The Physiologist's Friend Simulation API
A B C D E F G H I J L M N O P R S T U V W

A

AboutDialog - Class in ch.unizh.ini.friend.gui
The About dialog.
AboutDialog(Frame, boolean) - Constructor for class ch.unizh.ini.friend.gui.AboutDialog
Creates new form AboutDialog
AbstractAcceptsInput - Class in ch.unizh.ini.friend.simulation
Provides the infrastructure for a simulation component with many inputs.
AbstractAcceptsInput() - Constructor for class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Creates a new instance with currently no inputs.
AbstractAcceptsInput(int) - Constructor for class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Creates a new instance with currently no inputs and with the given initial capacity.
AbstractAcceptsInput(Collection) - Constructor for class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Creates a new instance with the given collection of inputs.
AbstractAcceptsInput(Object) - Constructor for class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Creates a new instance with the given input.
AbstractCell - Class in ch.unizh.ini.friend.simulation.cells
Default implementations for all cells.
AbstractCell() - Constructor for class ch.unizh.ini.friend.simulation.cells.AbstractCell
Creates a new instance with currently no inputs.
AbstractCell(int) - Constructor for class ch.unizh.ini.friend.simulation.cells.AbstractCell
Creates a new instance with currently no inputs and with the given initial capacity.
AbstractCell(Collection) - Constructor for class ch.unizh.ini.friend.simulation.cells.AbstractCell
Creates a new instance with the given collection of inputs.
AbstractCell(Object) - Constructor for class ch.unizh.ini.friend.simulation.cells.AbstractCell
Creates a new instance with the given input.
AbstractMonitor - Class in ch.unizh.ini.friend.simulation
Default implementation for a monitor.
AbstractMonitor() - Constructor for class ch.unizh.ini.friend.simulation.AbstractMonitor
Creates a new instance with currently no inputs.
AbstractMonitor(int) - Constructor for class ch.unizh.ini.friend.simulation.AbstractMonitor
Creates a new instance with currently no inputs and with the given initial capacity.
AbstractMonitor(Collection) - Constructor for class ch.unizh.ini.friend.simulation.AbstractMonitor
Creates a new instance with the given collection of inputs.
AbstractMonitor(ServesOutput) - Constructor for class ch.unizh.ini.friend.simulation.AbstractMonitor
Creates a new instance with the given input.
AbstractSimulation - Class in ch.unizh.ini.friend.simulation
Provides a few default implementations for the SimulationTask interface.
AbstractSimulation(SimulationStep) - Constructor for class ch.unizh.ini.friend.simulation.AbstractSimulation
Creates a new instance with the given simulation step.
AbstractSpikingCell - Class in ch.unizh.ini.friend.simulation.cells
Abstract class providing common methods for spiking cells.
AbstractSpikingCell() - Constructor for class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Creates a new instance with currently no inputs.
AbstractSpikingCell(int) - Constructor for class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Creates a new instance with currently no inputs and with the given initial capacity.
AbstractSpikingCell(Collection) - Constructor for class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Creates a new instance with the given collections of inputs.
AbstractSpikingCell(ServesOutput) - Constructor for class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Creates a new instance with the given input.
AbstractStimulus - Class in ch.unizh.ini.friend.stimulus
Provides default implementations for a stimulus, including it's foreground and background brightness, its shapes' container, and the transform applied to the shapes.
AbstractStimulus() - Constructor for class ch.unizh.ini.friend.stimulus.AbstractStimulus
 
AbstractSynapse - Class in ch.unizh.ini.friend.simulation.synapses
Default implementations for synapses.
AbstractSynapse() - Constructor for class ch.unizh.ini.friend.simulation.synapses.AbstractSynapse
Creates a new instance with currently no inputs.
AbstractSynapse(int) - Constructor for class ch.unizh.ini.friend.simulation.synapses.AbstractSynapse
Creates a new instance with currently no inputs and with the given initial capacity.
AbstractSynapse(Collection) - Constructor for class ch.unizh.ini.friend.simulation.synapses.AbstractSynapse
Creates a new instance with the given collection of inputs.
AbstractSynapse(Object) - Constructor for class ch.unizh.ini.friend.simulation.synapses.AbstractSynapse
Creates a new instance with the given input.
AbstractTransformable - Class in ch.unizh.ini.friend.graphics
Provides default implementations for all methods of Transformable except apply on which all other methods depend.
AbstractTransformable() - Constructor for class ch.unizh.ini.friend.graphics.AbstractTransformable
 
AcceptsInput - Interface in ch.unizh.ini.friend.simulation
Common interface to simulation components that accept inputs.
actionPerformed(ActionEvent) - Method in class ch.unizh.ini.friend.gui.FriendHelp
Shows the help system.
actionPerformed(ActionEvent) - Method in class ch.unizh.ini.friend.gui.StimulusAction.Brighten
Invoked when an action occurs.
actionPerformed(ActionEvent) - Method in class ch.unizh.ini.friend.gui.StimulusAction.BrightenBackground
Invoked when an action occurs.
actionPerformed(ActionEvent) - Method in class ch.unizh.ini.friend.gui.StimulusAction.Darken
Invoked when an action occurs.
actionPerformed(ActionEvent) - Method in class ch.unizh.ini.friend.gui.StimulusAction.DarkenBackground
Invoked when an action occurs.
actionPerformed(ActionEvent) - Method in class ch.unizh.ini.friend.gui.StimulusAction.FlipContrast
Invoked when an action occurs.
actionPerformed(ActionEvent) - Method in class ch.unizh.ini.friend.gui.StimulusAction.Rotate
Invoked when an action occurs.
actionPerformed(ActionEvent) - Method in class ch.unizh.ini.friend.simulation.TimedSimulation
Gets notified by the timer.
ActivityMeter - Class in ch.unizh.ini.friend.gui
Shows activity of monitored neuron.
ActivityMeter() - Constructor for class ch.unizh.ini.friend.gui.ActivityMeter
Creates new form ActivityMeter
activityMeter - Variable in class ch.unizh.ini.friend.gui.FriendGUI
the acitivyt meter
ADAPTATION_TIME_CONSTANT - Static variable in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
adaptation time constant of photoreceptor in seconds: 0.5f
addMarker() - Method in class ch.unizh.ini.friend.gui.TangentScreen
add a marker to the tangent screen
addPoint(float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Adds the given vertex at the end of the allready added vertices iff the resulting polygon is still convex, no three vertices co-linear and in counterclockwise order.
addPointOfIntersection(float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Adds a point to the polygon iff it isCompliant(x, y).
addPointSilently(float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Adds the given vertex at the end of the allready added vertices.
addShape(Transformable) - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
add a shape to the list of shapes making up the stimulus
addShape(Transformable) - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
add a shape to the list of shapes making up the stimulus
addSpikeListener(SpikeListener) - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
add a listener for all spikes.
addSpikeListener(SpikeListener) - Method in class ch.unizh.ini.friend.record.SimulationReporter
add a listener for all spikes.
addSpikeListener(SpikeListener) - Method in interface ch.unizh.ini.friend.record.SpikeEventSource
add a listener for all spikes.
addUpdateable(Updateable) - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
Adds an updateable to the simulation.
addUpdateable(Updateable) - Method in interface ch.unizh.ini.friend.simulation.SimulationTask
Adds an updateable to the simulation.
addUpdateable(Updateable) - Method in class ch.unizh.ini.friend.simulation.ThreadedSimulation
Adds an updateable to the simulation.
addUpdateable(Updateable) - Method in class ch.unizh.ini.friend.simulation.TimedSimulation
Adds an updateable to the simulation.
apply(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Applies the given transformation to the geometric object.
apply(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Applies the given transformation to the vertices of the polygon.
apply(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.ShapeList
Applies the given transformation to the geometric object.
apply(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Applies the given transformation to the geometric object.
apply(AffineTransform) - Method in interface ch.unizh.ini.friend.graphics.Transformable
Applies the given transformation to the geometric object.
area() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Calculates the area of this polygon.
area() - Method in interface ch.unizh.ini.friend.graphics.Intersectable
Computes the area of this geometric object.
area() - Method in class ch.unizh.ini.friend.graphics.ShapeList
Computes the total area of the shapes.
AudioOutput - Class in ch.unizh.ini.friend.simulation
Plays the output of a ServesOutput on the speaker, if the cell being played makes spikes.
AudioOutput() - Constructor for class ch.unizh.ini.friend.simulation.AudioOutput
Creates a now instance with no current input.
AudioOutput(ServesOutput) - Constructor for class ch.unizh.ini.friend.simulation.AudioOutput
Creates a new instance with the given input.
audioOutput - Variable in class ch.unizh.ini.friend.tests.AudioOutputTest
The audio output.
AudioOutputTest - Class in ch.unizh.ini.friend.tests
This class tests and demos the function of AudioOutput.
AudioOutputTest() - Constructor for class ch.unizh.ini.friend.tests.AudioOutputTest
Initializes the simulation.
averageInputs() - Method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Returns averaged inputs.

B

background - Variable in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
The background color.
BACKGROUND_BRIGHTNESS - Static variable in interface ch.unizh.ini.friend.stimulus.Stimulus
the default background brightness: 0.25f
backgroundExcitationDensity - Variable in class ch.unizh.ini.friend.stimulus.AbstractStimulus
The background excitation density.
BarStimulus - Class in ch.unizh.ini.friend.stimulus
A stimulus consisting of a single bar.
BarStimulus() - Constructor for class ch.unizh.ini.friend.stimulus.BarStimulus
Creates a new instance of BarStimulus with default size.
BarStimulus(float, float) - Constructor for class ch.unizh.ini.friend.stimulus.BarStimulus
Creates a new instance of BarStimulus with a width and height of the bar.
BarStimulus(float, float, float, float) - Constructor for class ch.unizh.ini.friend.stimulus.BarStimulus
Creates a new instance of BarStimulus with a width and height and center of the bar.
BipolarCell - Class in ch.unizh.ini.friend.simulation.cells
Implements a bipolar cell.
BipolarCell() - Constructor for class ch.unizh.ini.friend.simulation.cells.BipolarCell
Creates a new instance with currently no inputs.
BipolarCell(Collection) - Constructor for class ch.unizh.ini.friend.simulation.cells.BipolarCell
Creates a new instance with the given collections of inputs and weights.
brighten - Static variable in class ch.unizh.ini.friend.gui.StimulusAction
name of action that can happen to Stimulus
BRIGHTEN_BACKGROUND - Static variable in interface ch.unizh.ini.friend.stimulus.Stimulus
a command that a stimulus will accept.
BRIGHTEN_FOREGROUND - Static variable in interface ch.unizh.ini.friend.stimulus.Stimulus
a command that a stimulus will accept.
brightenBackground - Static variable in class ch.unizh.ini.friend.gui.StimulusAction
name of action that can happen to Stimulus
brightenBackground() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
make background brighter
brightenBackground() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
brightenBackground() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
make background brighter
brightenForeground() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
make foreground brighter
brightenForeground() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
brightenForeground() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
make foreground brighter
BRIGHTNESS_CHANGE_RATIO - Static variable in class ch.unizh.ini.friend.stimulus.AbstractStimulus
factor to change brightness of foreground or background by for AbstractStimulus.brightenForeground(), etc.
Browser - Class in ch.unizh.ini.friend.browser
from http://forum.java.sun.com/thread.jsp?
Browser() - Constructor for class ch.unizh.ini.friend.browser.Browser
 
BrowserControl - Class in ch.unizh.ini.friend.browser
A simple, static class to display a URL in the system browser.
BrowserControl() - Constructor for class ch.unizh.ini.friend.browser.BrowserControl
 
BrowserLauncher - Class in ch.unizh.ini.friend.browser
BrowserLauncher is a class that provides one static method, openURL, which opens the default web browser for the current user of the system to the given URL.
BufferedTransform - Interface in ch.unizh.ini.friend.graphics
Allows for uniform access to Transformable objects that want/need to buffer the transformations applied to them.

