span.sub(min);

	// allocate ASCII character array
	final char[] c = new char[w * h];
	for (int y = 1; y <= h; y++) {
		c[w * y - 1] = '\n'; // end of row
	}

	// loop over all available positions
	final Cursor<T> cursor = image.localizingCursor();
	final int[] pos = new int[image.numDimensions()];
	final T tmp = image.firstElement().copy();
	while (cursor.hasNext()) {
		cursor.fwd();
		cursor.localize(pos);
		final int index = w * pos[1] + pos[0];

		// normalized = (value - min) / (max - min)
		tmp.set(cursor.get());
		tmp.sub(min);
		final double normalized = tmp.getRealDouble() / span.getRealDouble();

		final int charLen = CHARS.length();
		final int charIndex = (int) (charLen * normalized);
		c[index] = CHARS.charAt(charIndex < charLen ? charIndex : charLen - 1);
	}

	return new String(c);
}
 

public static <I1, I2, O> void map(final RandomAccessibleInterval<I1> a,
	final IterableInterval<I2> b, final IterableInterval<O> c,
	final BinaryComputerOp<I1, I2, O> op)
{
	final RandomAccess<I1> aAccess = a.randomAccess();
	final Cursor<I2> bCursor = b.localizingCursor();
	final Cursor<O> cCursor = c.cursor();
	while (bCursor.hasNext()) {
		bCursor.fwd();
		aAccess.setPosition(bCursor);
		op.compute(aAccess.get(), bCursor.get(), cCursor.next());
	}
}
 

public static <I1, I2, O extends I1> void inplace(
	final IterableInterval<O> arg, final RandomAccessibleInterval<I2> in,
	final BinaryInplace1Op<I1, I2, O> op)
{
	final Cursor<O> argCursor = arg.localizingCursor();
	final RandomAccess<I2> inAccess = in.randomAccess();
	while (argCursor.hasNext()) {
		argCursor.fwd();
		inAccess.setPosition(argCursor);
		op.mutate1(argCursor.get(), inAccess.get());
	}
}
 

public static <I, O> void map(final IterableInterval<I> a,
	final RandomAccessibleInterval<O> b, final UnaryComputerOp<I, O> op,
	final long startIndex, final long stepSize, final long numSteps)
{
	if (numSteps <= 0) return;
	final Cursor<I> aCursor = a.localizingCursor();
	final RandomAccess<O> bAccess = b.randomAccess();

	for (long ctr = 0; ctr < numSteps; ctr++) {
		aCursor.jumpFwd(ctr == 0 ? startIndex + 1 : stepSize);
		bAccess.setPosition(aCursor);
		op.compute(aCursor.get(), bAccess.get());
	}
}
 

public static <I, O> void map(final IterableInterval<I> a,
	final RandomAccessibleInterval<O> b, final UnaryComputerOp<I, O> op)
{
	final Cursor<I> aCursor = a.localizingCursor();
	final RandomAccess<O> bAccess = b.randomAccess();
	while (aCursor.hasNext()) {
		aCursor.fwd();
		bAccess.setPosition(aCursor);
		op.compute(aCursor.get(), bAccess.get());
	}
}
 

@Override
public void compute(final RandomAccessibleInterval<T> op,
	final RandomAccessibleInterval<T> r)
{
	final IterableInterval<T> iterOp = Views.flatIterable(op);
	final IterableInterval<T> iterR = Views.flatIterable(r);

	long[] dim = new long[r.numDimensions()];
	r.dimensions(dim);
	Cursor<T> rc = iterR.cursor();
	Cursor<T> opc = iterOp.localizingCursor();
	// Fill with non background marker
	while (rc.hasNext()) {
		rc.next().setOne();
	}

	rc.reset();
	boolean border;
	// Flood fill from every background border voxel
	while (rc.hasNext()) {
		rc.next();
		opc.next();
		if (rc.get().get() && !opc.get().get()) {
			border = false;
			for (int i = 0; i < r.numDimensions(); i++) {
				if (rc.getLongPosition(i) == 0 || rc.getLongPosition(i) == dim[i] -
					1)
				{
					border = true;
					break;
				}
			}
			if (border) {
				floodFillComp.compute(op, rc, r);
			}
		}
	}
}
 

public static <A, I> void inplace(final RandomAccessibleInterval<A> arg,
	final IterableInterval<I> in, final BinaryInplace1Op<A, I, A> op,
	final long startIndex, final long stepSize, final long numSteps)
{
	if (numSteps <= 0) return;
	final RandomAccess<A> argAccess = arg.randomAccess();
	final Cursor<I> inCursor = in.localizingCursor();

	for (long ctr = 0; ctr < numSteps; ctr++) {
		inCursor.jumpFwd(ctr == 0 ? startIndex + 1 : stepSize);
		argAccess.setPosition(inCursor);
		op.mutate1(argAccess.get(), inCursor.get());
	}
}
 

public static <I, O> void map(final RandomAccessibleInterval<I> a,
	final IterableInterval<O> b, final UnaryComputerOp<I, O> op,
	final long startIndex, final long stepSize, final long numSteps)
{
	if (numSteps <= 0) return;
	final RandomAccess<I> aAccess = a.randomAccess();
	final Cursor<O> bCursor = b.localizingCursor();

	for (long ctr = 0; ctr < numSteps; ctr++) {
		bCursor.jumpFwd(ctr == 0 ? startIndex + 1 : stepSize);
		aAccess.setPosition(bCursor);
		op.compute(aAccess.get(), bCursor.get());
	}
}
 

