Package org.anchoranalysis.image.bean.threshold

Class ThresholderGlobal

Object

org.anchoranalysis.bean.AnchorBean<B>

org.anchoranalysis.bean.initializable.InitializableBean<T,NullInitialization>

org.anchoranalysis.bean.NullParametersBean<org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder>

org.anchoranalysis.image.bean.threshold.Thresholder

org.anchoranalysis.image.bean.threshold.ThresholderGlobal

public class ThresholderGlobal
extends Thresholder

Performs global thresholding.

This implies that the threshold-level is identical for every voxel.

The thresholding occurs inplace on the existing voxels i.e. a new buffer is not created.

An on voxel is placed in the buffer if voxel-value >= level or off otherwise.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
ThresholderGlobal()
ThresholderGlobal(CalculateLevel calculateLevel)

Method Summary

Modifier and Type	Method	Description
CalculateLevel	getCalculateLevel()
void	setCalculateLevel(CalculateLevel calculateLevel)
org.anchoranalysis.image.voxel.binary.BinaryVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>	threshold(org.anchoranalysis.image.voxel.VoxelsUntyped inputBuffer, org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte bvOut, Optional<org.anchoranalysis.math.histogram.Histogram> histogram, Optional<org.anchoranalysis.image.voxel.object.ObjectMask> objectMask)	Thresholds voxels (across a range of values) so that they have only binary range (i.e.

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

ThresholderGlobal

public ThresholderGlobal()

ThresholderGlobal

public ThresholderGlobal(CalculateLevel calculateLevel)

Method Details

threshold

public org.anchoranalysis.image.voxel.binary.BinaryVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer> threshold(org.anchoranalysis.image.voxel.VoxelsUntyped inputBuffer, org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte bvOut, Optional<org.anchoranalysis.math.histogram.Histogram> histogram, Optional<org.anchoranalysis.image.voxel.object.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.

bvOut - 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.

getCalculateLevel

public CalculateLevel getCalculateLevel()

setCalculateLevel

public void setCalculateLevel(CalculateLevel calculateLevel)