Contains all of CARLsim's core functionality. More...

#include <snn.h>

Public Member Functions
	SNN (const std::string &name, SimMode preferredSimMode, LoggerMode loggerMode, int randSeed)
	SNN Constructor. More...

	~SNN ()
	SNN Destructor. More...

void	biasWeights (short int connId, float bias, bool updateWeightRange=false)

short int	connect (int gIDpre, int gIDpost, ConnectionGeneratorCore *conn, float mulSynFast, float mulSynSlow, bool synWtType)

short int	connect (int gIDpre, int gIDpost, const std::string &_type, float initWt, float maxWt, float prob, uint8_t minDelay, uint8_t maxDelay, RadiusRF radius, float mulSynFast, float mulSynSlow, bool synWtType)
	make from each neuron in grpId1 to 'numPostSynapses' neurons in grpId2 More...

short int	connectCompartments (int grpIdLower, int grpIdUpper)

int	createGroup (const std::string &grpName, const Grid3D &grid, int neurType, int preferredPartition, ComputingBackend preferredBackend)
	Creates a group of Izhikevich spiking neurons. More...

int	createGroupLIF (const std::string &grpName, const Grid3D &grid, int neurType, int preferredPartition, ComputingBackend preferredBackend)
	Creates a group of LIF spiking neurons. More...

int	createSpikeGeneratorGroup (const std::string &grpName, const Grid3D &grid, int neurType, int preferredPartition, ComputingBackend preferredBackend)
	Creates a spike generator group (dummy-neurons, not Izhikevich spiking neurons) More...

void	exitSimulation (int val=1)
	deallocates all dynamical structures and exits More...

std::vector< float >	getConductanceAMPA (int grpId)

std::vector< float >	getConductanceGABAa (int grpId)

std::vector< float >	getConductanceGABAb (int grpId)

std::vector< float >	getConductanceNMDA (int grpId)

ConnectConfig	getConnectConfig (short int connectId)
	required for homeostasis More...

short int	getConnectId (int grpIdPre, int grpIdPost)
	find connection ID based on pre-post group pair, O(N) More...

float *	getCurrent ()
	temporary getter to return pointer to current[] More...

RangeDelay	getDelayRange (short int connId)
	returns the RangeDelay struct of a connection More...

uint8_t *	getDelays (int gGrpIdPre, int gGrpIdPost, int &numPreN, int &numPostN)
	Returns the delay information for all synaptic connections between a pre-synaptic and a post-synaptic neuron group. More...

int	getGroupEndNeuronId (int gGrpId)

Grid3D	getGroupGrid3D (int grpId)

int	getGroupId (std::string grpName)

std::string	getGroupName (int grpId)

GroupNeuromodulatorInfo	getGroupNeuromodulatorInfo (int grpId)

int	getGroupNumNeurons (int gGrpId)

int	getGroupStartNeuronId (int gGrpId)

GroupSTDPInfo	getGroupSTDPInfo (int grpId)

const FILE *	getLogFpDeb ()
	returns file pointer to debug log More...

const FILE *	getLogFpErr ()
	returns file pointer to error log More...

const FILE *	getLogFpInf ()
	function writes population weights from gIDpre to gIDpost to file fname in binary. More...

const FILE *	getLogFpLog ()
	returns file pointer to log file More...

LoggerMode	getLoggerMode ()

std::string	getNetworkName ()

Point3D	getNeuronLocation3D (int grpId, int relNeurId)

Point3D	getNeuronLocation3D (int neurId)

NeuronMonitor *	getNeuronMonitor (int grpId)
	Returns pointer to existing NeuronMonitor object, NULL else. More...

NeuronMonitorCore *	getNeuronMonitorCore (int grpId)

int	getNumCompartmentConnections ()

int	getNumConnections ()

int	getNumGroups ()

int	getNumNeurons ()

int	getNumNeuronsGen ()

int	getNumNeuronsGenExc ()

int	getNumNeuronsGenInh ()

int	getNumNeuronsReg ()

int	getNumNeuronsRegExc ()

int	getNumNeuronsRegInh ()

int	getNumSynapses ()

int	getNumSynapticConnections (short int connectionId)
	gets number of connections associated with a connection ID More...

int	getRandSeed ()

double	getRFDist3D (const RadiusRF &radius, const Point3D &pre, const Point3D &post)
	checks whether a point pre lies in the receptive field for point post More...

int	getSimTime ()

int	getSimTimeMs ()

int	getSimTimeSec ()

SpikeMonitor *	getSpikeMonitor (int grpId)
	Returns pointer to existing SpikeMonitor object, NULL else. More...

SpikeMonitorCore *	getSpikeMonitorCore (int grpId)

float *	getSTPu ()
	temporary getter to return pointer to stpu[] More...

float *	getSTPx ()
	temporary getter to return pointer to stpx[] More...

std::vector< std::vector< float > >	getWeightMatrix2D (short int connId)

RangeWeight	getWeightRange (short int connId)
	returns RangeWeight struct of a connection More...

bool	isConnectionPlastic (short int connId)
	returns whether synapses in connection are fixed (false) or plastic (true) More...

bool	isDopaminergicGroup (int gGrpId)

bool	isExcitatoryGroup (int gGrpId)

bool	isGroupWithHomeostasis (int grpId)
	returns whether group has homeostasis enabled (true) or not (false) More...

