Java Cursor类代码示例

import net.imglib2.Cursor; //导入依赖的package包/类
/**
 * Relabel the label map according to the tree labeling.
 * @param threshold , all pixel below threshold are set to 0 
 * @param percentFlooding , percent of the peak that will be flooded  (percent between label maximum and the threshold) 
 * @return a label image corresponding to the current tree labeling, threshold, percentFlooding parameters
 */
public Img<IntType> getLabelMap( float hMin, float threshold, float percentFlooding, boolean keepOrphanPeak){
	
	intensity = (IterableInterval<T>) intensity0;
	
	int nDims = segmentMap0.numDimensions();
	long[] dims = new long[nDims];
	segmentMap0.dimensions(dims);
	segmentMap = segmentMap0.factory().create(dims, segmentMap0.firstElement().createVariable() );
	Cursor<IntType> cursor = segmentMap.cursor();
	Cursor<IntType> cursor0 = segmentMap0.cursor();
	while(cursor0.hasNext()){
		cursor.next().set( cursor0.next().get() );
	}
	
	
	Img<IntType> labelMap = fillLabelMap2(hMin, threshold, percentFlooding, keepOrphanPeak);
	
	return labelMap;
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
public HWatershedLabeling(Img<T> input, float threshold, Connectivity connectivity)
{
	int nDims = input.numDimensions();
	long[] dims = new long[nDims];
	input.dimensions(dims);
	ImgFactory<IntType> imgFactoryIntType=null;
	try {
		imgFactoryIntType = input.factory().imgFactory( new IntType() );
	} catch (IncompatibleTypeException e) {
		e.printStackTrace();
	}
	
	if ( imgFactoryIntType != null )
	{
		this.labelMapMaxTree = imgFactoryIntType.create(dims, new IntType(0));
		Cursor<IntType> c_label = labelMapMaxTree.cursor();
		Cursor<T>       c_input = input.cursor();
		while( c_input.hasNext() )
		{
			c_label.next().setInteger( (int) c_input.next().getRealFloat() );
		}
	}
	
	this.threshold = threshold;
	this.connectivity = connectivity;
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
/**
 * @throws java.lang.Exception
 */
@BeforeClass
public static void setUpBeforeClass() throws Exception {

	final File testDir = new File(testDirPath);
	testDir.mkdirs();
	if (!(testDir.exists() && testDir.isDirectory()))
		throw new IOException("Could not create benchmark directory for HDF5Utils benchmark.");

	data = new short[64 * 64 * 64];
	final ImagePlus imp = new Opener().openURL("https://imagej.nih.gov/ij/images/t1-head-raw.zip");
	final ImagePlusImg<UnsignedShortType, ?> img = (ImagePlusImg<UnsignedShortType, ?>)(Object)ImagePlusImgs.from(imp);
	final Cursor<UnsignedShortType> cursor = Views.flatIterable(Views.interval(img, new long[]{100, 100, 30}, new long[]{163, 163, 93})).cursor();
	for (int i = 0; i < data.length; ++i)
		data[i] = (short)cursor.next().get();

	n5 = new N5FSWriter(testDirPath);
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
/**
 * Compute the partial derivative of source in a particular dimension.
 *
 * @param source
 *            source image, has to provide valid data in the interval of the
 *            gradient image plus a one pixel border in dimension.
 * @param target
 *            output image, the partial derivative of source in the
 *            specified dimension.
 * @param dimension
 *            along which dimension the partial derivatives are computed
 * @param <T> pixel type source
 * @param <S> pixel type target
 */
public static < T extends RealType< T >, S extends RealType< S > > void gradient(
		final RandomAccessible< T > source,
		final RandomAccessibleInterval< S > target,
		final int dimension )
{
	final Cursor< T > front = Views.flatIterable(
			Views.interval( source,
					Intervals.translate( target, 1, dimension ) ) ).cursor();
	final Cursor< T > back = Views.flatIterable(
			Views.interval( source,
					Intervals.translate( target, -1, dimension ) ) ).cursor();
	for( final S t : Views.flatIterable( target ) )
	{
		t.setReal( front.next().getRealDouble() - back.next().getRealDouble());
		t.mul( 0.5 );
	}
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
public static Img< UnsignedShortType > copyChannelUSST( final ImagePlus imp, final int channel )
{
	final int w, h, d;

