databionics.math
Class ParetoDensity

java.lang.Object
  databionics.math.Distances
      databionics.math.ParetoDensity

public class ParetoDensity
extends Distances

Compute the Pareto Density for all row vectors of a DoubleMatrix2D.

Field Summary

protected cern.colt.matrix.DoubleMatrix2D	centers the sphere centers
protected int	clusters the current number of expected clusters
protected cern.colt.matrix.DoubleMatrix1D	densities the list to hold the density values
protected cern.colt.matrix.DoubleMatrix1D	distancePercentiles
protected double	radius the current radius

Fields inherited from class databionics.math.Distances

data, data2d, distanceFunction, distances, log, n

Constructor Summary

ParetoDensity()

Method Summary

void	calculateDensities() Calculate the densities for a given radius The result is stored in the densities field.
void	calculateDistances() calculate pairwise distances and fill percentile vector
cern.colt.matrix.DoubleMatrix1D	densities() Return densities evaluated at centers.
cern.colt.matrix.DoubleMatrix2D	getCenters()
protected double	getClusterFactor(int i) Lookup table for cluster correction factors.
int	getClusters()
cern.colt.matrix.DoubleMatrix1D	getDensities() Return all Pareto density values of the rows in matrix.
cern.colt.matrix.DoubleMatrix1D	getDensityQuantiles() returning quantiles of calculated densities.
cern.colt.matrix.DoubleMatrix1D	getDistancePercentiles()
double	getMax() maximum of calculated densities
int	getMaxDensityIndex()
double	getMin() minimum of calculated densities
double	getParetoRadius() Calculate Pareto radius.
int	getPercentile() Get current percentile (closest to current radius)
double	getRadius() Get current radius
void	setCenters(cern.colt.matrix.DoubleMatrix2D centers)
void	setClusters(int clusters) Number of clusters, used for radius correction
void	setData(cern.colt.matrix.impl.DenseDoubleMatrix1D data) set one dimensional data
void	setData(cern.colt.matrix.impl.DenseDoubleMatrix1D[] data) set data matrix
void	setData(cern.colt.matrix.DoubleMatrix2D data) set data matrix with vectors in rows
void	setParetoRadius() Calculate and set Pareto radius.
void	setRadius(double r) Set radius directly
void	setRadius(int r) Set radius to distance percentile

Methods inherited from class databionics.math.Distances

get, getData, getDistanceFunction, getDistanceMatrix, getDistances, set, setData, setData, setDistanceFunction

Methods inherited from class java.lang.Object

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

Field Detail

distancePercentiles

protected cern.colt.matrix.DoubleMatrix1D distancePercentiles

radius

protected double radius

the current radius

clusters

protected int clusters

the current number of expected clusters

centers

protected cern.colt.matrix.DoubleMatrix2D centers

the sphere centers

densities

protected cern.colt.matrix.DoubleMatrix1D densities

the list to hold the density values

Constructor Detail

ParetoDensity

public ParetoDensity()

Method Detail

setRadius

public void setRadius(double r)

Set radius directly

Parameters:

Pareto - radius

getRadius

public double getRadius()

Get current radius

Returns:

radius

setRadius

public void setRadius(int r)

Set radius to distance percentile

Parameters:

percentile -

getPercentile

public int getPercentile()

Get current percentile (closest to current radius)

Returns:

percentile

getParetoRadius

public double getParetoRadius()

Calculate Pareto radius. For 1D data simply the 18%tile of the distances. For more dimensions iteratively search radius s.t. the median size of all hyperspheres is 20% of the data

Returns:

Pareto radius

setParetoRadius

public void setParetoRadius()

Calculate and set Pareto radius.

calculateDistances

public void calculateDistances()
                        throws java.lang.NullPointerException

calculate pairwise distances and fill percentile vector

Overrides:

calculateDistances in class Distances

Throws:

java.lang.NullPointerException

calculateDensities

public void calculateDensities()

Calculate the densities for a given radius The result is stored in the densities field.

getDensities

public cern.colt.matrix.DoubleMatrix1D getDensities()

Return all Pareto density values of the rows in matrix. If no radius is not set.ParetoRadius is called for density processing.

Returns:

list of density values

densities

public cern.colt.matrix.DoubleMatrix1D densities()

Return densities evaluated at centers.

Returns:

list of density values

getCenters

public cern.colt.matrix.DoubleMatrix2D getCenters()

Returns:

Returns the centers.

setCenters

public void setCenters(cern.colt.matrix.DoubleMatrix2D centers)

Parameters:

centers - The centers to set.

setData

public void setData(cern.colt.matrix.impl.DenseDoubleMatrix1D data)

set one dimensional data

Parameters:

data -

setData

public void setData(cern.colt.matrix.impl.DenseDoubleMatrix1D[] data)

set data matrix

Parameters:

data -

setData

public void setData(cern.colt.matrix.DoubleMatrix2D data)

set data matrix with vectors in rows

Overrides:

setData in class Distances

Parameters:

data - matrix

getClusters

public int getClusters()

Returns:

Returns the expected number of clusters.

setClusters

public void setClusters(int clusters)

Number of clusters, used for radius correction

Parameters:

clusters - The clusters to set.

getClusterFactor

protected double getClusterFactor(int i)

Lookup table for cluster correction factors.

Parameters:

clusters - The number of expected clusters.

getMax

public double getMax()

maximum of calculated densities

Returns:

getMin

public double getMin()

minimum of calculated densities

Returns:

getDensityQuantiles

public cern.colt.matrix.DoubleMatrix1D getDensityQuantiles()

returning quantiles of calculated densities. (if densities were not calculated before, getDensities() is called)

Returns:

quantiles of densities

getMaxDensityIndex

public int getMaxDensityIndex()

Returns:

Returns the distancePercentiles.

getDistancePercentiles

public cern.colt.matrix.DoubleMatrix1D getDistancePercentiles()

Returns:

Returns the distancePercentiles.