net.imglib2.algorithm.blocks.dfield

Class DisplacementFields

java.lang.Object

net.imglib2.algorithm.blocks.dfield.DisplacementFields

public final class DisplacementFields
extends Object

Utility methods for creating displacement fields from RealTransform.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	DisplacementFields.TransformedDisplacementField<D extends net.imglib2.type.NativeType<D> & net.imglib2.type.numeric.RealType<D>> A (zero-min) DisplacementField and the affine transform that turns displacement field coordinates into target coordinates.

Method Summary

Modifier and Type	Method and Description
static <D extends net.imglib2.type.NativeType<D> & net.imglib2.type.numeric.RealType<D>> net.imglib2.RandomAccessibleInterval<D>	createNormalized(net.imglib2.realtransform.RealTransform transform, net.imglib2.Dimensions dimensions, double[] spacing, double[] offset, D type) Sample the given RealTransform to create a normalized displacement field.
static DisplacementFields.TransformedDisplacementField<net.imglib2.type.numeric.real.DoubleType>	sample(net.imglib2.realtransform.RealTransform transform, net.imglib2.Interval interval, double[] spacing) Sample the given transform into a DisplacementField that can be used for interpolated lookup into a source image BlockSupplier with the displacementFieldAffine block operator.
static <D extends net.imglib2.type.NativeType<D> & net.imglib2.type.numeric.RealType<D>> DisplacementFields.TransformedDisplacementField<D>	sample(net.imglib2.realtransform.RealTransform transform, net.imglib2.Interval interval, double[] spacing, D type) Sample the given transform into a DisplacementField that can be used for interpolated lookup into a source image BlockSupplier with the displacementFieldAffine block operator.

Methods inherited from class java.lang.Object

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

Method Detail

sample

public static DisplacementFields.TransformedDisplacementField<net.imglib2.type.numeric.real.DoubleType> sample(net.imglib2.realtransform.RealTransform transform,
                                                                                                               net.imglib2.Interval interval,
                                                                                                               double[] spacing)

Sample the given transform into a DisplacementField that can be used for interpolated lookup into a source image BlockSupplier with the displacementFieldAffine block operator.

The transform is from target to source image coordinates.

The transform is sampled in the given interval with the given spacing between sample points.

Parameters:

transform - the transform to sample

interval - the interval in which to sample coordinates

spacing - the spacing between samples

Returns:

the (zero-min) DisplacementField and the transformFromField that turns displacement field coordinates into target coordinates (scaling by spacing and shifting to the min of interval).

sample

public static <D extends net.imglib2.type.NativeType<D> & net.imglib2.type.numeric.RealType<D>> DisplacementFields.TransformedDisplacementField<D> sample(net.imglib2.realtransform.RealTransform transform,
                                                                                                                                                          net.imglib2.Interval interval,
                                                                                                                                                          double[] spacing,
                                                                                                                                                          D type)

Sample the given transform into a DisplacementField that can be used for interpolated lookup into a source image BlockSupplier with the displacementFieldAffine block operator.

The transform is from target to source image coordinates.

The transform is sampled in the given interval with the given spacing between sample points.

Type Parameters:

D - displacement component type. should be DoubleType or FloatType.

Parameters:

transform - the transform to sample

interval - the interval in which to sample coordinates

spacing - the spacing between samples

type - displacement component type. should be DoubleType or FloatType.

Returns:

the (zero-min) DisplacementField and the transformFromField that turns displacement field coordinates into target coordinates (scaling by spacing and shifting to the min of interval).

createNormalized

public static <D extends net.imglib2.type.NativeType<D> & net.imglib2.type.numeric.RealType<D>> net.imglib2.RandomAccessibleInterval<D> createNormalized(net.imglib2.realtransform.RealTransform transform,
                                                                                                                                                         net.imglib2.Dimensions dimensions,
                                                                                                                                                         double[] spacing,
                                                                                                                                                         double[] offset,
                                                                                                                                                         D type)

Sample the given RealTransform to create a normalized displacement field.

A "normalized" field expresses displacements in units relative to the displacement grid's own pixel spacing. Consequently, downsampling the grid by a factor of N requires scaling the displacement vectors by 1/N to maintain normalization.

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

Type Parameters:

D - displacement component type. should be DoubleType or FloatType.

Parameters:

transform - the transform to sample

dimensions - dimensions of the displacement field to create (dimension 0 for the vector components will be prepended)

spacing - spacing of the samples

offset - offset of the samples

type - displacement component type. should be DoubleType or FloatType.

Returns:

the displacement field