	Img< UnsignedShortType > img = ArrayImgs.unsignedShorts( w = imp.getWidth(), h = imp.getHeight(), d = imp.getNSlices() );
	
	final Cursor< UnsignedShortType > c = img.cursor();

	for ( int z = 0; z < d; ++z )
	{
		final int[] pixels = (int[])imp.getStack().getProcessor( z + 1 ).getPixels();
		
		for ( int i = 0; i < w*h; ++i )
		{
			if ( channel == 0 )
				c.next().set( ( pixels[ i ] & 0xff0000) >> 16 );
			else if ( channel == 1 )
				c.next().set( ( pixels[ i ] & 0xff00 ) >> 8 );
			else
				c.next().set( pixels[ i ] & 0xff );
		}
	}
	
	return img;
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
public static Img< FloatType > copyChannel( final ImagePlus imp, final int channel )
{
	final int w, h, d;

	Img< FloatType > img = ArrayImgs.floats( w = imp.getWidth(), h = imp.getHeight(), d = imp.getNSlices() );
	
	final Cursor< FloatType > c = img.cursor();

	for ( int z = 0; z < d; ++z )
	{
		final int[] pixels = (int[])imp.getStack().getProcessor( z + 1 ).getPixels();
		
		for ( int i = 0; i < w*h; ++i )
		{
			if ( channel == 0 )
				c.next().set( ( pixels[ i ] & 0xff0000) >> 16 );
			else if ( channel == 1 )
				c.next().set( ( pixels[ i ] & 0xff00 ) >> 8 );
			else
				c.next().set( pixels[ i ] & 0xff );
		}
	}
	
	return img;
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
public static void main( String[] args )
{
	new ImageJ();
	
	Img< FloatType > img = ArrayImgs.floats( 500, 500 );
	BlendingRealRandomAccess blend = new BlendingRealRandomAccess(
			img,
			new float[]{ 100, 0 },
			new float[]{ 12, 150 } );
	
	Cursor< FloatType > c = img.localizingCursor();
	
	while ( c.hasNext() )
	{
		c.fwd();
		blend.setPosition( c );
		c.get().setReal( blend.get().getRealFloat() );
	}
	
	ImageJFunctions.show( img );
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
public static GenericTexture convertToGenericTexture( Dataset d ) {
    long width = d.getWidth();
    long height = d.getHeight();

    GLVector dims = new GLVector( width, height, 1 );
    int nChannels = 3;

    ByteBuffer bb = BufferUtils.BufferUtils.allocateByte((int) (width * height * nChannels));

    System.out.println("Size:" + width + " " +  height + " " + nChannels);

    Cursor cur = d.cursor();
    while( cur.hasNext() ) {
        cur.fwd();
        int val = ((UnsignedByteType) cur.get()).get();
        //System.out.println( (byte)val );
        bb.put( (byte) val );
        //bb.put((byte)(Math.random()*255));
    }
    bb.flip();

    return new GenericTexture("neverUsed", dims, nChannels, GLTypeEnum.UnsignedByte, bb, true, true, false);
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
public double[] minMax()
{
	double[] minmax = new double[ 2 ];
	minmax[ 0 ] = Double.MAX_VALUE;
	minmax[ 1 ] = Double.MIN_VALUE;
	
	Cursor<T> curs = Views.iterable( this.getSource( 0,0 ) ).cursor();
	
	while( curs.hasNext() )
	{
		double val = curs.next().getRealDouble();
		if( val < minmax[ 0 ])
			minmax[ 0 ] = val;
		else if( val > minmax[ 1 ])
			minmax[ 1 ] = val;
		
