auryn::Connection Class Reference

The abstract base class for all Connection objects in Auryn. More...

#include <Connection.h>

Inheritance diagram for auryn::Connection:

Collaboration diagram for auryn::Connection:

Public Member Functions
	Connection ()
	Connection (NeuronID rows, NeuronID cols)
	Connection (SpikingGroup *source, NeuronGroup *destination, TransmitterType transmitter=GLUT, std::string name="Connection")
virtual	~Connection ()
void	set_size (NeuronID i, NeuronID j)
void	set_name (std::string name)
	Set name of connection. More...
std::string	get_name ()
	Returns name of connection. 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...
AurynStateVector *	get_target_vector ()
	Returns target state vector if one is defined. More...
NeuronID	get_m_rows ()
	Get number of rows (presynaptic) in connection. More...
NeuronID	get_n_cols ()
	Get number of columns (postsynaptic) in connection. More...
TransmitterType	get_transmitter ()
	Returns transmitter type. More...
void	set_target (AurynWeight *ptr)
	Sets target state of this connection directly via a pointer. More...
void	set_target (AurynStateVector *ptr)
	Sets target state of this connection directly via a StateVector. More...
void	set_receptor (AurynStateVector *ptr)
	Same as set_target. More...
void	set_transmitter (AurynStateVector *ptr)
	Same as set_target. More...
void	set_transmitter (TransmitterType transmitter)
	Sets target state of this connection for a given receptor as one of Auryn's default transmitter types. More...
void	set_receptor (string state_name)
	Sets target state of this connection directly the name of a state vector. More...
void	set_target (string state_name)
	Same as set_receptor. More...
void	set_transmitter (string state_name)
	Same as set_receptor, but DEPRECATED. More...
void	set_source (SpikingGroup *source)
	Sets source SpikingGroup of this connection. More...
SpikingGroup *	get_source ()
	Returns pointer to the presynaptic group. More...
void	set_destination (NeuronGroup *source)
	Sets destination SpikingGroup of this connection. More...
NeuronGroup *	get_destination ()
	Returns pointer to the postsynaptic group. More...
virtual AurynWeight	get (NeuronID i, NeuronID j)=0
	Get weight value i,j if it exists. Otherwise the value is undefined. More...
virtual AurynWeight *	get_ptr (NeuronID i, NeuronID j)=0
	Return pointer to weight element i,j if it exists, otherwise return NULL. More...
virtual AurynWeight	get_data (NeuronID i)=0
	Return weight element as index in data array. More...
virtual void	set (NeuronID i, NeuronID j, AurynWeight value)=0
	Set existing weight element i,j with value. More...
virtual AurynLong	get_nonzero ()=0
	Return number of nonzero elements in this Connection. More...
virtual void	finalize ()=0
	Finalize Connection after initialization to prepare for use in simulation. More...
virtual void	propagate ()=0
	Propagate method to propagate spikes. Called by System run method. More...
virtual void	evolve ()
	Evolve method to update internal connection state. Called by System run method. More...
void	conditional_propagate ()
	DEPRECATED. (Such connections should not be registered in the first place) Calls propagate only if the postsynaptic NeuronGroup exists on the local rank. More...
Trace *	get_pre_trace (const AurynDouble tau)
	Returns a pointer to a presynaptic trace object. More...
Trace *	get_post_trace (const AurynDouble tau)
	Returns a pointer to a postsynaptic trace object. More...
Trace *	get_post_state_trace (const string state_name, const AurynDouble tau, const AurynDouble jump_size=0.0)
	Returns a pointer to a postsynaptic state trace object. More...
virtual void	stats (AurynDouble &mean, AurynDouble &std, StateID zid=0)=0
	Computes mean synaptic weight and std dev of all weights in this connection. More...
virtual bool	write_to_file (std::string filename)=0
	Implements save to file functionality. Also called in save_network_state from System class. More...
virtual bool	load_from_file (std::string filename)=0
	Implements load from file functionality. Also called in save_network_state from System class. More...
void	transmit (const NeuronID id, const AurynWeight amount)
	Default way to transmit a spike to a postsynaptic partner. More...
void	targeted_transmit (SpikingGroup *target_group, AurynStateVector *target_state, const NeuronID id, const AurynWeight amount)
	Transmits a spike to a given target group and state. More...
void	safe_transmit (NeuronID id, AurynWeight amount)
	Same as transmit but first checks if the target neuron exists and avoids segfaults that way (but it's also slower). More...
SpikeContainer *	get_pre_spikes ()
	Supplies pointer to SpikeContainer of all presynaptic spikes. More...
SpikeContainer *	get_post_spikes ()
	Returns pointer to SpikeContainer for postsynaptic spikes on this node. More...
void	add_number_of_spike_attributes (int x)
	Set up spike delay to accomodate x additional spike attributes. More...
AurynFloat	get_spike_attribute (const NeuronID i, const int attribute_id=0)
	Returns spike attribute belonging to the spike at position i in the get_spikes() SpikeContainer. More...

