GrowingCellLayer

java.lang.Object
- at.tuwien.ifs.somtoolbox.layers.GrowingCellLayer

All Implemented Interfaces:

Layer
```
public class GrowingCellLayer
extends java.lang.Object
implements Layer
```
Version:

$Id: GrowingCellLayer.java 3590 2010-05-21 10:43:45Z mayer $

Author:

Johannes Inführ, Andreas Zweng

Nested Class Summary
- Nested classes/interfaces inherited from interface at.tuwien.ifs.somtoolbox.layers.Layer
  Layer.GridLayout, Layer.GridTopology

Field Summary

Fields
Modifier and Type	Field and Description
`private float`	`alpha` Reduction Factor for signal counter
`private double`	`attractScale` Scaling Factor for gravity between Units
`private double`	`coherenceForceFactor` Scaling Factor for gravity between Units independent of connectedness/distance
`private InputData`	`data` Data used for training
`private int`	`dim` Dimensions of the input-data
`private javax.swing.JFrame`	`display` Frame used to display the CellUnits
`private double[]`	`emptyUnitMarkVector` Weight-Vector for Units that fill holes in unitfield
`private float`	`epsilonB` Adaption Factor of best matching unit
`private float`	`epsilonN` Adaption Factor of neighbors of best matching unit
`private float`	`eta` Cutoff-Value for normalized probability density
`private int`	`lamda` Number of adaption steps between adding/removing of Units
`private int`	`maxEpochs` Number of Iterations on the input data
`private DistanceMetric`	`metric` Distance Metric used for GrowingCellStructures
`private QualityMeasure`	`qualityMeasure` QualityMesure used for GrowingCellStructures
`private java.util.Random`	`rand` Random Nr Generator for Weight-Vector initialisation
`private double`	`repellingScale` Scaling Factor for repulsion between Units
`private java.util.List<GrowingCellTetraheder>`	`tetraheders` List of Tetraheders formed by the Units
`private GrowingCellUnit[][]`	`unitfield` Storagearray for Units for export
`private java.util.List<GrowingCellUnit>`	`units` List of Units that get trained

Constructor Summary

Constructors
Constructor and Description

GrowingCellLayer(int dim, boolean normalize, long randomSeed, InputData data)
Std.

