net.imglib2.img.basictypeaccess.array.FloatArray Java Examples

The following examples show how to use net.imglib2.img.basictypeaccess.array.FloatArray. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.
Example #1
Source File: MVDeconFFTThreads.java    From SPIM_Registration with GNU General Public License v2.0 6 votes vote down vote up 
@SuppressWarnings("unchecked")
final protected static void convolve2BlockCUDA(
		final Block blockStruct, final int deviceId, final Img< FloatType > image,
		final Img< FloatType > result, final Img< FloatType > block, final Img< FloatType > kernel2 )
{
	// ratio outside of the deconvolved space (psi) is 1
	blockStruct.copyBlock( Views.extendValue( image, new FloatType( 1.0f ) ), block );

	// convolve block with kernel2 using CUDA
	final float[] blockF = ((FloatArray)((ArrayImg< net.imglib2.type.numeric.real.FloatType, ? > )block).update( null ) ).getCurrentStorageArray();
	final float[] kernel2F = ((FloatArray)((ArrayImg< net.imglib2.type.numeric.real.FloatType, ? > )kernel2).update( null ) ).getCurrentStorageArray();

	MVDeconFFT.cuda.convolution3DfftCUDAInPlace(
			blockF, getCUDACoordinates( CUDAOutput.getImgSizeInt( block ) ),
			kernel2F, getCUDACoordinates( CUDAOutput.getImgSizeInt( kernel2 ) ),
			deviceId );

	blockStruct.pasteBlock( result, block );
}
Example #2
Source File: MVDeconFFTThreads.java    From SPIM_Registration with GNU General Public License v2.0 6 votes vote down vote up 
@SuppressWarnings("unchecked")
final protected static void convolve1BlockCUDA(
		final Block blockStruct, final int deviceId, final Img< FloatType > image,
		final Img< FloatType > result, final Img< FloatType > block, final Img< FloatType > kernel1, final int i )
{
	long time = System.currentTimeMillis();
	blockStruct.copyBlock( Views.extendMirrorSingle( image ), block );
	System.out.println( " block " + i + "(CPU  " + deviceId + "): copy " + (System.currentTimeMillis() - time) );

	// convolve block with kernel1 using CUDA
	time = System.currentTimeMillis();
	final float[] blockF = ((FloatArray)((ArrayImg< net.imglib2.type.numeric.real.FloatType, ? > )block).update( null ) ).getCurrentStorageArray();
	final float[] kernel1F = ((FloatArray)((ArrayImg< net.imglib2.type.numeric.real.FloatType, ? > )kernel1).update( null ) ).getCurrentStorageArray();
	
	MVDeconFFT.cuda.convolution3DfftCUDAInPlace(
			blockF, getCUDACoordinates( CUDAOutput.getImgSizeInt( block ) ),
			kernel1F, getCUDACoordinates( CUDAOutput.getImgSizeInt( kernel1 ) ),
			deviceId );
	System.out.println( " block " + i + "(CUDA " + deviceId + "): compute " + (System.currentTimeMillis() - time) );

	time = System.currentTimeMillis();
	blockStruct.pasteBlock( result, block );
	System.out.println( " block " + i + "(CPU  " + deviceId + "): paste " + (System.currentTimeMillis() - time) );
}
Example #3
Source File: FastFusionTools.java    From BigStitcher with GNU General Public License v2.0 6 votes vote down vote up 
public static void main(String[] args)
{
	final ImagePlus imp = IJ.openImage( "/Users/david/Desktop/stable HelaK-GFP-H2A.Z20000.tif" );
	new ImageJ();

	RandomAccessibleInterval< ? extends RealType > img = ImageJFunctions.wrapReal( imp );
	ArrayImg< FloatType, FloatArray > f = ArrayImgs.floats( 1024, 1024 );
	ArrayImg< FloatType, FloatArray > w = ArrayImgs.floats( 1024, 1024 );
	RandomAccessibleInterval< FloatType > interp = (RandomAccessibleInterval< FloatType >) getLinearInterpolation( img, new FloatType(), new float[] {0.5f,0.5f}, Executors.newSingleThreadExecutor() ).getA();
	
