AnimatLab  2
Test
FiringRateSim::Neurons::Neuron Class Reference

Firing Rate Neuron model. More...

#include <Neuron.h>

+ Inheritance diagram for FiringRateSim::Neurons::Neuron:
+ Collaboration diagram for FiringRateSim::Neurons::Neuron:

Public Member Functions

 Neuron ()
 Default constructor. More...
 
virtual ~Neuron ()
 Destructor. More...
 
virtual float AccommodationTimeConstant ()
 Gets the accomodation time constant. More...
 
virtual void AccommodationTimeConstant (float fltVal)
 Sets the accomodation time constant. More...
 
virtual void AddExternalI (float fltVal)
 Adds to the external current. More...
 
virtual void AddExternalNodeInput (int iTargetDataType, float fltInput)
 Adds an external node input. 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 AddSynapse (Synapse *lpSynapse)
 Adds a synapse to this neuron. More...
 
virtual void AddSynapse (std::string strXml, bool bDoNotInit)
 Adds a synapse using an xml packet. More...
 
virtual long CalculateSnapshotByteSize ()
 Calculates the snapshot byte size. More...
 
virtual void ClearSynapses ()
 Clears the synapses list. More...
 
virtual float Cn ()
 Gets the membrane capacitance. More...
 
virtual void Cn (float fltVal)
 Sets the membrane capacitance. More...
 
virtual void Copy (CStdSerialize *lpSource)
 
virtual float ExternalI ()
 Gets the external current. More...
 
virtual void ExternalI (float fltVal)
 Sets the external current. More...
 
virtual int FindSynapseListPos (std::string strID, bool bThrowError=true)
 Searches for a synapse with the specified ID and returns its position in the list. More...
 
virtual float FiringFreq (FiringRateModule *lpModule)
 Calculates the current firing frequency. More...
 
virtual float Fmin ()
 Gets the minimum firing frequency. More...
 
virtual void Fmin (float fltVal)
 Sets the minimum firing frequency. More...
 
virtual float Gain ()
 Gets the firing frequency gain. More...
 
virtual void Gain (float fltVal)
 Sets the firing frequency gain. More...
 
virtual bool GainType ()
 Gets the gain type. (Old way or new way) More...
 
virtual void GainType (bool bVal)
 Sets the gain type. (Old way or new way) More...
 
virtual float * GetDataPointer (const std::string &strDataType)
 Returns a float pointer to a data item of interest in this object. More...
 
virtual SynapseGetSynapse (int iIndex)
 Gets a synapse by its index in the array. More...
 
virtual CStdPtrArray< Synapse > * GetSynapses ()
 Gets a pointer to the synapses array. More...
 
virtual float Gn ()
 Gets the membrane conductance. More...
 
virtual void Gn (float fltVal)
 Sets the membrane conductance. More...
 
virtual float Iinit ()
 
virtual void Iinit (float fltVal)
 
virtual void Initialize ()
 Initializes this object. More...
 
virtual float InitTime ()
 
virtual void InitTime (float fltVal)
 
virtual void InjectCurrent (float fltVal)
 Injects current into this neuron. More...
 
virtual float IntrinsicCurrent ()
 Gets the intrinsic current. More...
 
virtual void IntrinsicCurrent (float fltVal)
 Sets the intrinsic current. More...
 
virtual void Load (CStdXml &oXml)
 
virtual void LoadKeyFrameSnapshot (byte *aryBytes, long &lIndex)
 Loads a key frame snapshot. More...
 
virtual unsigned char NeuronType ()
 Gets the neuron type. More...
 
virtual void QueryProperties (CStdPtrArray< TypeProperty > &aryProperties)
 
virtual float RelativeAccommodation ()
 Gets the relative accomodation. More...
 
virtual void RelativeAccommodation (float fltVal)
 Sets the relative accomodation. More...
 
virtual bool RemoveItem (const std::string &strItemType, const std::string &strID, bool bThrowError=true)
 Removes a child item from this parent. More...
 
virtual void RemoveSynapse (int iIndex)
 Removes the synapse described by iIndex. More...
 
virtual void RemoveSynapse (std::string strID, bool bThrowError=true)
 Removes the synapse by the GUID 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 SetSystemPointers (Simulator *lpSim, Structure *lpStructure, NeuralModule *lpModule, Node *lpNode, bool bVerify)
 Sets the system pointers. More...
 
virtual void StepSimulation ()
 Step the simulation for this object. More...
 
virtual void TimeStepModified ()
 Notification method that the time step modified has been modified. Objects should recalculate any slice times as needed. More...
 
virtual int TotalSynapses ()
 Gets the total number of synapses. More...
 
virtual bool UseAccom ()
 Gets whether to use accommodation. More...
 
virtual void UseAccom (bool bVal)
 Sets whether to use accommodation. More...
 