Constructors
Constructor and Description
`GrowingCellLayer(int dim, boolean normalize, long randomSeed, InputData data)` Std.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private void`	`addAttractingForce(GrowingCellUnit unitToMove, GrowingCellUnit unitForcing, double[] attractingForce)` Calculate the attracting force between unitToMove and unitForcing and store it in attractingForce
`private void`	`addRepellingForce(GrowingCellUnit unitToMove, GrowingCellUnit unitForcing, double[] force)` Calculate the repelling force between unitToMove and unitForcing and store it in force
`private void`	`analyzeDimension(GrowingCellUnit[][] data, int[] dimandoffset)` Analyses maximum extension of the Units in data and their offset
`private void`	`analyzeDimension(java.util.List<GrowingCellUnit> units, int[] dimandoffset)` Analyses maximum extension of the Units in units and their offset
`private double`	`calculateVoronoiEstimate(GrowingCellUnit u)` Calculates the voronoi region estimate for unit u
`private void`	`calculateVoronoiEstimate(java.util.List<GrowingCellUnit> neighborsToBe)` Sets the voronoiEstimate of all neighborsToBe
`private void`	`checkConsistency()` Checks consistency of tetraheders and units
`private void`	`clearMappedInput()` Clears the mapped Input of every unit
`private void`	`correctUnitPositions()` Correct Unit Positions so that they stay at the upper left corner (10,10) and don't drift away
`private void`	`decreaseSignalCounters()` Decrease SignalCoutners of units by alpha percent
`java.util.Collection<? extends GrowingCellStructures>`	`getAllSubMaps()`
`Unit[]`	`getAllUnits()` Returns an array of all units in the map layer; the specific order of the units is unspecified.
`double[][]`	`getComponentPlane(int component)` Returns a component plane of the component specified by the argument `component`.
`double[][]`	`getComponentPlane(int component, int z)` Returns a component plane of the component specified by the argument `component`.
`InputData`	`getData()`
`int`	`getDim()`
`private double`	`getDistance(double[] v1, double[] v2)`
`private GrowingCellUnit`	`getFarthestNeighbor(GrowingCellUnit unit)`
`Layer.GridLayout`	`getGridLayout()`
`Layer.GridTopology`	`getGridTopology()`
`java.lang.String`	`getIdString()` Returns the identification string of the map layer.
`private java.util.List<GrowingCellUnit>`	`getInsertionTopologicalNeighbors(GrowingCellUnit sfwinner, GrowingCellUnit sfpartner)`
`int`	`getLevel()` Returns the level of the map layer in a hierarchical model.
`double`	`getMapDistance(int x1, int y1, int z1, int x2, int y2, int z2)` Returns the distance between two units on the map grid.
`double`	`getMapDistance(Unit u1, Unit u2)` Returns the distance between two units on the map grid.
`DistanceMetric`	`getMetric()` Returns the metric used for distance calculation.
`int`	`getNumberOfMappedInputs()` Returns the total number of Inputs mapped on all units in the map layer.
`QualityMeasure`	`getQualityMeasure()` Returns the quality information.
`java.lang.String`	`getRevision()` Returns the revision string of this layer.
`private GrowingCellUnit`	`getSignalFrequencyWinner()`
`private java.util.List<GrowingCellUnit>`	`getTopologicalNeighbors(GrowingCellUnit unit)`
`private java.util.List<GrowingCellTetraheder>`	`getTouchedTetraheders(GrowingCellUnit u1, GrowingCellUnit u2)` Returns Tetraheders that have u1 and u2 in common
`Unit`	`getUnit(int x, int y)` Returns the `Unit` at the position specified by the `x` and `y` arguments.
`Unit`	`getUnit(int x, int y, int z)` Returns the `Unit` at the position specified by the `x` and `y` arguments.
`Unit`	`getUnitForDatum(java.lang.String name)` Returns the unit onto which the datum specified by its name by argument `name` is mapped.
`private GrowingCellUnit`	`getWinner(InputDatum input)`
`UnitDistance[]`	`getWinnersAndDistances(InputDatum input, int numWinners)`
`int`	`getXSize()` Returns the width of the map layer.
`int`	`getYSize()` Returns the height of the map layer.
`int`	`getZSize()` Returns the depth of the map layer.
`private void`	`mapCompleteData(InputData data)` Maps data to the units
`private void`	`prepareForOutput()` Moves the units for optimized space requirement The order along x and y axis stays the same, but the space between units gets reduced to 0, x is reduced before y so a narrow stripe along the y axis will emerge
`private void`	`removeUnits(java.util.List<GrowingCellUnit> unitsToRemove)` removes units specified in unitsToRemove and possible resulting disconnected units
`QualityMeasure`	`train(InputData data, float epsilonB, float epsilonN, float alpha, int lamda, float eta, SOMProperties props)` Trains the CellLayer with the given Parameters and returns the QualityMeasure
`private void`	`trainNormal(InputData data, ProgressListener progressWriter)` Trains the CellLayer with the secified InputData and logs to progressWriter
`private void`	`updateInsertSignalCounters(GrowingCellUnit newUnit, java.util.List<GrowingCellUnit> neighbors)` Updates the SignalCounters after an insert of a new unit
`private void`	`updatePositions()` Update the Position of Units in display-space by means of a simple physics simulation
`private void`	`updateWinnerAndNeighbors(GrowingCellUnit winner, InputDatum currentInput)` Updates the weight-vectors of winning unit and its neighbors

