Firing rate neural module. More...

#include <CsNeuralModule.h>

Inheritance diagram for AnimatCarlSim::CsNeuralModule:

Collaboration diagram for AnimatCarlSim::CsNeuralModule:

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

virtual	~CsNeuralModule ()
	Destructor. More...

virtual void	AddConnectionGenerator (std::string strID, CsConnectionGenerator *lpGen)

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	AddNeuronGroup (std::string strXml, bool bDoNotInit=false)
	Adds a neuron to the module. More...

virtual void	AddSynapse (CsSynapseGroup *lpSynapse)
	Adds a synapse to this module. More...

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

virtual void	ClearSynapses ()
	Clears the synapses list. More...

virtual CsConnectionGenerator *	FindConnectionGenerator (std::string strID, bool bThrowError=true)
	Searches for an item with the specified ID and sets its index in the array. More...

virtual int	FindNeuronGroupListPos (std::string strID, bool bThrowError=true)
	Searches for the neuron with the specified ID and returns its position in the list. 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 CsSynapseGroup *	GetSynapse (int iIndex)
	Gets a synapse by its index in the array. More...

virtual CStdPtrArray< CsSynapseGroup > *	GetSynapses ()
	Gets a pointer to the synapses array. More...

virtual void	Initialize ()
	Initializes this object. More...

virtual void	Kill (bool bState=true)
	Kills. More...

virtual void	Load (CStdXml &oXml)

virtual std::string	ModuleName ()
	Gets the module name. More...

virtual void	QueryProperties (CStdPtrArray< TypeProperty > &aryProperties)

virtual bool	RemoveItem (const std::string &strItemType, const std::string &strID, bool bThrowError=true)
	Removes a child item from this parent. More...

virtual void	RemoveNeuronGroup (std::string strID, bool bThrowError=true)
	Removes the neuron with the specified ID. 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 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	SimMode (int iMode)

virtual int	SimMode ()

virtual void	SimStarting ()
	When the simulation is starting we need to configure our NN and start our processing thread. More...

virtual void	SimStopping ()
	Called just before the simulation stops. More...

virtual unsigned int	SimulationStepInterval ()
	Tells the number of simulation steps that other components, like stimuli, will need to use for their step interval. More...

virtual CpuSNN *	SNN ()

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

virtual bool	stepUpdate (CpuSNN *s, int step)

virtual int	TotalSynapses ()
	Gets the total number of synapses. More...

virtual void	updateMonitors (CpuSNN *s, int step)

Public Member Functions inherited from AnimatSim::Behavior::ThreadedModule
	ThreadedModule (void)
	Default constructor. More...

virtual	~ThreadedModule (void)
	Destructor. More...

virtual float *	GetDataPointer (const std::string &strDataType)
	Returns a float pointer to a data item of interest in this object. More...

virtual void	PauseThread (bool bVal)

virtual bool	PauseThread ()

virtual void	QueryProperties (CStdPtrArray< TypeProperty > &aryProperties)
	Queries this object for a list of properties that can be changed using SetData. More...

virtual void	SetupThread ()
	This method is called after all connections to whatever control board have been made. It calls each parts SetupIO method. For example, We connect to a Firmata microcontroller like an Arduino, and then do a setup that could take some time. We should not attempt to setup any of the pins until after the board itself has been setup. After that we need to loop through and setup all the parts. More...

virtual void	ShutdownThread ()
	This method is called just before the IO thread is closed down. It gives the IO objects a chance to do any required cleanup. More...

virtual float	StepThreadDuration ()
	Gets the time duration required to perform one step of the thread for all parts in this control. More...

virtual bool	ThreadPaused ()

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...

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 float	TimeStep ()
	Gets the time step for this moudle in time units. More...

virtual void	TimeStep (float fltVal)
	Sets the Time step for this moudle in time units. More...

virtual short	TimeStepInterval ()
	Gets the time step interval. More...

virtual void	TimeStepInterval (short iVal)
	Sets ime step interval. More...

virtual void	VerifySystemPointers ()
	Verify that system pointers have been set correctly. More...

Public Member Functions inherited from AnimatSim::AnimatBase
	AnimatBase ()
	Constructs an AnimatBase object. More...

virtual	~AnimatBase ()
	Destroys the AnimatBase object.. More...

virtual void	AfterResetSimulation ()
	Called after a simulation reset for some objects. More...

virtual long	CalculateSnapshotByteSize ()
	Calculates the snapshot byte size. 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 void	LoadKeyFrameSnapshot (byte *aryBytes, long &lIndex)
	Loads a key frame snapshot. 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 void	SaveKeyFrameSnapshot (byte *aryBytes, long &lIndex)
	Saves a key frame snapshot. More...

