net.imglib2.realtransform

Class AffineTransform3D

java.lang.Object

net.imglib2.realtransform.AffineTransform3D

All Implemented Interfaces:

net.imglib2.concatenate.Concatenable<AffineGet>, net.imglib2.concatenate.PreConcatenable<AffineGet>, net.imglib2.EuclideanSpace, AffineGet, AffineSet, InvertibleRealTransform, RealTransform

public class AffineTransform3D
extends Object
implements AffineGet, AffineSet, net.imglib2.concatenate.Concatenable<AffineGet>, net.imglib2.concatenate.PreConcatenable<AffineGet>

3d-affine transformation.

Author:

Stephan Saalfeld

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	AffineTransform3D.AffineMatrix3D

Field Summary

Fields

Modifier and Type	Field and Description
protected AffineTransform3D.AffineMatrix3D	a
protected net.imglib2.RealPoint	d0
protected net.imglib2.RealPoint	d1
protected net.imglib2.RealPoint	d2
protected net.imglib2.RealPoint[]	ds
protected AffineTransform3D	inverse

Constructor Summary

Constructors

Modifier	Constructor and Description
	AffineTransform3D()
protected	AffineTransform3D(AffineTransform3D.AffineMatrix3D a)
protected	AffineTransform3D(AffineTransform3D inverse)

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.
void	applyInverse(double[] source, double[] target) Apply the inverse transform to a target vector to obtain a source vector.
void	applyInverse(float[] source, float[] target) Apply the inverse transform to a target vector to obtain a source vector.
void	applyInverse(net.imglib2.RealPositionable source, net.imglib2.RealLocalizable target) Apply the inverse transform to a target RealLocalizable to obtain a source RealPositionable.
net.imglib2.RealInterval	boundingInterval(net.imglib2.RealInterval interval, IntervalSamplingMethod samplingMethod) Estimate the RealInterval that bounds the given RealInterval after being transformed by a RealTransform.
AffineTransform3D	concatenate(AffineGet affine)
AffineTransform3D	concatenate(AffineTransform3D affine)
AffineTransform3D	copy() Create a deep copy of this RealTransform.
net.imglib2.RealLocalizable	d(int d) Get the constant partial differential vector for dimension d.
net.imglib2.FinalRealInterval	estimateBounds(net.imglib2.RealInterval interval) Calculate the boundary interval of an interval after it has been transformed.
double	get(int row, int column) Get a field of the n×(n+1) affine transformation matrix.
Class<AffineGet>	getConcatenableClass()
Class<AffineGet>	getPreConcatenableClass()
double[]	getRowPackedCopy() Get a copy of the n×(n+1) affine transformation matrix as a row packed array similar to Jama.
double[]	getTranslation() Initialize the translation with a given vector
void	identity() Set to identity transform
AffineTransform3D	inverse() Get the inverse transform.
protected void	invert()
boolean	isIdentity() Check if the RealTransform is identity.
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.
AffineTransform3D	preConcatenate(AffineGet affine)
AffineTransform3D	preConcatenate(AffineTransform3D affine)
void	rotate(int axis, double angle) Rotate
void	scale(double s) Scale
void	scale(double s0, double s1, double s2) Scale
void	set(AffineTransform3D m)
void	set(double... values) Set the n×(n+1) affine transformation matrix with row packed double values.
void	set(double[][] values) Set the n×(n+1) affine transformation matrix with double values from a [row][column] addressed array.
void	set(double m00, double m01, double m02, double m03, double m10, double m11, double m12, double m13, double m20, double m21, double m22, double m23) Set the affine matrix to: m00 m01 m02 m03 m10 m11 m12 m13 m20 m21 m22 m23
void	set(double value, int row, int column) Set a field of the n×(n+1) affine transformation matrix.
void	setTranslation(double... translationVector) Initialize the translation with a given vector
void	toArray(double[] data)
void	toMatrix(double[][] data)
String	toString()
void	translate(double... translationVector) Translation
protected void	updateDs()

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.imglib2.realtransform.RealTransform

apply, applyDimension, applyDimension, applyDimension

Field Detail

a

protected final AffineTransform3D.AffineMatrix3D a

d0

protected final net.imglib2.RealPoint d0

d1

protected final net.imglib2.RealPoint d1

d2

protected final net.imglib2.RealPoint d2

ds

protected final net.imglib2.RealPoint[] ds

inverse

protected final AffineTransform3D inverse

Constructor Detail

AffineTransform3D

public AffineTransform3D()

AffineTransform3D

protected AffineTransform3D(AffineTransform3D.AffineMatrix3D a)

AffineTransform3D

protected AffineTransform3D(AffineTransform3D inverse)

Method Detail

invert

protected void invert()

updateDs

protected void updateDs()

apply

public final 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()

applyInverse

public final void applyInverse(double[] source,
                               double[] target)

Description copied from interface: InvertibleRealTransform

Apply the inverse transform to a target vector to obtain a source vector.

