config
Class Config

java.lang.Object
  config.Config

public class Config
extends java.lang.Object

Configure the execution of the algorithm. If a parameter is not set manually, the default parameters are used. Valid parameter names and values are predefined in Constants.

Field Summary

private int	additionalDummyNodes Configure how many dummy nodes are added when using the Hungarian algorithm at any point of the matching process.
private double	alpha Configure the alpha in the path distance computation.
private java.lang.String	extractSimilarityWith configure which algorithm is used to extract the similarity from the path distance matrix.
private java.lang.String	finalMatchingWith Configure which algorithm is used for the final matching.
private java.lang.String	handleBadMatchings Configure how bad matchings are handled in the matching result.
private org.apache.log4j.Logger	logger logger instance
private int	numberOfSamplePoints Configure the number of the sampling points used to gain the skeleton path vector, that is, the size of the skeleton path vector.
private java.lang.String	pathdistance configure which path distance definition will be used.
private double	preprocessing Configure the threshold for the skeleton preprocessor.
private java.lang.String	useDenominator Configuring the computation for the path distance definition.
private java.lang.String	useEndnodeOrder Configure how end nodes will be ordered.
private java.lang.String	visualize Configure how the matching result is visualized.

Constructor Summary

Config()
Constructor.

Config(java.lang.String[] args)
Constructor.

Method Summary

int	getAdditionalDummyNodes() Get how many dummy nodes are added when executing HungarianAlgorithm
double	getAlpha() Get the configuration for the weighting factor alpha.
java.lang.String	getExtractSimilarityWith() Get the configuration which method is used to extract the similarity between two end nodes from their path distance matrix
java.lang.String	getFinalMatchingWith() Get the configuration which method is used to perform the final matching.
java.lang.String	getHandleBadMatchings() Get the configuration how bad matchings in the matching result are handled.
int	getNumberOfSamplePoints() Get the configuration how many sample points are used for the skeleton path vector creation.
java.lang.String	getPathDistance() Get the configuration which path distance measurement is used
double	getPreprocessing() Get the threshold for preprocessing the skeleton.
java.lang.String	getUseDenominator() Get the configuration if the denominators in the path distance computation are used.
java.lang.String	getUseEndnodeOrder() Get the configuration how end nodes are ordered.
java.lang.String	getVisualize() Get the configuration for the visualization.
private void	parseArguments(java.lang.String[] args) Parse the arguments specified in the constructor.
private void	setAdditionalDummyNodes(java.lang.String arg) Configure how many dummy nodes will be added when executing HungarianAlgorithm
private void	setAlpha(java.lang.String arg) Set the alpha value for path distance computation.
private void	setExtractSimilarityWith(java.lang.String arg) conigure which algorithm to use to extract end node similarities from path distance matrices.
private void	setFinalMatching(java.lang.String arg) Configure which function to use to perform the final matching.
private void	setHandleMatchings(java.lang.String arg) Configure how bad matchings will be handled
private void	setNumberOfSamplePoints(java.lang.String arg) Set the number of sample points for the skeleton path vector.
private void	setOrderingEndnodes(java.lang.String arg) Configure how end nodes will be ordered
private void	setPathDistance(java.lang.String arg) Configure which path distance measurement will be used.
private void	setPreprocessing(java.lang.String arg) Set the threshold for the preprocessor
private void	setUseDenominator(java.lang.String arg) Configure if to use denominator in path distance computation
private void	setVisualize(java.lang.String arg) set the visualization mode

Methods inherited from class java.lang.Object

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

Field Detail

logger

private final org.apache.log4j.Logger logger

logger instance

pathdistance

private java.lang.String pathdistance

configure which path distance definition will be used.

Possible values are:

• Constants.useOriginalPathDistance, which is the definition described in the paper.
• Constants.usePathLengthForPathDistance, when using this definition, only the paths' length is taken into account.

Default is Constants.useOriginalPathDistance.

extractSimilarityWith

private java.lang.String extractSimilarityWith

configure which algorithm is used to extract the similarity from the path distance matrix.

Possible values are:

• Constants.OSBfunctionUsedForMatchingCosts: OSBv5 will be used, which is order-preserving.
• Constants.HungarianfunctionUsedForMatchingCosts: HungarianAlgorithm will be used, which is not order-preserving, but is not able to skip elements in the matrix.

