inra.ijpb.morphology

Class MinimaAndMaxima3D

java.lang.Object

inra.ijpb.morphology.MinimaAndMaxima3D

public class MinimaAndMaxima3D
extends Object

A collection of static methods for computing regional and extended minima and maxima on 3D stacks. Supports integer and floating-point stacks, in 6 and 26 connectivities.

Regional extrema algorithms are based on flood-filling-like algorithms, whereas extended extrema and extrema imposition algorithms use geodesic reconstruction algorithm.

See the books of Serra and Soille for further details.

Author:

David Legland

See Also:

MinimaAndMaxima, Reconstruction3D, FloodFill

Method Summary

Modifier and Type	Method and Description
static ij.ImageStack	extendedMaxima(ij.ImageStack image, double dynamic) Computes the extended maxima in grayscale image image, keeping maxima with the specified dynamic, and using the default connectivity.
static ij.ImageStack	extendedMaxima(ij.ImageStack image, double dynamic, ij.ImageStack binaryMask) Computes the extended maxima in the grayscale image image, keeping maxima with the specified dynamic, restricted to the non-zero voxels of the binary mask, and using the default connectivity.
static ij.ImageStack	extendedMaxima(ij.ImageStack image, double dynamic, int conn) Computes the extended maxima in grayscale image image, keeping maxima with the specified dynamic, and using the specified connectivity.
static ij.ImageStack	extendedMaxima(ij.ImageStack image, double dynamic, int conn, ij.ImageStack binaryMask) Computes the extended maxima in the grayscale image image, keeping maxima with the specified dynamic, restricted to the non-zero voxels of the binary mask, and using the specified connectivity.
static ij.ImageStack	extendedMinima(ij.ImageStack image, double dynamic) Computes the extended minima in grayscale image image, keeping minima with the specified dynamic, and using the default connectivity.
static ij.ImageStack	extendedMinima(ij.ImageStack image, double dynamic, int conn) Computes the extended minima in grayscale image image, keeping minima with the specified dynamic, and using the specified connectivity.
static ij.ImageStack	imposeMaxima(ij.ImageStack image, ij.ImageStack maxima) Imposes the maxima given by marker image into the input image, using the default connectivity.
static ij.ImageStack	imposeMaxima(ij.ImageStack image, ij.ImageStack maxima, int conn) Imposes the maxima given by marker image into the input image, using the specified connectivity.
static ij.ImageStack	imposeMinima(ij.ImageStack image, ij.ImageStack minima) Imposes the minima given by marker image into the input image, using the default connectivity.
static ij.ImageStack	imposeMinima(ij.ImageStack image, ij.ImageStack minima, int conn) Imposes the minima given by marker image into the input image, using the specified connectivity.
static ij.ImageStack	regionalMaxima(ij.ImageStack image) Computes the regional maxima in 3D stack image, using the default connectivity.
static ij.ImageStack	regionalMaxima(ij.ImageStack image, int conn) Computes the regional maxima in grayscale image stack, using the specified connectivity.
static ij.ImageStack	regionalMaxima(ij.ImageStack image, int conn, ij.ImageStack mask) Computes the regional maxima in grayscale image stack, using the specified connectivity and binary mask.
static ij.ImageStack	regionalMaximaByReconstruction(ij.ImageStack image, int conn) Computes the regional maxima in 3D image stack, using the specified connectivity, and a slower algorithm (used for testing).
static ij.ImageStack	regionalMinima(ij.ImageStack image) Computes the regional minima in 3D image stack, using the default connectivity.
static ij.ImageStack	regionalMinima(ij.ImageStack image, int conn) Computes the regional minima in 3D stack image, using the specified connectivity.
static ij.ImageStack	regionalMinima(ij.ImageStack image, int conn, ij.ImageStack mask) Computes the regional minima in 3D image stack, using the specified connectivity.
static ij.ImageStack	regionalMinimaByReconstruction(ij.ImageStack image, int conn) Computes the regional minima in grayscale image image, using the specified connectivity, and a slower algorithm (used for testing).

Methods inherited from class java.lang.Object

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

Method Detail

regionalMaxima

public static final ij.ImageStack regionalMaxima(ij.ImageStack image)

Computes the regional maxima in 3D stack image, using the default connectivity.

Parameters:

image - the 3D image to process

Returns:

the regional maxima of input image

regionalMaxima

public static final ij.ImageStack regionalMaxima(ij.ImageStack image,
                                                 int conn)

Computes the regional maxima in grayscale image stack, using the specified connectivity.

Parameters:

image - the 3D image to process

conn - the connectivity for maxima, that should be either 6 or 26

Returns:

the regional maxima of input image

regionalMaximaByReconstruction

public static final ij.ImageStack regionalMaximaByReconstruction(ij.ImageStack image,
                                                                 int conn)

Computes the regional maxima in 3D image stack, using the specified connectivity, and a slower algorithm (used for testing).

Parameters:

image - the 3D image to process

conn - the connectivity for maxima, that should be either 6 or 26

Returns:

the regional maxima of input image

regionalMaxima

public static final ij.ImageStack regionalMaxima(ij.ImageStack image,
                                                 int conn,
                                                 ij.ImageStack mask)

Computes the regional maxima in grayscale image stack, using the specified connectivity and binary mask.