	RandomAccessibleInterval< FloatType > weight = new ArrayImgFactory( new FloatType() ).create( interp );
	applyWeights( interp, weight, new float[] {0.5f,0.5f}, new float[] {0,0}, new float[] {20,20}, false, Executors.newSingleThreadExecutor() );
	addTranslated( Views.iterable( interp ), f, new int[] {500, 700}, Executors.newSingleThreadExecutor() );
	addTranslated( Views.iterable( interp ), f, new int[] {400, 500}, Executors.newSingleThreadExecutor() );
	addTranslated( Views.iterable( weight ), w, new int[] {500, 700}, Executors.newSingleThreadExecutor() );
	addTranslated( Views.iterable( weight ), w, new int[] {400, 500}, Executors.newSingleThreadExecutor() );

	normalizeWeights( f, w, Executors.newSingleThreadExecutor() );
	
	ImageJFunctions.show( f );
}
Example #4
Source File: AbstractOpTest.java    From imagej-ops with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
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);
}
Example #5
Source File: LinearIntensityMap.java    From TrakEM2 with GNU General Public License v3.0 5 votes vote down vote up 
public static void main( final String[] args )
{
	new ImageJ();

	final double[] coefficients = new double[]{
			0, 2, 4, 8,
			1, 1, 1, 1,
			1, 10, 5, 1,
			1, 1, 1, 1,

			0, 10, 20, 30,
			40, 50, 60, 70,
			80, 90, 100, 110,
			120, 130, 140, 150
	};

	final LinearIntensityMap< DoubleType > transform = new LinearIntensityMap< DoubleType >( ArrayImgs.doubles( coefficients, 4, 4, 2 ) );

	//final ImagePlus imp = new ImagePlus( "http://upload.wikimedia.org/wikipedia/en/2/24/Lenna.png" );
	final ImagePlus imp1 = new ImagePlus( "http://fly.mpi-cbg.de/~saalfeld/Pictures/norway.jpg");

	final ArrayImg< FloatType, FloatArray > image1 = ArrayImgs.floats( ( float[] )imp1.getProcessor().convertToFloatProcessor().getPixels(), imp1.getWidth(), imp1.getHeight() );
	final ArrayImg< UnsignedByteType, ByteArray > image2 = ArrayImgs.unsignedBytes( ( byte[] )imp1.getProcessor().convertToByteProcessor().getPixels(), imp1.getWidth(), imp1.getHeight() );
	final ArrayImg< UnsignedShortType, ShortArray > image3 = ArrayImgs.unsignedShorts( ( short[] )imp1.getProcessor().convertToShortProcessor().getPixels(), imp1.getWidth(), imp1.getHeight() );
	final ArrayImg< ARGBType, IntArray > image4 = ArrayImgs.argbs( ( int[] )imp1.getProcessor().getPixels(), imp1.getWidth(), imp1.getHeight() );

	ImageJFunctions.show( ArrayImgs.doubles( coefficients, 4, 4, 2 ) );

	transform.run( image1 );
	transform.run( image2 );
	transform.run( image3 );
	transform.run( image4 );

	ImageJFunctions.show( image1 );
	ImageJFunctions.show( image2 );
	ImageJFunctions.show( image3 );
	ImageJFunctions.show( image4 );
}
Example #6
Source File: SCIFIOCellImgFactory.java    From scifio with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
@SuppressWarnings({ "unchecked", "rawtypes" })
private <A extends ArrayDataAccess<A>> SCIFIOCellLoader<T, A>
	createCellLoader(final NativeTypeFactory<T, A> typeFactory)
{
	switch (typeFactory.getPrimitiveType()) {
		case BYTE:
			return new SCIFIOCellLoader(new ByteArrayLoader(reader, subregion),
				o -> new ByteArray((byte[]) o));
		case CHAR:
			return new SCIFIOCellLoader(new CharArrayLoader(reader, subregion),
				o -> new CharArray((char[]) o));
		case DOUBLE:
			return new SCIFIOCellLoader(new DoubleArrayLoader(reader, subregion),
				o -> new DoubleArray((double[]) o));
		case FLOAT:
			return new SCIFIOCellLoader(new FloatArrayLoader(reader, subregion),
				o -> new FloatArray((float[]) o));
		case INT:
			return new SCIFIOCellLoader(new IntArrayLoader(reader, subregion),
				o -> new IntArray((int[]) o));
		case LONG:
			return new SCIFIOCellLoader(new LongArrayLoader(reader, subregion),
				o -> new LongArray((long[]) o));
		case SHORT:
			return new SCIFIOCellLoader(new ShortArrayLoader(reader, subregion),
				o -> new ShortArray((short[]) o));
		default:
			throw new IllegalArgumentException();
	}
}
Example #7
Source File: Block.java    From SPIM_Registration with GNU General Public License v2.0 5 votes vote down vote up 
private static final void copy3dArray( final int threadIdx, final int numThreads, final RandomAccessible< FloatType > source, final ArrayImg< FloatType, ? > block, final long[] offset )
{
	final int w = (int)block.dimension( 0 );
	final int h = (int)block.dimension( 1 );
	final int d = (int)block.dimension( 2 );

