DefaultFluorophore¶
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public class
DefaultFluorophore
extends 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.
Author: Marcel Stefko, Kyle M. Douglass
Constructors¶
DefaultFluorophore¶
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public
DefaultFluorophore
(PSFBuilder psfBuilder, Illumination illumination, double signal, StateSystem state_system, int start_state, 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 profile on the sample.
- signal – Number of photons per frame.
- state_system – Internal state system for this fluorophore
- start_state – 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.
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.
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.