	}
	return minmax;
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
@Test
public void testListDilateFull() {
	final List<Shape> shapes = new ArrayList<>();
	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());
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
public static <T extends RealType<T>> double moment1( IterableInterval<T> img, int d ){
	logger.debug("moment 1 ");

	double mom = 0; 
	int nd = img.numDimensions();

	if( d >= nd){
		logger.warn("Dimension for moment must be less than image dimensionality ... returning 0");
		return mom;
	}
	double[] loc = new double[nd];
	Cursor<T> lc = img.localizingCursor();
	while(lc.hasNext()){
		lc.next();
		lc.localize(loc);	
		mom +=  loc[d] * lc.get().getRealDouble();
	}

	logger.debug("result: " + mom);

	return mom;
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
@Test
public void UnshearIntervalTest() {
	Img<DoubleType> img = new ArrayImgFactory<DoubleType>().create(new int[] { 2, 2 }, new DoubleType());
	Cursor<DoubleType> imgC = img.cursor();
	while (imgC.hasNext()) {
		imgC.next().set(1);
	}

	Cursor<DoubleType> il2 = Views
			.unshear(Views.shear(Views.extendZero(img), 0, 1), new FinalInterval(new long[] { 0, 0 }, new long[] { 3, 3 }), 0, 1)
			.cursor();
	RandomAccess<DoubleType> opr = ops.transform()
			.unshearView(Views.shear(Views.extendZero(img), 0, 1), new FinalInterval(new long[] { 0, 0 }, new long[] { 3, 3 }), 0, 1)
			.randomAccess();

	while (il2.hasNext()) {
		il2.next();
		opr.setPosition(il2);
		assertEquals(il2.get().get(), opr.get().get(), 1e-10);
	}
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
static public Img<FloatType> correctIllumination(
		final Img<? extends RealType<?>> img,
		final Img<? extends RealType<?>> brightfield,
		final Img<? extends RealType<?>> darkfield,
		final double mean) {
	p("Start direct (correct illumination)...");
	long t0 = System.nanoTime();
	Img<FloatType> corrected = new ArrayImgFactory<FloatType>().create(img, new FloatType());
	final Cursor<FloatType> c = corrected.cursor();
	final Cursor<? extends RealType<?>> ci = img.cursor(),
										cb = brightfield.cursor(),
										cd = darkfield.cursor();
	while (c.hasNext()) {
		c.fwd();
		ci.fwd();
		cb.fwd();
		cd.fwd();
		c.get().setReal( (  (ci.get().getRealDouble() - cb.get().getRealDouble())
							  / (cb.get().getRealDouble() - cd.get().getRealDouble()))
							 * mean);
	}
	p("  elapsed: " + (System.nanoTime() - t0)/1000000.0 + "  image");
	return corrected;
}
 

import net.imglib2.Cursor; //导入依赖的package包/类
protected void assertComplexImagesEqual(final Img<ComplexFloatType> img1,
	final Img<ComplexFloatType> img2, final float delta)
{
	final Cursor<ComplexFloatType> c1 = img1.cursor();
	final Cursor<ComplexFloatType> c2 = img2.cursor();

	while (c1.hasNext()) {
		c1.fwd();
		c2.fwd();

		// assert that the inverse = the input within the error delta
		assertEquals(c1.get().getRealFloat(), c2.get().getRealFloat(), delta);
		// assert that the inverse = the input within the error delta
		assertEquals(c1.get().getImaginaryFloat(), c2.get().getImaginaryFloat(),
			delta);
	}

}
 

import net.imglib2.Cursor; //导入依赖的package包/类
/** Copy the contents from img to an ImagePlus; assumes containers are compatible. */
static public ImagePlus copyToFloatImagePlus(final Img<? extends RealType<?>> img, final String title) {
	ImagePlusImgFactory<FloatType> factory = new ImagePlusImgFactory<FloatType>();
	ImagePlusImg<FloatType, ?> iml = factory.create(img, new FloatType());
	Cursor<FloatType> c1 = iml.cursor();
	Cursor<? extends RealType<?>> c2 = img.cursor();
	while (c1.hasNext()) {
		c1.fwd();
		c2.fwd();
		c1.get().set(c2.get().getRealFloat());
	}
	try {
		ImagePlus imp = iml.getImagePlus();
		imp.setTitle(title);
		return imp;
	} catch (ImgLibException e) {
		e.printStackTrace();
		return null;
	}
}