de.lmu.ifi.dbs.elki.math.linearalgebra.pca

Class PCARunner<V extends NumberVector<?>>

java.lang.Object

de.lmu.ifi.dbs.elki.math.linearalgebra.pca.PCARunner<V>

Type Parameters:

V - Vector type

All Implemented Interfaces:

Parameterizable

Direct Known Subclasses:

PCAFilteredRunner

public class PCARunner<V extends NumberVector<?>>
extends Object
implements Parameterizable

Class to run PCA on given data. The various methods will start PCA at different places (e.g. with database IDs, database query results, a precomputed covariance matrix or eigenvalue decomposition). The runner can be parameterized by setting a covariance matrix builder (e.g. to a weighted covariance matrix builder)

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PCARunner.Parameterizer<V extends NumberVector<?>> Parameterization class.

Field Summary

Fields

Modifier and Type	Field and Description
protected CovarianceMatrixBuilder<V>	covarianceMatrixBuilder The covariance computation class.
static OptionID	PCA_COVARIANCE_MATRIX Parameter to specify the class to compute the covariance matrix, must be a subclass of CovarianceMatrixBuilder.

Constructor Summary

Constructors

Constructor and Description
PCARunner(CovarianceMatrixBuilder<V> covarianceMatrixBuilder) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
CovarianceMatrixBuilder<V>	getCovarianceMatrixBuilder() Get covariance matrix builder.
PCAResult	processCovarMatrix(Matrix covarMatrix) Process an existing covariance Matrix.
PCAResult	processDatabase(Relation<? extends V> database) Run PCA on the complete database.
PCAResult	processEVD(EigenvalueDecomposition evd) Process an existing eigenvalue decomposition.
PCAResult	processIds(DBIDs ids, Relation<? extends V> database) Run PCA on a collection of database IDs.
<D extends NumberDistance<D,?>> PCAResult	processQueryResult(DistanceDBIDList<D> results, Relation<? extends V> database) Run PCA on a QueryResult Collection.
void	setCovarianceMatrixBuilder(CovarianceMatrixBuilder<V> covarianceBuilder) Set covariance matrix builder.

Methods inherited from class java.lang.Object

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

Field Detail

PCA_COVARIANCE_MATRIX

public static final OptionID PCA_COVARIANCE_MATRIX

Parameter to specify the class to compute the covariance matrix, must be a subclass of CovarianceMatrixBuilder.

Default value: CovarianceMatrixBuilder

Key: -pca.covariance

covarianceMatrixBuilder

protected CovarianceMatrixBuilder<V extends NumberVector<?>> covarianceMatrixBuilder

The covariance computation class.

Constructor Detail

PCARunner

public PCARunner(CovarianceMatrixBuilder<V> covarianceMatrixBuilder)

Constructor.

Parameters:

covarianceMatrixBuilder - Class for computing the covariance matrix

Method Detail

processDatabase

public PCAResult processDatabase(Relation<? extends V> database)

Run PCA on the complete database.

Parameters:

database - the database used

Returns:

PCA result

processIds

public PCAResult processIds(DBIDs ids,
                   Relation<? extends V> database)

Run PCA on a collection of database IDs.

Parameters:

ids - a collection of ids

database - the database used

Returns:

PCA result

processQueryResult

public <D extends NumberDistance<D,?>> PCAResult processQueryResult(DistanceDBIDList<D> results,
                                                           Relation<? extends V> database)

Run PCA on a QueryResult Collection.

Type Parameters:

D - distance type

Parameters:

results - a collection of QueryResults

database - the database used

Returns:

PCA result

processCovarMatrix

public PCAResult processCovarMatrix(Matrix covarMatrix)

Process an existing covariance Matrix.

Parameters:

covarMatrix - the matrix used for performing pca

Returns:

PCA result

processEVD

public PCAResult processEVD(EigenvalueDecomposition evd)

Process an existing eigenvalue decomposition.

Parameters:

evd - eigenvalue decomposition to use

Returns:

PCA result

getCovarianceMatrixBuilder

public CovarianceMatrixBuilder<V> getCovarianceMatrixBuilder()

Get covariance matrix builder.

Returns:

covariance matrix builder in use

setCovarianceMatrixBuilder

public void setCovarianceMatrixBuilder(CovarianceMatrixBuilder<V> covarianceBuilder)

Set covariance matrix builder.

Parameters:

covarianceBuilder - New covariance matrix builder.