Inheritance diagram for AllIFNeurons:

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Collaboration diagram for AllIFNeurons:

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Public Member Functions
virtual void	setupVertices () override
	Setup the internal structure of the class (allocate memories).

virtual void	loadParameters ()

virtual void	printParameters () const

virtual void	createAllVertices (Layout &layout)

virtual string	toString (int index) const

virtual void	deserialize (istream &input)

virtual void	serialize (ostream &output) const

template<class Archive >
void	serialize (Archive &archive)
	Cereal serialization method.

The membrane time constant	f$ (R_m \cdot C_m)\f$ DeviceVector< BGFLOAT > Tau_

template<class Archive >
Cereal serialization method void	serialize (Archive &archive)

Public Member Functions inherited from AllSpikingNeurons
void	clearSpikeCounts ()
	Clear the spike counts out of all Neurons.

virtual void	registerHistoryVariables () override

template<class Archive >
void	serialize (Archive &archive)
	Cereal serialization method.

virtual void	advanceVertices (AllEdges &synapses, const EdgeIndexMap &edgeIndexMap)

virtual void	integrateVertexInputs (AllEdges &edges, EdgeIndexMap &edgeIndexMap)

uint64_t	getSpikeHistory (int index, int offIndex)

Public Member Functions inherited from AllVertices
virtual void	loadEpochInputs (uint64_t currentStep, uint64_t endStep)

template<class Archive >
void	serialize (Archive &archive)
	Cereal serialization method.

Public Attributes
DeviceVector< BGFLOAT >	Trefract_
	The length of the absolute refractory period. [units=sec; range=(0,1);].

DeviceVector< BGFLOAT >	Vthresh_
	If exceeds $V_{thresh}$ a spike is emmited. [units=V; range=(-10,100);].

DeviceVector< BGFLOAT >	Vrest_
	The resting membrane voltage. [units=V; range=(-1,1);].

DeviceVector< BGFLOAT >	Vreset_
	The voltage to reset to after a spike. [units=V; range=(-1,1);].

DeviceVector< BGFLOAT >	Vinit_
	The initial condition for at time . [units=V; range=(-1,1);].

DeviceVector< BGFLOAT >	Cm_

DeviceVector< BGFLOAT >	Rm_
	The membrane resistance [units=Ohm; range=(0,1e30)].

DeviceVector< BGFLOAT >	Inoise_
	The standard deviation of the noise to be added each integration time constant. [range=(0,1); units=A;].

DeviceVector< BGFLOAT >	Iinject_
	A constant current to be injected into the LIF neuron. [units=A; range=(-1,1);].

DeviceVector< BGFLOAT >	Isyn_

DeviceVector< int >	numStepsInRefractoryPeriod_
	The remaining number of time steps for the absolute refractory period.

DeviceVector< BGFLOAT >	C1_
	Internal constant for the exponential Euler integration of f$V_m .

Internal constant for the exponential Euler integration of f$V_m f$ DeviceVector< BGFLOAT >	C2_

Internal constant for the exponential Euler integration of f$V_m f$ DeviceVector< BGFLOAT >	I0_

The membrane voltage f$V_m f$[readonly;units=V;] DeviceVector< BGFLOAT >	Vm_

Public Attributes inherited from AllSpikingNeurons
DeviceVector< bool >	hasFired_
	The booleans which track whether the neuron has fired.

vector< EventBuffer >	vertexEvents_
	Holds at least one epoch's worth of event times for every vertex.

DeviceVector< BGFLOAT >	summationPoints_

Protected Member Functions
void	createNeuron (int neuronIndex, Layout &layout)

void	setNeuronDefaults (int index)

virtual void	initNeuronConstsFromParamValues (int neuronIndex, BGFLOAT deltaT)

void	readNeuron (istream &input, int i)

void	writeNeuron (ostream &output, int i) const

Protected Member Functions inherited from AllSpikingNeurons
virtual void	advanceNeuron (int index)=0

virtual void	fire (int index)

Additional Inherited Members
Protected Attributes inherited from AllSpikingNeurons
bool	fAllowBackPropagation_

Protected Attributes inherited from AllVertices
int	size_
	Total number of vertices.

log4cplus::Logger	fileLogger_

log4cplus::Logger	vertexLogger_
	TODO: Should check to see if this file name "neurons" is hardcoded and change it to vertices.

Detailed Description

Definition at line 41 of file AllIFNeurons.h.

