import net.imglib2.Localizable; //导入依赖的package包/类
/**
 * Visualise MSER. Add a 3sigma ellipse overlay to {@link #imp} in the given
 * color. Add a slice to {@link #stack} showing binary mask of MSER region.
 */
public void visualise( final Mser< T > mser, final Color color )
{
	final ByteProcessor byteProcessor = new ByteProcessor( w, h );
	final byte[] pixels = ( byte[] )byteProcessor.getPixels();
	for ( final Localizable l : mser )
	{
		final int x = l.getIntPosition( 0 );
		final int y = l.getIntPosition( 1 );
		pixels[ y * w + x ] = (byte)(255 & 0xff);
	}
	final String label = "" + mser.value();
	stack.addSlice( label, byteProcessor );

	final EllipseRoi ellipse = createEllipse( mser.mean(), mser.cov(), 3 );
	ellipse.setStrokeColor( color );
	ov.add( ellipse );
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
public static void print( PixelListComponentTree< IntType > tree )
{
	for ( PixelListComponent< IntType > component : tree )
	{
		System.out.println( component );

		for ( int r = 0; r < dimensions[1]; ++r )
		{
			System.out.print("| ");
			for ( int c = 0; c < dimensions[0]; ++c )
			{
				boolean set = false;
				for ( Localizable l : component )
					if( l.getIntPosition( 0 ) == c && l.getIntPosition( 1 ) == r )
						set = true;
				System.out.print( set ? "x " : ". " );
			}
			System.out.println("|");
		}

		System.out.println();
	}
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
/**
 * Gaussian Smooth of the input image using intermediate float format.
 * @param <T>
 * @param img
 * @param sigma
 * @return
 */
public static <T extends RealType<T> & NativeType<T>> RandomAccessibleInterval<T> gaussianSmooth(
		RandomAccessibleInterval<T> img, double[] sigma) {
	Interval interval = Views.iterable(img);

	ImgFactory<T> outputFactory = new ArrayImgFactory<T>();
	final long[] dim = new long[ img.numDimensions() ];
	img.dimensions(dim);
	RandomAccessibleInterval<T> output = outputFactory.create( dim,
			img.randomAccess().get().createVariable() );

	final long[] pos = new long[ img.numDimensions() ];
	Arrays.fill(pos, 0);
	Localizable origin = new Point(pos);

	ImgFactory<FloatType> tempFactory = new ArrayImgFactory<FloatType>();
	RandomAccessible<T> input = Views.extendMirrorSingle(img);
	Gauss.inFloat(sigma, input, interval, output, origin, tempFactory);

	return output;
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
public PhaseCorrelationPeak2(Localizable pcmPosition, double phaseCorr)
{
	this.pcmLocation = new Point( pcmPosition );
	this.shift = null;
	this.subpixelPcmLocation = null;
	this.subpixelShift = null;
	this.phaseCorr = phaseCorr;
	this.crossCorr = 0.0;
	this.nPixel = 0;
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
public static < T, U, V > void intersect(
		final RandomAccessible< T > source1,
		final RandomAccessible< U > source2,
		final RandomAccessible< V > target,
		final Shape shape,
		final Localizable seed,
		final Filter< Pair< Pair< T, U >, V >, Pair< Pair< T, U >, V > > filter,
		final Converter< Pair< T, U >, V > writer )
{
	final RandomAccessiblePair.RandomAccess access =
			new RandomAccessiblePair< >( new RandomAccessiblePair< >( source1, source2 ), target ).randomAccess();
	access.setPosition( seed );
	intersect( source1, source2, target, shape, seed, access.get().copy(), filter, writer );
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
@Override
public void move( final Localizable localizable )
{
	for ( int d = 0; d < n; ++d )
	{
		final int distance = localizable.getIntPosition( d );
		position[ d ] += distance;
	}
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
@Override
public void apply( final Localizable source, final Positionable target )
{
	assert source.numDimensions() >= numTargetDimensions && target.numDimensions() >= numTargetDimensions: "Dimensions do not match.";

	for ( int d = 0; d < numTargetDimensions; ++d )
		target.setPosition( apply( source.getIntPosition( d ) ), d );
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
@Override
public void applyInverse( final Positionable source, final Localizable target )
{
	assert source.numDimensions() >= numSourceDimensions && target.numDimensions() >= numSourceDimensions: "Dimensions do not match.";

	for ( int d = 0; d < numSourceDimensions; ++d )
		source.setPosition( applyInverse( target.getIntPosition( d ) ), d );
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
public final void initPositions(final Localizable l, final int offset) {
	for (int d=0; d<maxPositions.length; ++d) {
		final long p = l.getLongPosition(d);
		maxPositions[d] = p + offset;
		minPositions[d] = p + offset;
	}
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
@OpMethod(op = net.imagej.ops.morphology.floodFill.DefaultFloodFill.class)
public <T extends Type<T> & Comparable<T>> RandomAccessibleInterval<T>
	floodFill(final RandomAccessibleInterval<T> out,
		final RandomAccessibleInterval<T> in, final Localizable startPos,
		final Shape structElement)
{
	@SuppressWarnings("unchecked")
	final RandomAccessibleInterval<T> result =
		(RandomAccessibleInterval<T>) ops().run(
			net.imagej.ops.morphology.floodFill.DefaultFloodFill.class, out, in, startPos,
			structElement);
	return result;
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
@Override
public void compute(RandomAccessibleInterval<T> op0, Localizable loc,
	RandomAccessibleInterval<T> r)
{
	final RandomAccess<T> op0c = op0.randomAccess();
	op0c.setPosition(loc);
	final T fillValue = op0c.get().copy();
	FloodFill.fill(Views.extendValue(op0, fillValue), Views.extendValue(r, fillValue), loc, fillValue, structElement, new Filter<Pair<T,T >, Pair<T,T>>() {

