PhysicalFluorophore¶
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public class
PhysicalFluorophoreextends AbstractEmitter implements Fluorophore¶ A general fluorescent molecule which emits light. This class directly implements the methods of Observables, rather than extending AbstractObservable, because Java does not support multiple inheritance. TODO: IMPLEMENT TESTS FOR THIS CLASS.
Author: Marcel Stefko, Kyle M. Douglass
Constructors¶
PhysicalFluorophore¶
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public
PhysicalFluorophore(PSFBuilder psfBuilder, Illumination illumination, double quantumYield, double extinctionCoefficient, double secondsPerFrame, StateSystem stateSystem, int startState, double x, double y, double z)¶ Initialize fluorophore and calculate its pattern on camera
Parameters: - psfBuilder – The Builder for calculating microscope PSFs.
- illumination – The illumination at the fluorophore.
- quantumYield – The fluorophore’s quantumYield.
- extinctionCoefficient – The fluorophore’s extinction coefficient.
- secondsPerFrame – The length of a frame’s exposure time in seconds.
- stateSystem – Internal state system for this fluorophore
- startState – Initial state number
- x – x-position in pixels
- y – y-position in pixels
- z – z-position in pixels
Methods¶
addListener¶
deleteListener¶
getCurrentState¶
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public int
getCurrentState()¶ Returns the id of the fluorophore state system’s current state.
Returns: The id of the current state of the fluorophore’s state system.
getExtinctionCoefficient¶
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public double
getExtinctionCoefficient()¶ Returns the fluorophore extinction coefficient.
Returns: The fluorophore’s extinction coefficient.
getIllumination¶
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public Illumination
getIllumination()¶ Returns the fluorophore’s illumination profile.
Returns: The fluorophore’s illumination profile.
getIlluminationListener¶
getOnTimeThisFrame¶
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public double
getOnTimeThisFrame()¶ Returns the time spent in the emitting state during the previous frame. This time is the proportion of the frame’s duration; 1 corresponds to having spent the entirety of the frame in the emitting state.
Returns: The time spent in the emitting state.
getPhotonsThisFrame¶
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public double
getPhotonsThisFrame()¶ Returns the number of photons emitted during the previous frame.
Returns: The number of photons emitted during the previous frame.
getQuantumYield¶
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public double
getQuantumYield()¶ Returns the fluorophore’s quantum yield.
Returns: The fluorophore’s quantum yield.
getSecondsPerFrame¶
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public double
getSecondsPerFrame()¶ Returns the length of a camera exposure in seconds.
Returns: The length of a camera exposure in seconds.
getSignal¶
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public double
getSignal()¶ Returns the fluorophore’s number of photons per frame.
Returns: The number of photons per frame emitted by the fluorophore.
getX¶
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public double
getX()¶ Return the x-position of the fluorophore.
Returns: The fluorophore’s x-position.
getY¶
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public double
getY()¶ Return the y-position of the fluorophore.
Returns: The fluorophore’s y-position.
getZ¶
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public double
getZ()¶ Return the z-position of the fluorophore.
Returns: The fluorophore’s z-position.
isBleached¶
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public boolean
isBleached()¶ Informs if this emitter switched into the irreversible bleached state.
Returns: boolean, true if emitter is bleached
isOn¶
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public boolean
isOn()¶ Returns the current state of the emitter (on or off), but does not inform if this emitter is also bleached!
Returns: true-emitter is on, false-emitter is off
nextExponential¶
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protected final double
nextExponential(double mean)¶ Sample an random number from an exponential distribution
Parameters: - mean – mean of the distribution
Returns: random number from this distribution
notifyListeners¶
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public void
notifyListeners()¶ Notifies all subscribed listeners to a change in the Observable’s state. This method should only be called if setChanged() has been called.