AnimatLab  2
Test
FiringRateSim::FiringRateModule Class Reference

Firing rate neural module. More...

#include <FiringRateModule.h>

+ Inheritance diagram for FiringRateSim::FiringRateModule:
+ Collaboration diagram for FiringRateSim::FiringRateModule:

Public Member Functions

 FiringRateModule ()
 Default constructor. More...
 
virtual ~FiringRateModule ()
 Destructor. More...
 
bool ActiveArray ()
 Gets the active array. More...
 
void ActiveArray (bool bVal)
 Sets the active array. More...
 
virtual bool AddItem (const std::string &strItemType, const std::string &strXml, bool bThrowError=true, bool bDoNotInit=false)
 Adds a new object to this parent. More...
 
virtual void AddNeuron (std::string strXml, bool bDoNotInit=false)
 Adds a neuron to the module. More...
 
virtual long CalculateSnapshotByteSize ()
 Calculates the snapshot byte size. More...
 
virtual int FindNeuronListPos (std::string strID, bool bThrowError=true)
 Searches for the neuron with the specified ID and returns its position in the list. More...
 
bool InactiveArray ()
 Gets the inactive array. More...
 
void InactiveArray (bool bVal)
 Sets the inactive array. More...
 
virtual void Initialize ()
 Initializes this object. More...
 
virtual void Kill (bool bState=true)
 Kills. More...
 
virtual void Load (CStdXml &oXml)
 
virtual void LoadKeyFrameSnapshot (byte *aryBytes, long &lIndex)
 Loads a key frame snapshot. More...
 
virtual std::string ModuleName ()
 Gets the module name. More...
 
virtual void QueryProperties (CStdPtrArray< TypeProperty > &aryProperties)
 
virtual bool RemoveItem (const std::string &strItemType, const std::string &strID, bool bThrowError=true)
 Removes a child item from this parent. More...
 
virtual void RemoveNeuron (std::string strID, bool bThrowError=true)
 Removes the neuron with the specified ID. More...
 
virtual void ResetSimulation ()
 Resets the simulation back to time 0. More...
 
virtual void SaveKeyFrameSnapshot (byte *aryBytes, long &lIndex)
 Saves a key frame snapshot. More...
 
virtual bool SetData (const std::string &strDataType, const std::string &strValue, bool bThrowError=true)
 Set a variable based on a string data type name. More...
 
virtual void StepSimulation ()
 Step the simulation for this object. More...
 
- Public Member Functions inherited from AnimatSim::Behavior::NeuralModule
 NeuralModule ()
 Default constructor. More...
 
virtual ~NeuralModule ()
 Destructor. More...
 
virtual void AddExternalSynapse (AnimatSim::Link *lpSynapse)
 
virtual void AddExternalSynapse (std::string strXml, bool bDoNotInit)
 Adds a synapse using an xml packet. More...
 
virtual void AttachSourceAdapter (Adapter *lpAdapter)
 Attaches a source adapter. More...
 
virtual void AttachTargetAdapter (Adapter *lpAdapter)
 Attaches a target adapter. More...
 
virtual IStdClassFactoryClassFactory ()
 Gets the class factory. More...
 
virtual void ClassFactory (IStdClassFactory *lpFactory)
 
virtual int FindExternalSynapseListPos (std::string strID, bool bThrowError=true)
 Searches for a synapse with the specified ID and returns its position in the list. More...
 
virtual float * GetDataPointer (const std::string &strDataType)
 Returns a float pointer to a data item of interest in this object. More...
 
OrganismGetOrganism ()
 Gets the organism. More...
 