bool	isInhibitoryGroup (int gGrpId)

bool	isPoint3DinRF (const RadiusRF &radius, const Point3D &pre, const Point3D &post)

bool	isPoissonGroup (int gGrpId)

bool	isSimulationWithCOBA ()

bool	isSimulationWithCompartments ()

bool	isSimulationWithCUBA ()

bool	isSimulationWithFixedWeightsOnly ()

bool	isSimulationWithGABAbRise ()

bool	isSimulationWithHomeostasis ()

bool	isSimulationWithNMDARise ()

bool	isSimulationWithPlasticWeights ()

bool	isSimulationWithSTDP ()

bool	isSimulationWithSTP ()

void	loadSimulation (FILE *fid)

int	runNetwork (int _nsec, int _nmsec, bool printRunSummary)
	run the simulation for n sec More...

void	saveSimulation (FILE *fid, bool saveSynapseInfo=false)
	stores the pre and post synaptic neuron ids with the weight and delay More...

void	scaleWeights (short int connId, float scale, bool updateWeightRange=false)

void	setCompartmentParameters (int grpId, float couplingUp, float couplingDown)
	Coupling constants for the compartment are set using this method. More...

void	setConductances (bool isSet, int tdAMPA, int trNMDA, int tdNMDA, int tdGABAa, int trGABAb, int tdGABAb)
	Sets custom values for conductance decay (\tau_decay) or disables conductances alltogether These will be applied to all connections in a network For details on the ODE that is implemented refer to (Izhikevich et al, 2004), and for suitable values see (Dayan & Abbott, 2001). More...

ConnectionMonitor *	setConnectionMonitor (int grpIdPre, int grpIdPost, FILE *fid)
	sets up a network monitor registered with a callback to process the spikes. More...

void	setESTDP (int grpId, bool isSet, STDPType type, STDPCurve curve, float alphaPlus, float tauPlus, float alphaMinus, float tauMinus, float gamma)
	Set the spike-timing-dependent plasticity (STDP) for a neuron group. More...

void	setExternalCurrent (int grpId, const std::vector< float > &current)
	injects current (mA) into the soma of every neuron in the group More...

GroupMonitor *	setGroupMonitor (int grpId, FILE *fid)
	sets up a group monitor registered with a callback to process the spikes. More...

void	setHomeoBaseFiringRate (int groupId, float baseFiring, float baseFiringSD)
	Sets homeostatic target firing rate (enforced through homeostatic synaptic scaling) More...

void	setHomeostasis (int grpId, bool isSet, float homeoScale, float avgTimeScale)
	Sets the homeostasis parameters. g is the grpID, enable=true(false) enables(disables) homeostasis, homeostasisScale is strength of homeostasis compared to the strength of normal LTP/LTD from STDP (which is 1), and avgTimeScale is the time frame over which the average firing rate is averaged (it should be larger in scale than STDP timescales). More...

void	setIntegrationMethod (integrationMethod_t method, int numStepsPerMs)
	Sets the integration method and the number of integration steps per 1ms simulation time step. More...

void	setISTDP (int grpId, bool isSet, STDPType type, STDPCurve curve, float ab1, float ab2, float tau1, float tau2)
	Set the inhibitory spike-timing-dependent plasticity (STDP) with anti-hebbian curve for a neuron group. More...

void	setLogsFp (FILE fpInf=NULL, FILE fpErr=NULL, FILE fpDeb=NULL, FILE fpLog=NULL)
	Sets the file pointers for all log files file pointer NULL means don't change it. More...

void	setNeuromodulator (int grpId, float baseDP, float tauDP, float base5HT, float tau5HT, float baseACh, float tauACh, float baseNE, float tauNE)
	Sets baseline concentration and decay time constant of neuromodulators (DP, 5HT, ACh, NE) for a neuron group. More...

NeuronMonitor *	setNeuronMonitor (int gid, FILE *fid)
	sets up a neuron monitor registered with a callback to process the neuron state values, there can only be one NeuronMonitor per group More...

void	setNeuronParameters (int grpId, float izh_a, float izh_a_sd, float izh_b, float izh_b_sd, float izh_c, float izh_c_sd, float izh_d, float izh_d_sd)
	Sets the Izhikevich parameters a, b, c, and d of a neuron group. More...

void	setNeuronParameters (int grpId, float izh_C, float izh_C_sd, float izh_k, float izh_k_sd, float izh_vr, float izh_vr_sd, float izh_vt, float izh_vt_sd, float izh_a, float izh_a_sd, float izh_b, float izh_b_sd, float izh_vpeak, float izh_vpeak_sd, float izh_c, float izh_c_sd, float izh_d, float izh_d_sd)
	Sets the Izhikevich parameters C, k, vr, vt, a, b, vpeak, c, and d of a neuron group. More...

void	setNeuronParametersLIF (int grpId, int tau_m, int tau_ref, float vTh, float vReset, double minRmem, double maxRmem)
	Sets neuron parameters for a group of LIF spiking neurons. More...

void	setSpikeGenerator (int grpId, SpikeGeneratorCore *spikeGenFunc)
	sets up a spike generator More...

SpikeMonitor *	setSpikeMonitor (int gid, FILE *fid)
	sets up a spike monitor registered with a callback to process the spikes, there can only be one SpikeMonitor per group More...

void	setSpikeRate (int grpId, PoissonRate *spikeRate, int refPeriod)
	Sets the Poisson spike rate for a group. For information on how to set up spikeRate, see Section Poisson spike generators in the Tutorial. More...

