Nengo.ca

ca.nengo.model.muscle.impl
Class LinkSegmentModelImpl

java.lang.Object
  extended by ca.nengo.model.muscle.impl.LinkSegmentModelImpl
All Implemented Interfaces:
LinkSegmentModel, Node, Probeable, Resettable, SimulationMode.ModeConfigurable, VisiblyMutable, java.io.Serializable, java.lang.Cloneable

public class LinkSegmentModelImpl
extends java.lang.Object
implements LinkSegmentModel

Default implementation of LinkSegmentModel.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface ca.nengo.util.VisiblyMutable
VisiblyMutable.Event, VisiblyMutable.Listener, VisiblyMutable.NameChangeEvent, VisiblyMutable.NodeRemovedEvent
 
Constructor Summary
LinkSegmentModelImpl(java.lang.String name, DynamicalSystem dynamics, float timeStep)
           
 
Method Summary
 void addChangeListener(VisiblyMutable.Listener listener)
           
 LinkSegmentModel clone()
           
 void defineJoint(java.lang.String name, Function[] definition)
           
 void defineMuscle(int input, SkeletalMuscle muscle, Function length, Function momentArm)
           
 Node[] getChildren()
           
 java.lang.String getDocumentation()
           
 TimeSeries getHistory(java.lang.String stateName)
          Note that the units of TimeSeries' for a given state do not change over time (ie at different time steps).
 java.lang.String[] getJointNames()
           
 SimulationMode getMode()
           
 SkeletalMuscle[] getMuscles()
           
 java.lang.String getName()
           
 Origin getOrigin(java.lang.String name)
           
 Origin[] getOrigins()
           
 Termination getTermination(java.lang.String name)
           
 Termination[] getTerminations()
           
 java.util.Properties listStates()
           
 void removeChangeListener(VisiblyMutable.Listener listener)
           
 void reset(boolean randomize)
           
 void run(float startTime, float endTime)
          Runs the Node (including all its components), updating internal state and outputs as needed.
 void setDocumentation(java.lang.String text)
           
 void setMode(SimulationMode mode)
          Sets the object to run in either the given mode or the closest mode that it supports (all ModeConfigurables must support SimulationMode.DEFAULT, and must default to this mode).
 void setName(java.lang.String name)
           
 java.lang.String toScript(java.util.HashMap<java.lang.String,java.lang.Object> scriptData)
           
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

LinkSegmentModelImpl

public LinkSegmentModelImpl(java.lang.String name,
                            DynamicalSystem dynamics,
                            float timeStep)
Parameters:
name - Segment name
dynamics - Dynamical system governing function
timeStep - dt
Method Detail

defineJoint

public void defineJoint(java.lang.String name,
                        Function[] definition)
Parameters:
name - Name of joint
definition - 2 or 3 Functions of generalized coordinates, corresponding to (x,y) position of the joint or (x,y,z) position of the joint

defineMuscle

public void defineMuscle(int input,
                         SkeletalMuscle muscle,
                         Function length,
                         Function momentArm)
Parameters:
input - Which of the n inputs are we defining?
muscle - Muscle being defined
length - Function defining length?
momentArm - Function defining momentum?

getJointNames

public java.lang.String[] getJointNames()
Specified by:
getJointNames in interface LinkSegmentModel
Returns:
Names of joints
See Also:
LinkSegmentModel.getJointNames()

getMuscles

public SkeletalMuscle[] getMuscles()
Specified by:
getMuscles in interface LinkSegmentModel
Returns:
Array of SkeletalMuscles
See Also:
LinkSegmentModel.getMuscles()

getMode

public SimulationMode getMode()
Specified by:
getMode in interface SimulationMode.ModeConfigurable
Returns:
The SimulationMode in which the object is running
See Also:
SimulationMode.ModeConfigurable.getMode()

getName

public java.lang.String getName()
Specified by:
getName in interface Node
Returns:
Name of Node (must be unique in a Network)
See Also:
Node.getName()

setName

public void setName(java.lang.String name)
             throws StructuralException
Specified by:
setName in interface Node
Parameters:
name - The new name
Throws:
StructuralException - if name already exists?
See Also:
Node.setName(java.lang.String)

getOrigin

public Origin getOrigin(java.lang.String name)
                 throws StructuralException
Specified by:
getOrigin in interface Node
Parameters:
name - Name of an Origin on this Node
Returns:
The named Origin if it exists
Throws:
StructuralException - if the named Origin does not exist
See Also:
Node.getOrigin(java.lang.String)

getOrigins

public Origin[] getOrigins()
Specified by:
getOrigins in interface Node
Returns:
Sets of ouput channels (eg spiking outputs, gap junctional outputs, etc.)
See Also:
Node.getOrigins()