virtual bool UseNoise ()
 Gets whether to use noise. More...
 
virtual void UseNoise (bool bVal)
 Sets whether to use noise. More...
 
virtual void VerifySystemPointers ()
 Verify that system pointers have been set correctly. More...
 
virtual float Vn ()
 Gets the membrane voltage. More...
 
virtual float VNoiseMax ()
 Gets the maximum noise voltage. More...
 
virtual void VNoiseMax (float fltVal)
 Sets the maximum noise voltage. More...
 
virtual float Vrest ()
 Gets the rest potential. More...
 
virtual void Vrest (float fltVal)
 Sets the rest potential. More...
 
virtual float Vth ()
 Gets the voltage threshold for firing. More...
 
virtual void Vth (float fltVal)
 Sets the voltage threshold for firing. More...
 
- Public Member Functions inherited from AnimatSim::Node
 Node ()
 Default constructor. More...
 
virtual ~Node ()
 Destructor. More...
 
virtual bool Enabled ()
 Tells whether this node is enabled. More...
 
virtual void Enabled (bool bValue)
 Enables the node. More...
 
virtual int GetTargetDataTypeIndex (const std::string &strDataType)
 Used to convert a string target data type into an integer index. More...
 
virtual void Kill (bool bState=true)
 Kills. More...
 
virtual void QueryProperties (CStdPtrArray< TypeProperty > &aryProperties)
 Queries this object for a list of properties that can be changed using SetData. More...
 
virtual void SetSystemPointers (Simulator *lpSim, Structure *lpStructure, NeuralModule *lpModule, Node *lpNode, bool bVerify)
 Sets the system pointers. 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 NeuralModuleGetNeuralModule ()
 Gets the neural module. More...
 
virtual NodeGetNode ()
 Gets the node. More...
 
virtual SimulatorGetSimulator ()
 Gets the simulator pointer. 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 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 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 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

virtual float CalculateFiringFrequency (float fltVn, float fltVth)
 Calculates the firing frequency of the neuron. More...
 
virtual float CalculateIntrinsicCurrent (FiringRateModule *lpModule, float fltInputCurrent)
 Calculates the intrinsic current. More...
 
virtual float CalculateSynapticCurrent (FiringRateModule *lpModule)
 Calculates the total incoming synaptic current. More...
 
SynapseLoadSynapse (CStdXml &oXml)
 Loads a synapse. More...
 
- Protected Member Functions inherited from AnimatSim::Node
virtual void UpdateData ()
 Updates any reporting data for this time step. More...
 

Protected Attributes

CStdPtrArray< Synapse > m_arySynapses
 The array of synapses that are in-coming to this neuron.
 
float m_aryVn [2]
 Current and next Membrane voltage. Vn.
 
float m_aryVth [2]
 Current and next threshold voltage. Vth.
 
bool m_bGainType
 Tells whether to use the old type gain or new type gain.
 
bool m_bUseAccom
 true use accomodation
 
bool m_bUseNoise
 Tells if we should use noise or not.
 
float m_fltAccomTimeConst
 The accomodation time constant tells how fast the neuron accomodates to a new membrane potential.
 
float m_fltAccomTimeMod
 If we are setting the accomodation time constant through modulation then this keeps track of it.
 
float m_fltAdapterI
 current added from all of the adapters.
 
float m_fltAdapterMemoryI
 Used to allow datacharts to track current input from adapters.
 
float m_fltCn
 Membrane capacitance.
 
float m_fltDCTH
 expon decline working factor for thresh accomm
 
float m_fltExternalI
 Externally injected current.
 
float m_fltFiringFreq
 Current firing frequency.
 
float m_fltFmin
 Minimum Firing frequency.
 
float m_fltGain
 
float m_fltGn
 Membrane conductance.
 
float m_fltIinit
 The initialization current to turn on at the beginning of the simulation.
 
float m_fltInitTime
 The duration for how long the Iinit current is on at the beginning of the simulation.
 
float m_fltIntrinsicI
 Intrinsic current.
 
float m_fltInvCn
 Inverse membrane capacitance.
 
float m_fltRelativeAccom
 The relative accomodation rate.
 
float m_fltSynapticI
 Current synaptic current.
 
float m_fltTotalMemoryI
 Total current applied to the neuron.
 
float m_fltVn
 Current membrane voltage.
 
float m_fltVndisp
 this is the membrane voltage that is reported back to animatlab.
 
float m_fltVNoise
 This is the random noise that should be added to the membrane voltage at a timestep.
 
float m_fltVNoiseMax
 Tells the maximum noise to use when running sim.
 
float m_fltVrest
 this is the resting potential of the neuron.
 
float m_fltVth
 Firing frequency voltage threshold.
 
float m_fltVthadd
 The component added to Vthi for accomodation.
 
float m_fltVthdisp
 this is the theshold voltage that is reported back to animatlab.
 
float m_fltVthi
 Initial firing frequency voltage threshold.
 
