AgBasicPsdEvaluator (Morphokinetics)

java.lang.Object
- geneticAlgorithm.evaluationFunctions.AbstractEvaluator
- - geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
  - - geneticAlgorithm.evaluationFunctions.AgBasicPsdEvaluator

All Implemented Interfaces:

IEvaluation
```
public class AgBasicPsdEvaluator
extends AbstractPsdEvaluator
```
Author:

N. Ferrando, J. Alberdi-Rodriguez, E. Sanchez

Field Summary

Fields
Modifier and Type	Field and Description
`private double`	`g2g1`
`private double`	`g3g0`
`private double`	`g3g1`
`private double`	`g3g2`
`private double`	`g3g4`
`private double`	`g3g5`
`private double`	`g4g0`
`private double`	`g4g1`
`private double`	`g5g0`
`private double`	`g5g1`
`private double`	`g5g4`
`private double`	`hierarchyFrobeniusRef`
`private AgKmc`	`kmc`
`private int`	`kmcError`
`private PsdSignature2D`	`psd`
`private float[][]`	`sampledSurface`
`private boolean`	`searchEnergies`
`private int`	`simulationCount`
`private float`	`temperature` Temperature of the simulation.

Constructor Summary

Constructors
Constructor and Description
`AgBasicPsdEvaluator(AgKmc kmc, int repeats, int measureInterval, int psdSizeX, int psdSizeY, java.util.Set flags, java.lang.String hierarchyEvaluator, java.lang.String evolutionarySearchType, float temperature)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected double`	`calculateHierarchyError(Individual ind)` Calculates the hierarchy error based on the rates of Cox et al.
`protected double`	`calculateHierarchyErrorDiscrete(Individual ind)` If the difference is lower than 1, error is not added; otherwise, error is added by one.
`protected double`	`calculateHierarchyErrorFrobenius(Individual ind)`
`protected double`	`calculateHierarchyErrorFromReference(Individual ind)` Calculates the hierarchy error based on the rates of Cox et al.
`protected double`	`calculateHierarchyErrorOrder(Individual ind)` Adds the error if the next condition is not fulfilled: E_f > E_b > E_a > E_d > E_e > E_c g(3) > g(5) > g(4) > g(0) > g(2) > g(1)
`float[][]`	`calculatePsdFromIndividual(Individual ind)`
`void`	`dispose()`
`private double`	`getMaxIteration()`
`private double`	`getRate(double gene)`
`double[]`	`getRates(double[] genes)` Calculates rates from the genes.
`double[]`	`getRates6(double[] genes)` Calculates rates from the genes.
`int`	`getSimulationCount()` Method thought to be called from the main interface updater.
`float[][]`	`getSurface()`
`void`	`setHierarchy(double[] genes)` Sets the expected rates hierarchies, based on the objective rates (genes)
`private double`	`stepFunction(double division)`

Methods inherited from class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator
calculateFrobeniusNormErrorMatrix, evaluate, getCurrentDifference, getCurrentError, getCurrentIteration, getCurrentPopulation, getCurrentPsd, getCurrentSimulation, getIndividualCount, getMeasureInterval, getProgressPercent, getPsdSizeX, getPsdSizeY, getRepeats, hasKmcFailed, kmcHasFailed, resetKmcError, setCurrentPopulation, setCurrentSimulation, setExpectedSimulationTime, setPsd, setPsdSizeX, setPsdSizeY, setRepeats

Methods inherited from class geneticAlgorithm.evaluationFunctions.AbstractEvaluator
getWheight, setShowGraphics, setWheight, showGraphics

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

- Field Detail
  - kmc
```
private AgKmc kmc
```
  - g4g0
```
private double g4g0
```
  - g5g0
```
private double g5g0
```
  - g5g4
```
private double g5g4
```
  - g3g0
```
private double g3g0
```
  - g3g1
```
private double g3g1
```
  - g3g2
```
private double g3g2
```
  - g3g4
```
private double g3g4
```
  - g3g5
```
private double g3g5
```
  - g4g1
```
private double g4g1
```
  - g5g1
```
private double g5g1
```
  - g2g1
```
private double g2g1
```
  - hierarchyFrobeniusRef
```
private double hierarchyFrobeniusRef
```
  - searchEnergies
```
private boolean searchEnergies
```
  - psd
```
private PsdSignature2D psd
```
  - kmcError
```
private int kmcError
```
  - simulationCount
```
private int simulationCount
```
  - sampledSurface
```
private float[][] sampledSurface
```
  - temperature
```
private final float temperature
```
    Temperature of the simulation. Useful when searching for energies.
- Constructor Detail
  - AgBasicPsdEvaluator
```
public AgBasicPsdEvaluator(AgKmc kmc,
                           int repeats,
                           int measureInterval,
                           int psdSizeX,
                           int psdSizeY,
                           java.util.Set flags,
                           java.lang.String hierarchyEvaluator,
                           java.lang.String evolutionarySearchType,
                           float temperature)
```
- Method Detail
  - calculatePsdFromIndividual
```
public float[][] calculatePsdFromIndividual(Individual ind)
```
    Specified by:
    
    calculatePsdFromIndividual in class AbstractPsdEvaluator
  - getSurface
```
public float[][] getSurface()
```
    Specified by:
    
    getSurface in interface IEvaluation
    
    Overrides:
    
    getSurface in class AbstractEvaluator
  - getSimulationCount
```
public int getSimulationCount()
```
    Method thought to be called from the main interface updater.
    
