net.imglib2.algorithm.labeling

Class Watershed<T extends RealType<T>,L extends Comparable<L>>

java.lang.Object

net.imglib2.algorithm.labeling.Watershed<T,L>

All Implemented Interfaces:

Algorithm, OutputAlgorithm<Labeling<L>>

public class Watershed<T extends RealType<T>,L extends Comparable<L>>
extends Object
implements OutputAlgorithm<Labeling<L>>

Watershed algorithms. The watershed algorithm segments and labels an image using an analogy to a landscape. The image intensities are turned into the z-height of the landscape and the landscape is "filled with water" and the bodies of water label the landscape's pixels. Here is the reference for the original paper: Lee Vincent, Pierre Soille, Watersheds in digital spaces: An efficient algorithm based on immersion simulations, IEEE Trans. Pattern Anal. Machine Intell., 13(6) 583-598 (1991) Watersheds are often performed on the gradient of an intensity image or one where the edges of the object boundaries have been enhanced. The resulting image has a depressed object interior and a ridge which constrains the watershed boundary.

Author:

Lee Kamentsky

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	Watershed.PixelIntensity<U extends Comparable<U>>

Field Summary

Fields

Modifier and Type	Field and Description
protected RandomAccessibleInterval<T>	image
protected Labeling<L>	output
protected Labeling<L>	seeds

Constructor Summary

Constructors

Constructor and Description
Watershed()

Method Summary

Modifier and Type	Method and Description
boolean	checkInput()
String	getErrorMessage()
Labeling<L>	getResult()
boolean	process() The seeded watershed uses a pre-existing labeling of the space where the labels act as seeds for the output watershed.
void	setIntensityImage(RandomAccessibleInterval<T> image) Provide the intensity image to be watershedded.
void	setOutputLabeling(Labeling<L> outputLabeling) Set the output labeling where the results will be stored.
void	setSeeds(Labeling<L> seeds) Provide the seeds that mark the watersheds.
void	setStructuringElement(long[][] structuringElement) Set the structuring element that defines the connectivity

Methods inherited from class java.lang.Object

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

Field Detail

image

protected RandomAccessibleInterval<T extends RealType<T>> image

seeds

protected Labeling<L extends Comparable<L>> seeds

output

protected Labeling<L extends Comparable<L>> output

Constructor Detail

Watershed

public Watershed()

Method Detail

setIntensityImage

public void setIntensityImage(RandomAccessibleInterval<T> image)

Provide the intensity image to be watershedded.

Parameters:

image - the intensity image that defines the watershed landscape. Lower values will be labeled first.

setSeeds

public void setSeeds(Labeling<L> seeds)

Provide the seeds that mark the watersheds.

Parameters:

seeds - a labeling of the space, defining the first pixels in the space to be labeled. The seeded pixels will be similarly labeled in the output as will be their watershed neighbors.

setStructuringElement

public void setStructuringElement(long[][] structuringElement)

Set the structuring element that defines the connectivity

Parameters:

structuringElement - an array of offsets where each element of the array gives the offset of a connected pixel from a pixel of interest. You can use AllConnectedComponents.getStructuringElement to get an 8-connected (or N-dimensional equivalent) structuring element (all adjacent pixels + diagonals).

setOutputLabeling

public void setOutputLabeling(Labeling<L> outputLabeling)

Set the output labeling where the results will be stored. The class will provide one if none is supplied.

Parameters:

outputLabeling -

process

public boolean process()

The seeded watershed uses a pre-existing labeling of the space where the labels act as seeds for the output watershed. The analogy would be to use dyed liquids emanating from the seeded pixels, flowing to the local minima and then filling individual watersheds until the liquids meet at the boundaries. This implementation breaks ties by assigning the pixel to the label that occupied an adjacent pixel first.

Specified by:

process in interface Algorithm

checkInput

public boolean checkInput()

Specified by:

checkInput in interface Algorithm

getErrorMessage

public String getErrorMessage()

Specified by:

getErrorMessage in interface Algorithm

getResult

public Labeling<L> getResult()

Specified by:

getResult in interface OutputAlgorithm<Labeling<L extends Comparable<L>>>