Default is Constants.OSBfunctionUsedForMatchingCosts.

useEndnodeOrder

private java.lang.String useEndnodeOrder

Configure how end nodes will be ordered. This will have no effect on the result if extractSimilarityWith is set the Constants.HungarianfunctionUsedForMatchingCosts.

Possible values are

• Constants.defaultOrder: In 2D-matchings the end nodes are order by traversing the contour. In 3D - matchings, the end nodes are not ordered at all.
• Constants.orderByPathLength: When creating the path distance matrix for two end nodes i and i', the end nodes will be ordered according to their distance to i and i', respectively.

Default is Constants.defaultOrder

finalMatchingWith

private java.lang.String finalMatchingWith

Configure which algorithm is used for the final matching.

Possible values are:

• Constants.finalMatchingWithHungarian: uses HungarianAlgorithm for the final matching
• Constants.finalMatchingWithOSB: used OSBfinalMatching for the final matching

Default is Constants.finalMatchingWithHungarian

handleBadMatchings

private java.lang.String handleBadMatchings

Configure how bad matchings are handled in the matching result. Used only in 3D Matchings.

Possible values are:

• Constants.showAllMatchings: The matching results are not filtered at all
• Constants.deleteBadMatchingsByMean: The mean of all matching costs is computed. Afterwards, all matchings with a matching cost higher than the mean are deleted.
• Constants.deleteBadMatchingsByMeanAndStd: The mean and standard deviation of all matching costs is computed. Afterwards, all matchings with a matching cost higher than the resulting value are deleted.
• Constants.deleteBadMatchingsByMedian: The median of all matching costs is computed. Afterwards, all matchings with a matching cost higher than the median's matching costs are deleted.
• Constants.deleteBadMatchingsByAngleMean: The mean angle for the matching lines of all matchings are computed, for all three directions in the three-dimensional space. Afterwards, all matchings with a matching line with an angle higher than this value are deleted.
• Constants.deleteBadMatchingsByAngleMeanAndStd: The mean angle and standard deviation for the matching lines of all matchings are computed, for all three directions in the three-dimensional space. Afterwards, all matchings with a matching line with an angle higher than this value are deleted.

Default is Constants.showAllMatchings.

useDenominator

private java.lang.String useDenominator

Configuring the computation for the path distance definition.

Possible values are:

• Constants.useDefaultDenominator: Take denominators into account, as described in the paper
• Constants.dontUseDenominator: Don't use denominators in the computation of the path distance

Default is Constants.useDefaultDenominator

visualize

private java.lang.String visualize

Configure how the matching result is visualized.

Possible values are:

• Constants.showSkeleton: show only the skeleton in matching viewer
• Constants.showVolume: show voxelized volume in matching viewer
• Constants.showBoth: show both skeleton and volume.

Default is Constants.showBoth

additionalDummyNodes

private int additionalDummyNodes

Configure how many dummy nodes are added when using the Hungarian algorithm at any point of the matching process. This only has an effect if either finalMatchingWith is set to Constants.finalMatchingWithHungarian or this extractSimilarityWith is set to Constants.HungarianfunctionUsedForMatchingCosts.

Default is 0.

preprocessing

private double preprocessing

Configure the threshold for the skeleton preprocessor. All branches shorter than this threshold are removed from the skeleton.

Default is -1, that is, the skeleton won't be preprocessed at all.

numberOfSamplePoints

private int numberOfSamplePoints

Configure the number of the sampling points used to gain the skeleton path vector, that is, the size of the skeleton path vector. This only has an effect on the matching result if thispathdistance is set to Constants.useOriginalPathDistance.

Default is 50.

alpha

private double alpha

Configure the alpha in the path distance computation. This only has an effect on the matching result if thispathdistance is set to Constants.useOriginalPathDistance.

Default is 70.

Constructor Detail

Config

public Config(java.lang.String[] args)
       throws InvalidConfigParameterException

Constructor. Create a new configuration instance with the arguments passed as string array. Each parameter has to have the following format: =. All parameter names and values are predefined in Constants.