SimulatorGetSimulator ()
 Gets the simulator. More...
 
virtual bool NeedToStep (bool bIncrement)
 Tells whether this NeuralModule needs to call StepSimulation. More...
 
virtual void RemoveExternalSynapse (std::string strID, bool bThrowError=true)
 Removes the synapse by the GUID ID. More...
 
virtual void RemoveSourceAdapter (Adapter *lpAdapter)
 Removes a source adapter. More...
 
virtual void RemoveTargetAdapter (Adapter *lpAdapter)
 Removes a target adapter. More...
 
virtual void ResetStepCounter ()
 
virtual void SetSystemPointers (Simulator *lpSim, Structure *lpStructure, NeuralModule *lpModule, Node *lpNode, bool bVerify)
 Sets the system pointers. More...
 
virtual void StepAdapters ()
 Step adapters. More...
 
virtual float TimeStep ()
 Gets the time step for this moudle in time units. More...
 
virtual void TimeStep (float fltVal)
 Sets the Time step for this moudle in time units. More...
 
virtual short TimeStepInterval ()
 Gets the time step interval. More...
 
virtual void TimeStepInterval (short iVal)
 Sets ime step interval. More...
 
virtual void VerifySystemPointers ()
 Verify that system pointers have been set correctly. More...
 
- Public Member Functions inherited from AnimatSim::AnimatBase
 AnimatBase ()
 Constructs an AnimatBase object. More...
 
virtual ~AnimatBase ()
 Destroys the AnimatBase object.. More...
 
virtual void AfterResetSimulation ()
 Called after a simulation reset for some objects. More...
 
virtual void Copy (CStdSerialize *lpSource)
 
virtual void Enabled (bool bVal)
 Tells whether this item is enabled or not. This is not actually used for all objects, only specific ones. I am putting it in the base class though to prevent numerous duplications. More...
 
virtual bool Enabled ()
 Tells whether this item is enabled or not. This is not actually used for all objects, only specific ones. I am putting it in the base class though to prevent numerous duplications. More...
 
virtual NeuralModuleGetNeuralModule ()
 Gets the neural module. More...
 
virtual NodeGetNode ()
 Gets the node. More...
 
virtual StructureGetStructure ()
 Gets the structure for this node. More...
 
virtual bool HasProperty (const std::string &strName)
 Queries this object if it has a property with the given name. More...
 
virtual std::string ID ()
 Gets the unique GUID ID of this object. More...
 
virtual void ID (std::string strValue)
 Sets the unique GUID ID of the object. More...
 
virtual void Load (StdUtils::CStdXml &oXml)
 Loads the item using an XML data packet. More...
 
virtual std::string Name ()
 Gets the name of this object. More...
 
virtual void Name (std::string strValue)
 Sets the name of the object. Blank is acceptable. More...
 
virtual AnimatPropertyType PropertyType (const std::string &strName)
 
virtual void QueryProperties (CStdPtrArray< TypeProperty > &aryProperties)
 Queries this object for a list of properties that can be changed using SetData. More...
 
virtual void ReInitialize ()
 Re-initialize this object. More...
 
virtual void Reset ()
 Resets this object. More...
 
virtual void RigidBodyAdded (std::string strID)
 
virtual void RigidBodyRemoved (std::string strID)
 
virtual bool Selected ()
 Tells if this items is selected or not. More...
 
virtual void Selected (bool bValue, bool bSelectMultiple)
 Selects this object. More...
 
virtual bool SetData (const std::string &strDataType, const float fltValue, bool bThrowError=true)
 Set a variable based on a string data type name. More...
 
virtual bool SetData (const std::string &strDataType, const long lValue, bool bThrowError=true)
 Set a variable based on a string data type name. More...
 
virtual void SetSystemPointers (Simulator *lpSim, Structure *lpStructure, NeuralModule *lpModule, Node *lpNode, bool bVerify)
 Sets the system pointers. More...
 
virtual void SimPausing ()
 Called just before the simulation pauses. More...
 
virtual void SimStarting ()
 Called just before the simulation starts. More...
 
virtual void SimStopping ()
 Called just before the simulation stops. More...
 
virtual void TimeStepModified ()
 Notification method that the time step modified has been modified. Objects should recalculate any slice times as needed. More...
 
virtual std::string Type ()
 returns the string type name of this object. More...
 
virtual void Type (std::string strValue)
 Sets the class type for this object. More...
 
virtual void VisualSelectionModeChanged (int iNewMode)
 Visual selection mode changed. More...
 

Protected Member Functions

void LoadNetworkXml (CStdXml &oXml)
 Loads the network configuration. More...
 
NeuronLoadNeuron (CStdXml &oXml)
 Loads a neuron. More...
 