Member Function Documentation

◆ createAllVertices()

void AllIFNeurons::createAllVertices ( Layout & layout )

virtual

Creates all the Neurons and assigns initial data for them.

Parameters

layout Layout information of the neural network.

Creates all the Neurons and generates data for them.

Parameters

layout Layout information of the neural network.

Implements AllVertices.

Reimplemented in AllIZHNeurons.

Definition at line 102 of file AllIFNeurons.cpp.

◆ createNeuron()

void AllIFNeurons::createNeuron	(	int	i,
		Layout &	layout )

protected

Creates a single Neuron and generates data for it.

Parameters

neuronIndex	Index of the neuron to create.
layout	Layout information of the neural network.

Creates a single Neuron and generates data for it.

Parameters

i	Index of the neuron to create.
layout	Layout information of the neural network.

Definition at line 117 of file AllIFNeurons.cpp.

◆ deserialize()

void AllIFNeurons::deserialize ( istream & input )

virtual

Reads and sets the data for all neurons from input stream.

Parameters

input istream to read from.

Sets the data for Neurons to input's data.

Parameters

input istream to read from.

Reimplemented in AllIZHNeurons.

Definition at line 246 of file AllIFNeurons.cpp.

◆ initNeuronConstsFromParamValues()

void AllIFNeurons::initNeuronConstsFromParamValues	(	int	i,
		BGFLOAT	deltaT )

protectedvirtual

Initializes the Neuron constants at the indexed location.

Parameters

neuronIndex	Index of the Neuron.
deltaT	Inner simulation step duration

Initializes the Neuron constants at the indexed location.

Parameters

i	Index of the Neuron.
deltaT	Inner simulation step duration

Reimplemented in AllIZHNeurons.

Definition at line 190 of file AllIFNeurons.cpp.

◆ loadParameters()

void AllIFNeurons::loadParameters ( )

virtual

Load member variables from configuration file. Registered to OperationManager as Operation::loadParameters

Load member variables from configuration file. Registered to OperationManager as Operation::op::loadParameters

Implements AllVertices.

Definition at line 43 of file AllIFNeurons.cpp.

◆ printParameters()

void AllIFNeurons::printParameters ( ) const

virtual

Prints out all parameters of the neurons to logging file. Registered to OperationManager as Operation::printParameters

Reimplemented from AllVertices.

Reimplemented in AllIZHNeurons, and AllLIFNeurons.

Definition at line 76 of file AllIFNeurons.cpp.

◆ readNeuron()

void AllIFNeurons::readNeuron	(	istream &	input,
		int	i )

protected

Sets the data for Neuron #index to input's data.

Parameters

input	istream to read from.
i	index of the neuron (in neurons).

Definition at line 257 of file AllIFNeurons.cpp.

◆ serialize() [1/2]

template<class Archive >

Cereal serialization method void AllIFNeurons::serialize ( Archive & archive )

Definition at line 251 of file AllIFNeurons.h.

◆ serialize() [2/2]

void AllIFNeurons::serialize ( ostream & output ) const

virtual

Writes out the data in all neurons to output stream.

Parameters

output stream to write out to.ss.

Writes out the data in Neurons.

Parameters

output stream to write out to.

Reimplemented in AllIZHNeurons.

Definition at line 301 of file AllIFNeurons.cpp.

◆ setNeuronDefaults()

void AllIFNeurons::setNeuronDefaults ( int index )

protected

Set the Neuron at the indexed location to default values.

Parameters

index Index of the Neuron that the synapse belongs to.

Definition at line 172 of file AllIFNeurons.cpp.

◆ setupVertices()

void AllIFNeurons::setupVertices ( )

overridevirtual

Setup the internal structure of the class (allocate memories).

Setup the internal structure of the class. Allocate memories to store all neurons' state.

Reimplemented from AllSpikingNeurons.

Reimplemented in AllIZHNeurons.

Definition at line 18 of file AllIFNeurons.cpp.

◆ toString()

string AllIFNeurons::toString ( int index ) const

virtual

Outputs state of the neuron chosen as a string.

Parameters

index index of the neuron (in neurons) to output info from.

Returns: the complete state of the neuron.

Implements AllVertices.

Reimplemented in AllIZHNeurons.

Definition at line 220 of file AllIFNeurons.cpp.

◆ writeNeuron()

void AllIFNeurons::writeNeuron	(	ostream &	output,
		int	i ) const

protected

Writes out the data in the selected Neuron.

Parameters

output	stream to write out to.
i	index of the neuron (in neurons).