void	setSTP (int grpId, bool isSet, float STP_U, float STP_tau_u, float STP_tau_x)
	Sets STP params U, tau_u, and tau_x of a neuron group (pre-synaptically) CARLsim implements the short-term plasticity model of (Tsodyks & Markram, 1998; Mongillo, Barak, & Tsodyks, 2008) du/dt = -u/STP_tau_u + STP_U * (1-u-) * \delta(t-t_spk) dx/dt = (1-x)/STP_tau_x - u+ * x- * \delta(t-t_spk) dI/dt = -I/tau_S + A * u+ * x- * \delta(t-t_spk) where u- means value of variable u right before spike update, and x+ means value of variable x right after the spike update, and A is the synaptic weight. The STD effect is modeled by a normalized variable (0<=x<=1), denoting the fraction of resources that remain available after neurotransmitter depletion. The STF effect is modeled by a utilization parameter u, representing the fraction of available resources ready for use (release probability). Following a spike, (i) u increases due to spike-induced calcium influx to the presynaptic terminal, after which (ii) a fraction u of available resources is consumed to produce the post-synaptic current. Between spikes, u decays back to zero with time constant STP_tau_u (\tau_F), and x recovers to value one with time constant STP_tau_x (\tau_D). More...

void	setupNetwork ()
	build the network More...

void	setWeight (short int connId, int neurIdPre, int neurIdPost, float weight, bool updateWeightRange=false)
	sets the weight value of a specific synapse More...

void	setWeightAndWeightChangeUpdate (UpdateInterval wtANDwtChangeUpdateInterval, bool enableWtChangeDecay, float wtChangeDecay)
	Sets the weight and weight change update parameters. More...

void	startTesting (bool shallUpdateWeights=true)
	enters a testing phase, where all weight updates are disabled More...

void	stopTesting ()
	exits a testing phase, making weight updates possible again More...

void	updateConnectionMonitor (short int connId=ALL)
	polls connection weights More...

void	updateGroupMonitor (int grpId=ALL)
	access group status (currently the concentration of neuromodulator) More...

void	updateNeuronMonitor (int grpId=ALL)
	copy required neuron state values from ??? buffer to ??? buffer More...

void	updateSpikeMonitor (int grpId=ALL)
	copy required spikes from firing buffer to spike buffer More...

Static Public Attributes
static const unsigned int	MAJOR_VERSION = 4
	major release version, as in CARLsim X More...

static const unsigned int	MINOR_VERSION = 0
	minor release version, as in CARLsim 2.X More...

Detailed Description

**************************************************************************************************************** /// CPUSNN CORE CLASS **************************************************************************************************************** ///

This is a more elaborate description of our main class.

Definition at line 115 of file snn.h.

Constructor & Destructor Documentation

◆ SNN()

SNN	(	const std::string &	name,
		SimMode	preferredSimMode,
		LoggerMode	loggerMode,
		int	randSeed
	)

**************************************************************************************************************** /// PUBLIC METHODS **************************************************************************************************************** ///

Parameters

name	the symbolic name of a spiking neural network
loggerMode	log mode
randSeed	randomize seed of the random number generator

**************************************************************************************************************** /// CONSTRUCTOR / DESTRUCTOR **************************************************************************************************************** ///

Definition at line 77 of file snn_manager.cpp.

◆ ~SNN()

~SNN ( )

clean up all allocated resource

Definition at line 86 of file snn_manager.cpp.

Member Function Documentation

◆ biasWeights()

void biasWeights	(	short int	connId,
		float	bias,
		bool	updateWeightRange = `false`
	)

************************************************************************************************************ /// PUBLIC METHODS: INTERACTING WITH A SIMULATION ************************************************************************************************************ ///

Definition at line 916 of file snn_manager.cpp.

◆ connect() [1/2]

short int connect	(	int	gIDpre,
		int	gIDpost,
		ConnectionGeneratorCore *	conn,
		float	mulSynFast,
		float	mulSynSlow,
		bool	synWtType
	)

Definition at line 178 of file snn_manager.cpp.

◆ connect() [2/2]

short int connect	(	int	grpId1,
		int	grpId2,
		const std::string &	_type,
		float	initWt,
		float	maxWt,
		float	prob,
		uint8_t	minDelay,
		uint8_t	maxDelay,
		RadiusRF	radius,
		float	_mulSynFast,
		float	_mulSynSlow,
		bool	synWtType
	)

Creates synaptic projections from a pre-synaptic group to a post-synaptic group using a pre-defined primitive type.

Parameters

grpIdPre	ID of the pre-synaptic group
grpIdPost	ID of the post-synaptic group
connType	connection type. "random": random connectivity. "one-to-one": connect the i-th neuron in pre to the i-th neuron in post. "full": connect all neurons in pre to all neurons in post (no self-connections).
initWt	initial weight strength (arbitrary units); should be negative for inhibitory connections
maxWt	upper bound on weight strength (arbitrary units); should be negative for inhibitory connections
connProb	connection probability
minDelay	the minimum delay allowed (ms)
maxdelay	the maximum delay allowed (ms)
synWtType	(optional) connection type, either SYN_FIXED or SYN_PLASTIC, default = SYN_FIXED.
wtType	(optional) DEPRECATED

Returns: number of created synaptic projections

************************************************************************************************************ /// PUBLIC METHODS: SETTING UP A SIMULATION ************************************************************************************************************ ///

Definition at line 96 of file snn_manager.cpp.

◆ connectCompartments()

short int connectCompartments	(	int	grpIdLower,
		int	grpIdUpper
	)

Definition at line 217 of file snn_manager.cpp.

◆ createGroup()

int createGroup	(	const std::string &	grpName,
		const Grid3D &	grid,
		int	neurType,
		int	preferredPartition,
		ComputingBackend	preferredBackend
	)

Parameters

name	the symbolic name of a group
grid	Grid3D struct to create neurons on a 3D grid (x,y,z)
nType	the type of neuron

Definition at line 252 of file snn_manager.cpp.

