Package qupath.imagej.processing

Class MorphologicalReconstruction

java.lang.Object

qupath.imagej.processing.MorphologicalReconstruction

public class MorphologicalReconstruction
extends Object

Implementation of morphological reconstruction for ImageJ.

Constructor Summary

Constructors

Constructor	Description
MorphologicalReconstruction()

Method Summary

Modifier and Type	Method	Description
static ByteProcessor	binaryReconstruction(ByteProcessor bpMarker, ByteProcessor bpMask, boolean permitMaskChanges)	Alternative morphological reconstruction (based on ImageJ's FloodFiller) suitable for binary images only.
static ImageProcessor	closingByReconstruction(ImageProcessor ip, double radius)	Apply a morphological closing by reconstruction.
static ImageProcessor	findRegionalMaxima(ImageProcessor ip, float threshold, boolean outputBinary)	Find regional maxima using morphological reconstruction.
static void	imposeMaxima(FloatProcessor fp, Roi roi)	Ensure that a FloatProcessor only has region maxima within a specified Roi, using morphological reconstruction.
static void	imposeMaxima(FloatProcessor fp, ImageProcessor ipMask)	Ensure that a FloatProcessor only has region maxima within a specified mask, using morphological reconstruction.
static void	imposeMinima(FloatProcessor fp, Roi roi)	Ensure that a FloatProcessor only has region minima within a specified Roi, using morphological reconstruction.
static boolean	morphologicalReconstruction(ImageProcessor ipMarker, ImageProcessor ipMask)	Apply morphological operation using marker and mask images.
static ImageProcessor	openingByReconstruction(ImageProcessor ip, double radius)	Apply opening by reconstruction, with the specified minimum filter radius.
static boolean	validateMarkerMask(ImageProcessor ipMarker, ImageProcessor ipMask)	Check that marker and mask images have the same size, and ensure that marker pixels are <= mask pixels, making this if necessary.

Methods inherited from class java.lang.Object

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

Constructor Details

MorphologicalReconstruction

public MorphologicalReconstruction()

Method Details

binaryReconstruction

public static ByteProcessor binaryReconstruction(ByteProcessor bpMarker,
 ByteProcessor bpMask,
 boolean permitMaskChanges)

Alternative morphological reconstruction (based on ImageJ's FloodFiller) suitable for binary images only.

Parameters:

bpMarker -

bpMask -

permitMaskChanges -

Returns:

morphologicalReconstruction

public static boolean morphologicalReconstruction(ImageProcessor ipMarker,
 ImageProcessor ipMask)

Apply morphological operation using marker and mask images. The marker image is changed.

Parameters:

ipMarker -

ipMask -

Returns:

validateMarkerMask

public static boolean validateMarkerMask(ImageProcessor ipMarker,
 ImageProcessor ipMask)

Check that marker and mask images have the same size, and ensure that marker pixels are <= mask pixels, making this if necessary.

Parameters:

ipMarker -

ipMask -

Returns:

openingByReconstruction

public static ImageProcessor openingByReconstruction(ImageProcessor ip,
 double radius)

Apply opening by reconstruction, with the specified minimum filter radius.

Parameters:

ip -

radius -

Returns:

closingByReconstruction

public static ImageProcessor closingByReconstruction(ImageProcessor ip,
 double radius)

Apply a morphological closing by reconstruction.

Parameters:

ip - ImageProcessor to process

radius - minimum filter radius

Returns:

processed image

imposeMinima

public static void imposeMinima(FloatProcessor fp,
 Roi roi)

Ensure that a FloatProcessor only has region minima within a specified Roi, using morphological reconstruction.

Parameters:

fp -

roi -

imposeMaxima

public static void imposeMaxima(FloatProcessor fp,
 Roi roi)

Ensure that a FloatProcessor only has region maxima within a specified Roi, using morphological reconstruction.

Parameters:

fp -

roi -

imposeMaxima

public static void imposeMaxima(FloatProcessor fp,
 ImageProcessor ipMask)

Ensure that a FloatProcessor only has region maxima within a specified mask, using morphological reconstruction.

Parameters:

fp -

ipMask -

findRegionalMaxima

public static ImageProcessor findRegionalMaxima(ImageProcessor ip,
 float threshold,
 boolean outputBinary)

Find regional maxima using morphological reconstruction.

Parameters:

ip - input image

threshold - the extent to which a maximum must be greater than its surroundings

outputBinary - if true, the output is a binary image

Returns: