The Physiologist's Friend Simulation API

Serialized Form


Package ch.unizh.ini.friend.browser

Class ch.unizh.ini.friend.browser.Browser extends JFrame implements Serializable

Serialized Fields

enter

JTextField enter

contents

JEditorPane contents

Package ch.unizh.ini.friend.graphics

Class ch.unizh.ini.friend.graphics.ShapeList extends ArrayList implements Serializable


Package ch.unizh.ini.friend.gui

Class ch.unizh.ini.friend.gui.AboutDialog extends JDialog implements Serializable

Serialized Fields

tagName

String tagName

revision

String revision

tStampFileName

String tStampFileName

jPanel3

JPanel jPanel3

jPanel2

JPanel jPanel2

okButton

JButton okButton

jSeparator1

JSeparator jSeparator1

jPanel1

JPanel jPanel1

aboutLabel

JLabel aboutLabel

Class ch.unizh.ini.friend.gui.ActivityMeter extends JPanel implements Serializable

Serialized Fields

activity

float activity

activityFormat

NumberFormat activityFormat

negativeActivityBar

JProgressBar negativeActivityBar

positiveActivityBar

JProgressBar positiveActivityBar

jPanel1

JPanel jPanel1

activityTextField

JTextField activityTextField

Class ch.unizh.ini.friend.gui.ExceptionDialog extends JDialog implements Serializable

Serialized Fields

exceptionTextAreaScrollPane

JScrollPane exceptionTextAreaScrollPane

exceptionTextAreaPanel

JPanel exceptionTextAreaPanel

jPanel1

JPanel jPanel1

jSeparator1

JSeparator jSeparator1

exceptionSummaryTextField

JLabel exceptionSummaryTextField

buttonPanel

JPanel buttonPanel

okButton

JButton okButton

exeptionSummaryPanel

JPanel exeptionSummaryPanel

exceptionTextArea

JTextArea exceptionTextArea

returnStatus

int returnStatus

Class ch.unizh.ini.friend.gui.FriendGUI extends JFrame implements Serializable

Serialized Fields

simulationSetup

SimulationSetup simulationSetup

stimulus

Stimulus stimulus

tangentScreen

TangentScreen tangentScreen
the plotting area


statusPanel

StatusPanel statusPanel
the status panel.


