Sirene.h File Reference

Main inlcude file of the SiReNe Software. More...

#include <stdio.h>
#include <stdlib.h>
#include <malloc.h>
#include <sys/time.h>
#include <vector>
#include "GenLib.h"

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Data Structures
struct	SpikeEvent
	Description of a spike event. More...
struct	Neuron
	Description of a neuron. More...
struct	NeuralModel
	Description of a neural model containing neurons of the same type. More...
struct	SynapseModel
	Description of a synaptic model. More...
struct	Simul
	Description of an entire simulation. More...

Macros
#define	omp_get_thread_num()   0
	Alias to OpenMP function returning the thread number. More...
#define	omp_get_num_threads()   1
	Alias to OpenMP function returning the number of threads. More...
#define	QUIET   0
	Flag for minimal display in initialization. More...
#define	VERBOSE_CONFIG   1
	Flag for configuration display in initialization. More...
#define	VERBOSE_DETAILS   2
	Flag for detailed network display in initialization. More...
#define	VERBOSE_TIME   4
	Flag for execution time display after simulation. More...
#define	NO_RECORD   0
	0000000B flag value for no saving during the simulation More...
#define	SAVE_POTENTIALS   1
	0000001B flag value for saving the potentials during the simulation More...
#define	SAVE_VARIABLES   2
	0000010B flag value for saving the variables during the simulation More...
#define	SAVE_INPUT_CURRENTS   4
	0000100B flag value for saving the input currents during the simulation More...
#define	SAVE_SYNAPTIC_CURRENTS   8
	0001000B flag value for saving the synaptic currents during the simulation More...
#define	SAVE_LFP   16
	0010000B flag value for saving the LFP during the simulation More...
#define	SAVE_SPIKES   32
	0100000B flag value for saving the spike times and locations during the simulation More...
#define	SAVE_NBSPIKES   64
	1000000B flag value for saving the number of spikes during the simulation More...
#define	BUFFER_SIZE   1000000
	Spikes buffer size. More...
#define	NBMEMSTEP   2
	Number of stored time steps. More...
#define	MAXTHREADS   128
	Max number of threads. More...
#define	INPUT_CALL(chrono)
	Macro to be placed at the beginning of each function requiring execution time profiling (empty macro when time profiling is not activated) More...
#define	RETURN_CALL(chrono, cumul)
	Macro to be placed at the end of each function requiring execution time profiling (empty macro when time profiling is not activated) More...

Enumerations
enum	SynapticCurrentType { EXP_CURRENT =0, EXP_CURRENT_WITH_NOISE }
	Synaptic current types: exponential model wo/w noise (may be extended with other types of synaptic currents) More...
enum	InterpolatorType { NO_INTERP =0, LINEAR_INTERP, BEZIER_INTERP }
	Spike interpolation type: NO_INTERP=Spike at time step, LINEAR_INTERP=Lines, BEZIER_INTERP=Quadratic Bézier curve. More...

Functions
void	Iter (Simul *Simulation, double *TmpVar, double *TmpDer)
	Computation of one time-step from (t) to (t + dt) More...
void	Advance (Simul *Simulation)
	Simulation process over time-steps. More...
void	InitSimu (Simul *Simulation)
	Initialization of the simulation structure. More...
void	PrepareSimu (Simul *Simulation, ushort VerboseMask, ushort SaveMask, int ResultsInterval)
	Preparation of simulation data according to the neural network description. More...

Detailed Description

Data structures and main functions to simulate biological neuronal networks with adjustable properties (normal state, Parkinson's disease,...).

