de.unihalle.informatik.MiToBo.morphology

Class ComponentPostprocess

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class ComponentPostprocess
extends MTBOperator

Methods for post-processing components/pixels in binary images.

Thresholding algorithms yield binary images with distinct connected components of foreground pixels, i.e. regions. The routines of this operator provide functionality for post-processing such binary (unlabeled) component images. Exemplary post-processing steps might include linking/merging adjacent components or changing a component's morphological shape.

Note that the different processing modes may require different parameter settings. These settings have to be done explicitly by calling the corresponding setter-functions the class provides. If the parameters are not set by the user default values are used.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ComponentPostprocess.ProcessMode Processing mode identifiers.

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private double	compactnessTreshold Compactness threshold for components.
private boolean	diagonalNeighbors Flag for using 8-neighborhood.
private int	dilateMaskSize Mask size for topology-preserving dilation.
private Vector<Vector<Point2D.Double>>	endPointHash
private int	height
private MTBImage	inImg (Binary) Input image.
private int	maxCompDist Maximal distance of adjacent components.
private int	maxCompSize Minimal size of components in mode ERASE_SMALL_COMPS.
private int	maxVoronoiExpDist Voronoi expansion distance.
private int	minCompSize Minimal size of components in mode ERASE_SMALL_COMPS.
private ComponentPostprocess.ProcessMode	processMode Processing mode.
private MTBImage	resultImg Result image.
private double	roundnessThreshold Roundness threshold for components.
private int	width

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
ComponentPostprocess() Default constructor.
ComponentPostprocess(MTBImage img, ComponentPostprocess.ProcessMode pm) Default constructor.
ComponentPostprocess(MTBImage img, ComponentPostprocess.ProcessMode pm, int _minCompSize, int _maxCompDist, int maxVoroExpandDist) Deprecated.
ComponentPostprocess(MTBImage img, ComponentPostprocess.ProcessMode pm, int _minCompSize, int _maxCompDist, int maxVoroExpandDist, double _roundnessThreshold) Deprecated.

Method Summary

Modifier and Type	Method and Description
protected MTBImage	dilateComponentsTopologyPreserving(MTBImage lImg, int maskSize) Perform a dilation of the given image with given masksize, but preserve topology.
protected MTBImageByte	EraseLargeComponents(MTBImageByte binIP, int maxComponentSize) Function to remove large components from a binary image.
protected MTBImageByte	eraseNonCompactComponents(MTBImageByte binImage, double threshold) Function to remove all non compact/circular components of a binary image.
protected MTBImageByte	EraseRoundComponents(MTBImageByte binImage, double threshold) Remove components with small eccentricity.
protected MTBImageByte	EraseSmallComponents(MTBImageByte binIP, int minComponentSize) Function to remove small components from a binary image.
private void	foregroundToBackground(Vector<Point2D.Double> points, MTBImage image) Set the pixel value containing in a java.util.Vector of java.awt.geom.Points2D to 0.
double	getCompactnessThreshold() Returns the actual value of compactness threshold.
boolean	getDiagonalNeighbors() Get value of Parameter argument DiagonalNeighbors.
MTBImage	getInputImage() Get reference to the current input image.
int	getMaximalComponentDist() Returns the maximal component distance for linking.
int	getMaximalComponentSize() Returns the maximal valid component size for component removal.
int	getMaxVoronoiExpandDist() Returns the maximal distance of pixels considered in Voronoi expansion.
int	getMinimalComponentSize() Returns the minimal valid component size for component removal.
ComponentPostprocess.ProcessMode	getProcessMode() Get current process mode.
MTBImage	getResultImage() Get the result image after applying operator.
double	getRoundnessThreshold() Returns the currently active roundness threshold.
protected MTBImageByte	LinkAdjacentComponents(MTBImageByte binIP) Function for linking adjacent components/regions in a binary image.
protected MTBImageByte	LinkAdjacentPixels(MTBImageByte binIP, int maxDist) Function for linking adjacent pixels in a binary image.
protected void	operate()
void	setCompactnessThreshold(double _compactnessTrheshold) Set the compactness threshold for eliminating non compact components.
void	setDiagonalNeighbors(boolean value) If true 8-neighborhood, i.e. diagonal neighbors, will be used in mode 'VORONOI_EXPAND' for Voronoi dilation.
void	setDilateMaskSize(int mask) Specify mask size for topology-preserving dilation.
void	setInputImage(MTBImage img) Specify input image.
void	setMaximalComponentDistance(int _maxCompDist) Set maximal component/pixel distance for linking.
void	setMaximalComponentSize(int _maxCompSize) Set maximal component size for erasing large components.
void	setMaximalVoronoiExpansionDistance(int _maxVoroExpandDist) Set radius of dilation mask in Voronoi expansion.
void	setMinimalComponentSize(int _minCompSize) Set minimal component size for erasing small components.
void	setProcessMode(ComponentPostprocess.ProcessMode pm) Specify process mode.
void	setRoundnessThreshold(double _roundnessThreshold) Set roundness threshold for eliminating round components.
protected MTBImage	VoronoiExpandComponents(MTBImage labelImg, int maxDist) Deprecated. Implementation is quite slow, use method dilateComponentsTopologyPreserving(MTBImage, int).

