A B C D E F G H I J L M N O P Q R S T U V W Y

A

absoluteRefractionTime - Static variable in class mosaic.sim.neuron.ConstantPLThreshold
The globally constant absolute refraction time of the threshold.
activateAt(double) - Method in class mosaic.sim.neuron.ActiveVariable
Calls the respective method in timer
activateIn(double) - Method in class mosaic.sim.neuron.ActiveVariable
Calls the respective method in timer
active - Variable in class mosaic.sim.neuron.netinputs.TemporalCodedInput.Output
Set to true, when this output has scheduled a fire event, but has not fired until now (i.e. the current simulation time).
ActiveVariable - class mosaic.sim.neuron.ActiveVariable.
This class implements an active variable that has support for sending out VariableChangeEvents and for sending itself a TimeEvent, therefore being an active variable container.
ActiveVariable() - Constructor for class mosaic.sim.neuron.ActiveVariable
Creates a new timer object and registers this object as a listener for time events.
ActiveVariable(String) - Constructor for class mosaic.sim.neuron.ActiveVariable
Creates a new timer object and registers this object as a listener for time events.
addInput(NeuronOutput) - Method in class mosaic.sim.neuron.Neuron
This method adds another input to this Neuron, but the given input object does not have to be a Synpase, it just has to be some object implementing NeuronOutput.
addInputSynapse(Synapse) - Method in class mosaic.sim.neuron.Neuron
Adds a single synapse object to the list of input synapses.
addListenerVariable(Variable) - Method in class mosaic.sim.neuron.Neuron
This implementation of VariableChangeListener.addListenerVariable does nothing.
addListenerVariable(Variable) - Method in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
Implementation of VariableChangeListener: This implementation does nothing.
addOutput(NeuronInput) - Method in class mosaic.sim.neuron.NeuronOutputSupport
Adds a single NeuronInput object to the list of objects that should receive spike events sent by this object.
addOutput(NeuronInput) - Method in interface mosaic.sim.neuron.NeuronOutput
Add a spike event listener.
addSimEventComponent(SimEventComponent) - Method in class mosaic.sim.neuron.simulations.SOMPanel
 
addTimeEventComponent(SimEventComponent) - Method in class mosaic.sim.neuron.ActiveVariable
This implementation of TimeEventListener.addTimeEventComponent does nothing
addTimeEventComponent(SimEventComponent) - Method in class mosaic.sim.neuron.simulations.SOMPanel
 
addVectorOutputListener(VectorOutputListener) - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
Adds an output event listener.
addView(ScrollingView) - Method in class mosaic.sim.neuron.visualisation.ViewSynchronizer
Adds a view that should be synchronized with the already added views.
assertCond(boolean, String, String) - Static method in class mosaic.sim.neuron.Debug
Assert that a condition is true.
ATTRACTOR_SET - Static variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 

B

BasicTest1 - class mosaic.sim.neuron.examples.BasicTest1.
 
BasicTest1() - Constructor for class mosaic.sim.neuron.examples.BasicTest1
 
BasicTest1Panel - class mosaic.sim.neuron.examples.BasicTest1Panel.
 
BasicTest1Panel() - Constructor for class mosaic.sim.neuron.examples.BasicTest1Panel
 
brain - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
buffer - Variable in class mosaic.sim.neuron.PLPotential
This is only a buffer for the mergeSynapseResponse method, used for the enhanced merge sort in there.

C

calcSquareError(double[][], double[][]) - Method in class mosaic.sim.neuron.netoutputs.OutputFilter
Calculates the normalized (divided by number of elements in the matrix length) square difference between the given matrices.
calcSquareError(double[], double[]) - Method in class mosaic.sim.neuron.netoutputs.OutputFilter
Calculates the normalized (divided by the vector length) square difference between the given vectors.
calculateIntersectionPoint(PLFunction, double, double, int, PLFunction, double, double, int) - Method in class mosaic.sim.neuron.PLThreshold
 
calculateNextFireTime(Potential) - Method in class mosaic.sim.neuron.Threshold
Returns the next fire time of the associated Neuron, that is the first intersection between the threshold function and the given potential function.
calculateNextFireTime(Potential) - Method in class mosaic.sim.neuron.PLThreshold
Returns the next fire time of the associated neuron.
calculateRelativeRefractionTime() - Static method in class mosaic.sim.neuron.ConstantPLThreshold
Calculates the relative refraction time, that is the time until the threshold reaches its quiescent value again.
CBN - class mosaic.sim.neuron.simulations.CBN.
 
CBN() - Constructor for class mosaic.sim.neuron.simulations.CBN
 
CBNPanel - class mosaic.sim.neuron.simulations.CBNPanel.
 
CBNPanel() - Constructor for class mosaic.sim.neuron.simulations.CBNPanel
 
changeParameters(Synapse) - Method in interface mosaic.sim.neuron.Synapse.LearningMethod
 
changeParameters(Synapse) - Method in class mosaic.sim.neuron.simulations.SOMLearningMethod
 
changes - Variable in class mosaic.sim.neuron.PLPotential
This function specifies the future potential development, computed from the received synapse response functions (by mergeSynapseResponse).
clone() - Method in class mosaic.sim.neuron.Synapse
Returns a copy of the current object.
coderOneDim - Variable in class mosaic.sim.neuron.netinputs.ImageInput
This object is used as the coder when using one-dimensional (vector) input.
coderTwoDim - Variable in class mosaic.sim.neuron.netinputs.ImageInput
This object is used as the coder when using two-dimensional (matrix) input.
CodingException - exception mosaic.sim.neuron.CodingException.
This class represents an exception with the used spike coding.
CodingException(String) - Constructor for class mosaic.sim.neuron.CodingException
Creates a new CodingException with an error string.
colorModel - Variable in class mosaic.sim.neuron.netoutputs.ImageOutput
 
computeTimeOfFire() - Method in class mosaic.sim.neuron.Neuron
Computes the next fire time according to the current potential and threshold parameters.
ConstantPLSynapse - class mosaic.sim.neuron.ConstantPLSynapse.
This class represents a synapse using piecewiese linear functions, but with a constant shape for all synapse objects in the simulation.
ConstantPLSynapse(NeuronOutput, Neuron) - Constructor for class mosaic.sim.neuron.ConstantPLSynapse
Creates a synapse object and associates the pre- and postsynaptic neurons with it.
ConstantPLSynapse(NeuronOutput, Neuron, float) - Constructor for class mosaic.sim.neuron.ConstantPLSynapse
Creates a synapse object, associates the pre- and postsynaptic neurons with it and initializes the synaptic weight.
ConstantPLSynapse(NeuronOutput, Neuron, float, float) - Constructor for class mosaic.sim.neuron.ConstantPLSynapse
Creates a synapse object, associates the pre- and postsynaptic neurons with it and initializes the synaptic weight and delay
ConstantPLSynapse(NeuronOutput, Neuron, float, float, Synapse.LearningMethod) - Constructor for class mosaic.sim.neuron.ConstantPLSynapse
Creates a synapse object, associates the pre- and postsynaptic neurons with it and initializes the synaptic weight and delay
ConstantPLThreshold - class mosaic.sim.neuron.ConstantPLThreshold.
This class represents a threshold using piecewiese linear functions, but with a constant shape for all threshold objects in the simulation.
ConstantPLThreshold() - Constructor for class mosaic.sim.neuron.ConstantPLThreshold
Creates a ConstantPLThreshold object, but does no initialization.
currentLearningCycle - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
currentTimePosition - Variable in class mosaic.sim.neuron.visualisation.ScrollingView
The position on the time frame where to show the current simulation time.
cycleActive - Variable in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
This boolean variable is set to true whenever an output cycle is currently active.

