net.imglib2.realtransform

Class PositionFieldTransform

java.lang.Object

net.imglib2.realtransform.PositionFieldTransform

All Implemented Interfaces:

RealTransform

Direct Known Subclasses:

DisplacementFieldTransform

public class PositionFieldTransform
extends Object
implements RealTransform

A RealTransform by continuous coordinate 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 net.imglib2.RealRandomAccess<? extends net.imglib2.RealLocalizable>	access
protected int	numTargetDimensions

Constructor Summary

Constructors

Constructor and Description
PositionFieldTransform(net.imglib2.RandomAccessibleInterval<T> positions)
PositionFieldTransform(net.imglib2.RandomAccessibleInterval<T> positions, AffineGet pixelToPhysical)
PositionFieldTransform(net.imglib2.RandomAccessibleInterval<T> positions, double... spacing)
PositionFieldTransform(net.imglib2.RandomAccessibleInterval<T> positions, double[] spacing, double[] offset)
PositionFieldTransform(net.imglib2.RealRandomAccess<? extends net.imglib2.RealLocalizable> positionAccesses)
PositionFieldTransform(net.imglib2.RealRandomAccessible<? extends net.imglib2.RealLocalizable> positions)

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.
RealTransform	copy() Create a deep copy of this RealTransform.
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.DoubleType>	createPositionField(RealTransform transform, net.imglib2.Interval interval, double[] spacing) Creates a RandomAccessibleInterval of DoubleType containing the positions of a PositionFieldTransform for a given RealTransform.
static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.DoubleType>	createPositionField(RealTransform transform, net.imglib2.Interval interval, double[] spacing, double[] offset) Creates a RandomAccessibleInterval of DoubleType containing the positions of a PositionFieldTransform for a given RealTransform.
static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.RandomAccessibleInterval<T>	createPositionField(RealTransform transform, net.imglib2.Interval interval, double[] spacing, double[] offset, Supplier<net.imglib2.view.composite.RealComposite<T>> supplier) Creates a RandomAccessibleInterval containing the positions of a PositionFieldTransform for a given RealTransform.
static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.RandomAccessibleInterval<T>	createPositionField(RealTransform transform, net.imglib2.Interval interval, RealTransform gridTransform, Supplier<net.imglib2.view.composite.RealComposite<T>> supplier) Creates a RandomAccessibleInterval containing the positions of a PositionFieldTransform for a given RealTransform.
int	numSourceDimensions() Returns n, the minimal number of dimension of the source vector.
int	numTargetDimensions() Returns m, the minimal dimension of the target vector.

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

apply, applyDimension, applyDimension, applyDimension, boundingInterval, isIdentity

Field Detail

access

protected final net.imglib2.RealRandomAccess<? extends net.imglib2.RealLocalizable> access

numTargetDimensions

protected final int numTargetDimensions

Constructor Detail

PositionFieldTransform

public PositionFieldTransform(net.imglib2.RealRandomAccess<? extends net.imglib2.RealLocalizable> positionAccesses)

PositionFieldTransform

public PositionFieldTransform(net.imglib2.RealRandomAccessible<? extends net.imglib2.RealLocalizable> positions)

PositionFieldTransform

public PositionFieldTransform(net.imglib2.RandomAccessibleInterval<T> positions)

Type Parameters:

T - position type

Parameters:

positions - interleaved target coordinate, this means that the components of the target coordinates are in the 0th dimension

PositionFieldTransform

public PositionFieldTransform(net.imglib2.RandomAccessibleInterval<T> positions,
                              AffineGet pixelToPhysical)

Type Parameters:

T - position type

Parameters:

positions - interleaved target coordinate, this means that the components of the target coordinates are in the 0th dimension

pixelToPhysical - a transformation from pixel coordinates to physical coordinates

PositionFieldTransform

public PositionFieldTransform(net.imglib2.RandomAccessibleInterval<T> positions,
                              double... spacing)

Type Parameters:

T - position type

Parameters:

positions - interleaved target coordinate, this means that the components of the target coordinates are in the 0th dimension

spacing - the pixel spacing

PositionFieldTransform

public PositionFieldTransform(net.imglib2.RandomAccessibleInterval<T> positions,
                              double[] spacing,
                              double[] offset)

Type Parameters:

T - position type

Parameters:

positions - interleaved target coordinate, this means that the components of the target coordinates are in the 0th dimension

spacing - the pixel spacing

offset - the pixel offset

Method Detail

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()

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

Returns:

deep copy

createPositionField

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.DoubleType> createPositionField(RealTransform transform,
                                                                                                                 net.imglib2.Interval interval,
                                                                                                                 double[] spacing)

Creates a RandomAccessibleInterval of DoubleType containing the positions of a PositionFieldTransform 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 PositionFieldTransform.

Components of the positions 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 position 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 position field

createPositionField

public static net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.real.DoubleType> createPositionField(RealTransform transform,
                                                                                                                 net.imglib2.Interval interval,
                                                                                                                 double[] spacing,
                                                                                                                 double[] offset)

Creates a RandomAccessibleInterval of DoubleType containing the positions of a PositionFieldTransform 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 PositionFieldTransform.

Components of the positions 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 position 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 position field

createPositionField

public static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.RandomAccessibleInterval<T> createPositionField(RealTransform transform,
                                                                                                                           net.imglib2.Interval interval,
                                                                                                                           double[] spacing,
                                                                                                                           double[] offset,
                                                                                                                           Supplier<net.imglib2.view.composite.RealComposite<T>> supplier)

Creates a RandomAccessibleInterval containing the positions of a PositionFieldTransform 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 PositionFieldTransform.

Components of the positions 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 position 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 - output type

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 position field

createPositionField

public static <T extends net.imglib2.type.numeric.RealType<T>> net.imglib2.RandomAccessibleInterval<T> createPositionField(RealTransform transform,
                                                                                                                           net.imglib2.Interval interval,
                                                                                                                           RealTransform gridTransform,
                                                                                                                           Supplier<net.imglib2.view.composite.RealComposite<T>> supplier)

Creates a RandomAccessibleInterval containing the positions of a PositionFieldTransform 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 PositionFieldTransform.

Components of the positions 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 position 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 - output type

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 position field