◆ createGroupLIF()

int createGroupLIF	(	const std::string &	grpName,
		const Grid3D &	grid,
		int	neurType,
		int	preferredPartition,
		ComputingBackend	preferredBackend
	)

Parameters

grpName	the symbolic name of a group
grid	Grid3D struct to create neurons on a 3D grid (x,y,z)
neurType	the type of neuron
preferredPartition	defines the desired runtime partition for the group
preferredBackend	defines whether the group will be placed on CPU or GPU

Definition at line 302 of file snn_manager.cpp.

◆ createSpikeGeneratorGroup()

int createSpikeGeneratorGroup	(	const std::string &	grpName,
		const Grid3D &	grid,
		int	neurType,
		int	preferredPartition,
		ComputingBackend	preferredBackend
	)

Parameters

name	the symbolic name of a group
grid	Grid3D struct to create neurons on a 3D grid (x,y,z)
nType	the type of neuron, currently only support EXCITATORY NEURON

TODO:: :IS THIS NECESSARY?

Definition at line 349 of file snn_manager.cpp.

◆ exitSimulation()

void exitSimulation ( int val = 1 )

Definition at line 995 of file snn_manager.cpp.

◆ getConductanceAMPA()

std::vector< float > getConductanceAMPA ( int grpId )

Definition at line 1728 of file snn_manager.cpp.

◆ getConductanceGABAa()

std::vector< float > getConductanceGABAa ( int grpId )

Definition at line 1761 of file snn_manager.cpp.

◆ getConductanceGABAb()

std::vector< float > getConductanceGABAb ( int grpId )

Definition at line 1774 of file snn_manager.cpp.

◆ getConductanceNMDA()

std::vector< float > getConductanceNMDA ( int grpId )

Definition at line 1741 of file snn_manager.cpp.

◆ getConnectConfig()

ConnectConfig getConnectConfig ( short int connectId )

Definition at line 1717 of file snn_manager.cpp.

◆ getConnectId()

short int getConnectId	(	int	grpIdPre,
		int	grpIdPost
	)

**************************************************************************************************************** /// GETTERS / SETTERS **************************************************************************************************************** ///

Definition at line 1704 of file snn_manager.cpp.

◆ getCurrent()

float* getCurrent ( )

inline

TODO:: replace with NeuronMonitor

Definition at line 600 of file snn.h.

◆ getDelayRange()

RangeDelay getDelayRange ( short int connId )

Definition at line 1795 of file snn_manager.cpp.

◆ getDelays()

uint8_t * getDelays	(	int	gGrpIdPre,
		int	gGrpIdPost,
		int &	numPreN,
		int &	numPostN
	)

Parameters

gGrpIdPre	ID of pre-synaptic group
gGrpIdPost	ID of post-synaptic group
numPreN	return the number of pre-synaptic neurons
numPostN	retrun the number of post-synaptic neurons
delays	(optional) return the delay information for all synapses, default = NULL

Returns: delays information for all synapses

Definition at line 1802 of file snn_manager.cpp.

◆ getGroupEndNeuronId()

int getGroupEndNeuronId ( int gGrpId )

inline

Definition at line 558 of file snn.h.

◆ getGroupGrid3D()

Grid3D getGroupGrid3D ( int grpId )

Definition at line 1846 of file snn_manager.cpp.

◆ getGroupId()

int getGroupId ( std::string grpName )

Definition at line 1853 of file snn_manager.cpp.

◆ getGroupName()

std::string getGroupName ( int grpId )

Definition at line 1865 of file snn_manager.cpp.

◆ getGroupNeuromodulatorInfo()

GroupNeuromodulatorInfo getGroupNeuromodulatorInfo ( int grpId )

Definition at line 1901 of file snn_manager.cpp.

◆ getGroupNumNeurons()

int getGroupNumNeurons ( int gGrpId )

inline

Definition at line 559 of file snn.h.

◆ getGroupStartNeuronId()

int getGroupStartNeuronId ( int gGrpId )

inline

Definition at line 557 of file snn.h.

◆ getGroupSTDPInfo()

GroupSTDPInfo getGroupSTDPInfo ( int grpId )

Definition at line 1874 of file snn_manager.cpp.

◆ getLogFpDeb()

const FILE* getLogFpDeb ( )

inline

Definition at line 518 of file snn.h.

◆ getLogFpErr()

const FILE* getLogFpErr ( )

inline

Definition at line 516 of file snn.h.

◆ getLogFpInf()

const FILE* getLogFpInf ( )

inline

returns file pointer to info log

Definition at line 514 of file snn.h.

◆ getLogFpLog()

const FILE* getLogFpLog ( )

inline

Definition at line 520 of file snn.h.

◆ getLoggerMode()

LoggerMode getLoggerMode ( )

inline

Definition at line 554 of file snn.h.

◆ getNetworkName()

std::string getNetworkName ( )

inline

Definition at line 561 of file snn.h.

◆ getNeuronLocation3D() [1/2]

Point3D getNeuronLocation3D	(	int	grpId,
		int	relNeurId
	)

Definition at line 1932 of file snn_manager.cpp.

◆ getNeuronLocation3D() [2/2]

Point3D getNeuronLocation3D ( int neurId )

Definition at line 1916 of file snn_manager.cpp.

◆ getNeuronMonitor()

NeuronMonitor * getNeuronMonitor ( int grpId )

Definition at line 1981 of file snn_manager.cpp.

◆ getNeuronMonitorCore()

NeuronMonitorCore * getNeuronMonitorCore ( int grpId )

Returns pointer to existing NeuronMonitorCore object, NULL else. Should not be exposed to user interface

Definition at line 1992 of file snn_manager.cpp.

◆ getNumCompartmentConnections()

int getNumCompartmentConnections ( )

inline

Definition at line 568 of file snn.h.