Public Attributes
SpikingGroup *	src
	Pointer to the source group of this connection. More...
NeuronGroup *	dst
	Pointer to the destination group of this connection. More...

Protected Member Functions
virtual void	virtual_serialize (boost::archive::binary_oarchive &ar, const unsigned int version)
virtual void	virtual_serialize (boost::archive::binary_iarchive &ar, const unsigned int version)
void	init (TransmitterType transmitter=GLUT)

Protected Attributes
TransmitterType	trans
AurynStateVector *	target_state_vector
AurynFloat *	target
	A more direct reference on the first element of the target_state_vector. More...
NeuronID	number_of_spike_attributes
	Number of spike attributes to expect with each spike transmitted through this connection. More...
NeuronID	spike_attribute_offset
	Stores spike attribute offset in attribute array. More...

Friends
class	boost::serialization::access

Detailed Description

The abstract base class for all Connection objects in Auryn.

Connections are designed to take up spikes from a source a group that can spike in general (decendants of SpikingGroup) and to convey them to a group that can integrate spikes such as the children of NeuronGroup.

For that reason, when constructing any decendant of Connection you generally will have to specify a source (SpikingGroup) and a destination (NeuronGroup).

Constructor & Destructor Documentation

Connection() [1/3]

Connection::Connection

(

)

{
        init();
}

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Connection() [2/3]

Connection::Connection	(	NeuronID	rows,
		NeuronID	cols
	)

{
        init();
        set_size(rows,cols);
}

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Connection() [3/3]

Connection::Connection	(	SpikingGroup *	source,
		NeuronGroup *	destination,
		TransmitterType	transmitter = GLUT,
		std::string	name = "Connection"
	)

{
        set_source(source);
        set_destination(destination);
        m_rows = src->get_size();
        n_cols = dst->get_size();
        init(transmitter);
        set_name(name);
}

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~Connection()

Connection::~Connection ( )

virtual

{
}

Member Function Documentation

add_number_of_spike_attributes()

void Connection::add_number_of_spike_attributes

(

int

x

)

Set up spike delay to accomodate x additional spike attributes.

Spike attribute numbers can only be increased. This function can only be run during initialization.

{
        if ( x <= 0 ) {
                throw AurynSpikeAttributeSizeException();
        }

        number_of_spike_attributes += x; // we remember how many attributes are due to this connection
        src->inc_num_spike_attributes(x);
}

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conditional_propagate()

void Connection::conditional_propagate

(

)

DEPRECATED. (Such connections should not be registered in the first place) Calls propagate only if the postsynaptic NeuronGroup exists on the local rank.

{
        if ( dst->evolve_locally() ) 
                propagate();
}

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evolve()

void Connection::evolve ( )

virtual

Evolve method to update internal connection state. Called by System run method.

Reimplemented in auryn::TripletConnection, auryn::LPTripletConnection, auryn::MinimalTripletConnection, auryn::STPConnection, auryn::TripletScalingConnection, auryn::STDPwdConnection, auryn::RateModulatedConnection, and auryn::STDPConnection.

{

}

finalize()

virtual void auryn::Connection::finalize ( )

pure virtual

Finalize Connection after initialization to prepare for use in simulation.

Implemented in auryn::SparseConnection, auryn::TripletConnection, auryn::LPTripletConnection, auryn::MinimalTripletConnection, auryn::STDPwdConnection, auryn::TripletScalingConnection, auryn::STDPConnection, auryn::FanOutConnection, auryn::AllToAllConnection, auryn::DuplexConnection, and auryn::IdentityConnection.

get()

virtual AurynWeight auryn::Connection::get ( NeuronID  i, NeuronID  j  )

pure virtual

Get weight value i,j if it exists. Otherwise the value is undefined.

Implemented in auryn::SparseConnection, auryn::FanOutConnection, auryn::AllToAllConnection, and auryn::IdentityConnection.

get_data()

virtual AurynWeight auryn::Connection::get_data ( NeuronID  i )

pure virtual

Return weight element as index in data array.