- Protected Member Functions inherited from AnimatSim::Behavior::NeuralModule
virtual int FindAdapterListIndex (CStdArray< Adapter * > aryAdapters, std::string strID, bool bThrowError=true)
 
virtual AnimatSim::LinkLoadExternalSynapse (CStdXml &oXml)
 Loads an external synapse. More...
 
virtual void LoadExternalSynapses (CStdXml &oXml)
 Loads external synapses. More...
 

Protected Attributes

CStdPtrArray< Neuron > m_aryNeurons
 The array of neurons in this module.
 
bool m_bActiveArray
 
CStdIPoint m_oNetworkSize
 Size of the neural network.
 
- Protected Attributes inherited from AnimatSim::Behavior::NeuralModule
CStdPtrArray< AnimatSim::Linkm_aryExternalSynapses
 An array of external synapses connected to nodes within this module.
 
CStdArray< Adapter * > m_arySourceAdapters
 An array of source adapters for this module.
 
CStdArray< Adapter * > m_aryTargetAdapters
 An array of target adapters for this module.
 
float m_fltTimeStep
 The DT time step for this neural module in seconds.
 
short m_iTargetAdapterCount
 Number of target adapters.
 
short m_iTimeStepCount
 Count variable that keeps track of how many slices have occured since the last StepSimulation.
 
short m_iTimeStepInterval
 
IStdClassFactorym_lpClassFactory
 The pointer to the class factory for this module.
 
Organism * m_lpOrganism
 The pointer to the organism.
 
std::string m_strNeuralNetworkFile
 The string neural network file name.
 
std::string m_strProjectPath
 Full pathname of the string project file for this module.
 
- Protected Attributes inherited from AnimatSim::AnimatBase
bool m_bEnabled
 Tells if this item is enabled or not. If it is not enabled then it is not run.
 
bool m_bSelected
 Tells whether the object is selected or not.
 
AnimatSim::Behavior::NeuralModulem_lpModule
 The pointer to this items parentNeuralModule. If this is not relevant for this object then this is NULL.
 
Nodem_lpNode
 The pointer to this items parent Node. If this is not relevant for this object then this is NULL.
 
Simulatorm_lpSim
 The pointer to a Simulation.
 
AnimatSim::Environment::Structurem_lpStructure
 The pointer to this items parent Structure. If this is not relevant for this object then this is NULL.
 
std::string m_strID
 The unique Id for this object.
 
std::string m_strName
 The name for this object.
 
std::string m_strType
 The type for this object. Examples are Box, Plane, Neuron, etc..
 

Additional Inherited Members

- Static Public Member Functions inherited from AnimatSim::Behavior::NeuralModule
static NeuralModuleCastToDerived (AnimatBase *lpBase)
 

Detailed Description

Firing rate neural module.

This neural module implements a firing rate neural model. The firing rate model is a more abstract representation of the neuron than an integrate and fire system. This type of model assumes that there is a linear relationship between cell depolarization and firing rate. After the neuron has depolarized beyond its threshold its firing rate increases linearly between 0 and 1 relative to the membrane potential and a gain value. Synapses inject current into post-synaptic neurons based on the firing rate. The synaptic weight is the amount of current to inject, and this is multiplied by the firing rate of the pre-synaptic neuron. this model also has modulatory and gated synapses.
Another feature of this model is that there are a few different types of neruons. These primarily differ based on how they implement intrinsic currents. Intrinsic currents are currents that are internal to the neuron. An exmample of this is the pacemaker neuron that generates currents internally to model bursting behavior.

Author
dcofer
Date
3/29/2011

Definition at line 30 of file FiringRateModule.h.

Constructor & Destructor Documentation

FiringRateSim::FiringRateModule::FiringRateModule ( )

Default constructor.

Author
dcofer
Date
3/29/2011

Definition at line 22 of file FiringRateModule.cpp.

References m_bActiveArray, and AnimatSim::Behavior::NeuralModule::m_lpClassFactory.

FiringRateSim::FiringRateModule::~FiringRateModule ( )
virtual

Destructor.

