net.imglib2.realtransform

Class AbstractAffineTransform

java.lang.Object

net.imglib2.realtransform.AbstractAffineTransform

All Implemented Interfaces:

net.imglib2.EuclideanSpace, AffineGet, AffineSet, InvertibleRealTransform, RealTransform

Direct Known Subclasses:

AffineTransform

public abstract class AbstractAffineTransform
extends Object
implements AffineGet, AffineSet

An abstract implementation of an affine transformation that returns default values referring to the identity transformation for all fields. This implementation is not thread safe. Create a AffineGet.copy() for each consumer.

Author:

Stephan Saalfeld

Field Summary

Fields

Modifier and Type	Field and Description
protected Jama.Matrix	a
protected net.imglib2.RealPoint[]	ds
protected int	n
protected double[]	t
protected double[]	tmp

Constructor Summary

Constructors

Modifier	Constructor and Description
	AbstractAffineTransform(int n)
	AbstractAffineTransform(Jama.Matrix matrix)
protected	AbstractAffineTransform(Jama.Matrix a, double[] t)

Method Summary

Modifier and Type	Method and Description
void	apply(double[] source, double[] target) Apply the RealTransform to a source vector to obtain a target vector.
void	apply(float[] source, float[] target) Apply the RealTransform to a source vector to obtain a target vector.
void	apply(net.imglib2.RealLocalizable source, net.imglib2.RealPositionable target) Apply the RealTransform to a source RealLocalizable to obtain a target RealPositionable.
net.imglib2.RealInterval	boundingInterval(net.imglib2.RealInterval interval, IntervalSamplingMethod samplingMethdod) Estimate the RealInterval that bounds the given RealInterval after being transformed by a RealTransform.
net.imglib2.RealLocalizable	d(int d) Get the constant partial differential vector for dimension d.
double	get(int row, int column) Get a field of the n×(n+1) affine transformation matrix.
double[]	getRowPackedCopy() Get a copy of the n×(n+1) affine transformation matrix as a row packed array similar to Jama.
int	numDimensions()
int	numSourceDimensions() Returns n, the minimal number of dimension of the source vector.
int	numTargetDimensions() Returns m, the minimal dimension of the target vector.
protected void	updateDs()

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.imglib2.realtransform.AffineGet

copy, inverse

Methods inherited from interface net.imglib2.realtransform.InvertibleRealTransform

applyInverse, applyInverse, applyInverse

Methods inherited from interface net.imglib2.realtransform.RealTransform

apply, applyDimension, applyDimension, applyDimension, isIdentity

Methods inherited from interface net.imglib2.realtransform.AffineSet

set, set, set

Field Detail

n

protected final int n

a

protected final Jama.Matrix a

t

protected final double[] t

tmp

protected final double[] tmp

ds

protected final net.imglib2.RealPoint[] ds

Constructor Detail

AbstractAffineTransform

protected AbstractAffineTransform(Jama.Matrix a,
                                  double[] t)

AbstractAffineTransform

public AbstractAffineTransform(Jama.Matrix matrix)

AbstractAffineTransform

public AbstractAffineTransform(int n)

Method Detail

updateDs

protected void updateDs()

numDimensions

public int numDimensions()

Specified by:

numDimensions in interface net.imglib2.EuclideanSpace

numSourceDimensions

public int numSourceDimensions()

Description copied from interface: RealTransform

Returns n, the minimal number of dimension of the source vector.

Specified by:

numSourceDimensions in interface RealTransform

Returns:

the dimension of the source vector.

numTargetDimensions

public int numTargetDimensions()

Description copied from interface: RealTransform

Returns m, the minimal dimension of the target vector.

Specified by:

numTargetDimensions in interface RealTransform

Returns:

the dimension of the target vector.

apply

public void apply(double[] source,
                  double[] target)

Description copied from interface: RealTransform

Apply the RealTransform to a source vector to obtain a target vector.

Specified by:

apply in interface RealTransform

Parameters:

source - source coordinates, length must be >= RealTransform.numSourceDimensions()

target - set this to the target coordinates, length must be >= RealTransform.numTargetDimensions()

apply

public void apply(float[] source,
                  float[] target)

Description copied from interface: RealTransform

Apply the RealTransform to a source vector to obtain a target vector.

Specified by:

apply in interface RealTransform

Parameters:

source - source coordinates, length must be >= RealTransform.numSourceDimensions()

target - set this to the target coordinates, length must be >= RealTransform.numTargetDimensions()

apply

public void apply(net.imglib2.RealLocalizable source,
                  net.imglib2.RealPositionable target)

Description copied from interface: RealTransform

Apply the RealTransform to a source RealLocalizable to obtain a target RealPositionable.

Specified by:

apply in interface RealTransform

Parameters:

source - source coordinates, numDimensions() must be >= RealTransform.numSourceDimensions()

target - set this to the target coordinates, numDimensions() must be >= RealTransform.numTargetDimensions()

get

public double get(int row,
                  int column)

Description copied from interface: AffineGet

Get a field of the n×(n+1) affine transformation matrix.

Specified by:

get in interface AffineGet

Parameters:

row - the row index

column - the column index

Returns:

the value

getRowPackedCopy

public double[] getRowPackedCopy()

Description copied from interface: AffineGet

Get a copy of the n×(n+1) affine transformation matrix as a row packed array similar to Jama.

Specified by:

getRowPackedCopy in interface AffineGet

Returns:

the array of values

d

public net.imglib2.RealLocalizable d(int d)

Description copied from interface: AffineGet

Get the constant partial differential vector for dimension d.

Specified by:

d in interface AffineGet

Parameters:

d - the dimension

Returns:

the partial differential vector

boundingInterval

public net.imglib2.RealInterval boundingInterval(net.imglib2.RealInterval interval,
                                                 IntervalSamplingMethod samplingMethdod)

Description copied from interface: RealTransform

Estimate the RealInterval that bounds the given RealInterval after being transformed by a RealTransform.

For arbitrary transformations, it is not necessarily possible to directly calculate the resulting bounding box trivially, therefore, a sampling methods for coordinates in the source interval must be provided. RealTransforms that can calculate the bounding interval more efficiently than by sampling coordinates are encouraged to override this method and to ignore the provided sampling method.

Specified by:

boundingInterval in interface RealTransform

Parameters:

interval - the real interval

samplingMethdod - the method used to sample coordinates of the source interval

Returns:

the bounding interval