FiringRateModulem_lpFRModule
 Pointer to the parent FiringRateModule.
 
- Protected Attributes inherited from AnimatSim::Node
bool m_bInitEnabled
 Keeps track of the enabled state at sim startup.
 
float m_fltEnabled
 This is used for reporting the enabled state in a GetDataPointer call.
 
Organism * m_lpOrganism
 The pointer to this node's organism.
 
- 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::Node
static NodeCastToDerived (AnimatBase *lpBase)
 

Detailed Description

Firing Rate Neuron model.

This Neuron 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 35 of file FiringRateSim/Neuron.h.

Constructor & Destructor Documentation

FiringRateSim::Neurons::Neuron::~Neuron ( )
virtual

Destructor.

Author
dcofer
Date
3/29/2011

Definition at line 77 of file FiringRateSim/Neuron.cpp.

References m_arySynapses, and StdUtils::Std_TraceMsg().

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Member Function Documentation

float FiringRateSim::Neurons::Neuron::AccommodationTimeConstant ( )
virtual

Gets the accomodation time constant.

Author
dcofer
Date
3/29/2011
Returns
accomodation time constant.

Definition at line 412 of file FiringRateSim/Neuron.cpp.

References m_fltAccomTimeConst.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::AccommodationTimeConstant ( float  fltVal)
virtual

Sets the accomodation time constant.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 423 of file FiringRateSim/Neuron.cpp.

References m_bUseAccom, m_fltAccomTimeConst, m_fltDCTH, m_lpFRModule, and AnimatSim::Behavior::NeuralModule::TimeStep().

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void FiringRateSim::Neurons::Neuron::AddExternalI ( float  fltVal)
virtual

Adds to the external current.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value to add.

Definition at line 255 of file FiringRateSim/Neuron.cpp.

References m_fltExternalI.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::AddExternalNodeInput ( int  iTargetDataType,
float  fltInput 
)
virtual

Adds an external node input.

This is used by the adapter to add a new external value to this node. It is up to the node to interpret what that value means. For example, if it is a neuron then it can interpret it to be a current. This value is added to the current total so that multiple adapters can call this in a given time step. It is cleared out to zero at the beginning of the time step. You can now also specify which data you are adding to for this method call. This allows adapters to be setup to change multiple different variables in the system.

Author
dcofer
Date
6/16/2014
Parameters
iTargetDataTypeThe index of the target data type we are adding to.
fltInputThe new input.

Implements AnimatSim::Node.

Definition at line 923 of file FiringRateSim/Neuron.cpp.

References m_fltAdapterI, and m_fltAdapterMemoryI.

bool FiringRateSim::Neurons::Neuron::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 1099 of file FiringRateSim/Neuron.cpp.

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

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virtual void FiringRateSim::Neurons::Neuron::AddSynapse ( Synapse *  lpSynapse)
virtual

Adds a synapse to this neuron.

Author
dcofer
Date
3/29/2011
Parameters
[in,out]lpSynapsePointer to the synapse to add.

Referenced by AddItem(), and LoadSynapse().

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void FiringRateSim::Neurons::Neuron::AddSynapse ( std::string  strXml,
bool  bDoNotInit 
)
virtual

Adds a synapse using an xml packet.

Author
dcofer
Date
3/29/2011
Parameters
strXmlThe xml of the synapse to add.

Definition at line 597 of file FiringRateSim/Neuron.cpp.

References FiringRateSim::Synapses::Synapse::Initialize(), and LoadSynapse().

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float FiringRateSim::Neurons::Neuron::CalculateFiringFrequency ( float  fltVn,
float  fltVth 
)
protectedvirtual

Calculates the firing frequency of the neuron.

Author
dcofer
Date
3/29/2011
Parameters
fltVnThe membrane potential.
fltVthThe threshold potential.
Returns
The calculated firing frequency.

Definition at line 775 of file FiringRateSim/Neuron.cpp.

References m_bGainType, m_fltFmin, and m_fltGain.

Referenced by FiringFreq(), and StepSimulation().

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float FiringRateSim::Neurons::Neuron::CalculateIntrinsicCurrent ( FiringRateModule m_lpFRModule,
float  fltInputCurrent 
)
protectedvirtual

Calculates the intrinsic current.

Author
dcofer
Date
3/29/2011
Parameters
[in,out]m_lpFRModulePointer to the parent FiringRateModule.
fltInputCurrentThe input current.
Returns
The calculated intrinsic current.

Reimplemented in FiringRateSim::Neurons::RandomNeuron, FiringRateSim::Neurons::PacemakerNeuron, FiringRateSim::Neurons::BistableNeuron, and FiringRateSim::Neurons::TonicNeuron.

