Java ArrayImgs.floats方法代码示例

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
@Override
public RandomAccessibleInterval< FloatType > getFloatImage(
		int timepointId, boolean normalize, ImgLoaderHint... hints )
{
	final Random rnd = new Random( setupId );

	final Img< FloatType > img = ArrayImgs.floats( 512, 512, 86 );

	final float scale;
	
	if ( normalize )
		scale = 1;
	else
		scale = 20000;
	
	for ( final FloatType t : img )
		t.set( rnd.nextFloat() * scale);

	return img;
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的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.img.array.ArrayImgs; //导入方法依赖的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.img.array.ArrayImgs; //导入方法依赖的package包/类
final static public void main( final String[] args )
	{
		new ImageJ();
		final ImagePlus imp = new ImagePlus( "http://media.npr.org/images/picture-show-flickr-promo.jpg" );
		imp.show();

		final float[] pixels = ( float[] ) imp.getProcessor().convertToFloat().getPixels();
		final ArrayImg< FloatType, FloatArray > img = ArrayImgs.floats( pixels, imp.getWidth(), imp.getHeight() );

		final double[] lut = new double[ Math.max( imp.getWidth(), imp.getHeight() ) ];
		for ( int i = 0; i < lut.length; ++i )
			lut[ i ] = i + Math.pow( i, 1.5 );

		final SingleDimensionLUTRealTransform transform = new SingleDimensionLUTRealTransform( lut, 2, 2, 1 );
		final RealRandomAccessible< FloatType > source = Views.interpolate( Views.extendBorder( img ), new NLinearInterpolatorFactory< FloatType >() );
		final RandomAccessible< FloatType > target = new RealTransformRandomAccessible< FloatType, RealTransform >( source, transform );
		final RandomAccessible< FloatType > target2 = RealViews.transform( source, transform );

//		RealViews.transformReal(source, transform);

		ImageJFunctions.show( Views.interval( target, new FinalInterval( imp.getWidth(), imp.getHeight() ) ) );
		ImageJFunctions.show( Views.interval( target2, new FinalInterval( imp.getWidth(), imp.getHeight() ) ) );
	}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
public static void main( final String[] args ) throws ImgIOException
	{
		final String fn = "/home/tobias/workspace/data/DrosophilaWing.tif";
		final Img< FloatType > img = new ImgOpener().openImg( fn, new ArrayImgFactory< FloatType >(), new FloatType() );

		final long[] dims = new long[ img.numDimensions() ];
		img.dimensions( dims );
		final Img< FloatType > convolved = ArrayImgs.floats( dims );

		try
		{
			Gauss3.gauss( 3, Views.extendMirrorSingle( img ), convolved );
//			Gauss3.gauss( 5, img, Views.interval( convolved, Intervals.createMinSize( 200, 100, 200, 150 ) ) );
		}
		catch ( final IncompatibleTypeException e )
		{
			e.printStackTrace();
		}
		ImageJFunctions.show( convolved );
	}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
private static float[] createFloatArray(
	final RandomAccessibleInterval<FloatType> image)
{
	final long[] dims = Intervals.dimensionsAsLongArray(image);
	final ArrayImg<FloatType, FloatArray> dest = ArrayImgs.floats(dims);
	copy(image, dest);
	return dest.update(null).getCurrentStorageArray();
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
public static void main(String... args) {
	// SETUP
	final ImageJ imageJ = new ImageJ();
	final Random random = new Random();
	final int width = 100;
	final int height = 100;
	final int depth = 100;
	final int rotations = 100;
	final int bins = 100;
	final Img<FloatType> img = ArrayImgs.floats(width, height, depth);
	@SuppressWarnings("unchecked")
	final BinaryFunctionOp<ValuePair<Point3d, Vector3d>, Interval, Optional<ValuePair<DoubleType, DoubleType>>> intersectOp =
		(BinaryFunctionOp) Functions.binary(imageJ.op(), BoxIntersect.class,
			Optional.class, ValuePair.class, img);
	final BinaryHybridCFI1<Tuple3d, AxisAngle4d, Tuple3d> rotateOp = Hybrids
		.binaryCFI1(imageJ.op(), RotateAboutAxis.class, Tuple3d.class,
			new Vector3d(), new AxisAngle4d());

	// EXECUTE
	for (int i = 0; i < rotations; i++) {
		final AxisAngle4d rotation = RotateAboutAxis.randomAxisAngle();
		final LineGrid grid = createGrid(img, rotateOp, rotation, random);
		final Stream<Section> sections = createSections(img, grid, bins,
			intersectOp);
		sections.forEach(s -> sample(img, s, 1.0, random));
	}