C

centerAndSetVisible(int, int) - Method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
ch.unizh.ini.friend - package ch.unizh.ini.friend
The top level package.
ch.unizh.ini.friend.browser - package ch.unizh.ini.friend.browser
The classes in this package enable browsing to a web page.
ch.unizh.ini.friend.graphics - package ch.unizh.ini.friend.graphics
Graphics objects and interfaces.
ch.unizh.ini.friend.gui - package ch.unizh.ini.friend.gui
GUI objects, including the main GUI, the tangent screen, and the dialogs.
ch.unizh.ini.friend.record - package ch.unizh.ini.friend.record
Spike recording using the microphone input with SpikeReporter and SpikeEvent generation from these spikes.
ch.unizh.ini.friend.simulation - package ch.unizh.ini.friend.simulation
Code that simulates the cells.
ch.unizh.ini.friend.simulation.cells - package ch.unizh.ini.friend.simulation.cells
This package contains specific cell types, which are subclasses of AbstractCell.
ch.unizh.ini.friend.simulation.filter - package ch.unizh.ini.friend.simulation.filter
Filters used in the simulation.
ch.unizh.ini.friend.simulation.synapses - package ch.unizh.ini.friend.simulation.synapses
This package contains specific synapse types, which are subclasses of AbstractSynapse.
ch.unizh.ini.friend.stimulus - package ch.unizh.ini.friend.stimulus
The stimuli.
ch.unizh.ini.friend.tests - package ch.unizh.ini.friend.tests
Miscellaneous test classes.
ch.unizh.ini.friend.topology - package ch.unizh.ini.friend.topology
Classes that help assign a topology to the cells.
chooser - Variable in class ch.unizh.ini.friend.gui.ColorChooser
Color chooser used to show the dialog
clearMarkers() - Method in class ch.unizh.ini.friend.gui.TangentScreen
clear all markers
clearShapes() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
clear the list of shapes
clearShapes() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
clear the list of shapes
clearSpikeImage() - Method in class ch.unizh.ini.friend.gui.TangentScreen
clears recorded spikes and markers
clearSpikeListeners() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
remove all listeners
clearSpikeListeners() - Method in class ch.unizh.ini.friend.record.SimulationReporter
remove all listeners
clearSpikeListeners() - Method in interface ch.unizh.ini.friend.record.SpikeEventSource
remove all listeners
clone() - Method in class ch.unizh.ini.friend.graphics.AbstractTransformable
Clones this geometric object.
clone() - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Clones this geometric object.
clone() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Clones the polygon by allocating a new polygon and copying the array of coordinates.
clone() - Method in class ch.unizh.ini.friend.graphics.ShapeList
clones this list of shapes, including cloning of the members of the list
clone() - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Clones this geometric object.
clone() - Method in interface ch.unizh.ini.friend.graphics.Transformable
Clones this geometric object.
clone() - Method in class ch.unizh.ini.friend.simulation.SimpleOutputMonitor.Deliverable
Clone this.
clone() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
clones the foreground color, background color, and the tranformed ShapeList
clone() - Method in class ch.unizh.ini.friend.stimulus.ConcreteStimulus
clones the foreground density, background density, and the transformed ShapeList
cloneObject(Object) - Static method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Returns a deep-clone of the given object.
close() - Method in class ch.unizh.ini.friend.record.SpikeLogger
closes the file.
ColorChooser - Class in ch.unizh.ini.friend.gui
Adaptor for JColorChooser.
ColorChooser() - Constructor for class ch.unizh.ini.friend.gui.ColorChooser
Create a new instance.
colorChooser - Variable in class ch.unizh.ini.friend.gui.TangentScreen
Color-chooser to select the forground and background color of the (color) stimulus.
ColorPhotoreceptor - Class in ch.unizh.ini.friend.simulation.cells
A color-selective photoreceptor.
ColorPhotoreceptor(ConvexPolygon, ColorStimulus, int) - Constructor for class ch.unizh.ini.friend.simulation.cells.ColorPhotoreceptor
Creates a new color-selective photoreceptor.
ColorStimulus - Interface in ch.unizh.ini.friend.stimulus
A color stimulus has a foreground and background color.
ColorStimulusImpl - Class in ch.unizh.ini.friend.stimulus
Default implementation of the ColorStimulus interface.
ColorStimulusImpl() - Constructor for class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
Creates a new color stimulus.
compute(float) - Method in class ch.unizh.ini.friend.gui.StatusPanel
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.record.SimulationReporter
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.simulation.AudioOutput
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.simulation.cells.BipolarCell
Computes the new state of this bipolar cell.
compute(float) - Method in class ch.unizh.ini.friend.simulation.cells.HorizontalCell
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
Computes the new state of this photoreceptor.
compute(float) - Method in class ch.unizh.ini.friend.simulation.cells.PoissonSoma
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.simulation.SimpleOutputMonitor
Computes the new state of this component of the simulation.
compute(float) - Method in interface ch.unizh.ini.friend.simulation.Updateable
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.tests.OscillatingOutput
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.tests.OutputPrinter
Computes the new state of this component of the simulation.
compute(float) - Method in class ch.unizh.ini.friend.tests.TimePrinter
Computes the new state of this component of the simulation.
ConcreteSeparateTransforms - Class in ch.unizh.ini.friend.graphics
Provides the facilities to keep a geometric object in its original state while buffering applied transformations.
ConcreteSeparateTransforms(Transformable) - Constructor for class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Creates a new instance with the given geometric object
ConcreteStimulus - Class in ch.unizh.ini.friend.stimulus
Provides a generic implementation of a stimulus.
ConcreteStimulus() - Constructor for class ch.unizh.ini.friend.stimulus.ConcreteStimulus
creates a new instance of ConcreteStimulus with a null list of shapes.
ConcreteStimulus(ShapeList) - Constructor for class ch.unizh.ini.friend.stimulus.ConcreteStimulus
Creates a new instance with the given shapes.
ConcreteStimulus(Transformable) - Constructor for class ch.unizh.ini.friend.stimulus.ConcreteStimulus
create a ConcreteStimulus with a single Transformable shape.
connectOneToAll(Object, Collection) - Static method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Registers the given Object as an additional input of each of the AcceptInputs from the given collection.
connectOneToOne(Collection, Collection) - Static method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Registers the i-th Object from the first as an additional input of the i-th AcceptInput from the second given collection.
contains(Rectangle2D) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether the given rectangle is completely contained by this instance of ConvexPolygon.
contains(Point2D) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether the given point is contained by this instance of ConvexPolygon.
contains(double, double) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether the given point (x, y) is contained by this instance of ConvexPolygon.
contains(double, double, double, double) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether the given rectangle is completely contained by this instance of ConvexPolygon.
ConvexPolygon - Class in ch.unizh.ini.friend.graphics
This class implements the notion of a convex polygon.
ConvexPolygon() - Constructor for class ch.unizh.ini.friend.graphics.ConvexPolygon
Initializes xpoints and ypoints to three elements.
ConvexPolygon(int) - Constructor for class ch.unizh.ini.friend.graphics.ConvexPolygon
Initializes xpoints and ypoints to n elements.
ConvexPolygon(float[], int) - Constructor for class ch.unizh.ini.friend.graphics.ConvexPolygon
Ensures that the represented polygon is convex, no three vertices are co-linear and the vertices are in counterclockwise order.
ConvexPolygonIterator - Class in ch.unizh.ini.friend.graphics
ConvexPolygonIterator implements the PathIterator interface for ConvexPolygon.
ConvexPolygonIterator(ConvexPolygon) - Constructor for class ch.unizh.ini.friend.graphics.ConvexPolygonIterator
Constructor yielding an instance that iterates along the given polygon.
ConvexPolygonTest - Class in ch.unizh.ini.friend.tests
This class tests and demos the function of ConvexPolygon.
ConvexPolygonTest() - Constructor for class ch.unizh.ini.friend.tests.ConvexPolygonTest
Initializes the object.
currentSegment(double[]) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygonIterator
Fills the array with coordinates and returns the type of the current segment.
currentSegment(float[]) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygonIterator
Fills the array with coordinates and returns the type of the current segment.
CurrentTimeMillisBenchMark - Class in ch.unizh.ini.friend.tests
 
CurrentTimeMillisBenchMark() - Constructor for class ch.unizh.ini.friend.tests.CurrentTimeMillisBenchMark
Creates a new instance of CurrentTimeMillisBenchMark

D

darken - Static variable in class ch.unizh.ini.friend.gui.StimulusAction
name of action that can happen to Stimulus
DARKEN_BACKGROUND - Static variable in interface ch.unizh.ini.friend.stimulus.Stimulus
a command that a stimulus will accept.
DARKEN_FOREGROUND - Static variable in interface ch.unizh.ini.friend.stimulus.Stimulus
a command that a stimulus will accept.
darkenBackground - Static variable in class ch.unizh.ini.friend.gui.StimulusAction
name of action that can happen to Stimulus
darkenBackground() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
make background darker
darkenBackground() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
darkenBackground() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
make background darker
darkenForeground() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
make foreground darker
darkenForeground() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
darkenForeground() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
make foreground darker
DEFAULT_WEIGHT - Static variable in class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse
The default weight with which the input will be multiplied.
delay - Variable in class ch.unizh.ini.friend.gui.SimulationProperties
 
delay - Variable in class ch.unizh.ini.friend.simulation.AbstractSimulation
delay in ms between thread simulation update cycles
DELAY - Static variable in class ch.unizh.ini.friend.simulation.SimulationSetupFactory
default timer delay in ms: 5
delay - Static variable in class ch.unizh.ini.friend.simulation.SimulationSetupFactory
The delay between the timer events in milliseconds.
deliverable - Variable in class ch.unizh.ini.friend.simulation.SimpleOutputMonitor
The prototype of the deliverable.
DIAMETER - Static variable in class ch.unizh.ini.friend.stimulus.SpotStimulus
default diameter of bar: 1.0f
dir - Variable in class ch.unizh.ini.friend.topology.HexDirection
 
displayURL(String) - Static method in class ch.unizh.ini.friend.browser.BrowserControl
Display a file in the system browser.
doIntersect(float, float, float, float, float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether the two given lines intersect.
dotProd(float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Computes the dot product of the two given vectors.

E

E - Static variable in class ch.unizh.ini.friend.topology.HexDirection
a hex direction
EdgeStimulus - Class in ch.unizh.ini.friend.stimulus
A stimulus consisting of an edge, with reference (mouse) position centered along edge of the bar.
EdgeStimulus() - Constructor for class ch.unizh.ini.friend.stimulus.EdgeStimulus
Creates a new instance of EdgeStimulus with default parameters.
ExceptionDialog - Class in ch.unizh.ini.friend.gui
Shows an Exception in a dialog.
ExceptionDialog(JFrame, boolean) - Constructor for class ch.unizh.ini.friend.gui.ExceptionDialog
Creates new form ExceptionDialog
ExceptionDialog(JFrame, boolean, Exception, String) - Constructor for class ch.unizh.ini.friend.gui.ExceptionDialog
construct a new ExceptionDialog.
excitation() - Method in class ch.unizh.ini.friend.simulation.cells.ColorPhotoreceptor
Overridden to support color-specific excitation.
excitation() - Method in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
Calculate the exitation of the given object (photoreceptor) from the stimulus.
expand() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
expand by ratio Stimulus.RESIZE_RATIO in both dimensions
expand() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
expand by ratio Stimulus.RESIZE_RATIO in both dimensions