Implemented in auryn::SparseConnection, auryn::FanOutConnection, auryn::AllToAllConnection, and auryn::IdentityConnection.

get_destination()

NeuronGroup * Connection::get_destination

(

)

Returns pointer to the postsynaptic group.

{
        return dst;
}

get_file_name()

std::string Connection::get_file_name

(

)

Extracts the class name of the connection from the file name.

{
        std::string filename (strrchr(__FILE__, '/') ? strrchr(__FILE__, '/') + 1 : __FILE__);
        return filename;
}

get_log_name()

std::string Connection::get_log_name

(

)

Returns a string which is the combination of file and connection name for logging.

{
        std::stringstream oss;
        oss << get_name() << " ("
                << get_file_name() << "): ";
        return oss.str();
}

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get_m_rows()

NeuronID Connection::get_m_rows

(

)

Get number of rows (presynaptic) in connection.

Note that Matrices in Auryn have to be thought of as multiplied from the left. The number of rows thus corresponds to the maximum number of presynaptic cells.

{
        return m_rows;
}

get_n_cols()

NeuronID Connection::get_n_cols

(

)

Get number of columns (postsynaptic) in connection.

Note that Matrices in Auryn have to be thought of as multiplied from the left. The number of columns thus corresponds to the maximum number of postsynaptic cells.

{
        return n_cols;
}

get_name()

std::string Connection::get_name

(

)

Returns name of connection.

{
        return connection_name;
}

get_nonzero()

virtual AurynLong auryn::Connection::get_nonzero ( )

pure virtual

Return number of nonzero elements in this Connection.

Implemented in auryn::SparseConnection, auryn::IdentityConnection, auryn::FanOutConnection, and auryn::AllToAllConnection.

get_post_spikes()

SpikeContainer * Connection::get_post_spikes

(

)

Returns pointer to SpikeContainer for postsynaptic spikes on this node.

This corresponds to calling get_spikes_immediate() from the SpikingGroup. These spikes have been generated postsynaptically in the same timestep and have not been delayed yet. Equivalent to calling dst->get_spikes_immediate().

{
        return dst->get_spikes_immediate();
}

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get_post_state_trace()

Trace * Connection::get_post_state_trace	(	const string	state_name,
		const AurynDouble	tau,
		const AurynDouble	jump_size = 0.0
	)

Returns a pointer to a postsynaptic state trace object.

{
        return dst->get_post_state_trace(state_name, tau, jump_size);
}

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get_post_trace()

Trace * Connection::get_post_trace

(

const AurynDouble

tau

)

Returns a pointer to a postsynaptic trace object.

{
        return dst->get_post_trace(tau);
}

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get_pre_spikes()

SpikeContainer * Connection::get_pre_spikes

(

)

Supplies pointer to SpikeContainer of all presynaptic spikes.

This includes spikes from this group from all other nodes. This also means that these spikes have gone through the axonal dealy. Equivalent to calling src->get_spikes().

{
        return src->get_spikes();
}

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get_pre_trace()

Trace * Connection::get_pre_trace

(

const AurynDouble

tau

)

Returns a pointer to a presynaptic trace object.

{
        return src->get_pre_trace(tau);
}

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get_ptr()

virtual AurynWeight* auryn::Connection::get_ptr ( NeuronID  i, NeuronID  j  )

pure virtual

Return pointer to weight element i,j if it exists, otherwise return NULL.

Implemented in auryn::SparseConnection, auryn::FanOutConnection, auryn::AllToAllConnection, and auryn::IdentityConnection.

get_source()

SpikingGroup * Connection::get_source

(

)

Returns pointer to the presynaptic group.

{
        return src ;
}

get_spike_attribute()

AurynFloat Connection::get_spike_attribute	(	const NeuronID	i,
		const int	attribute_id = 0
	)

Returns spike attribute belonging to the spike at position i in the get_spikes() SpikeContainer.

{
        // We need to skip attributes by other Connection objects (spike_attribute_offset)
        // and other attributes from this Connection. Note that if attribute_id is larger
        // then number_of_spike_attributes the behavior will be undefined, but for performance
        // reasons we do not check for this here.
        NeuronID stackpos = spike_array_pos + (spike_attribute_offset+attribute_id)*src->get_spikes()->size();

        #ifdef DEBUG
        std::cout << "stack pos " << stackpos 
                << " value: " << std::setprecision(5) 
                << src->get_attributes()->at(stackpos) 
                << std::endl;
        #endif //DEBUG

        return src->get_attributes()->at(stackpos);
}

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get_target_vector()

AurynStateVector * Connection::get_target_vector

(

)

Returns target state vector if one is defined.

