Package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance

Class DistanceTransform3D

Object

AnchorBean<ChannelProvider>

InitializableBean<ChannelProvider,ImageInitialization>

ImageBean<ChannelProvider>

BeanProviderAsStackBase<ChannelProvider,Channel>

ChannelProvider

FromMaskBase

DistanceTransform3D

All Implemented Interfaces:

Provider<Channel>, ProviderAsStack

public class DistanceTransform3D
extends FromMaskBase

Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.

See Distance transform on Wikipedia.

A new channel is always created i.e. the input channel is unchanged.

The plugin uses aspect ratio (relative distance between z and xy slices) in its distance calculations.

As a simplification, when resolution is used, the XY plane is multipled by the average of the x and y dimensions.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
DistanceTransform3D()

Method Summary

Modifier and Type	Method	Description
Voxels<UnsignedByteBuffer>	createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer> voxels, Optional<Resolution> resolution, float multiplyByZRes)	Creates a distance map for binary voxels.
protected Channel	createFromMask(Mask mask)	Creates a Channel from the provided Mask.
float	getMultiplyBy()	A factor to multiply the distance values by.
boolean	isApplyResolution()	If true, multiplies the values by the x-resolution, if it exists.
boolean	isCreateShort()	If true, creates a short (16-bit) output instead of byte (8-bit).
boolean	isIgnoreZIfNaN()	If true and the z-resolution is undefined, the z dimension is ignored.
boolean	isSuppressZ()	If true, suppresses the z-dimension in distance calculations.
void	setApplyResolution(boolean applyResolution)	If true, multiplies the values by the x-resolution, if it exists.
void	setCreateShort(boolean createShort)	If true, creates a short (16-bit) output instead of byte (8-bit).
void	setIgnoreZIfNaN(boolean ignoreZIfNaN)	If true and the z-resolution is undefined, the z dimension is ignored.
void	setMultiplyBy(float multiplyBy)	A factor to multiply the distance values by.
void	setSuppressZ(boolean suppressZ)	If true, suppresses the z-dimension in distance calculations.

Methods inherited from class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase

get, getMask, setMask

Methods inherited from class org.anchoranalysis.image.bean.provider.ChannelProvider

getAsStack

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

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

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

DistanceTransform3D

public DistanceTransform3D()

Method Details

createFromMask

protected Channel createFromMask(Mask mask)
                          throws ProvisionFailedException

Description copied from class: FromMaskBase

Creates a Channel from the provided Mask.

Specified by:

createFromMask in class FromMaskBase

Parameters:

mask - the Mask to create the channel from

Returns:

the created Channel

Throws:

ProvisionFailedException - if the channel creation fails

createDistanceMapForVoxels

public Voxels<UnsignedByteBuffer> createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer> voxels,
 Optional<Resolution> resolution,
 float multiplyByZRes)
                                                      throws ProvisionFailedException

Creates a distance map for binary voxels.

Parameters:

voxels - the binary voxels to create a distance map for

resolution - the optional resolution of the voxels

multiplyByZRes - a factor to multiply the z-resolution by

Returns:

the distance map as Voxels of UnsignedByteBuffer

Throws:

ProvisionFailedException - if the distance map creation fails

isSuppressZ

public boolean isSuppressZ()

If true, suppresses the z-dimension in distance calculations.

setSuppressZ

public void setSuppressZ(boolean suppressZ)

If true, suppresses the z-dimension in distance calculations.

getMultiplyBy

public float getMultiplyBy()

A factor to multiply the distance values by.

setMultiplyBy

public void setMultiplyBy(float multiplyBy)

A factor to multiply the distance values by.

isCreateShort

public boolean isCreateShort()

If true, creates a short (16-bit) output instead of byte (8-bit).

setCreateShort

public void setCreateShort(boolean createShort)

If true, creates a short (16-bit) output instead of byte (8-bit).

isApplyResolution

public boolean isApplyResolution()

If true, multiplies the values by the x-resolution, if it exists.

setApplyResolution

public void setApplyResolution(boolean applyResolution)

If true, multiplies the values by the x-resolution, if it exists.

isIgnoreZIfNaN

public boolean isIgnoreZIfNaN()

If true and the z-resolution is undefined, the z dimension is ignored.

setIgnoreZIfNaN

public void setIgnoreZIfNaN(boolean ignoreZIfNaN)

If true and the z-resolution is undefined, the z dimension is ignored.