getTermination

public Termination getTermination(java.lang.String name)
                           throws StructuralException
Specified by:
getTermination in interface Node
Parameters:
name - Name of a Termination onto this Node
Returns:
The named Termination if it exists
Throws:
StructuralException - if the named Termination does not exist
See Also:
Node.getTermination(java.lang.String)

getTerminations

public Termination[] getTerminations()
Specified by:
getTerminations in interface Node
Returns:
Sets of input channels (these have the same dimension as corresponding Origins to which they are connected).
See Also:
Node.getTerminations()

run

public void run(float startTime,
                float endTime)
         throws SimulationException
Description copied from interface: Node
Runs the Node (including all its components), updating internal state and outputs as needed. Runs should be short (eg 1ms), because inputs can not be changed during a run, and outputs will only be communicated to other Nodes after a run.

Specified by:
run in interface Node
Parameters:
startTime - simulation time at which running starts (s)
endTime - simulation time at which running ends (s)
Throws:
SimulationException - if a problem is encountered while trying to run
See Also:
Node.run(float, float)

setMode

public void setMode(SimulationMode mode)
Description copied from interface: SimulationMode.ModeConfigurable
Sets the object to run in either the given mode or the closest mode that it supports (all ModeConfigurables must support SimulationMode.DEFAULT, and must default to this mode).

Specified by:
setMode in interface SimulationMode.ModeConfigurable
Parameters:
mode - SimulationMode in which it is desired that the object runs.
See Also:
SimulationMode.ModeConfigurable.setMode(ca.nengo.model.SimulationMode)

reset

public void reset(boolean randomize)
Specified by:
reset in interface Resettable
Parameters:
randomize - True indicates that the object should be reset to a randomly selected initial state (the object must be aware of the distribution from which to draw from). False indicates that the object should be reset to a fixed initial state (which it must also know). Some objects may not support randomization of the initial state, in which case a fixed state will be used in either case.
See Also:
Resettable.reset(boolean)

getHistory

public TimeSeries getHistory(java.lang.String stateName)
                      throws SimulationException
Description copied from interface: Probeable
Note that the units of TimeSeries' for a given state do not change over time (ie at different time steps). CAUTION: The TimeSeries should not contain a reference to any arrays that you are going to change later. The caller owns what you return.

Specified by:
getHistory in interface Probeable
Parameters:
stateName - A state variable name
Returns:
History of values for the named state variable. The history must cover the most recent network time step, and no more. There should be no overlap in the time points returned for different steps.
Throws:
SimulationException - if the Probeable does not have the requested state
See Also:
Probeable.getHistory(java.lang.String)

listStates

public java.util.Properties listStates()
Specified by:
listStates in interface Probeable
Returns:
List of state variable names, eg "V", and associated descriptions eg "membrane potential (mV)"
See Also:
Probeable.listStates()

getDocumentation

public java.lang.String getDocumentation()
Specified by:
getDocumentation in interface Node
Returns:
User-specified documentation for the Node, if any
See Also:
Node.getDocumentation()

setDocumentation

public void setDocumentation(java.lang.String text)
Specified by:
setDocumentation in interface Node
Parameters:
text - New user-specified documentation for the Node
See Also:
Node.setDocumentation(java.lang.String)

addChangeListener

public void addChangeListener(VisiblyMutable.Listener listener)
Specified by:
addChangeListener in interface VisiblyMutable
Parameters:
listener - Listener to add
See Also:
VisiblyMutable.addChangeListener(ca.nengo.util.VisiblyMutable.Listener)

removeChangeListener

public void removeChangeListener(VisiblyMutable.Listener listener)
Specified by:
removeChangeListener in interface VisiblyMutable
Parameters:
listener - Listener to remove
See Also:
VisiblyMutable.removeChangeListener(ca.nengo.util.VisiblyMutable.Listener)

clone

public LinkSegmentModel clone()
                       throws java.lang.CloneNotSupportedException
Specified by:
clone in interface Node
Overrides:
clone in class java.lang.Object
Returns:
An independent copy of the Node
Throws:
java.lang.CloneNotSupportedException - if clone can't be made

getChildren

public Node[] getChildren()
Specified by:
getChildren in interface Node

toScript

public java.lang.String toScript(java.util.HashMap<java.lang.String,java.lang.Object> scriptData)
                          throws ScriptGenException
Specified by:
toScript in interface Node
Parameters:
scriptData - Map of class parent and prefix data for generating python script
Returns:
Python script for generating the node
Throws:
ScriptGenException - if the node cannot be generated in script

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