flanagan.optics

Class Reflectivity

java.lang.Object

flanagan.optics.Reflectivity

public class Reflectivity
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
int	degreesOfFreedom
int	regressionOption

Constructor Summary

Constructors

Constructor and Description
Reflectivity(int n)

Method Summary

Modifier and Type	Method and Description
void	calcReflectivity(int wavelengthIndex, int angleIndex)
double[]	calcTEreflectivity(int wavelengthIndex, int angleIndex)
double[]	calcTMreflectivity(int wavelengthIndex, int angleIndex)
void	checkWhichCalculation()
void	fitAndPlotReflectivities(double[] experimentalReflectivities)
void	fitAndPlotReflectivities(double[] experimentalReflectivities, double[] errors)
void	fitAndPlotReflectivities(double[] experimentalReflectivities, double[] errors, java.lang.String graphTitle)
void	fitAndPlotReflectivities(double[] experimentalReflectivities, java.lang.String graphTitle)
void	fitAndPlotTransmissivities(double[] experimentalTransmissivities)
void	fitAndPlotTransmissivities(double[] experimentalTransmissivities, double[] errors)
void	fitAndPlotTransmissivities(double[] experimentalTransmissivities, double[] errors, java.lang.String graphTitle)
void	fitAndPlotTransmissivities(double[] experimentalTransmissivities, java.lang.String graphTitle)
void	fitEvanescentField(double[] experimentalEvanescentFieldIntensities)
void	fitEvanescentField(double[] experimentalEvanescentFieldIntensities, double fieldDistance)
void	fitEvanescentField(double[] experimentalEvanescentFieldIntensities, double[] errors)
void	fitEvanescentField(double[] experimentalEvanescentFieldIntensities, double[] errors, double fieldDistance)
void	fitReflectivities(double[] experimentalReflectivities)
void	fitReflectivities(double[] experimentalReflectivities, double[] errors)
void	fitTransmissivities(double[] experimentalTransmissivities)
void	fitTransmissivities(double[] experimentalTransmissivities, double[] errors)
double	fractionInTEmode()
double	fractionInTMmode()
java.lang.Object	getAbsorptionCoefficients()
double[]	getCalculatedData()
java.lang.Object	getEvanescentFields()
java.lang.Object	getEvanescentFields(double fieldDistance)
double[]	getIncidentAngles()
java.lang.Object	getKoVectors()
java.lang.Object	getKvectors()
java.lang.Object	getKxVectors()
java.lang.Object	getKzVectors()
java.lang.Object	getPenetrationDepths()
java.lang.Object	getPowerLoss()
double[]	getRadialFrequencies()
java.lang.Object	getReflectivities()
java.lang.Object	getRefractiveIndices()
java.lang.Object	getRelativeMagneticPermeabilities()
java.lang.Object	getTEreflectionCoefficients()
java.lang.Object	getTEreflectionPhaseShiftDeg()
java.lang.Object	getTEreflectionPhaseShiftRad()
java.lang.Object	getTEtransmissionCoefficients()
java.lang.Object	getTEtransmissionPhaseShiftDeg()
java.lang.Object	getTEtransmissionPhaseShiftRad()
double[]	getThicknesses()
java.lang.Object	getTMreflectionCoefficients()
java.lang.Object	getTMreflectionPhaseShiftDeg()
java.lang.Object	getTMreflectionPhaseShiftRad()
java.lang.Object	getTMtransmissionCoefficients()
java.lang.Object	getTMtransmissionPhaseShiftDeg()
java.lang.Object	getTMtransmissionPhaseShiftRad()
java.lang.Object	getTransmissionAnglesInDegrees()
java.lang.Object	getTransmissionAnglesInRadians()
java.lang.Object	getTransmissivities()
double[]	getWavelengths()
void	nonLinearRegression()
void	plotAbsTEreflectionCoefficients()
void	plotAbsTEreflectionCoefficients(java.lang.String legend)
void	plotAbsTEtransmissionCoefficients()
void	plotAbsTEtransmissionCoefficients(java.lang.String legend)
void	plotAbsTMreflectionCoefficients()
void	plotAbsTMreflectionCoefficients(java.lang.String legend)
void	plotAbsTMtransmissionCoefficients()
void	plotAbsTMtransmissionCoefficients(java.lang.String legend)
void	plotEvanescentFields()
void	plotEvanescentFields(double distanceIntoField)
void	plotEvanescentFields(double fieldDistance, java.lang.String legend)
void	plotEvanescentFields(java.lang.String legend)
