de.lmu.ifi.dbs.elki.distance.distancefunction.external
Class FileBasedFloatDistanceFunction<V extends DatabaseObject>

java.lang.Object
  de.lmu.ifi.dbs.elki.logging.AbstractLoggable
      de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizable
          de.lmu.ifi.dbs.elki.distance.AbstractMeasurementFunction<O,D>
              de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDistanceFunction<O,FloatDistance>
                  de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractFloatDistanceFunction<V>
                      de.lmu.ifi.dbs.elki.distance.distancefunction.external.FileBasedFloatDistanceFunction<V>

Type Parameters:

V - object type

All Implemented Interfaces:

DistanceFunction<V,FloatDistance>, MeasurementFunction<V,FloatDistance>, Parameterizable

public class FileBasedFloatDistanceFunction<V extends DatabaseObject>
extends AbstractFloatDistanceFunction<V>

Provides a DistanceFunction that is based on float distances given by a distance matrix of an external file.

Author:

Elke Achtert

Field Summary

private Map<Pair<Integer,Integer>,FloatDistance>	cache
static OptionID	MATRIX_ID OptionID for MATRIX_PARAM
private FileParameter	MATRIX_PARAM Parameter that specifies the name of the directory to be re-parsed.
private DistanceParser<V,FloatDistance>	parser
static OptionID	PARSER_ID OptionID for PARSER_PARAM
private ClassParameter<DistanceParser<V,FloatDistance>>	PARSER_PARAM Optional parameter to specify the parsers to provide a database, must extend DistanceParser.

Fields inherited from class de.lmu.ifi.dbs.elki.distance.AbstractMeasurementFunction

INFINITY_PATTERN

Fields inherited from class de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizable

optionHandler

Fields inherited from class de.lmu.ifi.dbs.elki.logging.AbstractLoggable

debug, logger

Constructor Summary

FileBasedFloatDistanceFunction()
Constructor

Method Summary

FloatDistance	distance(Integer id1, Integer id2) Returns the distance between the two objects specified by their objects ids.
FloatDistance	distance(Integer id1, V o2) Returns the distance between the two specified objects.
FloatDistance	distance(V o1, V o2) Computes the distance between two given DatabaseObjects according to this distance function.
private void	loadCache(File matrixfile)
List<String>	setParameters(List<String> args) Grabs all specified options from the option handler.
String	shortDescription() Returns a description of the class and the required parameters.

Methods inherited from class de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractFloatDistanceFunction

infiniteDistance, nullDistance, undefinedDistance, valueOf

Methods inherited from class de.lmu.ifi.dbs.elki.distance.distancefunction.AbstractDistanceFunction

isInfiniteDistance, isNullDistance, isUndefinedDistance

Methods inherited from class de.lmu.ifi.dbs.elki.distance.AbstractMeasurementFunction

getDatabase, matches, requiredInputPattern, setDatabase, setRequiredInputPattern

Methods inherited from class de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizable

addOption, addParameterizable, addParameterizable, checkGlobalParameterConstraints, collectOptions, getAttributeSettings, getParameters, rememberParametersExcept, removeOption, removeParameterizable

Methods inherited from class de.lmu.ifi.dbs.elki.logging.AbstractLoggable

debugFine, debugFiner, debugFinest, exception, progress, verbose, warning

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.lmu.ifi.dbs.elki.distance.MeasurementFunction

requiredInputPattern, setDatabase

Methods inherited from interface de.lmu.ifi.dbs.elki.utilities.optionhandling.Parameterizable

checkGlobalParameterConstraints, collectOptions, getParameters

Field Detail

MATRIX_ID

public static final OptionID MATRIX_ID

OptionID for MATRIX_PARAM

MATRIX_PARAM

private final FileParameter MATRIX_PARAM

Parameter that specifies the name of the directory to be re-parsed.

Key: -distance.matrix

PARSER_ID

public static final OptionID PARSER_ID

OptionID for PARSER_PARAM

PARSER_PARAM

private final ClassParameter<DistanceParser<V extends DatabaseObject,FloatDistance>> PARSER_PARAM

Optional parameter to specify the parsers to provide a database, must extend DistanceParser. If this parameter is not set, NumberDistanceParser is used as parser for all input files.

Key: -distance.parser

parser

private DistanceParser<V extends DatabaseObject,FloatDistance> parser

cache

private Map<Pair<Integer,Integer>,FloatDistance> cache

Constructor Detail

FileBasedFloatDistanceFunction

public FileBasedFloatDistanceFunction()

Constructor

Method Detail

distance

public FloatDistance distance(V o1,
                              V o2)

Computes the distance between two given DatabaseObjects according to this distance function.

Parameters:

o1 - first DatabaseObject

o2 - second DatabaseObject

Returns:

the distance between two given DatabaseObject according to this distance function

distance

public FloatDistance distance(Integer id1,
                              V o2)

Returns the distance between the two specified objects.

Specified by:

distance in interface DistanceFunction<V extends DatabaseObject,FloatDistance>

Overrides:

distance in class AbstractDistanceFunction<V extends DatabaseObject,FloatDistance>

Parameters:

id1 - first object id

o2 - second DatabaseObject

Returns:

the distance between the two objects specified by their objects ids

distance

public FloatDistance distance(Integer id1,
                              Integer id2)

Returns the distance between the two objects specified by their objects ids. If a cache is used, the distance value is looked up in the cache. If the distance does not yet exists in cache, it will be computed an put to cache. If no cache is used, the distance is computed.

Specified by:

distance in interface DistanceFunction<V extends DatabaseObject,FloatDistance>

Overrides:

distance in class AbstractDistanceFunction<V extends DatabaseObject,FloatDistance>

Parameters:

id1 - first object id

id2 - second object id

Returns:

the distance between the two objects specified by their objects ids

shortDescription

public String shortDescription()

Returns a description of the class and the required parameters. This description should be suitable for a usage description.

Specified by:

shortDescription in interface Parameterizable

Overrides:

shortDescription in class AbstractMeasurementFunction<V extends DatabaseObject,FloatDistance>

Returns:

String a description of the class and the required parameters

setParameters

public List<String> setParameters(List<String> args)
                           throws ParameterException

Description copied from class: AbstractParameterizable

Grabs all specified options from the option handler. Any extending class should call this method first and return the returned array without further changes, but after setting further required parameters. An example for overwriting this method taking advantage from the previously (in superclasses) defined options would be:

 {
   List remainingParameters = super.setParameters(args);
   // set parameters for your class
   // for example like this:
   if(isSet(MY_PARAM_VALUE_PARAM))
   {
      myParamValue = getParameterValue(MY_PARAM_VALUE_PARAM);
   }
   .
   .
   .
   return remainingParameters;
   // or in case of attributes requesting parameters themselves
   // return parameterizableAttribbute.setParameters(remainingParameters);
 }
 

Specified by:

setParameters in interface Parameterizable

Overrides:

setParameters in class AbstractParameterizable

Parameters:

args - parameters to set the attributes accordingly to

Returns:

a list containing the unused parameters

Throws:

ParameterException - in case of wrong parameter-setting

loadCache

private void loadCache(File matrixfile)
                throws IOException

Throws:

IOException