inra.ijpb.morphology

Class Morphology

java.lang.Object

inra.ijpb.morphology.Morphology

public class Morphology
extends Object

Collection of static methods for morphological filters, as well as an enumeration of available methods.

Example of use:

 ImageProcessor image = IJ.getImage().getProcessor();
 Strel se = SquareStrel.fromDiameter(5);
 ImageProcessor grad = Morphology.gradient(image, se);
 ImagePlus res = new ImagePlus("Gradient", grad);
 res.show(); 
 

Example of use with 3D image (stack):

 ImageStack image = IJ.getImage().getStack();
 Strel3D se = CubeStrel.fromDiameter(3);
 ImageStack grad = Morphology.gradient(image, se);
 ImagePlus res = new ImagePlus("Gradient3D", grad);
 res.show(); 
 

Or directly with an instance of ImagePlus:

 ImagePlus image = IJ.getImage();
 Strel se = SquareStrel.fromDiameter(5);
 ImagePlus res = Morphology.gradient(image, se);
 res.show(); 
 

Author:

David Legland

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Morphology.Operation A pre-defined set of basis morphological operations, that can be easily used with a GenericDialog.

Method Summary

Modifier and Type	Method and Description
static ij.ImagePlus	blackTopHat(ij.ImagePlus imagePlus, Strel3D strel) Computes black top hat (or "bottom hat") of the original image.
static ij.process.ImageProcessor	blackTopHat(ij.process.ImageProcessor image, Strel strel) Computes black top hat (or "bottom hat") of the original image.
static ij.ImageStack	blackTopHat(ij.ImageStack image, Strel3D strel) Computes black top hat (or "bottom hat") of the original image.
static ij.ImagePlus	closing(ij.ImagePlus imagePlus, Strel3D strel) Performs morphological closing on the input image.
static ij.process.ImageProcessor	closing(ij.process.ImageProcessor image, Strel strel) Performs closing on the input image.
static ij.ImageStack	closing(ij.ImageStack image, Strel3D strel) Performs morphological closing on the input 3D image.
static ij.ImagePlus	dilation(ij.ImagePlus imagePlus, Strel3D strel) Performs morphological dilation on the input image.
static ij.process.ImageProcessor	dilation(ij.process.ImageProcessor image, Strel strel) Performs morphological dilation on the input image.
static ij.ImageStack	dilation(ij.ImageStack image, Strel3D strel) Performs morphological dilation on the input 3D image.
static ij.ImagePlus	erosion(ij.ImagePlus imagePlus, Strel3D strel) Performs morphological erosion on the input image.
static ij.process.ImageProcessor	erosion(ij.process.ImageProcessor image, Strel strel) Performs morphological erosion on the input image.
static ij.ImageStack	erosion(ij.ImageStack image, Strel3D strel) Performs morphological erosion on the input 3D image.
static ij.ImagePlus	externalGradient(ij.ImagePlus imagePlus, Strel3D strel) Computes the morphological external gradient of the input image.
static ij.process.ImageProcessor	externalGradient(ij.process.ImageProcessor image, Strel strel) Computes the morphological external gradient of the input image.
static ij.ImageStack	externalGradient(ij.ImageStack image, Strel3D strel) Computes the morphological external gradient of the input 3D image.
static ij.ImagePlus	gradient(ij.ImagePlus imagePlus, Strel3D strel) Computes the morphological gradient of the input image.
static ij.process.ImageProcessor	gradient(ij.process.ImageProcessor image, Strel strel) Computes the morphological gradient of the input image.
static ij.ImageStack	gradient(ij.ImageStack image, Strel3D strel) Computes the morphological gradient of the input 3D image.
static ij.ImagePlus	internalGradient(ij.ImagePlus imagePlus, Strel3D strel) Computes the morphological internal gradient of the input image.
static ij.process.ImageProcessor	internalGradient(ij.process.ImageProcessor image, Strel strel) Computes the morphological internal gradient of the input image.
static ij.ImageStack	internalGradient(ij.ImageStack image, Strel3D strel) Computes the morphological internal gradient of the 3D input image.
static ij.ImagePlus	laplacian(ij.ImagePlus imagePlus, Strel3D strel) Computes the morphological Laplacian of the 3D input image.
static ij.process.ImageProcessor	laplacian(ij.process.ImageProcessor image, Strel strel) Computes the morphological Laplacian of the input image.
static ij.ImageStack	laplacian(ij.ImageStack image, Strel3D strel) Computes the morphological Laplacian of the 3D input image.
static ij.ImagePlus	opening(ij.ImagePlus imagePlus, Strel3D strel) Performs morphological opening on the input image.
static ij.process.ImageProcessor	opening(ij.process.ImageProcessor image, Strel strel) Performs morphological opening on the input image.
static ij.ImageStack	opening(ij.ImageStack image, Strel3D strel) Performs morphological opening on the input 3D image.
static ij.ImagePlus	whiteTopHat(ij.ImagePlus imagePlus, Strel3D strel) Computes white top hat of the original image.
static ij.process.ImageProcessor	whiteTopHat(ij.process.ImageProcessor image, Strel strel) Computes white top hat of the original image.
static ij.ImageStack	whiteTopHat(ij.ImageStack image, Strel3D strel) Computes 3D white top hat of the original image.

