#include <SpikeTimingStimGroup.h>

Inheritance diagram for auryn::SpikeTimingStimGroup:

Collaboration diagram for auryn::SpikeTimingStimGroup:

Public Member Functions
	SpikeTimingStimGroup (NeuronID n, string filename, string stimfile, StimulusGroupModeType stimulusmode=RANDOM, AurynFloat timeframe=0.0)
	Default constructor. More...

	SpikeTimingStimGroup (NeuronID n, string stimfile, StimulusGroupModeType stimulusmode=RANDOM, AurynFloat timeframe=0.0)
	Constructor without stimfile. Patterns can be loaded afterwards using the load_patterns method. More...

virtual	~SpikeTimingStimGroup ()

virtual void	evolve ()

Public Member Functions inherited from auryn::StimulusGroup
virtual unsigned int	get_num_stimuli ()
	Returns number of stimuli. More...

	StimulusGroup (NeuronID n, string filename, string stimfile, StimulusGroupModeType stimulusmode=RANDOM, AurynFloat baserate=1.0)
	Default constructor. More...

	StimulusGroup (NeuronID n, string stimfile, StimulusGroupModeType stimulusmode=RANDOM, AurynFloat baserate=1.0)
	Constructor without pattern file. Patterns can be loaded afterwards using the load_patterns method. More...

virtual	~StimulusGroup ()

void	set_baserate (AurynFloat baserate)
	Sets the baserate that is the rate at 1 activity. More...

void	set_maxrate (AurynFloat baserate)
	TODO. More...

void	set_stimulation_mode (StimulusGroupModeType mode)
	Sets the stimulation mode. Can be any of StimulusGroupModeType (MANUAL,RANDOM,SEQUENTIAL,SEQUENTIAL_REV). More...

void	set_all (AurynFloat val=0.0)
	Sets sets the activity of all units. More...

void	seed (int rndseed)
	Seeds the random number generator for all stimulus groups of the simulation. More...

AurynFloat	get_activity (NeuronID i)
	Gets the activity of unit i. More...

virtual void	load_patterns (string filename)
	Loads stimulus patterns from a designated pat file given. More...

virtual void	clear_patterns ()
	Clear stimulus patterns. More...

void	set_mean_off_period (AurynFloat period)
	Set mean quiet interval between consecutive stimuli. More...

void	set_mean_on_period (AurynFloat period)
	Set mean on period. More...

void	set_pattern_activity (unsigned int i)
	Function that loops over the stimulus/pattern vector and sets the activity verctor to the gamma values given with the pattern. More...

void	set_pattern_activity (unsigned int i, AurynFloat setval)
	Function that loops over the stimulus/pattern vector and sets the activity verctor to the given value. More...

virtual void	set_active_pattern (unsigned int i)
	This function is called internally and sets the activity level to a given active stimulus. More...

void	set_active_pattern (unsigned int i, AurynFloat default_value)
	This function is called internally and sets the activity level to a given active stimulus. More...

void	set_next_action_time (double time)

void	set_distribution (std::vector< double > probs)
	Setter for pattern probability distribution. More...

std::vector< double >	get_distribution ()
	Getter for pattern probability distribution. More...

double	get_distribution (int i)
	Getter for pattern i of the probability distribution. More...

unsigned int	get_stim_count ()
	Returns number of stimuli shown. More...

AurynTime	get_last_action_time ()
	returns the last action (stim on/off) time in units of AurynTime More...

AurynTime	get_last_onset_time ()
	returns the last stimulus onset time in units of AurynTime More...

AurynTime	get_last_offset_time ()
	returns the last stimulus offset time in units of AurynTime More...

AurynTime	get_next_action_time ()
	returns the next action (stim on/off) time in units of AurynTime More...

unsigned int	get_cur_stim ()
	returns the index of the current (or last – if not active anymore) active stimulus More...

bool	get_stim_active ()
	Returns true if currently a stimulus is active and false otherwise. More...

void	flat_distribution ()

void	normalize_distribution ()

std::vector< type_pattern > *	get_patterns ()

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 ()

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
AurynDouble	refractory_period
	Refractory period. More...

Public Attributes inherited from auryn::StimulusGroup
int	cur_stim_index
	Current stimulus index. More...

bool	stimulus_active
	Current stimulus active. More...

std::vector< type_pattern >	stimuli
	Vector containing all the stimuli. More...

