de.unihalle.informatik.MiToBo.filters.vesselness

Class StegerRidgeDetection2DWrapper

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.filters.vesselness.StegerRidgeDetection2DWrapper

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=false)
public class StegerRidgeDetection2DWrapper
extends MTBOperator
implements loci.common.StatusReporter

Wrapper for Ridge Detection plugin by Carsten Steger (and Thorsten Wagner).

Related publication:

• C. Steger, An unbiased detector of curvilinear structures, in IEEE Transactions on Pattern Analysis and Machine Intelligence, 20(2), pp.113–125, 1998

For details on parameters and functionality take a look at ...

• the website of the corresponding ImageJ plugin: http://imagej.net/Ridge_Detection
• the Github page with the source code: https://github.com/thorstenwagner/ij-ridgedetection

Author:

Birgit Moeller

Nested Class Summary

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
protected boolean	correctPosition Correct the line position if it has different contrast on each side of it.
protected boolean	darkLine If true, dark lines on bright background are extracted.
protected boolean	estimateWidth If true the widths of the lines are estimated.
protected boolean	extendLine If true lines are extended.
protected double	highContrast Highest grayscale value of the line.
protected MTBImageByte	inImg Input image to be processed.
protected double	lineWidth Line width.
protected double	lowContrast Lowest grayscale value of the line.
protected double	lowerThresh Lower threshold for filter responses.
protected double	maxLineLength Maximal line length.
protected double	minLineLength Minimal line length.
private static String	opIdentifier Identifier for outputs in verbose mode.
protected de.biomedical_imaging.ij.steger.OverlapOption	overlapOpt Mode for how to resolve overlaps of lines.
private MTBImageRGB	resultImage Output image.
private de.biomedical_imaging.ij.steger.Junctions	resultJunctions Detected junction points.
private de.biomedical_imaging.ij.steger.Lines	resultLines Detected lines.
protected double	sigma Sigma value of derivatives depending on line width.
protected Vector<loci.common.StatusListener>	statusListeners Vector of installed StatusListeners.
protected double	upperThresh Pixels with a response above this threshold are immidiately accepted.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
StegerRidgeDetection2DWrapper() Default constructor.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener statuslistener)
private void	callBackUpdateSigmaThresholds() Calculates values for mandatory parameters sigma, upperThresh and lowerThresh from optional parameters lineWidth, highContrast and lowContrast in case that one of the values changed.
static void	drawResultsToImage(MTBImageRGB image, de.biomedical_imaging.ij.steger.Lines lines, de.biomedical_imaging.ij.steger.Junctions junctions, boolean drawWidth, boolean showIDs) Draw results to given image.
de.biomedical_imaging.ij.steger.Junctions	getResultJunctions() Get detected junctions.
de.biomedical_imaging.ij.steger.Lines	getResultLines() Get detected lines.
void	notifyListeners(loci.common.StatusEvent e)
protected void	operate()
void	removeStatusListener(loci.common.StatusListener statuslistener)
void	setCorrectPosition(boolean cp) Specify if to correct line positions.
void	setDarkLine(boolean dark) Specify if to detect dark lines on bright background.
void	setEstimateWidth(boolean ew) Specify if to estimate width.
void	setExtendLine(boolean el) Specify if to extend lines.
void	setHighContrast(double highC) Specify high contrast.
void	setInputImage(MTBImageByte inputImage) Specify input image.
void	setLineWidth(double w) Specify line width.
void	setLowContrast(double lowC) Specify low contrast.
void	setLowerThresh(double lowerT) Specify lower threshold.
void	setMaxLineLength(double maxLength) Specify maximal line length.
void	setMinLineLength(double minLength) Specify minimal line length.
void	setOverlapOpt(de.biomedical_imaging.ij.steger.OverlapOption overlapOption) Specify overlap handling mode.
void	setSigma(double s) Specify sigma value.
void	setUpperThresh(double upperT) Specify upper threshold.
void	validateCustom()

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, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

opIdentifier

private static final String opIdentifier

Identifier for outputs in verbose mode.