	final long offsetX = offset[ 0 ];
	final long offsetY = offset[ 1 ];
	final long offsetZ = offset[ 2 ];
	final float[] blockArray = ((FloatArray)block.update( null ) ).getCurrentStorageArray();

	// define where we will query the RandomAccess on the source
	final FinalInterval interval = new FinalInterval( new long[] { offsetX, offsetY, offsetZ }, new long[] { offsetX + w - 1, offsetY + h - 1, offsetZ + d - 1 } );
	final RandomAccess< FloatType > randomAccess = source.randomAccess( interval );

	final long[] tmp = new long[]{ offsetX, offsetY, 0 };

	for ( int z = threadIdx; z < d; z += numThreads )
	{
		tmp[ 2 ] = z + offsetZ;
		randomAccess.setPosition( tmp );

		int i = z * h * w;

		for ( int y = 0; y < h; ++y )
		{
			randomAccess.setPosition( offsetX, 0 );

			for ( int x = 0; x < w; ++x )
			{
				blockArray[ i++ ] = randomAccess.get().get();
				randomAccess.fwd( 0 );
			}

			randomAccess.move( -w, 0 );
			randomAccess.fwd( 1 );
		}
	}
}
Example #8
Source File: MathNamespace.java    From imagej-ops with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
@OpMethod(op = net.imagej.ops.math.ConstantToPlanarImage.SubtractFloat.class)
public PlanarImg<FloatType, FloatArray> subtract(
	final PlanarImg<FloatType, FloatArray> image, final float value)
{
	@SuppressWarnings("unchecked")
	final PlanarImg<FloatType, FloatArray> result =
		(PlanarImg<FloatType, FloatArray>) ops().run(
			net.imagej.ops.Ops.Math.Subtract.class, image, value);
	return result;
}
Example #9
Source File: MathNamespace.java    From imagej-ops with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
@OpMethod(ops = {
	net.imagej.ops.math.ConstantToArrayImageP.SubtractFloat.class,
	net.imagej.ops.math.ConstantToArrayImage.SubtractFloat.class })
public ArrayImg<FloatType, FloatArray> subtract(
	final ArrayImg<FloatType, FloatArray> image, final float value)
{
	@SuppressWarnings("unchecked")
	final ArrayImg<FloatType, FloatArray> result =
		(ArrayImg<FloatType, FloatArray>) ops().run(Ops.Math.Subtract.NAME, image,
			value);
	return result;
}
Example #10
Source File: MathNamespace.java    From imagej-ops with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
@OpMethod(op = net.imagej.ops.math.ConstantToPlanarImage.MultiplyFloat.class)
public PlanarImg<FloatType, FloatArray> multiply(
	final PlanarImg<FloatType, FloatArray> image, final float value)
{
	@SuppressWarnings("unchecked")
	final PlanarImg<FloatType, FloatArray> result =
		(PlanarImg<FloatType, FloatArray>) ops().run(
			net.imagej.ops.Ops.Math.Multiply.class, image, value);
	return result;
}
Example #11
Source File: MathNamespace.java    From imagej-ops with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
@OpMethod(ops = { net.imagej.ops.math.ConstantToArrayImageP.AddFloat.class,
	net.imagej.ops.math.ConstantToArrayImage.AddFloat.class })
public ArrayImg<FloatType, FloatArray> add(
	final ArrayImg<FloatType, FloatArray> image, final float value)
{
	@SuppressWarnings("unchecked")
	final ArrayImg<FloatType, FloatArray> result =
		(ArrayImg<FloatType, FloatArray>) ops().run(Ops.Math.Add.NAME, image,
			value);
	return result;
}
Example #12