activityMeter

ActivityMeter activityMeter
the acitivyt meter


spikeReporter

SpikeReporter spikeReporter

help

FriendHelp help

fullScreenEnabled

boolean fullScreenEnabled

simulationEnabled

boolean simulationEnabled

cellButtonGroup

ButtonGroup cellButtonGroup

jSeparator2

JSeparator jSeparator2

jSeparator4

JSeparator jSeparator4

fadeSpikesCheckBoxMenuItem

JCheckBoxMenuItem fadeSpikesCheckBoxMenuItem

viewMenu

JMenu viewMenu

fileMenu

JMenu fileMenu

barRadioButtonMenuItem

JRadioButtonMenuItem barRadioButtonMenuItem

jSeparator5

JSeparator jSeparator5

quickStartMenuItem

JMenuItem quickStartMenuItem

brightenForegroundStimulus

JMenuItem brightenForegroundStimulus

colorSimulationButton

JRadioButtonMenuItem colorSimulationButton

exitMenuItem

JMenuItem exitMenuItem

toggleStimulusVisibility

JMenuItem toggleStimulusVisibility

jSeparator10

JSeparator jSeparator10

webPageMenuItem

JMenuItem webPageMenuItem

fullScreenCheckBoxMenuItem

JCheckBoxMenuItem fullScreenCheckBoxMenuItem

jSeparator7

JSeparator jSeparator7

menuBar

JMenuBar menuBar

simulationButtonGroup

ButtonGroup simulationButtonGroup

invertStimulusContrast

JMenuItem invertStimulusContrast

makeShorter

JMenuItem makeShorter

jSeparator9

JSeparator jSeparator9

hotkeytMenuItem

JMenuItem hotkeytMenuItem

fromMicrophoneMenuButtonItem

JRadioButtonMenuItem fromMicrophoneMenuButtonItem

recordMenu

JMenu recordMenu

hideCellNameMenuItem

JCheckBoxMenuItem hideCellNameMenuItem

makeWider

JMenuItem makeWider

jSeparator6

JSeparator jSeparator6

setPersistenceMenuItem

JMenuItem setPersistenceMenuItem

receptorViewMenuItem

JCheckBoxMenuItem receptorViewMenuItem

jPopupMenu1

JPopupMenu jPopupMenu1

jSeparator3

JSeparator jSeparator3

gratingRadioButtonMenuItem

JRadioButtonMenuItem gratingRadioButtonMenuItem

monochromeSimulationButton

JRadioButtonMenuItem monochromeSimulationButton

darkenBackgroundStimulus

JMenuItem darkenBackgroundStimulus

markScreenMenuItem

JMenuItem markScreenMenuItem

fromSimulationMenuButtonItem

JRadioButtonMenuItem fromSimulationMenuButtonItem

spotStimulusRadioButtonItem

JRadioButtonMenuItem spotStimulusRadioButtonItem

recordCheckBoxMenuItem

JCheckBoxMenuItem recordCheckBoxMenuItem

mutedViewMenuItem

JCheckBoxMenuItem mutedViewMenuItem

cellMenu

JMenu cellMenu

stimulusMenu

JMenu stimulusMenu

stimulusButtonGroup

ButtonGroup stimulusButtonGroup

makeTaller

JMenuItem makeTaller

edgeRadioButtonMenuItem

JRadioButtonMenuItem edgeRadioButtonMenuItem

recordButtonGroup

ButtonGroup recordButtonGroup

jSeparator8

JSeparator jSeparator8

simulationPropertiesMenuItem

JMenuItem simulationPropertiesMenuItem

brightenBackgroundStimulus

JMenuItem brightenBackgroundStimulus

simulationMenu

JMenu simulationMenu

darkenForegroundStimulus

JMenuItem darkenForegroundStimulus

makeNarrower

JMenuItem makeNarrower

jSeparator1

JSeparator jSeparator1

mysteryCellItem

JMenuItem mysteryCellItem

fillSpikesCheckBoxMenuItem

JCheckBoxMenuItem fillSpikesCheckBoxMenuItem

aboutMenuItem

JMenuItem aboutMenuItem

helpMenu

JMenu helpMenu

rotateStimulus

JMenuItem rotateStimulus

helpContents

JMenuItem helpContents

toggleSimulationRunning

JCheckBoxMenuItem toggleSimulationRunning

clearSpikesMenuItem

JMenuItem clearSpikesMenuItem

Class ch.unizh.ini.friend.gui.HelpDialog extends JDialog implements Serializable

Serialized Fields

jSeparator1

JSeparator jSeparator1
Deprecated. 

helpLabel

JLabel helpLabel
Deprecated. 

okButton

JButton okButton
Deprecated. 

Class ch.unizh.ini.friend.gui.LMSColorPreviewPanel extends JPanel implements Serializable

Serialized Fields

colorPanel

JPanel colorPanel

lValueLabel

JLabel lValueLabel

mValueLabel

JLabel mValueLabel

sValueLabel

JLabel sValueLabel

lProgressBar

JProgressBar lProgressBar

mProgressBar

JProgressBar mProgressBar

sProgressBar

JProgressBar sProgressBar

lmsFormat

NumberFormat lmsFormat

Class ch.unizh.ini.friend.gui.SimulationProperties extends JDialog implements Serializable

Serialized Fields

delay

int delay

nIterate

int nIterate

setup

SimulationSetup setup

task

SimulationTask task

jLabel1

JLabel jLabel1

jLabel2

JLabel jLabel2

simulationIterationNumberSlider

JSlider simulationIterationNumberSlider

jPanel2

JPanel jPanel2

okButton

JButton okButton

simulationDelaySlider

JSlider simulationDelaySlider

cancelButton

JButton cancelButton

jPanel1

JPanel jPanel1

Class ch.unizh.ini.friend.gui.StatusPanel extends JPanel implements Serializable

Serialized Fields

cellName

String cellName

activity

float activity

stimulusName

String stimulusName

setup

SimulationSetup setup

stimulus

Stimulus stimulus

cellVisibleEnabled

boolean cellVisibleEnabled

plottingEnabledTextField

JTextField plottingEnabledTextField

cellComboBox

JComboBox cellComboBox

Class ch.unizh.ini.friend.gui.StimulusAction extends AbstractAction implements Serializable

Serialized Fields

stimulus

Stimulus stimulus
the stimulus

Class ch.unizh.ini.friend.gui.StimulusAction.Brighten extends StimulusAction implements Serializable

Class ch.unizh.ini.friend.gui.StimulusAction.BrightenBackground extends StimulusAction implements Serializable

Class ch.unizh.ini.friend.gui.StimulusAction.Darken extends StimulusAction implements Serializable

Class ch.unizh.ini.friend.gui.StimulusAction.DarkenBackground extends StimulusAction implements Serializable