See Also:

Constant Field Values

inImg

@Parameter(label="Input Image",
           required=true,
           dataIOOrder=0,
           direction=IN,
           mode=STANDARD,
           description="Input image.")
protected transient MTBImageByte inImg

Input image to be processed.

sigma

@Parameter(label="Sigma",
           required=true,
           dataIOOrder=1,
           direction=IN,
           mode=STANDARD,
           description="Sigma of derivatives.")
protected double sigma

Sigma value of derivatives depending on line width.

lowerThresh

@Parameter(label="Lower Threshold",
           required=true,
           dataIOOrder=2,
           direction=IN,
           mode=STANDARD,
           description="Lower threshold for filter responses.")
protected double lowerThresh

Lower threshold for filter responses.

upperThresh

@Parameter(label="Upper Threshold",
           required=true,
           dataIOOrder=3,
           direction=IN,
           mode=STANDARD,
           description="Upper threshold for filter responses.")
protected double upperThresh

Pixels with a response above this threshold are immidiately accepted.

minLineLength

@Parameter(label="Minimum Line Length",
           required=true,
           dataIOOrder=4,
           direction=IN,
           mode=STANDARD,
           description="Minimum line length.")
protected double minLineLength

Minimal line length.

maxLineLength

@Parameter(label="Maximum Line Length",
           required=true,
           dataIOOrder=5,
           direction=IN,
           mode=STANDARD,
           description="Maximum line length.")
protected double maxLineLength

Maximal line length.

lineWidth

@Parameter(label="Line Width",
           required=false,
           dataIOOrder=1,
           direction=IN,
           mode=STANDARD,
           description="Line width.",
           callback="callBackUpdateSigmaThresholds",
           paramModificationMode=MODIFIES_VALUES_ONLY)
protected double lineWidth

Line width.

lowContrast

@Parameter(label="Low Contrast",
           required=false,
           dataIOOrder=2,
           direction=IN,
           mode=STANDARD,
           description="Low contrast.",
           callback="callBackUpdateSigmaThresholds",
           paramModificationMode=MODIFIES_VALUES_ONLY)
protected double lowContrast

Lowest grayscale value of the line.

highContrast

@Parameter(label="High Contrast",
           required=false,
           dataIOOrder=3,
           direction=IN,
           mode=STANDARD,
           description="High contrast.",
           callback="callBackUpdateSigmaThresholds",
           paramModificationMode=MODIFIES_VALUES_ONLY)
protected double highContrast

Highest grayscale value of the line.

darkLine

@Parameter(label="Dark Lines on Bright Background?",
           required=false,
           dataIOOrder=4,
           direction=IN,
           mode=STANDARD,
           description="Dark lines on bright background.")
protected boolean darkLine

If true, dark lines on bright background are extracted.

correctPosition

@Parameter(label="Correct Position?",
           required=false,
           dataIOOrder=5,
           direction=IN,
           mode=STANDARD,
           description="Line positions are corrected.")
protected boolean correctPosition

Correct the line position if it has different contrast on each side of it.

estimateWidth

@Parameter(label="Estimate Width?",
           required=false,
           dataIOOrder=6,
           direction=IN,
           mode=STANDARD,
           description="If true widths of lines are estimated.")
protected boolean estimateWidth

If true the widths of the lines are estimated.

extendLine

@Parameter(label="Extend Lines?",
           required=false,
           dataIOOrder=7,
           direction=IN,
           mode=STANDARD,
           description="If true lines are extended.")
protected boolean extendLine

If true lines are extended.

overlapOpt

@Parameter(label="Overlap Resolution Mode",
           required=false,
           dataIOOrder=8,
           direction=IN,
           mode=STANDARD,
           description="Mode for resolving overlaps of lines.")
protected de.biomedical_imaging.ij.steger.OverlapOption overlapOpt

Mode for how to resolve overlaps of lines.

resultImage

@Parameter(label="Result image",
           dataIOOrder=3,
           direction=OUT,
           description="Result image.")
private transient MTBImageRGB resultImage

Output image.

resultLines

private transient de.biomedical_imaging.ij.steger.Lines resultLines

Detected lines.

resultJunctions

private transient de.biomedical_imaging.ij.steger.Junctions resultJunctions

Detected junction points.

statusListeners

protected transient Vector<loci.common.StatusListener> statusListeners

Vector of installed StatusListeners.