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - units
```
private java.util.List<GrowingCellUnit> units
```
    List of Units that get trained
  - tetraheders
```
private java.util.List<GrowingCellTetraheder> tetraheders
```
    List of Tetraheders formed by the Units
  - data
```
private InputData data
```
    Data used for training
  - dim
```
private int dim
```
    Dimensions of the input-data
  - qualityMeasure
```
private QualityMeasure qualityMeasure
```
    QualityMesure used for GrowingCellStructures
  - metric
```
private DistanceMetric metric
```
    Distance Metric used for GrowingCellStructures
  - unitfield
```
private GrowingCellUnit[][] unitfield
```
    Storagearray for Units for export
  - emptyUnitMarkVector
```
private double[] emptyUnitMarkVector
```
    Weight-Vector for Units that fill holes in unitfield
  - rand
```
private java.util.Random rand
```
    Random Nr Generator for Weight-Vector initialisation
  - epsilonB
```
private float epsilonB
```
    Adaption Factor of best matching unit
  - epsilonN
```
private float epsilonN
```
    Adaption Factor of neighbors of best matching unit
  - alpha
```
private float alpha
```
    Reduction Factor for signal counter
  - lamda
```
private int lamda
```
    Number of adaption steps between adding/removing of Units
  - eta
```
private float eta
```
    Cutoff-Value for normalized probability density
  - maxEpochs
```
private int maxEpochs
```
    Number of Iterations on the input data
  - display
```
private javax.swing.JFrame display
```
    Frame used to display the CellUnits
  - attractScale
```
private double attractScale
```
    Scaling Factor for gravity between Units
  - repellingScale
```
private double repellingScale
```
    Scaling Factor for repulsion between Units
  - coherenceForceFactor
```
private double coherenceForceFactor
```
    Scaling Factor for gravity between Units independent of connectedness/distance
- Constructor Detail
  - GrowingCellLayer
```
public GrowingCellLayer(int dim,
                        boolean normalize,
                        long randomSeed,
                        InputData data)
```
    Std. Constructor for Cell Layers
    
    Parameters:
    
    dim - Dimensions of the InputData
    
    normalize - Wheter or not the Data is normalized
    
    randomSeed - Seed to use for random components
    
    data - InputData to be used for training
- Method Detail
  - getAllUnits
```
public Unit[] getAllUnits()
```
    Description copied from interface: Layer
    
    Returns an array of all units in the map layer; the specific order of the units is unspecified.
    
    Specified by:
    
    getAllUnits in interface Layer
  - getComponentPlane
```
public double[][] getComponentPlane(int component)
```
    Description copied from interface: Layer
    
    Returns a component plane of the component specified by the argument component. Returns null, if the argument component is out of range.
    
    Specified by:
    
    getComponentPlane in interface Layer
    
    Parameters:
    
    component - the index of the component.
    
    Returns:
    
    a double matrix containing the values of the weight vectors' respective components, or null if argument component is invalid.
  - getComponentPlane
```
public double[][] getComponentPlane(int component,
                                    int z)
```
    Description copied from interface: Layer
    
    Returns a component plane of the component specified by the argument component. Returns null, if the argument component is out of range.
    
    Specified by:
    
    getComponentPlane in interface Layer
    
    Parameters:
    
    component - the index of the component.
    
    z - TODO
    
    Returns:
    
    a double matrix containing the values of the weight vectors' respective components, or null if argument component is invalid.
  - getIdString
```
public java.lang.String getIdString()
```
    Description copied from interface: Layer
    
    Returns the identification string of the map layer.
    
    Specified by:
    
    getIdString in interface Layer
    
    Returns:
    
    the identification string of the map layer.
  - getLevel
```
public int getLevel()
```
    Description copied from interface: Layer
    
    Returns the level of the map layer in a hierarchical model.
    
    Specified by:
    
    getLevel in interface Layer
    
    Returns:
    
    the level of the map layer in a hierarchical model.
  - getMapDistance
```
public double getMapDistance(int x1,
                             int y1,
                             int z1,
                             int x2,
                             int y2,
                             int z2)
```
    Description copied from interface: Layer
    
    Returns the distance between two units on the map grid.
    
    Specified by:
    
    getMapDistance in interface Layer
    
    Parameters:
    
    x1 - the horizontal position of the first unit.
    
    y1 - the vertical position of the first unit.
    
    z1 - the height position of the first unit.
    
    x2 - the horizontal position of the second unit.
    
    y2 - the vertical position of the second unit.
    
    z2 - the height position of the second unit.
    