Parameters:

args - the configuration arguments

Throws:

InvalidConfigParameterException - if one of the configuration arguments is not valid

Config

public Config()
       throws InvalidConfigParameterException

Constructor. Create a new configuration without any arguments. All parameters are set to default.

Throws:

InvalidConfigParameterException - if an error orccured while creating the new configuration

Method Detail

parseArguments

private void parseArguments(java.lang.String[] args)
                     throws InvalidConfigParameterException

Parse the arguments specified in the constructor.

Parameters:

args - - the configuration array

Throws:

InvalidConfigParameterException - if one of the configuration arguments is not valid

setAdditionalDummyNodes

private void setAdditionalDummyNodes(java.lang.String arg)

Configure how many dummy nodes will be added when executing HungarianAlgorithm

Parameters:

arg - configuring argument

getAdditionalDummyNodes

public int getAdditionalDummyNodes()

Get how many dummy nodes are added when executing HungarianAlgorithm

Returns:

number of dummy nodes

setVisualize

private void setVisualize(java.lang.String arg)
                   throws InvalidConfigParameterException

set the visualization mode

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

setUseDenominator

private void setUseDenominator(java.lang.String arg)
                        throws InvalidConfigParameterException

Configure if to use denominator in path distance computation

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

setHandleMatchings

private void setHandleMatchings(java.lang.String arg)
                         throws InvalidConfigParameterException

Configure how bad matchings will be handled

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

setPreprocessing

private void setPreprocessing(java.lang.String arg)
                       throws InvalidConfigParameterException

Set the threshold for the preprocessor

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

setNumberOfSamplePoints

private void setNumberOfSamplePoints(java.lang.String arg)
                              throws InvalidConfigParameterException

Set the number of sample points for the skeleton path vector.

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

setAlpha

private void setAlpha(java.lang.String arg)
               throws InvalidConfigParameterException

Set the alpha value for path distance computation.

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

setFinalMatching

private void setFinalMatching(java.lang.String arg)
                       throws InvalidConfigParameterException

Configure which function to use to perform the final matching.

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

setOrderingEndnodes

private void setOrderingEndnodes(java.lang.String arg)
                          throws InvalidConfigParameterException

Configure how end nodes will be ordered

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

setExtractSimilarityWith

private void setExtractSimilarityWith(java.lang.String arg)
                               throws InvalidConfigParameterException

conigure which algorithm to use to extract end node similarities from path distance matrices.

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

setPathDistance

private void setPathDistance(java.lang.String arg)
                      throws InvalidConfigParameterException

Configure which path distance measurement will be used.

Parameters:

arg - configuring argument

Throws:

InvalidConfigParameterException

getExtractSimilarityWith

public java.lang.String getExtractSimilarityWith()

Get the configuration which method is used to extract the similarity between two end nodes from their path distance matrix

Returns:

method used to extract the similarity between two end nodes

getPathDistance

public java.lang.String getPathDistance()

Get the configuration which path distance measurement is used

Returns:

used path distance measurement

getUseEndnodeOrder

public java.lang.String getUseEndnodeOrder()

Get the configuration how end nodes are ordered.

Returns:

order of the end nodes

getFinalMatchingWith

public java.lang.String getFinalMatchingWith()

Get the configuration which method is used to perform the final matching.

Returns:

method to perform the final matching

getHandleBadMatchings

public java.lang.String getHandleBadMatchings()

Get the configuration how bad matchings in the matching result are handled.

Returns:

how bad matchings are handled

getNumberOfSamplePoints

public int getNumberOfSamplePoints()

Get the configuration how many sample points are used for the skeleton path vector creation.

Returns:

number of sample points

getAlpha

public double getAlpha()

Get the configuration for the weighting factor alpha.

Returns:

the weighting factor alpha

getVisualize

public java.lang.String getVisualize()

Get the configuration for the visualization.

Returns:

the visualization mode

getPreprocessing

public double getPreprocessing()

Get the threshold for preprocessing the skeleton.

Returns:

the minimum length all skeleton branches must have

getUseDenominator

public java.lang.String getUseDenominator()

Get the configuration if the denominators in the path distance computation are used.

Returns:

if the denominators in the path distance computation are used