Definition at line 822 of file FiringRateSim/Neuron.cpp.

Referenced by StepSimulation().

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long FiringRateSim::Neurons::Neuron::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.

Reimplemented in FiringRateSim::Neurons::RandomNeuron, and FiringRateSim::Neurons::PacemakerNeuron.

Definition at line 1136 of file FiringRateSim/Neuron.cpp.

References m_aryVn, m_fltExternalI, m_fltFiringFreq, m_fltIntrinsicI, m_fltSynapticI, and m_fltVn.

Referenced by FiringRateSim::Neurons::PacemakerNeuron::CalculateSnapshotByteSize(), and FiringRateSim::Neurons::RandomNeuron::CalculateSnapshotByteSize().

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float FiringRateSim::Neurons::Neuron::CalculateSynapticCurrent ( FiringRateModule m_lpFRModule)
protectedvirtual

Calculates the total incoming synaptic current.

Author
dcofer
Date
3/29/2011
Parameters
[in,out]m_lpFRModulePointer to the parent FiringRateModule.
Returns
The calculated synaptic current.

Definition at line 835 of file FiringRateSim/Neuron.cpp.

References AnimatSim::Link::Enabled(), FiringRateSim::Synapses::Synapse::FromNeuron(), m_arySynapses, and FiringRateSim::Synapses::Synapse::Process().

Referenced by StepSimulation().

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void FiringRateSim::Neurons::Neuron::ClearSynapses ( )
virtual

Clears the synapses list.

Author
dcofer
Date
3/29/2011

Definition at line 699 of file FiringRateSim/Neuron.cpp.

References m_arySynapses.

float FiringRateSim::Neurons::Neuron::Cn ( )
virtual

Gets the membrane capacitance.

Author
dcofer
Date
3/29/2011
Returns
membrane capacitance.

Definition at line 96 of file FiringRateSim/Neuron.cpp.

References m_fltCn.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::Cn ( float  fltVal)
virtual

Sets the membrane capacitance.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 107 of file FiringRateSim/Neuron.cpp.

References m_fltCn, m_fltInvCn, and StdUtils::Std_IsAboveMin().

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float FiringRateSim::Neurons::Neuron::ExternalI ( )
virtual

Gets the external current.

Author
dcofer
Date
3/29/2011
Returns
external current.

Definition at line 231 of file FiringRateSim/Neuron.cpp.

References m_fltExternalI.

void FiringRateSim::Neurons::Neuron::ExternalI ( float  fltVal)
virtual

Sets the external current.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 242 of file FiringRateSim/Neuron.cpp.

References m_fltExternalI.

int FiringRateSim::Neurons::Neuron::FindSynapseListPos ( std::string  strID,
bool  bThrowError = true 
)
virtual

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

Author
dcofer
Date
3/29/2011
Parameters
strIDGUID ID of the synapse to find.
bThrowErrortrue to throw error if no synapse is found.
Returns
The found synapse list position.

Definition at line 667 of file FiringRateSim/Neuron.cpp.

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

Referenced by RemoveSynapse().

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float FiringRateSim::Neurons::Neuron::FiringFreq ( FiringRateModule m_lpFRModule)
virtual

Calculates the current firing frequency.

Author
dcofer
Date
3/29/2011
Parameters
[in,out]m_lpFRModulePointer to a fast module.
Returns
firing frequency.

Definition at line 490 of file FiringRateSim/Neuron.cpp.

References FiringRateSim::FiringRateModule::ActiveArray(), CalculateFiringFrequency(), m_aryVn, and m_aryVth.

Referenced by FiringRateSim::Synapses::Synapse::CalculateCurrent(), FiringRateSim::Synapses::ModulatedSynapse::CalculateModulation(), FiringRateSim::Synapses::GatedSynapse::CalculateModulation(), and FiringRateSim::Synapses::ModulateNeuronPropSynapse::Process().

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float FiringRateSim::Neurons::Neuron::Fmin ( )
virtual

Gets the minimum firing frequency.

Author
dcofer
Date
3/29/2011
Returns
minimum firing frequency.

Definition at line 180 of file FiringRateSim/Neuron.cpp.

References m_fltFmin.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::Fmin ( float  fltVal)
virtual

Sets the minimum firing frequency.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 191 of file FiringRateSim/Neuron.cpp.

References m_fltFmin, and StdUtils::Std_IsAboveMin().

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float FiringRateSim::Neurons::Neuron::Gain ( )
virtual

Gets the firing frequency gain.

Author
dcofer
Date
3/29/2011
Returns
firing frequency gain.

Definition at line 206 of file FiringRateSim/Neuron.cpp.

References m_fltGain.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::Gain ( float  fltVal)
virtual

Sets the firing frequency gain.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 217 of file FiringRateSim/Neuron.cpp.