◆ getNumConnections()

int getNumConnections ( )

inline

Definition at line 566 of file snn.h.

◆ getNumGroups()

int getNumGroups ( )

inline

Definition at line 569 of file snn.h.

◆ getNumNeurons()

int getNumNeurons ( )

inline

Definition at line 570 of file snn.h.

◆ getNumNeuronsGen()

int getNumNeuronsGen ( )

inline

Definition at line 574 of file snn.h.

◆ getNumNeuronsGenExc()

int getNumNeuronsGenExc ( )

inline

Definition at line 575 of file snn.h.

◆ getNumNeuronsGenInh()

int getNumNeuronsGenInh ( )

inline

Definition at line 576 of file snn.h.

◆ getNumNeuronsReg()

int getNumNeuronsReg ( )

inline

Definition at line 571 of file snn.h.

◆ getNumNeuronsRegExc()

int getNumNeuronsRegExc ( )

inline

Definition at line 572 of file snn.h.

◆ getNumNeuronsRegInh()

int getNumNeuronsRegInh ( )

inline

Definition at line 573 of file snn.h.

◆ getNumSynapses()

int getNumSynapses ( )

inline

Definition at line 577 of file snn.h.

◆ getNumSynapticConnections()

int getNumSynapticConnections ( short int connectionId )

Definition at line 1949 of file snn_manager.cpp.

◆ getRandSeed()

int getRandSeed ( )

inline

Definition at line 579 of file snn.h.

◆ getRFDist3D()

double getRFDist3D	(	const RadiusRF &	radius,
		const Point3D &	pre,
		const Point3D &	post
	)

Definition at line 5071 of file snn_manager.cpp.

◆ getSimTime()

int getSimTime ( )

inline

Definition at line 581 of file snn.h.

◆ getSimTimeMs()

int getSimTimeMs ( )

inline

Definition at line 583 of file snn.h.

◆ getSimTimeSec()

int getSimTimeSec ( )

inline

Definition at line 582 of file snn.h.

◆ getSpikeMonitor()

SpikeMonitor * getSpikeMonitor ( int grpId )

Definition at line 1960 of file snn_manager.cpp.

◆ getSpikeMonitorCore()

SpikeMonitorCore * getSpikeMonitorCore ( int grpId )

Returns pointer to existing SpikeMonitorCore object, NULL else. Should not be exposed to user interface

Definition at line 1970 of file snn_manager.cpp.

◆ getSTPu()

float* getSTPu ( )

inline

TODO:: replace with NeuronMonitor or ConnectionMonitor

Definition at line 610 of file snn.h.

◆ getSTPx()

float* getSTPx ( )

inline

TODO:: replace with NeuronMonitor or ConnectionMonitor

Definition at line 613 of file snn.h.

◆ getWeightMatrix2D()

std::vector< std::vector< float > > getWeightMatrix2D ( short int connId )

TODO:: : modify this for multi-GPUs

Definition at line 6233 of file snn_manager.cpp.

◆ getWeightRange()

RangeWeight getWeightRange ( short int connId )

Definition at line 2003 of file snn_manager.cpp.

◆ isConnectionPlastic()

bool isConnectionPlastic ( short int connId )

Definition at line 4884 of file snn_manager.cpp.

◆ isDopaminergicGroup()

bool isDopaminergicGroup ( int gGrpId )

inline

Definition at line 624 of file snn.h.

◆ isExcitatoryGroup()

bool isExcitatoryGroup ( int gGrpId )

inline

Definition at line 621 of file snn.h.

◆ isGroupWithHomeostasis()

bool isGroupWithHomeostasis ( int grpId )

TODO:: : distinguish the function call at CONFIG_STATE and SETUP_STATE, where groupConfigs[0][] might not be available

Definition at line 4894 of file snn_manager.cpp.

◆ isInhibitoryGroup()

bool isInhibitoryGroup ( int gGrpId )

inline

Definition at line 622 of file snn.h.

◆ isPoint3DinRF()

bool isPoint3DinRF	(	const RadiusRF &	radius,
		const Point3D &	pre,
		const Point3D &	post
	)

TODO:: : not sure where this should go... maybe create some helper file?

Definition at line 5062 of file snn_manager.cpp.

◆ isPoissonGroup()

bool isPoissonGroup ( int gGrpId )

inline

Definition at line 623 of file snn.h.

◆ isSimulationWithCOBA()

bool isSimulationWithCOBA ( )

inline

Definition at line 634 of file snn.h.

◆ isSimulationWithCompartments()

bool isSimulationWithCompartments ( )

inline

Definition at line 633 of file snn.h.

◆ isSimulationWithCUBA()

bool isSimulationWithCUBA ( )

inline

Definition at line 635 of file snn.h.

◆ isSimulationWithFixedWeightsOnly()

bool isSimulationWithFixedWeightsOnly ( )

inline

Definition at line 638 of file snn.h.

◆ isSimulationWithGABAbRise()

bool isSimulationWithGABAbRise ( )

inline

Definition at line 637 of file snn.h.

◆ isSimulationWithHomeostasis()

bool isSimulationWithHomeostasis ( )

inline

Definition at line 639 of file snn.h.

◆ isSimulationWithNMDARise()

bool isSimulationWithNMDARise ( )

inline

Definition at line 636 of file snn.h.

◆ isSimulationWithPlasticWeights()

bool isSimulationWithPlasticWeights ( )

inline

Definition at line 640 of file snn.h.

◆ isSimulationWithSTDP()

bool isSimulationWithSTDP ( )

inline

Definition at line 641 of file snn.h.

◆ isSimulationWithSTP()

bool isSimulationWithSTP ( )

inline

Definition at line 642 of file snn.h.

