inra.ijpb.morphology.strel

Class AbstractStrel

java.lang.Object

inra.ijpb.algo.AlgoStub

inra.ijpb.morphology.strel.AbstractStrel3D

inra.ijpb.morphology.strel.AbstractStrel

All Implemented Interfaces:

Algo, Strel, Strel3D

Direct Known Subclasses:

AbstractInPlaceStrel, AbstractSeparableStrel, ChamferStrel, OrientedLineStrel

public abstract class AbstractStrel
extends AbstractStrel3D
implements Strel

Implementation basis for planar structuring elements. The aim of this class is mostly to allow the application of 2D structuring elements to 3D stacks, without having to write specific code in derived classes. Default implementations for 2D morphological operations are also provided. Morphological operations for stacks are implemented such that the planar strel is applied to each slice, and the result is added to the result stack.

Author:

David Legland

Nested Class Summary

Nested classes/interfaces inherited from interface inra.ijpb.morphology.Strel

Strel.Shape

Field Summary

Fields inherited from interface inra.ijpb.morphology.Strel

BACKGROUND, FOREGROUND

Constructor Summary

Constructors

Constructor and Description
AbstractStrel()

Method Summary

Modifier and Type	Method and Description
ij.process.ImageProcessor	addBorder(ij.process.ImageProcessor image) Adds a border around the image, to avoid edge effects when performing morphological closing or opening.
ij.process.ImageProcessor	closing(ij.process.ImageProcessor image) Performs a morphological closing on the input image, by applying first a dilation, then an erosion with the reversed structuring element.
ij.ImageStack	closing(ij.ImageStack stack) Performs a morphological closing on the input stack, by applying first a dilation, then an erosion with the reversed structuring element.
protected static int[][]	convertMaskToShifts(int[][] mask) Converts the specified (binary) mask into a series of shifts, assuming the offset of the mask is located at its center.
ij.process.ImageProcessor	cropBorder(ij.process.ImageProcessor image) Retrieve the portion of image that corresponds to the original image before adding border.
ij.process.ImageProcessor	dilation(ij.process.ImageProcessor image) Implements a default algorithm for dilation, that consists in iterating over the neighbors of each pixel to compute the maximum value.
ij.ImageStack	dilation(ij.ImageStack stack) Implements a default algorithm for dilation, that consists in iterating over the neighbors of each pixel to compute the maximum value.
ij.process.ImageProcessor	erosion(ij.process.ImageProcessor image) Implements a default algorithm for erosion, that consists in iterating over the neighbors of each pixel to compute the minimum value.
ij.ImageStack	erosion(ij.ImageStack stack) Implements a default algorithm for erosion, that consists in iterating over the neighbors of each pixel to compute the minimum value.
String	getChannelName() Returns the name of the channel currently processed, or null by default.
int[][][]	getMask3D() Returns the structuring element as a mask.
int[][]	getShifts3D() Returns the structuring element as a set of shifts.
ij.process.ImageProcessor	opening(ij.process.ImageProcessor image) Performs a morphological opening on the input image, by applying first an erosion, then a dilation with the reversed structuring element.
ij.ImageStack	opening(ij.ImageStack stack) Performs a morphological opening on the input stack, by applying first an erosion, then a dilation with the reversed structuring element.
void	setChannelName(String channelName) Sets the name of the currently processed channel.

Methods inherited from class inra.ijpb.morphology.strel.AbstractStrel3D

addBorder, convertMaskToShifts, cropBorder, fireProgressChanged, fireProgressChanged, fireStatusChanged, fireStatusChanged, showProgress, showProgress

Methods inherited from class inra.ijpb.algo.AlgoStub

addAlgoListener, removeAlgoListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface inra.ijpb.morphology.Strel

getMask, getOffset, getShifts, getSize, reverse

Methods inherited from interface inra.ijpb.morphology.Strel3D

showProgress, showProgress

Methods inherited from interface inra.ijpb.algo.Algo

addAlgoListener, removeAlgoListener

Constructor Detail

AbstractStrel

public AbstractStrel()

Method Detail

convertMaskToShifts

protected static final int[][] convertMaskToShifts(int[][] mask)

Converts the specified (binary) mask into a series of shifts, assuming the offset of the mask is located at its center.

Parameters:

mask - a binary mask as a 2D array (first index is y, second is x)

Returns:

the series of 2D shifts from offset/center, as n-by-2 array of signed integers. The first value corresponds to the shift in the x direction.

addBorder

public ij.process.ImageProcessor addBorder(ij.process.ImageProcessor image)

Adds a border around the image, to avoid edge effects when performing morphological closing or opening. The size of the border is determined by Strel size and offset. Replicated border strategy is used to expand image.

Parameters:

image - the image to pad

Returns:

the image with border extended.

See Also:

cropBorder(ImageProcessor)

cropBorder

public ij.process.ImageProcessor cropBorder(ij.process.ImageProcessor image)

Retrieve the portion of image that corresponds to the original image before adding border. The crop parameters are retrieved from strel size and offset. This method works together with the addBorder method. In practice, we retrieve the input image if we perform the following:

 ImageProcessor result = strel.cropBorder(strel.addBorder(inputImage));
 

Parameters:

image - the image to crop

Returns:

the image with strel padding removed.

