de.lmu.ifi.dbs.elki.utilities
Class DatabaseUtil

java.lang.Object
  de.lmu.ifi.dbs.elki.utilities.DatabaseUtil

public final class DatabaseUtil
extends Object

Class with Database-related utility functions such as centroid computation, covariances etc.

Author:

Erich Schubert

Constructor Summary

DatabaseUtil()

Method Summary

static <O extends NumberVector<O,?>> O	centroid(Database<O> database) Returns the centroid as a NumberVector object of the specified database.
static <V extends NumberVector<V,?>> V	centroid(Database<V> database, Collection<Integer> ids) Returns the centroid as a NumberVector object of the specified objects stored in the given database.
static <V extends NumberVector<V,?>> V	centroid(Database<V> database, Collection<Integer> ids, BitSet dimensions) Returns the centroid w.r.t. the dimensions specified by the given BitSet as a NumberVector object of the specified objects stored in the given database.
static <V extends NumberVector<V,?>> V	centroid(Database<V> database, Iterator<Integer> iter, BitSet bitSet) Returns the centroid w.r.t. the dimensions specified by the given BitSet as a NumberVector object of the specified objects stored in the given database.
static Vector	centroid(Matrix data) Returns the centroid as a Vector object of the specified data matrix.
static <NV extends NumberVector<NV,?>> Pair<NV,NV>	computeMinMax(Database<NV> database) Determines the minimum and maximum values in each dimension of all objects stored in the given database.
static <O extends NumberVector<O,?>> Matrix	covarianceMatrix(Database<O> database) Determines the covariance matrix of the objects stored in the given database.
static <O extends NumberVector<O,?>> Matrix	covarianceMatrix(Database<O> database, O centroid) Determines the covariance matrix of the objects stored in the given database w.r.t. the given centroid.
static <V extends NumberVector<V,?>> Matrix	covarianceMatrix(Database<V> database, Collection<Integer> ids) Determines the covariance matrix of the objects stored in the given database.
static Matrix	covarianceMatrix(Matrix data) Determines the d x d covariance matrix of the given n x d data matrix.
static <O extends DatabaseObject> Class<? extends DatabaseObject>	getBaseObjectClassExpensive(Database<O> database) Do a full inspection of the database to find the base object class.
static SortedSet<ClassLabel>	getClassLabels(Database<?> database) Retrieves all class labels within the database.
static String	getClassOrObjectLabel(Database<?> database, Integer objid) Get the class label or object label of an object in the database
static Collection<Integer>	getObjectsByLabelMatch(Database<?> database, Pattern name_pattern) Find object by matching their labels.
static <O extends DatabaseObject> Class<? extends O>	guessObjectClass(Database<O> database) Do a cheap guess at the databases object class.
static double[]	variances(Database<NumberVector<?,?>> database, NumberVector<?,?> centroid, Collection<Integer>[] ids) Determines the variances in each dimension of the specified objects stored in the given database.
static <O extends NumberVector<O,?>> double[]	variances(Database<O> database) Determines the variances in each dimension of all objects stored in the given database.
static <V extends NumberVector<V,?>> double[]	variances(Database<V> database, Collection<Integer> ids) Determines the variances in each dimension of the specified objects stored in the given database.
static <V extends NumberVector<V,?>> double[]	variances(Database<V> database, V centroid, Collection<Integer> ids) Determines the variances in each dimension of the specified objects stored in the given database.

Methods inherited from class java.lang.Object

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

Constructor Detail

DatabaseUtil

public DatabaseUtil()

Method Detail

centroid

public static <V extends NumberVector<V,?>> V centroid(Database<V> database,
                                                       Collection<Integer> ids)

Returns the centroid as a NumberVector object of the specified objects stored in the given database. The objects belonging to the specified ids must be instance of NumberVector.

Type Parameters:

V - Vector type

Parameters:

database - the database storing the objects

ids - the ids of the objects

Returns:

the centroid of the specified objects stored in the given database

Throws:

IllegalArgumentException - if the id list is empty

centroid

public static <V extends NumberVector<V,?>> V centroid(Database<V> database,
                                                       Collection<Integer> ids,
                                                       BitSet dimensions)

Returns the centroid w.r.t. the dimensions specified by the given BitSet as a NumberVector object of the specified objects stored in the given database. The objects belonging to the specified IDs must be instance of NumberVector.

Type Parameters:

V - Vector type

Parameters:

database - the database storing the objects

ids - the identifiable objects

dimensions - the BitSet representing the dimensions to be considered

Returns:

the centroid of the specified objects stored in the given database w.r.t. the specified subspace

Throws:

IllegalArgumentException - if the id list is empty

centroid

public static <V extends NumberVector<V,?>> V centroid(Database<V> database,
                                                       Iterator<Integer> iter,
                                                       BitSet bitSet)

Returns the centroid w.r.t. the dimensions specified by the given BitSet as a NumberVector object of the specified objects stored in the given database. The objects belonging to the specified ids must be instance of NumberVector.

Type Parameters:

V - Vector type

Parameters:

database - the database storing the objects

iter - iterator over the identifiable objects

bitSet - the bitSet specifying the dimensions to be considered

Returns:

the centroid of the specified objects stored in the given database

Throws:

IllegalArgumentException - if the id list is empty

centroid

public static <O extends NumberVector<O,?>> O centroid(Database<O> database)

Returns the centroid as a NumberVector object of the specified database. The objects must be instance of NumberVector.