D

debug - Static variable in class mosaic.sim.neuron.Debug
Debugging methods are enabled in the project only if this is set to true.
Debug - class mosaic.sim.neuron.Debug.
This class is used for debugging purposes, mainly for printing debug traces dependent on a trace level and for assertions (which will be supported natively in JDK 1.4 as soon as it becomes stable).
Debug() - Constructor for class mosaic.sim.neuron.Debug
 
delay - Variable in class mosaic.sim.neuron.PLSynapse
The delay of the synapse.
DELAY_INTERNEURON - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
dim - Variable in class mosaic.sim.neuron.netinputs.ImageInput
The dimension of the network input.
displayPotential - Variable in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
If set to true, the view displays the neuron potential.
displayThreshold - Variable in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
If set to true, the view displays the neuron threshold.
DOUBLE_INACCURACY_WINDOW - Static variable in class mosaic.sim.neuron.GlobalConstants
This constant specifies the inaccuracy window for double values.
drawPLFunction(LinkedList, Graphics, Color, Color) - Method in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
This method draws a piecewise linear function which has to be given as a linear list containing points in the world (not graphics) space as Point2D.Double objects.

E

enterMatrix(double[][]) - Method in interface mosaic.sim.neuron.netinputs.MatrixInputCoder
Enters a new real numbered input matrix into the simulation.
enterVector(double[]) - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput
Enters a new analog input vector into the simulation.
enterVector(double[]) - Method in interface mosaic.sim.neuron.netinputs.VectorInputCoder
Enters a new real numbered input vector into the simulation.
enterVector(double[]) - Method in class mosaic.sim.neuron.netinputs.RateCodedInputVector
Implementation of VectorInput.enterVector.

F

f - Variable in class mosaic.sim.neuron.PLFunction.FloatIntPair
 
FILENAME_COMPUTEDWEIGHTS - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
FILENAME_LEARNINGPARAMS - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
FILENAME_TRAININGSET - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
fired() - Method in class mosaic.sim.neuron.Threshold
This method can be overridden to process the firing event, but super() should be called
fired() - Method in class mosaic.sim.neuron.PLThreshold
This method is called by the associated neuron object whenever it fires.
fireIn(double) - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput.Output
Schedule firing in the specified time.
fireSpikeEvent() - Method in class mosaic.sim.neuron.NeuronOutputSupport
Sends a spike event to every registered NeuronInput listener object.
forwardedFirstEvent - Variable in class mosaic.sim.neuron.netoutputs.OutputFilter
True when an event has already been forwarded.
forwardMultipleEvents - Variable in class mosaic.sim.neuron.netoutputs.OutputFilter
When true, then multiple events will be forwarded.

G

getAbsoluteRefractionTime() - Method in class mosaic.sim.neuron.PLThreshold
Returns the absolute refraction time.
getAbsoluteRefractionTime() - Method in class mosaic.sim.neuron.ConstantPLThreshold
Implementation of PLThreshold.getAbsoluteRefractionTime().
getChanges() - Method in class mosaic.sim.neuron.PLPotential
Returns the currently computed piecewiese linear function describing the currently known future potential changes.
getColorModel() - Method in class mosaic.sim.neuron.netinputs.ImageInput
Returns the color model of the loaded image.
getCurrentPotential() - Method in class mosaic.sim.neuron.Neuron
Returns the current neuron potential.
getCurrentPotential() - Method in class mosaic.sim.neuron.Potential
Compute the current Neuron potential from the gradient changes.
getCurrentPotential() - Method in class mosaic.sim.neuron.PLPotential
Returns the current potential value (at the current simulation time).
getCurrentThreshold() - Method in class mosaic.sim.neuron.Threshold
Compute the current Neuron threshold from the gradient changes.
getCurrentThreshold() - Method in class mosaic.sim.neuron.PLThreshold
Compute the current Neuron threshold from the gradient changes.
getCurrentTimePosition() - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Returns the current time position.
getDelay() - Method in class mosaic.sim.neuron.PLSynapse
Gets the currently set synaptic delay.
getEndTime() - Method in class mosaic.sim.neuron.PLFunction
Calculates and returns the time when the function reaches 0.
getEndTime(double, int) - Method in class mosaic.sim.neuron.PLFunction
Calculates and returns the time when the function, starting with the given startValue as offset and when restricted to the first numSegments segments, reaches 0.
getFinishedSegments(double, boolean) - Method in class mosaic.sim.neuron.PLFunction
 