Methods inherited from class java.lang.Object

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

Method Detail

dilation

public static ij.ImagePlus dilation(ij.ImagePlus imagePlus,
                                    Strel3D strel)

Performs morphological dilation on the input image. Dilation is obtained by extracting the maximum value among pixels/voxels in the neighborhood given by the structuring element. This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for dilation

Returns:

the result of the dilation

See Also:

dilation(ImageProcessor, Strel), dilation(ImageStack, Strel3D), erosion(ImagePlus, Strel3D)

dilation

public static ij.process.ImageProcessor dilation(ij.process.ImageProcessor image,
                                                 Strel strel)

Performs morphological dilation on the input image. Dilation is obtained by extracting the maximum value among pixels in the neighborhood given by the structuring element. This methods is mainly a wrapper to the dilation method of the strel object.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for dilation

Returns:

the result of the dilation

See Also:

erosion(ImageProcessor, Strel), Strel.dilation(ImageProcessor)

dilation

public static ij.ImageStack dilation(ij.ImageStack image,
                                     Strel3D strel)

Performs morphological dilation on the input 3D image. Dilation is obtained by extracting the maximum value among voxels in the neighborhood given by the 3D structuring element.

Parameters:

image - the input 3D image to process (grayscale or RGB)

strel - the structuring element used for dilation

Returns:

the result of the dilation

erosion

public static ij.ImagePlus erosion(ij.ImagePlus imagePlus,
                                   Strel3D strel)

Performs morphological erosion on the input image. Erosion is obtained by extracting the minimum value among pixels/voxels in the neighborhood given by the structuring element. This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for erosion

Returns:

the result of the erosion

See Also:

erosion(ImageProcessor, Strel), erosion(ImageStack, Strel3D), dilation(ImagePlus, Strel3D)

erosion

public static ij.process.ImageProcessor erosion(ij.process.ImageProcessor image,
                                                Strel strel)

Performs morphological erosion on the input image. Erosion is obtained by extracting the minimum value among pixels in the neighborhood given by the structuring element. This methods is mainly a wrapper to the erosion method of the strel object.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for erosion

Returns:

the result of the erosion

See Also:

dilation(ImageProcessor, Strel), Strel.erosion(ImageProcessor)

erosion

public static ij.ImageStack erosion(ij.ImageStack image,
                                    Strel3D strel)

Performs morphological erosion on the input 3D image. Erosion is obtained by extracting the minimum value among voxels in the neighborhood given by the 3D structuring element.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for erosion

Returns:

the result of the erosion

opening

public static ij.ImagePlus opening(ij.ImagePlus imagePlus,
                                   Strel3D strel)

Performs morphological opening on the input image. The opening is obtained by performing an erosion followed by a dilation with the reversed structuring element. This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for erosion

Returns:

the result of the erosion

See Also:

opening(ImageProcessor, Strel), opening(ImageStack, Strel3D), closing(ImagePlus, Strel3D)

opening

public static ij.process.ImageProcessor opening(ij.process.ImageProcessor image,
                                                Strel strel)

Performs morphological opening on the input image. The opening is obtained by performing an erosion followed by a dilation with the reversed structuring element. This methods is mainly a wrapper to the opening method of the strel object.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for opening

Returns:

the result of the morphological opening

See Also:

closing(ImageProcessor, Strel), Strel.opening(ImageProcessor)

opening

public static ij.ImageStack opening(ij.ImageStack image,
                                    Strel3D strel)

Performs morphological opening on the input 3D image. The 3D opening is obtained by performing a 3D erosion followed by a 3D dilation with the reversed structuring element.

Parameters:

image - the input 3D image to process

strel - the structuring element used for opening

Returns:

the result of the 3D morphological opening

See Also:

closing(ImageStack, Strel3D), Strel3D.opening(ImageStack)

closing

public static ij.ImagePlus closing(ij.ImagePlus imagePlus,
                                   Strel3D strel)

Performs morphological closing on the input image. The opening is obtained by performing a dilation followed by an erosion with the reversed structuring element. This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for closing

Returns:

the result of the closing

See Also:

closing(ImageProcessor, Strel), closing(ImageStack, Strel3D), opening(ImagePlus, Strel3D)

closing

public static ij.process.ImageProcessor closing(ij.process.ImageProcessor image,
                                                Strel strel)

Performs closing on the input image. The closing is obtained by performing a dilation followed by an erosion with the reversed structuring element. This methods is mainly a wrapper to the opening method of the strel object.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for closing

Returns:

the result of the morphological closing

See Also:

opening(ImageProcessor, Strel), Strel.closing(ImageProcessor)

closing

public static ij.ImageStack closing(ij.ImageStack image,
                                    Strel3D strel)

Performs morphological closing on the input 3D image. The 3D closing is obtained by performing a 3D dilation followed by a 3D erosion with the reversed structuring element.

