Integrate and fire neural module. More...

#include <IntegrateFireModule.h>

Inheritance diagram for IntegrateFireSim::IntegrateFireNeuralModule:

Collaboration diagram for IntegrateFireSim::IntegrateFireNeuralModule:

Public Member Functions
	IntegrateFireNeuralModule ()
	Default constructor. More...

virtual	~IntegrateFireNeuralModule ()
	Destructor. More...

void	AbsoluteRefr (double dVal)
	Sets the absolute refractory period. More...

double	AbsoluteRefr ()
	Gets the absolute refractory period. 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)
	Adds a neuron by using xml. More...

virtual void	AddSynapse (std::string strXml, bool bDoNotInit)
	Adds a synapse by xml. More...

virtual void	AddSynapseType (std::string strXml, bool bDoNotInit)
	Adds a synapse type by xml. More...

void	AHPEquilPot (double dVal)
	Sets the after-hyperpolarizing equil potential for all neurons in the IGF module. More...

double	AHPEquilPot ()
	Gets the after-hyperpolarizing equil potential for all neurons in the IGF module. More...

void	CaEquilPot (double dVal)
	Sets the calcium equilibrium potential. More...

double	CaEquilPot ()
	Gets the calcium equilibrium potential. More...

virtual long	CalculateSnapshotByteSize ()
	Calculates the snapshot byte size. More...

void	CalcUpdate ()
	Calculates the update during the step of the simulation. More...

void	Cd (bool bVal)
	Sets whether Cadmium is applied to the nervous system. More...

bool	Cd ()
	Gets whether Cadmium is applied to the nervous system. More...

void	EndCriticalPeriod (double dVal)
	Sets the end time of the critical period. More...

double	EndCriticalPeriod ()
	Gets the end time of the critical period. More...

virtual int	FindElectricalListPos (std::string strID, bool bThrowError=true)
	Searches for an electrical synapse by the specified ID and returns its position in the list. More...

virtual int	FindNeuronListPos (std::string strID, bool bThrowError=true)
	Searches for a neuron by the specified ID and returns its position in the list. More...

virtual int	FindNonSpikingChemListPos (std::string strID, bool bThrowError=true)
	Searches for a non-spiking chemical synapse by the specified ID and returns its position in the list. More...

virtual int	FindSpikingChemListPos (std::string strID, bool bThrowError=true)
	Searches for a spiking chemical synapse by the specified ID and returns its position in the list. More...

virtual int	FindSynapseListPos (std::string strID, bool bThrowError=true)
	Searches for a synapse by the specified ID and returns its position in the list. More...

void	FreezeHebb (bool bVal)
	Sets whether to freeze hebbian learning. More...

bool	FreezeHebb ()
	Sets whether to freeze hebbian learning. More...

Connexion *	GetConnexionAt (int i)
	Gets a connexion at specified index. More...

int	GetConnexionCount ()
	Gets the connexion count. More...

double	GetCurrentTime ()
	Gets the current time. More...

ElectricalSynapse *	GetElecSynAt (int i)
	Gets an electrical synapse at the specified index. More...

int	GetElecSynCount ()
	Gets the electrical synapse count. More...

Neuron *	GetNeuronAt (int i)
	Gets a neuron at specified index. More...

int	GetNeuronCount ()
	Gets the neuron count. More...

NonSpikingChemicalSynapse *	GetNonSpikingChemSynAt (int i)
	Gets a non-spiking chemical synapse at the specified index. More...

int	GetNonSpikingChemSynCount ()
	Gets the non-spiking chemical synapse count. More...

double	GetScaleElecCond (double minG, double maxG, double jV, double ThreshV, double SaturateV)
	Gets a scale electrical conductance. More...

SpikingChemicalSynapse *	GetSpikingChemSynAt (int i)
	Gets a spiking chemical synapse at the specified array index. More...

int	GetSpikingChemSynCount ()
	Gets the spiking chemical synapse count. More...

double	GetTimeStep ()
	Gets the time step. More...

void	HH (bool bVal)
	Sets whether hodgkin-huxely model is used. More...

bool	HH ()
	Gets whether hodgkin-huxely model is used. 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...

void	PostCalc ()
	performs post-step calculations. More...

void	PreCalc ()
	Performs pre-step calculations. 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	RemoveSynapse (std::string strID, bool bThrowError=true)
	Removes the synapse with the specified ID. More...

virtual void	RemoveSynapseType (std::string strID, bool bThrowError=true)
	Removes the synapse type by ID. More...

void	ResetIDs ()
	Resets the integer IDs of the various objects when things move around in the array for some reason. More...

virtual void	ResetSimulation ()
	Resets the simulation back to time 0. More...

void	RetainHebbMemory (bool bVal)
	Sets whether to retain hebbian memory. More...

bool	RetainHebbMemory ()
	Gets whether to retain hebbian memory. More...

virtual void	SaveKeyFrameSnapshot (byte *aryBytes, long &lIndex)
	Saves a key frame snapshot. More...

void	ScaleCondForNonSpiking (double &G, double PreV, double ThreshV, double SaturateV)
	Scale conductance for non-spiking chemical synapse. More...