getFinishedSegments(double, int, double, boolean) - Method in class mosaic.sim.neuron.PLFunction
Returns the value of the function at the time of last gradient change before the given simulation time (computing all linear segments that have ended before the current simulation time).
getHeight() - Method in class mosaic.sim.neuron.netinputs.ImageInput
Returns the height of the loaded image.
getInput(int) - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
Returns the input object with the given index.
getInputSynapses() - Method in class mosaic.sim.neuron.Neuron
Returns the list of currently registerd input synapses.
getLastEventTime() - Method in class mosaic.sim.neuron.Synapse
Returns the time when this synapse has received the last spike.
getLastFireTime() - Method in class mosaic.sim.neuron.PLThreshold
Returns the last fire time of the associated neuron.
getLastStartTime() - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput
Returns the time when the last event was started.
getLastVector() - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput
Returns the last input vector.
getLastZeroTime() - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput
Return the time when the last event should end (or has ended).
getMasterSynapse() - Method in class mosaic.sim.neuron.Neuron
Returns the master synapse object used for creating new synapse objects on the fly in the method addInput().
getMultiplicator() - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput
Returns the multiplicator.
getNumSegments() - Method in class mosaic.sim.neuron.PLPotential
Returns the number of piecewiese linear segments that are currently valid in the changes function.
getOutput(int) - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput
Implementation of VectorInput.getOutput.
getOutput(int) - Method in interface mosaic.sim.neuron.netinputs.VectorInputCoder
Returns the output with the given index.
getOutput(int) - Method in class mosaic.sim.neuron.netinputs.RateCodedInputVector
Implementation of VectorInput.getOutput.
getOutput(int, int) - Method in interface mosaic.sim.neuron.netinputs.MatrixInputCoder
Returns the output with the given indices.
getOutputs() - Method in class mosaic.sim.neuron.NeuronOutputSupport
Returns the list of currently registered NeuronInput objects that should receive the spike events sent by this object.
getPotential() - Method in class mosaic.sim.neuron.Neuron
Returns the potential object.
getPriority() - Method in class mosaic.sim.neuron.Neuron
This implementation of VariableChangeListener.getPriority always returns 0.
getPriority() - Method in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
Implementation of VariableChangeListener: This implementation always returns 0.
getQuiescentValue() - Method in class mosaic.sim.neuron.PLThreshold
Returns the quiescent value.
getQuiescentValue() - Method in class mosaic.sim.neuron.ConstantPLThreshold
Implementation of PLThreshold.getQuiescentValue().
getRate() - Method in class mosaic.sim.neuron.netinputs.RateCodedInputSingle
Returns the currently used firing rate.
getReceivedTime() - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput.Input
Returns the time when the input has received its spike.
getReceiver() - Method in class mosaic.sim.neuron.Synapse
Returns the post-synaptic neuron that receives the forwarded spike events from this synapse.
getReferenceInput() - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
Returns the reference input.
getReferenceOutput() - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput
Returns the reference output.
getRelativeRefraction() - Method in class mosaic.sim.neuron.PLThreshold
Returns the relative refraction function.
getRelativeRefraction() - Method in class mosaic.sim.neuron.ConstantPLThreshold
Implementation of PLThreshold.getRelativeRefraction().
getRelativeRefractionStartValue() - Method in class mosaic.sim.neuron.PLThreshold
Returns the start value of the relative refraction function.
getRelativeRefractionStartValue() - Method in class mosaic.sim.neuron.ConstantPLThreshold
Implementation of PLThreshold.getRelativeRefractionStartValue().
getRelativeRefractionTime() - Method in class mosaic.sim.neuron.PLThreshold
Returns the relative refraction time.
getRelativeRefractionTime() - Method in class mosaic.sim.neuron.ConstantPLThreshold
Implementation of PLThreshold.getRelativeRefractionTime().
getResponse() - Static method in class mosaic.sim.neuron.ConstantPLSynapse
Implementation of PLSynapse.getResponse()
getResponseParameters() - Method in class mosaic.sim.neuron.Synapse
This function is called by the post-synaptic neuron to retrieve the parameters which describe how the neuron potential changes because of the receives spike event.
getResponseParameters() - Method in class mosaic.sim.neuron.PLSynapse
This implementation of Synapse.getResponseParameters returns an object of type PLFunction, i.e. 2 one-dimensional arrays describing the piecewise linear response function of this synapse.
getSampleModel() - Method in class mosaic.sim.neuron.netinputs.ImageInput
Returns the sample model of the loaded image.
getSender() - Method in class mosaic.sim.neuron.Synapse
Returns the pre-synaptic NeuronOutput object that sends spike events to this synapse.
getStandardResponse() - Method in class mosaic.sim.neuron.PLSynapse
getResponseParameters uses this method to retrieve the function gradients used for constructing the response object.
getStandardResponse() - Method in class mosaic.sim.neuron.ConstantPLSynapse
Implementation of PLSynapse.getStandardResponse()
getState() - Method in class mosaic.sim.neuron.PLThreshold
Returns the current internal state.
getSynchronizer() - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Returns the associated ViewSynchronizer.
getThreshold() - Method in class mosaic.sim.neuron.Neuron
Returns the threshold object.
getTMax() - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Returns the maximum simulation time shown.
getTMin() - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Returns the minimum simulation time shown.
getValueAtTime(double, int, double) - Method in class mosaic.sim.neuron.PLFunction
Returns the value of the function at the given time, starting with the given startValue and taking numSegments into account.
getValueObject() - Method in class mosaic.sim.neuron.NeuronOutputSupport
This implementation of AbstractVariable.getValueObject just returns the current object.
getValueObject() - Method in class mosaic.sim.neuron.Threshold
This implementation of AbstractVariable.getValueObject just returns the current object.
getValueObject() - Method in class mosaic.sim.neuron.Potential
This implementation of AbstractVariable.getValueObject just returns the current object.
getWeight() - Method in class mosaic.sim.neuron.PLSynapse
Gets the currently set synaptic weight.
getWidth() - Method in class mosaic.sim.neuron.netinputs.ImageInput
Returns the width of the loaded image.
getYMax() - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Returns the maximum vertical value shown.
getYMin() - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Returns the minimum vertical value shown.
GlobalConstants - class mosaic.sim.neuron.GlobalConstants.
This class contains some constants that are globally used within the framework.
GlobalConstants() - Constructor for class mosaic.sim.neuron.GlobalConstants
 
gradients - Variable in class mosaic.sim.neuron.PLFunction
The gradients of the linear segments.
gradientTimes - Variable in class mosaic.sim.neuron.PLFunction
The begin times of the linear segments.

H

hasReceivedSpike() - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput.Input
Returns true if this input has already received a spike.
Hopfield - class mosaic.sim.neuron.simulations.Hopfield.
 
Hopfield() - Constructor for class mosaic.sim.neuron.simulations.Hopfield
 
HopfieldPanel - class mosaic.sim.neuron.simulations.HopfieldPanel.
 
HopfieldPanel() - Constructor for class mosaic.sim.neuron.simulations.HopfieldPanel
 

I

i - Variable in class mosaic.sim.neuron.PLFunction.FloatIntPair
 
image - Variable in class mosaic.sim.neuron.netinputs.ImageInput
The image.
ImageInput - class mosaic.sim.neuron.netinputs.ImageInput.
This class reads an image and converts it to either a one-dimensional vector of dimension height*width or a two-dimensional matrix of dimension [height, width].
ImageInput(String, int) - Constructor for class mosaic.sim.neuron.netinputs.ImageInput
This constructor initializes the class for one-dimensional or two-dimensional input.
ImageOutput - class mosaic.sim.neuron.netoutputs.ImageOutput.
This class receives vector or matrix output events from some spike decoder and transforms the values into an image, which is immediately saved in the file given to the constructor.
ImageOutput(String, String, int, ColorModel, SampleModel) - Constructor for class mosaic.sim.neuron.netoutputs.ImageOutput
 
init() - Method in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
init() - Method in class mosaic.sim.neuron.netinputs.RateCodedInputSingle
Initialize the random number generator and start the spike firing.
init() - Method in class mosaic.sim.neuron.netinputs.RandomSpikeSource
Initialize the random number generator and start the spike firing.
init() - Method in class mosaic.sim.neuron.simulations.HopfieldPanel
 
init() - Method in class mosaic.sim.neuron.simulations.SOMPanel
 
init() - Method in class mosaic.sim.neuron.simulations.CBNPanel
 
init() - Method in class mosaic.sim.neuron.simulations.genesis.MultiCellPanel
 
input - Variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
input - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
INPUT_VECTOR - Static variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
inputs - Variable in class mosaic.sim.neuron.Neuron
This is the list of Synapses which receive spike events from another NeuronOutput object and forward the event to this Neuron object.
inputs - Variable in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
The inputs which receive the spike series.
inputs - Variable in class mosaic.sim.neuron.simulations.CBNPanel
 
interneurons - Variable in class mosaic.sim.neuron.simulations.CBNPanel
 
inWithoutRef - Variable in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
inWithRef - Variable in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
isActive() - Method in class mosaic.sim.neuron.ActiveVariable
Calls the respective method in timer
isActive() - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput.Output
Returns true if this output is still waiting to fire its spike.

J

jbInit() - Method in class mosaic.sim.neuron.examples.SpikeViewTest1Panel
 
jbInit() - Method in class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1Panel
 
jbInit() - Method in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
jbInit() - Method in class mosaic.sim.neuron.examples.BasicTest1Panel
 