Macro Definition Documentation

BUFFER_SIZE

#define BUFFER_SIZE   1000000

INPUT_CALL

#define INPUT_CALL

(

chrono

)

MAXTHREADS

#define MAXTHREADS   128

NBMEMSTEP

#define NBMEMSTEP   2

NO_RECORD

#define NO_RECORD   0

omp_get_num_threads

#define omp_get_num_threads

(

)

1

omp_get_thread_num

#define omp_get_thread_num

(

)

0

QUIET

#define QUIET   0

RETURN_CALL

#define RETURN_CALL	(		chrono,
			cumul
	)

SAVE_INPUT_CURRENTS

#define SAVE_INPUT_CURRENTS   4

SAVE_LFP

#define SAVE_LFP   16

SAVE_NBSPIKES

#define SAVE_NBSPIKES   64

SAVE_POTENTIALS

#define SAVE_POTENTIALS   1

SAVE_SPIKES

#define SAVE_SPIKES   32

SAVE_SYNAPTIC_CURRENTS

#define SAVE_SYNAPTIC_CURRENTS   8

SAVE_VARIABLES

#define SAVE_VARIABLES   2

VERBOSE_CONFIG

#define VERBOSE_CONFIG   1

VERBOSE_DETAILS

#define VERBOSE_DETAILS   2

VERBOSE_TIME

#define VERBOSE_TIME   4

Enumeration Type Documentation

InterpolatorType

enum InterpolatorType

Enumerator
NO_INTERP
LINEAR_INTERP
BEZIER_INTERP

SynapticCurrentType

enum SynapticCurrentType

Enumerator
EXP_CURRENT
EXP_CURRENT_WITH_NOISE

Function Documentation

Advance()

void Advance

(

Simul *

Simulation

)

---

Iterative process over the time-steps:

• Calls to the Iter() function to solve the ODE system of the network at each time-step

Possibility to save data like VARIABLES, POTENTIALS, INPUT_CURRENTS, SYNAPTIC_CURRENTS, LFP, SPIKES and NBSPIKES.
All files are saved in binary mode.

Parameters

Simulation

Structure where all simulation information is stored

References Simul::BufferSpikes, Simul::Chrono_Advance, Simul::CrtNum, Neuron::GlobalNumNeuron, INPUT_CALL, Neuron::InputCurrent, Simul::InputCurrentsFileName, Iter(), Simul::LFPFileName, MYFREE(), MYMALLOC(), Simul::NbSpikesFileName, Simul::NbSpInBuf, Simul::NeuralModels, NeuralModel::Neurons, NO_RECORD, Simul::NumberNeuralModels, NeuralModel::NumberOfNeurons, Neuron::NumberOfSpikes, Simul::NumberOfVariables, Neuron::PotentialIndex, Simul::PotentialsFileName, PrintTimes(), Simul::PrvNum, Simul::ResultsInterval, RETURN_CALL, SAVE_INPUT_CURRENTS, SAVE_LFP, SAVE_NBSPIKES, SAVE_POTENTIALS, SAVE_SPIKES, SAVE_SYNAPTIC_CURRENTS, SAVE_VARIABLES, Simul::SaveMask, Simul::sLFP, Simul::SpikesFile, Simul::SpikesFileName, Simul::Start, Neuron::SynapticCurrent, Simul::SynapticCurrentsFileName, Simul::t, Simul::Time_Advance, Simul::TimeStep, Simul::TotalNumberOfNeurons, Simul::TotalTimeSim, Simul::Variables, and Simul::VariablesFileName.

Referenced by main().

InitSimu()

void InitSimu

(

Simul *

Simulation

)

---

Parameters

Simulation

Structure where all simulation information is stored

References Simul::BufferSpikes, Simul::CrtNum, Simul::DVar, Euler(), Simul::InterpolationType, NBMEMSTEP, Simul::NbSpInBuf, Simul::NbThreads, Simul::NeuralModels, NO_INTERP, Simul::NumberNeuralModels, Simul::NumberOfVariables, Simul::NumberSynapseModels, Simul::NumericalMethod, Simul::PrvNum, Simul::RandGenerConnect, RandomConnections(), Simul::ResultsInterval, Simul::SaveMask, Simul::sLFP, Simul::SpikesFile, Simul::Start, Simul::SynapseModels, Simul::t, Simul::TimeStep, Simul::TotalNumberOfNeurons, Simul::TotalTimeSim, Simul::Variables, and Simul::VerboseMask.

