Package net.preibisch.mvrecon.process.interestpointdetection.methods.dog

Class DoGImgLib2

java.lang.Object

net.preibisch.mvrecon.process.interestpointdetection.methods.dog.DoGImgLib2

public class DoGImgLib2
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	DoGImgLib2.SpecialPoint

Field Summary

Fields

Modifier and Type	Field	Description
static int[]	blockSize
static boolean	silent

Constructor Summary

Constructors

Constructor	Description
DoGImgLib2()

Method Summary

Modifier and Type	Method	Description
static <T extends net.imglib2.type.numeric.RealType<T>> ArrayList<InterestPoint>	computeDoG(net.imglib2.RandomAccessible<T> input, net.imglib2.RandomAccessible<T> mask, net.imglib2.Interval interval, double sigma, double threshold, int localization, boolean findMin, boolean findMax, double minIntensity, double maxIntensity, int[] blockSize, ExecutorService service, CUDASeparableConvolution cuda, CUDADevice cudaDevice, boolean accurateCUDA, double percentGPUMem)
static <T extends net.imglib2.type.numeric.RealType<T>> ArrayList<InterestPoint>	computeDoG(net.imglib2.RandomAccessible<T> input, net.imglib2.RandomAccessible<T> mask, net.imglib2.Interval interval, double sigma, double threshold, int localization, boolean findMin, boolean findMax, double minIntensity, double maxIntensity, ExecutorService service)
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType>	computeGaussCUDA(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> inputFloatNonZeroMin, double[] sigma, CUDASeparableConvolution cuda, CUDADevice cudaDevice, boolean accurateCUDA, double percentGPUMem)
static int[]	computeNumBlocksDim(long memAvail, long memReq, double percentGPUMem, int n, String start)
static net.imglib2.util.Pair<double[][],Float>	computeSigmas(float initialSigma, int n)
static final <T extends net.imglib2.type.Type<T>> void	copy(net.imglib2.RandomAccessible<? extends T> source, net.imglib2.RandomAccessibleInterval<T> target)
static ArrayList<SimplePeak>	findPeaks(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> laPlace, net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> laPlaceMask, float minValue, ExecutorService service)
static int[]	getImgSizeInt(net.imglib2.Interval img)
protected static long[]	getKernelSize(double[] sigma)
protected static final DoGImgLib2.SpecialPoint	isSpecialPoint(net.imglib2.Cursor<net.imglib2.type.numeric.real.FloatType> neighborhoodCursor, float centerValue)
static void	main(String[] args)
static <T extends net.imglib2.type.numeric.RealType<T>> float[]	minMax(net.imglib2.RandomAccessibleInterval<T> img, net.imglib2.RandomAccessibleInterval<T> mask, ExecutorService service)
protected static int	numBlocks(int[] numBlocksDim)
protected static long	numPixels(net.imglib2.Dimensions dim, boolean accurate, double[] sigma)
static <T extends net.imglib2.type.numeric.RealType<T>> int	radiusDoG(double sigma)
protected static void	reduceBlockNumbers(int[] numBlocksDim, int numBlocks)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

silent

public static boolean silent

blockSize

public static int[] blockSize

Constructor Details

DoGImgLib2

public DoGImgLib2()

Method Details

main

public static void main(String[] args)

radiusDoG

public static <T extends net.imglib2.type.numeric.RealType<T>>
int radiusDoG(double sigma)

computeDoG

public static <T extends net.imglib2.type.numeric.RealType<T>>
ArrayList<InterestPoint> computeDoG(net.imglib2.RandomAccessible<T> input,
 net.imglib2.RandomAccessible<T> mask,
 net.imglib2.Interval interval,
 double sigma,
 double threshold,
 int localization,
 boolean findMin,
 boolean findMax,
 double minIntensity,
 double maxIntensity,
 ExecutorService service)

computeDoG

public static <T extends net.imglib2.type.numeric.RealType<T>>
ArrayList<InterestPoint> computeDoG(net.imglib2.RandomAccessible<T> input,
 net.imglib2.RandomAccessible<T> mask,
 net.imglib2.Interval interval,
 double sigma,
 double threshold,
 int localization,
 boolean findMin,
 boolean findMax,
 double minIntensity,
 double maxIntensity,
 int[] blockSize,
 ExecutorService service,
 CUDASeparableConvolution cuda,
 CUDADevice cudaDevice,
 boolean accurateCUDA,
 double percentGPUMem)

computeSigmas

public static net.imglib2.util.Pair<double[][],Float> computeSigmas(float initialSigma,
 int n)

findPeaks

public static ArrayList<SimplePeak> findPeaks(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> laPlace,
 net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> laPlaceMask,
 float minValue,
 ExecutorService service)

isSpecialPoint

protected static final DoGImgLib2.SpecialPoint isSpecialPoint(net.imglib2.Cursor<net.imglib2.type.numeric.real.FloatType> neighborhoodCursor,
 float centerValue)

copy

public static final <T extends net.imglib2.type.Type<T>>
void copy(net.imglib2.RandomAccessible<? extends T> source,
 net.imglib2.RandomAccessibleInterval<T> target)

minMax

public static <T extends net.imglib2.type.numeric.RealType<T>>
float[] minMax(net.imglib2.RandomAccessibleInterval<T> img,
 net.imglib2.RandomAccessibleInterval<T> mask,
 ExecutorService service)

computeGaussCUDA

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> computeGaussCUDA(net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.FloatType> inputFloatNonZeroMin,
 double[] sigma,
 CUDASeparableConvolution cuda,
 CUDADevice cudaDevice,
 boolean accurateCUDA,
 double percentGPUMem)

getImgSizeInt

public static int[] getImgSizeInt(net.imglib2.Interval img)

getKernelSize

protected static long[] getKernelSize(double[] sigma)

computeNumBlocksDim

public static int[] computeNumBlocksDim(long memAvail,
 long memReq,
 double percentGPUMem,
 int n,
 String start)

reduceBlockNumbers

protected static void reduceBlockNumbers(int[] numBlocksDim,
 int numBlocks)

numBlocks

protected static int numBlocks(int[] numBlocksDim)

numPixels

protected static long numPixels(net.imglib2.Dimensions dim,
 boolean accurate,
 double[] sigma)