jbInit() - Method in class mosaic.sim.neuron.simulations.genesis.MultiCellPanel
 

L

LAMBDA - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
set sufficiently large so that every competitive neuron actually fires
lastEventTime - Variable in class mosaic.sim.neuron.Synapse
The time when the last spike event has been received by this synapse.
lastFireTime - Variable in class mosaic.sim.neuron.PLThreshold
The simulation time when the associated neuron fired the last time.
lastMatrix - Variable in class mosaic.sim.neuron.netoutputs.OutputFilter
The last matrix that has been received - used for determining if an equilibrium has been reached.
lastStartTime - Variable in class mosaic.sim.neuron.netinputs.TemporalCodedInput
In this variable, the last (absolute) time of starting an input event is stored (the simulation time when enterVector was called).
lastState - Variable in class mosaic.sim.neuron.PLThreshold
The previous state of the neuron, can be one of STATE_*.
lastVector - Variable in class mosaic.sim.neuron.netinputs.TemporalCodedInput
In this variable, the last input vector that was entered using this object is stored.
lastVector - Variable in class mosaic.sim.neuron.netoutputs.OutputFilter
The last vector that has been received - used for determining if an equilibrium has been reached.
lastVectorWithoutRef - Variable in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
lastVectorWithRef - Variable in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
lastZeroTime - Variable in class mosaic.sim.neuron.netinputs.TemporalCodedInput
In this variable, the end of the last input cycle (the absolute simulation time marking the input value 0) is stored.
LATERAL_INHIBITION_WIDTH - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
LEARNING_CYCLES - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
learningMethod - Variable in class mosaic.sim.neuron.Synapse
The learning method to use whenever changing the synaptic parameters is to be done (e.g. when postNeuronFired() is called).
learningRate - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
LEARNINGRATE_FACTOR - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
LEARNINGRATE_START - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
level - Static variable in class mosaic.sim.neuron.Debug
Determines the debugging level, can be one of LEVEL_*.
LEVEL_ALL - Static variable in class mosaic.sim.neuron.Debug
Log everything that can be logged.
LEVEL_CRITICAL - Static variable in class mosaic.sim.neuron.Debug
Only log critical debug trace statements, this is minimal debugging.
LEVEL_ERROR - Static variable in class mosaic.sim.neuron.Debug
Log everything from LEVEL_CRITICAL and error messages.
LEVEL_INFO - Static variable in class mosaic.sim.neuron.Debug
Log everything from LEVEL_WARNING and info messages.
LEVEL_NONE - Static variable in class mosaic.sim.neuron.Debug
Log nothing.
LEVEL_TRACE - Static variable in class mosaic.sim.neuron.Debug
Log everything from LEVEL_INFO and print various traces for examining rhe program paths.
LEVEL_WARNING - Static variable in class mosaic.sim.neuron.Debug
Log everything from LEVEL_ERROR and warning messages.
listeners - Variable in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
The listeners which should receive outputEvents sent by this class.

M

main(String[]) - Static method in class mosaic.sim.neuron.examples.SpikeViewTest1
 
main(String[]) - Static method in class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1
 
main(String[]) - Static method in class mosaic.sim.neuron.examples.TemporalCodingTest1
 
main(String[]) - Static method in class mosaic.sim.neuron.examples.BasicTest1
 
main(String[]) - Static method in class mosaic.sim.neuron.simulations.Hopfield
 
main(String[]) - Static method in class mosaic.sim.neuron.simulations.SOM
 
main(String[]) - Static method in class mosaic.sim.neuron.simulations.CBN
 
main(String[]) - Static method in class mosaic.sim.neuron.simulations.genesis.MultiCell
 
masterSynapse - Variable in class mosaic.sim.neuron.Neuron
This is a master copy of the synapses that will be used for connecting neurons with each other.
MatrixInputCoder - interface mosaic.sim.neuron.netinputs.MatrixInputCoder.
This is an interface for giving a two-dimensional matrix of real numbered values to the network.
MatrixOutputListener - interface mosaic.sim.neuron.netoutputs.MatrixOutputListener.
This interface must be implemented by objects that want to receive the real numbered, two-dimensional matrices computed by the network.
maxCycleTime - Variable in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
This is the maximum time that an input cycle is allow to take.
maxSquareError - Variable in class mosaic.sim.neuron.netoutputs.OutputFilter
The maximum square error for determining if the received event is in an equilibrium state.
maxTime - Variable in class mosaic.sim.neuron.netinputs.RandomSpikeSource
The maximum time between two spike events.
mergeSynapseResponse(Object) - Method in class mosaic.sim.neuron.Potential
Merge a new synaptic response from one of the Neuron input synapses with the current potential function, resulting in a new potential function.
mergeSynapseResponse(Object) - Method in class mosaic.sim.neuron.PLPotential
Merges the synaptic response of an input synapse (probably caused by a spike received by that synapse) with the current potential function, thus forming a new potential function.
mosaic.sim.neuron - package mosaic.sim.neuron
 
mosaic.sim.neuron.examples - package mosaic.sim.neuron.examples
 
mosaic.sim.neuron.netinputs - package mosaic.sim.neuron.netinputs
 
mosaic.sim.neuron.netoutputs - package mosaic.sim.neuron.netoutputs
 
mosaic.sim.neuron.simulations - package mosaic.sim.neuron.simulations
 
mosaic.sim.neuron.simulations.genesis - package mosaic.sim.neuron.simulations.genesis
 
mosaic.sim.neuron.visualisation - package mosaic.sim.neuron.visualisation
 
MultiCell - class mosaic.sim.neuron.simulations.genesis.MultiCell.
 
MultiCell() - Constructor for class mosaic.sim.neuron.simulations.genesis.MultiCell
 
MultiCellPanel - class mosaic.sim.neuron.simulations.genesis.MultiCellPanel.
 
MultiCellPanel() - Constructor for class mosaic.sim.neuron.simulations.genesis.MultiCellPanel
 
multiplicator - Variable in class mosaic.sim.neuron.netinputs.TemporalCodedInput
This value is uses for computing the delay between the first spike event and following spikes depending on the difference in the input values.
multiplicator - Variable in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
Multiplicator for computing the analog value depending on the delay between the received spikes.

N

n1 - Variable in class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1Panel
 
n1 - Variable in class mosaic.sim.neuron.examples.BasicTest1Panel
 
n1 - Variable in class mosaic.sim.neuron.simulations.genesis.MultiCellPanel
 
n2 - Variable in class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1Panel
 
n2 - Variable in class mosaic.sim.neuron.examples.BasicTest1Panel
 
n2 - Variable in class mosaic.sim.neuron.simulations.genesis.MultiCellPanel
 
NEIGHBORHOOD_START - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
NEIGHBOURHOOD_DECREASE - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
Neuron - class mosaic.sim.neuron.Neuron.
This class represents a neuron, which is able to fire spike events (thus it implements the NeuronOutput interface) and receive spikes indirectly via Synapses.
Neuron() - Constructor for class mosaic.sim.neuron.Neuron
Default constructor with no arguments.
NeuronInput - interface mosaic.sim.neuron.NeuronInput.
This Interface specifies the capability of an object to act like an input of a neuron, i.e. the ability to receive spike events.
NeuronOutput - interface mosaic.sim.neuron.NeuronOutput.
This interface specifies the capability of an object to act like the output part of a neuron, i.e. the ability to send spike events.
NeuronOutputSupport - class mosaic.sim.neuron.NeuronOutputSupport.
This is a helper class for objects that want to emit spike events.
NeuronOutputSupport() - Constructor for class mosaic.sim.neuron.NeuronOutputSupport
Default constructor, initializes the output list.
neurons - Variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
neurons - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
next_Tout - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
nextMatrixListener - Variable in class mosaic.sim.neuron.netoutputs.OutputFilter
The object to which the filtered matrix events will be forwarded.
nextVectorListener - Variable in class mosaic.sim.neuron.netoutputs.OutputFilter
The object to which the filtered vector events will be forwarded.
NUMBER_INPUTS - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
NUMBER_INPUTS - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
NUMBER_NEURONS - Static variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
NUMBER_NEURONS - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
NUMBER_OUTPUTS - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
numSegments - Variable in class mosaic.sim.neuron.PLPotential
The current number of linear segments in the piecewise linear potential function 'changes'.