Referenced by main().

Iter()

void Iter	(	Simul *	Simulation,
		double *	TmpVar,
		double *	TmpDer
	)

---

Network state is computed at (t + dt) using a numerical method (Euler or Runge-Kutta 2).
Detection of spikes using the SpikeDetection() function.

Parameters

Simulation	Structure where all simulation information is stored
TmpVar	Variables array for intermediate time-steps computed in the numerical method
TmpDer	Derivatives array for intermediate time-steps computed in the numerical method

References Simul::Chrono_Iter, Simul::CrtNum, INPUT_CALL, Simul::NumericalMethod, Simul::PrvNum, RETURN_CALL, SpikeDetection(), Simul::t, Simul::Time_Iter, Simul::TimeStep, and UpdateModels().

Referenced by Advance().

PrepareSimu()

void PrepareSimu	(	Simul *	Simulation,
		ushort	VerboseMask,
		ushort	SaveMask,
		int	ResultsInterval
	)

---

Initialization of:

• Simulation structure:
  • SaveMask for data saving during the simulation
  • Time index PrvNum (previous time-step)
  • Crt (current time-step)
  • Time t0 = simulation starting point
  • Total number of neurons
  • Number of variables
  • Allocation of the variables array
  • Allocation of the derivatives of the variables array
  • Sum of the LFP
• Neuron structure:
  • Input/Synaptic current
  • Global number neuron
  • Number of parameters
  • Parameters
  • Synaptic current factor
  • Spike threshold
  • Potential index
  • Mid-time step potential
  • Mid-time step derivative of the potential
  • Number of spikes
  • Last spike time
• Message:
  • Display of initialization information
    • Initialization display is activated via the VerboseMask parameter
• Chrono:
  • Time initalization for each function

Parameters

Simulation	Structure where all simulation information is stored
VerboseMask	Mask of information to display
SaveMask	Mask of variables to save to file
ResultsInterval	Number of iterations between results display / save

References BUFFER_SIZE, Simul::BufferSpikes, Simul::Chrono_Init, Simul::ChronoStart, Simul::CrtNum, Simul::DVar, Neuron::dVMidStep, NeuralModel::FirstNeuronNumber, Neuron::GlobalNumNeuron, Neuron::InitialValues, INPUT_CALL, Neuron::InputCurrent, Neuron::LastSpikeTime, MAXTHREADS, MYMALLOC(), NBMEMSTEP, Simul::NbSpInBuf, Simul::NbThreads, NeuralModelPrint(), Simul::NeuralModels, NeuronPrint(), NeuralModel::Neurons, Simul::NumberNeuralModels, SynapseModel::NumberOfConnections, NeuralModel::NumberOfNeurons, Neuron::NumberOfParameters, NeuralModel::NumberOfParameters, Neuron::NumberOfSpikes, NeuralModel::NumberOfVariables, Simul::NumberOfVariables, Neuron::Parameters, NeuralModel::Parameters, Neuron::PotentialIndex, Simul::PrvNum, Simul::ResultsInterval, RETURN_CALL, Simul::SaveMask, Simul::sLFP, Neuron::SpikeTreshold, NeuralModel::SpikeTreshold, Simul::Start, SynapseModelPrint(), Simul::SynapseModels, Neuron::SynapticCurrent, Neuron::SynCurrentFactor, Simul::t, Simul::Time_Advance, Simul::Time_Detection, Simul::Time_Init, Simul::Time_Iter, Simul::Time_NumericalMethod, Simul::Time_RandGenConn, Simul::Time_SpikeProcessing, Simul::Time_UpdateModels, Simul::Time_UpdateNeuron, Simul::TimeStep, Simul::TotalNumberOfNeurons, Simul::TotalTimeSim, Simul::Variables, VERBOSE_CONFIG, VERBOSE_DETAILS, Simul::VerboseMask, and Neuron::VMidStep.

Referenced by main().