F

factory(String) - Static method in class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Returns an instance of a subclass of AbstractSpikingCell given by the name.
factory(String, Collection, Collection) - Static method in class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Returns an instance of a subclass of AbstractSpikingCell given by the name with the given collections of inputs and weights.
factory(String, int) - Static method in class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Returns an instance of a subclass of AbstractSpikingCell given by the name with currently no inputs and with the given initial capacity.
factory(String, ServesOutput, float) - Static method in class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Returns an instance of a subclass of AbstractSpikingCell given by the name with the given input and weight.
fatten() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
fatten by ratio Stimulus.RESIZE_RATIO
fatten() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
fatten by ratio Stimulus.RESIZE_RATIO
Filter - Interface in ch.unizh.ini.friend.simulation.filter
Common interface for filters.
filter(float, float) - Method in interface ch.unizh.ini.friend.simulation.filter.Filter
Returns the output of the filter based on the given input and the passed time.
filter(float, float) - Method in class ch.unizh.ini.friend.simulation.filter.HighPassFilter
Returns the output of the filter based on the given input and the passed time.
filter(float, float) - Method in class ch.unizh.ini.friend.simulation.filter.LowPassFilter
Returns the output of the filter based on the given input and the passed time.
finalize() - Method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
finalize() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
Release the line on finialization.
finalize() - Method in class ch.unizh.ini.friend.simulation.AudioOutput
Release the line on finialization.
findCenterCell(Collection) - Static method in class ch.unizh.ini.friend.topology.RetinotopicLocation
static helper that takes a list of cells, each Retinotopic, and finds the geometrically-center one.
findCorresponding(Retinotopic, Collection) - Static method in class ch.unizh.ini.friend.topology.RetinotopicLocation
finds the corresponding cell in another layer at this same retinotopic location This method is slow--not for runtime use.
findNearestNeighbor(Retinotopic, Collection, HexDirection) - Static method in class ch.unizh.ini.friend.topology.RetinotopicLocation
finds the nearst neighboring cell to me, in collection all, in direction dir.
flipContrast - Static variable in class ch.unizh.ini.friend.gui.StimulusAction
name of action that can happen to Stimulus
flipContrast() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
swap brightness of foreground and background
flipContrast() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
flipContrast() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
swap brightness of foreground and background
foreground - Variable in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
The foreground color.
FOREGROUND_BRIGHTNESS - Static variable in interface ch.unizh.ini.friend.stimulus.Stimulus
the default foreground brightness: 0.75f
foregroundExcitationDensity - Variable in class ch.unizh.ini.friend.stimulus.AbstractStimulus
The foreground excitation density.
FRAME_SCREEN_FRACTION - Static variable in class ch.unizh.ini.friend.gui.FriendGUI
fraction of screen horizontal occupied by Frame
FriendGUI - Class in ch.unizh.ini.friend.gui
Main GUI.
FriendGUI(SimulationSetup) - Constructor for class ch.unizh.ini.friend.gui.FriendGUI
Creates new form FriendGUI.
FriendGUI() - Constructor for class ch.unizh.ini.friend.gui.FriendGUI
Creates new form FriendGUI.
FriendHelp - Class in ch.unizh.ini.friend.gui
Shows help system.
FriendHelp(JFrame) - Constructor for class ch.unizh.ini.friend.gui.FriendHelp
Creates a new instance of FirendHelp.

G

gain - Variable in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
The gain of the high-pass output.
GanglionCell - Class in ch.unizh.ini.friend.simulation.cells
Represents a retinal ganglion cell.
GanglionCell() - Constructor for class ch.unizh.ini.friend.simulation.cells.GanglionCell
Creates a new instance of GanglionCell
GanglionCell(Collection) - Constructor for class ch.unizh.ini.friend.simulation.cells.GanglionCell
Creates a new instance with the given collections of inputs.
GanglionCell(ServesOutput) - Constructor for class ch.unizh.ini.friend.simulation.cells.GanglionCell
Creates a new instance with the given input.
geometry - Variable in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Transformable against which transformations are buffered
get() - Method in class ch.unizh.ini.friend.topology.HexDirection
gets the direction as a int, 0-5 CCW from east, non negative.
getAngle() - Method in class ch.unizh.ini.friend.topology.HexDirection
get angle in radians.
getArrayListInstance(ArrayList, float, ServesOutput, float) - Static method in class ch.unizh.ini.friend.simulation.cells.BipolarCell
Returns a list of BipolarCell with the given input weights.
getArrayListInstance(ArrayList) - Static method in class ch.unizh.ini.friend.simulation.cells.GanglionCell
Returns a list of GanglionCell with the default input weight and one input from the given list of inputs.
getArrayListInstance(ArrayList, ArrayList) - Static method in class ch.unizh.ini.friend.simulation.cells.GanglionCell
Returns a list of GanglionCells with positive/negative default input weight and one input from the given two list of inputs.
getArrayListInstance(ArrayList[], float[]) - Static method in class ch.unizh.ini.friend.simulation.cells.GanglionCell
Returns a list of GanglionCells with the given input weight and one input from the given list of inputs (for each array index).
getBackground() - Method in interface ch.unizh.ini.friend.stimulus.ColorStimulus
Returns the background excitation color of the stimulus.
getBackground() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
getBackgroundExcitationDensity() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
Returns the background excitation density of the stimulus.
getBackgroundExcitationDensity() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
getBackgroundExcitationDensity() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
Returns the background excitation density of the stimulus.
getBounds() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Computes a bounding box around this instance of ConvexPolygon.
getBounds2D() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Computes a bounding box around this instance of ConvexPolygon.
getCenter() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Computes the center of this ConvexPolygon.
getCollectionInstance(AcceptsInput, int) - Static method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Returns a collection of the given number of clones of the given object.
getColor() - Method in class ch.unizh.ini.friend.graphics.LMSColor
Returns the color in the sRGB color space.
getColorSimulationSetup() - Static method in class ch.unizh.ini.friend.simulation.SimulationSetupFactory
Creates a simulation setup for color vision cells.
getComplexCellInstance(String, Collection, Collection, Collection, Retinotopic, HexDirection) - Static method in class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Returns a new instance of ComplexCell.
getDelay() - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
 
getDelay() - Method in interface ch.unizh.ini.friend.simulation.SimulationTask
 
getDSSimpleCellInstance(String, Collection, Collection, Collection, Retinotopic, HexDirection) - Static method in class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Returns a new instance of a direction-selective simple cell, composed with input from two simple cells, one effectively shunting the input from the other.
getEvenSimpleCellInstance(String, Collection, Collection, Retinotopic, HexDirection) - Static method in class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Returns a new instance of a even-type simple cell.
getFallingArrayListInstance(ArrayList, ServesOutput) - Static method in class ch.unizh.ini.friend.simulation.cells.BipolarCell
Returns a list of BipolarCell with input weights for a falling output.
getForeground() - Method in interface ch.unizh.ini.friend.stimulus.ColorStimulus
Returns the foreground excitation color of the stimulus.
getForeground() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
getForegroundExcitationDensity() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
Returns the foreground excitation density of the stimulus.
getForegroundExcitationDensity() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
getForegroundExcitationDensity() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
Returns the foreground excitation density of the stimulus.
getGeometry() - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Returns the original geometric object.
getGeometry() - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Returns the original geometric object.
getGeometry() - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Returns the original geometric object.
getGradedOutput() - Method in class ch.unizh.ini.friend.simulation.cells.BipolarCell
returns the graded output from the cell
getGradedOutput() - Method in interface ch.unizh.ini.friend.simulation.cells.GradedCell
returns the graded output from the cell
getGradedOutput() - Method in class ch.unizh.ini.friend.simulation.cells.HorizontalCell
returns the graded output from the cell
getGradedOutput() - Method in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
returns the graded output from the cell
getHexagonalArrayListInstance(int, float, float, Stimulus, Collection) - Static method in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
Returns a hexagonal arranged list of hexagonal photoreceptors.
getHexagonalArrayLists(int, float, float, ColorStimulus, Collection) - Static method in class ch.unizh.ini.friend.simulation.cells.ColorPhotoreceptor
This method does almost the same as Photoreceptor#getHexagonalArrayListInstance.
getHystersis() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
 
getInput() - Method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Returns the first (if any) input.
getInput() - Method in class ch.unizh.ini.friend.simulation.AbstractMonitor
Returns the first (if any) input.
getInput() - Method in interface ch.unizh.ini.friend.simulation.AcceptsInput
Returns the first (if any) input.
getInputs() - Method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Returns a collection of all inputs to this simulation component.
getInputs() - Method in class ch.unizh.ini.friend.simulation.AbstractMonitor
Returns a collection of all inputs to this simulation component.
getInputs() - Method in interface ch.unizh.ini.friend.simulation.AcceptsInput
Returns a collection of all inputs to this simulation component.
getL() - Method in class ch.unizh.ini.friend.graphics.LMSColor
Returns the long-wavelength (red) component.
getLeakTime() - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Getter for property leakTime.
getLMSBackground() - Method in interface ch.unizh.ini.friend.stimulus.ColorStimulus
Returns the background excitation color of the stimulus.
getLMSBackground() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
getLMSForeground() - Method in interface ch.unizh.ini.friend.stimulus.ColorStimulus
Returns the foreground excitation color of the stimulus.
getLMSForeground() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
getM() - Method in class ch.unizh.ini.friend.graphics.LMSColor
Returns the middle-wavelength (green) component.
getMaxRate() - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Getter for property maxRate.
getMonitor(String) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
returns a particlar monitor by its key.
getMonitoredCell() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
returns the monitored cell
getMonitors() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Returns the monitors that are currently registered.
getName() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
 
getNGonInstance(float, float, float, int) - Static method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Creates an instance of ConvexPolygon initalizing it as a regular n-gon with the given radius of the enclosing circle and the given center.
getNGonInstance(float, int) - Static method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Creates an instance of ConvexPolygon initalizing it as a regular n-gon with the given radius of the enclosing circle and the center at (0,0).
getNGonInstance(int) - Static method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Creates an instance of ConvexPolygon initalizing it as a regular n-gon with radius 1.0 of the enclosing circle and the center at (0,0).
getNumberOfIterationsPerStep() - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
 
getNumberOfIterationsPerStep() - Method in class ch.unizh.ini.friend.simulation.SimulationStep
 
getNumberOfIterationsPerStep() - Method in interface ch.unizh.ini.friend.simulation.SimulationTask
 
getOddSimpleCellInstance(String, Collection, Collection, Retinotopic, HexDirection) - Static method in class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell
Returns a new instance of a odd-type simple cell.
getOffGanglions() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Return the retinal ganglion off-type cells
getOnGanglions() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Return the retinal ganglion on-type cells
getOutputCell(String) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
returns a particlar output cell by its key.
getOutputCells() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Returns the cells that can be monitored (listened to).
getParent() - Method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
getPathIterator(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Returns a PathIterator for this polygon, applying the transform if not null.
getPathIterator(AffineTransform, double) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Returns a PathIterator for this polygon, applying the transform if not null.
getPotasiumReversal() - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
 
getReceptorShapes() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Returns the shapes of the photoreceptors.
getRectangleInstance(float, float, float, float) - Static method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Creates an instance of ConvexPolygon initalizing it as a rectangle.
getRetinotopicLocation() - Method in class ch.unizh.ini.friend.simulation.cells.BipolarCell
return the RetinotopicLocaton of the cell
getRetinotopicLocation() - Method in class ch.unizh.ini.friend.simulation.cells.GanglionCell
return the RetinotopicLocaton of the cell
getRetinotopicLocation() - Method in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
return the RetinotopicLocaton of the cell
getRetinotopicLocation() - Method in interface ch.unizh.ini.friend.topology.Retinotopic
return the RetinotopicLocaton of the cell
getRisingArrayListInstance(ArrayList, ServesOutput) - Static method in class ch.unizh.ini.friend.simulation.cells.BipolarCell
Returns a list of BipolarCell with input weights for a rising output.
getRotation() - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Returns the buffered rotation.
getRotation() - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Returns the buffered rotation.
getRotation() - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Returns the buffered rotation.
getS() - Method in class ch.unizh.ini.friend.graphics.LMSColor
Returns the short-wavelength (blue) component.
getScaling() - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Returns the buffered scaling.
getScaling() - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Returns the buffered scaling.
getScaling() - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Returns the buffered scaling.
getShapes() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
return list of original (untransformed) shapes making up this stimulus
getShapes() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
return list of untransformed shapes making up this stimulus
getSimulatedCells() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Returns the cells that are simulated
getSimulation() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Returns the current simulation instance.
getSimulationSetup() - Method in class ch.unizh.ini.friend.gui.FriendGUI
 
getSimulationSetup() - Static method in class ch.unizh.ini.friend.simulation.SimulationSetupFactory
Creates the monchrome simulation setup.
getSimulationTask(SimulationStep) - Static method in class ch.unizh.ini.friend.simulation.SimulationSetupFactory
Creates a simulation task.
getSpikeListeners() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
 
getSpikeListeners() - Method in class ch.unizh.ini.friend.record.SimulationReporter
 
getSpikeListeners() - Method in interface ch.unizh.ini.friend.record.SpikeEventSource
 