References m_fltGain, and StdUtils::Std_IsAboveMin().

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bool FiringRateSim::Neurons::Neuron::GainType ( )
virtual

Gets the gain type. (Old way or new way)

Author
dcofer
Date
3/29/2011
Returns
true to use new way, false to use old way.

Definition at line 453 of file FiringRateSim/Neuron.cpp.

References m_bGainType.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::GainType ( bool  bVal)
virtual

Sets the gain type. (Old way or new way)

Author
dcofer
Date
3/29/2011
Parameters
bValtrue to use new way, false to use old way.

Definition at line 464 of file FiringRateSim/Neuron.cpp.

References m_bGainType.

float * FiringRateSim::Neurons::Neuron::GetDataPointer ( const std::string &  strDataType)
virtual

Returns a float pointer to a data item of interest in this object.

This is a generic method used to get a pointer to data variable of interest. It is used by a variety of systems in the simulation. The most prominent are the data charting and stimulus classes. Within this method we associate a variable with a string name. By passing in the name of the data type we are interested in we can recieve back a float pointer to that data type. We can use that to read or set the data item in other classes. For example, the data charting system gets the pointer and then each time it needs to log a data point it reads the value into an array.

Author
dcofer
Date
2/22/2011
Parameters
strDataTypename of the data item for which we are looking.
Returns
float pointer of the data item. If not found then it throws an exception.
Exceptions
IfDataType is not found.

Reimplemented from AnimatSim::AnimatBase.

Reimplemented in FiringRateSim::Neurons::PacemakerNeuron.

Definition at line 931 of file FiringRateSim/Neuron.cpp.

References m_fltAccomTimeMod, m_fltAdapterMemoryI, m_fltExternalI, m_fltFiringFreq, m_fltGn, m_fltIntrinsicI, m_fltSynapticI, m_fltTotalMemoryI, m_fltVndisp, m_fltVNoise, m_fltVrest, m_fltVthdisp, and StdUtils::Std_CheckString().

Referenced by FiringRateSim::Neurons::PacemakerNeuron::GetDataPointer(), FiringRateSim::Synapses::ModulateNeuronPropSynapse::Initialize(), and FiringRateSim::Synapses::ModulateNeuronPropSynapse::PropertyName().

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Synapse * FiringRateSim::Neurons::Neuron::GetSynapse ( int  iIndex)
virtual

Gets a synapse by its index in the array.

Author
dcofer
Date
3/29/2011
Parameters
iIndexZero-based index of the synaspe to return.
Returns
null if it fails, else the synapse.

Definition at line 649 of file FiringRateSim/Neuron.cpp.

References m_arySynapses.

CStdPtrArray< Synapse > * FiringRateSim::Neurons::Neuron::GetSynapses ( )
virtual

Gets a pointer to the synapses array.

Author
dcofer
Date
3/29/2011
Returns
Pointer to the synapses.

Definition at line 578 of file FiringRateSim/Neuron.cpp.

References m_arySynapses.

float FiringRateSim::Neurons::Neuron::Gn ( )
virtual

Gets the membrane conductance.

Author
dcofer
Date
3/29/2011
Returns
membrane conductance.

Definition at line 123 of file FiringRateSim/Neuron.cpp.

References m_fltGn.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::Gn ( float  fltVal)
virtual

Sets the membrane conductance.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 134 of file FiringRateSim/Neuron.cpp.

References m_fltGn, and StdUtils::Std_IsAboveMin().

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void FiringRateSim::Neurons::Neuron::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::AnimatBase.

Definition at line 864 of file FiringRateSim/Neuron.cpp.

References m_arySynapses, m_bUseAccom, m_fltAccomTimeConst, m_fltDCTH, m_lpFRModule, and AnimatSim::Behavior::NeuralModule::TimeStep().

Referenced by FiringRateSim::FiringRateModule::AddNeuron().

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void FiringRateSim::Neurons::Neuron::InjectCurrent ( float  fltVal)
virtual

Injects current into this neuron.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new current to add.

Definition at line 861 of file FiringRateSim/Neuron.cpp.

References m_fltExternalI.

float FiringRateSim::Neurons::Neuron::IntrinsicCurrent ( )
virtual

Gets the intrinsic current.

Author
dcofer
Date
3/29/2011
Returns
intrinsic current.

Reimplemented in FiringRateSim::Neurons::RandomNeuron, and FiringRateSim::Neurons::BistableNeuron.

Definition at line 503 of file FiringRateSim/Neuron.cpp.

References m_fltIntrinsicI.

void FiringRateSim::Neurons::Neuron::IntrinsicCurrent ( float  fltVal)
virtual

Sets the intrinsic current.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Reimplemented in FiringRateSim::Neurons::RandomNeuron, and FiringRateSim::Neurons::BistableNeuron.