AurynFloat	scale
	This is by how much the pattern gamma value is multiplied. The resulting value gives the x-times baseline activation. More...

bool	binary_patterns
	Switches to more efficient algorithm which ignores the gamma value. More...

AurynTime	refractory_period
	Enables a finite refractory time specified in AurynTime (only works for non-binary-pattern mode. More...

bool	randomintervals
	Determines if the Group is using random activation intervals. More...

bool	randomintensities
	Determines if the Group is using random activation intensities. More...

AurynDouble	background_rate
	Play random Poisson noise with this rate on all channels when no stim is active. More...

bool	background_during_stimulus
	Switch for background firing during stimulus. More...

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
virtual void	redraw ()

Protected Member Functions inherited from auryn::StimulusGroup
void	init (StimulusGroupModeType stimulusmode, string stimfile, AurynFloat baserate)

void	write_stimulus_file (AurynDouble time)

void	read_next_stimulus_from_file (AurynDouble &time, int &active, int &stimulusid)

void	set_activity (NeuronID i, AurynFloat val=0.0)

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...

Additional Inherited Members
Protected Attributes inherited from auryn::StimulusGroup
AurynTime *	ttl

AurynFloat *	activity

StimulusGroupModeType	stimulus_order

unsigned int	stimulation_count
	Counter variable for number of stimuli shown. More...

NeuronID	fgx

NeuronID	bgx

std::vector< double >	probabilities

AurynTime	next_action_time
	next stimulus time requiring change in rates More...

AurynTime	last_action_time
	last stimulus time requiring change in rates More...

AurynTime	last_stim_onset_time
	last stimulus onset time More...

AurynTime	last_stim_offset_time
	last stimulus offset time More...

AurynFloat	mean_off_period

AurynFloat	mean_on_period

AurynFloat	curscale

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

Static Protected Attributes inherited from auryn::StimulusGroup
static boost::mt19937	poisson_gen = boost::mt19937()

static boost::mt19937	order_gen = boost::mt19937()

static boost::uniform_01< boost::mt19937 >	order_die = boost::uniform_01<boost::mt19937> (order_gen)

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

Constructor & Destructor Documentation

◆ SpikeTimingStimGroup() [1/2]

SpikeTimingStimGroup::SpikeTimingStimGroup	(	NeuronID	n,
		std::string	filename,
		std::string	stimfile,
		StimulusGroupModeType	stimulusmode = `RANDOM`,
		AurynFloat	timeframe = `0.0`
	)

Default constructor.

                                                                                                                                                        : StimulusGroup( n, filename, stimfile, stimulusmode, timeframe ) 
 {
         init();
 }

◆ SpikeTimingStimGroup() [2/2]

SpikeTimingStimGroup::SpikeTimingStimGroup	(	NeuronID	n,
		std::string	stimfile,
		StimulusGroupModeType	stimulusmode = `RANDOM`,
		AurynFloat	timeframe = `0.0`
	)

Constructor without stimfile. Patterns can be loaded afterwards using the load_patterns method.

                                                                                                                                    : StimulusGroup( n, stimfile, stimulusmode, timeframe ) 
 {
         init();
 }

◆ ~SpikeTimingStimGroup()

SpikeTimingStimGroup::~SpikeTimingStimGroup ( )

virtual

42 {

43 }

Member Function Documentation

◆ evolve()

void SpikeTimingStimGroup::evolve ( )

virtual

Standard virtual evolve function

Reimplemented from auryn::StimulusGroup.

 {
         if ( !active ) return;
 
         if ( stimulus_active  ) { // during active stimulation
 
                 for ( NeuronID i = 0; i < get_rank_size() ; ++i ) {
                         // if ( ttl[i] ) { // DEBUG
                         //      std::cout << ttl[i] << " " << sys->get_clock() << std::endl;
                         // }
                         if ( ttl[i] == sys->get_clock() ) {
                                 push_spike(i);
                         }
                 }
 
         } else { // while stimulation is off
                 if ( background_rate ) {
                         boost::exponential_distribution<> dist(background_rate);
                         boost::variate_generator<boost::mt19937&, boost::exponential_distribution<> > die(poisson_gen, dist);
 
                         while ( bgx < get_rank_size() ) {
                                 push_spike ( bgx );
                                 AurynDouble r = die();
                                 bgx += 1+(NeuronID)(r/auryn_timestep); 
                         }
                         bgx -= get_rank_size();
                 }
         }
 
