IJPluginModel¶

public class IJPluginModel implements Serializable ¶

IJPluginModel for the InitializeSimulation window.

Author:	Kyle M. Douglass

Methods¶

build¶

public Microscope build()¶

Builds a microscope from the model parameters.

Returns:	A new microscope built from the model parameters.

getAnalyzerCurrentSelection¶

public String getAnalyzerCurrentSelection()¶

getBackgroundCurrentSelection¶

public String getBackgroundCurrentSelection()¶

getBackgroundRandomButtonText¶

public String getBackgroundRandomButtonText()¶

getBackgroundRandomFeatureSize¶

public double getBackgroundRandomFeatureSize()¶

getBackgroundRandomMaxValue¶

public float getBackgroundRandomMaxValue()¶

getBackgroundRandomMinValue¶

public float getBackgroundRandomMinValue()¶

getBackgroundRandomSeed¶

public int getBackgroundRandomSeed()¶

getBackgroundTifFile¶

public String getBackgroundTifFile()¶

getBackgroundTifFileButtonText¶

public String getBackgroundTifFileButtonText()¶

getBackgroundUniformButtonText¶

public String getBackgroundUniformButtonText()¶

getBackgroundUniformSignal¶

public float getBackgroundUniformSignal()¶

getCameraAduPerElectron¶

public double getCameraAduPerElectron()¶

getCameraBaseline¶

public int getCameraBaseline()¶

getCameraDarkCurrent¶

public double getCameraDarkCurrent()¶

getCameraEmGain¶

public int getCameraEmGain()¶

getCameraNX¶

public int getCameraNX()¶

getCameraNY¶

public int getCameraNY()¶

getCameraPixelSize¶

public double getCameraPixelSize()¶

getCameraQuantumEfficiency¶

public double getCameraQuantumEfficiency()¶

getCameraReadoutNoise¶

public double getCameraReadoutNoise()¶

getCameraThermalNoise¶

public double getCameraThermalNoise()¶

getControllerCurrentSelection¶

public String getControllerCurrentSelection()¶

getEmitters3DCheckBoxEnabled¶

public boolean getEmitters3DCheckBoxEnabled()¶

getEmitters3DMaxZ¶

public double getEmitters3DMaxZ()¶

getEmitters3DMinZ¶

public double getEmitters3DMinZ()¶

getEmittersCsvFile¶

public String getEmittersCsvFile()¶

getEmittersCsvFileButtonText¶

public String getEmittersCsvFileButtonText()¶

getEmittersCurrentSelection¶

public String getEmittersCurrentSelection()¶

getEmittersGridButtonText¶

public String getEmittersGridButtonText()¶

getEmittersGridSpacing¶

public int getEmittersGridSpacing()¶

getEmittersRandomButtonText¶

public String getEmittersRandomButtonText()¶

getEmittersRandomNumber¶

public int getEmittersRandomNumber()¶

getFiducialsNumber¶

public int getFiducialsNumber()¶

getFiducialsSignal¶

public double getFiducialsSignal()¶

getFluorophoreCurrentSelection¶

public String getFluorophoreCurrentSelection()¶

getFluorophorePalmText¶

public String getFluorophorePalmText()¶

getFluorophoreSignal¶

public double getFluorophoreSignal()¶

getFluorophoreSimpleText¶

public String getFluorophoreSimpleText()¶

getFluorophoreStormText¶

public String getFluorophoreStormText()¶

getFluorophoreTBl¶

public double getFluorophoreTBl()¶

getFluorophoreTOff¶

public double getFluorophoreTOff()¶

getFluorophoreTOn¶

public double getFluorophoreTOn()¶

getFluorophoreWavelength¶

public double getFluorophoreWavelength()¶

getLaserCurrentPower¶

public double getLaserCurrentPower()¶

getLaserMaxPower¶

public double getLaserMaxPower()¶

getLaserMinPower¶

public double getLaserMinPower()¶

getObjectiveMag¶

public double getObjectiveMag()¶

getObjectiveNa¶

public double getObjectiveNa()¶

getPalmKA¶

public double getPalmKA()¶

getPalmKB¶

public double getPalmKB()¶

getPalmKD1¶

public double getPalmKD1()¶

getPalmKD2¶

public double getPalmKD2()¶

getPalmKR1¶

public double getPalmKR1()¶

getPalmKR2¶

public double getPalmKR2()¶

getPalmSignal¶

public double getPalmSignal()¶

getPalmWavelength¶

public double getPalmWavelength()¶

getPsfCurrentSelection¶

public String getPsfCurrentSelection()¶

getPsfGaussian2dText¶

public String getPsfGaussian2dText()¶

getPsfGaussian3dText¶

public String getPsfGaussian3dText()¶

getPsfGibsonLanniMaxRadius¶

public int getPsfGibsonLanniMaxRadius()¶

getPsfGibsonLanniNg¶

public double getPsfGibsonLanniNg()¶

getPsfGibsonLanniNg0¶

public double getPsfGibsonLanniNg0()¶

getPsfGibsonLanniNi¶

public double getPsfGibsonLanniNi()¶

getPsfGibsonLanniNi0¶

public double getPsfGibsonLanniNi0()¶

getPsfGibsonLanniNs¶

public double getPsfGibsonLanniNs()¶

getPsfGibsonLanniNumBasis¶

public int getPsfGibsonLanniNumBasis()¶

getPsfGibsonLanniNumSamples¶

public int getPsfGibsonLanniNumSamples()¶

getPsfGibsonLanniOversampling¶

public int getPsfGibsonLanniOversampling()¶

getPsfGibsonLanniResPsf¶

public double getPsfGibsonLanniResPsf()¶

getPsfGibsonLanniResPsfAxial¶

public double getPsfGibsonLanniResPsfAxial()¶

getPsfGibsonLanniSizeX¶

public int getPsfGibsonLanniSizeX()¶

getPsfGibsonLanniSizeY¶

public int getPsfGibsonLanniSizeY()¶

getPsfGibsonLanniSolver¶

public String getPsfGibsonLanniSolver()¶

getPsfGibsonLanniText¶

public String getPsfGibsonLanniText()¶

getPsfGibsonLanniTg¶

public double getPsfGibsonLanniTg()¶

getPsfGibsonLanniTg0¶

public double getPsfGibsonLanniTg0()¶

getPsfGibsonLanniTi0¶

public double getPsfGibsonLanniTi0()¶

getStageX¶

public double getStageX()¶

getStageY¶

public double getStageY()¶

getStageZ¶

public double getStageZ()¶

getStormKBl¶

public double getStormKBl()¶

getStormKDark¶

public double getStormKDark()¶

getStormKDarkRecovery¶

public double getStormKDarkRecovery()¶

getStormKDarkRecoveryConstant¶

public double getStormKDarkRecoveryConstant()¶

getStormKTriplet¶

public double getStormKTriplet()¶

getStormKTripletRecovery¶

public double getStormKTripletRecovery()¶

getStormSignal¶

public double getStormSignal()¶

getStormWavelength¶

public double getStormWavelength()¶

read¶

public static IJPluginModel read(FileInputStream fileIn)¶

Loads a model from a file.

Parameters:	fileIn – The input stream from the file.

