auryn::IdentityConnection Class Reference

Provides a unity matrix like connectivity. More...

#include <IdentityConnection.h>

Inheritance diagram for auryn::IdentityConnection:

Collaboration diagram for auryn::IdentityConnection:

Public Member Functions
	IdentityConnection ()
	IdentityConnection (SpikingGroup *source, NeuronGroup *destination, AurynWeight weight=1.0, TransmitterType transmitter=GLUT, string name="Default IdentityConnection")
	IdentityConnection (SpikingGroup *source, NeuronGroup *destination, AurynWeight weight, NeuronID lo_row, NeuronID hi_row, NeuronID lo_col, NeuronID hi_col, TransmitterType transmitter=GLUT, string name="Cropped Identity Connection")
virtual	~IdentityConnection ()
virtual AurynWeight	get (NeuronID i, NeuronID j)
	Get weight value i,j if it exists. Otherwise the value is undefined. More...
virtual AurynWeight *	get_ptr (NeuronID i, NeuronID j)
	Return pointer to weight element i,j if it exists, otherwise return NULL. More...
virtual AurynWeight	get_data (NeuronID i)
	Return weight element as index in data array. More...
void	set_offset (int off)
void	set_every (NeuronID e)
virtual void	set_data (NeuronID i, AurynWeight value)
virtual void	set (NeuronID i, NeuronID j, AurynWeight value)
	Set existing weight element i,j with value. More...
void	finalize ()
	Finalize Connection after initialization to prepare for use in simulation. More...
AurynLong	get_nonzero ()
	Return number of nonzero elements in this Connection. More...
virtual void	propagate ()
	Propagate method to propagate spikes. Called by System run method. More...
virtual AurynDouble	sum ()
virtual void	stats (AurynDouble &mean, AurynDouble &std, StateID zid=0)
	Return stats for connection. More...
virtual bool	write_to_file (string filename)
	Implements save to file functionality. Also called in save_network_state from System class. More...
virtual bool	load_from_file (string filename)
	Implements load from file functionality. Also called in save_network_state from System class. More...
virtual AurynFloat	mean ()
std::vector< neuron_pair >	get_block (NeuronID lo_row, NeuronID lo_col, NeuronID hi_row, NeuronID hi_col)
Public Member Functions inherited from auryn::Connection
	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 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...
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...

Protected Member Functions
void	free ()
Protected Member Functions inherited from auryn::Connection
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)

Additional Inherited Members
Public Attributes inherited from auryn::Connection
SpikingGroup *	src
	Pointer to the source group of this connection. More...
NeuronGroup *	dst
	Pointer to the destination group of this connection. More...
Protected Attributes inherited from auryn::Connection
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...

Detailed Description

Provides a unity matrix like connectivity.

Constructor & Destructor Documentation

IdentityConnection() [1/3]

auryn::IdentityConnection::IdentityConnection

(

)

IdentityConnection() [2/3]

IdentityConnection::IdentityConnection	(	SpikingGroup *	source,
		NeuronGroup *	destination,
		AurynWeight	weight = 1.0,
		TransmitterType	transmitter = GLUT,
		std::string	name = "Default IdentityConnection"
	)

: Connection(source,destination,transmitter,name)
{
        init(weight);
}

IdentityConnection() [3/3]

IdentityConnection::IdentityConnection	(	SpikingGroup *	source,
		NeuronGroup *	destination,
		AurynWeight	weight,
		NeuronID	lo_row,
		NeuronID	hi_row,
		NeuronID	lo_col,
		NeuronID	hi_col,
		TransmitterType	transmitter = GLUT,
		std::string	name = "Cropped Identity Connection"
	)

: Connection(source,destination,transmitter)
{
        init(weight);
        lo_src = lo_row;
        hi_src = hi_row;
        lo_dst = lo_dst;
        hi_dst = hi_dst;
}

~IdentityConnection()

IdentityConnection::~IdentityConnection ( )

virtual

{
        free();
}

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Member Function Documentation

finalize()

void IdentityConnection::finalize ( )

virtual

Finalize Connection after initialization to prepare for use in simulation.