void	ScaleCondForVoltDep (double &G, double postV, double maxV, double minV, double scl)
	Scale conductance for volt dependance. More...

void	SetCurrentTime (double t)
	Sets the current time. 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...

void	SpikePeak (double dVal)
	Sets the spike peak. More...

double	SpikePeak ()
	Gets the spike peak. More...

void	SpikeStrength (double dVal)
	Sets the spike strength. More...

double	SpikeStrength ()
	Gets the spike strength. More...

void	StartCriticalPeriod (double dVal)
	Sets the start time of the critical period. More...

double	StartCriticalPeriod ()
	Gets the start time of the critical period. More...

virtual void	StepSimulation ()
	Step the simulation for this object. More...

virtual void	TimeStep (float fltVal)
	Sets the Time step. More...

virtual float	TimeStep ()
	Gets the time step. More...

virtual void	TimeStepModified ()
	Notification method that the time step modified has been modified. Objects should recalculate any slice times as needed. More...

void	TTX (bool bVal)
	Sets whether ttx is applied to the nervous system. More...

bool	TTX ()
	Gets whether ttx is applied to the nervous system. More...

void	UseCriticalPeriod (bool bVal)
	Sets whether to use critical period. More...

bool	UseCriticalPeriod ()
	Gets whether to use critical period. 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 IStdClassFactory *	ClassFactory ()
	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...

Organism *	GetOrganism ()
	Gets the organism. More...

Simulator *	GetSimulator ()
	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 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 NeuralModule *	GetNeuralModule ()
	Gets the neural module. More...

virtual Node *	GetNode ()
	Gets the node. More...

virtual Structure *	GetStructure ()
	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 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	InitSynapse (Connexion *pCx)
	Initialises the synapse. More...

Connexion *	LoadConnexion (CStdXml &oXml)
	Loads a connexion. More...

ElectricalSynapse *	LoadElecSyn (CStdXml &oXml, int iIndex)
	Loads an electrical synapse. More...

virtual void	LoadInternal (CStdXml &oXml)
	Interal method to load the module data. More...

Neuron *	LoadNeuron (CStdXml &oXml)
	Loads a neuron. More...

NonSpikingChemicalSynapse *	LoadNonSpikingChemSyn (CStdXml &oXml, int iIndex)
	Loads a non-spiking chemical synapse. More...

SpikingChemicalSynapse *	LoadSpikingChemSyn (CStdXml &oXml, int iIndex)
	Loads a spiking chemical synapse. More...

SynapseType *	LoadSynapseType (CStdXml &oXml)
	Loads a synapse type. More...

Protected Member Functions inherited from AnimatSim::Behavior::NeuralModule
virtual int	FindAdapterListIndex (CStdArray< Adapter * > aryAdapters, std::string strID, bool bThrowError=true)

virtual AnimatSim::Link *	LoadExternalSynapse (CStdXml &oXml)
	Loads an external synapse. More...

virtual void	LoadExternalSynapses (CStdXml &oXml)
	Loads external synapses. More...

Protected Attributes
CStdPtrArray< Connexion >	m_aryConnexion
	The array of connexions in this neural module.

CStdPtrArray< ElectricalSynapse >	m_aryElecSyn
	The array of electrical synapses in this neural module.

CStdPtrArray< Neuron >	m_aryNeurons
	The array of neurons in this neural module.

CStdPtrArray< NonSpikingChemicalSynapse >	m_aryNonSpikingChemSyn
	The array of non-spiking chemical synapses in this neural module.

CStdPtrArray< SpikingChemicalSynapse >	m_arySpikingChemSyn
	The array of spiking chem synapses in this neural module.

bool	m_bCd
	true if cadium is applied to the nervous system.

bool	m_bFreezeHebb
	true to freeze hebbian learning.

bool	m_bFreezeLearning
	true to freeze learning.

bool	m_bHH
	true if this nervous system is using a hodgkin-huxely model.

bool	m_bNeedInitialiseHebb
	true if hebbian learning needs to be initialized

bool	m_bRandomisedHebb
	true to randomise hebbian learning values.

bool	m_bRetainHebbMemory
	true to retain hebbian memory

bool	m_bTTX
	true if ttx drug is applied to the nervous system.

bool	m_bUseCriticalPeriod
	true to use critical period during hebbian learning.

double	m_dCurrentTime
	Current time of the simulation.

double	m_dEndCriticalPeriod
	The end time of the critical period for hebbian learning.

double	m_dStartCriticalPeriod
	The start time of the critical period for hebbian learning.

double	m_dTimeStep
	The time step of the neural module.

Protected Attributes inherited from AnimatSim::Behavior::NeuralModule
CStdPtrArray< AnimatSim::Link >	m_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

IStdClassFactory *	m_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::NeuralModule *	m_lpModule
	The pointer to this items parentNeuralModule. If this is not relevant for this object then this is NULL.

Node *	m_lpNode
	The pointer to this items parent Node. If this is not relevant for this object then this is NULL.

Simulator *	m_lpSim
	The pointer to a Simulation.

AnimatSim::Environment::Structure *	m_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 NeuralModule *	CastToDerived (AnimatBase *lpBase)

Detailed Description

Integrate and fire neural module.

This neural module implements the integrate and fire neural models.