		@Override
		public boolean accept(Pair<T, T> t, Pair<T, T> u) {
			return !t.getB().valueEquals(u.getB()) && t.getA().valueEquals(u.getA());
		}
	});
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
@SuppressWarnings({ "rawtypes", "unchecked" })
@Override
public void initialize() {
	createFunc = RAIs.function(ops(), CreateImgFromDimsAndType.class, in(), new BitType());
	floodFillComp = (BinaryComputerOp) Computers.binary(ops(),
		Ops.Morphology.FloodFill.class, RandomAccessibleInterval.class, in(),
		Localizable.class, structElement);
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
public static < T extends NumericType< T > > void gradientBackwardDifference( final RandomAccessible< T > source, final RandomAccessibleInterval< T > gradient, final int dimension, Localizable pos )
	{
		final int n = gradient.numDimensions();

		final long[] min = new long[ n ];
		for ( int d = 0; d < n; ++d ){
			if(d < (n-1)){
				min[d] = pos.getLongPosition(d);
			}else{
				min[d] = dimension;
			}
		}

		final RandomAccess< T > result = gradient.randomAccess();
		final RandomAccess< T > back = source.randomAccess( Intervals.translate( gradient, 1, dimension ) );
		final RandomAccess< T > ctr = source.randomAccess( gradient );

		result.setPosition( min );
		back.setPosition( min );
		back.bck( dimension );
		ctr.setPosition( min );

		// process pixel
		final T t = result.get();
		t.set( ctr.get() );
		t.sub( back.get() );

//		System.out.println(" bd " + result.get());
	}
 

import net.imglib2.Localizable; //导入依赖的package包/类
/**
		 * Compute the partial derivative of source in a particular dimension using a
		 * forward difference scheme.
		 *
		 * @param source
		 *            source image, has to provide valid data in the interval of the
		 *            gradient image plus a one pixel border in dimension.
		 * @param gradient
		 *            output image
		 * @param dimension
		 *            along which dimension the partial derivatives are computed
		 */
		public static < T extends NumericType< T > > void gradientForwardDifference( final RandomAccessible< T > source, final RandomAccessibleInterval< T > gradient, final int dimension, Localizable pos )
		{
			final int n = gradient.numDimensions();

			final long[] min = new long[ n ];
//			System.out.println("pos: " );
			for ( int d = 0; d < n; ++d ){
				if(d < (n-1)){
					min[d] = pos.getLongPosition(d);
				}else{
					min[d] = dimension;
				}
//				System.out.println("  " + min[d]);
			}
//			System.out.println("  ");


			final RandomAccess< T > result = gradient.randomAccess();
			final RandomAccess< T > ctr = source.randomAccess(  gradient );
			final RandomAccess< T > front = source.randomAccess( Intervals.translate( gradient, -1, dimension ) );

			result.setPosition( min );
			
			ctr.setPosition( min );
			
			front.setPosition( min );
			front.fwd( dimension );

			// process pixel
			final T t = result.get();
			t.set( front.get() );
			t.sub( ctr.get() );

//			System.out.println(" fd " + result.get());
			
		}
 

import net.imglib2.Localizable; //导入依赖的package包/类
public void move( final Localizable localizable )
{
	for ( int d = 0; d < n; ++d )
	{
		final long distance = localizable.getLongPosition( d );
		currentPos[ d ] += distance;
		currentMin[ d ] += distance;
		currentMax[ d ] += distance;
	}
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
public void setPosition( final Localizable localizable )
{
	for ( int d = 0; d < n; ++d )
	{
		final long position = localizable.getLongPosition( d );
		currentPos[ d ] = position;
		currentMin[ d ] = position + span.min( d );
		currentMax[ d ] = position + span.max( d );
	}
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
/**
 * 
 * Returns the signed distance function (phi) for an object, reconstructed
 * from the MGDM decomposition
 * 
 * 
 * @param pt the center point
 * @param lb the object
 * @return
 */
public final double labelSignedDistanceFunction(Localizable pt, int lb){
	
	RandomAccess<L> lbra = mgdmlabels.randomAccess();
	lbra.setPosition(pt);
	lbra.setPosition(0, ndims); //TODO double check me
	
	RandomAccess<FloatType> dra = mgdmfunctions.randomAccess();
	dra.setPosition(pt);
	dra.setPosition(0, ndims); //TODO double check me
	
	int l = lbra.get().getInteger();
	double out = 0;
	if( l == lb ){
		out = - dra.get().get();
	}
	
	for (int n = 0; n < nmgdm ; n++) {
		
		lbra.setPosition(n, ndims);
		l = lbra.get().getInteger();
		
		if ( l == lb){ break; }
		dra.setPosition(n, ndims);
		out += dra.get().get(); 
	}
	
	return out;
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
/**
 * 
 * Builds the signed distance function (phi) for an object, reconstructed
 * from the MGDM decomposition in a neighborhood around the input {@link Localizable}.
 * 
 * 
 * @param pt the center point
 * @param lb the object
 * @return
 */
public final void signedDistanceFunctionNeighborhood(Localizable pt, int lb){
	
	int[] pos = new int[ndims];
	pt.localize(pos);
	
	Cursor<DoubleType> c = phi.cursor();
	while(c.hasNext()){
		c.fwd();
		c.get().set( labelSignedDistanceFunction(c, lb));
	}
	
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
@Override
public void move(Localizable localizable)
{
	for (final RandomAccess< T > ra : RAs)
		ra.move( localizable);
}
 

import net.imglib2.Localizable; //导入依赖的package包/类
@Override
public void setPosition(Localizable localizable)
{
	for (final RandomAccess< T > ra : RAs)
		ra.setPosition( localizable );
}