net.imglib2.realtransform

Class DisplacementFieldTransform

java.lang.Object

net.imglib2.realtransform.PositionFieldTransform

net.imglib2.realtransform.DisplacementFieldTransform

All Implemented Interfaces:

RealTransform

Direct Known Subclasses:

DeformationFieldTransform

public class DisplacementFieldTransform
extends PositionFieldTransform

A RealTransform by continuous offset lookup.

Author:

Stephan Saalfeld <saalfelds@janelia.hhmi.org>, Caleb Hulbert <hulbertc@janelia.hhmi.org>, John Bogovic <bogovicj@janelia.hhmi.org>

Field Summary

Fields

Modifier and Type	Field and Description
protected int	numTargetDimensions

Fields inherited from class net.imglib2.realtransform.PositionFieldTransform

access

Constructor Summary

Constructors

Constructor and Description
DisplacementFieldTransform(RandomAccessibleInterval<T> displacements)
DisplacementFieldTransform(RandomAccessibleInterval<T> displacements, AffineGet pixelToPhysical)
DisplacementFieldTransform(RandomAccessibleInterval<T> displacements, double... spacing)
DisplacementFieldTransform(RandomAccessibleInterval<T> displacements, double[] spacing, double[] offset)
DisplacementFieldTransform(RealRandomAccess<? extends RealLocalizable> displacementsAccess)
DisplacementFieldTransform(RealRandomAccessible<? extends RealLocalizable> displacements)

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(RealLocalizable source, RealPositionable target) Apply the RealTransform to a source RealLocalizable to obtain a target RealPositionable.
RealTransform	copy() Create a deep copy of this RealTransform.
static RandomAccessibleInterval<DoubleType>	createDisplacementField(RealTransform transform, Interval interval, double[] spacing) Creates a RandomAccessibleInterval of DoubleType containing the displacements of a DisplacementFieldTransform for a given RealTransform.
static RandomAccessibleInterval<DoubleType>	createDisplacementField(RealTransform transform, Interval interval, double[] spacing, double[] offset) Creates a RandomAccessibleInterval of DoubleType containing the displacements of a DisplacementFieldTransform for a given RealTransform.
static <T extends RealType<T>> RandomAccessibleInterval<T>	createDisplacementField(RealTransform transform, Interval interval, double[] spacing, double[] offset, Supplier<RealComposite<T>> supplier) Creates a RandomAccessibleInterval containing the displacements of a DisplacementFieldTransform for a given RealTransform.
static <T extends RealType<T>> RandomAccessibleInterval<T>	createDisplacementField(RealTransform transform, Interval interval, RealTransform gridTransform, Supplier<RealComposite<T>> supplier) Creates a RandomAccessibleInterval containing the displacements of a DisplacementFieldTransform for a given RealTransform.
int	numTargetDimensions() Returns m, the minimal dimension of the target vector.

Methods inherited from class net.imglib2.realtransform.PositionFieldTransform

createPositionField, createPositionField, createPositionField, createPositionField, numSourceDimensions

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.RealTransform

isIdentity

Field Detail

numTargetDimensions

protected final int numTargetDimensions

Constructor Detail

DisplacementFieldTransform

public DisplacementFieldTransform(RealRandomAccess<? extends RealLocalizable> displacementsAccess)

DisplacementFieldTransform

public DisplacementFieldTransform(RealRandomAccessible<? extends RealLocalizable> displacements)

DisplacementFieldTransform

public DisplacementFieldTransform(RandomAccessibleInterval<T> displacements)

Type Parameters:

T - type of the displacements

Parameters:

displacements - interleaved displacement vectors, this means that the components of the displacement vectors are in the 0th dimension

DisplacementFieldTransform

public DisplacementFieldTransform(RandomAccessibleInterval<T> displacements,
                                  AffineGet pixelToPhysical)

Type Parameters:

T - type of the displacements

Parameters:

displacements - interleaved displacement vectors, this means that the components of the displacement vectors are in the 0th dimension

pixelToPhysical - a transformation from pixel coordinates to physical coordinates

DisplacementFieldTransform

public DisplacementFieldTransform(RandomAccessibleInterval<T> displacements,
                                  double... spacing)

Type Parameters:

T - type of the displacements

Parameters:

displacements - interleaved displacement vectors, this means that the components of the displacement vectors are in the 0th dimension

spacing - the pixel spacing

DisplacementFieldTransform

public DisplacementFieldTransform(RandomAccessibleInterval<T> displacements,
                                  double[] spacing,
                                  double[] offset)

Type Parameters:

T - type of the displacements

Parameters:

displacements - interleaved displacement vectors, this means that the components of the displacement vectors are in the 0th dimension

spacing - the pixel spacing

offset - the pixel offset

Method Detail

numTargetDimensions

public int numTargetDimensions()

Description copied from interface: RealTransform

Returns m, the minimal dimension of the target vector.