    Specified by:
    
    getSimulationCount in interface IEvaluation
    
    Overrides:
    
    getSimulationCount in class AbstractPsdEvaluator
    
    Returns:
    
    number of the current simulation
  - setHierarchy
```
public void setHierarchy(double[] genes)
```
    Sets the expected rates hierarchies, based on the objective rates (genes)
    
    Specified by:
    
    setHierarchy in class AbstractPsdEvaluator
    
    Parameters:
    
    genes -
  - calculateHierarchyErrorDiscrete
```
protected double calculateHierarchyErrorDiscrete(Individual ind)
```
    If the difference is lower than 1, error is not added; otherwise, error is added by one.
    
    Specified by:
    
    calculateHierarchyErrorDiscrete in class AbstractPsdEvaluator
    
    Parameters:
    
    ind -
    
    Returns:
    
    calculated error
  - stepFunction
```
private double stepFunction(double division)
```
  - calculateHierarchyErrorOrder
```
protected double calculateHierarchyErrorOrder(Individual ind)
```
    Adds the error if the next condition is not fulfilled: E_f > E_b > E_a > E_d > E_e > E_c g(3) > g(5) > g(4) > g(0) > g(2) > g(1)
    
    Parameters:
    
    ind -
    
    Returns:
    
    calculated error
  - calculateHierarchyErrorFromReference
```
protected double calculateHierarchyErrorFromReference(Individual ind)
```
    Calculates the hierarchy error based on the rates of Cox et al.
    
    Specified by:
    
    calculateHierarchyErrorFromReference in class AbstractPsdEvaluator
    
    Parameters:
    
    ind - Current individual
    
    Returns:
    
    normalised hierarchy error
  - calculateHierarchyErrorFrobenius
```
protected double calculateHierarchyErrorFrobenius(Individual ind)
```
  - calculateHierarchyError
```
protected double calculateHierarchyError(Individual ind)
```
    Calculates the hierarchy error based on the rates of Cox et al.
    
    Specified by:
    
    calculateHierarchyError in class AbstractPsdEvaluator
    
    Parameters:
    
    ind - Current individual
    
    Returns:
    
    hierarchy error, at least 6.52e-2
  - dispose
```
public void dispose()
```
    Specified by:
    
    dispose in class AbstractEvaluator
  - getRates
```
public double[] getRates(double[] genes)
```
    Calculates rates from the genes. Most of the rates are 0, the rest is calculated from the given genes.
    
    Parameters:
    
    genes -
    
    Returns:
    
    rates
  - getRates6
```
public double[] getRates6(double[] genes)
```
    Calculates rates from the genes. Most of the rates are 0, the rest is calculated from the given genes. Ratio (energy type) | ratio index 0) E_d (0,j) 1) E_c (1,1)(1,2)(1,6) 2) E_e (1,3)(1,5) 3) E_f (2,3)=(2,4)=(2,5)=(2,6)=(5,2)=(5,3)=(5,4)=(5,6) 4) E_a (2,2) 5) E_b (5,5)
    
    Parameters:
    
    genes -
    
    Returns:
    
    rates
  - getRate
```
private double getRate(double gene)
```
  - getMaxIteration
```
private double getMaxIteration()
```

Class AgBasicPsdEvaluator

Field Summary

Constructor Summary

Method Summary

Methods inherited from class geneticAlgorithm.evaluationFunctions.AbstractPsdEvaluator

Methods inherited from class geneticAlgorithm.evaluationFunctions.AbstractEvaluator

Methods inherited from class java.lang.Object

Field Detail

kmc

g4g0

g5g0

g5g4

g3g0

g3g1

g3g2

g3g4

g3g5

g4g1

g5g1

g2g1

hierarchyFrobeniusRef

searchEnergies

psd

kmcError

simulationCount

sampledSurface

temperature

Constructor Detail

AgBasicPsdEvaluator

Method Detail

calculatePsdFromIndividual

getSurface

getSimulationCount

setHierarchy

calculateHierarchyErrorDiscrete

stepFunction

calculateHierarchyErrorOrder

calculateHierarchyErrorFromReference

calculateHierarchyErrorFrobenius

calculateHierarchyError

dispose

getRates

getRates6

getRate

getMaxIteration