Parameters:

image - the 3D image to process

conn - the connectivity for maxima, that should be either 6 or 26

mask - the binary mask that restricts the processing

Returns:

the regional maxima of input image

regionalMinima

public static final ij.ImageStack regionalMinima(ij.ImageStack image)

Computes the regional minima in 3D image stack, using the default connectivity.

Parameters:

image - the 3D image to process

Returns:

the regional minima of input image

regionalMinima

public static final ij.ImageStack regionalMinima(ij.ImageStack image,
                                                 int conn)

Computes the regional minima in 3D stack image, using the specified connectivity.

Parameters:

image - the 3D image to process

conn - the connectivity for minima, that should be either 6 or 26

Returns:

the regional minima of input image

regionalMinimaByReconstruction

public static final ij.ImageStack regionalMinimaByReconstruction(ij.ImageStack image,
                                                                 int conn)

Computes the regional minima in grayscale image image, using the specified connectivity, and a slower algorithm (used for testing).

Parameters:

image - the 3D image to process

conn - the connectivity for minima, that should be either 6 or 26

Returns:

the regional minima of input image

regionalMinima

public static final ij.ImageStack regionalMinima(ij.ImageStack image,
                                                 int conn,
                                                 ij.ImageStack mask)

Computes the regional minima in 3D image stack, using the specified connectivity.

Parameters:

image - the 3D image to process

conn - the connectivity for minima, that should be either 6 or 26

mask - the binary mask that restricts processing

Returns:

the regional minima of input image

extendedMaxima

public static final ij.ImageStack extendedMaxima(ij.ImageStack image,
                                                 double dynamic)

Computes the extended maxima in grayscale image image, keeping maxima with the specified dynamic, and using the default connectivity.

Parameters:

image - the 3D image to process

dynamic - the difference between maxima and maxima boundary

Returns:

the extended maxima of input image

extendedMaxima

public static final ij.ImageStack extendedMaxima(ij.ImageStack image,
                                                 double dynamic,
                                                 int conn)

Computes the extended maxima in grayscale image image, keeping maxima with the specified dynamic, and using the specified connectivity.

Parameters:

image - the 3D image to process

dynamic - the difference between maxima and maxima boundary

conn - the connectivity for maxima, that should be either 6 or 26

Returns:

the extended maxima of input image

extendedMaxima

public static final ij.ImageStack extendedMaxima(ij.ImageStack image,
                                                 double dynamic,
                                                 ij.ImageStack binaryMask)

Computes the extended maxima in the grayscale image image, keeping maxima with the specified dynamic, restricted to the non-zero voxels of the binary mask, and using the default connectivity.

Parameters:

image - the 3D image to process

dynamic - the difference between maxima and maxima boundary

binaryMask - binary mask image to restrict region of application

Returns:

the extended maxima of input image

extendedMaxima

public static final ij.ImageStack extendedMaxima(ij.ImageStack image,
                                                 double dynamic,
                                                 int conn,
                                                 ij.ImageStack binaryMask)

Computes the extended maxima in the grayscale image image, keeping maxima with the specified dynamic, restricted to the non-zero voxels of the binary mask, and using the specified connectivity.

Parameters:

image - input grayscale image

dynamic - nonnegative scalar defining the depth threshold of maxima removal ("h" value in Soile, 1999)

conn - connectivity value (6 or 26)

binaryMask - binary mask image to restrict region of application

Returns:

the extended maxima of input image

extendedMinima

public static final ij.ImageStack extendedMinima(ij.ImageStack image,
                                                 double dynamic)

Computes the extended minima in grayscale image image, keeping minima with the specified dynamic, and using the default connectivity.

Parameters:

image - the 3D image to process

dynamic - the difference between minima and minima boundary

Returns:

the extended minima of input image

extendedMinima

public static final ij.ImageStack extendedMinima(ij.ImageStack image,
                                                 double dynamic,
                                                 int conn)

Computes the extended minima in grayscale image image, keeping minima with the specified dynamic, and using the specified connectivity.

Parameters:

image - the 3D image to process

dynamic - the difference between minima and minima boundary

conn - the connectivity for minima, that should be either 6 or 26

Returns:

the extended minima of input image

imposeMaxima

public static final ij.ImageStack imposeMaxima(ij.ImageStack image,
                                               ij.ImageStack maxima)

Imposes the maxima given by marker image into the input image, using the default connectivity.

Parameters:

image - the 3D image to process

maxima - a 3D binary image of maxima

Returns:

the result of maxima imposition

imposeMaxima

public static final ij.ImageStack imposeMaxima(ij.ImageStack image,
                                               ij.ImageStack maxima,
                                               int conn)

Imposes the maxima given by marker image into the input image, using the specified connectivity.

Parameters:

image - the 3D image to process

maxima - a 3D binary image of maxima

conn - the connectivity for maxima, that should be either 6 or 26

Returns:

the result of maxima imposition

imposeMinima

public static final ij.ImageStack imposeMinima(ij.ImageStack image,
                                               ij.ImageStack minima)

Imposes the minima given by marker image into the input image, using the default connectivity.

Parameters:

image - the 3D image to process

minima - a 3D binary image of minima

Returns:

the result of minima imposition

imposeMinima

public static final ij.ImageStack imposeMinima(ij.ImageStack image,
                                               ij.ImageStack minima,
                                               int conn)

Imposes the minima given by marker image into the input image, using the specified connectivity.

Parameters:

image - the 3D image to process

minima - a 3D binary image of minima

conn - the connectivity for minima, that should be either 6 or 26

Returns:

the result of minima imposition