Package elki.application.experiments

Class ORLibBenchmark

java.lang.Object

elki.application.AbstractApplication

elki.application.experiments.ORLibBenchmark

public class ORLibBenchmark
extends AbstractApplication

Load an ORlib problem to evaluate k-medoids clustering quality.

Since:

0.8.0

Author:

Erich Schubert

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ORLibBenchmark.Par<O>	Parameterization class.

Field Summary

Fields

Modifier and Type	Field	Description
private java.lang.Class<? extends ClusteringAlgorithm<?>>	alg	Clustering algorithm
private java.net.URI	file	Input file.
private KMedoidsInitialization<DBID>	init	Initialization method.
private int	k	Number of clusters override (optional)
private static Logging	LOG	Class logger.
private RandomFactory	rnd	Random generator for shuffling.

Fields inherited from class elki.application.AbstractApplication

REFERENCE, VERSION

Constructor Summary

Constructors

Constructor	Description
ORLibBenchmark(java.net.URI file, java.lang.Class<? extends ClusteringAlgorithm<?>> alg, KMedoidsInitialization<DBID> init, int k, RandomFactory rnd)	Constructor.

Method Summary

Modifier and Type	Method	Description
private static void	allShortestPaths(int n, double[] mat)	Floyd's all-pairs shortest paths
private static int	computeOffset(int x, int y)	Compute the offset within the file.
static void	main(java.lang.String[] args)	Main method, delegate to super class.
private double[]	randomShuffle(int n, double[] mat)	Random shuffle of the matrix.
private static double[]	readEdges(int n, TokenizedReader reader, Tokenizer tok)	Load the edge list.
void	run()	Runs the application.

Methods inherited from class elki.application.AbstractApplication

printErrorMessage, runCLIApplication, usage

Methods inherited from class java.lang.Object

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

Field Detail

LOG

private static final Logging LOG

Class logger.

file

private java.net.URI file

Input file.

alg

private java.lang.Class<? extends ClusteringAlgorithm<?>> alg

Clustering algorithm

init

private KMedoidsInitialization<DBID> init

Initialization method.

k

private int k

Number of clusters override (optional)

rnd

private RandomFactory rnd

Random generator for shuffling.

Constructor Detail

ORLibBenchmark

public ORLibBenchmark(java.net.URI file,
                      java.lang.Class<? extends ClusteringAlgorithm<?>> alg,
                      KMedoidsInitialization<DBID> init,
                      int k,
                      RandomFactory rnd)

Constructor.

Parameters:

file - Input file name

alg - Algorithm class

init - Random generator

k - Override for the number of clusters

rnd - Random generator for shuffling

Method Detail

run

public void run()

Description copied from class: AbstractApplication

Runs the application.

Specified by:

run in class AbstractApplication

readEdges

private static double[] readEdges(int n,
                                  TokenizedReader reader,
                                  Tokenizer tok)
                           throws java.io.IOException

Load the edge list.

Parameters:

n - Data set size

reader - Reader

tok - Tokenizer

Returns:

Matrix (missing values are infinity)

Throws:

java.io.IOException

allShortestPaths

private static void allShortestPaths(int n,
                                     double[] mat)

Floyd's all-pairs shortest paths

Parameters:

n - Number of nodes

mat - Matrix to complete

randomShuffle

private double[] randomShuffle(int n,
                               double[] mat)

Random shuffle of the matrix.

Parameters:

n - Data set size

mat - Matrix

Returns:

New matrix

computeOffset

private static int computeOffset(int x,
                                 int y)

Compute the offset within the file.

Parameters:

x - First coordinate

y - Second coordinate

Returns:

Linear offset

main

public static void main(java.lang.String[] args)

Main method, delegate to super class.

Parameters:

args - Command line arguments