Source File: MathNamespace.java    From imagej-ops with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
@OpMethod(op = net.imagej.ops.math.ConstantToPlanarImage.DivideFloat.class)
public PlanarImg<FloatType, FloatArray> divide(
	final PlanarImg<FloatType, FloatArray> image, final float value)
{
	@SuppressWarnings("unchecked")
	final PlanarImg<FloatType, FloatArray> result =
		(PlanarImg<FloatType, FloatArray>) ops().run(
			net.imagej.ops.Ops.Math.Divide.class, image, value);
	return result;
}
Example #13
Source File: MathNamespace.java    From imagej-ops with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
@OpMethod(ops = { net.imagej.ops.math.ConstantToArrayImageP.DivideFloat.class,
	net.imagej.ops.math.ConstantToArrayImage.DivideFloat.class })
public ArrayImg<FloatType, FloatArray> divide(
	final ArrayImg<FloatType, FloatArray> image, final float value)
{
	@SuppressWarnings("unchecked")
	final ArrayImg<FloatType, FloatArray> result =
		(ArrayImg<FloatType, FloatArray>) ops().run(Ops.Math.Divide.NAME, image,
			value);
	return result;
}
Example #14
Source File: MathNamespace.java    From imagej-ops with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
@OpMethod(op = net.imagej.ops.math.ConstantToPlanarImage.AddFloat.class)
public PlanarImg<FloatType, FloatArray> add(
	final PlanarImg<FloatType, FloatArray> image, final float value)
{
	@SuppressWarnings("unchecked")
	final PlanarImg<FloatType, FloatArray> result =
		(PlanarImg<FloatType, FloatArray>) ops().run(
			net.imagej.ops.Ops.Math.Add.class, image, value);
	return result;
}
Example #15
Source File: MathNamespace.java    From imagej-ops with BSD 2-Clause "Simplified" License 5 votes vote down vote up 
@OpMethod(ops = {
	net.imagej.ops.math.ConstantToArrayImageP.MultiplyFloat.class,
	net.imagej.ops.math.ConstantToArrayImage.MultiplyFloat.class })
public ArrayImg<FloatType, FloatArray> multiply(
	final ArrayImg<FloatType, FloatArray> image, final float value)
{
	@SuppressWarnings("unchecked")
	final ArrayImg<FloatType, FloatArray> result =
		(ArrayImg<FloatType, FloatArray>) ops().run(Ops.Math.Multiply.NAME, image,
			value);
	return result;
}
Example #16
Source File: Block.java    From SPIM_Registration with GNU General Public License v2.0 4 votes vote down vote up 
private static final void paste3d( final int threadIdx, final int numThreads, final ArrayImg< FloatType, ? > target, final ArrayImg< FloatType, ? > block, 
		final long[] effectiveOffset, final long[] effectiveSize, final long[] effectiveLocalOffset )
{
	// min position in the output
	final int minX = (int)effectiveOffset[ 0 ];
	final int minY = (int)effectiveOffset[ 1 ];
	final int minZ = (int)effectiveOffset[ 2 ];

	// max+1 of the output area
	final int maxY = (int)effectiveSize[ 1 ] + minY;
	final int maxZ = (int)effectiveSize[ 2 ] + minZ;

	// size of the output area
	final int sX = (int)effectiveSize[ 0 ];

	// min position in the output
	final int minXb = (int)effectiveLocalOffset[ 0 ];
	final int minYb = (int)effectiveLocalOffset[ 1 ];
	final int minZb = (int)effectiveLocalOffset[ 2 ];

	// size of the target image
	final int w = (int)target.dimension( 0 );
	final int h = (int)target.dimension( 1 );