    Returns:
    
    the distance between two units.
  - getMapDistance
```
public double getMapDistance(Unit u1,
                             Unit u2)
```
    Description copied from interface: Layer
    
    Returns the distance between two units on the map grid.
    
    Specified by:
    
    getMapDistance in interface Layer
    
    Parameters:
    
    u1 - the first unit.
    
    u2 - the second unit.
    
    Returns:
    
    the distance between two units.
  - getMetric
```
public DistanceMetric getMetric()
```
    Description copied from interface: Layer
    
    Returns the metric used for distance calculation.
    
    Specified by:
    
    getMetric in interface Layer
    
    Returns:
    
    the metric used for distance calculation.
  - getNumberOfMappedInputs
```
public int getNumberOfMappedInputs()
```
    Description copied from interface: Layer
    
    Returns the total number of Inputs mapped on all units in the map layer.
    
    Specified by:
    
    getNumberOfMappedInputs in interface Layer
  - getQualityMeasure
```
public QualityMeasure getQualityMeasure()
```
    Description copied from interface: Layer
    
    Returns the quality information.
    
    Specified by:
    
    getQualityMeasure in interface Layer
    
    Returns:
    
    the quality information, or null if not existent.
  - getRevision
```
public java.lang.String getRevision()
```
    Description copied from interface: Layer
    
    Returns the revision string of this layer. This string should be written to output files to be able to trace back the implementation revision based on the CVS revision a map was trained with.
    
    Specified by:
    
    getRevision in interface Layer
    
    Returns:
    
    the revision string of this layer.
  - getUnit
```
public Unit getUnit(int x,
                    int y)
             throws LayerAccessException
```
    Description copied from interface: Layer
    
    Returns the Unit at the position specified by the x and y arguments. A LayerAccessException is thrown, if the coordinates are invalid.
    
    Specified by:
    
    getUnit in interface Layer
    
    Parameters:
    
    x - the horizontal position on the map layer.
    
    y - the vertical position on the map layer.
    
    Returns:
    
    the unit at the specified position.
    
    Throws:
    
    LayerAccessException - if the coordinates are out of range.
  - getUnit
```
public Unit getUnit(int x,
                    int y,
                    int z)
             throws LayerAccessException
```
    Description copied from interface: Layer
    
    Returns the Unit at the position specified by the x and y arguments. A LayerAccessException is thrown, if the coordinates are invalid.
    
    Specified by:
    
    getUnit in interface Layer
    
    Parameters:
    
    x - the horizontal position on the map layer.
    
    y - the vertical position on the map layer.
    
    z - TODO
    
    Returns:
    
    the unit at the specified position.
    
    Throws:
    
    LayerAccessException - if the coordinates are out of range.
  - getUnitForDatum
```
public Unit getUnitForDatum(java.lang.String name)
```
    Description copied from interface: Layer
    
    Returns the unit onto which the datum specified by its name by argument name is mapped.
    
    Specified by:
    
    getUnitForDatum in interface Layer
    
    Parameters:
    
    name - the name of the input datum to be searched for.
    
    Returns:
    
    the unit onto which the datum is mapped, or null if the datum is not found on the map.
  - getXSize
```
public int getXSize()
```
    Description copied from interface: Layer
    
    Returns the width of the map layer.
    
    Specified by:
    
    getXSize in interface Layer
    
    Returns:
    
    the width of the map layer.
  - getYSize
```
public int getYSize()
```
    Description copied from interface: Layer
    
    Returns the height of the map layer.
    
    Specified by:
    
    getYSize in interface Layer
    
    Returns:
    
    the height of the map layer.
  - getZSize
```
public int getZSize()
```
    Description copied from interface: Layer
    
    Returns the depth of the map layer.
    