Definition at line 312 of file AllIFNeurons.cpp.

Member Data Documentation

◆ C1_

DeviceVector<BGFLOAT> AllIFNeurons::C1_

Internal constant for the exponential Euler integration of f$V_m .

Definition at line 208 of file AllIFNeurons.h.

◆ C2_

Internal constant for the exponential Euler integration of f$V_m f$ DeviceVector<BGFLOAT> AllIFNeurons::C2_

Definition at line 211 of file AllIFNeurons.h.

◆ Cm_

DeviceVector<BGFLOAT> AllIFNeurons::Cm_

The membrane capacitance $C_m$ [range=(0,1); units=F;] Used to initialize Tau (no use after that)

Definition at line 187 of file AllIFNeurons.h.

◆ I0_

Internal constant for the exponential Euler integration of f$V_m f$ DeviceVector<BGFLOAT> AllIFNeurons::I0_

Definition at line 214 of file AllIFNeurons.h.

◆ Iinject_

DeviceVector<BGFLOAT> AllIFNeurons::Iinject_

A constant current to be injected into the LIF neuron. [units=A; range=(-1,1);].

Definition at line 196 of file AllIFNeurons.h.

◆ Inoise_

DeviceVector<BGFLOAT> AllIFNeurons::Inoise_

The standard deviation of the noise to be added each integration time constant. [range=(0,1); units=A;].

Definition at line 193 of file AllIFNeurons.h.

◆ Isyn_

DeviceVector<BGFLOAT> AllIFNeurons::Isyn_

What the hell is this used for??? It does not seem to be used; seems to be a candidate for deletion. Possibly from the old code before using a separate summation point The synaptic input current.

Definition at line 202 of file AllIFNeurons.h.

◆ numStepsInRefractoryPeriod_

DeviceVector<int> AllIFNeurons::numStepsInRefractoryPeriod_

The remaining number of time steps for the absolute refractory period.

Definition at line 205 of file AllIFNeurons.h.

◆ Rm_

DeviceVector<BGFLOAT> AllIFNeurons::Rm_

The membrane resistance $R_m$ [units=Ohm; range=(0,1e30)].

Definition at line 190 of file AllIFNeurons.h.

◆ Trefract_

DeviceVector<BGFLOAT> AllIFNeurons::Trefract_

The length of the absolute refractory period. [units=sec; range=(0,1);].

Definition at line 171 of file AllIFNeurons.h.

◆ Vinit_

DeviceVector<BGFLOAT> AllIFNeurons::Vinit_

The initial condition for $V_m$ at time $t=0$ . [units=V; range=(-1,1);].

Definition at line 183 of file AllIFNeurons.h.

◆ Vm_

The membrane voltage f$V_m f$ [readonly; units=V;] DeviceVector<BGFLOAT> AllIFNeurons::Vm_

Definition at line 217 of file AllIFNeurons.h.

◆ Vreset_

DeviceVector<BGFLOAT> AllIFNeurons::Vreset_

The voltage to reset $V_m$ to after a spike. [units=V; range=(-1,1);].

Definition at line 180 of file AllIFNeurons.h.

◆ Vrest_

DeviceVector<BGFLOAT> AllIFNeurons::Vrest_

The resting membrane voltage. [units=V; range=(-1,1);].

Definition at line 177 of file AllIFNeurons.h.

◆ Vthresh_

DeviceVector<BGFLOAT> AllIFNeurons::Vthresh_

If $V_m$ exceeds $V_{thresh}$ a spike is emmited. [units=V; range=(-10,100);].

Definition at line 174 of file AllIFNeurons.h.

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

Simulator/Vertices/Neuro/AllIFNeurons.h
Simulator/Vertices/Neuro/AllIFNeurons.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ createAllVertices()

◆ createNeuron()

◆ deserialize()

◆ initNeuronConstsFromParamValues()

◆ loadParameters()

◆ printParameters()

◆ readNeuron()

◆ serialize() [1/2]

◆ serialize() [2/2]

◆ setNeuronDefaults()

◆ setupVertices()

◆ toString()

◆ writeNeuron()

Member Data Documentation

◆ C1_

◆ C2_

◆ Cm_

◆ I0_

◆ Iinject_

◆ Inoise_

◆ Isyn_

◆ numStepsInRefractoryPeriod_

◆ Rm_

◆ Trefract_

◆ Vinit_

◆ Vm_

◆ Vreset_

◆ Vrest_

◆ Vthresh_