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

virtual std::string	Type ()
	returns the string type name of this object. More...

virtual void	Type (std::string strValue)
	Sets the class type for this object. More...

virtual void	VisualSelectionModeChanged (int iNewMode)
	Visual selection mode changed. More...

Protected Member Functions
virtual void	CloseThread ()

void	LoadNetworkXml (CStdXml &oXml)
	Loads the network configuration. More...

CsNeuronGroup *	LoadNeuronGroup (CStdXml &oXml)
	Loads a neuron. More...

CsSynapseGroup *	LoadSynapse (CStdXml &oXml)
	Loads a synapse. More...

virtual void	SetCARLSimulation ()

virtual void	StepThread ()
	This method is called from within the IO thread. It calls StepIO for each part. More...

virtual void	WaitForNeuralToCatchUp ()

virtual void	WaitForPhysicsToCatchUp ()

Protected Member Functions inherited from AnimatSim::Behavior::ThreadedModule
virtual void	ExitPause ()
	This method is waits until the m_bIOPaused flag is set back to false. More...

virtual void	ExitThread ()

virtual void	ProcessThread ()

virtual void	StartPause ()
	This method is waits until the m_bIOPaused flag is set to true. More...

virtual void	StartThread ()

virtual void	WaitForThreadNotifyReady ()

virtual void	WaitTillPaused ()
	This method is waits until the m_bIOPaused flag is set to true. More...

virtual void	WaitWhilePaused ()
	This method is waits until the m_bPauseIO flag is set back to false. 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
CStdPtrMap< std::string, CsConnectionGenerator >	m_aryGenerators

CStdPtrArray< CsNeuronGroup >	m_aryNeuronGroups
	The array of neuron groups in this module.

CStdPtrArray< CsSynapseGroup >	m_arySynapses
	The array of synapses in this module.

bool	m_bWaitingForNeuralToCatchUp
	True if the physics simulation has finished and is waiting on the neural sim to catch up.

bool	m_bWaitingForPhysicsToCatchUp
	True if the neural simulation has finished and is waiting on the physics sim to catch up.

float	m_fltNeuralTime
	The current time of the neural simulation.

int	m_iSimMode
	The mode of the simulation. GPU vs CPU.

CpuSNN *	m_lpSNN
	Pointer to the CARLsim simulator.

Protected Attributes inherited from AnimatSim::Behavior::ThreadedModule
bool	m_bPauseThread
	Set to true to pause the thread processing. Set back to false to resume it.

bool	m_bSetupComplete
	Set to true once the thread is setup correctly.

bool	m_bSetupStarted
	Set to true once the thread begins its setup.

bool	m_bStopThread
	Flags the thread processing loop to exit.

bool	m_bThreadPaused
	Is set to true once the thread loop is paused.

bool	m_bThreadProcessing
	True while the io thread processing loop is going on.

bool	m_bWaitingForThreadNotify
	Used to signal to the IO thread that we are waiting for their return signal.

float	m_fltStepThreadDuration
	The time it takes to perform a step of the IO for all parts in this control.

boost::thread	m_Thread
	Thread responsible for doing IO processing.

boost::interprocess::interprocess_condition	m_WaitForSetupCond
	Condition used to determine when the IO is setup.

boost::interprocess::interprocess_mutex	m_WaitForSetupMutex
	Mutex responsible for waiting until the IO is finished setting up.

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::ThreadedModule
static ThreadedModule *	CastToDerived (AnimatBase *lpBase)

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

Detailed Description

Firing rate neural module.

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

Author: dcofer

Date: 3/29/2011

Definition at line 35 of file CsNeuralModule.h.

Constructor & Destructor Documentation

AnimatCarlSim::CsNeuralModule::CsNeuralModule ( )

Default constructor.

Author: dcofer

Date: 3/29/2011

Definition at line 20 of file CsNeuralModule.cpp.

References m_bWaitingForNeuralToCatchUp, m_bWaitingForPhysicsToCatchUp, m_fltNeuralTime, AnimatSim::Behavior::NeuralModule::m_fltTimeStep, m_iSimMode, AnimatSim::Behavior::NeuralModule::m_lpClassFactory, and m_lpSNN.

AnimatCarlSim::CsNeuralModule::~CsNeuralModule ( )

virtual

Destructor.

Author: dcofer

Date: 3/29/2011

Definition at line 37 of file CsNeuralModule.cpp.

References m_aryNeuronGroups, m_arySynapses, and StdUtils::Std_TraceMsg().

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Member Function Documentation

bool AnimatCarlSim::CsNeuralModule::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 552 of file CsNeuralModule.cpp.

