Package org.anchoranalysis.image.bean.threshold

Class Thresholder

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

Direct Known Subclasses:

ThresholderGlobal

public abstract class Thresholder
extends NullParametersBean<org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder>

Thresholds voxels to create a binary-voxels using global thresholding.

Author:

Owen Feehan

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	Thresholder()

Method Summary

Modifier and Type	Method	Description
org.anchoranalysis.image.voxel.binary.BinaryVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>	threshold(org.anchoranalysis.image.voxel.VoxelsUntyped voxels)	Like threshold(VoxelsUntyped) but using default binary-values.
org.anchoranalysis.image.voxel.binary.BinaryVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>	threshold(org.anchoranalysis.image.voxel.VoxelsUntyped voxels, org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte binaryValues)	Like threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the thresholding to the entire set of voxels.
abstract org.anchoranalysis.image.voxel.binary.BinaryVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>	threshold(org.anchoranalysis.image.voxel.VoxelsUntyped voxels, org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte binaryValues, 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.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

Thresholder

protected Thresholder()

Method Details

threshold

public org.anchoranalysis.image.voxel.binary.BinaryVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer> threshold(org.anchoranalysis.image.voxel.VoxelsUntyped voxels) throws OperationFailedException

Like threshold(VoxelsUntyped) but using default binary-values.

The default values are off(0) and on(255).

Parameters:

voxels - the voxels to be thresholded.

Returns:

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

Throws:

OperationFailedException - if the thresholding operation cannot complete successfully.

threshold

public org.anchoranalysis.image.voxel.binary.BinaryVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer> threshold(org.anchoranalysis.image.voxel.VoxelsUntyped voxels, org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte binaryValues) throws OperationFailedException

Like threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the thresholding to the entire set of voxels.

The thresholder does not accept a histogram as input.

Parameters:

voxels - the voxels to be thresholded.

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

Returns:

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

Throws:

OperationFailedException - if the thresholding operation cannot complete successfully.

threshold

public abstract org.anchoranalysis.image.voxel.binary.BinaryVoxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer> threshold(org.anchoranalysis.image.voxel.VoxelsUntyped voxels, org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte binaryValues, Optional<org.anchoranalysis.math.histogram.Histogram> histogram, Optional<org.anchoranalysis.image.voxel.object.ObjectMask> objectMask) throws OperationFailedException

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.

Parameters:

voxels - 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.