auryn::FileInputGroup Class Reference

Reads spikes from a ras file and emits them as SpikingGroup in a simulation. More...

#include <FileInputGroup.h>

Inheritance diagram for auryn::FileInputGroup:

Collaboration diagram for auryn::FileInputGroup:

Public Member Functions
	FileInputGroup (NeuronID n, string filename, bool loop=false, AurynFloat delay=0.0)
	Default constructor. More...
	FileInputGroup (NeuronID n)
	Constructor which does not load spikes. More...
virtual	~FileInputGroup ()
virtual void	evolve ()
	Virtual pure evolve function which needs to be implemented by derived classes. More...
void	set_loop_grid (AurynDouble grid_size)
	Aligned loop blocks to a temporal grid of this size. More...
void	load_spikes (std::string filename)
	Load spikes from file. More...
void	add_spike (double spiketime, NeuronID neuron_id=0)
	Adds a spike to the buffer manually and then temporally sorts the buffer. More...
void	sort_spikes ()
	Sorts spikes by time. More...
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
bool	playinloop
	Switch that activates the loop mode of FileInputGroup when set to true. More...
AurynTime	time_delay
	Time delay after each replay of the input pattern in loop mode (default 0s) 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

Additional Inherited Members
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...
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::SpikingGroup
static AurynTime *	clock_ptr = NULL

Detailed Description

Reads spikes from a ras file and emits them as SpikingGroup in a simulation.

FileInputGroup first reads the entire ras file into memory and emits the spikes then during the simulation without file access. It supports looping over the input spikes by setting the loop argument with the constructor to true.

Constructor & Destructor Documentation

FileInputGroup() [1/2]

FileInputGroup::FileInputGroup	(	NeuronID	n,
		std::string	filename,
		bool	loop = false,
		AurynFloat	delay = 0.0
	)

Default constructor.

: SpikingGroup( n , RANKLOCK )
{
        init();
        playinloop = loop;
        if ( playinloop ) set_loop_grid(auryn_timestep);
        time_delay = (AurynTime) (delay/auryn_timestep);
        time_offset = 0;
        load_spikes(filename);
}

Here is the call graph for this function:

FileInputGroup() [2/2]

FileInputGroup::FileInputGroup

(

NeuronID

n

)

Constructor which does not load spikes.

Use this constructor if you want to init the group without a filename containing spikes. Spikes can be added after initialization by calling load_spikes(filename) or by adding spikes one by one using add_spike(spiketime, neuron_id).

                                           : SpikingGroup(n, RANKLOCK ) 
{
        playinloop = false;
        time_delay = 0;
        time_offset = 0;
        init();
}

~FileInputGroup()

FileInputGroup::~FileInputGroup ( )

virtual

{
}

Member Function Documentation

add_spike()

void FileInputGroup::add_spike	(	double	spiketime,
		NeuronID	neuron_id = 0
	)

Adds a spike to the buffer manually and then temporally sorts the buffer.

Parameters

spiketime	the spike time
neuron_id	the neuron you want to spike with neuron_id < size of the group

{
                SpikeEvent_type event;
                event.time = spiketime/auryn_timestep;
                event.neuronID = neuron_id;
                input_spikes.push_back(event);
                sort_spikes();
}

Here is the call graph for this function:

evolve()

void FileInputGroup::evolve ( )

virtual

Virtual pure evolve function which needs to be implemented by derived classes.

The evolve function is called during simulations in every timestep by the System class. It updates the internal state of the spiking group and pushes spikes which are generated in this timestep to the axonal output delay (SpikeDelay).

Implements auryn::SpikingGroup.

{
        if (active && input_spikes.size()) {
                // when reset_time is reached reset the spike_iterator to The beginning and update time offset
                if ( sys->get_clock() == reset_time ) {
                        spike_iter = input_spikes.begin(); 
                        time_offset = sys->get_clock();
                        // std::cout << "set to" << reset_time*auryn_timestep << " " << time_offset << std::endl;
                }

                while ( spike_iter != input_spikes.end() && (*spike_iter).time <= get_offset_clock() ) {
                        spikes->push_back((*spike_iter).neuronID);
                        ++spike_iter;
                        // std::cout << "spike " << sys->get_time() << std::endl;
                }

                // TODO Fix the bug which eats the first spike
                if ( spike_iter==input_spikes.end() && reset_time < sys->get_clock() && playinloop ) { // at last spike on file set new reset time
                        // schedule reset for next grid point after delay
                        reset_time = get_next_grid_point(sys->get_clock());
                        // std::cout << "set rt" << reset_time << std::endl;
                }
        }
}

Here is the call graph for this function:

load_spikes()

void FileInputGroup::load_spikes

(

std::string

filename

)

Load spikes from file.

{
        std::ifstream spkfile;
        input_spikes.clear();

        if ( evolve_locally() ) {
                spkfile.open(filename.c_str(),std::ifstream::in);
                if (!spkfile) {
                        std::cerr << "Can't open input file " << filename << std::endl;
                        std::exit(1);
                }
        }

        char buffer[255];
        while ( spkfile.getline(buffer, 256) ) {
                SpikeEvent_type event;
                std::stringstream line ( buffer ) ;
                double t_tmp;
                line >> t_tmp;
                event.time = t_tmp/auryn_timestep;
                line >> event.neuronID;
                if ( localrank(event.neuronID) ) {
                        input_spikes.push_back(event);
                        // std::cout << event.time << std::endl;
                }
        }
        spkfile.close();

        sort_spikes();

        std::stringstream oss;
        oss << get_log_name() << ":: Finished loading " << input_spikes.size() 
                << " spike events";
        logger->info(oss.str());

        spike_iter = input_spikes.begin();
}

Here is the call graph for this function:

set_loop_grid()

void FileInputGroup::set_loop_grid

(

AurynDouble

grid_size

)

Aligned loop blocks to a temporal grid of this size.

The grid is applied after the delay. It's mostly there to facilitate the synchronization of certain events or readouts. If no grid is defined the last input spike time will define the end of the loop window (which often could be a fractional time).

{
        playinloop = true;
        if ( grid_size > 0.0 ) {
                loop_grid_size = 1.0/auryn_timestep*grid_size;
                if ( loop_grid_size == 0 ) loop_grid_size = 1;
        }
}

sort_spikes()

void FileInputGroup::sort_spikes

(

)

Sorts spikes by time.

Spikes need to be sorted befure a run otherwise the behavior of this SpikingGroup is undefined

{
        std::sort (input_spikes.begin(), input_spikes.end(), time_compare);
}

Here is the call graph for this function:

Member Data Documentation

playinloop

bool auryn::FileInputGroup::playinloop

Switch that activates the loop mode of FileInputGroup when set to true.

time_delay

AurynTime auryn::FileInputGroup::time_delay

Time delay after each replay of the input pattern in loop mode (default 0s)

---

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

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