Author: dcofer

Date: 3/30/2011

Definition at line 21 of file IntegrateFireModule.h.

Constructor & Destructor Documentation

IntegrateFireSim::IntegrateFireNeuralModule::IntegrateFireNeuralModule ( )

Default constructor.

Author: dcofer

Date: 3/30/2011

Definition at line 29 of file IntegrateFireModule.cpp.

References m_bCd, m_bFreezeHebb, m_bFreezeLearning, m_bHH, m_bNeedInitialiseHebb, m_bRandomisedHebb, m_bTTX, m_bUseCriticalPeriod, m_dCurrentTime, m_dEndCriticalPeriod, m_dStartCriticalPeriod, m_dTimeStep, and AnimatSim::Behavior::NeuralModule::m_lpClassFactory.

IntegrateFireSim::IntegrateFireNeuralModule::~IntegrateFireNeuralModule ( )

virtual

Destructor.

Author: dcofer

Date: 3/30/2011

Definition at line 62 of file IntegrateFireModule.cpp.

References m_aryNeurons, m_arySpikingChemSyn, and StdUtils::Std_TraceMsg().

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Member Function Documentation

void IntegrateFireSim::IntegrateFireNeuralModule::AbsoluteRefr ( double dVal )

Sets the absolute refractory period.

Author: dcofer

Date: 3/30/2011

Parameters

dVal	The new value.

Definition at line 407 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dAbsoluteRefr, m_dTimeStep, and IntegrateFireSim::Neuron::m_lAbsoluteRefr.

double IntegrateFireSim::IntegrateFireNeuralModule::AbsoluteRefr ( )

Gets the absolute refractory period.

Author: dcofer

Date: 3/30/2011

Returns: refractory period.

Definition at line 421 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dAbsoluteRefr.

Referenced by SetData().

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bool IntegrateFireSim::IntegrateFireNeuralModule::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

strItemType	String descriptor of the type of item that is being created.
strXml	XML packet that is used to create and load the new item.
bThrowError	If 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 1696 of file IntegrateFireModule.cpp.

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

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void IntegrateFireSim::IntegrateFireNeuralModule::AddNeuron	(	std::string	strXml,
		bool	bDoNotInit
	)

virtual

Adds a neuron by using xml.

Author: dcofer

Date: 3/30/2011

Parameters

strXml The string xml to load.

Definition at line 1573 of file IntegrateFireModule.cpp.

References LoadNeuron(), and PreCalc().

Referenced by AddItem().

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void IntegrateFireSim::IntegrateFireNeuralModule::AddSynapse	(	std::string	strXml,
		bool	bDoNotInit
	)

virtual

Adds a synapse by xml.

Author: dcofer

Date: 3/30/2011

Parameters

strXml The xml to load.

Definition at line 1608 of file IntegrateFireModule.cpp.

References LoadConnexion(), and PreCalc().

Referenced by AddItem().

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void IntegrateFireSim::IntegrateFireNeuralModule::AddSynapseType	(	std::string	strXml,
		bool	bDoNotInit
	)

virtual

Adds a synapse type by xml.

Author: dcofer

Date: 3/30/2011

Parameters

strXml The xml to load.

Definition at line 1627 of file IntegrateFireModule.cpp.

References LoadSynapseType(), and PreCalc().

Referenced by AddItem().

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void IntegrateFireSim::IntegrateFireNeuralModule::AHPEquilPot ( double dVal )

Sets the after-hyperpolarizing equil potential for all neurons in the IGF module.

Author: dcofer

Date: 2/1/2012

Parameters

dVal	Sets the value.

Definition at line 431 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dAHPEquilPot.

double IntegrateFireSim::IntegrateFireNeuralModule::AHPEquilPot ( )

Gets the after-hyperpolarizing equil potential for all neurons in the IGF module.

Author: dcofer

Date: 2/1/2012

Returns: Gets the value.

Definition at line 441 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dAHPEquilPot.

Referenced by SetData().

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void IntegrateFireSim::IntegrateFireNeuralModule::CaEquilPot ( double dVal )

Sets the calcium equilibrium potential.

Author: dcofer

Date: 3/30/2011

Parameters

dVal	The new value.

Definition at line 387 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dCaEquilPot.

double IntegrateFireSim::IntegrateFireNeuralModule::CaEquilPot ( )

Gets the calcium equilibrium potential.

Author: dcofer

Date: 3/30/2011

Returns: potential.

Definition at line 397 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dCaEquilPot.

Referenced by SetData().

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virtual long IntegrateFireSim::IntegrateFireNeuralModule::CalculateSnapshotByteSize ( )

inlinevirtual

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 202 of file IntegrateFireModule.h.

void IntegrateFireSim::IntegrateFireNeuralModule::CalcUpdate ( )

Calculates the update during the step of the simulation.

Author: dcofer

Date: 3/30/2011

Definition at line 1128 of file IntegrateFireModule.cpp.

Referenced by StepSimulation().

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void IntegrateFireSim::IntegrateFireNeuralModule::Cd ( bool bVal )

Sets whether Cadmium is applied to the nervous system.

Author: dcofer

Date: 3/30/2011

Parameters

bVal	true to use cadmium.

Definition at line 159 of file IntegrateFireModule.cpp.

