de.unihalle.informatik.MiToBo.apps.cellMorphology.paceQuant.segmentation.anisotropicFilters

Class SegConfigFilters

java.lang.Object

de.unihalle.informatik.MiToBo.apps.cellMorphology.paceQuant.segmentation.anisotropicFilters.SegConfigFilters

@ALDParametrizedClass
public class SegConfigFilters
extends Object

Configurator object for pavement cell detection based on vesselness filters.

Author:

Birgit Moeller

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	allowBranchPointsInSpines Flag to enable/disable check for branch points in spines.
private PaCeQuant.GapCloseMode	gapMode Mode for closing gaps.
private int	naiveGapThreshold Maximal distance of gaps in naive mode to be closed.
private double	niblackVarianceThresh Niblack threshold.
private boolean	runParallel Flag to enable/disable parallel execution.
private GaussFilter.SigmaInterpretation	sigmaMeaning Gaussian smoothing configuration.
private PaCeQuant.SpineLengthDefine	spineLengthDefine Spine length interpretation.
private double	spineLengthMax Maximal length of admissible spines.

Constructor Summary

Constructors

Constructor and Description
SegConfigFilters() Default constructor.

Method Summary

Modifier and Type	Method and Description
PaCeQuant.GapCloseMode	getGapMode() Get current gap mode selection
double	getMaxSpineLength() Maximal length of admissible spines.
int	getNaiveGapThreshold() Get threshold for closing gaps in naive mode.
double	getNiblackVarianceThreshold() Get variance threshold for Niblack thresholding.
GaussFilter.SigmaInterpretation	getSigmaMeaning() Get interpretation for sigma values.
PaCeQuant.SpineLengthDefine	getSpineLengthInterpretation() Get interpretation of spine length parameter.
boolean	isAllowedBranchPointsInSpines() Request how to deal with branch points in spines.
boolean	runParallelMode() Check if parallelization should be used.

Methods inherited from class java.lang.Object

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

Field Detail

runParallel

@ALDClassParameter(label="Run in parallel?",
                   dataIOOrder=-1)
private boolean runParallel

Flag to enable/disable parallel execution.

gapMode

@ALDClassParameter(label="Heuristic for Gap Closing",
                   dataIOOrder=0)
private PaCeQuant.GapCloseMode gapMode

Mode for closing gaps.

naiveGapThreshold

@ALDClassParameter(label="  - End-point distance for naive heuristic",
                   dataIOOrder=1)
private int naiveGapThreshold

Maximal distance of gaps in naive mode to be closed.

sigmaMeaning

@ALDClassParameter(label="Gaussian Sigma Interpretation",
                   dataIOOrder=10)
private GaussFilter.SigmaInterpretation sigmaMeaning

Gaussian smoothing configuration.

niblackVarianceThresh

@ALDClassParameter(label="Niblack threshold",
                   dataIOOrder=11)
private double niblackVarianceThresh

Niblack threshold.

spineLengthDefine

@ALDClassParameter(label="Spine Length Interpretation",
                   dataIOOrder=12)
private PaCeQuant.SpineLengthDefine spineLengthDefine

Spine length interpretation.

spineLengthMax

@ALDClassParameter(label="Maximal spine length",
                   dataIOOrder=13)
private double spineLengthMax

Maximal length of admissible spines.

allowBranchPointsInSpines

@ALDClassParameter(label="Allow Branch Points in Spines?",
                   dataIOOrder=14)
private boolean allowBranchPointsInSpines

Flag to enable/disable check for branch points in spines.

Constructor Detail

SegConfigFilters

public SegConfigFilters()

Default constructor.

Method Detail

runParallelMode

public boolean runParallelMode()

Check if parallelization should be used.

Returns:

If true, parallelization is desired.

getGapMode

public PaCeQuant.GapCloseMode getGapMode()

Get current gap mode selection

Returns:

Selected gap mode.

getNaiveGapThreshold

public int getNaiveGapThreshold()

Get threshold for closing gaps in naive mode.

Returns:

Maximal value for gaps to be closed.

getSigmaMeaning

public GaussFilter.SigmaInterpretation getSigmaMeaning()

Get interpretation for sigma values.

Returns:

Interpretation for sigma values for Gaussian mask.

getNiblackVarianceThreshold

public double getNiblackVarianceThreshold()

Get variance threshold for Niblack thresholding.

Returns:

Selected variance threshold.

getSpineLengthInterpretation

public PaCeQuant.SpineLengthDefine getSpineLengthInterpretation()

Get interpretation of spine length parameter.

Returns:

Either absolute or relative.

getMaxSpineLength

public double getMaxSpineLength()

Maximal length of admissible spines.

Returns:

Maximal length for spines.

isAllowedBranchPointsInSpines

public boolean isAllowedBranchPointsInSpines()

Request how to deal with branch points in spines.

Returns:

If true, branch points in spines are tolerated.