Neural module. More...

#include <NeuralModule.h>

Inheritance diagram for AnimatSim::Behavior::NeuralModule:

Collaboration diagram for AnimatSim::Behavior::NeuralModule:

Public Member Functions
	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 void	Initialize ()
	Initializes this object. More...

virtual std::string	ModuleName ()=0
	Gets the module name. 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	ResetSimulation ()
	Resets the simulation back to time 0. 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 void	StepSimulation ()
	Step the simulation for this object. 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 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	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	Kill (bool bState=true)
	Kills. 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	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 bool	RemoveItem (const std::string &strItemType, const std::string &strID, bool bThrowError=true)
	Removes a child item from this parent. 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 std::string &strValue, bool bThrowError=true)
	Set a variable based on a string data type name. More...

virtual bool	SetData (const std::string &strDataType, const float fltValue, bool bThrowError=true)
	Set a variable based on a string data type name. More...

virtual bool	SetData (const std::string &strDataType, const long lValue, bool bThrowError=true)
	Set a variable based on a string data type name. More...

virtual void	SetSystemPointers (Simulator lpSim, Structure lpStructure, NeuralModule lpModule, Node lpNode, bool bVerify)
	Sets the system pointers. More...

virtual void	SimPausing ()
	Called just before the simulation pauses. More...

virtual void	SimStarting ()
	Called just before the simulation starts. More...

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

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

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

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

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

Static Public Member Functions
static NeuralModule *	CastToDerived (AnimatBase *lpBase)

Protected Member Functions
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< 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..

Detailed Description

Neural module.

An organism is a structure with a nervous system (NervousSystem). The nervous system contains one or more neural modules. A neural module performs the processing for a given neural model library (firing rate, integrate and fire, etc.). Each neural module can operate with an independent time step. Elements in one module can interact with elements in an another by using adapters to connect them. The module has a list of target adapters. At each time step of the module it calls StepSimulation to add an external value to the target node in another module.

Author: dcofer

Date: 2/24/2011

Definition at line 29 of file NeuralModule.h.

Constructor & Destructor Documentation

AnimatSim::Behavior::NeuralModule::NeuralModule ( )

Default constructor.

Author: dcofer

Date: 2/24/2011

Definition at line 64 of file NeuralModule.cpp.

References m_fltTimeStep, m_iTargetAdapterCount, m_iTimeStepCount, m_iTimeStepInterval, m_lpClassFactory, m_lpOrganism, and AnimatSim::AnimatBase::m_lpSim.

AnimatSim::Behavior::NeuralModule::~NeuralModule ( )

virtual

Destructor.

This deletes the class factory when destroyed.

Author: dcofer

Date: 2/24/2011

Definition at line 85 of file NeuralModule.cpp.

References m_arySourceAdapters, m_aryTargetAdapters, m_lpClassFactory, and StdUtils::Std_TraceMsg().

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Member Function Documentation

void AnimatSim::Behavior::NeuralModule::AddExternalSynapse	(	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 326 of file NeuralModule.cpp.

References StdUtils::CStdXml::Deserialize(), StdUtils::CStdXml::FindChildElement(), StdUtils::CStdXml::FindElement(), AnimatSim::AnimatBase::Initialize(), and LoadExternalSynapse().

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virtual void AnimatSim::Behavior::NeuralModule::AttachSourceAdapter ( Adapter * lpAdapter )

virtual

Attaches a source adapter.

This adds the specified adapter to this module. It can then process the adapters during a step of the simulation.

Author: dcofer

Date: 3/18/2011

Parameters

[in,out] lpAdapter Pointer to an adapter.

virtual void AnimatSim::Behavior::NeuralModule::AttachTargetAdapter ( Adapter * lpAdapter )

virtual

Attaches a target adapter.

This adds the specified adapter to this module. It can then process the adapters during a step of the simulation.

Author: dcofer

Date: 3/18/2011

Parameters

[in,out] lpAdapter Pointer to an adapter.

IStdClassFactory * AnimatSim::Behavior::NeuralModule::ClassFactory ( )

virtual

Gets the class factory.

Author: dcofer

Date: 2/24/2011

Returns: null if it fails, else.

Definition at line 110 of file NeuralModule.cpp.

References m_lpClassFactory.

int AnimatSim::Behavior::NeuralModule::FindExternalSynapseListPos	(	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 364 of file NeuralModule.cpp.

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

Referenced by RemoveExternalSynapse().