Class ch.unizh.ini.friend.gui.StimulusAction.FlipContrast extends StimulusAction implements Serializable

Class ch.unizh.ini.friend.gui.StimulusAction.Rotate extends StimulusAction implements Serializable

Class ch.unizh.ini.friend.gui.TangentScreen extends JPanel implements Serializable

Serialized Fields

colorChooser

ColorChooser colorChooser
Color-chooser to select the forground and background color of the (color) stimulus.


simulationSetup

SimulationSetup simulationSetup

stimulus

Stimulus stimulus

showPhotoreceptorsEnabled

boolean showPhotoreceptorsEnabled

stimulusControlEnabled

boolean stimulusControlEnabled

mouseTransform

AffineTransform mouseTransform

mousePosition

Point mousePosition

spikeTriggeredStimuli

ch.unizh.ini.friend.gui.TangentScreen.SpikeTriggeredStimuli spikeTriggeredStimuli

markers

ch.unizh.ini.friend.gui.TangentScreen.Markers markers
the markers that the user has placed


dirty

Rectangle2D dirty

spikeImage

Image spikeImage

spikeGraphics

Graphics2D spikeGraphics

viewport

JViewport viewport

foregroundMenuItem

JMenuItem foregroundMenuItem

brightenMenuItem

JMenuItem brightenMenuItem

backgroundMenuItem

JMenuItem backgroundMenuItem

darkenBackgroundMenuItem

JMenuItem darkenBackgroundMenuItem

stimulusControlPopupMenu

JPopupMenu stimulusControlPopupMenu

invertContrastMenuItem

JMenuItem invertContrastMenuItem

rotateMenuItem

JMenuItem rotateMenuItem

darkenMenuItem

JMenuItem darkenMenuItem

brightenBackgroundMenuItem

JMenuItem brightenBackgroundMenuItem

Package ch.unizh.ini.friend.record

Class ch.unizh.ini.friend.record.SimulationReporter extends AbstractMonitor implements Serializable

Serialized Fields

setup

SimulationSetup setup

startTime

long startTime

lastInput

Object lastInput

lastSpikingCellReturn

boolean lastSpikingCellReturn

listeners

LinkedList<E> listeners

reportingEnabled

boolean reportingEnabled

Class ch.unizh.ini.friend.record.SpikeEvent extends EventObject implements Serializable

Serialized Fields

time

long time

Class ch.unizh.ini.friend.record.SpikePlotter extends JFrame implements Serializable

Serialized Fields

reporter

SpikeReporter reporter

p

Point p

panel

JPanel panel

image

BufferedImage image

dim

Dimension dim

g

Graphics2D g

stimSize

int stimSize

stimAspectRatio

int stimAspectRatio

spikeSize

int spikeSize

font

Font font

spikePositionJitter

int spikePositionJitter

rand

Random rand

spikeLogger

SpikeLogger spikeLogger

startTime

long startTime

dimOp

RescaleOp dimOp

Package ch.unizh.ini.friend.simulation

Class ch.unizh.ini.friend.simulation.AbstractAcceptsInput extends Object implements Serializable

Serialized Fields

inputs

Collection<E> inputs
The input components for this one.

Class ch.unizh.ini.friend.simulation.AbstractMonitor extends AbstractAcceptsInput implements Serializable

Class ch.unizh.ini.friend.simulation.AudioOutput extends AbstractMonitor implements Serializable

Serialized Fields

spikeSound

SpikeSound spikeSound

muted

boolean muted

lastInput

Object lastInput

lastSpikingCellReturn

boolean lastSpikingCellReturn

Class ch.unizh.ini.friend.simulation.SimpleOutputMonitor extends AbstractMonitor implements Serializable

Serialized Fields

deliverable

SimpleOutputMonitor.Deliverable deliverable
The prototype of the deliverable.


updateInterval

long updateInterval
The update interval in milliseconds.


nextUpdate

long nextUpdate
The time of the next update.

Class ch.unizh.ini.friend.simulation.SimulationSetup.NoSuchCellException extends RuntimeException implements Serializable


Package ch.unizh.ini.friend.simulation.cells

Class ch.unizh.ini.friend.simulation.cells.AbstractCell extends AbstractAcceptsInput implements Serializable

Serialized Fields

value

float value
The current value.


newValue

float newValue
The new output value.

