inra.ijpb.morphology.strel

Class AbstractStrel3D

java.lang.Object

inra.ijpb.algo.AlgoStub

inra.ijpb.morphology.strel.AbstractStrel3D

All Implemented Interfaces:

Algo, Strel3D

Direct Known Subclasses:

AbstractInPlaceStrel3D, AbstractSeparableStrel3D, AbstractStrel, BallStrel, ChamferStrel3D, Cross3DStrel, EllipsoidStrel, ExtrudedStrel

public abstract class AbstractStrel3D
extends AlgoStub
implements Strel3D

Implementation basis for 3D structuring elements

Author:

David Legland

Nested Class Summary

Nested classes/interfaces inherited from interface inra.ijpb.morphology.Strel3D

Strel3D.Shape

Field Summary

Fields inherited from interface inra.ijpb.morphology.Strel3D

BACKGROUND, FOREGROUND

Constructor Summary

Constructors

Constructor and Description
AbstractStrel3D()

Method Summary

Modifier and Type	Method and Description
ij.ImageStack	addBorder(ij.ImageStack image) Adds a border around the image, to avoid edge effects when performing morphological closing or opening.
ij.ImageStack	closing(ij.ImageStack image) 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.ImageStack	cropBorder(ij.ImageStack image) Retrieve the portion of image that corresponds to the original image before adding border.
ij.ImageStack	dilation(ij.ImageStack image) Implements a default algorithm for dilation, that consists in iterating over the neighbors of each pixel to compute the maximum value.
ij.ImageStack	erosion(ij.ImageStack image) Implements a default algorithm for erosion, that consists in iterating over the neighbors of each pixel to compute the minimum value.
protected void	fireProgressChanged(AlgoEvent evt)
protected void	fireProgressChanged(Object source, double step, double total)
protected void	fireStatusChanged(AlgoEvent evt)
protected void	fireStatusChanged(Object source, String message)
ij.ImageStack	opening(ij.ImageStack image) Performs a morphological opening on the input stack, by applying first an erosion, then a dilation with the reversed structuring element.
boolean	showProgress() Returns a boolean flag indicating whether or not this structuring element should display its progress or not
void	showProgress(boolean b) Specifies if this structuring element should display its progress.

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.Strel3D

getMask3D, getOffset, getShifts3D, getSize, reverse

Methods inherited from interface inra.ijpb.algo.Algo

addAlgoListener, removeAlgoListener

Constructor Detail

AbstractStrel3D

public AbstractStrel3D()

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 3D array (first index is z, second is y, last one is x)

Returns:

the series of 3D 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.ImageStack addBorder(ij.ImageStack 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(ImageStack)

cropBorder

public ij.ImageStack cropBorder(ij.ImageStack 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:

 ImageStack result = strel3d.cropBorder(strel3d.addBorder(inputImage));
 

Parameters:

image - the image to crop

Returns:

the image with strel padding removed.

See Also:

addBorder(ImageStack)

showProgress

public boolean showProgress()

Description copied from interface: Strel3D

Returns a boolean flag indicating whether or not this structuring element should display its progress or not

Specified by:

showProgress in interface Strel3D

Returns:

a boolean flag with value true if progress should be displayed

showProgress

public void showProgress(boolean b)

Description copied from interface: Strel3D

Specifies if this structuring element should display its progress.

Specified by:

showProgress in interface Strel3D

Parameters:

b - a boolean flag with value true if progress should be displayed

dilation

public ij.ImageStack dilation(ij.ImageStack 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 Strel3D

Parameters:

image - the input image

Returns:

the result of dilation with this structuring element

See Also:

Strel3D.getShifts3D(), erosion(ImageStack)

erosion

public ij.ImageStack erosion(ij.ImageStack 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 Strel3D

Parameters:

image - the input image

Returns:

the result of erosion with this structuring element

See Also:

Strel3D.getShifts3D(), dilation(ImageStack)

closing

public ij.ImageStack closing(ij.ImageStack image)

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

Parameters:

image - the input image

Returns:

the result of closing with this structuring element

See Also:

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

opening

public ij.ImageStack opening(ij.ImageStack image)

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

Parameters:

image - the input image

Returns:

the result of closing with this structuring element

See Also:

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

fireProgressChanged

protected void fireProgressChanged(Object source,
                                   double step,
                                   double total)

Overrides:

fireProgressChanged in class AlgoStub

fireProgressChanged

protected void fireProgressChanged(AlgoEvent evt)

Overrides:

fireProgressChanged in class AlgoStub

fireStatusChanged

protected void fireStatusChanged(Object source,
                                 String message)

Overrides:

fireStatusChanged in class AlgoStub

fireStatusChanged

protected void fireStatusChanged(AlgoEvent evt)

Overrides:

fireStatusChanged in class AlgoStub