{
        return target_state_vector;
}

get_transmitter()

TransmitterType Connection::get_transmitter

(

)

Returns transmitter type.

This is one of Auryn default transmitter types. It essentially characterizes an array of a state vector to which this Connections weight will be added upon synaptic transmission.

{
        return trans;
}

init()

void Connection::init ( TransmitterType  transmitter = GLUT )

protected

{
        set_transmitter(transmitter);

        // set a default name based on the neuron group names
        std::stringstream s;
        s <<   src->get_name() 
                << " -> "
                << dst->get_name();
        set_name(s.str());

        // init default parameters
        number_of_spike_attributes = 0;

        // Here we store how many spike attributes have already been 
        // added to the stack due to other connections having the same
        // source SpikingGroup. 
        spike_attribute_offset = src->get_num_spike_attributes();
}

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load_from_file()

virtual bool auryn::Connection::load_from_file ( std::string  filename )

pure virtual

Implements load from file functionality. Also called in save_network_state from System class.

Implemented in auryn::SparseConnection, auryn::RateModulatedConnection, auryn::FanOutConnection, auryn::AllToAllConnection, and auryn::IdentityConnection.

propagate()

virtual void auryn::Connection::propagate ( )

pure virtual

Propagate method to propagate spikes. Called by System run method.

Implemented in auryn::SparseConnection, auryn::TripletConnection, auryn::LPTripletConnection, auryn::MinimalTripletConnection, auryn::STPConnection, auryn::TripletScalingConnection, auryn::STDPwdConnection, auryn::RateModulatedConnection, auryn::PairInteractionConnection, auryn::SymmetricSTDPConnection, auryn::DelayConnection, auryn::STDPConnection, auryn::FanOutConnection, auryn::AllToAllConnection, auryn::ABSConnection, auryn::IdentityConnection, and auryn::TripletDecayConnection.

safe_transmit()

void Connection::safe_transmit	(	NeuronID	id,
		AurynWeight	amount
	)

Same as transmit but first checks if the target neuron exists and avoids segfaults that way (but it's also slower).

{
        if ( dst->localrank(id) )
                transmit( id, amount );
}

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set()

virtual void auryn::Connection::set ( NeuronID  i, NeuronID  j, AurynWeight  value  )

pure virtual

Set existing weight element i,j with value.

Implemented in auryn::SparseConnection, auryn::FanOutConnection, auryn::AllToAllConnection, and auryn::IdentityConnection.

set_destination()

void Connection::set_destination

(

NeuronGroup *

source

)

Sets destination SpikingGroup of this connection.

{
        dst = destination;
}

set_name()

void Connection::set_name

(

std::string

name

)

Set name of connection.

The name will appear in error messages and save files

{
        connection_name = name;
}

set_receptor() [1/2]

void Connection::set_receptor

(

AurynStateVector *

ptr

)

Same as set_target.

{
        set_target(ptr);
}

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set_receptor() [2/2]

void Connection::set_receptor

(

string

state_name

)

Sets target state of this connection directly the name of a state vector.

{
        set_receptor(dst->get_state_vector(state_name));
}

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set_size()

void Connection::set_size	(	NeuronID	i,
		NeuronID	j
	)

{
        m_rows = i;
        n_cols = j;
}

set_source()

void Connection::set_source

(

SpikingGroup *

source

)

Sets source SpikingGroup of this connection.

{
        src = source;
}

set_target() [1/3]

void Connection::set_target

(

AurynWeight *

ptr

)

Sets target state of this connection directly via a pointer.

{
        target = ptr;
}

set_target() [2/3]

void Connection::set_target

(

AurynStateVector *

ptr

)

Sets target state of this connection directly via a StateVector.

{
        // get_state_vector and other functions return the NULL
        // vector, for instance, when the corresponding vector
        // has zero size. We catch that first.
        if ( ptr == NULL ) return; 
        target_state_vector = ptr;
        set_target(ptr->data);
}

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set_target() [3/3]

void Connection::set_target

(

string

state_name

)

Same as set_receptor.

{
        set_receptor(state_name);
}

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set_transmitter() [1/3]

void auryn::Connection::set_transmitter

(

AurynStateVector *

ptr

)

Same as set_target.

set_transmitter() [2/3]

void Connection::set_transmitter

(

TransmitterType

transmitter

)

Sets target state of this connection for a given receptor as one of Auryn's default transmitter types.