getSpikeMemoryDepth() - Method in class ch.unizh.ini.friend.gui.TangentScreen
 
getSpikeRateMeasurementWindow() - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Getter for property spikeRateMeasurementWindow.
getStartingCellName() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Gets the starting cell name.
getStep() - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
Returns the simulation step instance.
getStep() - Method in interface ch.unizh.ini.friend.simulation.SimulationTask
Returns the simulation step instance.
getStimulus() - Method in class ch.unizh.ini.friend.gui.TangentScreen
get the displayed stimulus
getStimulus() - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Returns the current stimulus instance.
getTau() - Method in class ch.unizh.ini.friend.simulation.cells.HorizontalCell
Getter for property tau.
getTau() - Method in class ch.unizh.ini.friend.simulation.filter.HighPassFilter
Getter for property tau.
getTau() - Method in class ch.unizh.ini.friend.simulation.filter.LowPassFilter
Getter for property tau.
getThreshold() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
 
getThreshold() - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Getter for property threshold.
getTime() - Method in class ch.unizh.ini.friend.record.SpikeEvent
 
getTransformation() - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Returns the buffered generic transformation.
getTransformation() - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Returns the buffered generic transformation.
getTransformation() - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Returns the buffered generic transformation.
getTransformed() - Method in interface ch.unizh.ini.friend.graphics.BufferedTransform
Returns a Transformable with the buffered tranformation applied.
getTransformed() - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Returns the transformed geometric object.
getTransformed() - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Returns the transformed geometric object.
getTransformed() - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Returns a Transformable with the buffered tranformation applied.
getTransformedShapes() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
return transformed shapes.
getTransformedShapes() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
get list of transformed shapes.
getTransforms() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
return transforms operating on this stimulus
getTransforms() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
return transforms on this stimulus.
getTranslation() - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Returns the buffered translation.
getTranslation() - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Returns the buffered translation.
getTranslation() - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Returns the buffered translation.
getUpdateables() - Method in class ch.unizh.ini.friend.simulation.SimulationStep
Returns the collection of Updateable.
getWeight() - Method in class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse
Returns the weight with which the input will be multiplied.
getWindingRule() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygonIterator
Returns the winding rule for determining the interior of the path.
GifViewerWindow - Class in ch.unizh.ini.friend.gui
 
GifViewerWindow(Image) - Constructor for class ch.unizh.ini.friend.gui.GifViewerWindow
 
GifViewerWindow(Applet, String) - Constructor for class ch.unizh.ini.friend.gui.GifViewerWindow
 
GifViewerWindow(String) - Constructor for class ch.unizh.ini.friend.gui.GifViewerWindow
 
GradedCell - Interface in ch.unizh.ini.friend.simulation.cells
A cell that produced a graded output.
GratingStimulus - Class in ch.unizh.ini.friend.stimulus
A grating stimulus, which consists of a set of BarStimulus with a specified spatial period.
GratingStimulus() - Constructor for class ch.unizh.ini.friend.stimulus.GratingStimulus
Creates a new instance of GratingStimulus with default spatial period GratingStimulus.PERIOD.
GratingStimulus(float) - Constructor for class ch.unizh.ini.friend.stimulus.GratingStimulus
Creates a new instance of GratingStimulus with specified spatial period.

H

hb - Variable in class ch.unizh.ini.friend.gui.FriendHelp
the HelpBroker
HEIGHT - Static variable in class ch.unizh.ini.friend.stimulus.BarStimulus
default height of bar: 0.5f
HelpDialog - Class in ch.unizh.ini.friend.gui
Deprecated. Replaced by the help system
HelpDialog(Frame, boolean) - Constructor for class ch.unizh.ini.friend.gui.HelpDialog
Deprecated. Creates new form JDialog
HELPSET_URL - Static variable in class ch.unizh.ini.friend.gui.FriendHelp
relative URL of help set file
HexDirection - Class in ch.unizh.ini.friend.topology
Represents a topological direction in the hexagonal arrangement of cells in the retina.
HexDirection() - Constructor for class ch.unizh.ini.friend.topology.HexDirection
Creates a new instance of Direction with direction set to -1.
HexDirection(int) - Constructor for class ch.unizh.ini.friend.topology.HexDirection
Creates new instance with given direction.
hideGifFile(GifViewerWindow) - Static method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
highPass - Variable in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
A high-pass filter that is used to compute the transient gain.
HighPassFilter - Class in ch.unizh.ini.friend.simulation.filter
A high-pass filter.
HighPassFilter(float, float) - Constructor for class ch.unizh.ini.friend.simulation.filter.HighPassFilter
Creates a new instance of HighPassFilter with the given time constant and the given last output of the corresponding low-pass filter.
HorizontalCell - Class in ch.unizh.ini.friend.simulation.cells
Cell that averages the inputs and outputs the lowpass-filtered value.
HorizontalCell() - Constructor for class ch.unizh.ini.friend.simulation.cells.HorizontalCell
Creates a new instance with currently no inputs.
HorizontalCell(int) - Constructor for class ch.unizh.ini.friend.simulation.cells.HorizontalCell
Creates a new instance with currently no inputs and with the given initial capacity.
HorizontalCell(Collection) - Constructor for class ch.unizh.ini.friend.simulation.cells.HorizontalCell
Creates a new instance with the given collections of inputs and weights.
hs - Variable in class ch.unizh.ini.friend.gui.FriendHelp
the HelpSet

I

init() - Method in class ch.unizh.ini.friend.simulation.SimulationStep
(Re-)Initializes this instance at the begin of the simulation.
INPUT_WEIGHT - Static variable in class ch.unizh.ini.friend.simulation.cells.BipolarCell
The default input weight.
INPUT_WEIGHT - Static variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
The default input weight.
inputs - Variable in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
The input components for this one.
IntegrateFireCell - Class in ch.unizh.ini.friend.simulation.cells
Implementation of a spiking cell with an integrate-and-fire spike mechanism.
IntegrateFireCell() - Constructor for class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Creates a new instance with currently no inputs.
IntegrateFireCell(int) - Constructor for class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Creates a new instance with currently no inputs and with the given initial capacity.
IntegrateFireCell(Collection) - Constructor for class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Creates a new instance with the given collections of inputs.
IntegrateFireCell(ServesOutput) - Constructor for class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Creates a new instance with the given input.
integrateInputs() - Method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Returns summed inputs.
integrationPotential - Variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
The currently integrated membrane potential.
intersect(float, float, float, float, float, float, float, float, float[]) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Intersects the two given lines and stores the intersection point in the given array.
intersect(Intersectable) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Intersects this convex polygon with n vertices with the given convex polygon with m vertices and returns the intersection which is again a convex polygon with at most n+m vertices.
intersect(Intersectable) - Method in interface ch.unizh.ini.friend.graphics.Intersectable
Computes the area of intersection between this object and the given other object.
intersect(Intersectable) - Method in class ch.unizh.ini.friend.graphics.ShapeList
Computes the area of intersection between this and the given other object.
Intersectable - Interface in ch.unizh.ini.friend.graphics
Declares the interface for a Transformable that can be intersected with another shape.
intersects(Rectangle2D) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether the given rectangle intersects with this polygon.
intersects(double, double, double, double) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether the given rectangle intersects with this polygon.
isCellNameVisible() - Method in class ch.unizh.ini.friend.gui.StatusPanel
is cell name visible?
isColorVersionEnabled() - Method in class ch.unizh.ini.friend.Main
is the color version of PhysioFriend running
isCompliant() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether the represented polygon is convex, has no three co-linear vertices and the vertices are counterclockwise ordered.
isCompliant(float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether the polygon obtained by adding the given point (x,y) at the end would still be convex, have no three co-linear vertices and have the vertices in counterclockwise order.
isDone() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygonIterator
Returns true iff the end of the iteration is reached.
isInHalfPlane(float, float, float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether (x,y) is on the left of the straight line defined by (x1,y1) and (x2, y2) (looking from the first to the second), including the line itself.
isInPolygon(float, float, ConvexPolygon) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether a given point is in the given polygon.
isMuted() - Method in class ch.unizh.ini.friend.simulation.AudioOutput
is audio muted?
isOn() - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
Returns true if the simulation is running.
isPhotoreceptorsShown() - Method in class ch.unizh.ini.friend.gui.TangentScreen
are photoreceptor locations being shown?
isReporting() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
 
isReporting() - Method in class ch.unizh.ini.friend.record.SimulationReporter
 
isReporting() - Method in interface ch.unizh.ini.friend.record.SpikeReporter
 
isSpike() - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
is the cell making a spike now?
isSpike() - Method in class ch.unizh.ini.friend.simulation.cells.PoissonSoma
Is the cell making a spike now?
isSpike() - Method in interface ch.unizh.ini.friend.simulation.cells.SpikingCell
is the cell making a spike now?
isSpikeFadeEnabled() - Method in class ch.unizh.ini.friend.gui.TangentScreen
 
isSpikeFillEnabled() - Method in class ch.unizh.ini.friend.gui.TangentScreen
 
isStimulusControlEnabled() - Method in class ch.unizh.ini.friend.gui.TangentScreen
is mouse/keyboard control of stimulus enabled?
isStrictlyInHalfPlane(float, float, float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether (x,y) is on the left of the straight line defined by (x1,y1) and (x2, y2) (looking from the first to the second), excluding the line itself.
isVisible() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
is stimulus hidden by its foreground brightness being set to the background?
isVisible() - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
isVisible() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
is stimulus hidden by its foreground brightness being set to the background?
isWindowsPlatform() - Static method in class ch.unizh.ini.friend.browser.BrowserControl
Try to determine whether this application is running under Windows or some other platform by examing the "os.name" property.

J

jitter() - Method in class ch.unizh.ini.friend.record.SpikePlotter
 

L

L_CONE - Static variable in class ch.unizh.ini.friend.simulation.cells.ColorPhotoreceptor
Red selective (L cone) photoreceptor type.
lastForeground - Variable in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
leakTime - Variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
The leak time constant in seconds.
lengthen() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
lengthen by ratio Stimulus.RESIZE_RATIO
lengthen() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
lengthen by ratio Stimulus.RESIZE_RATIO
LMSColor - Class in ch.unizh.ini.friend.graphics
Represents a color in the LMS color space.
LMSColor(Color) - Constructor for class ch.unizh.ini.friend.graphics.LMSColor
Creates a new color instance in the LMS color space.
LMSColorPreviewPanel - Class in ch.unizh.ini.friend.gui
This panel can be used to replace the default preview panel of JColorChooser: JColorChooser chooser = new JColorChooser(); JPanel preview = new LMSColorPreviewPanel(); chooser.getSelectionModel().addChangeListener(previewPanel); chooser.setPreviewPanel(previewPanel); Issue: JColorChooser is somewhat buggy and the preview window might not work with Java <= 1.4.2 [1].
LMSColorPreviewPanel() - Constructor for class ch.unizh.ini.friend.gui.LMSColorPreviewPanel
Create a default instance.
lowPass - Variable in class ch.unizh.ini.friend.simulation.cells.HorizontalCell
A low-pass filter.
lowPass - Variable in class ch.unizh.ini.friend.simulation.filter.HighPassFilter
The corresponding low-pass filter
LowPassFilter - Class in ch.unizh.ini.friend.simulation.filter
A low-pass filter.
LowPassFilter(float, float) - Constructor for class ch.unizh.ini.friend.simulation.filter.LowPassFilter
Creates a new instance of LowPassFilter with the given time constant and the given last output.

