auryn::NeuronGroup Class Reference

Abstract base class for all neuron groups. More...

#include <NeuronGroup.h>

Inheritance diagram for auryn::NeuronGroup:

Collaboration diagram for auryn::NeuronGroup:

Public Member Functions
	NeuronGroup (NeuronID n, NodeDistributionMode mode=AUTO)
	Default constructor. More...
	NeuronGroup (NeuronID n, double loadmultiplier, NeuronID total)
	Old default constructor. More...
virtual	~NeuronGroup ()
virtual void	clear ()=0
void	set_state (std::string name, AurynState val)
	Conveniently sets all values in a state vector identified by name in this group. More...
void	set_state (std::string name, NeuronID i, AurynState val)
	Conveniently sets a single value of element i in a state vector identified by name in this group. More...
virtual AurynStateVector *	get_default_exc_target ()
	Returns default exc target input. More...
virtual AurynStateVector *	get_default_inh_target ()
	Returns default inh target input. More...
void	random_mem (AurynState mean=-60e-3, AurynState sigma=5e-3)
virtual void	init_state ()
void	safe_tadd (NeuronID id, AurynWeight amount, TransmitterType t=GLUT)
void	tadd (NeuronID id, AurynWeight amount, TransmitterType t=GLUT)
void	tadd (AurynStateVector *state, NeuronID id, AurynWeight amount)
Public Member Functions inherited from auryn::SpikingGroup
void	add_state_vector (std::string key, AurynStateVector *state_vector)
	Adds a state vector passed as an argument to the dictinary. More...
void	remove_state_vector (std::string key)
	Removes a state vector passed as an argument to the dictinary. More...
AurynStateVector *	find_state_vector (std::string key)
	Returns existing state vector by name or NULL if it does not exist. More...
AurynStateVector *	get_state_vector (std::string key)
	Creates a new or returns an existing state vector by name. More...
AurynStateVector *	get_existing_state_vector (std::string key)
	Returns an existing state with the supplied name. More...
AurynStateVector *	create_state_vector (std::string key)
	Creates a new state vector and throws an exception if a vector with the same name exists. More...
AurynState *	get_state_variable (std::string key)
	Creates a new group-wide state variable or returns an existing group-wide variable by name then returns a pointer to it. More...
void	randomize_state_vector_gauss (std::string state_vector_name, AurynState mean, AurynState sigma, int seed=12239)
	Randomizes the content of a state vector with Gaussian random numbers. Seeding is MPI save. More...
	SpikingGroup (NeuronID size, NodeDistributionMode mode=AUTO)
	Default constructor. More...
virtual	~SpikingGroup ()
	Default destructor. More...
virtual void	evolve_traces ()
	Evolves traces. More...
void	set_name (std::string s)
	Set connection name. More...
std::string	get_name ()
	Retrieves the groups name. More...
std::string	get_file_name ()
	Extracts the class name of the connection from the file name. More...
std::string	get_log_name ()
	Returns a string which is the combination of file and connection name for logging. More...
void	inc_num_spike_attributes (int x)
	Instructs SpikingGroup to increase the number of spike attributes by x. More...
int	get_num_spike_attributes ()
virtual void	evolve ()=0
	Virtual pure evolve function which needs to be implemented by derived classes. More...
void	conditional_evolve ()
	Conditional evolve functino which is called by System. More...
unsigned int	get_locked_rank ()
	Returns locked rank for SpikingGroups which are not distributed across all ranks. More...