void	plotFit(java.lang.String graphTitle2)
void	plotPenetrationDepths()
void	plotPenetrationDepths(java.lang.String graphLegend)
void	plotPowerLosses()
void	plotPowerLosses(java.lang.String legend)
void	plotReflectivities()
void	plotReflectivities(java.lang.String legend)
void	plotSimulation(java.lang.String graphLegend, java.lang.String graphLegendExtra, java.lang.String yLegend, java.lang.String yUnits, java.lang.Object yValuesObject)
void	plotTEreflectionPhaseShiftDeg()
void	plotTEreflectionPhaseShiftDeg(java.lang.String legend)
void	plotTEreflectionPhaseShiftRad()
void	plotTEreflectionPhaseShiftRad(java.lang.String legend)
void	plotTEtransmissionPhaseShiftDeg()
void	plotTEtransmissionPhaseShiftDeg(java.lang.String legend)
void	plotTEtransmissionPhaseShiftRad()
void	plotTEtransmissionPhaseShiftRad(java.lang.String legend)
void	plotTMreflectionPhaseShiftDeg()
void	plotTMreflectionPhaseShiftDeg(java.lang.String legend)
void	plotTMreflectionPhaseShiftRad()
void	plotTMreflectionPhaseShiftRad(java.lang.String legend)
void	plotTMtransmissionPhaseShiftDeg()
void	plotTMtransmissionPhaseShiftDeg(java.lang.String legend)
void	plotTMtransmissionPhaseShiftRad()
void	plotTMtransmissionPhaseShiftRad(java.lang.String legend)
void	plotTransmissionAngles()
void	plotTransmissionAngles(java.lang.String legend)
void	plotTransmissivities()
void	plotTransmissivities(java.lang.String legend)
void	relativeMagneticPermeabilities(double[][] relativeMagneticPermeabilities)
void	resetPlotAxisAsFrequency()
void	resetPlotAxisAsRadians()
void	resetPlotAxisAsWavelength()
void	scan()
void	setAbsorptionCoefficientEstimateIndices(int[] indices)
void	setAbsorptionCoefficients(double[] absorptionCoefficients)
void	setAbsorptionCoefficients(double[][] absorptionCoefficients)
void	setAbsorptionCoefficients(double[] absorptionCoefficients, int layerNumber)
void	setAbsorptionCoefficients(double absorptionCoefficient, int layerNumber)
void	setFrequency(double frequency)
void	setFrequency(double[] frequency)
void	setFrequency(double freqLow, double freqHigh, int nFreq)
void	setImagRefractIndexEstimateIndices(int[] indices)
void	setImagRelativeMagneticPermeabilityEstimateIndices(int[] indices)
void	setIncidentAngle(double incidentAngle)
void	setIncidentAngle(double[] incidentAngle)
void	setIncidentAngle(double angleLow, double angleHigh, int nAngles)
void	setMode(double modeAngle)
void	setMode(java.lang.String mode)
void	setRealRefractIndexEstimateIndices(int[] indices)
void	setRealRelativeMagneticPermeabilityEstimateIndices(int[] indices)
void	setRefractiveIndices(Complex[] refractiveIndices)
void	setRefractiveIndices(Complex[][] refractiveIndices)
void	setRefractiveIndices(Complex[] refractiveIndices, int layerNumber)
void	setRefractiveIndices(Complex refractiveIndex, int layerNumber)
void	setRefractiveIndices(double[] refractiveIndices)
void	setRefractiveIndices(double[][] refractiveIndices)
void	setRefractiveIndices(double[] refractiveIndices, int layerNumber)
void	setRefractiveIndices(double refractiveIndex, int layerNumber)
void	setRelativeMagneticPermeabilities(Complex[] relativeMagneticPermeabilities)
void	setRelativeMagneticPermeabilities(Complex[][] relativeMagneticPermeabilities)
void	setRelativeMagneticPermeabilities(Complex[] relativeMagneticPermeabilities, int layerNumber)
void	setRelativeMagneticPermeabilities(Complex relativeMagneticPermeability, int layerNumber)
void	setRelativeMagneticPermeabilities(double[] relativeMagneticPermeabilities)
void	setRelativeMagneticPermeabilities(double[] relativeMagneticPermeabilities, int layerNumber)
void	setRelativeMagneticPermeabilities(double relativeMagneticPermeability, int layerNumber)
void	setThicknesses(double[] thick)
void	setThicknesses(double thickness, int layerNumber)
void	setThicknessEstimatesIndices(int[] indices)
void	setWavelength(double wavelength)
void	setWavelength(double[] wavelengths)
void	setWavelength(double lambdaLow, double lambdaHigh, int nLambda)