Definition at line 514 of file FiringRateSim/Neuron.cpp.

References m_fltIntrinsicI.

void FiringRateSim::Neurons::Neuron::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.

Reimplemented in FiringRateSim::Neurons::RandomNeuron, and FiringRateSim::Neurons::PacemakerNeuron.

Definition at line 1163 of file FiringRateSim/Neuron.cpp.

References m_aryVn, m_fltExternalI, m_fltFiringFreq, m_fltIntrinsicI, m_fltSynapticI, and m_fltVn.

Referenced by FiringRateSim::Neurons::PacemakerNeuron::LoadKeyFrameSnapshot(), and FiringRateSim::Neurons::RandomNeuron::LoadKeyFrameSnapshot().

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Synapse * FiringRateSim::Neurons::Neuron::LoadSynapse ( CStdXml &  oXml)
protected

Loads a synapse.

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

Definition at line 1257 of file FiringRateSim/Neuron.cpp.

References AddSynapse(), AnimatSim::Simulator::CreateObject(), m_lpFRModule, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_lpStructure, and FiringRateSim::Synapses::Synapse::SetSystemPointers().

Referenced by AddSynapse().

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unsigned char FiringRateSim::Neurons::Neuron::NeuronType ( )
virtual

Gets the neuron type.

Author
dcofer
Date
3/29/2011
Returns
neuron type.

Reimplemented in FiringRateSim::Neurons::PacemakerNeuron, FiringRateSim::Neurons::RandomNeuron, FiringRateSim::Neurons::BistableNeuron, and FiringRateSim::Neurons::TonicNeuron.

Definition at line 525 of file FiringRateSim/Neuron.cpp.

float FiringRateSim::Neurons::Neuron::RelativeAccommodation ( )
virtual

Gets the relative accomodation.

Author
dcofer
Date
3/29/2011
Returns
relative accomodation.

Definition at line 376 of file FiringRateSim/Neuron.cpp.

References m_fltRelativeAccom.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::RelativeAccommodation ( float  fltVal)
virtual

Sets the relative accomodation.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 387 of file FiringRateSim/Neuron.cpp.

References m_bUseAccom, m_fltAccomTimeConst, m_fltDCTH, m_fltRelativeAccom, m_lpFRModule, StdUtils::Std_InValidRange(), and AnimatSim::Behavior::NeuralModule::TimeStep().

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bool FiringRateSim::Neurons::Neuron::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 1117 of file FiringRateSim/Neuron.cpp.

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

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void FiringRateSim::Neurons::Neuron::RemoveSynapse ( int  iIndex)
virtual

Removes the synapse described by iIndex.

Author
dcofer
Date
3/29/2011
Parameters
iIndexZero-based index of the synapse in the array.

Definition at line 617 of file FiringRateSim/Neuron.cpp.

References m_arySynapses.

Referenced by RemoveItem().

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void FiringRateSim::Neurons::Neuron::RemoveSynapse ( std::string  strID,
bool  bThrowError = true 
)
virtual

Removes the synapse by the GUID ID.

Author
dcofer
Date
3/29/2011
Parameters
strIDGUID ID for the synapse to remove.
bThrowErrortrue to throw error if synaspe not found.

Definition at line 633 of file FiringRateSim/Neuron.cpp.

References FindSynapseListPos(), and m_arySynapses.

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void FiringRateSim::Neurons::Neuron::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::Node.

Reimplemented in FiringRateSim::Neurons::RandomNeuron, FiringRateSim::Neurons::PacemakerNeuron, and FiringRateSim::Neurons::BistableNeuron.

Definition at line 896 of file FiringRateSim/Neuron.cpp.

References m_arySynapses, m_aryVn, m_aryVth, m_fltAccomTimeMod, m_fltAdapterI, m_fltAdapterMemoryI, m_fltExternalI, m_fltFiringFreq, m_fltIntrinsicI, m_fltSynapticI, m_fltTotalMemoryI, m_fltVn, m_fltVndisp, m_fltVNoise, m_fltVrest, m_fltVth, m_fltVthadd, m_fltVthdisp, m_fltVthi, and AnimatSim::Node::ResetSimulation().

Referenced by FiringRateSim::Neurons::BistableNeuron::ResetSimulation(), FiringRateSim::Neurons::PacemakerNeuron::ResetSimulation(), and FiringRateSim::Neurons::RandomNeuron::ResetSimulation().

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void FiringRateSim::Neurons::Neuron::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.

Reimplemented in FiringRateSim::Neurons::RandomNeuron, and FiringRateSim::Neurons::PacemakerNeuron.

Definition at line 1142 of file FiringRateSim/Neuron.cpp.