Constructor Detail

StegerRidgeDetection2DWrapper

public StegerRidgeDetection2DWrapper()
                              throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

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

Method Detail

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Overrides:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

operate

protected void operate()

Specified by:

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

setInputImage

public void setInputImage(MTBImageByte inputImage)

Specify input image.

Parameters:

inputImage - Input image to process.

setSigma

public void setSigma(double s)

Specify sigma value.

Parameters:

s - Sigma value.

setLowerThresh

public void setLowerThresh(double lowerT)

Specify lower threshold.

Parameters:

lowerT - Lower threshold to apply.

setUpperThresh

public void setUpperThresh(double upperT)

Specify upper threshold.

Parameters:

upperT - Upper threshold to apply.

setMinLineLength

public void setMinLineLength(double minLength)

Specify minimal line length.

Parameters:

minLength - The mininmal line length to apply.

setMaxLineLength

public void setMaxLineLength(double maxLength)

Specify maximal line length.

Parameters:

maxLength - The maximal line length to apply.

setLineWidth

public void setLineWidth(double w)

Specify line width.

Parameters:

w - Line width to apply.

setHighContrast

public void setHighContrast(double highC)

Specify high contrast.

Parameters:

highC - High contrast value to apply.

setLowContrast

public void setLowContrast(double lowC)

Specify low contrast.

Parameters:

lowC - Low contrast value to apply.

setDarkLine

public void setDarkLine(boolean dark)

Specify if to detect dark lines on bright background.

Parameters:

dark - If true dark lines on bright background are assumed.

setCorrectPosition

public void setCorrectPosition(boolean cp)

Specify if to correct line positions.

Parameters:

cp - If true positions will be corrected.

setEstimateWidth

public void setEstimateWidth(boolean ew)

Specify if to estimate width.

Parameters:

ew - If true line width will be estimated.

setExtendLine

public void setExtendLine(boolean el)

Specify if to extend lines.

Parameters:

el - If true lines will be extended.

setOverlapOpt

public void setOverlapOpt(de.biomedical_imaging.ij.steger.OverlapOption overlapOption)

Specify overlap handling mode.

Parameters:

overlapOption - The option to use for resolving overlaps.

getResultLines

public de.biomedical_imaging.ij.steger.Lines getResultLines()

Get detected lines.

Returns:

Set of detected lines.

getResultJunctions

public de.biomedical_imaging.ij.steger.Junctions getResultJunctions()

Get detected junctions.

Returns:

Set of detected junctions.

callBackUpdateSigmaThresholds

private void callBackUpdateSigmaThresholds()
                                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Calculates values for mandatory parameters sigma, upperThresh and lowerThresh from optional parameters lineWidth, highContrast and lowContrast in case that one of the values changed.

Throws:

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

drawResultsToImage

public static void drawResultsToImage(MTBImageRGB image,
                                      de.biomedical_imaging.ij.steger.Lines lines,
                                      de.biomedical_imaging.ij.steger.Junctions junctions,
                                      boolean drawWidth,
                                      boolean showIDs)

Draw results to given image.

This code is adapted from the method Lines_.displayContours().

Parameters:

image - Image to which to draw the lines.

lines - Lines to draw.

junctions - If not null, junction points to draw

drawWidth - If true, width of lines is also drawn.

showIDs - If true, IDs are drawn to image.

addStatusListener

public void addStatusListener(loci.common.StatusListener statuslistener)

Specified by:

addStatusListener in interface loci.common.StatusReporter

notifyListeners

public void notifyListeners(loci.common.StatusEvent e)

Specified by:

notifyListeners in interface loci.common.StatusReporter

removeStatusListener

public void removeStatusListener(loci.common.StatusListener statuslistener)

Specified by:

removeStatusListener in interface loci.common.StatusReporter