setAnalyzerCurrentSelection¶

public void setAnalyzerCurrentSelection(String text)¶

setBackgroundCurrentSelection¶

public void setBackgroundCurrentSelection(String currentSelection)¶

setBackgroundRandomButtonText¶

public void setBackgroundRandomButtonText(String text)¶

setBackgroundRandomFeatureSize¶

public void setBackgroundRandomFeatureSize(double featureSize)¶

setBackgroundRandomMaxValue¶

public void setBackgroundRandomMaxValue(float maxValue)¶

setBackgroundRandomMinValue¶

public void setBackgroundRandomMinValue(float minValue)¶

setBackgroundRandomSeed¶

public void setBackgroundRandomSeed(int seed)¶

setBackgroundTifFile¶

public void setBackgroundTifFile(String filename)¶

setBackgroundTifFileButtonText¶

public void setBackgroundTifFileButtonText(String text)¶

setBackgroundUniformButtonText¶

public void setBackgroundUniformButtonText(String text)¶

setBackgroundUniformSignal¶

public void setBackgroundUniformSignal(float signal)¶

setCameraAduPerElectron¶

public void setCameraAduPerElectron(double aduPerElectron)¶

setCameraBaseline¶

public void setCameraBaseline(int baseline)¶

setCameraDarkCurrent¶

public void setCameraDarkCurrent(double darkCurrent)¶

setCameraEmGain¶

public void setCameraEmGain(int emGain)¶

setCameraNX¶

public void setCameraNX(int nX)¶

setCameraNY¶

public void setCameraNY(int nY)¶

setCameraPixelSize¶

public void setCameraPixelSize(double pixelSize)¶

setCameraQuantumEfficiency¶

public void setCameraQuantumEfficiency(double quantumEfficiency)¶

setCameraReadoutNoise¶

public void setCameraReadoutNoise(double readoutNoise)¶

setCameraThermalNoise¶

public void setCameraThermalNoise(double thermalNoise)¶

setControllerCurrentSelection¶

public void setControllerCurrentSelection(String text)¶

setEmitters3DCheckBoxEnabled¶

public void setEmitters3DCheckBoxEnabled(boolean enabled)¶

setEmitters3DMaxZ¶

public void setEmitters3DMaxZ(double max)¶

setEmitters3DMinZ¶

public void setEmitters3DMinZ(double min)¶

setEmittersCsvFile¶

public void setEmittersCsvFile(String filename)¶

setEmittersCsvFileButtonText¶

public void setEmittersCsvFileButtonText(String text)¶

setEmittersCurrentSelection¶

public void setEmittersCurrentSelection(String currentSelection)¶

setEmittersGridButtonText¶

public void setEmittersGridButtonText(String text)¶

setEmittersGridSpacing¶

public void setEmittersGridSpacing(int spacing)¶

setEmittersRandomButtonText¶

public void setEmittersRandomButtonText(String text)¶

setEmittersRandomNumber¶

public void setEmittersRandomNumber(int number)¶

setFiducialsNumber¶

public void setFiducialsNumber(int number)¶

setFiducialsSignal¶

public void setFiducialsSignal(double signal)¶

setFluorophoreCurrentSelection¶

public void setFluorophoreCurrentSelection(String text)¶

setFluorophorePalmText¶

public void setFluorophorePalmText(String text)¶

setFluorophoreSignal¶

public void setFluorophoreSignal(double signal)¶

setFluorophoreSimpleText¶

public void setFluorophoreSimpleText(String text)¶

setFluorophoreStormText¶

public void setFluorophoreStormText(String text)¶

setFluorophoreTBl¶

public void setFluorophoreTBl(double tBl)¶

setFluorophoreTOff¶

public void setFluorophoreTOff(double tOff)¶

setFluorophoreTOn¶

public void setFluorophoreTOn(double tOn)¶

