auryn::VoltageMonitor Class Reference

Records the membrane potential from one unit from the source neuron group to a file. More...

#include <VoltageMonitor.h>

Inheritance diagram for auryn::VoltageMonitor:

Collaboration diagram for auryn::VoltageMonitor:

Public Member Functions
	VoltageMonitor (NeuronGroup *source, NeuronID id, string filename, AurynDouble stepsize=auryn_timestep)
virtual	~VoltageMonitor ()
void	execute ()
Public Member Functions inherited from auryn::StateMonitor
	StateMonitor (SpikingGroup *source, NeuronID id, string statename, string filename, AurynDouble sampling_interval=auryn_timestep)
	Standard constructor. More...
	StateMonitor (AurynStateVector *state, NeuronID id, string filename, AurynDouble sampling_interval=auryn_timestep)
	Alternative constructor. More...
	StateMonitor (AurynSynStateVector *state, NeuronID id, string filename, AurynDouble sampling_interval=auryn_timestep)
	Alternative constructor for synaptic states. More...
	StateMonitor (Trace *trace, NeuronID id, string filename, AurynDouble sampling_interval=auryn_timestep)
	Trace constructor. More...
void	record_for (AurynDouble time=10.0)
	Sets relative time at which to stop recording. More...
void	set_stop_time (AurynDouble time=10.0)
	Set an absolute time when to stop recording. More...
void	set_step_size (int step=1)
	Sets the step size. More...
virtual	~StateMonitor ()
Public Member Functions inherited from auryn::Monitor
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...
Public Member Functions inherited from auryn::Device
	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 ()

Public Attributes
AurynTime	paste_spikes
	Paste spikes switch (default = true) More...
Public Attributes inherited from auryn::StateMonitor
bool	enable_compression
	Switch to enable/disable output compression. More...
Public Attributes inherited from auryn::Monitor
bool	active
	Standard active switch. More...
Public Attributes inherited from auryn::Device
bool	active
	Standard active switch. More...

Protected Member Functions
void	init ()
	Standard initialization. More...
Protected Member Functions inherited from auryn::StateMonitor
void	init (string filename, AurynDouble stepsize)
	Standard initialization. More...
Protected Member Functions inherited from auryn::Monitor
virtual void	open_output_file (std::string filename)
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::Device
void	init ()
	Standard initializer to be called by the constructor. More...

Additional Inherited Members
Protected Attributes inherited from auryn::StateMonitor
SpikingGroup *	src
	The source SpikingGroup to record from. More...
AurynState *	target_variable
	Target variable. More...
AurynState	lastval
	Last value (used for compression) More...
AurynState	lastder
NeuronID	nid
	The source neuron id to record from. More...
AurynTime	ssize
	The step size (sampling interval) in units of auryn_timestep. More...
AurynTime	t_stop
	Defines the maximum recording time in AurynTime to save space. More...
Protected Attributes inherited from auryn::Monitor
std::ofstream	outfile
std::string	fname
std::string	default_file_extension
Protected Attributes inherited from auryn::Device
std::string	device_name
	Identifying name for device. More...

Detailed Description

Records the membrane potential from one unit from the source neuron group to a file.

The Monitor records the membrane potential of a single cell from a NeuronGroup. Per default the timestep is simulator precision and the Monitor pastes a spike of height VOLTAGEMONITOR_PASTED_SPIKE_HEIGHT by reading out the the current spikes. For performance it is adviced to use the StateMonitor which does not do any spike pasting.

Constructor & Destructor Documentation

VoltageMonitor()

VoltageMonitor::VoltageMonitor	(	NeuronGroup *	source,
		NeuronID	id,
		std::string	filename,
		AurynDouble	stepsize = auryn_timestep
	)

                                                                                                          : StateMonitor(source, id, "mem", filename, stepsize)
{
        if ( !source->localrank(id) ) return; // do not anything if the neuron is not on the local rank
        gid = id; // we also need the global id to scan for spikes, but StateMonitor only sets the rank id (nid)
        init();
}

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~VoltageMonitor()

VoltageMonitor::~VoltageMonitor ( )

virtual

{
}

Member Function Documentation

execute()

void VoltageMonitor::execute ( )

virtual

Virtual execute function to be called at the end of central simulation loop in System

Reimplemented from auryn::StateMonitor.

{
        if ( auryn::sys->get_clock() < t_stop ) {
                // we output spikes irrespectively of the sampling interval, because 
                // the membrane potential isn't a smooth function for most IF models when
                // they spike, so it's easy to "miss" a spike otherwise
                double voltage = *target_variable;
                if ( paste_spikes ) {
                        SpikeContainer * spikes = src->get_spikes_immediate();
                        for ( int i = 0 ; i < spikes->size() ; ++i ) {
                                if ( spikes->at(i) == gid ) {
                                        voltage = VOLTAGEMONITOR_PASTED_SPIKE_HEIGHT;
                                        outfile << (auryn::sys->get_time()) << " " << voltage << "\n";
                                        return;
                                }
                        }
                }
                if ( (auryn::sys->get_clock())%ssize==0 )
                        outfile << (auryn::sys->get_time()) << " " << voltage << "\n";
        }
}

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init()

void VoltageMonitor::init ( )

protected

Standard initialization.

{
        paste_spikes = true;
        target_variable = src->get_state_vector("mem")->ptr(nid);
}

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Member Data Documentation

paste_spikes

AurynTime auryn::VoltageMonitor::paste_spikes

Paste spikes switch (default = true)

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

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