◆ loadSimulation()

void loadSimulation ( FILE * fid )

reads the network state from file Reads a CARLsim network file. Such a file can be created using SNN:writeNetwork.

Definition at line 1001 of file snn_manager.cpp.

◆ runNetwork()

int runNetwork	(	int	_nsec,
		int	_nmsec,
		bool	printRunSummary
	)

Parameters

[in] printRunSummary whether to print a basic summary of the run at the end

************************************************************************************************************ /// PUBLIC METHODS: RUNNING A SIMULATION ************************************************************************************************************ ///

Definition at line 794 of file snn_manager.cpp.

◆ saveSimulation()

void saveSimulation	(	FILE *	fid,
		bool	saveSynapseInfo = `false`
	)

TODO:: : replace with faster version

Definition at line 1411 of file snn_manager.cpp.

◆ scaleWeights()

void scaleWeights	(	short int	connId,
		float	scale,
		bool	updateWeightRange = `false`
	)

Definition at line 1006 of file snn_manager.cpp.

◆ setCompartmentParameters()

void setCompartmentParameters	(	int	grpId,
		float	couplingUp,
		float	couplingDown
	)

Parameters

grpId	the symbolic name of a group
couplingUp	the coupling constant for upper connections
couplingDown	the coupling constant for lower connections

Definition at line 393 of file snn_manager.cpp.

◆ setConductances()

void setConductances	(	bool	isSet,
		int	tdAMPA,
		int	trNMDA,
		int	tdNMDA,
		int	tdGABAa,
		int	trGABAb,
		int	tdGABAb
	)

Parameters

isSet	enables the use of COBA mode
tAMPA	time _constant of AMPA decay (ms); for example, 5.0
tNMDA	time constant of NMDA decay (ms); for example, 150.0
tGABAa	time constant of GABAa decay (ms); for example, 6.0
tGABAb	time constant of GABAb decay (ms); for example, 150.0

Definition at line 409 of file snn_manager.cpp.

◆ setConnectionMonitor()

ConnectionMonitor * setConnectionMonitor	(	int	grpIdPre,
		int	grpIdPost,
		FILE *	fid
	)

Parameters

[in]	grpIdPre	ID of the pre-synaptic neuron group
[in]	grpIdPost	ID of the post-synaptic neuron group
[in]	connectionMon	ConnectionMonitorCore class

TODO:: : distinguish the function call at CONFIG_STATE and SETUP_STATE, where group(connect)Config[] might not be available

Definition at line 1125 of file snn_manager.cpp.

◆ setESTDP()

void setESTDP	(	int	grpId,
		bool	isSet,
		STDPType	type,
		STDPCurve	curve,
		float	alphaPlus,
		float	tauPlus,
		float	alphaMinus,
		float	tauMinus,
		float	gamma
	)

Definition at line 621 of file snn_manager.cpp.

◆ setExternalCurrent()

void setExternalCurrent	(	int	grpId,
		const std::vector< float > &	current
	)

Definition at line 1378 of file snn_manager.cpp.

◆ setGroupMonitor()

GroupMonitor * setGroupMonitor	(	int	gGrpId,
		FILE *	fid
	)

Parameters

[in]	grpId	ID of the neuron group
[in]	fid	file pointer for recording group status (neuromodulators)

TODO:: : distinguish the function call at CONFIG_STATE and SETUP_STATE, where groupConfigs[0][] might not be available

Definition at line 1088 of file snn_manager.cpp.

◆ setHomeoBaseFiringRate()

void setHomeoBaseFiringRate	(	int	groupId,
		float	baseFiring,
		float	baseFiringSD
	)

Definition at line 481 of file snn_manager.cpp.

◆ setHomeostasis()

void setHomeostasis	(	int	grpId,
		bool	isSet,
		float	homeoScale,
		float	avgTimeScale
	)

Definition at line 461 of file snn_manager.cpp.

◆ setIntegrationMethod()

void setIntegrationMethod	(	integrationMethod_t	method,
		int	numStepsPerMs
	)

Definition at line 497 of file snn_manager.cpp.

◆ setISTDP()

void setISTDP	(	int	grpId,
		bool	isSet,
		STDPType	type,
		STDPCurve	curve,
		float	ab1,
		float	ab2,
		float	tau1,
		float	tau2
	)

TODO:: : separate STDPType to ESTDPType and ISTDPType

Definition at line 654 of file snn_manager.cpp.

◆ setLogsFp()

void setLogsFp	(	FILE *	fpInf = `NULL`,
		FILE *	fpErr = `NULL`,
		FILE *	fpDeb = `NULL`,
		FILE *	fpLog = `NULL`
	)

************************************************************************************************************ /// PUBLIC METHODS: PLOTTING / LOGGING ************************************************************************************************************ ///

Definition at line 1672 of file snn_manager.cpp.

◆ setNeuromodulator()

void setNeuromodulator	(	int	grpId,
		float	baseDP,
		float	tauDP,
		float	base5HT,
		float	tau5HT,
		float	baseACh,
		float	tauACh,
		float	baseNE,
		float	tauNE
	)

Parameters

groupId	the symbolic name of a group
baseDP	the baseline concentration of Dopamine
tauDP	the decay time constant of Dopamine
base5HT	the baseline concentration of Serotonin
tau5HT	the decay time constant of Serotonin
baseACh	the baseline concentration of Acetylcholine
tauACh	the decay time constant of Acetylcholine
baseNE	the baseline concentration of Noradrenaline
tauNE	the decay time constant of Noradrenaline

Definition at line 597 of file snn_manager.cpp.