O

output - Variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
output(int, String) - Static method in class mosaic.sim.neuron.Debug
Output some message if the currently set debugging level is equal to or higher than the given minimum debugging level.
outputEvent(double[]) - Method in class mosaic.sim.neuron.netoutputs.OutputFilter
Implementation of VectorOutputListener.outputEvent.
outputEvent(double[]) - Method in interface mosaic.sim.neuron.netoutputs.VectorOutputListener
Receive the system output as a real numbered vector.
outputEvent(double[]) - Method in class mosaic.sim.neuron.netoutputs.ImageOutput
Implementation of VectorOutputListener.outputEvent.
outputEvent(double[][]) - Method in interface mosaic.sim.neuron.netoutputs.MatrixOutputListener
Receive the system output as a real numbered matrix.
outputEvent(double[][]) - Method in class mosaic.sim.neuron.netoutputs.OutputFilter
Implementation of MatrixOutputListener.outputEvent.
outputEvent(double[][]) - Method in class mosaic.sim.neuron.netoutputs.ImageOutput
Implementation of MatrixOutputListener.outputEvent.
OutputFilter - class mosaic.sim.neuron.netoutputs.OutputFilter.
This class is a decorator for output listeners, enabling the filtering of output events: - first of all, it can pass only the first event and filter out all subsequent ones - secondly, events can be forwarded when the have reached an equilibrium, i.e. they do not change anymore within a given error range The constructor intializes the filter.
OutputFilter(VectorOutputListener, MatrixOutputListener, boolean, boolean, double) - Constructor for class mosaic.sim.neuron.netoutputs.OutputFilter
Constructs an OuptutFilter object and initializes the mamber variables according to the given parameters.
outputs - Variable in class mosaic.sim.neuron.NeuronOutputSupport
This is the list of NeuronInput objects which should be notified whenever this object emits a spike event.
outputs - Variable in class mosaic.sim.neuron.netinputs.TemporalCodedInput
The list of outputs that used for emitting spike events.
outputs - Variable in class mosaic.sim.neuron.netinputs.RateCodedInputVector
The list of outputs that used for emitting spike events.
outputs - Variable in class mosaic.sim.neuron.simulations.CBNPanel
 
outWithoutRef - Variable in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
outWithRef - Variable in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 

P

paintComponent(Graphics) - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Overrides the default implementation from JPanel to indicate the current simulation time with a vertical line.
paintComponent(Graphics) - Method in class mosaic.sim.neuron.visualisation.SpikeView
Overrides the default method and paints the spikes received in the past as vertical lines.
paintComponent(Graphics) - Method in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
Overrides the default and draws the piecewise linear functions for the neuron threshold and potential.
panel - Variable in class mosaic.sim.neuron.simulations.SOMLearningMethod
 
passivate() - Method in class mosaic.sim.neuron.ActiveVariable
Calls the respective method in timer
PLFunction - class mosaic.sim.neuron.PLFunction.
This class represents a piecewise linear mathematical function in a finite timeframe with a finite number of linear segments.
PLFunction.FloatIntPair - class mosaic.sim.neuron.PLFunction.FloatIntPair.
Aargh !
PLFunction.FloatIntPair(PLFunction) - Constructor for class mosaic.sim.neuron.PLFunction.FloatIntPair
 
PLFunction(int) - Constructor for class mosaic.sim.neuron.PLFunction
The default constructor initializes both arrays with the same length.
PLNeuronInternalView - class mosaic.sim.neuron.visualisation.PLNeuronInternalView.
This class implements a view for the potential and threshold functions of a neuron, thus its internal states.
PLNeuronInternalView(String, boolean, boolean) - Constructor for class mosaic.sim.neuron.visualisation.PLNeuronInternalView
Creates a PLNeuronInternalView and initializes it.
PLNeuronInternalViewTest1 - class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1.
 
PLNeuronInternalViewTest1() - Constructor for class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1
 
PLNeuronInternalViewTest1Panel - class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1Panel.
 
PLNeuronInternalViewTest1Panel() - Constructor for class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1Panel
 
PLPotential - class mosaic.sim.neuron.PLPotential.
This class represents a neuron potential described by a piecewise linear mathematical function.
PLPotential(int) - Constructor for class mosaic.sim.neuron.PLPotential
Initializes lastValue and numSegments with 0 and allocates changes and buffer with maxSegements linear segments.
PLSynapse - class mosaic.sim.neuron.PLSynapse.
This class represents synapses with piecewise linear response functions.
PLSynapse(NeuronOutput, Neuron) - Constructor for class mosaic.sim.neuron.PLSynapse
Initializes the sender and receiver objects (by calling the super() constructor) and the weight and delay values with default.
PLSynapse(NeuronOutput, Neuron, float) - Constructor for class mosaic.sim.neuron.PLSynapse
Calls the constructor with two parameters, but also allows to specify the synapse weight.
PLSynapse(NeuronOutput, Neuron, float, float) - Constructor for class mosaic.sim.neuron.PLSynapse
Calls the constructor with three parameters, but also allows to specify the synapse delay.
PLSynapse(NeuronOutput, Neuron, float, float, Synapse.LearningMethod) - Constructor for class mosaic.sim.neuron.PLSynapse
Calls the constructor with four parameters, but also allows to specify the learning method.
PLThreshold - class mosaic.sim.neuron.PLThreshold.
This class implements a threshold with piecewise linear functions.
PLThreshold() - Constructor for class mosaic.sim.neuron.PLThreshold
Creates a PLThreshold object and sets its state to STATE_QUIESCENT.
postNeuronFired() - Method in class mosaic.sim.neuron.Synapse
The neuron calls this method whenever it fires a spike event to notify its input synapses of its firing.
potential - Variable in class mosaic.sim.neuron.Neuron
The inner potential of this neuron.
potential - Variable in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
A reference to the neuron potential object.
Potential - class mosaic.sim.neuron.Potential.
This class represent the potential of a neuron.
Potential() - Constructor for class mosaic.sim.neuron.Potential
Creates a potential object.
Potential(String) - Constructor for class mosaic.sim.neuron.Potential
Creates a potential object with a name (mainly useful during debugging).
potentialFunction - Variable in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
The currently used potential function.
printMatrix(double[][], boolean) - Method in class mosaic.sim.neuron.simulations.SOMPanel
 
processSimEvent(SimEvent) - Method in class mosaic.sim.neuron.Neuron
This method is called by the simulation framework when a time event occurs.
processSimEvent(SimEvent) - Method in class mosaic.sim.neuron.PLThreshold
This method is called by the simulation framework whenever a time event occurs.
processSimEvent(SimEvent) - Method in class mosaic.sim.neuron.PLPotential
This method is called by the simulation framework whenever a time event occurs.
processSimEvent(SimEvent) - Method in class mosaic.sim.neuron.netinputs.RateCodedInputSingle
This method is called by the simulation framework whenever a time event occurs.
processSimEvent(SimEvent) - Method in class mosaic.sim.neuron.netinputs.TemporalCodedInput.Output
This method is called by the simulation framework whenever a time event occurs.
processSimEvent(SimEvent) - Method in class mosaic.sim.neuron.netinputs.RandomSpikeSource
This method is called by the simulation framework whenever a time event occurs.
processSimEvent(SimEvent) - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
This method is called by the simulation framework whenever a time event for this object occurs.
processSimEvent(SimEvent) - Method in class mosaic.sim.neuron.simulations.SOMPanel
 
propertyChange(PropertyChangeEvent) - Method in class mosaic.sim.neuron.Neuron
This implementation of VariableChangeListener.propertyChange does nothing.
propertyChange(PropertyChangeEvent) - Method in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
Implementation of VariableChangeListener: This implementation does nothing.

