auryn::BurstRateMonitor Class Reference

Monitor class to record population firing rates. More...

#include <BurstRateMonitor.h>

Inheritance diagram for auryn::BurstRateMonitor:

Collaboration diagram for auryn::BurstRateMonitor:

Public Member Functions
	BurstRateMonitor (SpikingGroup *source, string filename="", AurynDouble binsize=0.1)
	Default Constructor. More...
virtual	~BurstRateMonitor ()
	Default Destructor. More...
void	set_tau (double tau)
	Sets burst detector time constant. More...
void	execute ()
	Implementation of necessary execute() function. More...

Public Attributes
AurynStateVector *	burst_state
	Burst state. More...

Protected Member Functions
void	init (SpikingGroup *source, string filename, AurynDouble binsize)
	Default init method. More...
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)
Protected Member Functions inherited from auryn::Monitor
virtual void	open_output_file (std::string filename)
virtual void	flush ()
	Flush to file. More...
	Monitor (std::string filename, std::string default_extension="dat")
	Standard constructor with file name. More...
	Monitor ()
	Constructor which does not open a text file for output. More...
std::string	generate_filename (std::string name_hint="")
	Generates a default filename from the device ID. More...
virtual	~Monitor ()
	Standard destructor. More...
Protected Member Functions inherited from auryn::Device
void	init ()
	Standard initializer to be called by the constructor. More...
	Device ()
	Standard constructor. More...
void	set_name (std::string s)
	Set device name. More...
std::string	get_name ()
	Get device name. More...
int	get_id ()
	Get numeric device id. More...
virtual	~Device ()
	Standard destructor. More...
virtual void	evolve ()

Protected Attributes
SpikingGroup *	src
	The source SpikingGroup. More...
Protected Attributes inherited from auryn::Monitor
std::ofstream	outfile
std::string	fname
std::string	default_file_extension
bool	active
	Standard active switch. More...
Protected Attributes inherited from auryn::Device
std::string	device_name
	Identifying name for device. More...
bool	active
	Standard active switch. More...

Detailed Description

Monitor class to record population firing rates.

Instances of this class record the population firing rate of the src SpikingGroup assigned. Binning is done discretely in bins of size bsize that is directly transformed in discrete AurynTime steps. The default

Constructor & Destructor Documentation

BurstRateMonitor()

BurstRateMonitor::BurstRateMonitor	(	SpikingGroup *	source,
		std::string	filename = "",
		AurynDouble	binsize = 0.1
	)

Default Constructor.

Parameters

                                                                                                 : Monitor(filename)
{
        init(source,filename,binsize);
}

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~BurstRateMonitor()

BurstRateMonitor::~BurstRateMonitor ( )

virtual

Default Destructor.

{
}

Member Function Documentation

execute()

void BurstRateMonitor::execute ( )

virtual

Implementation of necessary execute() function.

Reimplemented from auryn::Device.

{
        if ( src->evolve_locally() ) {

                // loop over all spikes to separate events from bursts
                SpikeContainer::const_iterator spk;
                for ( spk = src->get_spikes_immediate()->begin() ; 
                                spk < src->get_spikes_immediate()->end() ; 
                                ++spk ) {

                        const NeuronID s = src->global2rank(*spk);

                        // detect first spike in bursts and non-burst spikes 
                        if ( post_trace->get(s) < thr ) { 
                                ++event_counter;
                                burst_state->set(s,-1.0);
                        } else // detect second spike in burst
                        if ( burst_state->get(s) < 0.0 ) { 
                                ++burst_counter;
                                burst_state->set(s,1);
                        }
                }


                // record to file every now and then
                if (auryn::sys->get_clock()%ssize==0) {
                        const double burst_rate = scaleconst*burst_counter;
                        const double event_rate = scaleconst*event_counter;
                        burst_counter = 0;
                        event_counter = 0;
                        // outfile << std::setiosflags(ios::fixed) << std::setprecision(3);
                        outfile << auryn::sys->get_time() 
                                << " " << burst_rate 
                                << " " << event_rate << "\n";
                }

                // last_post_val->copy(post_trace);
        }
}

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init()

void BurstRateMonitor::init ( SpikingGroup *  source, std::string  filename, AurynDouble  binsize  )

protected

Default init method.

{
        auryn::sys->register_device(this);

        src = source;
        scaleconst = 1.0/binsize/src->get_rank_size();
        ssize = (1.0*binsize/auryn_timestep);
        if ( ssize < 1 ) ssize = 1;
        event_counter = 0;
        burst_counter = 0;

        const double default_tau = 16e-3;
        post_trace = src->get_post_trace(default_tau);
        burst_state = src->get_state_vector("_burst_state");

        set_tau(default_tau);
        thr = 1.0+std::exp(-1.0);


        std::stringstream oss;
        oss << "BurstRateMonitor:: Setting binsize " << binsize << "s";
        auryn::logger->msg(oss.str(),NOTIFICATION);

}

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set_tau()

void BurstRateMonitor::set_tau

(

double

tau

)

Sets burst detector time constant.

{
        post_trace->set_timeconstant(tau);
}

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virtual_serialize() [1/2]

void BurstRateMonitor::virtual_serialize ( boost::archive::binary_oarchive &  ar, const unsigned int  version  )

protectedvirtual

Functions necesssary for serialization and loading saving to netstate files.

Reimplemented from auryn::Monitor.

{
        ar & burst_counter ;
        ar & event_counter ;
}

virtual_serialize() [2/2]

void BurstRateMonitor::virtual_serialize ( boost::archive::binary_iarchive &  ar, const unsigned int  version  )

protectedvirtual

Reimplemented from auryn::Monitor.

{
        ar & burst_counter ;
        ar & event_counter ;
}

Member Data Documentation

burst_state

AurynStateVector* auryn::BurstRateMonitor::burst_state

Burst state.

src

SpikingGroup* auryn::BurstRateMonitor::src

protected

The source SpikingGroup.

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

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