References m_bCd.

Referenced by IntegrateFireSim::Neuron::CalcUpdate().

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bool IntegrateFireSim::IntegrateFireNeuralModule::Cd ( )

Gets whether Cadmium is applied to the nervous system.

Author: dcofer

Date: 3/30/2011

Returns: true if Cd applied, false else.

Definition at line 169 of file IntegrateFireModule.cpp.

References m_bCd.

Referenced by LoadInternal(), and SetData().

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void IntegrateFireSim::IntegrateFireNeuralModule::EndCriticalPeriod ( double dVal )

Sets the end time of the critical period.

Author: dcofer

Date: 3/30/2011

Parameters

dVal	The new value.

Definition at line 307 of file IntegrateFireModule.cpp.

References m_dEndCriticalPeriod.

double IntegrateFireSim::IntegrateFireNeuralModule::EndCriticalPeriod ( )

Gets the end time of the critical period.

Author: dcofer

Date: 3/30/2011

Returns: end time.

Definition at line 317 of file IntegrateFireModule.cpp.

References m_dEndCriticalPeriod.

Referenced by LoadInternal(), and SetData().

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int IntegrateFireSim::IntegrateFireNeuralModule::FindElectricalListPos	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

Searches for an electrical synapse by the specified ID and returns its position in the list.

Author: dcofer

Date: 3/30/2011

Parameters

strID	GUID ID for the synapse.
bThrowError	true to throw error if synapse not found.

Returns: The found synapse list position.

Definition at line 1430 of file IntegrateFireModule.cpp.

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

Referenced by RemoveSynapseType().

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int IntegrateFireSim::IntegrateFireNeuralModule::FindNeuronListPos	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

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

Author: dcofer

Date: 3/30/2011

Parameters

strID	GUID ID for the neuron.
bThrowError	true to throw error if neuron not found.

Returns: The found neuron list position.

Definition at line 1326 of file IntegrateFireModule.cpp.

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

Referenced by RemoveNeuron().

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int IntegrateFireSim::IntegrateFireNeuralModule::FindNonSpikingChemListPos	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

Searches for a non-spiking chemical synapse by the specified ID and returns its position in the list.

Author: dcofer

Date: 3/30/2011

Parameters

strID	GUID ID for the synapse.
bThrowError	true to throw error if synapse not found.

Returns: The found synapse list position.

Definition at line 1404 of file IntegrateFireModule.cpp.

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

Referenced by RemoveSynapseType().

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int IntegrateFireSim::IntegrateFireNeuralModule::FindSpikingChemListPos	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

Searches for a spiking chemical synapse by the specified ID and returns its position in the list.

Author: dcofer

Date: 3/30/2011

Parameters

strID	GUID ID for the synapse.
bThrowError	true to throw error if synapse not found.

Returns: The found synapse list position.

Definition at line 1378 of file IntegrateFireModule.cpp.

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

Referenced by RemoveSynapseType().

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int IntegrateFireSim::IntegrateFireNeuralModule::FindSynapseListPos	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

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

Author: dcofer

Date: 3/30/2011

Parameters

strID	GUID ID for the synapse.
bThrowError	true to throw error if synapse not found.

Returns: The found synapse list position.

Definition at line 1352 of file IntegrateFireModule.cpp.

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

Referenced by RemoveSynapse().

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void IntegrateFireSim::IntegrateFireNeuralModule::FreezeHebb ( bool bVal )

Sets whether to freeze hebbian learning.

Author: dcofer

Date: 3/30/2011

Parameters

bVal	true to freeze.

Definition at line 327 of file IntegrateFireModule.cpp.

References m_bFreezeHebb.

bool IntegrateFireSim::IntegrateFireNeuralModule::FreezeHebb ( )

Sets whether to freeze hebbian learning.

Author: dcofer

Date: 3/30/2011

Returns: true if frozen, false else.

Definition at line 337 of file IntegrateFireModule.cpp.

References m_bFreezeHebb.

Referenced by LoadInternal(), and SetData().

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Connexion * IntegrateFireSim::IntegrateFireNeuralModule::GetConnexionAt ( int i )

Gets a connexion at specified index.

Author: dcofer

Date: 3/30/2011

Parameters

i	The index.

Returns: Pointer to the connexion at.

Definition at line 149 of file IntegrateFireModule.cpp.

References m_aryConnexion.

Referenced by CalcUpdate(), PostCalc(), PreCalc(), and ResetIDs().

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int IntegrateFireSim::IntegrateFireNeuralModule::GetConnexionCount ( )

Gets the connexion count.

Author: dcofer

Date: 3/30/2011

Returns: The connexion count.

Definition at line 137 of file IntegrateFireModule.cpp.

References m_aryConnexion.

Referenced by CalcUpdate(), PostCalc(), PreCalc(), and ResetIDs().

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double IntegrateFireSim::IntegrateFireNeuralModule::GetCurrentTime ( )

Gets the current time.

Author: dcofer

Date: 3/30/2011

Returns: The current time.

Definition at line 95 of file IntegrateFireModule.cpp.

References m_dCurrentTime.

Referenced by IntegrateFireSim::Neuron::CalculateFiringFreq().