Implements auryn::Connection.

{
}

free()

void IdentityConnection::free ( )

protected

{
}

get()

AurynWeight IdentityConnection::get ( NeuronID  i, NeuronID  j  )

virtual

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

Implements auryn::Connection.

{
        if ( i == j ) return connection_weight;
        else return 0;
}

get_block()

std::vector< neuron_pair > IdentityConnection::get_block	(	NeuronID	lo_row,
		NeuronID	lo_col,
		NeuronID	hi_row,
		NeuronID	hi_col
	)

Returns a vector of ConnectionsID of a block specified by the arguments

{
        std::vector<neuron_pair> clist;
        for ( NeuronID i = lo_row ; i < hi_row ; ++i ) {
                for ( NeuronID j =  lo_col ; j < hi_col ; ++j ) {
                        if ( i == j ) {
                                neuron_pair a;
                                a.i = i;
                                a.j = j;
                                clist.push_back( a );
                        }
                }
        }
        return clist;
}

get_data()

AurynWeight IdentityConnection::get_data ( NeuronID  i )

virtual

Return weight element as index in data array.

Implements auryn::Connection.

{
        return 0;
}

get_nonzero()

AurynLong IdentityConnection::get_nonzero ( )

virtual

Return number of nonzero elements in this Connection.

Implements auryn::Connection.

{
        return std::min(src->get_pre_size(),dst->get_post_size());
}

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get_ptr()

AurynWeight * IdentityConnection::get_ptr ( NeuronID  i, NeuronID  j  )

virtual

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

Implements auryn::Connection.

{
        if ( i == j ) return &connection_weight;
        else return NULL;
}

load_from_file()

bool IdentityConnection::load_from_file ( string  filename )

virtual

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

Implements auryn::Connection.

{
        return true; // TODO fake but what else ? 
}

mean()

AurynFloat IdentityConnection::mean ( )

virtual

{
        AurynDouble m,s;
        stats(m,s);
        return m;
}

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propagate()

void IdentityConnection::propagate ( )

virtual

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

Implements auryn::Connection.

{
        SpikeContainer::const_iterator spikes_end = src->get_spikes()->end();
        for (SpikeContainer::const_iterator spike = src->get_spikes()->begin() ;
                        spike != spikes_end ; ++spike ) {
                if ( *spike%every == 0 )
                        safe_transmit( ( *spike/every ) + offset , connection_weight ); 
                // IMPORTANT the use of safe_transmit
                // is important here since there is 
                // no weight matrix with only the 
                // corresponding columns
        }
}

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set()

void IdentityConnection::set ( NeuronID  i, NeuronID  j, AurynWeight  value  )

virtual

Set existing weight element i,j with value.

Implements auryn::Connection.

{
}

set_data()

void IdentityConnection::set_data ( NeuronID  i, AurynWeight  value  )

virtual

{
}

set_every()

void IdentityConnection::set_every

(

NeuronID

e

)

{
        if ( e != 0 ) {
                every = e;
                auryn::logger->parameter("every",(int)every);
        }
}

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set_offset()

void IdentityConnection::set_offset

(

int

off

)

{
        offset = off;
        auryn::logger->parameter("offset",(int)offset);
}

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stats()

void IdentityConnection::stats ( AurynDouble &  mean, AurynDouble &  std, StateID  zid = 0  )

virtual

Return stats for connection.

Note that IdentityConnection does not support complex matrix states yet

Implements auryn::Connection.

{
        mean = connection_weight;
        std = 0;
}

sum()

AurynDouble IdentityConnection::sum ( )

virtual

{
        return connection_weight*get_nonzero();
}

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write_to_file()

bool IdentityConnection::write_to_file ( string  filename )

virtual

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

Implements auryn::Connection.

{
        return true; // TODO fake but what else ? 
}

---

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

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