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

inImg

@Parameter(label="Input Image",
           required=true,
           dataIOOrder=-10,
           direction=IN,
           description="(Binary) input image.")
private transient MTBImage inImg

(Binary) Input image.

processMode

@Parameter(label="Process Mode",
           required=true,
           dataIOOrder=-9,
           direction=IN,
           description="Process mode.")
private ComponentPostprocess.ProcessMode processMode

Processing mode.

minCompSize

@Parameter(label="Min. Component Size",
           required=false,
           direction=IN,
           dataIOOrder=-8,
           description="Minimal component size, smaller ones are deleted.")
private int minCompSize

Minimal size of components in mode ERASE_SMALL_COMPS.

maxCompSize

@Parameter(label="Max. Component Size",
           required=false,
           direction=IN,
           dataIOOrder=-8,
           description="Maximal component size, larger ones are deleted.")
private int maxCompSize

Minimal size of components in mode ERASE_SMALL_COMPS.

maxCompDist

@Parameter(label="Max. Distance of Componens",
           required=false,
           direction=IN,
           dataIOOrder=-6,
           description="Maximum allowed distance of components to be linked.")
private int maxCompDist

Maximal distance of adjacent components.

maxVoronoiExpDist

@Parameter(label="Max. Voronoi Expansion Distance",
           required=false,
           direction=IN,
           dataIOOrder=-4,
           description="Distance to which components are expanded in Voronoi expansion mode.")
private int maxVoronoiExpDist

Voronoi expansion distance.

diagonalNeighbors

@Parameter(label="Use Diagonal Neighbors?   ",
           required=false,
           direction=IN,
           dataIOOrder=-10,
           description="Flag for considering 8-neighborhood instead of 4-NB")
private boolean diagonalNeighbors

Flag for using 8-neighborhood.

roundnessThreshold

@Parameter(label="Roundness Threshold",
           required=false,
           direction=IN,
           dataIOOrder=-2,
           description="Threshold for removing round components,  larger values enforce greater eccentricity of surviving components.")
private double roundnessThreshold

Roundness threshold for components.

compactnessTreshold

@Parameter(label="Compactness Threshold",
           required=false,
           direction=IN,
           dataIOOrder=-7,
           description="The theshold for removing noncompact components, larger values enforce more compact regions")
private double compactnessTreshold

Compactness threshold for components.

dilateMaskSize

@Parameter(label="Dilate Mask Size",
           required=false,
           direction=IN,
           dataIOOrder=-7,
           description="Dilation mask size.")
private int dilateMaskSize

Mask size for topology-preserving dilation.

resultImg

@Parameter(label="Result Image",
           required=true,
           direction=OUT,
           description="Result image")
private transient MTBImage resultImg

Result image.

width

private transient int width

height

private transient int height

endPointHash

private transient Vector<Vector<Point2D.Double>> endPointHash

Constructor Detail

ComponentPostprocess

public ComponentPostprocess()
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ComponentPostprocess

public ComponentPostprocess(MTBImage img,
                            ComponentPostprocess.ProcessMode pm)
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Note that parameters for the chosen processing mode have to be set explicitly. Parameters for other modes are ignored.

Parameters:

img - Image to work on.

pm - Process mode of operator.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException -

ComponentPostprocess

@Deprecated
public ComponentPostprocess(MTBImage img,
                                        ComponentPostprocess.ProcessMode pm,
                                        int _minCompSize,
                                        int _maxCompDist,
                                        int maxVoroExpandDist)
                                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Deprecated.