◆ setNeuronMonitor()

NeuronMonitor * setNeuronMonitor	(	int	gid,
		FILE *	fid
	)

Parameters

grpId	ID of the neuron group
neuronMon	(optional) neuronMonitor class

Returns: NeuronMonitor* pointer to a NeuronMonitor object

Definition at line 1222 of file snn_manager.cpp.

◆ setNeuronParameters() [1/2]

void setNeuronParameters	(	int	grpId,
		float	izh_a,
		float	izh_a_sd,
		float	izh_b,
		float	izh_b_sd,
		float	izh_c,
		float	izh_c_sd,
		float	izh_d,
		float	izh_d_sd
	)

Parameter values for each neuron are given by a normal distribution with mean _a, _b, _c, _d and standard deviation _a_sd, _b_sd, _c_sd, and _d_sd, respectively

Parameters

_groupId	the symbolic name of a group
_a	the mean value of izhikevich parameter a
_a_sd	the standard deviation value of izhikevich parameter a
_b	the mean value of izhikevich parameter b
_b_sd	the standard deviation value of izhikevich parameter b
_c	the mean value of izhikevich parameter c
_c_sd	the standard deviation value of izhikevich parameter c
_d	the mean value of izhikevich parameter d
_d_sd	the standard deviation value of izhikevich parameter d

Definition at line 505 of file snn_manager.cpp.

◆ setNeuronParameters() [2/2]

void setNeuronParameters	(	int	grpId,
		float	izh_C,
		float	izh_C_sd,
		float	izh_k,
		float	izh_k_sd,
		float	izh_vr,
		float	izh_vr_sd,
		float	izh_vt,
		float	izh_vt_sd,
		float	izh_a,
		float	izh_a_sd,
		float	izh_b,
		float	izh_b_sd,
		float	izh_vpeak,
		float	izh_vpeak_sd,
		float	izh_c,
		float	izh_c_sd,
		float	izh_d,
		float	izh_d_sd
	)

Parameter values for each neuron are given by a normal distribution with mean _C, _k, _vr, _vt, _a, _b, _vpeak, _c, and _d and standard deviation _C_sd, _k_sd, _vr_sd, _vt_sd, _a_sd, _b_sd, _vpeak_sd, _c_sd, and _d_sd, respectively

Parameters

_groupId	the symbolic name of a group
_C	the mean value of izhikevich parameter C
_C_sd	the standart deviation value of izhikevich parameter C
_k	the mean value of izhikevich parameter k
_k_sd	the standart deviation value of izhikevich parameter k
_vr	the mean value of izhikevich parameter vr
_vr_sd	the standart deviation value of izhikevich parameter vr
_vt	the mean value of izhikevich parameter vt
_vt_sd	the standart deviation value of izhikevich parameter vt
_a	the mean value of izhikevich parameter a
_a_sd	the standard deviation value of izhikevich parameter a
_b	the mean value of izhikevich parameter b
_b_sd	the standard deviation value of izhikevich parameter b
_vpeak	the mean value of izhikevich parameter vpeak
_vpeak_sd	the standart deviation value of izhikevich parameter vpeak
_c	the mean value of izhikevich parameter c
_c_sd	the standard deviation value of izhikevich parameter c
_d	the mean value of izhikevich parameter d
_d_sd	the standard deviation value of izhikevich parameter d

Definition at line 530 of file snn_manager.cpp.

◆ setNeuronParametersLIF()

void setNeuronParametersLIF	(	int	grpId,
		int	tau_m,
		int	tau_ref,
		float	vTh,
		float	vReset,
		double	minRmem,
		double	maxRmem
	)

Parameters

[in]	grpId	group ID
[in]	tau_m	Membrane time constant in ms (controls decay/leak)
[in]	tau_ref	absolute refractory period in ms
[in]	vTh	Threshold voltage for firing (must be > vReset)
[in]	vReset	Membrane potential resets to this value immediately after spike
[in]	minRmem	minimum membrane resistance
[in]	maxRmem	maximum membrane resistance

Definition at line 575 of file snn_manager.cpp.

◆ setSpikeGenerator()

void setSpikeGenerator	(	int	gGrpId,
		SpikeGeneratorCore *	spikeGenFunc
	)

TODO:: : distinguish the function call at CONFIG_STATE and SETUP_STATE, where groupConfigs[0][] might not be available

Definition at line 1174 of file snn_manager.cpp.

◆ setSpikeMonitor()

SpikeMonitor * setSpikeMonitor	(	int	gid,
		FILE *	fid
	)

Parameters

grpId	ID of the neuron group
spikeMon	(optional) spikeMonitor class

Returns: SpikeMonitor* pointer to a SpikeMonitor object

Definition at line 1182 of file snn_manager.cpp.

◆ setSpikeRate()

void setSpikeRate	(	int	gGrpId,
		PoissonRate *	ratePtr,
		int	refPeriod
	)

Input arguments:

Parameters

grpId	ID of the neuron group
spikeRate	pointer to a PoissonRate instance
refPeriod	(optional) refractive period, default = 1

TODO:: : distinguish the function call at CONFIG_STATE and RUN_STATE, where groupConfigs[0][] might not be available

Definition at line 1271 of file snn_manager.cpp.

◆ setSTP()

void setSTP	(	int	grpId,
		bool	isSet,
		float	STP_U,
		float	STP_tau_u,
		float	STP_tau_x
	)

Parameters

[in]	grpId	pre-synaptic group id. STP will apply to all neurons of that group!
[in]	isSet	a flag whether to enable/disable STP
[in]	STP_tau_u	decay constant of u (\tau_F)
[in]	STP_tau_x	decay constant of x (\tau_D)

Definition at line 700 of file snn_manager.cpp.