Q

quiescentValue - Static variable in class mosaic.sim.neuron.ConstantPLThreshold
 

R

rand - Variable in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
rand - Static variable in class mosaic.sim.neuron.netinputs.RandomSpikeSource
The random number generator used for getting the fire times.
rand - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
RandomSpikeSource - class mosaic.sim.neuron.netinputs.RandomSpikeSource.
This class implements a random spike source with a configurable maximum interval between two emitted spikes.
RandomSpikeSource(double) - Constructor for class mosaic.sim.neuron.netinputs.RandomSpikeSource
Creates a RandomSpikeSource with the given maxTime.
rate - Variable in class mosaic.sim.neuron.netinputs.RateCodedInputSingle
This is the current firing rate, specified by 1 / delay_between_spikes .
RateCodedInputSingle - class mosaic.sim.neuron.netinputs.RateCodedInputSingle.
This class implements a single spike source using rate coding.
RateCodedInputSingle() - Constructor for class mosaic.sim.neuron.netinputs.RateCodedInputSingle
Constructs a new RateCodedInput object and initializes the rate with 0 (disables the input).
RateCodedInputSingle(double) - Constructor for class mosaic.sim.neuron.netinputs.RateCodedInputSingle
Constructs a new RateCodedInput object.
RateCodedInputVector - class mosaic.sim.neuron.netinputs.RateCodedInputVector.
This class implements a spike source using rate coding.
RateCodedInputVector(int) - Constructor for class mosaic.sim.neuron.netinputs.RateCodedInputVector
Creates a new TemporalCodedInput object and initializes the outputs.
realTimeStarted - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
receivedSpike - Variable in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput.Input
Set to true when this input has already received a spike event in this output cycle.
receivedTime - Variable in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput.Input
The simulation time when the spike event was reveived by this input.
receiver - Variable in class mosaic.sim.neuron.Synapse
The post-synaptic neuron that should receive the forwarded spike events.
RECEPTIVE_FIELD_WIDTH - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
reference - Variable in class mosaic.sim.neuron.netinputs.TemporalCodedInput
The reference output, used optionally.
reference - Variable in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
An optional reference input representing the analog value "0".
REFRACTION_TIME - Static variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
REFRACTION_TIME - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
relativeRefraction - Static variable in class mosaic.sim.neuron.ConstantPLThreshold
 
relativeRefractionStartValue - Static variable in class mosaic.sim.neuron.ConstantPLThreshold
 
relativeRefractionTime - Static variable in class mosaic.sim.neuron.ConstantPLThreshold
The globally constant relative refraction time, that is the time after the quiescent value is reached again.
removeInput(NeuronOutput) - Method in class mosaic.sim.neuron.Neuron
Removes a NeuronOutput object from the input list of this neuron.
removeInputSynapse(Synapse) - Method in class mosaic.sim.neuron.Neuron
Removes a single synapse object from the list of input synapses.
removeListenerVariable(Variable) - Method in class mosaic.sim.neuron.Neuron
This implementation of VariableChangeListener.removeListenerVariable does nothing.
removeListenerVariable(Variable) - Method in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
Implementation of VariableChangeListener: This implementation does nothing.
removeOutput(NeuronInput) - Method in class mosaic.sim.neuron.NeuronOutputSupport
Removes a single NeuronInput object from the list of objects that should receive spike events sent by this object.
removeOutput(NeuronInput) - Method in interface mosaic.sim.neuron.NeuronOutput
Remove a spike event listener.
removeOutputEventListener(VectorOutputListener) - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
Removes an output event listener.
removeSimEventComponent(SimEventComponent) - Method in class mosaic.sim.neuron.simulations.SOMPanel
 
removeTimeEventComponent(SimEventComponent) - Method in class mosaic.sim.neuron.ActiveVariable
This implementation of TimeEventListener.addTimeEventComponent does nothing
removeTimeEventComponent(SimEventComponent) - Method in class mosaic.sim.neuron.simulations.SOMPanel
 
removeView(ScrollingView) - Method in class mosaic.sim.neuron.visualisation.ViewSynchronizer
Removes a view that should no longer be synchronized with the already added views.
reset() - Method in class mosaic.sim.neuron.Neuron
This overrides the default behaviour of reset() by also resetting the associated potential and threshold objects.
reset() - Method in class mosaic.sim.neuron.PLThreshold
Overrides the default behaviour of reset by also clearing the internal state variables.
reset() - Method in class mosaic.sim.neuron.PLPotential
Overrides the default behaviour of reset by also clearing the internal buffers for the future potential function (actually just setting the length to zero).
reset() - Method in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
reset() - Method in class mosaic.sim.neuron.netinputs.RateCodedInputSingle
Reset the spike source.
reset() - Method in class mosaic.sim.neuron.netinputs.RandomSpikeSource
Reset the spike source.
reset() - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput.Input
Resets the input after the output cycle is completed.
reset() - Method in class mosaic.sim.neuron.simulations.HopfieldPanel
 
reset() - Method in class mosaic.sim.neuron.simulations.SOMPanel
 
reset() - Method in class mosaic.sim.neuron.simulations.CBNPanel
 
reset() - Method in class mosaic.sim.neuron.simulations.genesis.MultiCellPanel
 
response - Static variable in class mosaic.sim.neuron.ConstantPLSynapse
The global piecewise linear function.
RISING_GRADIENT - Static variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
RISING_GRADIENT - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
RISING_TIME - Static variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
RISING_TIME - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 

S

s1 - Variable in class mosaic.sim.neuron.examples.SpikeViewTest1Panel
 
s1 - Variable in class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1Panel
 
s1 - Variable in class mosaic.sim.neuron.examples.BasicTest1Panel
 
s2 - Variable in class mosaic.sim.neuron.examples.SpikeViewTest1Panel
 
s2 - Variable in class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1Panel
 
s2 - Variable in class mosaic.sim.neuron.examples.BasicTest1Panel
 
sampleModel - Variable in class mosaic.sim.neuron.netoutputs.ImageOutput
 
savePB - Variable in class mosaic.sim.neuron.netoutputs.ImageOutput
 
scheduleNextFiring() - Method in class mosaic.sim.neuron.Neuron
This method calculates the next firing time of this neuron (by using the method computeTimeOfFire) and schedules the neuron for activation at this time if a firing occurs or deactivates it if no firing will occur.
ScrollingView - class mosaic.sim.neuron.visualisation.ScrollingView.
This class implements a horizontally scrolling view for 2D trajectories.
ScrollingView(String) - Constructor for class mosaic.sim.neuron.visualisation.ScrollingView
Creates a ScroolingView.
ScrollingView(String, ViewSynchronizer) - Constructor for class mosaic.sim.neuron.visualisation.ScrollingView
Creates a ScrollingView and associates a ViewSynchronizer with it.
scrollToSimulationTime(double) - Method in class mosaic.sim.neuron.visualisation.ScrollingView
This method scrolls the view horizontally, so that the current simulation time is contained within the view.
scrollToSimulationTime(double) - Method in class mosaic.sim.neuron.visualisation.ViewSynchronizer
Scrolls all registered ScrollingViews horizontally so that they show the same current simulation time.
sender - Variable in class mosaic.sim.neuron.Synapse
The pre-synaptic object that sends spike events to this synapse.
setAbsoluteRefractionTime(float) - Static method in class mosaic.sim.neuron.ConstantPLThreshold
Set the globally constant absolute refraction time.
setCoder(MatrixInputCoder) - Method in class mosaic.sim.neuron.netinputs.ImageInput
 