M

M_CONE - Static variable in class ch.unizh.ini.friend.simulation.cells.ColorPhotoreceptor
Green selective (M cone) photoreceptor type.
main(String[]) - Static method in class ch.unizh.ini.friend.browser.Browser
 
main(String[]) - Static method in class ch.unizh.ini.friend.browser.BrowserControl
Simple example.
main(String[]) - Static method in class ch.unizh.ini.friend.gui.AboutDialog
 
main(String[]) - Static method in class ch.unizh.ini.friend.gui.ExceptionDialog
 
main(String[]) - Static method in class ch.unizh.ini.friend.gui.FriendGUI
 
main(String[]) - Static method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
main(String[]) - Static method in class ch.unizh.ini.friend.gui.HelpDialog
Deprecated.  
main(String[]) - Static method in class ch.unizh.ini.friend.gui.SimulationProperties
 
main(String[]) - Static method in class ch.unizh.ini.friend.gui.SplashScreen
 
Main - Class in ch.unizh.ini.friend
Main class for the Physiologist's Friend program.
Main(String[]) - Constructor for class ch.unizh.ini.friend.Main
run friend by instantiating a new Main: new Main()
main(String[]) - Static method in class ch.unizh.ini.friend.Main
run this to run Friend
main(String[]) - Static method in class ch.unizh.ini.friend.record.MicrophoneReporter
test class by just printing . when it gets spikes
main(String[]) - Static method in class ch.unizh.ini.friend.record.SpikePlotter
 
main(String[]) - Static method in class ch.unizh.ini.friend.stimulus.BarStimulus
 
main(String[]) - Static method in class ch.unizh.ini.friend.stimulus.GratingStimulus
 
main(String[]) - Static method in class ch.unizh.ini.friend.tests.AudioOutputTest
Bootstraps the application.
main(String[]) - Static method in class ch.unizh.ini.friend.tests.ConvexPolygonTest
Gets the whole thing started.
main(String[]) - Static method in class ch.unizh.ini.friend.tests.CurrentTimeMillisBenchMark
 
main(String[]) - Static method in class ch.unizh.ini.friend.tests.PhotoreceptorTest
Bootstraps the application.
main(String[]) - Static method in class ch.unizh.ini.friend.tests.SimulationTest
Bootstraps the application.
main(String[]) - Static method in class ch.unizh.ini.friend.tests.SpikeSoundTest
run this to play a randomly genrated spike train
main(String[]) - Static method in class ch.unizh.ini.friend.tests.SpikeSoundTestGUI
 
main(String[]) - Static method in class ch.unizh.ini.friend.tests.SystemTimeBaseTest
 
main(String[]) - Static method in class ch.unizh.ini.friend.tests.SystemTimeTest
 
main(String[]) - Static method in class ch.unizh.ini.friend.topology.HexDirection
tests HexDirection
main(String[]) - Static method in class ch.unizh.ini.friend.topology.RetinotopicLocation
 
makeBarShape() - Static method in class ch.unizh.ini.friend.stimulus.StimulusShapeFactory
returns a bar shape
makeEdgeShape() - Static method in class ch.unizh.ini.friend.stimulus.StimulusShapeFactory
returns an edge shape
makeGratingShape() - Static method in class ch.unizh.ini.friend.stimulus.StimulusShapeFactory
returns grating shapes
makeSpotShape() - Static method in class ch.unizh.ini.friend.stimulus.StimulusShapeFactory
returns a spot shape
MAX_SPIKE_RATE - Static variable in class ch.unizh.ini.friend.simulation.cells.PoissonSoma
Spike rate at weightedInputs() == 1.0f.
maxRate - Variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
the maximum spike rate, measured in spikes/IntegrateFireCell.SPIKE_RATE_TIME_SCALE.
MicrophoneReporter - Class in ch.unizh.ini.friend.record
Uses the microphone input to detect and generate SpikeEvent's.
MicrophoneReporter(SimulationSetup) - Constructor for class ch.unizh.ini.friend.record.MicrophoneReporter
 
MicrophoneReporter() - Constructor for class ch.unizh.ini.friend.record.MicrophoneReporter
Creates a new instance of SpikeTest.
monitoredCell - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
the monitored cell.
monitors - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
Monitors that can be configured to listen to a specific cell.

N

NE - Static variable in class ch.unizh.ini.friend.topology.HexDirection
a hex direction
newBackgroundExcitationDensity - Variable in class ch.unizh.ini.friend.stimulus.AbstractStimulus
The new background excitation density.
newForegroundExcitationDensity - Variable in class ch.unizh.ini.friend.stimulus.AbstractStimulus
The new foreground excitation density.
newShape - Variable in class ch.unizh.ini.friend.stimulus.AbstractStimulus
the new set of shapes
newSpike - Variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Encodes whether the cell will make a spike after the next IntegrateFireCell.update().
newValue - Variable in class ch.unizh.ini.friend.simulation.cells.AbstractCell
The new output value.
next() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygonIterator
Moves the iterator to the next segment.
nextUpdate - Variable in class ch.unizh.ini.friend.simulation.SimpleOutputMonitor
The time of the next update.
nIterate - Variable in class ch.unizh.ini.friend.gui.SimulationProperties
 
nIterate - Variable in class ch.unizh.ini.friend.simulation.SimulationStep
number of times to iterate for a single step
npoints - Variable in class ch.unizh.ini.friend.graphics.ConvexPolygon
The number of vertices (xpoints and ypoints may have more elements than vertices present).
NSIDES - Static variable in class ch.unizh.ini.friend.stimulus.SpotStimulus
number of side of the polygon making up the stimulus: 6
NUM_CONES - Static variable in class ch.unizh.ini.friend.simulation.cells.ColorPhotoreceptor
Total number of cone types.
NW - Static variable in class ch.unizh.ini.friend.topology.HexDirection
a hex direction

O

offGanglions - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
the off-type ganglion cells
on - Variable in class ch.unizh.ini.friend.simulation.AbstractSimulation
False iff the simulation should stop.
onGanglions - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
the on-type ganglion cells
open() - Method in class ch.unizh.ini.friend.record.SpikeLogger
open the file for output.
openURL(String) - Static method in class ch.unizh.ini.friend.browser.BrowserLauncher
Attempts to open the default web browser to the given URL.
OscillatingOutput - Class in ch.unizh.ini.friend.tests
Simple waveform generator.
OscillatingOutput() - Constructor for class ch.unizh.ini.friend.tests.OscillatingOutput
 
output() - Method in class ch.unizh.ini.friend.simulation.cells.AbstractCell
Returns the current output value of the component.
output - Variable in class ch.unizh.ini.friend.simulation.filter.LowPassFilter
The last output.
output() - Method in interface ch.unizh.ini.friend.simulation.ServesOutput
Returns the current output value of the component.
output() - Method in class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse
Returns the current output value of the component.
outputCells - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
The cells that can be monitored.
OutputPrinter - Class in ch.unizh.ini.friend.tests
Prints the output value of an ServesOutput instance to a stream.
OutputPrinter(Collection, String, String, PrintStream) - Constructor for class ch.unizh.ini.friend.tests.OutputPrinter
Initializes the instance to prepend a given string and append another given string on output on the given stream.
OutputPrinter(ServesOutput, String, String, PrintStream) - Constructor for class ch.unizh.ini.friend.tests.OutputPrinter
Initializes the instance to prepend a given string and append another given string on output on the given stream.

P

paint(Graphics) - Method in class ch.unizh.ini.friend.tests.ConvexPolygonTest
Paints all shapes and intersections to a Graphics2D instance.
paint(Graphics) - Method in class ch.unizh.ini.friend.tests.PhotoreceptorTest
Paints all graphical components.
paint(Graphics) - Method in class ch.unizh.ini.friend.tests.SimulationTest
Draws the intersection, the photoreceptor shapes and the stimulus.
paintComponent(Graphics) - Method in class ch.unizh.ini.friend.gui.TangentScreen
Draws the background and stimulus in the tangent screen.
PERIOD - Static variable in class ch.unizh.ini.friend.stimulus.GratingStimulus
the default spatial period of the grating: 2.0f.
Photoreceptor - Class in ch.unizh.ini.friend.simulation.cells
This class implements the notion of a photoreceptor.
Photoreceptor(ConvexPolygon, Stimulus) - Constructor for class ch.unizh.ini.friend.simulation.cells.Photoreceptor
Creates a new photoreceptor with a given shape and attached to a given stimulus and a certain gain in higher frequencies.
PhotoreceptorTest - Class in ch.unizh.ini.friend.tests
This class tests and demos the function of Photoreceptor.
PhotoreceptorTest() - Constructor for class ch.unizh.ini.friend.tests.PhotoreceptorTest
Computes the intersections of the stimulus and the photoreceptors and displays the resulting area.
play() - Method in class ch.unizh.ini.friend.gui.SpikeSound
plays the spike sound once.
play(int) - Method in class ch.unizh.ini.friend.gui.SpikeSound
 
pointInHalfPlane(float, float, float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Determines whether (x,y) is on the left, right of or on the straight line defined by (x1,y1) and (x2, y2) (looking from the first to the second), including the line itself.
points - Variable in class ch.unizh.ini.friend.graphics.ConvexPolygon
The coordinates of the vertices, as x,y pairs.
PoissonSoma - Class in ch.unizh.ini.friend.simulation.cells
A poisson spiking mechanism.
PoissonSoma() - Constructor for class ch.unizh.ini.friend.simulation.cells.PoissonSoma
 
post - Variable in class ch.unizh.ini.friend.tests.OutputPrinter
The string to append to the ouput.
potasiumReversal - Variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Potasium reversal potential.
pre - Variable in class ch.unizh.ini.friend.tests.OutputPrinter
The string to prepend to the ouput.
previousTime - Variable in class ch.unizh.ini.friend.simulation.SimulationStep
Time during previous step.
putMonitor(String, AcceptsInput) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
put a an object into the monitors map.
putOutputCell(String, Object) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
put a an object into the output cells map.

R

r - Variable in class ch.unizh.ini.friend.simulation.cells.PoissonSoma
The pseudo-random generator.
receptorShapes - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
The shapes of the photoreceptors.
refillFrame() - Method in class ch.unizh.ini.friend.gui.TangentScreen
resize this TangentScreen to fill the parent container
refresh(Color) - Method in class ch.unizh.ini.friend.gui.LMSColorPreviewPanel
Refresh view.
removeNotify() - Method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
removeShape(Transformable) - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
remove a shape from the list of shapes
removeShape(Transformable) - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
remove a shape from the list of shapes
removeSpikeListener(SpikeListener) - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
removes a listener
removeSpikeListener(SpikeListener) - Method in class ch.unizh.ini.friend.record.SimulationReporter
removes a listener
removeSpikeListener(SpikeListener) - Method in interface ch.unizh.ini.friend.record.SpikeEventSource
removes a listener
removeUpdateable(Updateable) - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
Removes an updateable from the simulation.
removeUpdateable(Updateable) - Method in interface ch.unizh.ini.friend.simulation.SimulationTask
Removes an updateable from the simulation.
removeUpdateable(Updateable) - Method in class ch.unizh.ini.friend.simulation.ThreadedSimulation
Removes an updateable from the simulation.
removeUpdateable(Updateable) - Method in class ch.unizh.ini.friend.simulation.TimedSimulation
Removes an updateable from the simulation.
RESIZE_RATIO - Static variable in interface ch.unizh.ini.friend.stimulus.Stimulus
ratio by which to resize dimensions of stimulus
RET_CANCEL - Static variable in class ch.unizh.ini.friend.gui.ExceptionDialog
A return status code - returned if Cancel button has been pressed
RET_OK - Static variable in class ch.unizh.ini.friend.gui.ExceptionDialog
A return status code - returned if OK button has been pressed
Retinotopic - Interface in ch.unizh.ini.friend.topology
Represents a cell with a RetinotopicLocation.
RetinotopicLocation - Class in ch.unizh.ini.friend.topology
Represents a location of a retinotopic cell in the 2d image plane.
RetinotopicLocation(Point2D) - Constructor for class ch.unizh.ini.friend.topology.RetinotopicLocation
constructs a RetinotopicLocation from a Point2D.
rotate(float) - Method in class ch.unizh.ini.friend.graphics.AbstractTransformable
Rotates the geometric object by the given angle around the origin.
rotate(float, float, float) - Method in class ch.unizh.ini.friend.graphics.AbstractTransformable
Rotates the geometric object by the given angle around the given point.
rotate(float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Rotates the geometric object by the given angle around the origin.
rotate(float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Rotates the geometric object by the given angle around the given point.
rotate(float) - Method in class ch.unizh.ini.friend.graphics.ShapeList
Rotates the geometric object by the given angle around the origin.
rotate(float, float, float) - Method in class ch.unizh.ini.friend.graphics.ShapeList
Rotates the geometric object by the given angle around the given point.
rotate(float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Rotates the geometric object by the given angle around the origin.
rotate(float, float, float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Rotates the geometric object by the given angle around the given point.
rotate(float, float, float) - Method in interface ch.unizh.ini.friend.graphics.Transformable
Rotates the geometric object by the given angle around the given point.
rotate(float) - Method in interface ch.unizh.ini.friend.graphics.Transformable
Rotates the geometric object by the given angle around the origin.
rotate - Static variable in class ch.unizh.ini.friend.gui.StimulusAction
name of action that can happen to Stimulus
rotate(int) - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
rotate by n*Stimulus.ROTATE_BY
rotate(int) - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
rotate by n*Stimulus.ROTATE_BY
ROTATE_BY - Static variable in interface ch.unizh.ini.friend.stimulus.Stimulus
unit angle by which to rotate stimulus in radians: 0.5235987901687622f
rotateCCW() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
rotate CCW by Stimulus.ROTATE_BY
rotateCCW() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
rotate CCW by Stimulus.ROTATE_BY
rotateCW() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
rotate CW by Stimulus.ROTATE_BY
rotateCW() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
rotate CW by Stimulus.ROTATE_BY
rotateTo(float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Rotates the geometric object by the given angle around the origin.
rotateTo(float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Rotates the geometric object by the given angle around the given point.
rotateTo(float, float, float) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Rotates the geometric object by the given angle around the given point.
rotateTo(float) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Rotates the geometric object by the given angle around the origin.
rotateTo(float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Rotates the geometric object by the given angle around the origin.
rotateTo(float, float, float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Rotates the geometric object by the given angle around the given point.
rotation - Variable in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
The rotations.
run() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
grabs samples from microphone input and generates SpikeEvent's whenver spikes are detected.
run() - Method in class ch.unizh.ini.friend.simulation.ThreadedSimulation
The main-loop of the simulation.