Parameters:

image - the input 3D image to process

strel - the structuring element used for closing

Returns:

the result of the 3D morphological closing

See Also:

opening(ImageStack, Strel3D), Strel3D.opening(ImageStack)

whiteTopHat

public static ij.ImagePlus whiteTopHat(ij.ImagePlus imagePlus,
                                       Strel3D strel)

Computes white top hat of the original image. The white top hat is obtained by subtracting the result of an opening from the original image. The white top hat enhances light structures smaller than the structuring element. This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for closing

Returns:

the result of the closing

See Also:

whiteTopHat(ImageProcessor, Strel), whiteTopHat(ImageStack, Strel3D), blackTopHat(ImagePlus, Strel3D)

whiteTopHat

public static ij.process.ImageProcessor whiteTopHat(ij.process.ImageProcessor image,
                                                    Strel strel)

Computes white top hat of the original image. The white top hat is obtained by subtracting the result of an opening from the original image. The white top hat enhances light structures smaller than the structuring element.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for white top-hat

Returns:

the result of the white top-hat

See Also:

blackTopHat(ImageProcessor, Strel), opening(ImageProcessor, Strel)

whiteTopHat

public static ij.ImageStack whiteTopHat(ij.ImageStack image,
                                        Strel3D strel)

Computes 3D white top hat of the original image. The white top hat is obtained by subtracting the result of an opening from the original image. The white top hat enhances light structures smaller than the structuring element.

Parameters:

image - the input 3D image to process

strel - the structuring element used for white top-hat

Returns:

the result of the 3D white top-hat

See Also:

blackTopHat(ImageStack, Strel3D), opening(ImageStack, Strel3D)

blackTopHat

public static ij.ImagePlus blackTopHat(ij.ImagePlus imagePlus,
                                       Strel3D strel)

Computes black top hat (or "bottom hat") of the original image. The black top hat is obtained by subtracting the original image from the result of a closing. The black top hat enhances dark structures smaller than the structuring element. This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for closing

Returns:

the result of the closing

See Also:

blackTopHat(ImageProcessor, Strel), blackTopHat(ImageStack, Strel3D), whiteTopHat(ImagePlus, Strel3D)

blackTopHat

public static ij.process.ImageProcessor blackTopHat(ij.process.ImageProcessor image,
                                                    Strel strel)

Computes black top hat (or "bottom hat") of the original image. The black top hat is obtained by subtracting the original image from the result of a closing. The black top hat enhances dark structures smaller than the structuring element.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for black top-hat

Returns:

the result of the black top-hat

See Also:

whiteTopHat(ImageProcessor, Strel), closing(ImageProcessor, Strel)

blackTopHat

public static ij.ImageStack blackTopHat(ij.ImageStack image,
                                        Strel3D strel)

Computes black top hat (or "bottom hat") of the original image. The black top hat is obtained by subtracting the original image from the result of a closing. The black top hat enhances dark structures smaller than the structuring element.

Parameters:

image - the input 3D image to process

strel - the structuring element used for black top-hat

Returns:

the result of the 3D black top-hat

See Also:

whiteTopHat(ImageStack, Strel3D), closing(ImageStack, Strel3D)

gradient

public static ij.ImagePlus gradient(ij.ImagePlus imagePlus,
                                    Strel3D strel)

Computes the morphological gradient of the input image. The morphological gradient is obtained by from the difference of image dilation and image erosion computed with the same structuring element. This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for closing

Returns:

the result of the closing

See Also:

gradient(ImageProcessor, Strel), gradient(ImageStack, Strel3D), internalGradient(ImagePlus, Strel3D), externalGradient(ImagePlus, Strel3D)

gradient

public static ij.process.ImageProcessor gradient(ij.process.ImageProcessor image,
                                                 Strel strel)

Computes the morphological gradient of the input image. The morphological gradient is obtained by from the difference of image dilation and image erosion computed with the same structuring element.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for morphological gradient

Returns:

the result of the morphological gradient

See Also:

erosion(ImageProcessor, Strel), dilation(ImageProcessor, Strel)

gradient

public static ij.ImageStack gradient(ij.ImageStack image,
                                     Strel3D strel)

Computes the morphological gradient of the input 3D image. The morphological gradient is obtained by from the difference of image dilation and image erosion computed with the same structuring element.