         // update stimulus properties
         if ( auryn::sys->get_clock() >= next_action_time ) { // action required
                 last_action_time = next_action_time; // store last time before updating next_action_time
 
                 if ( stimuli.size() == 0 ) {
                         set_next_action_time(10); // TODO make this a bit smarter at some point -- i.e. could send this to the end of time 
                         return;
                 }
 
                 write_stimulus_file(auryn_timestep*(auryn::sys->get_clock()));
 
                 if ( stimulus_order == STIMFILE )  {
                         AurynDouble t = 0.0;
                         int a,i;
                         while ( t <= auryn::sys->get_time() ) {
                                 read_next_stimulus_from_file(t,a,i);
                                 next_action_time = (AurynTime) (t/auryn_timestep);
                                 if (a==0) stimulus_active = true; 
                                         else stimulus_active = false;
                                 cur_stim_index = i;
                                 // std::cout << auryn::sys->get_time() << " " << t << " " << a << " " << i << std::endl;
                         }
                 } else { // we have to generate stimulus times
 
                         if ( stimulus_active ) { // stimulus was active and going inactive now
 
                                 set_all( 0.0 ); // turns off currently active stimulus 
                                 stimulus_active = false ;
                                 last_stim_offset_time = sys->get_clock();
 
                                 if ( randomintervals ) {
                                         boost::exponential_distribution<> dist(1./mean_off_period);
                                         boost::variate_generator<boost::mt19937&, boost::exponential_distribution<> > die(order_gen, dist);
                                         next_action_time = auryn::sys->get_clock() + (AurynTime)(std::max(0.0,die()+refractory_period)/auryn_timestep);
                                 } else {
                                         next_action_time = auryn::sys->get_clock() + (AurynTime)((mean_off_period+refractory_period)/auryn_timestep);
                                 }
                         } else { // stimulus was not active and is going active now
                                 if ( active && stimuli.size() ) { // the group is active and there are stimuli in the array
 
                                         // chooses stimulus according to schema specified in stimulusmode
                                         double draw, cummulative;
                                         switch ( stimulus_order ) {
                                                 case RANDOM:
                                                         // TODO make this less greedy 
                                                         // and do not compute this every draw
                                                         draw = order_die();
                                                         cummulative = 0; 
                                                         stimulation_count++;
                                                         cur_stim_index = 0;
                                                         // std::cout.precision(5);
                                                         // std::cout << " draw " << draw <<  std::endl;
                                                         for ( unsigned int i = 0 ; i < probabilities.size() ; ++i ) {
                                                                 cummulative += probabilities[i];
                                                                 // std::cout << cummulative << std::endl;
                                                                 if ( draw <= cummulative ) {
                                                                         cur_stim_index = i;
                                                                         break;
                                                                 }
                                                         }
                                                 break;
                                                 case SEQUENTIAL:
                                                         cur_stim_index = (cur_stim_index+1)%stimuli.size();
                                                 break;
                                                 case SEQUENTIAL_REV:
                                                         --cur_stim_index;
                                                         if ( cur_stim_index <= 0 ) 
                                                                 cur_stim_index = stimuli.size() - 1 ;
                                                 break;
                                                 case MANUAL:
                                                 default:
                                                 break;
                                         }
 
                                         // sets the activity
                                         set_active_pattern( cur_stim_index, 1e20 ); // puts default spikes into the not forseeable future
                                         stimulus_active = true;
                                         last_stim_onset_time = sys->get_clock();
 
                                         next_action_time = auryn::sys->get_clock() + (AurynTime)(mean_on_period/auryn_timestep);
                                 }
                         }
                         write_stimulus_file(auryn_timestep*(auryn::sys->get_clock()+1));
                 }
         }
 }

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◆ redraw()

void SpikeTimingStimGroup::redraw ( )

protectedvirtual

Draw all Time-To-Live (ttls) typically after changing the any of the activiteis

Reimplemented from auryn::StimulusGroup.

 {
         for ( NeuronID i = 0; i < get_rank_size() ; ++i ) {
                 ttl[i] = sys->get_clock() + activity[i]/auryn_timestep;
         }
 }

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Member Data Documentation

◆ refractory_period

AurynDouble auryn::SpikeTimingStimGroup::refractory_period

Refractory period.

Refractory period in seconds gets adde to the potentially stochastic off time and ensures a minimum interval between stimuli.

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

/home/zenke/auryn/src/auryn/SpikeTimingStimGroup.h
/home/zenke/auryn/src/auryn/SpikeTimingStimGroup.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members