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ElectricalSynapse * IntegrateFireSim::IntegrateFireNeuralModule::GetElecSynAt ( int i )

Gets an electrical synapse at the specified index.

Author: dcofer

Date: 3/30/2011

Parameters

i	The index.

Returns: null if it fails, else the elec syn at.

Definition at line 507 of file IntegrateFireModule.cpp.

References m_aryElecSyn.

int IntegrateFireSim::IntegrateFireNeuralModule::GetElecSynCount ( )

Gets the electrical synapse count.

Author: dcofer

Date: 3/30/2011

Returns: The electrical synapse count.

Definition at line 495 of file IntegrateFireModule.cpp.

References m_aryElecSyn.

Neuron * IntegrateFireSim::IntegrateFireNeuralModule::GetNeuronAt ( int i )

Gets a neuron at specified index.

Author: dcofer

Date: 3/30/2011

Parameters

i	The index.

Returns: Pointer to the neuron at.

Definition at line 127 of file IntegrateFireModule.cpp.

References m_aryNeurons.

Referenced by CalcUpdate(), PostCalc(), and PreCalc().

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int IntegrateFireSim::IntegrateFireNeuralModule::GetNeuronCount ( )

Gets the neuron count.

Author: dcofer

Date: 3/30/2011

Returns: The neuron count.

Definition at line 115 of file IntegrateFireModule.cpp.

References m_aryNeurons.

Referenced by CalcUpdate(), PostCalc(), and PreCalc().

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NonSpikingChemicalSynapse * IntegrateFireSim::IntegrateFireNeuralModule::GetNonSpikingChemSynAt ( int i )

Gets a non-spiking chemical synapse at the specified index.

Author: dcofer

Date: 3/30/2011

Parameters

i	The index.

Returns: null if it fails, else the non spiking chem syn at.

Definition at line 485 of file IntegrateFireModule.cpp.

References m_aryNonSpikingChemSyn.

int IntegrateFireSim::IntegrateFireNeuralModule::GetNonSpikingChemSynCount ( )

Gets the non-spiking chemical synapse count.

Author: dcofer

Date: 3/30/2011

Returns: The non-spiking chemical synapse count.

Definition at line 473 of file IntegrateFireModule.cpp.

References m_aryNonSpikingChemSyn.

double IntegrateFireSim::IntegrateFireNeuralModule::GetScaleElecCond	(	double	minG,
		double	maxG,
		double	jV,
		double	ThreshV,
		double	SaturateV
	)

Gets a scale electrical conductance.

Author: dcofer

Date: 3/30/2011

Parameters

minG	The minimum conductance.
maxG	The maximum conductance.
jV	The juntional voltage.
ThreshV	The threshold voltage.
SaturateV	The saturate voltage.

Returns: The scale electrical conductance.

Definition at line 930 of file IntegrateFireModule.cpp.

Referenced by CalcUpdate().

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SpikingChemicalSynapse * IntegrateFireSim::IntegrateFireNeuralModule::GetSpikingChemSynAt ( int i )

Gets a spiking chemical synapse at the specified array index.

Author: dcofer

Date: 3/30/2011

Parameters

i	The index.

Returns: null if it fails, else the spiking chem syn at.

Definition at line 463 of file IntegrateFireModule.cpp.

References m_arySpikingChemSyn.

Referenced by IntegrateFireSim::Neuron::CalcUpdate(), and IntegrateFireSim::Neuron::PreCalc().

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int IntegrateFireSim::IntegrateFireNeuralModule::GetSpikingChemSynCount ( )

Gets the spiking chemical synapse count.

Author: dcofer

Date: 3/30/2011

Returns: The count.

Definition at line 451 of file IntegrateFireModule.cpp.

References m_arySpikingChemSyn.

Referenced by IntegrateFireSim::Neuron::CalcUpdate(), and IntegrateFireSim::Neuron::PreCalc().

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double IntegrateFireSim::IntegrateFireNeuralModule::GetTimeStep ( )

Gets the time step.

Author: dcofer

Date: 3/30/2011

Returns: The time step.

Definition at line 105 of file IntegrateFireModule.cpp.

References m_dTimeStep.

Referenced by IntegrateFireSim::Neuron::CalcUpdate().

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void IntegrateFireSim::IntegrateFireNeuralModule::HH ( bool bVal )

Sets whether hodgkin-huxely model is used.

Author: dcofer

Date: 3/30/2011

Parameters

bVal	true to use HH.

Definition at line 199 of file IntegrateFireModule.cpp.

References m_bHH.

Referenced by IntegrateFireSim::Neuron::CalcUpdate(), and IntegrateFireSim::Neuron::CalcUpdateFinal().

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bool IntegrateFireSim::IntegrateFireNeuralModule::HH ( )

Gets whether hodgkin-huxely model is used.

Author: dcofer

Date: 3/30/2011

Returns: true if HH used, false else.

Definition at line 209 of file IntegrateFireModule.cpp.

References m_bHH.

Referenced by LoadInternal(), and SetData().

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void IntegrateFireSim::IntegrateFireNeuralModule::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 1789 of file IntegrateFireModule.cpp.

References PreCalc().

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void IntegrateFireSim::IntegrateFireNeuralModule::InitSynapse ( Connexion * pCx )

protected

Initialises the synapse.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out] pCx Pointer to the connection to initialize.