S

S_CONE - Static variable in class ch.unizh.ini.friend.simulation.cells.ColorPhotoreceptor
Blue selective (S cone) photoreceptor type.
SAMPLE_RATE - Static variable in class ch.unizh.ini.friend.gui.SpikeSound
sample rate in Hz
scale(float, float) - Method in class ch.unizh.ini.friend.graphics.AbstractTransformable
Scales the geometric object by the given values in x- and y-coordinates with the origin as center.
scale(float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.AbstractTransformable
Scales the geometric object by the given values in x- and y-coordinates with the given center (x, y).
scale(float, float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Scales the geometric object by the given values in x- and y-coordinates with the origin as center.
scale(float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Scales the geometric object by the given values in x- and y-coordinates with the given center (x, y).
scale(float, float) - Method in class ch.unizh.ini.friend.graphics.ShapeList
Scales the geomtric object by the given values in x- and y-coordinates with the origin as center.
scale(float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.ShapeList
Scales the geomtric object by the given values in x- and y-coordinates with the given center (x, y).
scale(float, float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Scales the geomtric object by the given values in x- and y-coordinates with the origin as center.
scale(float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Scales the geomtric object by the given values in x- and y-coordinates with the given center (x, y).
scale(float, float, float, float) - Method in interface ch.unizh.ini.friend.graphics.Transformable
Scales the geomtric object by the given values in x- and y-coordinates with the given center (x, y).
scale(float, float) - Method in interface ch.unizh.ini.friend.graphics.Transformable
Scales the geomtric object by the given values in x- and y-coordinates with the origin as center.
scaleTo(float, float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Scales the geomtric object by the given values in x- and y-coordinates with the origin as center.
scaleTo(float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Scales the geomtric object by the given values in x- and y-coordinates with the given center (x, y).
scaleTo(float, float, float, float) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Scales the geomtric object by the given values in x- and y-coordinates with the given center (x, y).
scaleTo(float, float) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Scales the geomtric object by the given values in x- and y-coordinates with the origin as center.
scaleTo(float, float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Scales the geomtric object by the given values in x- and y-coordinates with the origin as center.
scaleTo(float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Scales the geomtric object by the given values in x- and y-coordinates with the given center (x, y).
scaling - Variable in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
The scalings.
ScalingSynapse - Class in ch.unizh.ini.friend.simulation.synapses
A simple scaling synapse.
ScalingSynapse(float) - Constructor for class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse
Creates a new instance with currently no inputs and the given scaling factor.
ScalingSynapse() - Constructor for class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse
Creates a new instance with currently no inputs and the default weight.
ScalingSynapse(Collection, float) - Constructor for class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse
Creates a new instance with the given collection of inputs and weight.
ScalingSynapse(ServesOutput, float) - Constructor for class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse
Creates a new instance with the given input and weight.
SCREEN_DIMENSION - Static variable in class ch.unizh.ini.friend.gui.TangentScreen
Dimension of tangent screen in our user (stimulus) coordinates.
SCREEN_MULTIPLE - Static variable in class ch.unizh.ini.friend.stimulus.GratingStimulus
size of the grating stimulus as a multiple of the screen size
SE - Static variable in class ch.unizh.ini.friend.topology.HexDirection
a hex direction
SeparateTransforms - Interface in ch.unizh.ini.friend.graphics
Provides the interface to keep a geometric object in its original state while buffering applied transformations separately.
ServesOutput - Interface in ch.unizh.ini.friend.simulation
This interface is provided by all components that offer an output in the simulation.
set(int) - Method in class ch.unizh.ini.friend.topology.HexDirection
sets the direction
setActivity(float) - Method in class ch.unizh.ini.friend.gui.ActivityMeter
Set the cell activity level shown.
setBackground(Color) - Method in interface ch.unizh.ini.friend.stimulus.ColorStimulus
Sets the background excitation color of the stimulus.
setBackground(Color) - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
setBackgroundExcitationDensity(float) - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
Sets the background excitation density of the stimulus.
setBackgroundExcitationDensity(float) - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
Sets the background excitation density of the stimulus.
setCellName(String) - Method in class ch.unizh.ini.friend.gui.StatusPanel
Set the name of the cell being listened to.
setCellNameVisible(boolean) - Method in class ch.unizh.ini.friend.gui.StatusPanel
sets visibility of cell name.
setDelay(long) - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
set the timer delay in ms between each simulation step
setDelay(long) - Method in interface ch.unizh.ini.friend.simulation.SimulationTask
set the timer delay in ms between each simulation step
setForeground(Color) - Method in interface ch.unizh.ini.friend.stimulus.ColorStimulus
Sets the foreground excitation color of the stimulus.
setForeground(Color) - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
setForegroundExcitationDensity(float) - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
Sets the foreground excitation density of the stimulus.
setForegroundExcitationDensity(float) - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
Sets the foreground excitation density of the stimulus.
setGeometry(Transformable) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Sets the original geometric object.
setGeometry(Transformable) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Sets the original geometric object.
setGeometry(Transformable) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Sets the original geometric object.
setHystersis(byte) - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
sets the hystersis for spike detection.
setInput(ServesOutput) - Method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Sets the first (and only) input.
setInput(ServesOutput) - Method in class ch.unizh.ini.friend.simulation.AbstractMonitor
Sets the first (and only) input.
setInput(ServesOutput) - Method in interface ch.unizh.ini.friend.simulation.AcceptsInput
Sets the first (and only) input.
setInputs(Collection) - Method in class ch.unizh.ini.friend.simulation.AbstractAcceptsInput
Sets the collection of all inputs to this simulation component.
setInputs(Collection) - Method in class ch.unizh.ini.friend.simulation.AbstractMonitor
Sets the collection of all inputs to this simulation component.
setInputs(Collection) - Method in interface ch.unizh.ini.friend.simulation.AcceptsInput
Sets the collection of all inputs to this simulation component to the given.
setLeakTime(float) - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Setter for property leakTime.
setLocation(int, int) - Method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
setMaxRate(float) - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Setter for property maxRate.
setMonitoredCell(String) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
set the monitored cell in the simulation using the String key.
setMonitoredCell(ServesOutput) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
set the monitored cell in the simulation directly.
setMonitors(Map) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Sets the Map of monitors.
setMuted(boolean) - Method in class ch.unizh.ini.friend.simulation.AudioOutput
sets audio muted.
setName(String) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
 
setNumberOfIterationsPerStep(int) - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
set the number of iterations over the updateables for each step.
setNumberOfIterationsPerStep(int) - Method in class ch.unizh.ini.friend.simulation.SimulationStep
 
setNumberOfIterationsPerStep(int) - Method in interface ch.unizh.ini.friend.simulation.SimulationTask
set the number of iterations over the updateables for each step.
setOffGanglions(Collection) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
 
setOnGanglions(Collection) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
 
setOutputCells(Map) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Sets the cells that can be monitored (listened to).
setPhotoreceptorsShown(boolean) - Method in class ch.unizh.ini.friend.gui.TangentScreen
enable showing the locations of the photoreceptors
setPlottingEnabled(boolean) - Method in class ch.unizh.ini.friend.gui.StatusPanel
set plotting running now status
setPotasiumReversal(float) - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
 
setReceptorShapes(ArrayList) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Sets the shapes of the photoreceptors.
setRetinotopicLocation(RetinotopicLocation) - Method in class ch.unizh.ini.friend.simulation.cells.BipolarCell
set the location
setRetinotopicLocation(RetinotopicLocation) - Method in class ch.unizh.ini.friend.simulation.cells.GanglionCell
set the location
setRetinotopicLocation(RetinotopicLocation) - Method in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
set the location
setRetinotopicLocation(RetinotopicLocation) - Method in interface ch.unizh.ini.friend.topology.Retinotopic
set the location
setRotation(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Sets the buffered rotation.
setRotation(AffineTransform) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Sets the buffered rotation.
setRotation(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Sets the buffered rotation.
setScaling(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Sets the buffered scaling.
setScaling(AffineTransform) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Sets the buffered scaling.
setScaling(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Sets the buffered scaling.
setShapes(ShapeList) - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
set list of untransformed shapes making up stimulus.
setShapes(ShapeList) - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
set list of shapes making up stimulus
setSimulatedCells(List) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Sets the cells that are simulated
setSimulation(SimulationTask) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Sets the current simulation instance.
setSimulationSetup(SimulationSetup) - Method in class ch.unizh.ini.friend.gui.FriendGUI
sets the SimulationSetup to simulate.
setSimulationSetup(SimulationSetup) - Method in class ch.unizh.ini.friend.gui.StatusPanel
sets the SimulationSetup.
setSimulationSetup(SimulationSetup) - Method in class ch.unizh.ini.friend.gui.TangentScreen
sets the SimulationSetup
setSize(Dimension) - Method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
setSpikeFadeEnabled(boolean) - Method in class ch.unizh.ini.friend.gui.TangentScreen
 
setSpikeFillEnabled(boolean) - Method in class ch.unizh.ini.friend.gui.TangentScreen
 
setSpikeMemoryDepth(int) - Method in class ch.unizh.ini.friend.gui.TangentScreen
 
setSpikeRateMeasurementWindow(float) - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Setter for property spikeRateMeasurementWindow.
setStartingCellName(String) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Sets the starting cell Name.
setStimulus(Stimulus) - Method in class ch.unizh.ini.friend.gui.TangentScreen
set the stimulus displayed.
setStimulus(Stimulus) - Method in class ch.unizh.ini.friend.simulation.SimulationSetup
Sets the current stimulus instance.
setStimulusControlEnabled(boolean) - Method in class ch.unizh.ini.friend.gui.TangentScreen
set mouse/keyboard control of stimulus enabled
setTau(float) - Method in class ch.unizh.ini.friend.simulation.cells.HorizontalCell
Setter for property tau.
setTau(float) - Method in class ch.unizh.ini.friend.simulation.filter.HighPassFilter
Setter for property tau.
setTau(float) - Method in class ch.unizh.ini.friend.simulation.filter.LowPassFilter
Setter for property tau.
setThreshold(byte) - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
sets the threshold for detecting spikes.
setThreshold(float) - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Setter for property threshold.
setTime(long) - Method in class ch.unizh.ini.friend.record.SpikeEvent
 