setCoder(VectorInputCoder) - Method in class mosaic.sim.neuron.netinputs.ImageInput
Initializes the Spike coder.
setCurrentTimePosition(double) - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Sets the current time position.
setDelay(float) - Method in class mosaic.sim.neuron.PLSynapse
Sets the synaptic delay.
setInputSynapses(Synapse[]) - Method in class mosaic.sim.neuron.Neuron
Set the list of registered input synapses.
setLearningMethod(Synapse.LearningMethod) - Method in class mosaic.sim.neuron.Synapse
Sets the learning method.
setMasterSynapse(Synapse) - Method in class mosaic.sim.neuron.Neuron
Sets the master synapse object used for creating new synapse objects on the fly in the method addInput().
setOutputs(NeuronInput[]) - Method in class mosaic.sim.neuron.NeuronOutputSupport
Sets the list of currently registered NeuronInput objects that should receive the spike events sent by this object.
setPotential(Potential) - Method in class mosaic.sim.neuron.Neuron
Sets the potential object.
setQuiescentValue(float) - Static method in class mosaic.sim.neuron.ConstantPLThreshold
Set the globally constant quiescent value of the threshold.
setRate(double) - Method in class mosaic.sim.neuron.netinputs.RateCodedInputSingle
Sets the currently used firing rate.
setReceiver(Neuron) - Method in class mosaic.sim.neuron.Synapse
Sets the post-synaptic neuron that receives the forwarded spike events from this synapse.
setRelativeRefraction(PLFunction) - Static method in class mosaic.sim.neuron.ConstantPLThreshold
Set the globally constant relative refraction function.
setRelativeRefractionStartValue(float) - Static method in class mosaic.sim.neuron.ConstantPLThreshold
Set the globally constant relative refraction start value.
setResponse(PLFunction) - Static method in class mosaic.sim.neuron.ConstantPLSynapse
Used to set the globally constant shape of the synapse response function.
setSender(NeuronOutput) - Method in class mosaic.sim.neuron.Synapse
Sets the pre-synaptic NeuronOutput object that sends spike events to this synapse.
setSynchronizer(ViewSynchronizer) - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Sets the associated ViewSynchronizer.
setThreshold(Threshold) - Method in class mosaic.sim.neuron.Neuron
Sets the threshold object.
setTMax(double) - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Sets the maximum simulation time shown.
setTMin(double) - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Sets the minimum simulation time shown.
setWeight(float) - Method in class mosaic.sim.neuron.PLSynapse
Sets the synaptic weight.
setYMax(double) - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Sets the maximum vertical value shown.
setYMin(double) - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Sets the minimum vertical value shown.
SHOW_ANYTHING - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
SHOW_INTERNEURONS_FIRING - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
SHOW_NEURON_DETAILS - Static variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
SHOW_NEURON_DETAILS - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
SHOW_NEURON_DETAILS - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
SOM - class mosaic.sim.neuron.simulations.SOM.
 
SOM() - Constructor for class mosaic.sim.neuron.simulations.SOM
 
SOMLearningMethod - class mosaic.sim.neuron.simulations.SOMLearningMethod.
Note that we do NOT use weight normalization after each learning cycle here - this is closer to the biological model.
SOMLearningMethod(SOMPanel) - Constructor for class mosaic.sim.neuron.simulations.SOMLearningMethod
 
SOMPanel - class mosaic.sim.neuron.simulations.SOMPanel.
The construction in here is exactly as chapter 11 of the PHD Thesis of Berthold Ruf describes.
SOMPanel() - Constructor for class mosaic.sim.neuron.simulations.SOMPanel
 
spikeColor - Variable in class mosaic.sim.neuron.visualisation.SpikeView
The color in which the spikes are painted.
spikeEvent(NeuronOutput) - Method in class mosaic.sim.neuron.Synapse
This is the implementation of the NeuronInput interface.
spikeEvent(NeuronOutput) - Method in interface mosaic.sim.neuron.NeuronInput
Receive a simple spike event.
spikeEvent(NeuronOutput) - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput.Input
This function is the implementation of NeuronInput.spikeEvent and is called when a spike event is received.
spikeEvent(NeuronOutput) - Method in class mosaic.sim.neuron.visualisation.SpikeView
This method is the implementation of the NeuronInput interface and is used to receive spikes.
spikeEventFrom(Synapse) - Method in class mosaic.sim.neuron.Neuron
This method is called by the synapses from the inputs list whenever they receive a spike event from their sender object.
spikeEventOccured() - Method in class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
This method is called by the input objects whenever a spike event has been received.
spikeHeight - Variable in class mosaic.sim.neuron.visualisation.SpikeView
The height for the vertical lines indicating the spikes.
spikePosition - Variable in class mosaic.sim.neuron.visualisation.SpikeView
The vertical starting position for the vertical lines indicating the spikes.
spikes - Variable in class mosaic.sim.neuron.visualisation.SpikeView
The spike events that occured in the past.
SpikeView - class mosaic.sim.neuron.visualisation.SpikeView.
This class implements a scrolling spike view where spikes are simply drawn as vertical lines marking the simulation time points when the spikes occured.
SpikeView(String) - Constructor for class mosaic.sim.neuron.visualisation.SpikeView
Creates a SpikeView with the given title.
SpikeView(String, Color) - Constructor for class mosaic.sim.neuron.visualisation.SpikeView
Creates a SpikeView with the given title and painting the spikes in the given color.
SpikeViewTest1 - class mosaic.sim.neuron.examples.SpikeViewTest1.
 
SpikeViewTest1() - Constructor for class mosaic.sim.neuron.examples.SpikeViewTest1
 
SpikeViewTest1Panel - class mosaic.sim.neuron.examples.SpikeViewTest1Panel.
 
SpikeViewTest1Panel() - Constructor for class mosaic.sim.neuron.examples.SpikeViewTest1Panel
 
startInput() - Method in class mosaic.sim.neuron.netinputs.ImageInput
This method really starts the network input and should only be called after the coder has been initialized with setCoder().
startNewCycle() - Method in class mosaic.sim.neuron.simulations.SOMLearningMethod
 
state - Variable in class mosaic.sim.neuron.PLThreshold
The current state of the neuron, can be one of STATE_*.
STATE_ABSOLUTE_REFRACTION - Static variable in class mosaic.sim.neuron.PLThreshold
The absolute refraction state means that the threshold is infinite (the associated neuron can not fire in any case).
STATE_QUIESCENT - Static variable in class mosaic.sim.neuron.PLThreshold
The quiescent state means that the threshold is constant (not changing over the time as long as the associated neuron does not fire).
STATE_RELATIVE_REFRACTION - Static variable in class mosaic.sim.neuron.PLThreshold
The relative refraction state means that the threshold is higher than the quiescent value, but approaches the quiescent value.
Synapse - class mosaic.sim.neuron.Synapse.
This class represents synapses, which are the connections between neurons.
SYNAPSE_DELAYS - Static variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
SYNAPSE_DELAYS - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
Synapse.LearningMethod - interface mosaic.sim.neuron.Synapse.LearningMethod.
This interface is used for external learning algorithms that are non-local to the synapse.
Synapse(NeuronOutput, Neuron) - Constructor for class mosaic.sim.neuron.Synapse
A synapse object needs a pre-synaptic NeuronOutput object and a post-synaptic neuron.
Synapse(NeuronOutput, Neuron, Synapse.LearningMethod) - Constructor for class mosaic.sim.neuron.Synapse
Does the same as Synapse(NeuronOutput pre, Neuron post), but also sets the learning method.
synapseResponse - Variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
synapseResponse - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
synapseResponse - Variable in class mosaic.sim.neuron.simulations.CBNPanel
 
synapsesDoneInCycle - Variable in class mosaic.sim.neuron.simulations.SOMLearningMethod
 
sync - Variable in class mosaic.sim.neuron.examples.SpikeViewTest1Panel
 
sync - Variable in class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1Panel
 
sync - Variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
sync - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
sync - Variable in class mosaic.sim.neuron.simulations.CBNPanel
 
sync - Variable in class mosaic.sim.neuron.simulations.genesis.MultiCellPanel
 
synchronizer - Variable in class mosaic.sim.neuron.visualisation.ScrollingView
The ViewSynchronizer used to synchronize with other ScrollingViews.