Default constructor. A new empty meta data object is initialized.

Parameters:

img - Image to work on.

pm - Process mode of operator.

_minCompSize - Minimal region size for eliminating small comps.

_maxCompDist - Maximal region distance in linking.

maxVoroExpandDist - Max. distance of pixel considered in Voronoi expansion.

Note: Depending on the process mode each time only one of the parameters is actually in use.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ComponentPostprocess

@Deprecated
public ComponentPostprocess(MTBImage img,
                                        ComponentPostprocess.ProcessMode pm,
                                        int _minCompSize,
                                        int _maxCompDist,
                                        int maxVoroExpandDist,
                                        double _roundnessThreshold)
                                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Deprecated.

Default constructor. A new empty meta data object is initialized.

Parameters:

img -

pm - Process mode of operator.

_minCompSize -

_maxCompDist -

maxVoroExpandDist -

_roundnessThreshold -

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

setInputImage

public void setInputImage(MTBImage img)

Specify input image.

Parameters:

img - Image to process.

setProcessMode

public void setProcessMode(ComponentPostprocess.ProcessMode pm)

Specify process mode.

Parameters:

pm - Process mode of operator.

setMinimalComponentSize

public void setMinimalComponentSize(int _minCompSize)

Set minimal component size for erasing small components.

Only used in mode 'ERASE_SMALL_COMPS'.

Parameters:

_minCompSize -

setMaximalComponentSize

public void setMaximalComponentSize(int _maxCompSize)

Set maximal component size for erasing large components.

Only used in mode 'ERASE_LARGE_COMPS'.

setMaximalComponentDistance

public void setMaximalComponentDistance(int _maxCompDist)

Set maximal component/pixel distance for linking.

Only used in modes 'LINK_ADJ_COMPS' and 'LINK_ADJ_PIXELS'.

setMaximalVoronoiExpansionDistance

public void setMaximalVoronoiExpansionDistance(int _maxVoroExpandDist)

Set radius of dilation mask in Voronoi expansion.

Only used in mode 'VORONOI_EXPAND'.

Parameters:

_maxVoroExpandDist -

setRoundnessThreshold

public void setRoundnessThreshold(double _roundnessThreshold)

Set roundness threshold for eliminating round components.

Only used in mode 'ERASE_ROUND_COMPS'.

Parameters:

_roundnessThreshold -

setCompactnessThreshold

public void setCompactnessThreshold(double _compactnessTrheshold)

Set the compactness threshold for eliminating non compact components.

Parameters:

_compactnessTrheshold -

setDilateMaskSize

public void setDilateMaskSize(int mask)

Specify mask size for topology-preserving dilation.

Parameters:

mask - Mask size to apply

setDiagonalNeighbors

public void setDiagonalNeighbors(boolean value)

If true 8-neighborhood, i.e. diagonal neighbors, will be used in mode 'VORONOI_EXPAND' for Voronoi dilation.

Parameters:

value -

getInputImage

public MTBImage getInputImage()

Get reference to the current input image.

Returns:

Input image to work on.

getProcessMode

public ComponentPostprocess.ProcessMode getProcessMode()

Get current process mode.

Returns:

Process mode of the component process.

getMinimalComponentSize

public int getMinimalComponentSize()

Returns the minimal valid component size for component removal.

Returns:

getMaximalComponentSize

public int getMaximalComponentSize()

Returns the maximal valid component size for component removal.

Returns:

getMaximalComponentDist

public int getMaximalComponentDist()

Returns the maximal component distance for linking.

Returns:

getMaxVoronoiExpandDist

public int getMaxVoronoiExpandDist()

Returns the maximal distance of pixels considered in Voronoi expansion.

Returns:

getDiagonalNeighbors

public boolean getDiagonalNeighbors()

Get value of Parameter argument DiagonalNeighbors.

Returns:

value of DiagonalNeighbors

getRoundnessThreshold

public double getRoundnessThreshold()

Returns the currently active roundness threshold.

Returns:

getCompactnessThreshold

public double getCompactnessThreshold()

Returns the actual value of compactness threshold.

Returns:

getResultImage

public MTBImage getResultImage()

Get the result image after applying operator. Attention, reference might be null.

Returns:

Reference to result image.

