Watershed (ImgLib2 Javadocs 0-SNAPSHOT API)

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>>

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

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()

Constructors
Constructor and Description
`Watershed()`

Method Summary

All Methods Instance Methods Concrete Methods
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>>>

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

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

image

seeds

output

Constructor Detail

Watershed

Method Detail

setIntensityImage

setSeeds

setStructuringElement

setOutputLabeling

process

checkInput

getErrorMessage

getResult