T

T - Variable in class mosaic.sim.neuron.simulations.SOMPanel
calculated from the above constants - the length of an input / output interval
TemporalCodedInput - class mosaic.sim.neuron.netinputs.TemporalCodedInput.
This class implements a spike source using temporal coding.
TemporalCodedInput.Output - class mosaic.sim.neuron.netinputs.TemporalCodedInput.Output.
This inner class implements the spike outputs of the TemporalCodedInput class.
TemporalCodedInput.Output(TemporalCodedInput) - Constructor for class mosaic.sim.neuron.netinputs.TemporalCodedInput.Output
 
TemporalCodedInput(int, double, boolean) - Constructor for class mosaic.sim.neuron.netinputs.TemporalCodedInput
Creates a new TemporalCodedInput object and initializes the outputs.
TemporalCodedOutput - class mosaic.sim.neuron.netoutputs.TemporalCodedOutput.
This class implements a system output class.
TemporalCodedOutput.Input - class mosaic.sim.neuron.netoutputs.TemporalCodedOutput.Input.
This inner class implements the inputs of TemporalCodedOutput, i.e. the objects receiving the spike events from the system.
TemporalCodedOutput.Input(TemporalCodedOutput) - Constructor for class mosaic.sim.neuron.netoutputs.TemporalCodedOutput.Input
 
TemporalCodedOutput(int, double, boolean, double) - Constructor for class mosaic.sim.neuron.netoutputs.TemporalCodedOutput
Creates a TemporalCodedOuput object and initializes the input objects.
TemporalCodingTest1 - class mosaic.sim.neuron.examples.TemporalCodingTest1.
 
TemporalCodingTest1() - Constructor for class mosaic.sim.neuron.examples.TemporalCodingTest1
 
TemporalCodingTest1Panel - class mosaic.sim.neuron.examples.TemporalCodingTest1Panel.
 
TemporalCodingTest1Panel() - Constructor for class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
threshold - Variable in class mosaic.sim.neuron.Neuron
The inner threshold of this neuron.
threshold - Variable in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
A reference to the neuron threshold object.
Threshold - class mosaic.sim.neuron.Threshold.
This class represents a Neuron threshold.
THRESHOLD - Static variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
THRESHOLD - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 
Threshold() - Constructor for class mosaic.sim.neuron.Threshold
Creates a Threshold object.
Threshold(String) - Constructor for class mosaic.sim.neuron.Threshold
Creates a Threshold object with a name (mainly useful during debugging).
thresholdFunction - Variable in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
The currently used threshold function.
timer - Variable in class mosaic.sim.neuron.ActiveVariable
 
timer - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
title - Variable in class mosaic.sim.neuron.visualisation.ScrollingView
The title of the view.
tmax - Variable in class mosaic.sim.neuron.visualisation.ScrollingView
The maximum time (horizontal) shown in the view.
tmin - Variable in class mosaic.sim.neuron.visualisation.ScrollingView
The minimum time (horizontal) shown in the view.
toString() - Method in class mosaic.sim.neuron.PLFunction
Returns the function as string.
toString(int) - Method in class mosaic.sim.neuron.PLFunction
Returns the first numSegments linear segments of this function as string.
TRAINING_SET - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
TRAINING_SET_SIZE - Static variable in class mosaic.sim.neuron.simulations.SOMPanel
 

U

updateView() - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Updates the current view (by calling scrollToSimulationTime with the current simulation time) when no ViewSynchronizer is associated or uses to associated ViewSynchronizer to scroll all synchronized views.
USE_INTERNEURON_SYNAPSES - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
Only synapses for inhibitive feedback do not seem to be enough.
USE_INTERNEURONS - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 

V

v1 - Variable in class mosaic.sim.neuron.examples.SpikeViewTest1Panel
 
v2 - Variable in class mosaic.sim.neuron.examples.SpikeViewTest1Panel
 
variableChange(VariableChangeEvent) - Method in class mosaic.sim.neuron.Neuron
This method is called by the simulation framework whenever a variable that this object is listening on changes.
variableChange(VariableChangeEvent) - Method in class mosaic.sim.neuron.visualisation.PLNeuronInternalView
Implementation of VariableChangeListener: This method is called by the simulation framework whenever a variable that this object is listening on changes.
VectorInputCoder - interface mosaic.sim.neuron.netinputs.VectorInputCoder.
This is an interface for giving a one-dimensional vector of real numbered values to the network.
vectorLength - Static variable in class mosaic.sim.neuron.examples.TemporalCodingTest1Panel
 
VectorOutputListener - interface mosaic.sim.neuron.netoutputs.VectorOutputListener.
This interface must be implemented by objects that want to receive the real numbered, one-dimensional vectors computed by the network.
views - Variable in class mosaic.sim.neuron.examples.PLNeuronInternalViewTest1Panel
 
views - Variable in class mosaic.sim.neuron.simulations.HopfieldPanel
 
views - Variable in class mosaic.sim.neuron.simulations.SOMPanel
 
views - Variable in class mosaic.sim.neuron.simulations.CBNPanel
 
views - Variable in class mosaic.sim.neuron.simulations.genesis.MultiCellPanel
 
views - Variable in class mosaic.sim.neuron.visualisation.ViewSynchronizer
The list of views that should be synchronized.
ViewSynchronizer - class mosaic.sim.neuron.visualisation.ViewSynchronizer.
This class is able to synchronize multiple ScrollingViews so that they always show the same current simulation time.
ViewSynchronizer() - Constructor for class mosaic.sim.neuron.visualisation.ViewSynchronizer
Creates a ViewSynchronizer.

W

waitForEquilibrium - Variable in class mosaic.sim.neuron.netoutputs.OutputFilter
When true, then only those events will be forwarded that are only marginally different from the previous.
weight - Variable in class mosaic.sim.neuron.PLSynapse
The weight of the synapse, i.e. its strenght.
WEIGHT_INPUTS - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
WEIGHT_INTERNEURON_BACKWARD - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
WEIGHT_INTERNEURON_FORWARD - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
 
WEIGHT_LATERAL - Static variable in class mosaic.sim.neuron.simulations.CBNPanel
If this parameter is set to 0, the simulation gets a significant speedup.
width - Variable in class mosaic.sim.neuron.netoutputs.ImageOutput
 
worldToGraphics(double, double) - Method in class mosaic.sim.neuron.visualisation.ScrollingView
Transform world coordinates to screen graphics coordinates.

Y

ymax - Variable in class mosaic.sim.neuron.visualisation.ScrollingView
The maximum vertical value shown in the view.
ymin - Variable in class mosaic.sim.neuron.visualisation.ScrollingView
The minimum vertical value shown in the view.

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