Author
dcofer
Date
3/29/2011

Definition at line 34 of file FiringRateModule.cpp.

References m_aryNeurons, and StdUtils::Std_TraceMsg().

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Member Function Documentation

bool FiringRateSim::FiringRateModule::ActiveArray ( )

Gets the active array.

Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This tells which of these array elements is currently the active one.

Author
dcofer
Date
3/29/2011
Returns
true for array element 1, false for array element 0.

Definition at line 58 of file FiringRateModule.cpp.

References m_bActiveArray.

Referenced by FiringRateSim::Neurons::Neuron::FiringFreq(), FiringRateSim::Neurons::PacemakerNeuron::StepSimulation(), and FiringRateSim::Neurons::Neuron::StepSimulation().

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void FiringRateSim::FiringRateModule::ActiveArray ( bool  bVal)

Sets the active array.

Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This sets which of these array elements is currently the active one.

Author
dcofer
Date
3/29/2011
Parameters
bValtrue for array element 1, false for array element 0.

Definition at line 72 of file FiringRateModule.cpp.

References m_bActiveArray.

bool FiringRateSim::FiringRateModule::AddItem ( const std::string &  strItemType,
const std::string &  strXml,
bool  bThrowError = true,
bool  bDoNotInit = false 
)
virtual

Adds a new object to this parent.

Generic method to add a new child item to this parent by specifying a string item type descriptor and an xml packet that can be used to load in the new object. The GUI uses this method to create new items that were added with the user interface. The item type lets the method determine what type of item is being created, like synapse, neuron, body part, etc.. It then gets the modulename, classname, and type from the xml and calls CreateObject to create the appropriate type of object. Then it passes in the xml packet to the new objects load method and does any needed initialization and adds it to the parent.

Author
dcofer
Date
2/22/2011
Parameters
strItemTypeString descriptor of the type of item that is being created.
strXmlXML packet that is used to create and load the new item.
bThrowErrorIf true then throw an error if there is a problem, otherwise return false.
Returns
true if it succeeds, false if it fails.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 243 of file FiringRateModule.cpp.

References AddNeuron(), and StdUtils::Std_CheckString().

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void FiringRateSim::FiringRateModule::AddNeuron ( std::string  strXml,
bool  bDoNotInit = false 
)
virtual

Adds a neuron to the module.

Author
dcofer
Date
3/29/2011
Parameters
strXmlThe xml to use when loading the neuron.

Definition at line 216 of file FiringRateModule.cpp.

References FiringRateSim::Neurons::Neuron::Initialize(), and LoadNeuron().

Referenced by AddItem().

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long FiringRateSim::FiringRateModule::CalculateSnapshotByteSize ( )
virtual

Calculates the snapshot byte size.

Sometimes the user may want to capture a snapshot of the simulation at a given point in time, and then be able to go back to that specific point. To do this we grab a snapshot of all the data in the system, including the neural variables. We essentially serialize the data into a binary format for later re-use. This method calculates the number of bytes that will be required to store the entire object.

Author
dcofer
Date
2/24/2011
Returns
The calculated snapshot byte size.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 283 of file FiringRateModule.cpp.

References m_aryNeurons.

int FiringRateSim::FiringRateModule::FindNeuronListPos ( std::string  strID,
bool  bThrowError = true 
)
virtual

Searches for the neuron with the specified ID and returns its position in the list.

Author
dcofer
Date
3/29/2011
Parameters
strIDGUID ID of the neruon to find.
bThrowErrortrue to throw error if nothing found.
Returns
The found neuron list position.

Definition at line 127 of file FiringRateModule.cpp.

References AnimatSim::AnimatBase::ID(), m_aryNeurons, StdUtils::Std_ToUpper(), and StdUtils::Std_Trim().

Referenced by RemoveNeuron().

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bool FiringRateSim::FiringRateModule::InactiveArray ( )

Gets the inactive array.

Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This tells which of these array elements is currently the inactive one.

Author
dcofer
Date
3/29/2011
Returns
true for array element 1, false for array element 0.

Definition at line 88 of file FiringRateModule.cpp.

References m_bActiveArray.