unsigned int	get_locked_range ()
	Returns locked range of ranks for SpikingGroups which are not distributed across all ranks. More...
SpikeContainer *	get_spikes ()
	Returns pointer to a spike container that contains spikes which arrive in this timestep from all neurons in this group. More...
SpikeContainer *	get_spikes_immediate ()
	Returns pointer to SpikeContainer of spikes generated during the last evolve() step. More...
AttributeContainer *	get_attributes ()
	Returns pointer to Attributecontainer for usage in propagating Connection objects. Same as get_spikes_immediate(), however might be overwritten to contain Spikes that have been delayed. More...
AttributeContainer *	get_attributes_immediate ()
	Returns pointer to Attributecontainer of spikes generated during the last evolve() step. More...
NeuronID	get_size ()
	Returns the size of the group. More...
NeuronID	get_pre_size ()
	Returns the size of the group. More...
NeuronID	calculate_rank_size (int rank=-1)
	Determines rank size and stores it in local variable. More...
NeuronID	get_rank_size ()
	Returns the size on this rank. More...
NeuronID	get_post_size ()
	Returns the size on this rank. More...
void	set_clock_ptr (AurynTime *clock)
bool	evolve_locally ()
	Returns true if the calling instance has units which are integrated on the current rank. More...
NeuronID	get_uid ()
	Get the unique ID of the class. More...
Trace *	get_pre_trace (AurynFloat x)
	Returns a pre trace with time constant x. More...
void	add_pre_trace (Trace *tr)
	Adds trace to pretrace stack of a connection. More...
Trace *	get_post_trace (AurynFloat x)
	Returns a post trace with time constant x. More...
void	add_post_trace (Trace *tr)
	Adds trace to posttrace stack of a connection. More...
void	push_spike (NeuronID spike)
	Pushes a local NeuronID as spike into the axonal SpikeDelay buffer. More...
void	push_attribute (AurynFloat attrib)
	Pushes a spike attribute into the axonal SpikeDelay buffer. More...
void	clear_spikes ()
	Clears all spikes stored in the delays which is useful to reset a network during runtime. More...
Trace *	get_post_state_trace (std::string state_name="mem", AurynFloat tau=10e-3, AurynFloat b=0.0)
	Returns a post trace of a neuronal state variable e.g. the membrane potential with time constant tau. More...
Trace *	get_post_state_trace (AurynStateVector *state, AurynFloat tau=10e-3, AurynFloat b=0.0)
	Returns a post trace of a neuronal state variable specified by pointer. More...
void	set_delay (int d)
	Sets axonal delay for this SpikingGroup. More...
virtual bool	write_to_file (const char *filename)
	Writes current states of SpikingGroup to human-readible textfile if implemented in derived class. More...
virtual bool	load_from_file (const char *filename)
	Reads current states of SpikingGroup to human-readible textfile if implemented in derived class. More...
NeuronID	ranksize ()
	Returns size (num of neurons) on the current rank. More...
NeuronID	global2rank (NeuronID i)
	Converts global NeuronID within the SpikingGroup to the local NeuronID on this rank. More...
NeuronID	rank2global (NeuronID i)
	Converts local NeuronID from the local rank to a global NeuronID. More...
bool	localrank (NeuronID i)
	Checks if the global NeuronID i is integrated on this MPI rank. More...
NeuronID	get_vector_size ()
	Rank size but rounded up to multiples of 4 (or potentially some other and larger number in future versions) for SSE compatibility. More...

