Brain

java.lang.Object
- brain.Brain

All Implemented Interfaces:

java.io.Serializable, java.lang.Runnable
```
public class Brain
extends java.lang.Object
implements java.lang.Runnable, java.io.Serializable
```
modules for the cognitive system

Module: general interface for all components (modules) DhanModule: the dHAN module, implements the `Module' interface PatternInputModule: the input module, implements the `Module' interface

classical auxiliary classes

OneAdaptVar

a single adaptive signal

OneStimulus

class representing an individual external stimuli

OneStimulusContainer

class managing sets of stimuli

OneCenter

representing a globally defined active center (AC)

OneCluster

a general clique; contains a sequence of active centers

OneCycle

a general cycle; contains a sequence of active clusters

abstract auxiliary facilities

FacilPrint

general printing to file facility

FacilCliqueNet

generates networks with a given distribution of cliques

RandomGraphs

facility for the analysis of general random graphs

FacilStimuli

facility to generate sets of test stimuli

classes for the statistical analysis

StatNet

general network-theoretical statistics facility

StatActiClus

facility for finding/evaluation of cliques/cycles/history

StatBiasLearn

monitors from-bias-learning of DhanModule-type modules

StatTimeManagement

monitors time to finish a simulation run

list of important output files

time series of data

Brain_dhan.acti

activities x_i(t)

Brain_dhan.rate

growth rate r_i(t)

Brain_dhan.rateInt

internal contribution to growth rate r_i(t)

Brain_dhan.res

reservoir phi_i(t)

Brain_dhan.bias

bias b(t)

Brain_dhan.backRate

input grows rates

Brain_dhan.backStandDev

standard deviation of incoming link-strength

Brain_dhan.diffModuleSignal

the diffusive learning signal

Brain_dhan.synchro

an effective measure of clique formation

Brain_dhan.actiClus

time series of clusters (cliques) activated

Brain_dhan.actiClusStat

how many times a given cluster was activated

Brain_dhan.actiRate

auxiliary rates

Brain_input.stim

time series of input stimuli

input files

Brain_dhan.ass

cliques (associations) when reading network from file

Brain_input.patt

input stimuli

Brain_input.refPatt

reference patterns for analyzing purposes

output files (generated at the end)

Brain_dhan_input.cliqRecFields

the receptive fields in (input) of cliques in (input)

Brain_dhan_input.cliqRefPatt

the response of cliques in (dhanModule) with respect to reference patterns in (input)

Brain_dhan.cliq

all cliques in dhanModule module

Brain_dhan.stat

statistics like degree distribution

Brain_dhan.statBackLinks

bin-statistics of the backward links

Brain_dhan_input.backLinks

backlinks connecting (input)-->(dhanModule)

Brain_dhan.acSequence

time sequences of active clusters of a module formed out of Brain_dhan.actiClus

Brain_dhan.statCycle

statistical properties of cycles of active clusters in Brain_dhan.actiClus

auxiliary files

Brain_dhan.fig

xfig picture of network

Brain_dhan.learn

an auxiliary learning analysis

output-file name convention
Brain_(module1)_(module2)_(...).datatyp where (module..) are the name of the modules involved in data extraction.
instructions for developers :: compatibility with the monitoring interface (GUI)
module member variable `memberVariable' is observable in GUI if present in member variable 'guiObservables[]' module member variable `memberVariable' is changable by the GUI if public and not static if a member variable `memberVariable' has only a finite number of allowed values put these in `memberVariableAllowedValues'; when `memberVariableAllowedValues' is present, then `memberVariable' is changeable through the GUI
actually implemented types of diffusive module signals
DhanModule :: novelty signal, cliques activated by backward links
actually used type of receptors for the inter- and inter-modular diffusive control
"backwardLearning" :: DhanModule - learning of backward links Entry point with global variables. Modules like `DhanModule' extend this Brain and acquire such access to the HashMap `modules' which contains all (other) components.

Since:

2008

See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected javax.swing.event.EventListenerList`	`changeListeners` Listeners to be notified of module changes.
`double`	`clusterSearchTimeInterval` Time interval for searching for active clusters.
`java.io.File`	`dataDirectory`
`java.io.File`	`dataInputDirectory`
`java.io.File`	`dataOutputDirectory`
`static java.text.DateFormat`	`DATE_FORMAT`
`static java.io.File`	`DEFAULT_DATA_DIRECTORY`
`static java.io.File`	`DEFAULT_DATA_INPUT_DIRECTORY`
`static java.io.File`	`DEFAULT_DATA_OUTPUT_DIRECTORY`
`static java.io.File`	`RESOURCES_DIRECTORY`
`static java.lang.String`	`VERSION`

Constructor Summary

Constructors
Constructor and Description

Brain()