setFluorophoreWavelength¶

public void setFluorophoreWavelength(double wavelength)¶

setLaserCurrentPower¶

public void setLaserCurrentPower(double currentPower)¶

setLaserMaxPower¶

public void setLaserMaxPower(double maxPower)¶

setLaserMinPower¶

public void setLaserMinPower(double minPower)¶

setObjectiveMag¶

public void setObjectiveMag(double mag)¶

setObjectiveNa¶

public void setObjectiveNa(double na)¶

setPalmKA¶

public void setPalmKA(double kA)¶

setPalmKB¶

public void setPalmKB(double kB)¶

setPalmKD1¶

public void setPalmKD1(double kD1)¶

setPalmKD2¶

public void setPalmKD2(double kD2)¶

setPalmKR1¶

public void setPalmKR1(double kR1)¶

setPalmKR2¶

public void setPalmKR2(double kR2)¶

setPalmSignal¶

public void setPalmSignal(double signal)¶

setPalmWavelength¶

public void setPalmWavelength(double wavelength)¶

setPsfCurrentSelection¶

public void setPsfCurrentSelection(String text)¶

setPsfGaussian2dText¶

public void setPsfGaussian2dText(String text)¶

setPsfGaussian3dText¶

public void setPsfGaussian3dText(String text)¶

setPsfGibsonLanniMaxRadius¶

public void setPsfGibsonLanniMaxRadius(int maxRadius)¶

setPsfGibsonLanniNg¶

public void setPsfGibsonLanniNg(double ng)¶

setPsfGibsonLanniNg0¶

public void setPsfGibsonLanniNg0(double ng0)¶

setPsfGibsonLanniNi¶

public void setPsfGibsonLanniNi(double ni)¶

setPsfGibsonLanniNi0¶

public void setPsfGibsonLanniNi0(double ni0)¶

setPsfGibsonLanniNs¶

public void setPsfGibsonLanniNs(double ns)¶

setPsfGibsonLanniNumBasis¶

public void setPsfGibsonLanniNumBasis(int numBasis)¶

setPsfGibsonLanniNumSamples¶

public void setPsfGibsonLanniNumSamples(int numSamples)¶

setPsfGibsonLanniOversampling¶

public void setPsfGibsonLanniOversampling(int oversampling)¶

setPsfGibsonLanniResPsf¶

public void setPsfGibsonLanniResPsf(double resPsf)¶

setPsfGibsonLanniResPsfAxial¶

public void setPsfGibsonLanniResPsfAxial(double resPsfAxial)¶

setPsfGibsonLanniSizeX¶

public void setPsfGibsonLanniSizeX(int sizeX)¶

setPsfGibsonLanniSizeY¶

public void setPsfGibsonLanniSizeY(int sizeY)¶

setPsfGibsonLanniSolver¶

public void setPsfGibsonLanniSolver(String solver)¶

setPsfGibsonLanniText¶

public void setPsfGibsonLanniText(String text)¶

setPsfGibsonLanniTg¶

public void setPsfGibsonLanniTg(double tg)¶

setPsfGibsonLanniTg0¶

public void setPsfGibsonLanniTg0(double tg0)¶

setPsfGibsonLanniTi0¶

public void setPsfGibsonLanniTi0(double ti0)¶

setStageX¶

public void setStageX(double x)¶

setStageY¶

public void setStageY(double y)¶

setStageZ¶

public void setStageZ(double z)¶

setStormKBl¶

public void setStormKBl(double kBl)¶

setStormKDark¶

public void setStormKDark(double kDark)¶

setStormKDarkRecovery¶

public void setStormKDarkRecovery(double kDarkRecovery)¶

setStormKDarkRecoveryConstant¶

public void setStormKDarkRecoveryConstant(double kDarkRecoveryConstant)¶

setStormKTriplet¶

public void setStormKTriplet(double kTriplet)¶

setStormKTripletRecovery¶

public void setStormKTripletRecovery(double kTripletRecovery)¶

setStormSignal¶

public void setStormSignal(double signal)¶

setStormWavelength¶

public void setStormWavelength(double wavelength)¶

write¶

public void write(FileOutputStream fileOut)¶

Saves the model’s state to a file.

Parameters:	fileOut – The output stream to the file.