References m_aryVn, m_fltExternalI, m_fltFiringFreq, m_fltIntrinsicI, m_fltSynapticI, and m_fltVn.

Referenced by FiringRateSim::Neurons::PacemakerNeuron::SaveKeyFrameSnapshot(), and FiringRateSim::Neurons::RandomNeuron::SaveKeyFrameSnapshot().

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bool FiringRateSim::Neurons::Neuron::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::Node.

Reimplemented in FiringRateSim::Neurons::RandomNeuron, FiringRateSim::Neurons::PacemakerNeuron, FiringRateSim::Neurons::BistableNeuron, and FiringRateSim::Neurons::TonicNeuron.

Definition at line 977 of file FiringRateSim/Neuron.cpp.

References AccommodationTimeConstant(), AddExternalI(), Cn(), Fmin(), Gain(), GainType(), Gn(), RelativeAccommodation(), StdUtils::Std_CheckString(), StdUtils::Std_ToBool(), VNoiseMax(), Vrest(), and Vth().

Referenced by FiringRateSim::Neurons::TonicNeuron::SetData(), FiringRateSim::Neurons::BistableNeuron::SetData(), FiringRateSim::Neurons::PacemakerNeuron::SetData(), and FiringRateSim::Neurons::RandomNeuron::SetData().

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void FiringRateSim::Neurons::Neuron::SetSystemPointers ( Simulator *  lpSim,
Structure *  lpStructure,
NeuralModule *  lpModule,
Node lpNode,
bool  bVerify 
)
virtual

Sets the system pointers.

There are a number of system pointers that are needed for use in the objects. The primariy one being a pointer to the simulation object itself so that you can get global parameters like the scale units and so on. However, each object may need other types of pointers as well, for example neurons need to have a pointer to their parent structure/organism, and to the NeuralModule they reside within. So different types of objects will need different sets of system pointers. We call this method to set the pointers just after creation and before Load is called. We then call VerifySystemPointers here, during Load and during Initialize in order to ensure that the correct pointers have been set for each type of objects. These pointers can then be safely used throughout the rest of the system.

Author
dcofer
Date
3/2/2011
Parameters
[in,out]lpSimThe pointer to a simulation.
[in,out]lpStructureThe pointer to the parent structure.
[in,out]lpModuleThe pointer to the parent module module.
[in,out]lpNodeThe pointer to the parent node.
bVerifytrue to call VerifySystemPointers.

Definition at line 876 of file FiringRateSim/Neuron.cpp.

References m_lpFRModule, and VerifySystemPointers().

Referenced by FiringRateSim::FiringRateModule::LoadNeuron().

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void FiringRateSim::Neurons::Neuron::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::AnimatBase.

Reimplemented in FiringRateSim::Neurons::PacemakerNeuron, and FiringRateSim::Neurons::BistableNeuron.

Definition at line 710 of file FiringRateSim/Neuron.cpp.

References FiringRateSim::FiringRateModule::ActiveArray(), CalculateFiringFrequency(), CalculateIntrinsicCurrent(), CalculateSynapticCurrent(), FiringRateSim::FiringRateModule::InactiveArray(), m_aryVn, m_aryVth, AnimatSim::AnimatBase::m_bEnabled, m_bUseAccom, m_bUseNoise, m_fltAccomTimeMod, m_fltAdapterI, m_fltDCTH, m_fltExternalI, m_fltFiringFreq, m_fltGn, m_fltIinit, m_fltInitTime, m_fltIntrinsicI, m_fltInvCn, m_fltRelativeAccom, m_fltSynapticI, m_fltTotalMemoryI, m_fltVn, m_fltVndisp, m_fltVNoise, m_fltVNoiseMax, m_fltVrest, m_fltVth, m_fltVthadd, m_fltVthdisp, m_fltVthi, m_lpFRModule, AnimatSim::AnimatBase::m_lpSim, StdUtils::Std_FRand(), AnimatSim::Simulator::Time(), and AnimatSim::Behavior::NeuralModule::TimeStep().

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

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void FiringRateSim::Neurons::Neuron::TimeStepModified ( )
virtual

Notification method that the time step modified has been modified. Objects should recalculate any slice times as needed.

Author
dcofer
Date
1/28/2012

Reimplemented from AnimatSim::AnimatBase.

Definition at line 702 of file FiringRateSim/Neuron.cpp.

References m_bUseAccom, m_fltAccomTimeConst, m_fltDCTH, m_lpFRModule, and AnimatSim::Behavior::NeuralModule::TimeStep().

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int FiringRateSim::Neurons::Neuron::TotalSynapses ( )
virtual

Gets the total number of synapses.

Author
dcofer
Date
3/29/2011
Returns
The total number of synapses.

Definition at line 690 of file FiringRateSim/Neuron.cpp.