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

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void AnimatCarlSim::CsNeuralModule::AddNeuronGroup	(	std::string	strXml,
		bool	bDoNotInit = `false`
	)

virtual

Adds a neuron to the module.

Author: dcofer

Date: 3/29/2011

Parameters

strXml The xml to use when loading the neuron.

Definition at line 393 of file CsNeuralModule.cpp.

References AnimatCarlSim::CsNeuronGroup::Initialize(), and LoadNeuronGroup().

Referenced by AddItem().

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void AnimatCarlSim::CsNeuralModule::AddSynapse ( CsSynapseGroup * lpSynapse )

virtual

Adds a synapse to this module.

Author: dcofer

Date: 9/28/2014

Parameters

[in,out] lpSynapse Pointer to the synapse to add.

Definition at line 432 of file CsNeuralModule.cpp.

References m_arySynapses.

Referenced by AddItem(), and LoadSynapse().

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void AnimatCarlSim::CsNeuralModule::AddSynapse	(	std::string	strXml,
		bool	bDoNotInit
	)

virtual

Adds a synapse using an xml packet.

Author: dcofer

Date: 3/29/2011

Parameters

strXml The xml of the synapse to add.

Definition at line 447 of file CsNeuralModule.cpp.

References AnimatCarlSim::CsSynapseGroup::Initialize(), and LoadSynapse().

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void AnimatCarlSim::CsNeuralModule::ClearSynapses ( )

virtual

Clears the synapses list.

Author: dcofer

Date: 3/29/2011

Definition at line 549 of file CsNeuralModule.cpp.

References m_arySynapses.

CsConnectionGenerator * AnimatCarlSim::CsNeuralModule::FindConnectionGenerator	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

Searches for an item with the specified ID and sets its index in the array.

Author: dcofer

Date: 10/2/2014

Parameters

strID	ID of item to find.
bThrowError	true to throw error if not found.

Returns: If bThrowError is false and item is not found it returns NULL, otherwise if it is found then it returns pointer to the item.

Exceptions

If	bThrowError is true and no item with the specified ID is found then an exception is thrown.

Definition at line 92 of file CsNeuralModule.cpp.

References m_aryGenerators, and StdUtils::Std_CheckString().

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int AnimatCarlSim::CsNeuralModule::FindNeuronGroupListPos	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

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

Author: dcofer

Date: 3/29/2011

Parameters

strID	GUID ID of the neruon to find.
bThrowError	true to throw error if nothing found.

Returns: The found neuron list position.

Definition at line 134 of file CsNeuralModule.cpp.

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

Referenced by RemoveNeuronGroup().

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int AnimatCarlSim::CsNeuralModule::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

strID	GUID ID of the synapse to find.
bThrowError	true to throw error if no synapse is found.

Returns: The found synapse list position.

Definition at line 517 of file CsNeuralModule.cpp.

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

Referenced by RemoveSynapse().

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CsSynapseGroup * AnimatCarlSim::CsNeuralModule::GetSynapse ( int iIndex )

virtual

Gets a synapse by its index in the array.

Author: dcofer

Date: 3/29/2011

Parameters

iIndex Zero-based index of the synaspe to return.

Returns: null if it fails, else the synapse.

Definition at line 499 of file CsNeuralModule.cpp.

References m_arySynapses.

CStdPtrArray< CsSynapseGroup > * AnimatCarlSim::CsNeuralModule::GetSynapses ( )

virtual

Gets a pointer to the synapses array.

Author: dcofer

Date: 3/29/2011

Returns: Pointer to the synapses.

Definition at line 428 of file CsNeuralModule.cpp.

References m_arySynapses.

void AnimatCarlSim::CsNeuralModule::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 322 of file CsNeuralModule.cpp.

References m_aryNeuronGroups, m_arySynapses, and AnimatSim::AnimatBase::m_lpStructure.

void AnimatCarlSim::CsNeuralModule::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 115 of file CsNeuralModule.cpp.

References m_aryNeuronGroups.

void AnimatCarlSim::CsNeuralModule::LoadNetworkXml ( CStdXml & oXml )

protected

Loads the network configuration.

Author: dcofer

Date: 3/29/2011

Parameters

[in,out] oXml The xml to load.

Definition at line 627 of file CsNeuralModule.cpp.

References AnimatSim::Simulator::AddToObjectList(), AnimatSim::AnimatBase::ID(), LoadNeuronGroup(), LoadSynapse(), m_aryNeuronGroups, m_iSimMode, AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_strID, AnimatSim::AnimatBase::m_strName, AnimatSim::AnimatBase::m_strType, AnimatSim::AnimatBase::Name(), and AnimatSim::AnimatBase::Type().