The most common transmitter types are GLUT and GABA. The postsynaptic NeuronGroup needs to make use of the g_ampa or g_gaba state vectors (AurynStateVector) for this to work.

{
        trans = transmitter;
        if ( dst->evolve_locally() ) {
                switch ( transmitter ) {
                        case GABA:
                                set_target(dst->get_default_inh_target());
                                break;
                        case MEM:
                                set_target(dst->get_state_vector("mem"));
                                break;
                        case CURSYN:
                                set_target(dst->get_state_vector("g_cursyn"));
                                break;
                        case NMDA:
                                set_target(dst->get_state_vector("g_nmda"));
                                break;
                        case GLUT:
                        case AMPA:
                        default:
                                set_target(dst->get_default_exc_target());
                }
        } else set_target((AurynWeight *)NULL);
}

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set_transmitter() [3/3]

void Connection::set_transmitter

(

string

state_name

)

Same as set_receptor, but DEPRECATED.

{
        set_receptor(state_name);
}

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stats()

virtual void auryn::Connection::stats ( AurynDouble &  mean, AurynDouble &  std, StateID  zid = 0  )

pure virtual

Computes mean synaptic weight and std dev of all weights in this connection.

Implemented in auryn::SparseConnection, auryn::FanOutConnection, auryn::AllToAllConnection, and auryn::IdentityConnection.

targeted_transmit()

void auryn::Connection::targeted_transmit ( SpikingGroup *  target_group, AurynStateVector *  target_state, const NeuronID  id, const AurynWeight  amount  )

inline

Transmits a spike to a given target group and state.

The method exposes the transmit interface and should not be used unless you know exactly what you are doing.

{
        const NeuronID localid = target_group->global2rank(id);
        target_state->data[localid]+=amount;
}

transmit()

void auryn::Connection::transmit ( const NeuronID  id, const AurynWeight  amount  )

inline

Default way to transmit a spike to a postsynaptic partner.

The method adds a given amount to the respective element in the target/transmitter array of the postsynaptic neuron specifeid by id. This is a new approach which replaces tadd to old method, increments transmitter specific state variables in neuron id. It turned out much faster that way, because the transmit function is one of the most often called function in the simulation and it can be efficiently inlined by the compiler.

{
        targeted_transmit(dst, target_state_vector, id, amount);
}

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virtual_serialize() [1/2]

virtual void auryn::Connection::virtual_serialize ( boost::archive::binary_oarchive &  ar, const unsigned int  version  )

inlineprotectedvirtual

Serialization function for saving the Connection state. Implement in derived classes to save additional information.

Reimplemented in auryn::SparseConnection, and auryn::DelayConnection.

        {
                ar & m_rows & n_cols & connection_name;
        }

virtual_serialize() [2/2]

virtual void auryn::Connection::virtual_serialize ( boost::archive::binary_iarchive &  ar, const unsigned int  version  )

inlineprotectedvirtual

Serialization function for loading the Connection state. Implement in derived classes to save additional information.

Reimplemented in auryn::SparseConnection, and auryn::DelayConnection.

        {
                ar & m_rows & n_cols & connection_name;
        }

write_to_file()

virtual bool auryn::Connection::write_to_file ( std::string  filename )

pure virtual

Implements save to file functionality. Also called in save_network_state from System class.

Implemented in auryn::SparseConnection, auryn::RateModulatedConnection, auryn::FanOutConnection, auryn::AllToAllConnection, and auryn::IdentityConnection.

Friends And Related Function Documentation

boost::serialization::access

friend class boost::serialization::access

friend

Member Data Documentation

dst

NeuronGroup* auryn::Connection::dst

Pointer to the destination group of this connection.

number_of_spike_attributes

NeuronID auryn::Connection::number_of_spike_attributes

protected

Number of spike attributes to expect with each spike transmitted through this connection.

Should only be set through methods called during init.

spike_attribute_offset

NeuronID auryn::Connection::spike_attribute_offset

protected

Stores spike attribute offset in attribute array.

src

SpikingGroup* auryn::Connection::src

Pointer to the source group of this connection.

target

AurynFloat* auryn::Connection::target

protected

A more direct reference on the first element of the target_state_vector.

The logic of connection is that when the simulation starts *target points to the first element of an array with AurynWeight type which has the post_size of the target group. Each presynaptic spike will then trigger addition the values stored as weights in some weight matrix to that group.

target_state_vector

AurynStateVector* auryn::Connection::target_state_vector

protected

trans

TransmitterType auryn::Connection::trans

protected

---

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

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