Methods inherited from class java.lang.Object

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

Field Detail

regressionOption

public int regressionOption

degreesOfFreedom

public int degreesOfFreedom

Constructor Detail

Reflectivity

public Reflectivity(int n)

Method Detail

setMode

public void setMode(java.lang.String mode)

setMode

public void setMode(double modeAngle)

fractionInTEmode

public double fractionInTEmode()

fractionInTMmode

public double fractionInTMmode()

setIncidentAngle

public void setIncidentAngle(double incidentAngle)

setIncidentAngle

public void setIncidentAngle(double[] incidentAngle)

setIncidentAngle

public void setIncidentAngle(double angleLow,
                             double angleHigh,
                             int nAngles)

getIncidentAngles

public double[] getIncidentAngles()

setThicknesses

public void setThicknesses(double[] thick)

setThicknesses

public void setThicknesses(double thickness,
                           int layerNumber)

getThicknesses

public double[] getThicknesses()

setWavelength

public void setWavelength(double[] wavelengths)

setFrequency

public void setFrequency(double[] frequency)

setWavelength

public void setWavelength(double lambdaLow,
                          double lambdaHigh,
                          int nLambda)

setFrequency

public void setFrequency(double freqLow,
                         double freqHigh,
                         int nFreq)

setWavelength

public void setWavelength(double wavelength)

setFrequency

public void setFrequency(double frequency)

getWavelengths

public double[] getWavelengths()

getRadialFrequencies

public double[] getRadialFrequencies()

setRefractiveIndices

public void setRefractiveIndices(Complex[][] refractiveIndices)

setRefractiveIndices

public void setRefractiveIndices(double[][] refractiveIndices)

setRefractiveIndices

public void setRefractiveIndices(Complex[] refractiveIndices)

setRefractiveIndices

public void setRefractiveIndices(double[] refractiveIndices)

setRefractiveIndices

public void setRefractiveIndices(Complex[] refractiveIndices,
                                 int layerNumber)

setRefractiveIndices

public void setRefractiveIndices(double[] refractiveIndices,
                                 int layerNumber)

setRefractiveIndices

public void setRefractiveIndices(Complex refractiveIndex,
                                 int layerNumber)

setRefractiveIndices

public void setRefractiveIndices(double refractiveIndex,
                                 int layerNumber)

getRefractiveIndices

public java.lang.Object getRefractiveIndices()

setAbsorptionCoefficients

public void setAbsorptionCoefficients(double[] absorptionCoefficients)

setAbsorptionCoefficients

public void setAbsorptionCoefficients(double[][] absorptionCoefficients)

setAbsorptionCoefficients

public void setAbsorptionCoefficients(double[] absorptionCoefficients,
                                      int layerNumber)

setAbsorptionCoefficients

public void setAbsorptionCoefficients(double absorptionCoefficient,
                                      int layerNumber)

getAbsorptionCoefficients

public java.lang.Object getAbsorptionCoefficients()

setRelativeMagneticPermeabilities

public void setRelativeMagneticPermeabilities(Complex[][] relativeMagneticPermeabilities)

relativeMagneticPermeabilities

public void relativeMagneticPermeabilities(double[][] relativeMagneticPermeabilities)

setRelativeMagneticPermeabilities

public void setRelativeMagneticPermeabilities(Complex[] relativeMagneticPermeabilities)

setRelativeMagneticPermeabilities

public void setRelativeMagneticPermeabilities(double[] relativeMagneticPermeabilities)

setRelativeMagneticPermeabilities

public void setRelativeMagneticPermeabilities(Complex[] relativeMagneticPermeabilities,
                                              int layerNumber)

setRelativeMagneticPermeabilities

public void setRelativeMagneticPermeabilities(double[] relativeMagneticPermeabilities,
                                              int layerNumber)

setRelativeMagneticPermeabilities

public void setRelativeMagneticPermeabilities(Complex relativeMagneticPermeability,
                                              int layerNumber)

setRelativeMagneticPermeabilities

public void setRelativeMagneticPermeabilities(double relativeMagneticPermeability,
                                              int layerNumber)

getRelativeMagneticPermeabilities

public java.lang.Object getRelativeMagneticPermeabilities()

getReflectivities

public java.lang.Object getReflectivities()

getTEreflectionCoefficients

public java.lang.Object getTEreflectionCoefficients()

getTMreflectionCoefficients

public java.lang.Object getTMreflectionCoefficients()

getTransmissivities

public java.lang.Object getTransmissivities()

getPowerLoss

public java.lang.Object getPowerLoss()

getTransmissionAnglesInRadians

public java.lang.Object getTransmissionAnglesInRadians()