Constructors
Constructor and Description
`Brain()`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addChangeListener(javax.swing.event.ChangeListener listener)`
`void`	`addLogger(java.lang.Object object, java.lang.reflect.AccessibleObject accessibleObject, java.io.File file)`
`void`	`addLogger(java.lang.Object object, java.lang.String fieldOrMethod)` User friendly version of method `addLogger`.
`void`	`addModule(Module module)` Adds a module to this brain.
`void`	`calculateSimulationStatistics()` Calculates statistics for data analysis.
`void`	`closeLoggers()`
`static Brain`	`createDefaultGrosBrain()`
`static Brain`	`createDefaultLinkerhandBrain()`
`void`	`exportGraphvizGraph(java.io.File gvFile)`
`void`	`exportGraphvizGraph(java.io.File gvFile, double lowerLinkBound, double upperLinkBound)`
`double`	`getLogInterval()`
`java.util.Set<Module>`	`getModules()` Get modules of brain.
`Module[]`	`getModules(java.lang.Class<?> clas)`
`static Module[]`	`getModules(java.lang.Class<?> clas, Module[] modules)` Get modules of given class (or subclasses) from given modules.
`int`	`getSimulationSleepDelay()` Returns getGlobalTimeDelayMillis.
`double`	`getTime()` Returns the time for Online Monitoring Purposes
`double`	`getTimeDelta()` Returns the timeDelta for Online Monitoring Purposes
`long`	`getTimeStepNumber()` Returns the timeStepNumber for Online Monitoring Purposes
`boolean`	`hasModule(Module module)`
`boolean`	`isSuspended()` Tests whether the simulation is suspended.
`static Brain`	`load(java.io.File file)` Deserializes brain (and its modules) from the given file.
`static Module`	`loadModule(java.lang.reflect.Constructor<?> constructor, java.lang.Object[] arguments)` Loads a module to the system given the concrete constructor and all of its arguments.
`static void`	`main(java.lang.String[] args)` Main routine to start the Brain simulation program.
`protected void`	`notifyStateChanged(javax.swing.event.ChangeEvent event)`
`void`	`performLogging()`
`void`	`performOneTimeStep(double timeDelta)`
`void`	`printGraphvizGraphs()` Prints default Graphviz files for the current network.
`void`	`printLogFileHeaders()`
`void`	`printModuleSetup()`
`void`	`removeChangeListener(javax.swing.event.ChangeListener listener)`
`void`	`removeLogger(java.lang.Object object)`
`void`	`removeLogger(java.lang.Object object, java.lang.reflect.Field field)`
`void`	`removeModule(Module module)` Removes a module from this brain.
`void`	`resume()` Resumes the current simulation.
`void`	`run()` The global dynamics.
`static void`	`save(Brain brain, java.io.File file)` Serializes the given brain object (and its modules) to the given file.
`void`	`save(java.io.File file)` Serializes the current brain (and its modules) to the given file.
`void`	`setDataOutputDirectory(java.io.File file)`
`void`	`setLogInterval(double logInterval)`
`void`	`setSimulationSleepDelay(int simulationSleepDelay)` Sets simulationSleepDelay.
`void`	`setTime(double time)` Sets the time member variable.
`void`	`setTimeDelta(double timeDelta)` Sets the timeDelta member variable.
`void`	`setTimeDeltaAndDuration(double timeDelta, double duration)` Sets the timeDelta member variable.
`void`	`setTimeStepNumber(long timeStepNumber)` Sets the timeStepNumber member variable.
`void`	`suspend()` Suspends the current simulation.
`java.lang.String`	`toString()` Basic toString method.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - dataDirectory
```
public final transient java.io.File dataDirectory
```
  - dataInputDirectory
```
public final transient java.io.File dataInputDirectory
```
  - dataOutputDirectory
```
public transient java.io.File dataOutputDirectory
```
  - DATE_FORMAT
```
public static final java.text.DateFormat DATE_FORMAT
```
  - DEFAULT_DATA_DIRECTORY
```
public static final java.io.File DEFAULT_DATA_DIRECTORY
```
  - DEFAULT_DATA_INPUT_DIRECTORY
```
public static final java.io.File DEFAULT_DATA_INPUT_DIRECTORY
```
  - DEFAULT_DATA_OUTPUT_DIRECTORY
```
public static java.io.File DEFAULT_DATA_OUTPUT_DIRECTORY
```
  - RESOURCES_DIRECTORY
```
public static final java.io.File RESOURCES_DIRECTORY
```
  - VERSION
```
public static final java.lang.String VERSION
```
    See Also:
    Constant Field Values
  - changeListeners
```
protected transient javax.swing.event.EventListenerList changeListeners
```
    Listeners to be notified of module changes. This field is marked transient, because AccessibleObjects (Fields, …) are not serializable. There (de-)serialization of that field is done by the methods readObject and writeObject.
  - clusterSearchTimeInterval
```
public double clusterSearchTimeInterval
```
    Time interval for searching for active clusters. The default value for `clusterSearchTimeInterval' may be changed at run-time.
- Constructor Detail
  - Brain
```
public Brain()
```
- Method Detail
  - createDefaultGrosBrain
```
public static Brain createDefaultGrosBrain()
                                    throws java.io.FileNotFoundException
```
    Throws:
    