Specified by:

numTargetDimensions in interface RealTransform

Overrides:

numTargetDimensions in class PositionFieldTransform

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

Overrides:

apply in class PositionFieldTransform

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

Overrides:

apply in class PositionFieldTransform

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(RealLocalizable source,
                  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

Overrides:

apply in class PositionFieldTransform

Parameters:

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

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

copy

public RealTransform 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 RealTransform

Overrides:

copy in class PositionFieldTransform

Returns:

deep copy

createDisplacementField

public static RandomAccessibleInterval<DoubleType> createDisplacementField(RealTransform transform,
                                                                           Interval interval,
                                                                           double[] spacing)

Creates a RandomAccessibleInterval of DoubleType containing the displacements of a DisplacementFieldTransform for a given RealTransform. This can be useful for saving a transformation as a displacement field, but generally should be not used to create a DisplacementFieldTransform.

Components of the displacements are in the 0th dimension, the extents of the field are given by the given Interval. The output interval will therefore be of size:
[ transform.numTargetDimensions(), interval.dimension(0), ..., interval.dimension( N-1 )]

The spacing parameter specifies how the discrete coordinates of the output displacement field map to the input source coordinates of the transform.

Parameters:

transform - the transform to be converted

interval - interval

spacing - the spacing of the grid

Returns:

the displacement field

createDisplacementField

public static RandomAccessibleInterval<DoubleType> createDisplacementField(RealTransform transform,
                                                                           Interval interval,
                                                                           double[] spacing,
                                                                           double[] offset)

Creates a RandomAccessibleInterval of DoubleType containing the displacements of a DisplacementFieldTransform for a given RealTransform. This can be useful for saving a transformation as a displacement field, but generally should be not used to create a DisplacementFieldTransform.

Components of the displacements are in the 0th dimension, the extents of the field are given by the given Interval. The output interval will therefore be of size:
[ transform.numTargetDimensions(), interval.dimension(0), ..., interval.dimension( N-1 )]

The spacing and offset parameters specify how the discrete coordinates of the output displacement field map to the input source coordinates of the transform.

Parameters:

transform - the transform to be converted

interval - interval

spacing - the spacing of the grid

offset - the offset of the output in physical units

Returns:

the displacement field

createDisplacementField

public static <T extends RealType<T>> RandomAccessibleInterval<T> createDisplacementField(RealTransform transform,
                                                                                          Interval interval,
                                                                                          double[] spacing,
                                                                                          double[] offset,
                                                                                          Supplier<RealComposite<T>> supplier)

Creates a RandomAccessibleInterval containing the displacements of a DisplacementFieldTransform for a given RealTransform. This can be useful for saving a transformation as a displacement field, but generally should be not used to create a DisplacementFieldTransform.

Components of the displacements are in the 0th dimension, the extents of the field are given by the given Interval. The output interval will therefore be of size:
[ transform.numTargetDimensions(), interval.dimension(0), ..., interval.dimension( N-1 )]

The spacing and offset parameters specify how the discrete coordinates of the output displacement field map to the input source coordinates of the transform.

The given supplier determines the output type and must provide RealComposites of size greater than or equal to the transforms target dimension. For example,

  () -> DoubleType.createVector(transform.numTargetDimensions())
 

Type Parameters:

T - the type of the output

Parameters:

transform - the transform to be converted

interval - interval

spacing - the spacing of the grid

offset - the offset of the output in physical units

supplier - supplier for intermediate RealComposite type

Returns:

the displacement field

createDisplacementField

public static <T extends RealType<T>> RandomAccessibleInterval<T> createDisplacementField(RealTransform transform,
                                                                                          Interval interval,
                                                                                          RealTransform gridTransform,
                                                                                          Supplier<RealComposite<T>> supplier)

Creates a RandomAccessibleInterval containing the displacements of a DisplacementFieldTransform for a given RealTransform. This can be useful for saving a transformation as a displacement field, but generally should be not used to create a DisplacementFieldTransform.

Components of the displacements are in the 0th dimension, the extents of the field are given by the given Interval. The output interval will therefore be of size:
[ transform.numTargetDimensions(), interval.dimension(0), ..., interval.dimension( N-1 )]

The RealTransform specifies how the discrete coordinates of the output displacement field map to the input source coordinates of the transform, i.e. it enables setting the spacing and offset of the displacement field grid.

The given supplier determines the output type and must provide RealComposites of size greater than or equal to the transforms target dimension. For example,

  () -> DoubleType.createVector(transform.numTargetDimensions())
 

Type Parameters:

T - the type of the output

Parameters:

transform - the transform to be converted

interval - interval

gridTransform - transformation from the discrete grid to the transform's source coordinates

supplier - supplier for intermediate RealComposite type

Returns:

the displacement field