Specified by:

applyInverse in interface InvertibleRealTransform

Parameters:

source - set this to the source coordinates.

target - target coordinates.

applyInverse

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

Description copied from interface: InvertibleRealTransform

Apply the inverse transform to a target vector to obtain a source vector.

Specified by:

applyInverse in interface InvertibleRealTransform

Parameters:

source - set this to the source coordinates.

target - target coordinates.

applyInverse

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

Description copied from interface: InvertibleRealTransform

Apply the inverse transform to a target RealLocalizable to obtain a source RealPositionable.

Specified by:

applyInverse in interface InvertibleRealTransform

Parameters:

source - set this to the source coordinates.

target - target coordinates.

concatenate

public final AffineTransform3D concatenate(AffineTransform3D affine)

concatenate

public final AffineTransform3D concatenate(AffineGet affine)

Specified by:

concatenate in interface net.imglib2.concatenate.Concatenable<AffineGet>

copy

public AffineTransform3D copy()

Description copied from interface: RealTransform

Create a deep copy of this RealTransform.

Deep copying is required to make sure that stateful RealTransforms can be duplicated for concurrent code.

Specified by:

copy in interface AffineGet

Specified by:

copy in interface InvertibleRealTransform

Specified by:

copy in interface RealTransform

Returns:

deep copy

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

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

getConcatenableClass

public Class<AffineGet> getConcatenableClass()

Specified by:

getConcatenableClass in interface net.imglib2.concatenate.Concatenable<AffineGet>

getPreConcatenableClass

public Class<AffineGet> getPreConcatenableClass()

Specified by:

getPreConcatenableClass in interface net.imglib2.concatenate.PreConcatenable<AffineGet>

inverse

public AffineTransform3D inverse()

Description copied from interface: InvertibleRealTransform

Get the inverse transform.

Specified by:

inverse in interface AffineGet

Specified by:

inverse in interface InvertibleRealTransform

Returns:

the inverse transform

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.

preConcatenate

public final AffineTransform3D preConcatenate(AffineTransform3D affine)

preConcatenate

public final AffineTransform3D preConcatenate(AffineGet affine)

Specified by:

preConcatenate in interface net.imglib2.concatenate.PreConcatenable<AffineGet>

rotate

public void rotate(int axis,
                   double angle)

Rotate

Parameters:

axis - 0=x, 1=y, 2=z

angle - angle in radians

scale

public void scale(double s)

Scale

Parameters:

s - scale factor

scale

public void scale(double s0,
                  double s1,
                  double s2)

Scale

Parameters:

s0 - scale factor for dimension 0

s1 - scale factor for dimension 1

s2 - scale factor for dimension 2

translate

public void translate(double... translationVector)

Translation

Parameters:

translationVector - vector describing the translation

getTranslation

public double[] getTranslation()

Initialize the translation with a given vector

Returns:

vector with 3 elements describing the translation

setTranslation

public void setTranslation(double... translationVector)

Initialize the translation with a given vector

Parameters:

translationVector - the translation

identity

public void identity()

Set to identity transform

set

public final void set(AffineTransform3D m)

set

public final void set(double m00,
                      double m01,
                      double m02,
                      double m03,
                      double m10,
                      double m11,
                      double m12,
                      double m13,
                      double m20,
                      double m21,
                      double m22,
                      double m23)

Set the affine matrix to:

 m00 m01 m02 m03
 m10 m11 m12 m13
 m20 m21 m22 m23
 

Parameters:

m00 - element 0,0

m01 - element 0,1

m02 - element 0,2

m03 - element 0,3

m10 - element 1,0

m11 - element 1,1

m12 - element 1,2

m13 - element 1,3

m20 - element 2,0

m21 - element 2,1

m22 - element 2,2

m23 - element 2,3

toArray

public void toArray(double[] data)

toMatrix

public void toMatrix(double[][] data)

toString

public final String toString()

Overrides:

toString in class Object

set

public void set(double value,
                int row,
                int column)

Description copied from interface: AffineSet

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

Specified by:

set in interface AffineSet

Parameters:

value - the value

row - the row index

column - the column index

set

public void set(double... values)

Description copied from interface: AffineSet

Set the n×(n+1) affine transformation matrix with row packed double values.

Specified by:

set in interface AffineSet

Parameters:

values - the lines of values

set

public void set(double[][] values)

Description copied from interface: AffineSet

Set the n×(n+1) affine transformation matrix with double values from a [row][column] addressed array.

Specified by:

set in interface AffineSet

Parameters:

values - a 2d array of values

estimateBounds

public net.imglib2.FinalRealInterval estimateBounds(net.imglib2.RealInterval interval)

Calculate the boundary interval of an interval after it has been transformed.

Parameters:

interval - the original bounds

Returns:

the new bounds

isIdentity

public boolean isIdentity()

Description copied from interface: RealTransform

Check if the RealTransform is identity.

Specified by:

isIdentity in interface RealTransform

Returns:

true if identity

boundingInterval

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

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

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

Returns:

the bounding interval