    Specified by:
    
    getZSize in interface Layer
    
    Returns:
    
    the depth of the map layer.
  - getWinnersAndDistances
```
public UnitDistance[] getWinnersAndDistances(InputDatum input,
                                             int numWinners)
```
  - getDim
```
public int getDim()
```
  - getAllSubMaps
```
public java.util.Collection<? extends GrowingCellStructures> getAllSubMaps()
```
  - train
```
public QualityMeasure train(InputData data,
                            float epsilonB,
                            float epsilonN,
                            float alpha,
                            int lamda,
                            float eta,
                            SOMProperties props)
```
    Trains the CellLayer with the given Parameters and returns the QualityMeasure
    
    Parameters:
    
    data - InputData
    
    epsilonB - Adaption factor for best matching unit
    
    epsilonN - Adaption factor for neighbours of best matching unit
    
    alpha - Reduction factor for Signalcount
    
    lamda - Interval between Adding/Removing of Units
    
    eta - Cutoff-Value for normalised probability density
    
    props - Additional properties to use (numIterations==maximum number of epochs, quality measure name)
  - mapCompleteData
```
private void mapCompleteData(InputData data)
```
    Maps data to the units
    
    Parameters:
    
    data - InputData to map
  - clearMappedInput
```
private void clearMappedInput()
```
    Clears the mapped Input of every unit
  - trainNormal
```
private void trainNormal(InputData data,
                         ProgressListener progressWriter)
```
    Trains the CellLayer with the secified InputData and logs to progressWriter
    
    Parameters:
    
    data - Data used for training
    
    progressWriter - ProgressListener for logging
  - updatePositions
```
private void updatePositions()
```
    Update the Position of Units in display-space by means of a simple physics simulation
  - correctUnitPositions
```
private void correctUnitPositions()
```
    Correct Unit Positions so that they stay at the upper left corner (10,10) and don't drift away
  - addAttractingForce
```
private void addAttractingForce(GrowingCellUnit unitToMove,
                                GrowingCellUnit unitForcing,
                                double[] attractingForce)
```
    Calculate the attracting force between unitToMove and unitForcing and store it in attractingForce
    
    Parameters:
    
    unitToMove - unit to be moved
    
    unitForcing - unit which applies the force
    
    attractingForce - vector to add the resulting force to
  - addRepellingForce
```
private void addRepellingForce(GrowingCellUnit unitToMove,
                               GrowingCellUnit unitForcing,
                               double[] force)
```
    Calculate the repelling force between unitToMove and unitForcing and store it in force
    
    Parameters:
    
    unitToMove - unit to be moved
    
    unitForcing - unit which applies the fore
    
    force - vector to add the resulting force to
  - removeUnits
```
private void removeUnits(java.util.List<GrowingCellUnit> unitsToRemove)
```
    removes units specified in unitsToRemove and possible resulting disconnected units
    
    Parameters:
    
    unitsToRemove - the units that need to be removed
  - checkConsistency
```
private void checkConsistency()
```
    Checks consistency of tetraheders and units
  - updateInsertSignalCounters
```
private void updateInsertSignalCounters(GrowingCellUnit newUnit,
                                        java.util.List<GrowingCellUnit> neighbors)
```
    Updates the SignalCounters after an insert of a new unit
    
    Parameters:
    
    newUnit - the new inserted unit
    
    neighbors - the neighbors of that unit
  - calculateVoronoiEstimate
```
private void calculateVoronoiEstimate(java.util.List<GrowingCellUnit> neighborsToBe)
```
    Sets the voronoiEstimate of all neighborsToBe
    
    Parameters:
    
    neighborsToBe - Units that get an updated estimate
  - calculateVoronoiEstimate
```
private double calculateVoronoiEstimate(GrowingCellUnit u)
```
    Calculates the voronoi region estimate for unit u
    
    Parameters:
    
    u - Unit to calculate the estimate for
    
    Returns:
    
    the calculated voronoi region volume estimate
  - getTouchedTetraheders
```
private java.util.List<GrowingCellTetraheder> getTouchedTetraheders(GrowingCellUnit u1,
                                                                    GrowingCellUnit u2)
```
    Returns Tetraheders that have u1 and u2 in common
    
    Parameters:
    
    u1 - CellUnit 1
    
    u2 - CellUnit 2
    
    Returns:
    