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Specified by:

operate in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

EraseSmallComponents

protected MTBImageByte EraseSmallComponents(MTBImageByte binIP,
                                            int minComponentSize)
                                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                            de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Function to remove small components from a binary image.

Small components are components that have a size below the given threshold. Suitable for noise reduction in binary images.

Parameters:

binIP - binary input image

minComponentSize - minimum size of valid components

Returns:

image with too small components erased

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

EraseLargeComponents

protected MTBImageByte EraseLargeComponents(MTBImageByte binIP,
                                            int maxComponentSize)
                                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                            de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Function to remove large components from a binary image.

Large components are components that have a size above the given threshold.

Parameters:

binIP - binary input image

maxComponentSize - maximum size of valid components

Returns:

image with too large components erased

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

EraseRoundComponents

protected MTBImageByte EraseRoundComponents(MTBImageByte binImage,
                                            double threshold)
                                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                            de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Remove components with small eccentricity.

Parameters:

binImage - Input image.

threshold - Eccentricity threshold.

Returns:

Result image.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

eraseNonCompactComponents

protected MTBImageByte eraseNonCompactComponents(MTBImageByte binImage,
                                                 double threshold)
                                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                 de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Function to remove all non compact/circular components of a binary image.

Parameters:

binImage - The input image.

threshold - The threshold of compactness

Returns:

A binary image with all regions removed who got a compactness less threshold

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

LinkAdjacentComponents

protected MTBImageByte LinkAdjacentComponents(MTBImageByte binIP)
                                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Function for linking adjacent components/regions in a binary image.

This function processes a binary image with foreground objects being white. Based on an initial component labeling step and subsequent skeletonization of resulting components, adjacent components are linked by a line of width one pixel in the result image.

The criterion for two components to be adjacent is defined based on the distance of pairs of skeleton endpoints of both components. If there exists at least one pair of endpoints between two components with a distance below the given threshold, the components are linked. If there is more than one pair of such points, the pair with the smallest distance is selected to be linked to each other.

Parameters:

binIP - input binary image with regions

Returns:

binary image where adjacent components are linked by a line of width 1 pixel

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

LinkAdjacentPixels

protected MTBImageByte LinkAdjacentPixels(MTBImageByte binIP,
                                          int maxDist)
                                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                          de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Function for linking adjacent pixels in a binary image.

This function processes a binary image containing only isolated pixels in the foreground. The foreground color is white. Based on the given maximal distance adjacent pixels are linked together to components. The result is comparable to a single-linkage clustering. As result an image is returned where adjacent pixels are linked to each other by a line of width one.

Note that the behaviour of the function is undefined if there are foreground objects present in the image other than single pixels!

Parameters:

binIP - input binary image with regions

maxDist -

Returns:

binary image where adjacent pixels are linked by a line of width 1 pixel

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException -

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

VoronoiExpandComponents

@Deprecated
protected MTBImage VoronoiExpandComponents(MTBImage labelImg,
                                                       int maxDist)
                                                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Deprecated. Implementation is quite slow, use method dilateComponentsTopologyPreserving(MTBImage, int).

Dilate components, but avoid merges with adjacent components.

Each component is dilated up to the maximum given pixel distance. However, the dilation is stopped immediately if its continuation would cause the component to merge with one of its neighbors.

Note that this method is not tuned for efficiency and it is really, really slow. As an alternative you can use the processing mode ComponentPostprocess.ProcessMode.DILATE_TOPOLOGY_PRESERVING or the method dilateComponentsTopologyPreserving(MTBImage, int), respectively, based on a Chamfer distance transformation and being much faster.

Parameters:

labelImg - Input image.

maxDist - Size of dilation mask to apply.

Returns:

Resulting binary image.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

dilateComponentsTopologyPreserving

protected MTBImage dilateComponentsTopologyPreserving(MTBImage lImg,
                                                      int maskSize)
                                               throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                      de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Perform a dilation of the given image with given masksize, but preserve topology.

Parameters:

lImg - Input label image.

maskSize - Size of dilation mask.

Returns:

Dilated label image.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

foregroundToBackground

private void foregroundToBackground(Vector<Point2D.Double> points,
                                    MTBImage image)

Set the pixel value containing in a java.util.Vector of java.awt.geom.Points2D to 0.

This is a private helper method.

Parameters:

points -

image -