Class ch.unizh.ini.friend.simulation.cells.AbstractSpikingCell extends AbstractCell implements Serializable

Class ch.unizh.ini.friend.simulation.cells.BipolarCell extends AbstractCell implements Serializable

Serialized Fields

offset

float offset

location

RetinotopicLocation location

Class ch.unizh.ini.friend.simulation.cells.ColorPhotoreceptor extends Photoreceptor implements Serializable

Serialized Fields

coneType

int coneType

Class ch.unizh.ini.friend.simulation.cells.GanglionCell extends IntegrateFireCell implements Serializable

Serialized Fields

location

RetinotopicLocation location

Class ch.unizh.ini.friend.simulation.cells.HorizontalCell extends AbstractCell implements Serializable

Serialized Fields

tau

float tau
the lowpass time constant of the HorizontalCell


lowPass

Filter lowPass
A low-pass filter.

Class ch.unizh.ini.friend.simulation.cells.IntegrateFireCell extends AbstractSpikingCell implements Serializable

Serialized Fields

leakTime

float leakTime
The leak time constant in seconds.


threshold

float threshold
The threshold where the cell will fire.


potasiumReversal

float potasiumReversal
Potasium reversal potential. The cell potential will not go below this value. This is the lower power rail of the cell. It prevents the cell from becoming infinitely hyperpolarized.


spikeRateMeasurementWindow

float spikeRateMeasurementWindow
spike rate measurement time window in seconds. The spike rate is measured with a fading memory of this duration.


rateMeasurementFilter

LowPassFilter rateMeasurementFilter

spike

boolean spike
Encodes whether the cell is making a spike now.


newSpike

boolean newSpike
Encodes whether the cell will make a spike after the next IntegrateFireCell.update().


integrationPotential

float integrationPotential
The currently integrated membrane potential.


maxRate

float maxRate
the maximum spike rate, measured in spikes/IntegrateFireCell.SPIKE_RATE_TIME_SCALE.


time

float time

lastSpikeTime

float lastSpikeTime

Class ch.unizh.ini.friend.simulation.cells.Photoreceptor extends AbstractCell implements Serializable

Serialized Fields

shape

ConvexPolygon shape
The shape of this photoreceptor.


stimulus

Stimulus stimulus
The stimulus for this photoreceptor (and likely the whole simulation).


gain

float gain
The gain of the high-pass output.


highPass

Filter highPass
A high-pass filter that is used to compute the transient gain.


location

RetinotopicLocation location

Class ch.unizh.ini.friend.simulation.cells.PoissonSoma extends AbstractSpikingCell implements Serializable

Serialized Fields

r

Random r
The pseudo-random generator.


Package ch.unizh.ini.friend.simulation.synapses

Class ch.unizh.ini.friend.simulation.synapses.AbstractSynapse extends AbstractAcceptsInput implements Serializable

Class ch.unizh.ini.friend.simulation.synapses.ScalingSynapse extends AbstractSynapse implements Serializable

Serialized Fields

weight

float weight
The weight with which the input will be multiplied.


Package ch.unizh.ini.friend.tests

Class ch.unizh.ini.friend.tests.ConvexPolygonTest extends JPanel implements Serializable

Serialized Fields

shapes

ArrayList<E> shapes
List of shapes to draw.


intersections

ArrayList<E> intersections
List of intersections to fill.


width

float width
Width of the visible area.


height

float height
Height of the visible area.

Class ch.unizh.ini.friend.tests.OscillatingOutput extends AbstractCell implements Serializable

Serialized Fields

vt

float vt
Virtual time.


vdt

float vdt
Virtual dt per iteration.

Class ch.unizh.ini.friend.tests.OutputPrinter extends AbstractMonitor implements Serializable

Serialized Fields

pre

String pre
The string to prepend to the ouput.


post

String post
The string to append to the ouput.


stream

PrintStream stream
The stream to print to.

Class ch.unizh.ini.friend.tests.PhotoreceptorTest extends JPanel implements Serializable

Serialized Fields

stimulus

Stimulus stimulus

shapes

ArrayList<E> shapes
Shapes of the photo receptors.


intersections

ArrayList<E> intersections
Intersections between the shapes of the photoreceptors and the stimulus.


receptors

ArrayList<E> receptors
The photoreceptors.

Class ch.unizh.ini.friend.tests.SimulationTest extends JPanel implements Serializable

Serialized Fields

setup

SimulationSetup setup
The simulation setup.

Class ch.unizh.ini.friend.tests.SpikeSoundTestGUI extends JFrame implements Serializable

Serialized Fields

jSlider1

JSlider jSlider1

Package ch.unizh.ini.friend.topology

Class ch.unizh.ini.friend.topology.RetinotopicLocation extends Point2D.Float implements Serializable


http://www.ini.unizh.ch/~tobi/friend