net.imglib2.algorithm.bspline

Class BSplineDecomposition<T extends net.imglib2.type.numeric.RealType<T>,S extends net.imglib2.type.numeric.RealType<S>>

java.lang.Object

net.imglib2.algorithm.bspline.BSplineDecomposition<T,S>

Type Parameters:

T - image type

S - coefficient type

All Implemented Interfaces:

Consumer<net.imglib2.RandomAccessibleInterval<S>>

public class BSplineDecomposition<T extends net.imglib2.type.numeric.RealType<T>,S extends net.imglib2.type.numeric.RealType<S>>
extends Object
implements Consumer<net.imglib2.RandomAccessibleInterval<S>>

Compute Bspline coefficients from an image.

Author:

John Bogovic

Field Summary

Fields

Modifier and Type	Field and Description
protected double[]	Ci
protected net.imglib2.RandomAccessible<T>	img
protected int	initHorizon
protected boolean	isPadded
protected int	numberOfPoles
protected int	order
protected net.imglib2.Interval	originalInterval
protected double[]	padding
protected int	paddingWidth
protected double[]	poles
protected net.imglib2.RandomAccessibleInterval<S>	tmpCoefStorage
protected double	tolerance

Constructor Summary

Constructors

Constructor and Description
BSplineDecomposition(int order, net.imglib2.RandomAccessible<T> img)
BSplineDecomposition(net.imglib2.RandomAccessible<T> img)

Method Summary

Modifier and Type	Method and Description
void	accept(net.imglib2.RandomAccessibleInterval<S> coefficients)
void	acceptUnpadded(net.imglib2.RandomAccessibleInterval<S> coefficients) Compute coefficients.
static double	gainFromPoles(double[] poles)
net.imglib2.RandomAccessible<T>	getImage()
static net.imglib2.iterator.IntervalIterator	getIterator(net.imglib2.Interval interval, int dim)
static net.imglib2.iterator.IntervalIterator	getIterator(net.imglib2.Interval paddedInterval, net.imglib2.Interval originalInterval, int dim)
protected static <T extends net.imglib2.type.numeric.RealType<T>> void	initializeAntiCausalCoefficients(double z, double c, T previous, net.imglib2.RandomAccess<T> coefs)
protected static <T extends net.imglib2.type.numeric.RealType<T>> double	initializeCausalCoefficients(double z, double tolerance, int dimension, net.imglib2.RandomAccess<T> dataAccess) Data must be 1d or permuted such that the first dimension is the dimension to be iterated over.
static double[]	poles(int splineOrder) Returns the poles for the filter for a spline of a given order.
static double[]	polesCi(double[] poles)
<S extends net.imglib2.type.numeric.RealType<S>,T extends net.imglib2.type.numeric.RealType<T>> void	recursion1d(net.imglib2.RandomAccess<T> srcAccess, net.imglib2.RandomAccess<S> destAccess, double z, double Ci, S previous, long N, int dimension) Compute a 1d forward-backward recursion to compute bspline coefficients.
static <S extends net.imglib2.type.numeric.RealType<S>,T extends net.imglib2.type.numeric.RealType<T>> void	recursion1dUnpadded(net.imglib2.RandomAccess<T> srcAccess, net.imglib2.RandomAccess<S> destAccess, S previous, long N, int dimension, double tolerance, int numberOfPoles, double[] poles, double[] Ci) Compute a 1d forward-backward recursion to compute bspline coefficients.
void	setPadded(boolean isPadded)
String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.function.Consumer

andThen

Field Detail

order

protected final int order

numberOfPoles

protected final int numberOfPoles

poles

protected final double[] poles

Ci

protected final double[] Ci

img

protected final net.imglib2.RandomAccessible<T extends net.imglib2.type.numeric.RealType<T>> img

tolerance

protected double tolerance

paddingWidth

protected int paddingWidth

initHorizon

protected int initHorizon

padding

protected double[] padding

tmpCoefStorage

protected net.imglib2.RandomAccessibleInterval<S extends net.imglib2.type.numeric.RealType<S>> tmpCoefStorage

originalInterval

protected net.imglib2.Interval originalInterval

isPadded

protected boolean isPadded

Constructor Detail

BSplineDecomposition

public BSplineDecomposition(int order,
                            net.imglib2.RandomAccessible<T> img)