	// size of the block image
	final int wb = (int)block.dimension( 0 );
	final int hb = (int)block.dimension( 1 );

	final float[] blockArray = ((FloatArray)block.update( null ) ).getCurrentStorageArray();
	final float[] targetArray = ((FloatArray)target.update( null ) ).getCurrentStorageArray();
			
	for ( int z = minZ + threadIdx; z < maxZ; z += numThreads )
	{
		final int zBlock = z - minZ + minZb;
		
		int iTarget = z * h * w + minY * w + minX;
		int iBlock = zBlock * hb * wb + minYb * wb + minXb;
		
		for ( int y = minY; y < maxY; ++y )
		{
			copyX( blockArray, targetArray, sX, iTarget, iBlock );

			iTarget += w;
			iBlock += wb;
		}
	}
}
Example #17
Source File: DifferenceOfGaussianCUDA.java    From SPIM_Registration with GNU General Public License v2.0 4 votes vote down vote up 
@Override
public boolean process()
{
	// do not operate at the edge, 80% of the memory is a good idea I think
	final long memAvail = Math.round( cudaDevice.getFreeDeviceMemory() * ( percentGPUMem / 100.0 ) );
	final long imgBytes = numPixels() * 4 * 2; // float, two images on the card at once

	final long[] numBlocksDim = net.imglib2.util.Util.int2long( computeNumBlocksDim( memAvail, imgBytes, percentGPUMem, img.numDimensions(), "CUDA-Device " + cudaDevice.getDeviceId() ) );
	final BlockGenerator< Block > generator;

	if ( accurate )
		generator = new BlockGeneratorVariableSizePrecise( numBlocksDim );
	else
		generator = new BlockGeneratorVariableSizeSimple( numBlocksDim );

	final Block[] blocks = generator.divideIntoBlocks( getImgSize( img ), getKernelSize( sigma ) );

	if ( !accurate && blocks.length == 1 && ArrayImg.class.isInstance( img ) )
	{
		IOFunctions.println( "Conovlving image as one single block." );
		long time = System.currentTimeMillis();

		// copy the only directly into the result
		blocks[ 0 ].copyBlock( img, result );
		long copy = System.currentTimeMillis();
		IOFunctions.println( "Copying data took " + ( copy - time ) + "ms" );

		// convolve
		final float[] resultF = ((FloatArray)((ArrayImg< net.imglib2.type.numeric.real.FloatType, ? > )result).update( null ) ).getCurrentStorageArray();
		cudaconvolve.gauss( resultF, getImgSizeInt( result ), sigma, OutOfBounds.EXTEND_BORDER_PIXELS, 0 );
		IOFunctions.println( "Convolution took " + ( System.currentTimeMillis() - copy ) + "ms using device=" + cudaDevice.getDeviceName() + " (id=" + cudaDevice.getDeviceId() + ")" );

		// no copy back required
	}
	else
	{
		final RandomAccessible< net.imglib2.type.numeric.real.FloatType > input;
		
		if ( accurate )
			input = Views.extendMirrorSingle( img );
		else
			input = img;
		
		for( final Block block : blocks )
		{
			//long time = System.currentTimeMillis();
			final ArrayImg< net.imglib2.type.numeric.real.FloatType, FloatArray > imgBlock = ArrayImgs.floats( block.getBlockSize() );

			// copy the block
			block.copyBlock( input, imgBlock );
			//long copy = System.currentTimeMillis();
			//IOFunctions.println( "Copying block took " + ( copy - time ) + "ms" );

			// convolve
			final float[] imgBlockF = ((FloatArray)((ArrayImg< net.imglib2.type.numeric.real.FloatType, ? > )imgBlock).update( null ) ).getCurrentStorageArray();
			cudaconvolve.gauss( imgBlockF, getImgSizeInt( imgBlock ), sigma, OutOfBounds.EXTEND_BORDER_PIXELS, 0 );
			//long convolve = System.currentTimeMillis();
			//IOFunctions.println( "Convolution took " + ( convolve - copy ) + "ms using device=" + cudaDevice.getDeviceName() + " (id=" + cudaDevice.getDeviceId() + ")" );

			// no copy back required
			block.pasteBlock( result, imgBlock );
			//IOFunctions.println( "Pasting block took " + ( System.currentTimeMillis() - convolve ) + "ms" );
		}
	}

	return true;
}
Example #18
Source File: FloatArrayLoader.java    From scifio with BSD 2-Clause "Simplified" License 4 votes vote down vote up 
@Override
public FloatArray emptyArray(final int entities) {
	return new FloatArray(entities);
}