Public Attributes
AurynStateVector *	mem
AurynStateVector *	g_ampa
AurynStateVector *	g_gaba
AurynStateVector *	g_nmda
AurynStateVector *	thr
Public Attributes inherited from auryn::SpikingGroup
SpikeDelay *	delay
bool	active
	Toggles group active. More...
std::map< std::string, AurynStateVector * >	state_vectors
std::map< std::string, AurynState >	state_variables

Protected Member Functions
void	init ()
void	free ()
Protected Member Functions inherited from auryn::SpikingGroup
virtual void	load_input_line (NeuronID i, const char *buf)
virtual std::string	get_output_line (NeuronID i)
virtual void	virtual_serialize (boost::archive::binary_oarchive &ar, const unsigned int version)
	Implementatinon of serialize function for writing. More...
virtual void	virtual_serialize (boost::archive::binary_iarchive &ar, const unsigned int version)
	Implementatinon of serialize function for reading. More...
void	free ()
	Frees potentially allocated memory. More...

Protected Attributes
AurynStateVector *	default_exc_target_state
AurynStateVector *	default_inh_target_state
Protected Attributes inherited from auryn::SpikingGroup
std::vector< Trace * >	pretraces
	Pretraces. More...
std::vector< Trace * >	posttraces
	Posttraces. More...
std::vector< Trace * >	post_state_traces
	Post state traces. More...
std::vector< AurynFloat >	post_state_traces_spike_biases
std::vector< AurynStateVector * >	post_state_traces_states
std::string	group_name
	Identifying name for object. More...
NeuronID	size
	Stores the size of the group. More...
NeuronID	rank_size
	Stores the size of the group on this rank. More...
SpikeContainer *	spikes
	SpikeContainers to store spikes produced during one step of evolve. More...
AttributeContainer *	attribs

Additional Inherited Members
Static Protected Attributes inherited from auryn::SpikingGroup
static AurynTime *	clock_ptr = NULL

Detailed Description

Abstract base class for all neuron groups.

This class constitutes the abstract forefather of all neuron groups in the simulator. It serves as target for Connection objects and is directly derived from SpikingGroup. It directly allocated the memory for mem (membrane potential) and the synaptic conductantes (g_ampa, g_gaba, g_nmda) as well as a vector to store the thresholds. The detailed implementation of the evolve() function depends on the children of NeuronGroup.

Constructor & Destructor Documentation

NeuronGroup() [1/2]

NeuronGroup::NeuronGroup	(	NeuronID	n,
		NodeDistributionMode	mode = AUTO
	)

Default constructor.

                                                               : SpikingGroup( n, mode )
{
        if ( evolve_locally() ) init();
}

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NeuronGroup() [2/2]

NeuronGroup::NeuronGroup	(	NeuronID	n,
		double	loadmultiplier,
		NeuronID	total
	)

Old default constructor.

Deprecated:

                                                                          : SpikingGroup( n )
{
        logger->warning("Using deprecated constructor of NeuronGroup with loadmultiplier. This feature is discontinued and the constructor will be removed in future versions.");
        if ( evolve_locally() ) init();
}

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~NeuronGroup()

NeuronGroup::~NeuronGroup ( )

virtual

Default destructor

{
        if ( evolve_locally() ) free();
}

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Member Function Documentation

clear()

virtual void auryn::NeuronGroup::clear ( )

pure virtual

Implemented in auryn::AdExGroup, auryn::ModSynIFGroup, auryn::IFGroup, auryn::NaudGroup, auryn::IafPscExpGroup, auryn::TIFGroup, auryn::IzhikevichGroup, auryn::SRM0Group, auryn::CubaIFGroup, auryn::AIFGroup, auryn::IafPscDeltaGroup, and auryn::AIF2Group.

free()

void NeuronGroup::free ( )

protected

Called by default destructor

{
}

get_default_exc_target()

AurynStateVector * NeuronGroup::get_default_exc_target ( )

virtual

Returns default exc target input.

{
        return default_exc_target_state;
}

get_default_inh_target()

AurynStateVector * NeuronGroup::get_default_inh_target ( )

virtual

Returns default inh target input.

{
        return default_inh_target_state;
}

init()

void NeuronGroup::init ( )

protected

Init procedure called by default constructor.

{               group_name = "NeuronGroup";

                // std::stringstream oss;
                // oss << description_std::string << " init";
                // auryn::logger->msg(oss.str(),VERBOSE);

                mem = get_state_vector("mem");
                thr = get_state_vector("thr");
                g_ampa = get_state_vector("g_ampa");
                g_gaba = get_state_vector("g_gaba");
                g_nmda = get_state_vector("g_nmda");

                default_exc_target_state = g_ampa;
                default_inh_target_state = g_gaba;

