Package org.anchoranalysis.plugin.imagej.bean.threshold

Class ThresholderSimpleFillHoles2D

Object

AnchorBean<VoxelsThresholder>

InitializableBean<VoxelsThresholder,NullInitialization>

NullParametersBean<VoxelsThresholder>

Thresholder

ThresholderSimpleFillHoles2D

public class ThresholderSimpleFillHoles2D
extends Thresholder

A thresholder that applies a simple intensity threshold and then fills holes in 2D.

This thresholder first applies an intensity threshold to create a binary image, and then uses ImageJ's "fill" morphological operation to fill holes in each 2D slice.

Constructor Summary

Constructors

Constructor	Description
ThresholderSimpleFillHoles2D()
ThresholderSimpleFillHoles2D(int minIntensity)	Creates a new ThresholderSimpleFillHoles2D instance.

Method Summary

Modifier and Type	Method	Description
int	getMinIntensity()	The minimum intensity value for thresholding.
void	setMinIntensity(int minIntensity)	The minimum intensity value for thresholding.
BinaryVoxels<UnsignedByteBuffer>	threshold(VoxelsUntyped inputBuffer, BinaryValuesByte binaryValues, Optional<Histogram> histogram, Optional<ObjectMask> objectMask)	Thresholds voxels (across a range of values) so that they have only binary range (i.e. two voxel values representing on and off).

Methods inherited from class org.anchoranalysis.image.bean.threshold.Thresholder

threshold, threshold

Methods inherited from class org.anchoranalysis.bean.NullParametersBean

initializeRecursive, onInitialization, onInitialization

Methods inherited from class org.anchoranalysis.bean.initializable.InitializableBean

getInitialization, getLogger, getPropertyInitializer, initialize, initializeRecursive, initRecursiveWithInitializer, isInitialized

Methods inherited from class org.anchoranalysis.bean.AnchorBean

checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

Methods inherited from class java.lang.Object

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

Constructor Details

ThresholderSimpleFillHoles2D

public ThresholderSimpleFillHoles2D()

ThresholderSimpleFillHoles2D

public ThresholderSimpleFillHoles2D(int minIntensity)

Creates a new ThresholderSimpleFillHoles2D instance.

Parameters:

minIntensity - The minimum intensity value for thresholding.

Voxels with intensity greater than or equal to this value are considered foreground.

Method Details

threshold

public BinaryVoxels<UnsignedByteBuffer> threshold(VoxelsUntyped inputBuffer,
 BinaryValuesByte binaryValues,
 Optional<Histogram> histogram,
 Optional<ObjectMask> objectMask)
                                           throws OperationFailedException

Description copied from class: Thresholder

Thresholds voxels (across a range of values) so that they have only binary range (i.e. two voxel values representing on and off).

If a mask is used, the voxels outside the object-mask are left unchanged. They will be either identical to the input-volume or 0 if a new buffer needs to be created.

Specified by:

threshold in class Thresholder

Parameters:

inputBuffer - the voxels to be thresholded.

binaryValues - what binary values to be used in the output.

histogram - a histogram if it's available, which must exactly match the intensity-values of voxels after any object-mask is applied. This exists for calculation efficiency.

objectMask - an object-mask to restrict thresholding to only some region(s) of the voxels.

Returns:

a binary-channel as described above, which may possibly reuse the input voxel-buffers.

Throws:

OperationFailedException - if the thresholding operation cannot complete successfully.

getMinIntensity

public int getMinIntensity()

The minimum intensity value for thresholding.

Voxels with intensity greater than or equal to this value are considered foreground.

setMinIntensity

public void setMinIntensity(int minIntensity)

The minimum intensity value for thresholding.

Voxels with intensity greater than or equal to this value are considered foreground.