@Override
public void compute(final IterableInterval<I> input, final O output) {

	double moment01 = 0;

	final Cursor<I> cur = input.localizingCursor();
	while (cur.hasNext()) {
		cur.fwd();
		double y = cur.getDoublePosition(1);
		double val = cur.get().getRealDouble();
		moment01 += y * val;
	}

	output.setReal(moment01);
}
 

@Override
public void compute(final IterableInterval<I> input, final O output) {

	double moment00 = 0;

	final Cursor<I> cur = input.localizingCursor();
	while (cur.hasNext()) {
		cur.fwd();
		double val = cur.get().getRealDouble();
		moment00 += val;
	}

	output.setReal(moment00);
}
 

@Override
public void compute(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 ZernikeMoment calculate(final IterableInterval<T> ii) {

	final double width2 = (ii.dimension(0) - 1) / 2.0;
	final double height2 = (ii.dimension(1) - 1) / 2.0;

	final double centerX = width2 + ii.min(0);
	final double centerY = height2 + ii.min(1);

	final double radius = Math.sqrt(width2 * width2 + height2 * height2);

	// Compute pascal's triangle for binomal coefficients: d[x][y] equals (x
	// over y)
	final double[][] d = computePascalsTriangle(order);

	// initialize zernike moment
	final ZernikeMoment moment = initZernikeMoment(order, repetition, d);

	// get the cursor of the iterable interval
	final Cursor<? extends RealType<?>> cur = ii.localizingCursor();

	// run over iterable interval
	while (cur.hasNext()) {
		cur.fwd();

		// get 2d centered coordinates
		final int x = (int) (cur.getIntPosition(0) - ii.min(0));
		final int y = (int) (cur.getIntPosition(1) - ii.min(1));

		final double xm = (x - centerX) / radius;
		final double ym = (y - centerY) / radius;

		final double r = Math.sqrt(xm * xm + ym * ym);
		if (r <= 1 && cur.get().getRealDouble() != 0.0) {
			// calculate theta for this position
			final double theta = Math.atan2(xm, ym);
			moment.getZm().add(multiplyExp(1, moment.getP().evaluate(r), theta, moment.getM()));
		}
	}
	// normalization
	normalize(moment.getZm(), moment.getN(), getNumberOfPixelsInUnitDisk(radius));
	return moment;
}
 

@Override
public double[][] calculate(final IterableInterval<T> input) {

	double[][] matrix = new double[nrGreyLevels][nrGreyLevels];

	final Cursor<T> cursor = input.localizingCursor();
  final Pair<T, T> minMax = minmax.calculate(input);

	double localMin = minMax.getA().getRealDouble();
	double localMax = minMax.getB().getRealDouble();

	final int[][][] pixels = new int[(int) input.dimension(2)][(int) input
			.dimension(1)][(int) input.dimension(0)];

	final int minimumX = (int) input.min(0);
	final int minimumY = (int) input.min(1);
	final int minimumZ = (int) input.min(2);
	
	final double diff = localMax - localMin;
	while (cursor.hasNext()) {
		cursor.fwd();
		pixels[cursor.getIntPosition(2) - minimumZ][cursor
				.getIntPosition(1) - minimumY][cursor
				.getIntPosition(0) - minimumX] = (int) (((cursor
				.get().getRealDouble() - localMin) / diff) * (nrGreyLevels - 1));
	}

	
	final double orientationAtX = orientation.getValueAtDim(0) * distance;
	final double orientationAtY = orientation.getValueAtDim(1) * distance;
	final double orientationAtZ = orientation.getValueAtDim(2) * distance;

	int nrPairs = 0;
	for (int z = 0; z < pixels.length; z++) {
		for (int y = 0; y < pixels[z].length; y++) {
			for (int x = 0; x < pixels[z][y].length; x++) {

				// ignore pixels not in mask
				if (pixels[z][y][x] == Integer.MAX_VALUE) {
					continue;
				}

				// get second pixel
				final int sx = (int) (x + orientationAtX);
				final int sy = (int) (y + orientationAtY);
				final int sz = (int) (z + orientationAtZ);

				// second pixel in interval and mask
				if (sx >= 0 && sy >= 0 && sz >= 0 && sz < pixels.length
						&& sy < pixels[sz].length
						&& sx < pixels[sz][sy].length
						&& pixels[sz][sy][sx] != Integer.MAX_VALUE) {

					matrix[pixels[z][y][x]][pixels[sz][sy][sx]]++;
					nrPairs++;

				}
			}
		}
	}

	// normalize matrix
	if (nrPairs > 0) {
		double divisor = 1.0 / nrPairs;
		for (int row = 0; row < matrix.length; row++) {
			for (int col = 0; col < matrix[row].length; col++) {
				matrix[row][col] *= divisor;
			}
		}
	}

	return matrix;
}