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float * AnimatSim::Behavior::NeuralModule::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

strDataType name 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

If	DataType is not found.

Reimplemented from AnimatSim::AnimatBase.

Reimplemented in AnimatSim::Behavior::ThreadedModule.

Definition at line 476 of file NeuralModule.cpp.

References AnimatSim::AnimatBase::GetDataPointer(), m_fltTimeStep, and StdUtils::Std_CheckString().

Referenced by AnimatSim::Behavior::ThreadedModule::GetDataPointer().

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Organism * AnimatSim::Behavior::NeuralModule::GetOrganism ( )

Gets the organism.

Author: dcofer

Date: 2/24/2011

Returns: returns the organism.

Definition at line 144 of file NeuralModule.cpp.

References m_lpOrganism.

Simulator * AnimatSim::Behavior::NeuralModule::GetSimulator ( )

virtual

Gets the simulator.

Author: dcofer

Date: 2/24/2011

Returns: returns the simulator.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 132 of file NeuralModule.cpp.

References AnimatSim::AnimatBase::m_lpSim.

Referenced by IntegrateFireSim::IntegrateFireNeuralModule::LoadInternal(), and IntegrateFireSim::IntegrateFireNeuralModule::RemoveSynapseType().

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void AnimatSim::Behavior::NeuralModule::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.

Reimplemented in IntegrateFireSim::IntegrateFireNeuralModule, AnimatCarlSim::CsNeuralModule, FiringRateSim::FiringRateModule, and AnimatSim::Behavior::PhysicsNeuralModule.

Definition at line 226 of file NeuralModule.cpp.

References m_aryExternalSynapses, m_fltTimeStep, and TimeStep().

Referenced by AnimatSim::Behavior::NervousSystem::AddNeuralModule(), AnimatSim::Behavior::PhysicsNeuralModule::Initialize(), and AnimatSim::Behavior::NervousSystem::Initialize().

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AnimatSim::Link * AnimatSim::Behavior::NeuralModule::LoadExternalSynapse ( CStdXml & oXml )

protectedvirtual

Loads an external synapse.

Author: dcofer

Date: 3/29/2011

Parameters

[in,out] oXml The xml to load.

Returns: Pointer to the created synapse.

Definition at line 419 of file NeuralModule.cpp.

References AnimatSim::Simulator::CreateObject(), StdUtils::CStdXml::GetChildString(), StdUtils::CStdXml::IntoElem(), AnimatSim::AnimatBase::Load(), AnimatSim::AnimatBase::m_lpSim, AnimatSim::AnimatBase::m_lpStructure, StdUtils::CStdXml::OutOfElem(), and AnimatSim::Link::SetSystemPointers().

Referenced by AddExternalSynapse(), and LoadExternalSynapses().

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void AnimatSim::Behavior::NeuralModule::LoadExternalSynapses ( CStdXml & oXml )

protectedvirtual

Loads external synapses.

Author: dcofer

Date: 10/15/2014

Parameters

[in,out] oXml The xml to load.

Returns: Pointer to the created synapse.

Definition at line 389 of file NeuralModule.cpp.

References StdUtils::CStdXml::FindChildByIndex(), StdUtils::CStdXml::FindChildElement(), StdUtils::CStdXml::IntoChildElement(), LoadExternalSynapse(), StdUtils::CStdXml::NumberOfChildren(), and StdUtils::CStdXml::OutOfElem().

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

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virtual std::string AnimatSim::Behavior::NeuralModule::ModuleName ( )

pure virtual

Gets the module name.

Author: dcofer

Date: 3/18/2011

Returns: Module name.

Implemented in IntegrateFireSim::IntegrateFireNeuralModule, AnimatCarlSim::CsNeuralModule, FiringRateSim::FiringRateModule, and AnimatSim::Behavior::PhysicsNeuralModule.

Referenced by AnimatSim::Behavior::NervousSystem::AddNeuralModule().

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bool AnimatSim::Behavior::NeuralModule::NeedToStep ( bool bIncrement )

virtual

Tells whether this NeuralModule needs to call StepSimulation.

This is determined by the m_iTimeStepInterval. We only step on some whole number interval of the physics time step.

Author: dcofer

Date: 3/18/2011

Returns: true if it succeeds, false if it fails.

Definition at line 250 of file NeuralModule.cpp.