Definition at line 1023 of file IntegrateFireModule.cpp.

Referenced by PreCalc().

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void IntegrateFireSim::IntegrateFireNeuralModule::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

bState true to state.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 1763 of file IntegrateFireModule.cpp.

References m_aryNeurons.

Connexion * IntegrateFireSim::IntegrateFireNeuralModule::LoadConnexion ( CStdXml & oXml )

protected

Loads a connexion.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out] oXml The xml to use when loading the connection.

Returns: Pointer to the connexion.

Definition at line 850 of file IntegrateFireModule.cpp.

References m_aryConnexion, AnimatSim::AnimatBase::m_lpSim, and AnimatSim::AnimatBase::m_lpStructure.

Referenced by AddSynapse(), and LoadInternal().

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ElectricalSynapse * IntegrateFireSim::IntegrateFireNeuralModule::LoadElecSyn	(	CStdXml &	oXml,
		int	iIndex
	)

protected

Loads an electrical synapse.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out]	oXml	The xml to use when loading the synapse.
	iIndex	Index where the synpase will be added in the array.

Returns: Pointer to the synapse.

Definition at line 808 of file IntegrateFireModule.cpp.

References m_aryElecSyn, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_lpStructure, and IntegrateFireSim::Synapses::SynapseType::SynapseTypeID().

Referenced by LoadInternal(), and LoadSynapseType().

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void IntegrateFireSim::IntegrateFireNeuralModule::LoadInternal ( CStdXml & oXml )

protectedvirtual

Interal method to load the module data.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out] oXml The xml to load.

Definition at line 529 of file IntegrateFireModule.cpp.

References Cd(), EndCriticalPeriod(), FreezeHebb(), AnimatSim::Behavior::NeuralModule::GetSimulator(), HH(), AnimatSim::AnimatBase::ID(), LoadConnexion(), LoadElecSyn(), LoadNeuron(), LoadNonSpikingChemSyn(), LoadSpikingChemSyn(), m_aryNeurons, IntegrateFireSim::Neuron::m_dAbsoluteRefr, IntegrateFireSim::Neuron::m_dAHPEquilPot, IntegrateFireSim::Neuron::m_dCaEquilPot, IntegrateFireSim::Neuron::m_dSpikePeak, IntegrateFireSim::Neuron::m_dSpikeStrength, m_dTimeStep, AnimatSim::Behavior::NeuralModule::m_fltTimeStep, IntegrateFireSim::Neuron::m_lAbsoluteRefr, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_strID, AnimatSim::AnimatBase::m_strName, AnimatSim::AnimatBase::m_strType, AnimatSim::AnimatBase::Name(), RetainHebbMemory(), StartCriticalPeriod(), StdUtils::Std_InValidRange(), TTX(), AnimatSim::AnimatBase::Type(), UseCriticalPeriod(), and AnimatSim::Behavior::NeuralModule::VerifySystemPointers().

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virtual void IntegrateFireSim::IntegrateFireNeuralModule::LoadKeyFrameSnapshot	(	byte *	aryBytes,
		long &	lIndex
	)

inlinevirtual

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]	aryBytes	The array of bytes where the data is being stored.
[in,out]	lIndex	Current zero-based index of the read position in the array.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 204 of file IntegrateFireModule.h.

Neuron * IntegrateFireSim::IntegrateFireNeuralModule::LoadNeuron ( CStdXml & oXml )

protected

Loads a neuron.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out] oXml The xml to use when loading the neuron.

Returns: Pointer to the neuron.

Definition at line 650 of file IntegrateFireModule.cpp.

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

Referenced by AddNeuron(), and LoadInternal().

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NonSpikingChemicalSynapse * IntegrateFireSim::IntegrateFireNeuralModule::LoadNonSpikingChemSyn	(	CStdXml &	oXml,
		int	iIndex
	)

protected

Loads a non-spiking chemical synapse.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out]	oXml	The xml to use when loading the synapse.
	iIndex	Index where the synpase will be added in the array.

Returns: Pointer to the synapse.

Definition at line 765 of file IntegrateFireModule.cpp.

References m_aryNonSpikingChemSyn, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_lpStructure, and IntegrateFireSim::Synapses::SynapseType::SynapseTypeID().

Referenced by LoadInternal(), and LoadSynapseType().

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SpikingChemicalSynapse * IntegrateFireSim::IntegrateFireNeuralModule::LoadSpikingChemSyn	(	CStdXml &	oXml,
		int	iIndex
	)

protected

Loads a spiking chemical synapse.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out]	oXml	The xml to use when loading the synapse.
	iIndex	Index where the synpase will be added in the array.

Returns: Pointer to the spiking chemical synapse.

Definition at line 722 of file IntegrateFireModule.cpp.

References m_arySpikingChemSyn, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_lpStructure, and IntegrateFireSim::Synapses::SynapseType::SynapseTypeID().

Referenced by LoadInternal(), and LoadSynapseType().

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SynapseType * IntegrateFireSim::IntegrateFireNeuralModule::LoadSynapseType ( CStdXml & oXml )

protected

Loads a synapse type.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out] oXml The xml to use when loading the synapse type.