    java.io.FileNotFoundException
  - createDefaultLinkerhandBrain
```
public static Brain createDefaultLinkerhandBrain()
```
  - main
```
public static void main(java.lang.String[] args)
```
    Main routine to start the Brain simulation program.
    
    Parameters:
    args - Arguments for the program. Use --help to get a list.
  - printModuleSetup
```
public void printModuleSetup()
```
  - printGraphvizGraphs
```
public void printGraphvizGraphs()
```
    Prints default Graphviz files for the current network. All Modules with intra- and inter-links are printed. Prints three versions: only excitatory links, only inhibitory links, all links.
  - run
```
public void run()
```
    The global dynamics. Contains the loop over time-steps for the numerical integration of the differential equations for the time-development.
    
    Specified by:
    
    run in interface java.lang.Runnable
  - performOneTimeStep
```
public void performOneTimeStep(double timeDelta)
```
  - getLogInterval
```
public double getLogInterval()
```
  - setLogInterval
```
public void setLogInterval(double logInterval)
```
  - performLogging
```
public void performLogging()
```
  - setDataOutputDirectory
```
public void setDataOutputDirectory(java.io.File file)
```
  - printLogFileHeaders
```
public void printLogFileHeaders()
```
  - addLogger
```
public void addLogger(java.lang.Object object,
             java.lang.reflect.AccessibleObject accessibleObject,
             java.io.File file)
```
  - addLogger
```
public void addLogger(java.lang.Object object,
             java.lang.String fieldOrMethod)
```
    User friendly version of method addLogger. The accessible object (field, method, …) will be search for given a string. First fields, than methods. The filename will be created automatically according to the observed object and the accessible object, viz. the method or field to observe.
    
    Parameters:
    object -
    fieldOrMethod -
  - removeLogger
```
public void removeLogger(java.lang.Object object)
```
  - removeLogger
```
public void removeLogger(java.lang.Object object,
                java.lang.reflect.Field field)
```
  - closeLoggers
```
public void closeLoggers()
```
  - addChangeListener
```
public void addChangeListener(javax.swing.event.ChangeListener listener)
```
  - removeChangeListener
```
public void removeChangeListener(javax.swing.event.ChangeListener listener)
```
  - notifyStateChanged
```
protected void notifyStateChanged(javax.swing.event.ChangeEvent event)
```
  - hasModule
```
public boolean hasModule(Module module)
```
  - addModule
```
public void addModule(Module module)
```
    Adds a module to this brain. Adds its afferent modules as well as they are also necessarily being updated as time evolves.
    
    Parameters:
    module - Module to add.
  - removeModule
```
public void removeModule(Module module)
```
    Removes a module from this brain.
    
    Parameters:
    module - Module to remove.
  - getModules
```
public Module[] getModules(java.lang.Class<?> clas)
```
  - getModules
```
public static Module[] getModules(java.lang.Class<?> clas,
                  Module[] modules)
```
    Get modules of given class (or subclasses) from given modules.
    
    Parameters:
    clas - Class to filter the modules for.
    modules - Modules to search for instances.
    
    Returns:
    Modules of desired type.
  - getModules
```
public java.util.Set<Module> getModules()
```
    Get modules of brain.
    
    Returns:
    modules of brain.
  - getTimeStepNumber
```
public long getTimeStepNumber()
```
    Returns the timeStepNumber for Online Monitoring Purposes
    
    Returns:
    timeStepNumber
  - setTimeStepNumber
```
public void setTimeStepNumber(long timeStepNumber)
```
    Sets the timeStepNumber member variable.
    
    Parameters:
    timeStepNumber -
  - getTimeDelta
```
public double getTimeDelta()
```
    Returns the timeDelta for Online Monitoring Purposes
    
    Returns:
    timeDelta
  - setTimeDelta
```
public void setTimeDelta(double timeDelta)
```
    Sets the timeDelta member variable.
    
    Parameters:
    timeDelta -
  - setTimeDeltaAndDuration
```
public void setTimeDeltaAndDuration(double timeDelta,
                           double duration)
```
    Sets the timeDelta member variable.
    
    Parameters:
    timeDelta -
  - getTime
```
public double getTime()
```
    Returns the time for Online Monitoring Purposes
    
    Returns:
    time
  - loadModule
```
public static Module loadModule(java.lang.reflect.Constructor<?> constructor,
                java.lang.Object[] arguments)
                         throws java.lang.IllegalArgumentException
```
    Loads a module to the system given the concrete constructor and all of its arguments.
    