Referenced by FiringRateSim::Neurons::PacemakerNeuron::StepSimulation(), and FiringRateSim::Neurons::Neuron::StepSimulation().

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void FiringRateSim::FiringRateModule::InactiveArray ( bool  bVal)

Sets the inactive array.

Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This sets which of these array elements is currently the inactive one.

Author
dcofer
Date
3/29/2011
Parameters
bValtrue for array element 1, false for array element 0.

Definition at line 102 of file FiringRateModule.cpp.

References m_bActiveArray.

void FiringRateSim::FiringRateModule::Initialize ( )
virtual

Initializes this object.

After an object is loaded in it must be initialized before it can be used. This allows the object to retrieve any pointers or setup memory that it will need during execution. Each object is responsible for initializing any of its child objects, so you simply need to call this method on the containing class to init all child objects. It also calls VerifySystemPointers to make sure that the system pointers have been setup correctly.

Author
dcofer
Date
3/1/2011

Reimplemented from AnimatSim::Behavior::NeuralModule.

Definition at line 152 of file FiringRateModule.cpp.

References m_aryNeurons, and AnimatSim::AnimatBase::m_lpStructure.

void FiringRateSim::FiringRateModule::Kill ( bool  bState = true)
virtual

Kills.

Called to kill the organism, nervous system, neurons, and body parts. All neural items are disabled to prevent any further neural activity, and all joints are disabled to allow free rotation, and all biomechancical components are disabled so they can no longer produce forces. This method is only relevant to these types of objects, but I am putting the definition in the base class because a variety of different types of classes all need this method and I want it consolidated. Those classes that do not need it do not have to call it or do anything when it is called.

Author
dcofer
Date
3/3/2011
Parameters
bStatetrue to state.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 108 of file FiringRateModule.cpp.

References m_aryNeurons.

void FiringRateSim::FiringRateModule::LoadKeyFrameSnapshot ( byte *  aryBytes,
long &  lIndex 
)
virtual

Loads a key frame snapshot.

Sometimes the user may want to capture a snapshot of the simulation at a given point in time, and then be able to go back to that specific point. To do this we grab a snapshot of all the data in the system, including the neural variables. We essentially serialize the data into a binary format for later re-use. This method goes through each module and loads its data from the byte array.

Author
dcofer
Date
2/24/2011
Parameters
[in,out]aryBytesThe array of bytes where the data is being stored.
[in,out]lIndexCurrent zero-based index of the read position in the array.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 302 of file FiringRateModule.cpp.

References m_aryNeurons.

void FiringRateSim::FiringRateModule::LoadNetworkXml ( CStdXml &  oXml)
protected
Neuron * FiringRateSim::FiringRateModule::LoadNeuron ( CStdXml &  oXml)
protected

Loads a neuron.

Author
dcofer
Date
3/29/2011
Parameters
[in,out]oXmlThe xml to load for the neuron.
Returns
Pointer to the loaded neuron.

Definition at line 382 of file FiringRateModule.cpp.

References AnimatSim::Simulator::CreateObject(), m_aryNeurons, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_lpStructure, and FiringRateSim::Neurons::Neuron::SetSystemPointers().

Referenced by AddNeuron(), and LoadNetworkXml().

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std::string FiringRateSim::FiringRateModule::ModuleName ( )
virtual

Gets the module name.

Author
dcofer
Date
3/29/2011
Returns
.

Implements AnimatSim::Behavior::NeuralModule.

Definition at line 45 of file FiringRateModule.cpp.

bool FiringRateSim::FiringRateModule::RemoveItem ( const std::string &  strItemType,
const std::string &  strID,
bool  bThrowError = true 
)
virtual

Removes a child item from this parent.

This is a generic method that is used to delete a child object from this parent. The GUI uses this method to remove objects from the simulation that have been deleted in the UI. The item type lets the method determine what type of item is being deleted, like synapse, neuron, body part, etc.. The ID is then used to delete that specific item.

Author
dcofer
Date
2/22/2011
Parameters
strItemTypeString descriptor of the type of item that is being created.
strIDUnique ID of the item that will be removed.
bThrowErrorIf true then throw an error if there is a problem, otherwise return false.
Returns
true if it succeeds, false if it fails.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 262 of file FiringRateModule.cpp.