    Tetraheders which are connected to u1 and u2
  - getInsertionTopologicalNeighbors
```
private java.util.List<GrowingCellUnit> getInsertionTopologicalNeighbors(GrowingCellUnit sfwinner,
                                                                         GrowingCellUnit sfpartner)
```
    Returns:
    
    CellUnits which will be neighbors of a new unit between sfwinner and sfpartner
  - getSignalFrequencyWinner
```
private GrowingCellUnit getSignalFrequencyWinner()
```
    Returns:
    
    CellUnit with highest signal frequency
  - decreaseSignalCounters
```
private void decreaseSignalCounters()
```
    Decrease SignalCoutners of units by alpha percent
  - updateWinnerAndNeighbors
```
private void updateWinnerAndNeighbors(GrowingCellUnit winner,
                                      InputDatum currentInput)
```
    Updates the weight-vectors of winning unit and its neighbors
    
    Parameters:
    
    winner - the winning unit
    
    currentInput - current input vector
  - getTopologicalNeighbors
```
private java.util.List<GrowingCellUnit> getTopologicalNeighbors(GrowingCellUnit unit)
```
    Returns:
    
    the topological neighbours of the unit
  - getWinner
```
private GrowingCellUnit getWinner(InputDatum input)
```
    Returns:
    
    unit closest to input
  - getFarthestNeighbor
```
private GrowingCellUnit getFarthestNeighbor(GrowingCellUnit unit)
```
    Returns:
    
    topological neighbor with the largest distance to unit
  - getDistance
```
private double getDistance(double[] v1,
                           double[] v2)
```
    Returns:
    
    Distance between v1 and v2
  - getData
```
public InputData getData()
```
    Returns:
    
    InputData that is used for training
  - prepareForOutput
```
private void prepareForOutput()
```
    Moves the units for optimized space requirement The order along x and y axis stays the same, but the space between units gets reduced to 0, x is reduced before y so a narrow stripe along the y axis will emerge
  - analyzeDimension
```
private void analyzeDimension(GrowingCellUnit[][] data,
                              int[] dimandoffset)
```
    Analyses maximum extension of the Units in data and their offset
    
    Parameters:
    
    data - array with units (with null Objects)
  - analyzeDimension
```
private void analyzeDimension(java.util.List<GrowingCellUnit> units,
                              int[] dimandoffset)
```
    Analyses maximum extension of the Units in units and their offset
    
    Parameters:
    
    units - List of Units without null elements
  - getGridLayout
```
public Layer.GridLayout getGridLayout()
```
    Specified by:
    
    getGridLayout in interface Layer
  - getGridTopology
```
public Layer.GridTopology getGridTopology()
```
    Specified by:
    
    getGridTopology in interface Layer

Class GrowingCellLayer

Nested Class Summary

Nested classes/interfaces inherited from interface at.tuwien.ifs.somtoolbox.layers.Layer

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

units

tetraheders

data

dim

qualityMeasure

metric

unitfield

emptyUnitMarkVector

rand

epsilonB

epsilonN

alpha

lamda

eta

maxEpochs

display

attractScale

repellingScale

coherenceForceFactor

Constructor Detail

GrowingCellLayer

Method Detail

getAllUnits

getComponentPlane

getComponentPlane

getIdString

getLevel

getMapDistance

getMapDistance

getMetric

getNumberOfMappedInputs

getQualityMeasure

getRevision

getUnit

getUnit

getUnitForDatum

getXSize

getYSize

getZSize

getWinnersAndDistances

getDim

getAllSubMaps

train

mapCompleteData

clearMappedInput

trainNormal

updatePositions

correctUnitPositions

addAttractingForce

addRepellingForce

removeUnits

checkConsistency

updateInsertSignalCounters

calculateVoronoiEstimate

calculateVoronoiEstimate

getTouchedTetraheders

getInsertionTopologicalNeighbors

getSignalFrequencyWinner

decreaseSignalCounters

updateWinnerAndNeighbors

getTopologicalNeighbors

getWinner

getFarthestNeighbor

getDistance

getData

prepareForOutput

analyzeDimension

analyzeDimension

getGridLayout

getGridTopology