getTransmissionAnglesInDegrees

public java.lang.Object getTransmissionAnglesInDegrees()

getTEtransmissionCoefficients

public java.lang.Object getTEtransmissionCoefficients()

getTMtransmissionCoefficients

public java.lang.Object getTMtransmissionCoefficients()

getTEreflectionPhaseShiftDeg

public java.lang.Object getTEreflectionPhaseShiftDeg()

getTEreflectionPhaseShiftRad

public java.lang.Object getTEreflectionPhaseShiftRad()

getTMreflectionPhaseShiftDeg

public java.lang.Object getTMreflectionPhaseShiftDeg()

getTMreflectionPhaseShiftRad

public java.lang.Object getTMreflectionPhaseShiftRad()

getTEtransmissionPhaseShiftDeg

public java.lang.Object getTEtransmissionPhaseShiftDeg()

getTEtransmissionPhaseShiftRad

public java.lang.Object getTEtransmissionPhaseShiftRad()

getTMtransmissionPhaseShiftDeg

public java.lang.Object getTMtransmissionPhaseShiftDeg()

getTMtransmissionPhaseShiftRad

public java.lang.Object getTMtransmissionPhaseShiftRad()

getEvanescentFields

public java.lang.Object getEvanescentFields(double fieldDistance)

getEvanescentFields

public java.lang.Object getEvanescentFields()

getPenetrationDepths

public java.lang.Object getPenetrationDepths()

getKoVectors

public java.lang.Object getKoVectors()

getKzVectors

public java.lang.Object getKzVectors()

getKvectors

public java.lang.Object getKvectors()

getKxVectors

public java.lang.Object getKxVectors()

resetPlotAxisAsFrequency

public void resetPlotAxisAsFrequency()

resetPlotAxisAsRadians

public void resetPlotAxisAsRadians()

resetPlotAxisAsWavelength

public void resetPlotAxisAsWavelength()

plotReflectivities

public void plotReflectivities()

plotReflectivities

public void plotReflectivities(java.lang.String legend)

plotTransmissivities

public void plotTransmissivities()

plotTransmissivities

public void plotTransmissivities(java.lang.String legend)

plotPowerLosses

public void plotPowerLosses()

plotPowerLosses

public void plotPowerLosses(java.lang.String legend)

plotTransmissionAngles

public void plotTransmissionAngles()

plotTransmissionAngles

public void plotTransmissionAngles(java.lang.String legend)

plotAbsTEreflectionCoefficients

public void plotAbsTEreflectionCoefficients()

plotAbsTEreflectionCoefficients

public void plotAbsTEreflectionCoefficients(java.lang.String legend)

plotAbsTMreflectionCoefficients

public void plotAbsTMreflectionCoefficients()

plotAbsTMreflectionCoefficients

public void plotAbsTMreflectionCoefficients(java.lang.String legend)

plotAbsTEtransmissionCoefficients

public void plotAbsTEtransmissionCoefficients()

plotAbsTEtransmissionCoefficients

public void plotAbsTEtransmissionCoefficients(java.lang.String legend)

plotAbsTMtransmissionCoefficients

public void plotAbsTMtransmissionCoefficients()

plotAbsTMtransmissionCoefficients

public void plotAbsTMtransmissionCoefficients(java.lang.String legend)

plotEvanescentFields

public void plotEvanescentFields()

plotEvanescentFields

public void plotEvanescentFields(double distanceIntoField)

plotEvanescentFields

public void plotEvanescentFields(double fieldDistance,
                                 java.lang.String legend)

plotEvanescentFields

public void plotEvanescentFields(java.lang.String legend)

plotPenetrationDepths

public void plotPenetrationDepths()

plotPenetrationDepths

public void plotPenetrationDepths(java.lang.String graphLegend)

plotTEreflectionPhaseShiftDeg

public void plotTEreflectionPhaseShiftDeg()

plotTEreflectionPhaseShiftDeg

public void plotTEreflectionPhaseShiftDeg(java.lang.String legend)

plotTMreflectionPhaseShiftDeg

public void plotTMreflectionPhaseShiftDeg()

plotTMreflectionPhaseShiftDeg

public void plotTMreflectionPhaseShiftDeg(java.lang.String legend)

plotTEreflectionPhaseShiftRad

public void plotTEreflectionPhaseShiftRad()

plotTEreflectionPhaseShiftRad

public void plotTEreflectionPhaseShiftRad(java.lang.String legend)

plotTMreflectionPhaseShiftRad

public void plotTMreflectionPhaseShiftRad()

