org.anchoranalysis.plugin.fiji.bean.define

Class AddDistanceTransform

Object

AnchorBean<DefineAdder>

DefineAdderBean

DefineAdderWithPrefixBean

AddDistanceTransform

All Implemented Interfaces:

DefineAdder

public class AddDistanceTransform
extends DefineAdderWithPrefixBean

Performs a Watershed on distance transform by bundling together several other beans.

The distance transform is Euclidean.

This is used to avoid repetitive bean-definitions in Define, but while still providing visualization of all the intermediate steps that occur during the transformation, which are typically vital for visualization.

For now, it only works in 2D, but can be easily extended for 3D.

The steps are:

1. Find connected components of a binary mask.
2. Find the distance transform of the above.
3. Invert the distance transform.
4. Find minima points from the above.
5. Merge minima points that occur within a certain distance (they become the same object, but it can be disconnected voxelwise).
6. Create seeds by drawing a line between the merged-minima-points so they are now connected.
7. Apply the watershed transformation using the seeds to create segments.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor and Description
AddDistanceTransform()

Method Summary

Modifier and Type	Method and Description
void	addTo(Define define) Adds items to define.
String	getBinaryInputChannelID() The ID of the binary input mask that determines the region of the Watershed.
float	getDistanceTransformMultiplyBy() Multiplies the distance transform by this factor to make it more meaningful in a short.
double	getDistanceTransformSmoothSigmaMeters() If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below.
UnitValueDistance	getMaxDistanceBetweenMinima()
double	getMaxDistanceDeltaContour() The maximum distance allowed between two seeds in terms of their values in the distance map
UnitValueVolume	getMinVolumeConnectedComponent()
void	setBinaryInputChannelID(String binaryInputChannelID) The ID of the binary input mask that determines the region of the Watershed.
void	setDistanceTransformMultiplyBy(float distanceTransformMultiplyBy) Multiplies the distance transform by this factor to make it more meaningful in a short.
void	setDistanceTransformSmoothSigmaMeters(double distanceTransformSmoothSigmaMeters) If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below.
void	setMaxDistanceBetweenMinima(UnitValueDistance maxDistanceBetweenMinima)
void	setMaxDistanceDeltaContour(double maxDistanceDeltaContour) The maximum distance allowed between two seeds in terms of their values in the distance map
void	setMinVolumeConnectedComponent(UnitValueVolume minVolumeConnectedComponent)

Methods inherited from class DefineAdderWithPrefixBean

addWithName, getPrefix, resolveName, setPrefix

Methods inherited from class AnchorBean

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

Methods inherited from class Object

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

Constructor Detail

AddDistanceTransform

public AddDistanceTransform()

Method Detail

addTo

public void addTo(Define define)
           throws DefineAddException

Description copied from interface: DefineAdder

Adds items to define.

What items are added varies by implementation.

Parameters:

define - where to add items to

Throws:

DefineAddException - if the items cannot be added successfully.

getBinaryInputChannelID

public String getBinaryInputChannelID()

The ID of the binary input mask that determines the region of the Watershed.

setBinaryInputChannelID

public void setBinaryInputChannelID(String binaryInputChannelID)

The ID of the binary input mask that determines the region of the Watershed.

getMinVolumeConnectedComponent

public UnitValueVolume getMinVolumeConnectedComponent()

setMinVolumeConnectedComponent

public void setMinVolumeConnectedComponent(UnitValueVolume minVolumeConnectedComponent)

getDistanceTransformMultiplyBy

public float getDistanceTransformMultiplyBy()

Multiplies the distance transform by this factor to make it more meaningful in a short.

setDistanceTransformMultiplyBy

public void setDistanceTransformMultiplyBy(float distanceTransformMultiplyBy)

Multiplies the distance transform by this factor to make it more meaningful in a short.

getDistanceTransformSmoothSigmaMeters

public double getDistanceTransformSmoothSigmaMeters()

If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below.

setDistanceTransformSmoothSigmaMeters

public void setDistanceTransformSmoothSigmaMeters(double distanceTransformSmoothSigmaMeters)

If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below.

getMaxDistanceBetweenMinima

public UnitValueDistance getMaxDistanceBetweenMinima()

setMaxDistanceBetweenMinima

public void setMaxDistanceBetweenMinima(UnitValueDistance maxDistanceBetweenMinima)

getMaxDistanceDeltaContour

public double getMaxDistanceDeltaContour()

The maximum distance allowed between two seeds in terms of their values in the distance map

setMaxDistanceDeltaContour

public void setMaxDistanceDeltaContour(double maxDistanceDeltaContour)

The maximum distance allowed between two seeds in terms of their values in the distance map