Parameters:

image - the input 3D image to process

strel - the structuring element used for morphological gradient

Returns:

the result of the 3D morphological gradient

See Also:

erosion(ImageStack, Strel3D), dilation(ImageStack, Strel3D)

laplacian

public static ij.ImagePlus laplacian(ij.ImagePlus imagePlus,
                                     Strel3D strel)

Computes the morphological Laplacian of the 3D input image. The morphological gradient is obtained from the difference of the external gradient with the internal gradient, both computed with the same structuring element. Homogeneous regions appear as gray. This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for closing

Returns:

the result of the closing

See Also:

laplacian(ImageProcessor, Strel), laplacian(ImageStack, Strel3D), internalGradient(ImagePlus, Strel3D), externalGradient(ImagePlus, Strel3D)

laplacian

public static ij.process.ImageProcessor laplacian(ij.process.ImageProcessor image,
                                                  Strel strel)

Computes the morphological Laplacian of the input image. The morphological Laplacian is obtained from the difference of the external gradient with the internal gradient, both computed with the same structuring element. Homogeneous regions appear as gray.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for morphological laplacian

Returns:

the result of the morphological laplacian

See Also:

erosion(ImageProcessor, Strel), dilation(ImageProcessor, Strel)

laplacian

public static ij.ImageStack laplacian(ij.ImageStack image,
                                      Strel3D strel)

Computes the morphological Laplacian of the 3D input image. The morphological gradient is obtained from the difference of the external gradient with the internal gradient, both computed with the same structuring element. Homogeneous regions appear as gray.

Parameters:

image - the input 3D image to process

strel - the structuring element used for morphological laplacian

Returns:

the result of the 3D morphological laplacian

See Also:

externalGradient(ImageStack, Strel3D), internalGradient(ImageStack, Strel3D)

internalGradient

public static ij.ImagePlus internalGradient(ij.ImagePlus imagePlus,
                                            Strel3D strel)

Computes the morphological internal gradient of the input image. The morphological internal gradient is obtained by from the difference of original image with the result of an erosion. This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for closing

Returns:

the result of the closing

See Also:

internalGradient(ImageProcessor, Strel), internalGradient(ImageStack, Strel3D), gradient(ImagePlus, Strel3D), externalGradient(ImagePlus, Strel3D)

internalGradient

public static ij.process.ImageProcessor internalGradient(ij.process.ImageProcessor image,
                                                         Strel strel)

Computes the morphological internal gradient of the input image. The morphological internal gradient is obtained by from the difference of original image with the result of an erosion.

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for morphological internal gradient

Returns:

the result of the morphological internal gradient

See Also:

erosion(ImageProcessor, Strel), gradient(ImageProcessor, Strel), externalGradient(ImageProcessor, Strel)

internalGradient

public static ij.ImageStack internalGradient(ij.ImageStack image,
                                             Strel3D strel)

Computes the morphological internal gradient of the 3D input image. The morphological internal gradient is obtained by from the difference of original image with the result of an erosion.

Parameters:

image - the input image to process

strel - the structuring element used for morphological internal gradient

Returns:

the result of the 3D morphological internal gradient

See Also:

erosion(ImageStack, Strel3D), gradient(ImageStack, Strel3D), externalGradient(ImageStack, Strel3D)

externalGradient

public static ij.ImagePlus externalGradient(ij.ImagePlus imagePlus,
                                            Strel3D strel)

Computes the morphological external gradient of the input image. The morphological external gradient is obtained by from the difference of the result of a dilation and of the original image . This methods is called the equivalent static method for ImageProcessor or ImageStack, and creates a new ImagePlus instance with the result.

Parameters:

imagePlus - the input image to process

strel - the structuring element used for closing

Returns:

the result of the closing

See Also:

externalGradient(ImageProcessor, Strel), externalGradient(ImageStack, Strel3D), gradient(ImagePlus, Strel3D), internalGradient(ImagePlus, Strel3D)

externalGradient

public static ij.process.ImageProcessor externalGradient(ij.process.ImageProcessor image,
                                                         Strel strel)

Computes the morphological external gradient of the input image. The morphological external gradient is obtained by from the difference of the result of a dilation and of the original image .

Parameters:

image - the input image to process (grayscale or RGB)

strel - the structuring element used for morphological external gradient

Returns:

the result of the morphological external gradient

See Also:

dilation(ImageProcessor, Strel)

externalGradient

public static ij.ImageStack externalGradient(ij.ImageStack image,
                                             Strel3D strel)

Computes the morphological external gradient of the input 3D image. The morphological external gradient is obtained by from the difference of the result of a dilation and of the original image .

Parameters:

image - the input image to process

strel - the structuring element used for morphological external gradient

Returns:

the result of the 3D morphological external gradient

See Also:

dilation(ImageStack, Strel3D), internalGradient(ImageStack, Strel3D)