plotTMreflectionPhaseShiftRad

public void plotTMreflectionPhaseShiftRad(java.lang.String legend)

plotTEtransmissionPhaseShiftDeg

public void plotTEtransmissionPhaseShiftDeg()

plotTEtransmissionPhaseShiftDeg

public void plotTEtransmissionPhaseShiftDeg(java.lang.String legend)

plotTMtransmissionPhaseShiftDeg

public void plotTMtransmissionPhaseShiftDeg()

plotTMtransmissionPhaseShiftDeg

public void plotTMtransmissionPhaseShiftDeg(java.lang.String legend)

plotTEtransmissionPhaseShiftRad

public void plotTEtransmissionPhaseShiftRad()

plotTEtransmissionPhaseShiftRad

public void plotTEtransmissionPhaseShiftRad(java.lang.String legend)

plotTMtransmissionPhaseShiftRad

public void plotTMtransmissionPhaseShiftRad()

plotTMtransmissionPhaseShiftRad

public void plotTMtransmissionPhaseShiftRad(java.lang.String legend)

plotSimulation

public void plotSimulation(java.lang.String graphLegend,
                           java.lang.String graphLegendExtra,
                           java.lang.String yLegend,
                           java.lang.String yUnits,
                           java.lang.Object yValuesObject)

checkWhichCalculation

public void checkWhichCalculation()

scan

public void scan()

calcReflectivity

public void calcReflectivity(int wavelengthIndex,
                             int angleIndex)

calcTEreflectivity

public double[] calcTEreflectivity(int wavelengthIndex,
                                   int angleIndex)

calcTMreflectivity

public double[] calcTMreflectivity(int wavelengthIndex,
                                   int angleIndex)

setThicknessEstimatesIndices

public void setThicknessEstimatesIndices(int[] indices)

setRealRefractIndexEstimateIndices

public void setRealRefractIndexEstimateIndices(int[] indices)

setImagRefractIndexEstimateIndices

public void setImagRefractIndexEstimateIndices(int[] indices)

setAbsorptionCoefficientEstimateIndices

public void setAbsorptionCoefficientEstimateIndices(int[] indices)

setRealRelativeMagneticPermeabilityEstimateIndices

public void setRealRelativeMagneticPermeabilityEstimateIndices(int[] indices)

setImagRelativeMagneticPermeabilityEstimateIndices

public void setImagRelativeMagneticPermeabilityEstimateIndices(int[] indices)

fitReflectivities

public void fitReflectivities(double[] experimentalReflectivities)

fitReflectivities

public void fitReflectivities(double[] experimentalReflectivities,
                              double[] errors)

fitAndPlotReflectivities

public void fitAndPlotReflectivities(double[] experimentalReflectivities)

fitAndPlotReflectivities

public void fitAndPlotReflectivities(double[] experimentalReflectivities,
                                     java.lang.String graphTitle)

fitAndPlotReflectivities

public void fitAndPlotReflectivities(double[] experimentalReflectivities,
                                     double[] errors)

fitAndPlotReflectivities

public void fitAndPlotReflectivities(double[] experimentalReflectivities,
                                     double[] errors,
                                     java.lang.String graphTitle)

fitTransmissivities

public void fitTransmissivities(double[] experimentalTransmissivities)

fitTransmissivities

public void fitTransmissivities(double[] experimentalTransmissivities,
                                double[] errors)

fitAndPlotTransmissivities

public void fitAndPlotTransmissivities(double[] experimentalTransmissivities)

fitAndPlotTransmissivities

public void fitAndPlotTransmissivities(double[] experimentalTransmissivities,
                                       java.lang.String graphTitle)

fitAndPlotTransmissivities

public void fitAndPlotTransmissivities(double[] experimentalTransmissivities,
                                       double[] errors)

fitAndPlotTransmissivities

public void fitAndPlotTransmissivities(double[] experimentalTransmissivities,
                                       double[] errors,
                                       java.lang.String graphTitle)

fitEvanescentField

public void fitEvanescentField(double[] experimentalEvanescentFieldIntensities)

fitEvanescentField

public void fitEvanescentField(double[] experimentalEvanescentFieldIntensities,
                               double[] errors)

fitEvanescentField

public void fitEvanescentField(double[] experimentalEvanescentFieldIntensities,
                               double fieldDistance)

fitEvanescentField

public void fitEvanescentField(double[] experimentalEvanescentFieldIntensities,
                               double[] errors,
                               double fieldDistance)

nonLinearRegression

public void nonLinearRegression()

getCalculatedData

public double[] getCalculatedData()

plotFit

public void plotFit(java.lang.String graphTitle2)