Package elki.distance.external

Class FileBasedSparseDoubleDistance

java.lang.Object

elki.distance.AbstractDatabaseDistance<DBID>

elki.distance.AbstractDBIDRangeDistance

elki.distance.external.FileBasedSparseDoubleDistance

All Implemented Interfaces:

DBIDDistance, DBIDRangeDistance, Distance<DBID>

public class FileBasedSparseDoubleDistance
extends AbstractDBIDRangeDistance

Distance function that is based on double distances given by a distance matrix of an external ASCII file.

Note: parsing an ASCII file is rather expensive.

See AsciiDistanceParser for the default input format.

TODO: use a double[] instead of the hash map?

Since:

0.1

Author:

Elke Achtert, Erich Schubert

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	FileBasedSparseDoubleDistance.Par	Parameterization class.

Nested classes/interfaces inherited from class elki.distance.AbstractDatabaseDistance

AbstractDatabaseDistance.Instance<O>

Field Summary

Fields

Modifier and Type	Field	Description
private it.unimi.dsi.fastutil.longs.Long2DoubleOpenHashMap	cache	The distance cache
protected double	defaultDistance	Distance to return when not defined otherwise.
private static Logging	LOG	Class logger.
private java.net.URI	matrixfile	Input file of distance matrix
private int	max	Minimum and maximum IDs seen.
private int	min	Minimum and maximum IDs seen.
private DistanceParser	parser	Distance parser

Constructor Summary

Constructors

Constructor	Description
FileBasedSparseDoubleDistance(DistanceParser parser, java.net.URI matrixfile, double defaultDistance)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	checkRange(DBIDRange range)	Validate the range of DBIDs to use.
double	distance(int i1, int i2)	Compute the distance for two integer offsets.
boolean	equals(java.lang.Object obj)
<O extends DBID> DistanceQuery<O>	instantiate(Relation<O> relation)	Instantiate with a database to get the actual distance query.
protected void	loadCache(int size, java.io.InputStream in)	Fill cache from an input stream.
protected static long	makeKey(int i1, int i2)	Combine two integer ids into a long value.

Methods inherited from class elki.distance.AbstractDBIDRangeDistance

distance, getInputTypeRestriction

Methods inherited from class java.lang.Object

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

Methods inherited from interface elki.distance.Distance

isMetric, isSquared, isSymmetric

Field Detail

LOG

private static final Logging LOG

Class logger.

cache

private it.unimi.dsi.fastutil.longs.Long2DoubleOpenHashMap cache

The distance cache

parser

private DistanceParser parser

Distance parser

matrixfile

private java.net.URI matrixfile

Input file of distance matrix

min

private int min

Minimum and maximum IDs seen.

max

private int max

Minimum and maximum IDs seen.

defaultDistance

protected double defaultDistance

Distance to return when not defined otherwise.

Constructor Detail

FileBasedSparseDoubleDistance

public FileBasedSparseDoubleDistance(DistanceParser parser,
                                     java.net.URI matrixfile,
                                     double defaultDistance)

Constructor.

Parameters:

parser - Parser

matrixfile - input file

defaultDistance - Default distance (when undefined)

Method Detail

instantiate

public <O extends DBID> DistanceQuery<O> instantiate(Relation<O> relation)

Description copied from interface: Distance

Instantiate with a database to get the actual distance query.

Specified by:

instantiate in interface Distance<DBID>

Overrides:

instantiate in class AbstractDBIDRangeDistance

Parameters:

relation - The representation to use

Returns:

Actual distance query.

distance

public double distance(int i1,
                       int i2)

Description copied from interface: DBIDRangeDistance

Compute the distance for two integer offsets.

Parameters:

i1 - First offset

i2 - Second offset

Returns:

Distance

loadCache

protected void loadCache(int size,
                         java.io.InputStream in)

Fill cache from an input stream.

Parameters:

size - Expected size

in - Input stream

makeKey

protected static final long makeKey(int i1,
                                    int i2)

Combine two integer ids into a long value.

Parameters:

i1 - First id

i2 - Second id

Returns:

Combined value

checkRange

public void checkRange(DBIDRange range)

Description copied from interface: DBIDRangeDistance

Validate the range of DBIDs to use. This will log a warning if an obvious mismatch was found.

Parameters:

range - DBID range

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object