References RemoveNeuron(), and StdUtils::Std_CheckString().

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void FiringRateSim::FiringRateModule::RemoveNeuron ( std::string  strID,
bool  bThrowError = true 
)
virtual

Removes the neuron with the specified ID.

Author
dcofer
Date
3/29/2011
Parameters
strIDGUID ID for the neuron.
bThrowErrortrue to throw error if neuron found.

Definition at line 237 of file FiringRateModule.cpp.

References FindNeuronListPos(), and m_aryNeurons.

Referenced by RemoveItem().

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void FiringRateSim::FiringRateModule::ResetSimulation ( )
virtual

Resets the simulation back to time 0.

This method calls the ResetSimulation method on all subitems in order to reset the simulation back to the beginning.

Author
dcofer
Date
3/1/2011

Reimplemented from AnimatSim::Behavior::NeuralModule.

Definition at line 142 of file FiringRateModule.cpp.

References m_aryNeurons.

void FiringRateSim::FiringRateModule::SaveKeyFrameSnapshot ( byte *  aryBytes,
long &  lIndex 
)
virtual

Saves a key frame snapshot.

Sometimes the user may want to capture a snapshot of the simulation at a given point in time, and then be able to go back to that specific point. To do this we grab a snapshot of all the data in the system, including the neural variables. We essentially serialize the data into a binary format for later re-use. This method goes through each module and saves its data into the byte array.

Author
dcofer
Date
2/24/2011
Parameters
[in,out]aryBytesThe array of bytes where the data is being stored.
[in,out]lIndexCurrent zero-based index of the write position in the array.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 294 of file FiringRateModule.cpp.

References m_aryNeurons.

bool FiringRateSim::FiringRateModule::SetData ( const std::string &  strDataType,
const std::string &  strValue,
bool  bThrowError = true 
)
virtual

Set a variable based on a string data type name.

This is a generic method that can be used to set any variable in an AnimatBase object by specifying the name of the variable and a string representation of that data. The GUI uses this method to set data into variables in the simulation when the user changes them in the UI. The value string can be as simple as a float or int, or as complex as an xml packet. It is the developers responsibilty to know what type of data is needed and to process it accordingly.

Author
dcofer
Date
2/22/2011
Parameters
strDataTypestring name of the data type to set.
strValueThe string value of the data. It is up to the developer to determine what this should be. For example, in most cases it is simply a float and you just have to convert it to a float and make the appropriate mutator method call. However, it can be any type of string, including an entire xml packet. It is the developers responsibility to know how to set and process the data as required.
bThrowErrortrue to throw error if there is a problem. If false then it will not return an error, just return false.
Returns
true if it succeeds, false if it fails.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 181 of file FiringRateModule.cpp.

References StdUtils::Std_CheckString(), and AnimatSim::Behavior::NeuralModule::TimeStep().

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void FiringRateSim::FiringRateModule::StepSimulation ( )
virtual

Step the simulation for this object.

This is called on an object each time it is stepped in the simulation. this is where its simulation code is processed. However, StepSimulation is not necessarily called every single time that the simulation as a whole is stepped. A good example of this is that neural modules can have different integration time steps. So a firing rate module may have a DT of 0.5 ms, while an integrate and fire model may have one of 0.1 ms. So the firing rate module would only get its StepSimulation method called every 5th time that the other module was called. This is all handed in the StepSimulation method of the Simulator and NervousSystem.

Author
dcofer
Date
3/1/2011

Reimplemented from AnimatSim::Behavior::NeuralModule.

Definition at line 166 of file FiringRateModule.cpp.

References m_aryNeurons, and m_bActiveArray.

Member Data Documentation

bool FiringRateSim::FiringRateModule::m_bActiveArray
protected

Within the neuron it keeps a two bit array to keep track of the previous and current membrane potential calculations. This tells which of these array elements is currently the active one.

Definition at line 41 of file FiringRateModule.h.

Referenced by ActiveArray(), FiringRateModule(), InactiveArray(), and StepSimulation().


The documentation for this class was generated from the following files: