Module org.bonej.bonej_plugins

Package org.bonej.wrapperPlugins.wrapperUtils

Class HyperstackUtils

java.lang.Object

org.bonej.wrapperPlugins.wrapperUtils.HyperstackUtils

public final class HyperstackUtils
extends Object

A static class containing utilities for splitting an n-dimensional hyperstack into arbitrary subspaces

Doesn't copy the subspaces, rather provides HyperstackUtils.Subspace objects, which contain a RandomAccessibleInterval that can be used to traverse a certain subspace. Each HyperstackUtils.Subspace also contains metadata, which locates the subspace in the hyperspace.

The code works for now, but a refactor is in place if/when ImgPlus API changes or is replaced by another metadata rich class.

If you want to split a hyperspace into {X, Y, T} subspaces, and the hyperspace has more than one time dimension, *all* of the time dimensions will be lumped into {X, Y, T₁, T₂, .. T_n} subspaces. That is, instead of {X, Y, T₁}, {X, Y, T₂}, .. {X, Y, T_n}.

Author:

Richard Domander

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	HyperstackUtils.Subspace<T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>	A class which stores a subspace interval of an n-dimensional hyperspace, and metadata

Method Summary

Modifier and Type	Method	Description
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> Stream<HyperstackUtils.Subspace<T>>	split3DSubspaces(net.imagej.ImgPlus<T> hyperStack)	Splits the hyperstack into {X, Y, Z} subspaces.
static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>> Stream<HyperstackUtils.Subspace<T>>	splitSubspaces(net.imagej.ImgPlus<T> hyperStack, Collection<net.imagej.axis.AxisType> subspaceTypes)	Splits the hyperstack into subspaces defined by the given axes.

Methods inherited from class java.lang.Object

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

Method Details

split3DSubspaces

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
Stream<HyperstackUtils.Subspace<T>> split3DSubspaces(net.imagej.ImgPlus<T> hyperStack)

Splits the hyperstack into {X, Y, Z} subspaces.

Type Parameters:

T - type of the elements in the image.

Parameters:

hyperStack - an N-dimensional image.

Returns:

a stream of all the subspaces found.

See Also:

• splitSubspaces(ImgPlus, Collection)

splitSubspaces

public static <T extends net.imglib2.type.numeric.RealType<T> & net.imglib2.type.NativeType<T>>
Stream<HyperstackUtils.Subspace<T>> splitSubspaces(net.imagej.ImgPlus<T> hyperStack,
 Collection<net.imagej.axis.AxisType> subspaceTypes)

Splits the hyperstack into subspaces defined by the given axes.

If all the given axis types are not found in the hyperstack, gives subspaces of the found types. If none of the types are found, returns an empty stream. For example, if you want to split a {X, Y, C, T} hyperstack into {X, Y, Z}, returns all the {X, Y} subspaces.

NB Assumes that the given ImgPlus has the necessary metadata, i.e. its CalibratedAxis have AxisType.

Type Parameters:

T - type of the elements in the image.

Parameters:

hyperStack - an N-dimensional image.

subspaceTypes - the types of the axis in the desired subspace.

Returns:

a stream of all the subspaces found.