setTransformation(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Sets the buffered generic transformation.
setTransformation(AffineTransform) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Sets the buffered generic transformation.
setTransformation(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Sets the buffered generic transformation.
setTransforms(SeparateTransforms) - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
set the transforms of this stimulus.
setTransforms(SeparateTransforms) - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
set the transforms of this stimulus.
setTranslation(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Sets the buffered translation.
setTranslation(AffineTransform) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Sets the buffered translation.
setTranslation(AffineTransform) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Sets the buffered translation.
setup - Variable in class ch.unizh.ini.friend.tests.AudioOutputTest
The simulation setup.
setup - Variable in class ch.unizh.ini.friend.tests.SimulationTest
The simulation setup.
setValue(float) - Method in class ch.unizh.ini.friend.simulation.SimpleOutputMonitor.Deliverable
Sets the value carried by this deliverable.
setVisible(boolean) - Method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
setVisible(boolean) - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
set state of stimulus to be hidden or shown.
setVisible(boolean) - Method in class ch.unizh.ini.friend.stimulus.ColorStimulusImpl
 
setVisible(boolean) - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
set state of stimulus to be hidden or shown.
setWeight(float) - Method in class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse
Sets the weight with which the input will be multiplied.
shape - Variable in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
The shape of this photoreceptor.
ShapeList - Class in ch.unizh.ini.friend.graphics
An ArrayList of shapes which are Transformable and Intersectable as a whole.
ShapeList() - Constructor for class ch.unizh.ini.friend.graphics.ShapeList
Creates a new instance of ShapeList with an empty shape list.
ShapeList(Transformable) - Constructor for class ch.unizh.ini.friend.graphics.ShapeList
creates a new ShapeList initialized with the given shape.
ShapeList() - Method in class ch.unizh.ini.friend.graphics.ShapeList
string regpresentation of ShapeList
shapes - Variable in class ch.unizh.ini.friend.stimulus.AbstractStimulus
the list of original (untransformed) shapes making up the stimulus
shorten() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
make shorter by ratio Stimulus.RESIZE_RATIO
shorten() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
shorten by ratio Stimulus.RESIZE_RATIO
showDialog(Component, String, Color) - Method in class ch.unizh.ini.friend.gui.ColorChooser
Show a modal color-chooser dialog.
showGifFile(String, int, int) - Static method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
showGifFile(Image, int, int) - Static method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
shrink() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
shrink by ratio Stimulus.RESIZE_RATIO in both dimensions
shrink() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
shrink by ratio Stimulus.RESIZE_RATIO in both dimensions
signedArea(float, float, float, float, float, float) - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Calculates the twice the signed area of the defined by the given three vertices p1, p2 and p3, where the sign is positive iff (p1p2p3) form a counterclockwise cycle.
SimpleOutputMonitor - Class in ch.unizh.ini.friend.simulation
Provides synchronization between the gui and the simulation needed for the gui to monitor the output of a simulation component.
SimpleOutputMonitor(SimpleOutputMonitor.Deliverable) - Constructor for class ch.unizh.ini.friend.simulation.SimpleOutputMonitor
Creates a new instance of SimpleOutputMonitor
SimpleOutputMonitor(SimpleOutputMonitor.Deliverable, ServesOutput) - Constructor for class ch.unizh.ini.friend.simulation.SimpleOutputMonitor
Creates a new instance of SimpleOutputMonitor with the given input.
SimpleOutputMonitor.Deliverable - Class in ch.unizh.ini.friend.simulation
An abstract class whose heirs' instances can be passed to invokeLater() by an instance of SimpleOutputMonitor.
SimpleOutputMonitor.Deliverable() - Constructor for class ch.unizh.ini.friend.simulation.SimpleOutputMonitor.Deliverable
 
simulatedCells - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
The cells that are simulated.
simulation - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
The simulation.
SIMULATION_UPDATE_INTERVAL_MS - Static variable in class ch.unizh.ini.friend.gui.FriendGUI
the interval in ms between simulation updates
SimulationProperties - Class in ch.unizh.ini.friend.gui
 
SimulationProperties(Frame, boolean, SimulationSetup) - Constructor for class ch.unizh.ini.friend.gui.SimulationProperties
Creates new form SimulationProperties
SimulationReporter - Class in ch.unizh.ini.friend.record
Generates a SpikeEvent when it detects that the simulation's monitored cell has made a spike.
SimulationReporter(SimulationSetup) - Constructor for class ch.unizh.ini.friend.record.SimulationReporter
Creates a new instance of SpikeEventMonitor
SimulationSetup - Class in ch.unizh.ini.friend.simulation
A collection of references to objects that together describe the current state of the simulation.
SimulationSetup() - Constructor for class ch.unizh.ini.friend.simulation.SimulationSetup
 
SimulationSetup.NoSuchCellException - Exception in ch.unizh.ini.friend.simulation
indicates we tried to monitor a nonexistent cell
SimulationSetup.NoSuchCellException(String) - Constructor for exception ch.unizh.ini.friend.simulation.SimulationSetup.NoSuchCellException
 
SimulationSetupFactory - Class in ch.unizh.ini.friend.simulation
Factory methods for creating instances of SimulationSetup.
SimulationSetupFactory() - Constructor for class ch.unizh.ini.friend.simulation.SimulationSetupFactory
 
SimulationStep - Class in ch.unizh.ini.friend.simulation
Implements a single iteration in the simulation process.
SimulationStep(Collection, float) - Constructor for class ch.unizh.ini.friend.simulation.SimulationStep
Creates a new instance of SimulationStep with the specified Collection of Updateable instances and a specified speed multiplier.
SimulationTask - Interface in ch.unizh.ini.friend.simulation
The interface of a simulation for the controlling thread.
SimulationTest - Class in ch.unizh.ini.friend.tests
This class tests and demos the function of Simulation.
SimulationTest() - Constructor for class ch.unizh.ini.friend.tests.SimulationTest
Initializes the intersections, initializes the simulation, registers an OuputPrinter instance to each cell and starts a new thread for the simulation.
SIZE - Static variable in class ch.unizh.ini.friend.simulation.SimulationSetupFactory
size of one edge of retinal array.
speed - Variable in class ch.unizh.ini.friend.simulation.SimulationStep
The scalar 'real-time' will be multiplied with.
spike - Variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Encodes whether the cell is making a spike now.
SPIKE_AMPLITUDE - Static variable in class ch.unizh.ini.friend.gui.SpikeSound
amplitude of spike sound.
SPIKE_DURATION_MS - Static variable in class ch.unizh.ini.friend.gui.SpikeSound
duration of spike sound in ms
SPIKE_RATE_TIME_SCALE - Static variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
spike rate time scale in seconds.
SpikeEvent - Class in ch.unizh.ini.friend.record
Represents a spike.
SpikeEvent(Object) - Constructor for class ch.unizh.ini.friend.record.SpikeEvent
Creates a new instance of SpikeEvent.
SpikeEvent(Object, long) - Constructor for class ch.unizh.ini.friend.record.SpikeEvent
Creates a new instance of SpikeEvent
SpikeEventSource - Interface in ch.unizh.ini.friend.record
Classes that are sources of SpikeEvent's implement this interface, so that SpikeListener's can register themselves to receive spikes.
SpikeListener - Interface in ch.unizh.ini.friend.record
SpikeListeners should implement this interface in order to be able to register themselves as recipients of spike events.
SpikeLogger - Class in ch.unizh.ini.friend.record
Logs SpikeEvent's to a File.
SpikeLogger(File) - Constructor for class ch.unizh.ini.friend.record.SpikeLogger
 
SpikeLogger(File, Object) - Constructor for class ch.unizh.ini.friend.record.SpikeLogger
 
spikeOccurred(SpikeEvent) - Method in class ch.unizh.ini.friend.gui.TangentScreen
called by spike source (SpikeReporter) when a spike is detected
spikeOccurred(SpikeEvent) - Method in interface ch.unizh.ini.friend.record.SpikeListener
called by spike source (SpikeReporter) when a spike is detected
spikeOccurred(SpikeEvent) - Method in class ch.unizh.ini.friend.record.SpikeLogger
called by spike source (SpikeReporter) when a spike is detected
spikeOccurred(SpikeEvent) - Method in class ch.unizh.ini.friend.record.SpikePlotter
called by spike source (SpikeReporter) when a spike is detected
spikeOccurred(SpikeEvent) - Method in class ch.unizh.ini.friend.record.SpikePrinter
called by spike source (SpikeReporter) when a spike is detected
SpikePlotter - Class in ch.unizh.ini.friend.record
 
SpikePlotter() - Constructor for class ch.unizh.ini.friend.record.SpikePlotter
 
SpikePrinter - Class in ch.unizh.ini.friend.record
 
SpikePrinter() - Constructor for class ch.unizh.ini.friend.record.SpikePrinter
 
spikeRate - Static variable in class ch.unizh.ini.friend.tests.SpikeSoundTest
 
spikeRateMeasurementWindow - Variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
spike rate measurement time window in seconds.
SpikeReporter - Interface in ch.unizh.ini.friend.record
Interface that is implemented by objects that can report spikes.
SpikeSound - Class in ch.unizh.ini.friend.gui
Plays a spike sound on the speaker.
SpikeSound() - Constructor for class ch.unizh.ini.friend.gui.SpikeSound
Creates a new instance of SpikeSound
SpikeSoundTest - Class in ch.unizh.ini.friend.tests
Tests SpikeSound by generating a Poisson spike sequence controlled by a slider.
SpikeSoundTest() - Constructor for class ch.unizh.ini.friend.tests.SpikeSoundTest
 
SpikeSoundTestGUI - Class in ch.unizh.ini.friend.tests
Makes a tiny GUI for testing spike sound generation.
SpikeSoundTestGUI() - Constructor for class ch.unizh.ini.friend.tests.SpikeSoundTestGUI
Creates new form SpikeSoundTestGUI
SpikingCell - Interface in ch.unizh.ini.friend.simulation.cells
A cell that makes spike output.
SPLASH_DURATION - Static variable in class ch.unizh.ini.friend.Main
time to show splash screen in ms: 5500L
SPLASH_IMAGE - Static variable in class ch.unizh.ini.friend.Main
location of splash screen image for original (monochrome) version of PhysioFriend relative to class root: "ch/unizh/ini/friend/SplashScreen.gif"
SPLASH_IMAGE_COLOR - Static variable in class ch.unizh.ini.friend.Main
location of splash screen image for color version of PhysioFriend relative to class root: "ch/unizh/ini/friend/SplashScreen-color.gif"
SplashScreen - Class in ch.unizh.ini.friend.gui
Shows a splash screen image.
SplashScreen() - Constructor for class ch.unizh.ini.friend.gui.SplashScreen
 
SpotStimulus - Class in ch.unizh.ini.friend.stimulus
A stimulus consisting of a single bar.
SpotStimulus() - Constructor for class ch.unizh.ini.friend.stimulus.SpotStimulus
Creates a new instance of BarStimulus with default size.
SpotStimulus(float) - Constructor for class ch.unizh.ini.friend.stimulus.SpotStimulus
Creates a new instance of SpotStimulus with the given diameter.
st - Variable in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
The object to wrap.
start() - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
Starts the simulation.
start() - Method in interface ch.unizh.ini.friend.simulation.SimulationTask
Starts the simulation.
start() - Method in class ch.unizh.ini.friend.simulation.ThreadedSimulation
Starts the thread on the main-loop.
start() - Method in class ch.unizh.ini.friend.simulation.TimedSimulation
Starts the simulation (timer).
startingCellName - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
The cell which is monitored first.
startReporting() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
starts acquisition from microphone port and generation of SpikeEvent's.
startReporting() - Method in class ch.unizh.ini.friend.record.SimulationReporter
starts acquisition of spikes and generation of SpikeEvent's.
startReporting() - Method in interface ch.unizh.ini.friend.record.SpikeReporter
starts acquisition of spikes and generation of SpikeEvent's.
startSimulation() - Method in class ch.unizh.ini.friend.gui.FriendGUI
start the simulation running.
stateChanged(ChangeEvent) - Method in class ch.unizh.ini.friend.gui.LMSColorPreviewPanel
Listen if the color changes.
STATUS_HEIGHT - Static variable in class ch.unizh.ini.friend.gui.FriendGUI
height of status panel in pixels
statusPanel - Variable in class ch.unizh.ini.friend.gui.FriendGUI
the status panel.
StatusPanel - Class in ch.unizh.ini.friend.gui
Shows the status of the simulation, and more important, displays a combo box that users use to choose the cell to be monitored.
StatusPanel(SimulationSetup, Stimulus) - Constructor for class ch.unizh.ini.friend.gui.StatusPanel
Creates new form StatusPanel
step - Variable in class ch.unizh.ini.friend.simulation.AbstractSimulation
The simulation step.
step() - Method in class ch.unizh.ini.friend.simulation.SimulationStep
Makes all the cells first Updateable.compute(float), and then all the cells then Updateable.update() for a single simulation step.
stimulus - Variable in class ch.unizh.ini.friend.gui.StimulusAction
the stimulus
stimulus - Variable in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
The stimulus for this photoreceptor (and likely the whole simulation).
stimulus - Variable in class ch.unizh.ini.friend.simulation.SimulationSetup
The stimulus.
Stimulus - Interface in ch.unizh.ini.friend.stimulus
Interface that a stimulus has to implement.
StimulusAction - Class in ch.unizh.ini.friend.gui
Actions that can happen to the stimulus.
StimulusAction() - Constructor for class ch.unizh.ini.friend.gui.StimulusAction
Creates a new instance of StimulusAction
StimulusAction(String) - Constructor for class ch.unizh.ini.friend.gui.StimulusAction
 