References m_arySynapses.

bool FiringRateSim::Neurons::Neuron::UseAccom ( )
virtual

Gets whether to use accommodation.

Author
dcofer
Date
3/29/2011
Returns
true to use accommodation, false else.

Definition at line 330 of file FiringRateSim/Neuron.cpp.

References m_bUseAccom.

void FiringRateSim::Neurons::Neuron::UseAccom ( bool  bVal)
virtual

Sets whether to use accommodation.

Author
dcofer
Date
3/29/2011
Parameters
bValtrue to use accommodation, false else.

Definition at line 340 of file FiringRateSim/Neuron.cpp.

References m_bUseAccom, m_fltAccomTimeConst, m_fltDCTH, m_lpFRModule, and AnimatSim::Behavior::NeuralModule::TimeStep().

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bool FiringRateSim::Neurons::Neuron::UseNoise ( )
virtual

Gets whether to use noise.

Author
dcofer
Date
3/29/2011
Returns
true if it uses noise, false else.

Definition at line 307 of file FiringRateSim/Neuron.cpp.

References m_bUseNoise.

void FiringRateSim::Neurons::Neuron::UseNoise ( bool  bVal)
virtual

Sets whether to use noise.

Author
dcofer
Date
3/29/2011
Parameters
bValtrue to use noise.

Definition at line 317 of file FiringRateSim/Neuron.cpp.

References m_bUseNoise.

void FiringRateSim::Neurons::Neuron::VerifySystemPointers ( )
virtual

Verify that system pointers have been set correctly.

The system pointers should be set just after an object is created. However, if for some reason it was not then this could cause read/write memory access errors later on because we would be using NULL pointers. This method is called during SetSystemPointers, Load, and Initialize to verify that the pointers for that type of object have been set correctly. We are calling three different places to ensure that it is checked before use. For example, if you are doing a Load call then you want to check it before attempting the load, but there may be an object that does not Load, but only does Initialize. So we need to check it there as well.

Author
dcofer
Date
3/4/2011

Reimplemented from AnimatSim::Node.

Definition at line 885 of file FiringRateSim/Neuron.cpp.

References AnimatSim::AnimatBase::ID(), m_lpFRModule, AnimatSim::Node::m_lpOrganism, and AnimatSim::AnimatBase::m_strID.

Referenced by SetSystemPointers().

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float FiringRateSim::Neurons::Neuron::Vn ( )
virtual

Gets the membrane voltage.

Author
dcofer
Date
3/29/2011
Returns
membrane voltage.

Definition at line 477 of file FiringRateSim/Neuron.cpp.

References m_fltVn.

float FiringRateSim::Neurons::Neuron::VNoiseMax ( )
virtual

Gets the maximum noise voltage.

Author
dcofer
Date
3/29/2011
Returns
maximum noise voltage.

Definition at line 296 of file FiringRateSim/Neuron.cpp.

References m_fltVNoiseMax.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::VNoiseMax ( float  fltVal)
virtual

Sets the maximum noise voltage.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 358 of file FiringRateSim/Neuron.cpp.

References m_bUseNoise, and m_fltVNoiseMax.

float FiringRateSim::Neurons::Neuron::Vrest ( )
virtual

Gets the rest potential.

Author
dcofer
Date
3/29/2011
Returns
rest potential.

Definition at line 268 of file FiringRateSim/Neuron.cpp.

References m_fltVrest.

Referenced by SetData().

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void FiringRateSim::Neurons::Neuron::Vrest ( float  fltVal)
virtual

Sets the rest potential.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 279 of file FiringRateSim/Neuron.cpp.

References m_fltVndisp, m_fltVrest, m_fltVthi, AnimatSim::AnimatBase::m_lpSim, AnimatSim::Simulator::SimRunning(), and Vth().

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float FiringRateSim::Neurons::Neuron::Vth ( )
virtual

Gets the voltage threshold for firing.

Author
dcofer
Date
3/29/2011
Returns
voltage threshold.

Definition at line 149 of file FiringRateSim/Neuron.cpp.

References m_fltVth.

Referenced by SetData(), and Vrest().

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void FiringRateSim::Neurons::Neuron::Vth ( float  fltVal)
virtual

Sets the voltage threshold for firing.

Author
dcofer
Date
3/29/2011
Parameters
fltValThe new value.

Definition at line 160 of file FiringRateSim/Neuron.cpp.

References m_aryVth, m_fltVrest, m_fltVth, m_fltVthadd, m_fltVthdisp, and m_fltVthi.

Member Data Documentation

float FiringRateSim::Neurons::Neuron::m_fltGain
protected

Firing frequency gain. This is multiplied by the membrane voltage that is above the threshold to determine the firing rate.

Definition at line 55 of file FiringRateSim/Neuron.h.

Referenced by CalculateFiringFrequency(), Gain(), and Neuron().


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