Type Parameters:

O - Vector type

Parameters:

database - the database storing the objects

Returns:

the centroid of the specified objects stored in the given database

Throws:

IllegalArgumentException - if the database is empty

centroid

public static Vector centroid(Matrix data)

Returns the centroid as a Vector object of the specified data matrix.

Parameters:

data - the data matrix, where the data vectors are column vectors

Returns:

the centroid of the specified data matrix

covarianceMatrix

public static <V extends NumberVector<V,?>> Matrix covarianceMatrix(Database<V> database,
                                                                    Collection<Integer> ids)

Determines the covariance matrix of the objects stored in the given database.

Type Parameters:

V - Vector type

Parameters:

database - the database storing the objects

ids - the ids of the objects

Returns:

the covariance matrix of the specified objects

covarianceMatrix

public static <O extends NumberVector<O,?>> Matrix covarianceMatrix(Database<O> database)

Determines the covariance matrix of the objects stored in the given database.

Type Parameters:

O - Vector type

Parameters:

database - the database storing the objects

Returns:

the covariance matrix of the specified objects

covarianceMatrix

public static <O extends NumberVector<O,?>> Matrix covarianceMatrix(Database<O> database,
                                                                    O centroid)

Determines the covariance matrix of the objects stored in the given database w.r.t. the given centroid.

Type Parameters:

O - Vector type

Parameters:

database - the database storing the objects

centroid - the centroid of the database

Returns:

the covariance matrix of the specified objects

covarianceMatrix

public static Matrix covarianceMatrix(Matrix data)

Determines the d x d covariance matrix of the given n x d data matrix.

Parameters:

data - the database storing the objects

Returns:

the covariance matrix of the given data matrix.

variances

public static <O extends NumberVector<O,?>> double[] variances(Database<O> database)

Determines the variances in each dimension of all objects stored in the given database.

Type Parameters:

O - Vector type

Parameters:

database - the database storing the objects

Returns:

the variances in each dimension of all objects stored in the given database

variances

public static <V extends NumberVector<V,?>> double[] variances(Database<V> database,
                                                               Collection<Integer> ids)

Determines the variances in each dimension of the specified objects stored in the given database. Returns variances(database, centroid(database, ids), ids)

Type Parameters:

V - Vector type

Parameters:

database - the database storing the objects

ids - the ids of the objects

Returns:

the variances in each dimension of the specified objects

variances

public static <V extends NumberVector<V,?>> double[] variances(Database<V> database,
                                                               V centroid,
                                                               Collection<Integer> ids)

Determines the variances in each dimension of the specified objects stored in the given database.

Type Parameters:

V - Vector type

Parameters:

database - the database storing the objects

ids - the ids of the objects

centroid - the centroid or reference vector of the ids

Returns:

the variances in each dimension of the specified objects

variances

public static double[] variances(Database<NumberVector<?,?>> database,
                                 NumberVector<?,?> centroid,
                                 Collection<Integer>[] ids)

Determines the variances in each dimension of the specified objects stored in the given database.

Parameters:

database - the database storing the objects

ids - the array of ids of the objects to be considered in each dimension

centroid - the centroid or reference vector of the ids

Returns:

the variances in each dimension of the specified objects

computeMinMax

public static <NV extends NumberVector<NV,?>> Pair<NV,NV> computeMinMax(Database<NV> database)

Determines the minimum and maximum values in each dimension of all objects stored in the given database.

Type Parameters:

NV - vector type

Parameters:

database - the database storing the objects

Returns:

Minimum and Maximum vector for the hyperrectangle

getClassLabels

public static SortedSet<ClassLabel> getClassLabels(Database<?> database)

Retrieves all class labels within the database.

Parameters:

database - the database to be scanned for class labels

Returns:

a set comprising all class labels that are currently set in the database

guessObjectClass

public static <O extends DatabaseObject> Class<? extends O> guessObjectClass(Database<O> database)

Do a cheap guess at the databases object class.

Type Parameters:

O - Restriction type

Parameters:

database - Database

Returns:

Class of first object in the Database.

getBaseObjectClassExpensive

public static <O extends DatabaseObject> Class<? extends DatabaseObject> getBaseObjectClassExpensive(Database<O> database)

Do a full inspection of the database to find the base object class. Note: this can be an abstract class or interface! TODO: Implement a full search for shared superclasses. But since currently the databases will always use only once class, this is not yet implemented.

Type Parameters:

O - Restriction type

Parameters:

database - Database

Returns:

Superclass of all objects in the database

getObjectsByLabelMatch

public static Collection<Integer> getObjectsByLabelMatch(Database<?> database,
                                                         Pattern name_pattern)

Find object by matching their labels.

Parameters:

database - Database to search in

name_pattern - Name to match against class or object label

Returns:

found cluster or it throws an exception.

getClassOrObjectLabel

public static String getClassOrObjectLabel(Database<?> database,
                                           Integer objid)

Get the class label or object label of an object in the database

Parameters:

database - Database

objid - Object ID

Returns:

String representation of label or object label