Returns: Pointer to the synapse type.

Definition at line 691 of file IntegrateFireModule.cpp.

References LoadElecSyn(), LoadNonSpikingChemSyn(), LoadSpikingChemSyn(), m_aryElecSyn, m_aryNonSpikingChemSyn, m_arySpikingChemSyn, and StdUtils::Std_ToUpper().

Referenced by AddSynapseType().

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std::string IntegrateFireSim::IntegrateFireNeuralModule::ModuleName ( )

virtual

Gets the module name.

Author: dcofer

Date: 3/30/2011

Returns: module name.

Implements AnimatSim::Behavior::NeuralModule.

Definition at line 517 of file IntegrateFireModule.cpp.

void IntegrateFireSim::IntegrateFireNeuralModule::PostCalc ( )

performs post-step calculations.

Author: dcofer

Date: 3/30/2011

Definition at line 998 of file IntegrateFireModule.cpp.

References GetConnexionAt(), GetConnexionCount(), GetNeuronAt(), GetNeuronCount(), IntegrateFireSim::Synapses::Connexion::m_HebbList, IntegrateFireSim::Synapses::Connexion::m_TransitCx, IntegrateFireSim::Neuron::PostCalc(), and IntegrateFireSim::Utilities::DoubleList::Release().

Referenced by ResetSimulation().

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void IntegrateFireSim::IntegrateFireNeuralModule::PreCalc ( )

Performs pre-step calculations.

Author: dcofer

Date: 3/30/2011

Definition at line 1061 of file IntegrateFireModule.cpp.

References GetConnexionAt(), GetConnexionCount(), GetNeuronAt(), GetNeuronCount(), InitSynapse(), m_arySpikingChemSyn, m_bNeedInitialiseHebb, m_bRandomisedHebb, IntegrateFireSim::Neuron::m_dAbsoluteRefr, m_dCurrentTime, IntegrateFireSim::Neuron::m_dDT, IntegrateFireSim::Synapses::SpikingChemicalSynapse::m_dFacilD, IntegrateFireSim::Synapses::SpikingChemicalSynapse::m_dFacilDecay, m_dTimeStep, IntegrateFireSim::Neuron::m_lAbsoluteRefr, IntegrateFireSim::Neuron::PreCalc(), and ResetIDs().

Referenced by AddNeuron(), AddSynapse(), AddSynapseType(), Initialize(), RemoveNeuron(), RemoveSynapse(), RemoveSynapseType(), ResetSimulation(), IntegrateFireSim::Synapses::Connexion::SetData(), TimeStep(), and TimeStepModified().

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bool IntegrateFireSim::IntegrateFireNeuralModule::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

strItemType	String descriptor of the type of item that is being created.
strID	Unique ID of the item that will be removed.
bThrowError	If 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 1728 of file IntegrateFireModule.cpp.

References AnimatSim::Behavior::NeuralModule::RemoveExternalSynapse(), RemoveNeuron(), RemoveSynapse(), RemoveSynapseType(), and StdUtils::Std_CheckString().

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void IntegrateFireSim::IntegrateFireNeuralModule::RemoveNeuron	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

Removes the neuron with the specified ID.

Author: dcofer

Date: 3/30/2011

Parameters

strID	GUID ID for the neuron to remove.
bThrowError	true to throw error if no neuron is found.

Definition at line 1593 of file IntegrateFireModule.cpp.

References FindNeuronListPos(), m_aryNeurons, and PreCalc().

Referenced by RemoveItem().

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void IntegrateFireSim::IntegrateFireNeuralModule::RemoveSynapse	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

Removes the synapse with the specified ID.

Author: dcofer

Date: 3/30/2011

Parameters

strID	GUUId for the string.
bThrowError	true to throw error.

Definition at line 1647 of file IntegrateFireModule.cpp.

References FindSynapseListPos(), m_aryConnexion, and PreCalc().

Referenced by RemoveItem().

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void IntegrateFireSim::IntegrateFireNeuralModule::RemoveSynapseType	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

Removes the synapse type by ID.

Author: dcofer

Date: 3/31/2011

Parameters

strID	GUID ID for the synapse type to remove.
bThrowError	true to throw error if synapse type was not found.

Definition at line 1663 of file IntegrateFireModule.cpp.

References AnimatSim::Simulator::FindByID(), FindElectricalListPos(), FindNonSpikingChemListPos(), FindSpikingChemListPos(), AnimatSim::Behavior::NeuralModule::GetSimulator(), m_aryElecSyn, m_aryNonSpikingChemSyn, m_arySpikingChemSyn, PreCalc(), StdUtils::Std_ToUpper(), and AnimatSim::AnimatBase::Type().

Referenced by RemoveItem().

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void IntegrateFireSim::IntegrateFireNeuralModule::ResetIDs ( )

Resets the integer IDs of the various objects when things move around in the array for some reason.

Author: dcofer

Date: 3/30/2011

Definition at line 886 of file IntegrateFireModule.cpp.

References GetConnexionAt(), GetConnexionCount(), m_aryElecSyn, m_aryNeurons, m_aryNonSpikingChemSyn, m_arySpikingChemSyn, and IntegrateFireSim::Synapses::Connexion::ResetIDs().

