Package org.anchoranalysis.plugin.fiji.bean.threshold

Class ThresholderAutoIJ

Object

AnchorBean<VoxelsThresholder>

InitializableBean<VoxelsThresholder,NullInitialization>

NullParametersBean<VoxelsThresholder>

Thresholder

ThresholderAutoIJ

public class ThresholderAutoIJ
extends Thresholder

Applies automatic thresholding using ImageJ's Auto_Threshold plugin.

Constructor Summary

Constructors

Constructor	Description
ThresholderAutoIJ()

Method Summary

Modifier and Type	Method	Description
String	getMethod()	The thresholding method to use.
boolean	isNoBlack()	If true, the thresholding algorithm will not consider black pixels (value 0) in its calculations.
void	setMethod(String method)	The thresholding method to use.
void	setNoBlack(boolean noBlack)	If true, the thresholding algorithm will not consider black pixels (value 0) in its calculations.
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

ThresholderAutoIJ

public ThresholderAutoIJ()

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.

getMethod

public String getMethod()

The thresholding method to use.

One of the following strings to identify ImageJ's thresholding algorithms: Default, Huang, "Intermodes", "IsoData", "Li", "MaxEntropy", "Mean", "MinError(I)", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag", "Triangle", "Yen"

An empty string will use the Default method.

setMethod

public void setMethod(String method)

The thresholding method to use.

One of the following strings to identify ImageJ's thresholding algorithms: Default, Huang, "Intermodes", "IsoData", "Li", "MaxEntropy", "Mean", "MinError(I)", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag", "Triangle", "Yen"

An empty string will use the Default method.

isNoBlack

public boolean isNoBlack()

If true, the thresholding algorithm will not consider black pixels (value 0) in its calculations.

setNoBlack

public void setNoBlack(boolean noBlack)

If true, the thresholding algorithm will not consider black pixels (value 0) in its calculations.