See Also:

addBorder(ImageProcessor)

dilation

public ij.process.ImageProcessor dilation(ij.process.ImageProcessor image)

Implements a default algorithm for dilation, that consists in iterating over the neighbors of each pixel to compute the maximum value. The neighbors are obtained via the getShifts() method.

Specified by:

dilation in interface Strel

Parameters:

image - the input image

Returns:

the result of dilation with this structuring element

See Also:

Strel.getShifts(), erosion(ImageProcessor)

erosion

public ij.process.ImageProcessor erosion(ij.process.ImageProcessor image)

Implements a default algorithm for erosion, that consists in iterating over the neighbors of each pixel to compute the minimum value. The neighbors are obtained via the getShifts() method.

Specified by:

erosion in interface Strel

Parameters:

image - the input image

Returns:

the result of erosion with this structuring element

See Also:

Strel.getShifts(), dilation(ImageProcessor)

closing

public ij.process.ImageProcessor closing(ij.process.ImageProcessor image)

Performs a morphological closing on the input image, by applying first a dilation, then an erosion with the reversed structuring element.

Specified by:

closing in interface Strel

Parameters:

image - the input image

Returns:

the result of closing with this structuring element

See Also:

dilation(ij.process.ImageProcessor), erosion(ij.process.ImageProcessor), opening(ij.process.ImageProcessor), Strel3D.reverse()

opening

public ij.process.ImageProcessor opening(ij.process.ImageProcessor image)

Performs a morphological opening on the input image, by applying first an erosion, then a dilation with the reversed structuring element.

Specified by:

opening in interface Strel

Parameters:

image - the input image

Returns:

the result of opening with this structuring element

See Also:

dilation(ij.process.ImageProcessor), erosion(ij.process.ImageProcessor), closing(ij.process.ImageProcessor), Strel3D.reverse()

getMask3D

public int[][][] getMask3D()

Description copied from interface: Strel3D

Returns the structuring element as a mask. Each value is either 0 or 255. The first index corresponds to the z position, the second index to the y direction, and the third one to the x position.

Specified by:

getMask3D in interface Strel3D

Returns:

the mask of the structuring element

getShifts3D

public int[][] getShifts3D()

Description copied from interface: Strel3D

Returns the structuring element as a set of shifts. The size of the result is N-by-3, where N is the number of elements of the structuring element. The first value corresponds to the shift in the x direction.

Specified by:

getShifts3D in interface Strel3D

Returns:

a set of shifts

setChannelName

public void setChannelName(String channelName)

Sets the name of the currently processed channel.

Specified by:

setChannelName in interface Strel

Parameters:

channelName - the name of the currently processed channel

getChannelName

public String getChannelName()

Returns the name of the channel currently processed, or null by default.

Specified by:

getChannelName in interface Strel

Returns:

the name of the currently processed channel

dilation

public ij.ImageStack dilation(ij.ImageStack stack)

Description copied from class: AbstractStrel3D

Implements a default algorithm for dilation, that consists in iterating over the neighbors of each pixel to compute the maximum value. The neighbors are obtained via the getShifts() method.

Specified by:

dilation in interface Strel3D

Overrides:

dilation in class AbstractStrel3D

Parameters:

stack - the input image

Returns:

the result of dilation with this structuring element

See Also:

Strel3D.getShifts3D(), AbstractStrel3D.erosion(ImageStack)

erosion

public ij.ImageStack erosion(ij.ImageStack stack)

Description copied from class: AbstractStrel3D

Implements a default algorithm for erosion, that consists in iterating over the neighbors of each pixel to compute the minimum value. The neighbors are obtained via the getShifts() method.

Specified by:

erosion in interface Strel3D

Overrides:

erosion in class AbstractStrel3D

Parameters:

stack - the input image

Returns:

the result of erosion with this structuring element

See Also:

Strel3D.getShifts3D(), AbstractStrel3D.dilation(ImageStack)

closing

public ij.ImageStack closing(ij.ImageStack stack)

Description copied from class: AbstractStrel3D

Performs a morphological closing on the input stack, by applying first a dilation, then an erosion with the reversed structuring element.

Specified by:

closing in interface Strel3D

Overrides:

closing in class AbstractStrel3D

Parameters:

stack - the input image

Returns:

the result of closing with this structuring element

See Also:

AbstractStrel3D.dilation(ImageStack), AbstractStrel3D.erosion(ImageStack), AbstractStrel3D.opening(ImageStack), Strel3D.reverse()

opening

public ij.ImageStack opening(ij.ImageStack stack)

Description copied from class: AbstractStrel3D

Performs a morphological opening on the input stack, by applying first an erosion, then a dilation with the reversed structuring element.

Specified by:

opening in interface Strel3D

Overrides:

opening in class AbstractStrel3D

Parameters:

stack - the input image

Returns:

the result of closing with this structuring element

See Also:

AbstractStrel3D.dilation(ImageStack), AbstractStrel3D.erosion(ImageStack), AbstractStrel3D.closing(ImageStack), Strel3D.reverse()