StimulusAction(String, Icon) - Constructor for class ch.unizh.ini.friend.gui.StimulusAction
 
StimulusAction.Brighten - Class in ch.unizh.ini.friend.gui
brightens the stimulus
StimulusAction.Brighten(Stimulus) - Constructor for class ch.unizh.ini.friend.gui.StimulusAction.Brighten
 
StimulusAction.BrightenBackground - Class in ch.unizh.ini.friend.gui
brightens background
StimulusAction.BrightenBackground(Stimulus) - Constructor for class ch.unizh.ini.friend.gui.StimulusAction.BrightenBackground
 
StimulusAction.Darken - Class in ch.unizh.ini.friend.gui
darkens the stimulus
StimulusAction.Darken(Stimulus) - Constructor for class ch.unizh.ini.friend.gui.StimulusAction.Darken
 
StimulusAction.DarkenBackground - Class in ch.unizh.ini.friend.gui
darkens background
StimulusAction.DarkenBackground(Stimulus) - Constructor for class ch.unizh.ini.friend.gui.StimulusAction.DarkenBackground
 
StimulusAction.FlipContrast - Class in ch.unizh.ini.friend.gui
Swaps foreground and background brightnesses.
StimulusAction.FlipContrast(Stimulus) - Constructor for class ch.unizh.ini.friend.gui.StimulusAction.FlipContrast
 
StimulusAction.Rotate - Class in ch.unizh.ini.friend.gui
rotates the stimulus.
StimulusAction.Rotate(Stimulus) - Constructor for class ch.unizh.ini.friend.gui.StimulusAction.Rotate
 
StimulusShapeFactory - Class in ch.unizh.ini.friend.stimulus
A helper class with static methods for making standard stimulus shapes.
stop() - Method in class ch.unizh.ini.friend.simulation.AbstractSimulation
Stops the simulation.
stop() - Method in interface ch.unizh.ini.friend.simulation.SimulationTask
Stops the simulation.
stop() - Method in class ch.unizh.ini.friend.simulation.ThreadedSimulation
Tells the main-loop to stop by the end of the current iteration.
stop() - Method in class ch.unizh.ini.friend.simulation.TimedSimulation
Stops the simulation (timer).
stopReporting() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
removes all spike event listeners, ends thread after first stopping microphone acquisition.
stopReporting() - Method in class ch.unizh.ini.friend.record.SimulationReporter
removes all spike event listeners, ends thread after first stopping microphone acquisition.
stopReporting() - Method in interface ch.unizh.ini.friend.record.SpikeReporter
ends thread after first stopping microphone acquisition.
stopSimulation() - Method in class ch.unizh.ini.friend.gui.FriendGUI
stops the simulation.
stream - Variable in class ch.unizh.ini.friend.tests.OutputPrinter
The stream to print to.
stream - Variable in class ch.unizh.ini.friend.tests.TimePrinter
The stream to print to.
SW - Static variable in class ch.unizh.ini.friend.topology.HexDirection
a hex direction
SynchronizedSeparateTransforms - Class in ch.unizh.ini.friend.graphics
Wrapper for SeperateTransforms to be thread-safe.
SynchronizedSeparateTransforms(SeparateTransforms) - Constructor for class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Creates a new instance that wraps the given object
SystemTimeBaseTest - Class in ch.unizh.ini.friend.tests
Tries to find the resolution of SystemTimeBase.getNanoseconds() (from the Java Media Framwork).
SystemTimeBaseTest() - Constructor for class ch.unizh.ini.friend.tests.SystemTimeBaseTest
 
SystemTimeTest - Class in ch.unizh.ini.friend.tests
Tries to find the resolution of System.getCurrentMillis().
SystemTimeTest() - Constructor for class ch.unizh.ini.friend.tests.SystemTimeTest
 

T

tangentScreen - Variable in class ch.unizh.ini.friend.gui.FriendGUI
the plotting area
TangentScreen - Class in ch.unizh.ini.friend.gui
Represents the plotting "tangent screen" -- the screen on which experimentalists display stimuli to characterize or measure cell responses.
TangentScreen(SimulationSetup) - Constructor for class ch.unizh.ini.friend.gui.TangentScreen
Creates new form TangentScreen.
tanh(float) - Static method in class ch.unizh.ini.friend.simulation.cells.BipolarCell
Computes the tanh(x).
tau - Variable in class ch.unizh.ini.friend.simulation.cells.HorizontalCell
the lowpass time constant of the HorizontalCell
tau - Variable in class ch.unizh.ini.friend.simulation.filter.LowPassFilter
The time constant.
thin() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
thin by ratio Stimulus.RESIZE_RATIO
thin() - Method in interface ch.unizh.ini.friend.stimulus.Stimulus
thin by ratio Stimulus.RESIZE_RATIO
thread - Variable in class ch.unizh.ini.friend.simulation.ThreadedSimulation
The simulation thread.
ThreadedSimulation - Class in ch.unizh.ini.friend.simulation
Implementation of the simulation loop in a separate thread.
ThreadedSimulation(SimulationStep) - Constructor for class ch.unizh.ini.friend.simulation.ThreadedSimulation
Creates a new instance with the given simulation step.
ThreadedSimulation(SimulationStep, long) - Constructor for class ch.unizh.ini.friend.simulation.ThreadedSimulation
 
threshold - Variable in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
The threshold where the cell will fire.
TimedSimulation - Class in ch.unizh.ini.friend.simulation
Implementation of the simulation loop with the javax.swing.Timer mechanism.
TimedSimulation(SimulationStep, int) - Constructor for class ch.unizh.ini.friend.simulation.TimedSimulation
Creates a new instance with the given simulation step.
TimePrinter - Class in ch.unizh.ini.friend.tests
Prints the time dt, which is passed to all Updateable instances, to a stream.
TimePrinter(PrintStream) - Constructor for class ch.unizh.ini.friend.tests.TimePrinter
Initializes the instance to print to the given stream.
timer - Variable in class ch.unizh.ini.friend.simulation.TimedSimulation
The simulation timer.
timeScale - Variable in class ch.unizh.ini.friend.simulation.SimulationStep
Time scale.
toFront() - Method in class ch.unizh.ini.friend.gui.GifViewerWindow
 
toggleSimulation() - Method in class ch.unizh.ini.friend.gui.FriendGUI
toggle simulation running
toString() - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
return string representation of the transforms
toString() - Method in class ch.unizh.ini.friend.graphics.ConvexPolygon
Returns a String-representation of the polygon.
toString() - Method in class ch.unizh.ini.friend.graphics.LMSColor
Returns a string representation of this LMSColor.
toString() - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
return string representation of the transforms
toString() - Method in class ch.unizh.ini.friend.record.SpikeEvent
 
toString() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
String representation of stimulus
toString() - Method in class ch.unizh.ini.friend.topology.HexDirection
returns int direction, 0-5 CCW from east and non negative
Transformable - Interface in ch.unizh.ini.friend.graphics
Interface a transformable geometric object might implement.
transformation - Variable in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
The generic transformations.
transformed - Variable in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
A transformed clone, null if uncached.
transforms - Variable in class ch.unizh.ini.friend.stimulus.AbstractStimulus
The transforms of the stimulus.
TRANSIENT_GAIN - Static variable in class ch.unizh.ini.friend.simulation.cells.Photoreceptor
the transient gain of the photoreceptor, as a multiple of the DC gain: 5.0f
translate(float, float) - Method in class ch.unizh.ini.friend.graphics.AbstractTransformable
Translates the geometric object by the given coordinates.
translate(float, float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Translates the geometric object by the given coordinates.
translate(float, float) - Method in class ch.unizh.ini.friend.graphics.ShapeList
Translates the geometric object by the given coordinates.
translate(float, float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Translates the geometric object by the given coordinates.
translate(float, float) - Method in interface ch.unizh.ini.friend.graphics.Transformable
Translates the geometric object by the given coordinates.
translateTo(float, float) - Method in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
Translates the geometric object by the given coordinates.
translateTo(float, float) - Method in interface ch.unizh.ini.friend.graphics.SeparateTransforms
Translates the geometric object by the given coordinates.
translateTo(float, float) - Method in class ch.unizh.ini.friend.graphics.SynchronizedSeparateTransforms
Translates the geometric object by the given coordinates.
translation - Variable in class ch.unizh.ini.friend.graphics.ConcreteSeparateTransforms
The translations.

U

update() - Method in class ch.unizh.ini.friend.gui.StatusPanel
Updates the actual state to the newly computed - aka double-buffering.
update() - Method in class ch.unizh.ini.friend.record.MicrophoneReporter
Updates the actual state to the newly computed - aka double-buffering.
update() - Method in class ch.unizh.ini.friend.simulation.AbstractMonitor
Updates the actual state to the newly computed - aka double-buffering.
update() - Method in class ch.unizh.ini.friend.simulation.cells.AbstractCell
Updates the actual state to the newly computed - aka double-buffering.
update() - Method in class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell
Updates the actual state to the newly computed - aka double-buffering.
update() - Method in interface ch.unizh.ini.friend.simulation.Updateable
Updates the actual state to the newly computed - aka double-buffering.
update() - Method in class ch.unizh.ini.friend.stimulus.AbstractStimulus
Updates the actual state to the newly computed - aka double-buffering.
update() - Method in class ch.unizh.ini.friend.stimulus.ConcreteStimulus
Updates the actual state to the newly computed - AKA double-buffering.
update() - Method in class ch.unizh.ini.friend.tests.TimePrinter
Updates the actual state to the newly computed - aka double-buffering.
Updateable - Interface in ch.unizh.ini.friend.simulation
This interface provides members common to all classes that participate in a simulation.
updateables - Variable in class ch.unizh.ini.friend.simulation.SimulationStep
The collection of updateable objects.
updateInterval - Variable in class ch.unizh.ini.friend.simulation.SimpleOutputMonitor
The update interval in milliseconds.
URL_HOME - Static variable in class ch.unizh.ini.friend.gui.FriendGUI
the URL string for home page: "http://www.ini.unizh.ch/~tobi/friend"

V

value - Variable in class ch.unizh.ini.friend.simulation.cells.AbstractCell
The current value.
value - Variable in class ch.unizh.ini.friend.simulation.SimpleOutputMonitor.Deliverable
The value carried by this deliverable.
vdt - Variable in class ch.unizh.ini.friend.tests.OscillatingOutput
Virtual dt per iteration.
vt - Variable in class ch.unizh.ini.friend.tests.OscillatingOutput
Virtual time.

W

W - Static variable in class ch.unizh.ini.friend.topology.HexDirection
a hex direction
weight - Variable in class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse
The weight with which the input will be multiplied.
WIDTH - Static variable in class ch.unizh.ini.friend.stimulus.BarStimulus
default wdith of bar: 6.0f

A B C D E F G H I J L M N O P R S T U V W
http://www.ini.unizh.ch/~tobi/friend