    Parameters:
    constructor - Constructor of the module class to create the module instance from.
    arguments - Arguments for the given constructor.
    
    Throws:
    
    java.lang.IllegalArgumentException
  - setTime
```
public void setTime(double time)
```
    Sets the time member variable.
    
    Parameters:
    time - Time of the simulation.
  - isSuspended
```
public boolean isSuspended()
```
    Tests whether the simulation is suspended.
    
    Returns:
    true if the simulation is suspended, false otherwise.
  - suspend
```
public void suspend()
```
    Suspends the current simulation.
  - resume
```
public void resume()
```
    Resumes the current simulation.
  - toString
```
public java.lang.String toString()
```
    Basic toString method.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    Returns the string "Brain".
  - save
```
public void save(java.io.File file)
```
    Serializes the current brain (and its modules) to the given file. The filename has to end with either ".ser" or ".xml". If it ends with ".ser" the writeObject method is used, while if it ends with ".xml" the XStream serialization is used.
  - save
```
public static void save(Brain brain,
        java.io.File file)
```
    Serializes the given brain object (and its modules) to the given file. The filename has to end with either ".ser" or ".xml". If it ends with ".ser" the writeObject method is used, while if it ends with ".xml" the XStream serialization is used.
    
    Parameters:
    brain - Object of class Brain to serialize.
    file - File to write the serialization to.
  - load
```
public static Brain load(java.io.File file)
                  throws java.lang.ClassNotFoundException,
                         java.io.IOException
```
    Deserializes brain (and its modules) from the given file. The filename has to end with either ".ser" or ".xml". If it ends with ".ser" the readObject method is used, while if it ends with ".xml" the XStream deserialization is used.
    
    Throws:
    
    java.lang.ClassNotFoundException
    
    java.io.IOException
  - calculateSimulationStatistics
```
public void calculateSimulationStatistics()
```
    Calculates statistics for data analysis.
  - getSimulationSleepDelay
```
public int getSimulationSleepDelay()
```
    Returns getGlobalTimeDelayMillis.
    
    Returns:
    Number of milliseconds the program has to sleep in every loop in oder to delay execution of small and fast systems.
    See Also:
    simulationSleepDelay
  - setSimulationSleepDelay
```
public void setSimulationSleepDelay(int simulationSleepDelay)
```
    Sets simulationSleepDelay.
    
    Parameters:
    simulationSleepDelay - - Number of milliseconds the program has to sleep in every loop in oder to delay execution of small and fast systems. *
    See Also:
    simulationSleepDelay
  - exportGraphvizGraph
```
public void exportGraphvizGraph(java.io.File gvFile)
                         throws java.io.FileNotFoundException
```
    Throws:
    
    java.io.FileNotFoundException
  - exportGraphvizGraph
```
public void exportGraphvizGraph(java.io.File gvFile,
                       double lowerLinkBound,
                       double upperLinkBound)
                         throws java.io.FileNotFoundException
```
    Throws:
    
    java.io.FileNotFoundException

Class Brain

modules for the cognitive system

classical auxiliary classes

abstract auxiliary facilities

classes for the statistical analysis

list of important output files

time series of data

input files

output files (generated at the end)

auxiliary files

output-file name convention

instructions for developers :: compatibility with the monitoring interface (GUI)

actually implemented types of diffusive module signals

actually used type of receptors for the inter- and inter-modular diffusive control

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

dataDirectory

dataInputDirectory

dataOutputDirectory

DATE_FORMAT

DEFAULT_DATA_DIRECTORY

DEFAULT_DATA_INPUT_DIRECTORY

DEFAULT_DATA_OUTPUT_DIRECTORY

RESOURCES_DIRECTORY

VERSION

changeListeners

clusterSearchTimeInterval

Constructor Detail

Brain

Method Detail

createDefaultGrosBrain

createDefaultLinkerhandBrain

main

printModuleSetup

printGraphvizGraphs

run

performOneTimeStep

getLogInterval

setLogInterval

performLogging

setDataOutputDirectory

printLogFileHeaders

addLogger

addLogger

removeLogger

removeLogger

closeLoggers

addChangeListener

removeChangeListener

notifyStateChanged

hasModule

addModule

removeModule

getModules

getModules

getModules

getTimeStepNumber

setTimeStepNumber

getTimeDelta

setTimeDelta

setTimeDeltaAndDuration

getTime

loadModule

setTime

isSuspended

suspend

resume

toString

save

save

load

calculateSimulationStatistics

getSimulationSleepDelay

setSimulationSleepDelay

exportGraphvizGraph

exportGraphvizGraph