de.lmu.ifi.dbs.elki.algorithm.projection

Class DenseAffinityMatrix

java.lang.Object

de.lmu.ifi.dbs.elki.algorithm.projection.DenseAffinityMatrix

All Implemented Interfaces:

AffinityMatrix

public class DenseAffinityMatrix
extends java.lang.Object
implements AffinityMatrix

Dense affinity matrix storage. TODO: it is likely faster to store this in a 1-d array when possible.

Since:

0.7.5

Author:

Erich Schubert

Field Summary

Fields

Modifier and Type	Field and Description
(package private) ArrayDBIDs	ids Indexed objects.
(package private) double[][]	pij Dense storage.

Constructor Summary

Constructors

Constructor and Description
DenseAffinityMatrix(double[][] affinities, ArrayDBIDs ids) Constructor.

Method Summary

Modifier and Type	Method and Description
double	get(int i, int j) Get an entry by absolute position.
int	iter(int x) Iterator over non-zero features only.
int	iterAdvance(int x, int iter) Advance the iterator to the next position.
DBIDArrayIter	iterDBIDs() Array iterator over the stored objects.
int	iterDim(int x, int iter) Get the dimension an iterator points to.
boolean	iterValid(int x, int iter) Test the iterator position for validity.
double	iterValue(int x, int iter) Get the value an iterator points to.
void	scale(double d) Scale the whole matrix with a constant factor d.
int	size() Number of rows.

Methods inherited from class java.lang.Object

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

Field Detail

pij

double[][] pij

Dense storage.

ids

ArrayDBIDs ids

Indexed objects.

Constructor Detail

DenseAffinityMatrix

public DenseAffinityMatrix(double[][] affinities,
                           ArrayDBIDs ids)

Constructor.

Parameters:

affinities - Raw affinity matrix

ids - Indexed objects

Method Detail

get

public double get(int i,
                  int j)

Description copied from interface: AffinityMatrix

Get an entry by absolute position. Note: this may be expensive on sparse matrixes.

Specified by:

get in interface AffinityMatrix

Parameters:

i - Row

j - Column

Returns:

Entry

scale

public void scale(double d)

Description copied from interface: AffinityMatrix

Scale the whole matrix with a constant factor d. This is used to add/remove early exaggeration of tSNE.

Specified by:

scale in interface AffinityMatrix

Parameters:

d - Scaling factor.

size

public int size()

Description copied from interface: AffinityMatrix

Number of rows.

Specified by:

size in interface AffinityMatrix

Returns:

Size

iterDBIDs

public DBIDArrayIter iterDBIDs()

Description copied from interface: AffinityMatrix

Array iterator over the stored objects.

Specified by:

iterDBIDs in interface AffinityMatrix

Returns:

DBID iterator

iter

public int iter(int x)

Description copied from interface: AffinityMatrix

Iterator over non-zero features only. Note: depending on the underlying implementation, this may or may not be the dimension. Use AffinityMatrix.iterDim(int, int) to get the actual dimension. In fact, usually this will be the ith non-zero value, assuming an array representation. Think of this number as an iterator. But for efficiency, it has a primitive type, so it does not require garbage collection. With Java 10 value types, we will likely be able to make this both type-safe and highly efficient again. Intended usage:

 
 for (int iter = v.iter(x); v.iterValid(x, iter); iter = v.iterAdvance(x, iter)) {
   final int dim = v.iterDim(x, iter);
   final int val = v.iterValue(x, iter);
 }
 
 

Important: you need to use the return value of iterAdvance for the next iteration, or you will have an endless loop.

Specified by:

iter in interface AffinityMatrix

Parameters:

x - Point to get the neighbors for

Returns:

Identifier for the first non-zero dimension, not necessarily the dimension!

iterAdvance

public int iterAdvance(int x,
                       int iter)

Description copied from interface: AffinityMatrix

Advance the iterator to the next position.

Specified by:

iterAdvance in interface AffinityMatrix

iter - Previous iterator position

Returns:

Next iterator position

iterDim

public int iterDim(int x,
                   int iter)

Description copied from interface: AffinityMatrix

Get the dimension an iterator points to.

Specified by:

iterDim in interface AffinityMatrix

iter - Iterator position

Returns:

Dimension the iterator refers to

iterValue

public double iterValue(int x,
                        int iter)

Description copied from interface: AffinityMatrix

Get the value an iterator points to.

Specified by:

iterValue in interface AffinityMatrix

iter - Iterator position

Returns:

Dimension the iterator refers to

iterValid

public boolean iterValid(int x,
                         int iter)

Description copied from interface: AffinityMatrix

Test the iterator position for validity.

Specified by:

iterValid in interface AffinityMatrix

iter - Iterator position

Returns:

true when it refers to a valid position.