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

Class PCARunner

java.lang.Object

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

Direct Known Subclasses:

PCAFilteredRunner

public class PCARunner
extends Object

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)

Author:

Erich Schubert

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PCARunner.Parameterizer Parameterization class.

Field Summary

Fields

Modifier and Type	Field and Description
protected CovarianceMatrixBuilder	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 covarianceMatrixBuilder) Constructor.

Method Summary

Methods

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

The covariance computation class.

Constructor Detail

PCARunner

public PCARunner(CovarianceMatrixBuilder covarianceMatrixBuilder)

Constructor.

Parameters:

covarianceMatrixBuilder - Class for computing the covariance matrix

Method Detail

processDatabase

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

Run PCA on the complete database.

Parameters:

database - the database used

Returns:

PCA result

processIds

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

Run PCA on a collection of database IDs.

Parameters:

ids - a collection of ids

database - the database used

Returns:

PCA result

processQueryResult

public PCAResult processQueryResult(DoubleDBIDList results,
                           Relation<? extends NumberVector> database)

Run PCA on a QueryResult Collection.

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 getCovarianceMatrixBuilder()

Get covariance matrix builder.

Returns:

covariance matrix builder in use

setCovarianceMatrixBuilder

public void setCovarianceMatrixBuilder(CovarianceMatrixBuilder covarianceBuilder)

Set covariance matrix builder.

Parameters:

covarianceBuilder - New covariance matrix builder.