	// DISPLAY RESULT
	final ImgPlus<FloatType> image = new ImgPlus<>(img, "Sampling count",
		new DefaultLinearAxis(Axes.X), new DefaultLinearAxis(Axes.Y),
		new DefaultLinearAxis(Axes.Z));
	imageJ.launch(args);
	imageJ.ui().show(image);
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
public static void main(final String... args) {
	// SETUP
	final ImageJ imageJ = new ImageJ();
	final Random random = new Random();
	final int width = 100;
	final int height = 100;
	final int depth = 100;
	final int rotations = 100;
	final int bins = 100;
	final Img<FloatType> img = ArrayImgs.floats(width, height, depth, 3);
	@SuppressWarnings("unchecked")
	final BinaryFunctionOp<ValuePair<Point3d, Vector3d>, Interval, Optional<ValuePair<DoubleType, DoubleType>>> intersectOp =
		(BinaryFunctionOp) Functions.binary(imageJ.op(), BoxIntersect.class,
			Optional.class, ValuePair.class, img);
	final BinaryHybridCFI1<Tuple3d, AxisAngle4d, Tuple3d> rotateOp = Hybrids
		.binaryCFI1(imageJ.op(), RotateAboutAxis.class, Tuple3d.class,
			new Vector3d(), new AxisAngle4d());

	// EXECUTE
	for (int i = 0; i < rotations; i++) {
		final AxisAngle4d rotation = RotateAboutAxis.randomAxisAngle();
		final LineGrid grid = createGrid(img, rotateOp, rotation, random);
		final Stream<Section> sections = createSections(img, grid, bins,
			intersectOp);
		sections.forEach(s -> sample(img, s, 1.0, random));
	}

	// DISPLAY RESULTS
	// Swap channel- and z-axes swapped so that image displays OK.
	final IntervalView<FloatType> displayView = Views.permute(img, 3, 2);
	final Img<FloatType> displayImg = ImgView.wrap(displayView, img.factory());
	final ImgPlus<FloatType> image = new ImgPlus<>(displayImg,
		"Sampling directions", new DefaultLinearAxis(Axes.X),
		new DefaultLinearAxis(Axes.Y), new DefaultLinearAxis(Axes.CHANNEL),
		new DefaultLinearAxis(Axes.Z));
	imageJ.launch(args);
	imageJ.ui().show(image);
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
final static public void main( final String[] args )
	{

		new ImageJ();
		final ImagePlus imp = new ImagePlus( "http://media.npr.org/images/picture-show-flickr-promo.jpg" );
		imp.show();

		final float[] pixels = ( float[] ) imp.getProcessor().convertToFloat().getPixels();
		final ArrayImg< FloatType, FloatArray > img = ArrayImgs.floats( pixels, imp.getWidth(), imp.getHeight() );

		final double[] lut = new double[ Math.max( imp.getWidth(), imp.getHeight() ) ];
		for ( int i = 0; i < lut.length; ++i )
			lut[ i ] = i + Math.pow( i, 1.5 );

		final LUTRealTransform transform = new LUTRealTransform( lut, 2, 2 );
		final RealRandomAccessible< FloatType > source = Views.interpolate( Views.extendBorder( img ), new NLinearInterpolatorFactory< FloatType >() );
		final RandomAccessible< FloatType > target = new RealTransformRandomAccessible< FloatType, RealTransform >( source, transform );
		final RandomAccessible< FloatType > target2 = RealViews.transform( source, transform );

//		RealViews.transformReal(source, transform);

		final ArrayImg< FloatType, FloatArray > targetImg = ArrayImgs.floats( imp.getWidth(), imp.getHeight() );
		render( source, targetImg, transform, 0.05 );

		ImageJFunctions.show( Views.interval( target, new FinalInterval( imp.getWidth(), imp.getHeight() ) ) );
		ImageJFunctions.show( Views.interval( target2, new FinalInterval( imp.getWidth(), imp.getHeight() ) ) );
		ImageJFunctions.show( targetImg );
	}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
private static Img<FloatType> generateFloatImg(final float[] values) {

		final float[] array =
			new float[(int) Intervals.numElements(new FinalInterval(dims))];

		if (array.length != values.length) {
			throw new RuntimeException("Number of values doesn't match dimmensions");
		}

		for (int i = 0; i < array.length; i++) {
			array[i] = values[i];
		}

		return ArrayImgs.floats(array, dims);
	}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
public ArrayImg<FloatType, FloatArray> generateFloatArrayTestImg(
	final boolean fill, final long... dims)
{
	final float[] array = new float[(int) Intervals.numElements(
		new FinalInterval(dims))];

	if (fill) {
		seed = 17;
		for (int i = 0; i < array.length; i++) {
			array[i] = (float) pseudoRandom() / (float) Integer.MAX_VALUE;
		}
	}

	return ArrayImgs.floats(array, dims);
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
@Test
public void regressionTest() throws Exception {