◆ setupNetwork()

void setupNetwork ( )

Parameters

[in] removeTempMemory remove temp memory after building network

************************************************************************************************************ /// PUBLIC METHODS: GENERATE A SIMULATION ************************************************************************************************************ ///

Definition at line 773 of file snn_manager.cpp.

◆ setWeight()

void setWeight	(	short int	connId,
		int	neurIdPre,
		int	neurIdPost,
		float	weight,
		bool	updateWeightRange = `false`
	)

Definition at line 1287 of file snn_manager.cpp.

◆ setWeightAndWeightChangeUpdate()

void setWeightAndWeightChangeUpdate	(	UpdateInterval	wtANDwtChangeUpdateInterval,
		bool	enableWtChangeDecay,
		float	wtChangeDecay
	)

Parameters

[in]	wtANDwtChangeUpdateInterval	the interval between two wt (weight) and wtChange (weight change) update.
[in]	enableWtChangeDecay	enable weight change decay
[in]	wtChangeDecay	the decay ratio of weight change (wtChange)

Definition at line 724 of file snn_manager.cpp.

◆ startTesting()

void startTesting ( bool shallUpdateWeights = true )

Definition at line 6181 of file snn_manager.cpp.

◆ stopTesting()

void stopTesting ( )

Definition at line 6208 of file snn_manager.cpp.

◆ updateConnectionMonitor()

void updateConnectionMonitor ( short int connId = ALL )

Definition at line 6219 of file snn_manager.cpp.

◆ updateGroupMonitor()

void updateGroupMonitor ( int grpId = ALL )

Definition at line 6280 of file snn_manager.cpp.

◆ updateNeuronMonitor()

void updateNeuronMonitor ( int gGrpId = ALL )

This function is public in SNN, but it should probably not be a public user function in CARLsim. It is usually called once every 1000ms by the core to update neuron state value binaries and NeuronMonitor objects. In GPU mode, it will first copy the neuron state info to the host. The input argument can either be a specific group ID or keyword ALL (for all groups). Core and utility functions can call updateNeuronMonitor at any point in time. The function will automatically determine the last time it was called, and update SpikeMonitor information only if necessary.

TODO:: : modify this for multi-GPUs

Definition at line 6590 of file snn_manager.cpp.

◆ updateSpikeMonitor()

void updateSpikeMonitor ( int gGrpId = ALL )

This function is public in SNN, but it should probably not be a public user function in CARLsim. It is usually called once every 1000ms by the core to update spike binaries and SpikeMonitor objects. In GPU mode, it will first copy the firing info to the host. The input argument can either be a specific group ID or keyword ALL (for all groups). Core and utility functions can call updateSpikeMonitor at any point in time. The function will automatically determine the last time it was called, and update SpikeMonitor information only if necessary.

TODO:: : modify this for multi-GPUs

Definition at line 6479 of file snn_manager.cpp.

Member Data Documentation

◆ MAJOR_VERSION

const unsigned int MAJOR_VERSION = 4

static

Definition at line 138 of file snn.h.

◆ MINOR_VERSION

const unsigned int MINOR_VERSION = 0

static

Definition at line 139 of file snn.h.

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

Public Member Functions

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SNN()

◆ ~SNN()

Member Function Documentation

◆ biasWeights()

◆ connect() [1/2]

◆ connect() [2/2]

◆ connectCompartments()

◆ createGroup()

◆ createGroupLIF()

◆ createSpikeGeneratorGroup()

◆ exitSimulation()

◆ getConductanceAMPA()

◆ getConductanceGABAa()

◆ getConductanceGABAb()

◆ getConductanceNMDA()

◆ getConnectConfig()

◆ getConnectId()

◆ getCurrent()

◆ getDelayRange()

◆ getDelays()

◆ getGroupEndNeuronId()

◆ getGroupGrid3D()

◆ getGroupId()

◆ getGroupName()

◆ getGroupNeuromodulatorInfo()

◆ getGroupNumNeurons()

◆ getGroupStartNeuronId()

◆ getGroupSTDPInfo()

◆ getLogFpDeb()

◆ getLogFpErr()

◆ getLogFpInf()

◆ getLogFpLog()

◆ getLoggerMode()

◆ getNetworkName()

◆ getNeuronLocation3D() [1/2]

◆ getNeuronLocation3D() [2/2]

◆ getNeuronMonitor()

◆ getNeuronMonitorCore()

◆ getNumCompartmentConnections()

◆ getNumConnections()

◆ getNumGroups()

◆ getNumNeurons()

◆ getNumNeuronsGen()

◆ getNumNeuronsGenExc()

◆ getNumNeuronsGenInh()

◆ getNumNeuronsReg()

◆ getNumNeuronsRegExc()

◆ getNumNeuronsRegInh()

◆ getNumSynapses()

◆ getNumSynapticConnections()

◆ getRandSeed()

◆ getRFDist3D()

◆ getSimTime()

◆ getSimTimeMs()

◆ getSimTimeSec()

◆ getSpikeMonitor()

◆ getSpikeMonitorCore()

◆ getSTPu()

◆ getSTPx()

◆ getWeightMatrix2D()

◆ getWeightRange()

◆ isConnectionPlastic()

◆ isDopaminergicGroup()

◆ isExcitatoryGroup()

◆ isGroupWithHomeostasis()

◆ isInhibitoryGroup()

◆ isPoint3DinRF()

◆ isPoissonGroup()

◆ isSimulationWithCOBA()

◆ isSimulationWithCompartments()

◆ isSimulationWithCUBA()

◆ isSimulationWithFixedWeightsOnly()

◆ isSimulationWithGABAbRise()

◆ isSimulationWithHomeostasis()

◆ isSimulationWithNMDARise()

◆ isSimulationWithPlasticWeights()