References m_iTimeStepCount, and m_iTimeStepInterval.

void AnimatSim::Behavior::NeuralModule::RemoveExternalSynapse	(	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 347 of file NeuralModule.cpp.

References FindExternalSynapseListPos(), and m_aryExternalSynapses.

Referenced by IntegrateFireSim::IntegrateFireNeuralModule::RemoveItem().

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virtual void AnimatSim::Behavior::NeuralModule::RemoveSourceAdapter ( Adapter * lpAdapter )

virtual

Removes a source adapter.

This removes the specified adapter from this module.

Author: dcofer

Date: 3/18/2011

Parameters

[in,out] lpAdapter Pointer to an adapter.

virtual void AnimatSim::Behavior::NeuralModule::RemoveTargetAdapter ( Adapter * lpAdapter )

virtual

Removes a target adapter.

This removes the specified adapter from this module.

Author: dcofer

Date: 3/18/2011

Parameters

[in,out] lpAdapter Pointer to an adapter.

void AnimatSim::Behavior::NeuralModule::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::AnimatBase.

Reimplemented in IntegrateFireSim::IntegrateFireNeuralModule, AnimatCarlSim::CsNeuralModule, FiringRateSim::FiringRateModule, and AnimatSim::Behavior::PhysicsNeuralModule.

Definition at line 486 of file NeuralModule.cpp.

References m_aryExternalSynapses.

Referenced by AnimatSim::Behavior::NervousSystem::ResetSimulation().

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virtual void AnimatSim::Behavior::NeuralModule::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]	lpSim	The pointer to a simulation.
[in,out]	lpStructure	The pointer to the parent structure.
[in,out]	lpModule	The pointer to the parent module module.
[in,out]	lpNode	The pointer to the parent node.
	bVerify	true to call VerifySystemPointers.

Referenced by AnimatSim::Behavior::NervousSystem::LoadNeuralModule().

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void AnimatSim::Behavior::NeuralModule::StepAdapters ( )

virtual

Step adapters.

Author: dcofer

Date: 2/25/2012

Definition at line 500 of file NeuralModule.cpp.

References AnimatSim::AnimatBase::Enabled(), m_aryTargetAdapters, and m_iTargetAdapterCount.

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void AnimatSim::Behavior::NeuralModule::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 IntegrateFireSim::IntegrateFireNeuralModule, AnimatCarlSim::CsNeuralModule, and FiringRateSim::FiringRateModule.

Definition at line 493 of file NeuralModule.cpp.

References m_aryExternalSynapses.

float AnimatSim::Behavior::NeuralModule::TimeStep ( )

virtual

Gets the time step for this moudle in time units.

Author: dcofer

Date: 3/18/2011

Returns: Time units for this modules time step.

Reimplemented in IntegrateFireSim::IntegrateFireNeuralModule, and AnimatSim::Behavior::PhysicsNeuralModule.

Definition at line 190 of file NeuralModule.cpp.

References m_fltTimeStep.

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void AnimatSim::Behavior::NeuralModule::TimeStep ( float fltVal )

virtual

Sets the Time step for this moudle in time units.

This method calculates the required m_iTimeStepInterval.

Author: dcofer

Date: 3/18/2011

Parameters

fltVal The flt value.

Reimplemented in IntegrateFireSim::IntegrateFireNeuralModule, and AnimatSim::Behavior::PhysicsNeuralModule.

Definition at line 203 of file NeuralModule.cpp.

References m_fltTimeStep, m_iTimeStepInterval, AnimatSim::AnimatBase::m_lpSim, StdUtils::Std_IsAboveMin(), AnimatSim::Simulator::TimeStep(), and TimeStepInterval().

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short AnimatSim::Behavior::NeuralModule::TimeStepInterval ( )

virtual

Gets the time step interval.

The m_iTimeStepInterval is the number of time slices between that this module must wait before stepping again.

Author: dcofer

Date: 2/24/2011

Returns: .

Definition at line 159 of file NeuralModule.cpp.

References m_iTimeStepInterval.

Referenced by TimeStep().

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void AnimatSim::Behavior::NeuralModule::TimeStepInterval ( short iVal )

virtual

Sets ime step interval.

Author: dcofer

Date: 2/24/2011

Parameters

iVal	New time step interval.

Exceptions

new	value must be greater than zero.

Definition at line 174 of file NeuralModule.cpp.

References m_iTimeStepInterval, and StdUtils::Std_IsAboveMin().

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void AnimatSim::Behavior::NeuralModule::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.