	// load in input image and expected output image.
	Img<FloatType> inputImg = (Img<FloatType>) ops.run(
		net.imagej.ops.image.equation.DefaultEquation.class,
		"Math.tan(0.3*p[0]) + Math.tan(0.1*p[1])");
	Img<FloatType> expectedOutput = ((Img<FloatType>) openFloatImg(
		"Result.tif"));

	// create ouput image
	long[] dims = new long[inputImg.numDimensions()];
	inputImg.dimensions(dims);
	Img<FloatType> actualOutput = ArrayImgs.floats(dims);

	// scale over which the filter operates (sensitivity)
	int scale = 1;

	// physical spacing between data points (1,1 since I got it from the
	// computer)
	double[] spacing = { 1, 1 };

	// run the op
	ops.run(net.imagej.ops.filter.vesselness.DefaultFrangi.class, actualOutput,
		inputImg, spacing, scale);

	// compare the output image data to that stored in the file.
	Cursor<FloatType> cursor = Views.iterable(actualOutput).localizingCursor();
	RandomAccess<FloatType> actualRA = actualOutput.randomAccess();
	RandomAccess<FloatType> expectedRA = expectedOutput.randomAccess();

	while (cursor.hasNext()) {
		cursor.fwd();
		actualRA.setPosition(cursor);
		expectedRA.setPosition(cursor);
		assertEquals(expectedRA.get().get(), actualRA.get().get(), 0);
	}
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
@Override
public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
{
	try
	{
		final MultipageTiffReader r = new MultipageTiffReader( mmFile );

		final ArrayImg< FloatType, ? > img = ArrayImgs.floats( r.width(), r.height(), r.depth() );
		final BasicViewDescription< ? > vd = sequenceDescription.getViewDescriptions().get( view );

		populateImage( img, vd, r );

		if ( normalize )
			normalize( img );

		updateMetaDataCache( view, r.width(), r.height(), r.depth(), r.calX(), r.calY(), r.calZ() );

		r.close();

		return img;
	}
	catch ( Exception e )
	{
		IOFunctions.printlnSafe( "Failed to load viewsetup=" + view.getViewSetupId() + " timepoint=" + view.getTimePointId() + ": " + e );
		e.printStackTrace();
		return null;
	}
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
@Override
public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
{
	final BasicViewDescription< ? > vd = sd.getViewDescriptions().get( view );
	final Dimensions d = vd.getViewSetup().getSize();
	final VoxelDimensions dv = vd.getViewSetup().getVoxelSize();

	final ArrayImg< FloatType, ? > img = ArrayImgs.floats( d.dimension( 0 ), d.dimension( 1 ), d.dimension(  2 ) );

	final String ampOrPhaseDir;

	if ( vd.getViewSetup().getAttribute( Channel.class ).getId() == ampChannelId )
		ampOrPhaseDir = amplitudeDir;
	else if ( vd.getViewSetup().getAttribute( Channel.class ).getId() ==  phaseChannelId )
		ampOrPhaseDir = phaseDir;
	else
		throw new RuntimeException( "viewSetupId=" + view.getViewSetupId() + " is not Amplitude nor phase." );

	populateImage( img, directory, stackDir, ampOrPhaseDir, zPlanes, timepoints.get( view.getTimePointId() ), extension );

	if ( normalize )
		normalize( img );

	updateMetaDataCache( view, (int)d.dimension( 0 ), (int)d.dimension( 1 ), (int)d.dimension( 2 ), dv.dimension( 0 ), dv.dimension( 1 ), dv.dimension( 2 ) );

	return img;
}
 

import net.imglib2.img.array.ArrayImgs; //导入方法依赖的package包/类
public static void main( String[] args )
{
	// define the blocksize so that it is one single block
	final RandomAccessibleInterval< FloatType > block = ArrayImgs.floats( 384, 384 );
	final long[] blockSize = new long[ block.numDimensions() ];
	block.dimensions( blockSize );

	final RandomAccessibleInterval< FloatType > image = ArrayImgs.floats( 1024, 1024 );
	final long[] imgSize = new long[ image.numDimensions() ];
	image.dimensions( imgSize );

	// whatever the kernel size is (extra size/2 in general)
	final long[] kernelSize = new long[]{ 16, 32 };

	final BlockGeneratorFixedSizePrecise blockGenerator = new BlockGeneratorFixedSizePrecise( blockSize );
	final Block[] blocks = blockGenerator.divideIntoBlocks( imgSize, kernelSize );

	int i = 0;

	for ( final Block b : blocks )
	{
		// copy data from the image to the block (including extra space for outofbounds/real image data depending on kernel size)
		b.copyBlock( Views.extendMirrorDouble( image ), block );

		// do something with the block (e.g. also multithreaded, cluster, ...)
		for ( final FloatType f : Views.iterable( block ) )
			f.set( i );

		++i;

		// write the block back (use a temporary image if multithreaded or in general not all are copied first)
		b.pasteBlock( image, block );
	}

	ImageJFunctions.show( image );
}