net.imglib2.algorithm.componenttree.pixellist

Class PixelListComponentTree<T extends net.imglib2.type.Type<T>>

java.lang.Object

net.imglib2.algorithm.componenttree.pixellist.PixelListComponentTree<T>

Type Parameters:

T - value type of the input image.

All Implemented Interfaces:

Iterable<PixelListComponent<T>>, ComponentForest<PixelListComponent<T>>, ComponentTree<PixelListComponent<T>>, PartialComponent.Handler<net.imglib2.algorithm.componenttree.pixellist.PixelListPartialComponent<T>>

public final class PixelListComponentTree<T extends net.imglib2.type.Type<T>>
extends Object
implements ComponentTree<PixelListComponent<T>>, Iterable<PixelListComponent<T>>, PartialComponent.Handler<net.imglib2.algorithm.componenttree.pixellist.PixelListPartialComponent<T>>

Component tree of an image stored as a tree of PixelListComponents. This class is used both to represent and build the tree.

TODO Add support for non-zero-min RandomAccessibleIntervals. (Currently, we assume that the input image is a zero-min interval.)

Author:

Tobias Pietzsch

Method Summary

Modifier and Type	Method and Description
static <T extends net.imglib2.type.numeric.RealType<T>> PixelListComponentTree<T>	buildComponentTree(net.imglib2.RandomAccessibleInterval<T> input, T type, boolean darkToBright) Build a component tree from an input image.
static <T extends net.imglib2.type.Type<T>> PixelListComponentTree<T>	buildComponentTree(net.imglib2.RandomAccessibleInterval<T> input, T maxValue, Comparator<T> comparator) Build a component tree from an input image.
static <T extends net.imglib2.type.Type<T>> PixelListComponentTree<T>	buildComponentTree(net.imglib2.RandomAccessibleInterval<T> input, T maxValue, Comparator<T> comparator, net.imglib2.img.ImgFactory<net.imglib2.type.numeric.integer.LongType> imgFactory) Build a component tree from an input image.
static <T extends net.imglib2.type.numeric.RealType<T>> PixelListComponentTree<T>	buildComponentTree(net.imglib2.RandomAccessibleInterval<T> input, T type, net.imglib2.img.ImgFactory<net.imglib2.type.numeric.integer.LongType> imgFactory, boolean darkToBright) Build a component tree from an input image.
void	emit(net.imglib2.algorithm.componenttree.pixellist.PixelListPartialComponent<T> partialComponent) BuildComponentTree calls this for every completed component.
Iterator<PixelListComponent<T>>	iterator() Returns an iterator over all connected components in the tree.
PixelListComponent<T>	root() Get the root component.
Set<PixelListComponent<T>>	roots() Get the root component.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Method Detail

buildComponentTree

public static <T extends net.imglib2.type.numeric.RealType<T>> PixelListComponentTree<T> buildComponentTree(net.imglib2.RandomAccessibleInterval<T> input,
                                                                                                            T type,
                                                                                                            boolean darkToBright)

Build a component tree from an input image. Calls buildComponentTree(RandomAccessibleInterval, RealType, ImgFactory, boolean) using an ArrayImgFactory or CellImgFactory depending on input image size.

Parameters:

input - the input image.

type - a variable of the input image type.

darkToBright - whether to apply thresholds from dark to bright (true) or bright to dark (false)

Returns:

component tree of the image.

buildComponentTree

public static <T extends net.imglib2.type.numeric.RealType<T>> PixelListComponentTree<T> buildComponentTree(net.imglib2.RandomAccessibleInterval<T> input,
                                                                                                            T type,
                                                                                                            net.imglib2.img.ImgFactory<net.imglib2.type.numeric.integer.LongType> imgFactory,
                                                                                                            boolean darkToBright)

Build a component tree from an input image.

Parameters:

input - the input image.

type - a variable of the input image type.

imgFactory - used for creating the PixelList image (see PixelListPartialComponentGenerator).

darkToBright - whether to apply thresholds from dark to bright (true) or bright to dark (false)

Returns:

component tree of the image.

buildComponentTree

public static <T extends net.imglib2.type.Type<T>> PixelListComponentTree<T> buildComponentTree(net.imglib2.RandomAccessibleInterval<T> input,
                                                                                                T maxValue,
                                                                                                Comparator<T> comparator)

Build a component tree from an input image. Calls buildComponentTree(RandomAccessibleInterval, Type, Comparator, ImgFactory) using an ArrayImgFactory or CellImgFactory depending on input image size.

Parameters:

input - the input image.

maxValue - a value (e.g., grey-level) greater than any occurring in the input image.

comparator - determines ordering of threshold values.

Returns:

component tree of the image.

buildComponentTree

public static <T extends net.imglib2.type.Type<T>> PixelListComponentTree<T> buildComponentTree(net.imglib2.RandomAccessibleInterval<T> input,
                                                                                                T maxValue,
                                                                                                Comparator<T> comparator,
                                                                                                net.imglib2.img.ImgFactory<net.imglib2.type.numeric.integer.LongType> imgFactory)

Build a component tree from an input image.

Parameters:

input - the input image.

maxValue - a value (e.g., grey-level) greater than any occurring in the input image.

comparator - determines ordering of threshold values.

imgFactory - used for creating the PixelList image PixelListPartialComponentGenerator.

Returns:

component tree of the image.

emit

public void emit(net.imglib2.algorithm.componenttree.pixellist.PixelListPartialComponent<T> partialComponent)

Description copied from interface: PartialComponent.Handler

BuildComponentTree calls this for every completed component. NOTE THAT THE COMPONENT IS RE-USED BY BuildComponentTree! That is, after calling emit() new pixels may be added, etc. Do not store the component object but rather copy the relevant data!

Specified by:

emit in interface PartialComponent.Handler<net.imglib2.algorithm.componenttree.pixellist.PixelListPartialComponent<T extends net.imglib2.type.Type<T>>>

Parameters:

partialComponent - a completed component

iterator

public Iterator<PixelListComponent<T>> iterator()

Returns an iterator over all connected components in the tree.

Specified by:

iterator in interface Iterable<PixelListComponent<T extends net.imglib2.type.Type<T>>>

Returns:

iterator over all connected components in the tree.

root

public PixelListComponent<T> root()

Get the root component.

Specified by:

root in interface ComponentTree<PixelListComponent<T extends net.imglib2.type.Type<T>>>

Returns:

root component.

roots

public Set<PixelListComponent<T>> roots()

Get the root component.

Specified by:

roots in interface ComponentForest<PixelListComponent<T extends net.imglib2.type.Type<T>>>

Returns:

a singleton set containing the root component.