BSplineDecomposition

public BSplineDecomposition(net.imglib2.RandomAccessible<T> img)

Method Detail

setPadded

public void setPadded(boolean isPadded)

getImage

public net.imglib2.RandomAccessible<T> getImage()

polesCi

public static double[] polesCi(double[] poles)

gainFromPoles

public static double gainFromPoles(double[] poles)

accept

public void accept(net.imglib2.RandomAccessibleInterval<S> coefficients)

Specified by:

accept in interface Consumer<net.imglib2.RandomAccessibleInterval<S extends net.imglib2.type.numeric.RealType<S>>>

acceptUnpadded

public void acceptUnpadded(net.imglib2.RandomAccessibleInterval<S> coefficients)

Compute coefficients.

Parameters:

coefficients - the interval and destination in which to store coefficients.

getIterator

public static net.imglib2.iterator.IntervalIterator getIterator(net.imglib2.Interval paddedInterval,
                                                                net.imglib2.Interval originalInterval,
                                                                int dim)

getIterator

public static net.imglib2.iterator.IntervalIterator getIterator(net.imglib2.Interval interval,
                                                                int dim)

recursion1dUnpadded

public static <S extends net.imglib2.type.numeric.RealType<S>,T extends net.imglib2.type.numeric.RealType<T>> void recursion1dUnpadded(net.imglib2.RandomAccess<T> srcAccess,
                                                                                                                                       net.imglib2.RandomAccess<S> destAccess,
                                                                                                                                       S previous,
                                                                                                                                       long N,
                                                                                                                                       int dimension,
                                                                                                                                       double tolerance,
                                                                                                                                       int numberOfPoles,
                                                                                                                                       double[] poles,
                                                                                                                                       double[] Ci)

Compute a 1d forward-backward recursion to compute bspline coefficients. Stores results in the destAccess, reads data from srcAccess. srcAccess and destAccess can look into the same RandomAccessible, but need to be different (RandomAccess)es It is the caller's responsibility to ensure the access are positioned correctly before calling.

Parameters:

srcAccess - access for the data

destAccess - access to write results into

previous - a temporary variable

N - width of the recursion

dimension - the dimension along which to operate

tolerance - tolerance for initializing coefficients

numberOfPoles - number of poles

poles - the poles

Ci - Ci

recursion1d

public <S extends net.imglib2.type.numeric.RealType<S>,T extends net.imglib2.type.numeric.RealType<T>> void recursion1d(net.imglib2.RandomAccess<T> srcAccess,
                                                                                                                        net.imglib2.RandomAccess<S> destAccess,
                                                                                                                        double z,
                                                                                                                        double Ci,
                                                                                                                        S previous,
                                                                                                                        long N,
                                                                                                                        int dimension)

Compute a 1d forward-backward recursion to compute bspline coefficients. Stores results in the destAccess, reads data from srcAccess. srcAccess and destAccess can look into the same RandomAccessible, but need to be different (RandomAccess)es It is the caller's responsibility to ensure the access are positioned correctly before calling. See also ITK's: Core/ImageFunction/include/itkBSplineDecompositionImageFilter.hxx

Parameters:

srcAccess - access for the data

destAccess - access to write results into

previous - a temporary variable

N - width of the recursion

dimension - the dimension along which to operate

initializeAntiCausalCoefficients

protected static <T extends net.imglib2.type.numeric.RealType<T>> void initializeAntiCausalCoefficients(double z,
                                                                                                        double c,
                                                                                                        T previous,
                                                                                                        net.imglib2.RandomAccess<T> coefs)

initializeCausalCoefficients

protected static <T extends net.imglib2.type.numeric.RealType<T>> double initializeCausalCoefficients(double z,
                                                                                                      double tolerance,
                                                                                                      int dimension,
                                                                                                      net.imglib2.RandomAccess<T> dataAccess)

Data must be 1d or permuted such that the first dimension is the dimension to be iterated over. See Box 2 of Unser 1999

toString

public String toString()

Overrides:

toString in class Object

poles

public static double[] poles(int splineOrder)

Returns the poles for the filter for a spline of a given order. See Unser, 1997. Part II, Table I for Pole values. See ITK's: Modules/Core/ImageFunction/include/itkBSplineDecompositionImageFilter.hxx

Parameters:

splineOrder - the order of the bspline

Returns:

an array of the poles