#ifndef CODE_ALIGNED_SSE_INSTRUCTIONS
                // checking via default if those arrays are aligned
                if ( auryn_AlignOffset( mem->size, mem->data, sizeof(float), 16) 
                                || auryn_AlignOffset( thr->size, thr->data, sizeof(float), 16) 
                                || auryn_AlignOffset( g_ampa->size, g_ampa->data, sizeof(float), 16) 
                                || auryn_AlignOffset( g_nmda->size, g_nmda->data, sizeof(float), 16) 
                                || auryn_AlignOffset( g_gaba->size, g_gaba->data, sizeof(float), 16)  
                   ) 
                        throw AurynMemoryAlignmentException();
#endif
}

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init_state()

void NeuronGroup::init_state ( )

virtual

{

}

random_mem()

void NeuronGroup::random_mem	(	AurynState	mean = -60e-3,
		AurynState	sigma = 5e-3
	)

{
        randomize_state_vector_gauss("mem",mean,sigma,42);
        init_state();
}

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safe_tadd()

void NeuronGroup::safe_tadd	(	NeuronID	id,
		AurynWeight	amount,
		TransmitterType	t = GLUT
	)

{
        if (localrank(id))
                tadd(id, amount, t);
}

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set_state() [1/2]

void NeuronGroup::set_state	(	std::string	name,
		AurynState	val
	)

Conveniently sets all values in a state vector identified by name in this group.

This sets all values in a state vector identified by its string name. All string identified operations are slow, so do not use them in evolve or propagate functions, but only for initialization.

Parameters

name	The state name to address
val	The value to set all entries to

{
        AurynStateVector * tmp = find_state_vector(name);
        if (tmp) tmp->set_all(val);
        else { logger->warning("State not found."); }
}

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set_state() [2/2]

void NeuronGroup::set_state	(	std::string	name,
		NeuronID	i,
		AurynState	val
	)

Conveniently sets a single value of element i in a state vector identified by name in this group.

Parameters

name	The state name to address
i	The local neuron id to set (this needs to be a translated value for MPI simulations)
val	The value to set all entries to.

{
        AurynStateVector * tmp = find_state_vector(name);
        if (tmp) { tmp->set(i,val); }
        else { logger->warning("State not found."); }
}

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tadd() [1/2]

void NeuronGroup::tadd	(	NeuronID	id,
		AurynWeight	amount,
		TransmitterType	t = GLUT
	)

Adds given transmitter to neuron as from a synaptic event. DEPRECATED. Moving slowly to SparseConnection transmit.

{
        NeuronID localid = global2rank(id);
        switch ( t ) {
                case GABA:
                        g_gaba->add_specific(localid,amount);
                        break;
                case MEM:
                        mem->add_specific(localid,amount);
                        break;
                case NMDA:
                        g_nmda->add_specific(localid,amount);
                        break;
                case GLUT:
                case AMPA:
                default:
                        g_ampa->add_specific(localid,amount);
        }
}

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tadd() [2/2]

void NeuronGroup::tadd	(	AurynStateVector *	state,
		NeuronID	id,
		AurynWeight	amount
	)

Adds given amount of transmitter to neuron state/id.

{
        NeuronID localid = global2rank(id);
        state->add_specific( localid, amount);
}

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Member Data Documentation

default_exc_target_state

AurynStateVector* auryn::NeuronGroup::default_exc_target_state

protected

default_inh_target_state

AurynStateVector* auryn::NeuronGroup::default_inh_target_state

protected

g_ampa

AurynStateVector* auryn::NeuronGroup::g_ampa

Stores the AMPA conductances of each point neuron.

g_gaba

AurynStateVector* auryn::NeuronGroup::g_gaba

Stores the GABA conductances of each point neuron.

g_nmda

AurynStateVector* auryn::NeuronGroup::g_nmda

Stores the NMDA conductances of each point neuron.

mem

AurynStateVector* auryn::NeuronGroup::mem

Stores the membrane potentials.

thr

AurynStateVector* auryn::NeuronGroup::thr

Stores threshold terms for moving thresholds.

TODO Remove and move to downstream.

---

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

• /home/zenke/auryn/src/auryn/NeuronGroup.h
• /home/zenke/auryn/src/auryn/NeuronGroup.cpp