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CsNeuronGroup * AnimatCarlSim::CsNeuralModule::LoadNeuronGroup ( CStdXml & oXml )

protected

Loads a neuron.

Author: dcofer

Date: 3/29/2011

Parameters

[in,out] oXml The xml to load for the neuron.

Returns: Pointer to the loaded neuron.

Definition at line 682 of file CsNeuralModule.cpp.

References AnimatSim::Simulator::CreateObject(), m_aryNeuronGroups, AnimatSim::AnimatBase::m_lpSim, and AnimatSim::AnimatBase::m_lpStructure.

Referenced by AddNeuronGroup(), and LoadNetworkXml().

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CsSynapseGroup * AnimatCarlSim::CsNeuralModule::LoadSynapse ( CStdXml & oXml )

protected

Loads a synapse.

Author: dcofer

Date: 3/29/2011

Parameters

[in,out] oXml The xml to load.

Returns: Pointer to the created synapse.

Definition at line 728 of file CsNeuralModule.cpp.

References AddSynapse(), AnimatSim::Simulator::CreateObject(), AnimatSim::AnimatBase::m_lpSim, and AnimatSim::AnimatBase::m_lpStructure.

Referenced by AddSynapse(), and LoadNetworkXml().

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std::string AnimatCarlSim::CsNeuralModule::ModuleName ( )

virtual

Gets the module name.

Author: dcofer

Date: 3/29/2011

Returns: .

Implements AnimatSim::Behavior::NeuralModule.

Definition at line 49 of file CsNeuralModule.cpp.

bool AnimatCarlSim::CsNeuralModule::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 575 of file CsNeuralModule.cpp.

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

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void AnimatCarlSim::CsNeuralModule::RemoveNeuronGroup	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

Removes the neuron with the specified ID.

Author: dcofer

Date: 3/29/2011

Parameters

strID	GUID ID for the neuron.
bThrowError	true to throw error if neuron found.

Definition at line 414 of file CsNeuralModule.cpp.

References FindNeuronGroupListPos(), and m_aryNeuronGroups.

Referenced by RemoveItem().

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void AnimatCarlSim::CsNeuralModule::RemoveSynapse ( int iIndex )

virtual

Removes the synapse described by iIndex.

Author: dcofer

Date: 3/29/2011

Parameters

iIndex Zero-based index of the synapse in the array.

Definition at line 467 of file CsNeuralModule.cpp.

References m_arySynapses.

Referenced by RemoveItem().

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void AnimatCarlSim::CsNeuralModule::RemoveSynapse	(	std::string	strID,
		bool	bThrowError = `true`
	)

virtual

Removes the synapse by the GUID ID.

Author: dcofer

Date: 3/29/2011

Parameters

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

Definition at line 483 of file CsNeuralModule.cpp.

References FindSynapseListPos(), and m_arySynapses.

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void AnimatCarlSim::CsNeuralModule::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 303 of file CsNeuralModule.cpp.

References m_aryNeuronGroups, m_arySynapses, m_fltNeuralTime, and AnimatSim::Behavior::ThreadedModule::ShutdownThread().

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bool AnimatCarlSim::CsNeuralModule::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 351 of file CsNeuralModule.cpp.

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

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void AnimatCarlSim::CsNeuralModule::SimStarting ( )

virtual

When the simulation is starting we need to configure our NN and start our processing thread.

When the simulation starts we need to re-run our configuration to setup the neural network in CARLsim and then start our processing loop.

Author: dcofer

Date: 10/1/2014

Reimplemented from AnimatSim::AnimatBase.

Definition at line 280 of file CsNeuralModule.cpp.

References m_arySynapses, and AnimatSim::Behavior::ThreadedModule::m_bThreadProcessing.

void AnimatCarlSim::CsNeuralModule::SimStopping ( )

virtual

Called just before the simulation stops.

This method is called on each AnimatBase object when the simulation stops. It allows it to perform any intialization prior to the stop of the simulation that is needed.

Author: dcofer

Date: 3/1/2011

Reimplemented from AnimatSim::AnimatBase.

Definition at line 296 of file CsNeuralModule.cpp.

References AnimatSim::Behavior::ThreadedModule::ShutdownThread().

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unsigned int AnimatCarlSim::CsNeuralModule::SimulationStepInterval ( )

virtual

Tells the number of simulation steps that other components, like stimuli, will need to use for their step interval.

Author: dcofer

Date: 10/11/2014

Returns: Step interval for the UpdateSteps of this module.

Definition at line 69 of file CsNeuralModule.cpp.

References AnimatSim::AnimatBase::m_lpSim.

void AnimatCarlSim::CsNeuralModule::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.