org.incenp.imagej

Class Masking

java.lang.Object

org.incenp.imagej.Masking

public class Masking
extends Object

A class of helper methods to create and manipulate binary masks.

Field Summary

Fields

Modifier and Type	Field and Description
static int	CLOSE_OPEN_MASK Performs a round of close/open operations when creating a mask.
static int	NO_DUPLICATE Avoid duplicating the source image when possible.
static int	WHITE_MASK Treats white pixels are masked.

Constructor Summary

Constructors

Constructor and Description
Masking()

Method Summary

Modifier and Type	Method and Description
static ij.process.ImageProcessor	applyMask(ij.process.ImageProcessor source, ij.process.ImageProcessor mask) Apply a binary mask to another image by performing a AND operation.
static ij.process.ImageProcessor	applyMask(ij.process.ImageProcessor source, ij.process.ImageProcessor mask, BinaryOperator operator, int options) Apply a binary mask to another image.
static ij.process.ImageProcessor	createMask(ij.process.ImageProcessor processor, ThresholdingMethod method, int parameter) Create a binary mask by thresholding a source image.
static ij.process.ImageProcessor	createMask(ij.process.ImageProcessor processor, ThresholdingMethod method, int parameter, int options) Creates a binary mask by thresholding a source image.

Methods inherited from class java.lang.Object

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

Field Detail

WHITE_MASK

public static final int WHITE_MASK

Treats white pixels are masked. With this option, methods in that class that create or manipulate masks consider white pixels as being masked, instead of black pixels. E.g., when creating a mask by automatic thresholding, pixels above the threshold are set to white instead of black; when applying a mask to another image, pixels from the source image are masked by the white pixels in the mask.

See Also:

Constant Field Values

CLOSE_OPEN_MASK

public static final int CLOSE_OPEN_MASK

Performs a round of close/open operations when creating a mask.

See Also:

Constant Field Values

NO_DUPLICATE

public static final int NO_DUPLICATE

Avoid duplicating the source image when possible.

See Also:

Constant Field Values

Constructor Detail

Masking

public Masking()

Method Detail

createMask

public static ij.process.ImageProcessor createMask(ij.process.ImageProcessor processor,
                                                   ThresholdingMethod method,
                                                   int parameter,
                                                   int options)

Creates a binary mask by thresholding a source image. This method is intended to provide an unified interface to both ImageJ's native AutoThresholder and Fiji's Auto_Local_Threshold plugin.

Parameters:

processor - the source image to create a mask from

method - the thresholding algorithm to apply

parameter - for the ThresholdingMethod.FIXED method, this is directly the threshold to apply; for the local thresholding methods, this is the radius to consider; global thresholding methods don't use this parameter

options - flags to alter the behavior of this method; see constant fields defined in this class

Returns:

the newly created binary mask

createMask

public static ij.process.ImageProcessor createMask(ij.process.ImageProcessor processor,
                                                   ThresholdingMethod method,
                                                   int parameter)

Create a binary mask by thresholding a source image. This method is similiar to createMask(ImageProcessor, ThresholdingMethod, int, int) but uses the CLOSE_OPEN_MASK flag and does not allow to set other flags.

Parameters:

processor - the source image to create a mask from

method - the thresholding algorithm to apply

parameter - for the ThresholdingMethod.FIXED method, this is directly the threshold to apply; for the local thresholding methods, this is the radius to consider; global thresholding methods don't use this parameter

Returns:

the newly generated binary mask

applyMask

public static ij.process.ImageProcessor applyMask(ij.process.ImageProcessor source,
                                                  ij.process.ImageProcessor mask,
                                                  BinaryOperator operator,
                                                  int options)

Apply a binary mask to another image.

Parameters:

source - the image to apply the mask to

mask - the mask to apply

operator - the binary operator defining the operation to perform with the mask

options - flags to alter the behavior of this method; see constant fields defined in this classfields defined in this class

Returns:

the resulting image

applyMask

public static ij.process.ImageProcessor applyMask(ij.process.ImageProcessor source,
                                                  ij.process.ImageProcessor mask)

Apply a binary mask to another image by performing a AND operation. This method is similar to applyMask(ImageProcessor, ImageProcessor, BinaryOperator, int) but with the default AND operation and without any flag.

Parameters:

source - the image to apply the mask to

mask - the mask to apply

Returns:

the resulting image