Referenced by PreCalc().

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void IntegrateFireSim::IntegrateFireNeuralModule::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 1770 of file IntegrateFireModule.cpp.

References m_aryConnexion, m_aryNeurons, m_dCurrentTime, PostCalc(), and PreCalc().

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void IntegrateFireSim::IntegrateFireNeuralModule::RetainHebbMemory ( bool bVal )

Sets whether to retain hebbian memory.

Author: dcofer

Date: 3/30/2011

Parameters

bVal	true to retain.

Definition at line 247 of file IntegrateFireModule.cpp.

References m_bRetainHebbMemory.

bool IntegrateFireSim::IntegrateFireNeuralModule::RetainHebbMemory ( )

Gets whether to retain hebbian memory.

Author: dcofer

Date: 3/30/2011

Returns: true if retaining, false else.

Definition at line 257 of file IntegrateFireModule.cpp.

References m_bRetainHebbMemory.

Referenced by LoadInternal(), and SetData().

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virtual void IntegrateFireSim::IntegrateFireNeuralModule::SaveKeyFrameSnapshot	(	byte *	aryBytes,
		long &	lIndex
	)

inlinevirtual

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]	aryBytes	The array of bytes where the data is being stored.
[in,out]	lIndex	Current zero-based index of the write position in the array.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 203 of file IntegrateFireModule.h.

void IntegrateFireSim::IntegrateFireNeuralModule::ScaleCondForNonSpiking	(	double &	G,
		double	PreV,
		double	ThreshV,
		double	SaturateV
	)

Scale conductance for non-spiking chemical synapse.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out]	G	The conductance to scale.
	PreV	The pre-synaptic voltage.
	ThreshV	The threshold voltage.
	SaturateV	The saturate voltage.

Definition at line 984 of file IntegrateFireModule.cpp.

Referenced by CalcUpdate().

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void IntegrateFireSim::IntegrateFireNeuralModule::ScaleCondForVoltDep	(	double &	G,
		double	postV,
		double	maxV,
		double	minV,
		double	scl
	)

Scale conductance for volt dependance.

Author: dcofer

Date: 3/30/2011

Parameters

[in,out]	G	The conductance to scale.
	postV	The post-synaptic voltage.
	maxV	The maximum voltage.
	minV	The minimum voltage.
	scl	The scale factor.

Definition at line 954 of file IntegrateFireModule.cpp.

Referenced by IntegrateFireSim::Neuron::CalcUpdate().

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void IntegrateFireSim::IntegrateFireNeuralModule::SetCurrentTime ( double t )

Sets the current time.

Author: dcofer

Date: 3/30/2011

Parameters

t time.

Definition at line 85 of file IntegrateFireModule.cpp.

References m_dCurrentTime.

bool IntegrateFireSim::IntegrateFireNeuralModule::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

strDataType	string name of the data type to set.
strValue	The 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.
bThrowError	true 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 1447 of file IntegrateFireModule.cpp.

References AbsoluteRefr(), AHPEquilPot(), CaEquilPot(), Cd(), EndCriticalPeriod(), FreezeHebb(), HH(), RetainHebbMemory(), SpikePeak(), SpikeStrength(), StartCriticalPeriod(), StdUtils::Std_CheckString(), StdUtils::Std_ToBool(), TimeStep(), TTX(), and UseCriticalPeriod().

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void IntegrateFireSim::IntegrateFireNeuralModule::SpikePeak ( double dVal )

Sets the spike peak.

Author: dcofer

Date: 3/30/2011

Parameters

dVal	The new value.

Definition at line 347 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dSpikePeak.

double IntegrateFireSim::IntegrateFireNeuralModule::SpikePeak ( )

Gets the spike peak.

Author: dcofer

Date: 3/30/2011

Returns: spike peak.

Definition at line 357 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dSpikePeak.

Referenced by SetData().

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void IntegrateFireSim::IntegrateFireNeuralModule::SpikeStrength ( double dVal )

Sets the spike strength.

Author: dcofer

Date: 3/30/2011

Parameters

dVal	The new value.

Definition at line 367 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dSpikeStrength.

double IntegrateFireSim::IntegrateFireNeuralModule::SpikeStrength ( )

Gets the spike strength.

Author: dcofer

Date: 3/30/2011

Returns: spike strength.

Definition at line 377 of file IntegrateFireModule.cpp.

References IntegrateFireSim::Neuron::m_dSpikeStrength.

Referenced by SetData().

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void IntegrateFireSim::IntegrateFireNeuralModule::StartCriticalPeriod ( double dVal )

Sets the start time of the critical period.

Author: dcofer

Date: 3/30/2011

Parameters

dVal	The new value.

Definition at line 287 of file IntegrateFireModule.cpp.

References m_dStartCriticalPeriod.

double IntegrateFireSim::IntegrateFireNeuralModule::StartCriticalPeriod ( )

Gets the start time of the critical period.

Author: dcofer

Date: 3/30/2011

Returns: start time.

Definition at line 297 of file IntegrateFireModule.cpp.

References m_dStartCriticalPeriod.

Referenced by LoadInternal(), and SetData().

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void IntegrateFireSim::IntegrateFireNeuralModule::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.