#include <pynn.hpp>

Inheritance diagram for cypress::PyNN:

Collaboration diagram for cypress::PyNN:

Classes
class	PyNNSimulatorNotFound

Public Member Functions
	PyNN (const std::string &simulator, const Json &setup=Json())

	~PyNN () override

Real	timestep ()

std::unordered_set< const NeuronType * >	supported_neuron_types () const override

std::string	name () const override

const std::string &	simulator () const

const std::string &	normalised_simulator () const

const std::vector< std::string > &	imports () const

std::string	nmpi_platform () const

Json	setup () const

void	run (NetworkBase &network, Real duration=0.0) const

Static Public Member Functions
static std::vector< std::string >	simulators ()

static std::string	get_import (const std::vector< std::string > &imports, const std::string &simulator)

static int	get_pynn_version ()

static int	get_neo_version ()

static py::dict	json_to_dict (Json json)

static std::string	get_neuron_class (const NeuronType &neuron_type)

static void	init_logger ()

static py::object	create_source_population (const PopulationBase &pop, py::module &pynn)

static py::object	create_homogeneous_pop (const PopulationBase &pop, py::module &pynn, bool &init_available)

static void	set_inhomogeneous_parameters (const PopulationBase &pop, py::object &pypop, bool init_available=false)

static void	set_homogeneous_rec (const PopulationBase &pop, py::object &pypop)

static void	set_inhomogenous_rec (const PopulationBase &pop, py::object &pypop, py::module &pynn)

static py::object	get_pop_view (const py::module &pynn, const py::object &py_pop, const PopulationBase &c_pop, const size_t &start, const size_t &end)

static py::object	get_connector7 (const ConnectionDescriptor &conn, const py::module &pynn)

static py::object	get_connector (const std::string &connector_name, const py::module &pynn, const Real &additional_parameter, const bool allow_self_connections)

static py::object	group_connect (const std::vector< PopulationBase > &populations, const std::vector< py::object > &pypopulations, const ConnectionDescriptor &conn, const py::module &pynn, const bool nest_flag, const Real timestep=0.0)

static py::object	group_connect (const std::vector< PopulationBase > &populations, const std::vector< py::object > &pypopulations, const ConnectionDescriptor &conn, const py::module &pynn, const Real nest_flag)=delete

static py::object	group_connect7 (const std::vector< PopulationBase > &populations, const std::vector< py::object > &pypopulations, const ConnectionDescriptor &conn, const py::module &pynn)

static std::tuple< py::object, py::object >	list_connect (const std::vector< py::object > &pypopulations, const ConnectionDescriptor conn, const py::module &pynn, const bool current_based, const Real timestep=0.0)

static std::tuple< py::object, py::object >	list_connect (const std::vector< py::object > &pypopulations, const ConnectionDescriptor conn, const py::module &pynn, const Real current_based)=delete

static std::tuple< py::object, py::object >	list_connect7 (const std::vector< py::object > &pypopulations, const ConnectionDescriptor conn, const py::module &pynn)

template<typename T >
static Matrix< T >	matrix_from_numpy (const py::object &object, bool transposed=false)

static void	fetch_data_nest (const std::vector< PopulationBase > &populations, const std::vector< py::object > &pypopulations)

static void	fetch_data_spinnaker (const std::vector< PopulationBase > &populations, const std::vector< py::object > &pypopulations)

static void	fetch_data_neo (const std::vector< PopulationBase > &populations, const std::vector< py::object > &pypopulations)

static void	spikey_run (NetworkBase &source, Real duration, py::module &pynn, py::dict dict)

static py::object	spikey_create_source_population (const PopulationBase &pop, py::module &pynn)

static py::object	spikey_create_homogeneous_pop (const PopulationBase &pop, py::module &pynn)

static void	spikey_set_homogeneous_rec (const PopulationBase &pop, py::object &pypop, py::module &pynn)

static void	spikey_set_inhomogeneous_rec (const PopulationBase &pop, py::object &pypop, py::module pynn)

static void	spikey_set_inhomogeneous_parameters (const PopulationBase &pop, py::object &pypop)

static void	spikey_get_spikes (PopulationBase pop, py::object &pypop)

static void	spikey_get_voltage (NeuronBase neuron, py::module &pynn)

Protected Member Functions
void	do_run (NetworkBase &network, Real duration) const override

Protected Attributes
std::string	m_simulator

std::string	m_normalised_simulator

std::vector< std::string >	m_imports

bool	m_keep_log

Json	m_setup

Detailed Description

The Backend class is an abstract base class which provides the facilities for network execution.

Constructor & Destructor Documentation

cypress::PyNN::PyNN	(	const std::string &	simulator,
		const Json &	setup = `Json()`
	)

Constructor of the PyNN backend. Throws an exception if the given PyNN backend does not exist.

Parameters

simulator	is the name of the simulator backend to be used by PyNN. Use the static backends method to list available backends.
setup	contains additional setup information that should be passed to the backend.

cypress::PyNN::~PyNN ( )

override

Destructor of the PyNN class.

Member Function Documentation

static py::object cypress::PyNN::create_homogeneous_pop	(	const PopulationBase &	pop,
		py::module &	pynn,
		bool &	init_available
	)

static

Creates a PyNN population with homogeneous parameters, inhomogeneous parameters can be set with set_inhomogeneous_parameters afterwards.

Parameters

pop	The cypress population
pynn	the PyNN instance

Returns: handler for the PyNN population

static py::object cypress::PyNN::create_source_population	(	const PopulationBase &	pop,
		py::module &	pynn
	)

static

Creates a PyNN source population

Parameters

pop	The cypress population
pynn	the PyNN instance

Returns: handler for the PyNN population

void cypress::PyNN::do_run	(	NetworkBase &	network,
		Real	duration
	)		const

overrideprotectedvirtual

Abstract method which has to be implemented by the backend.

Implements cypress::Backend.

static void cypress::PyNN::fetch_data_neo	(	const std::vector< PopulationBase > &	populations,
		const std::vector< py::object > &	pypopulations
	)

static

Fetch all data (spikes, traces) from NEO. This is a general method

Parameters

populations	Cypress populations
pypopulations	PyNN populations

static void cypress::PyNN::fetch_data_nest	(	const std::vector< PopulationBase > &	populations,
		const std::vector< py::object > &	pypopulations
	)

static

Fetch all data (spikes, traces) from nest. This is faster than using NEO.

Parameters

populations	Cypress populations
pypopulations	PyNN populations

static void cypress::PyNN::fetch_data_spinnaker	(	const std::vector< PopulationBase > &	populations,
		const std::vector< py::object > &	pypopulations
	)

static

Fetch all data (spikes, traces) from spiNNaker. This is faster than using NEO.

Parameters

populations	Cypress populations
pypopulations	PyNN populations

static py::object cypress::PyNN::get_connector	(	const std::string &	connector_name,
		const py::module &	pynn,
		const Real &	additional_parameter,
		const bool	allow_self_connections
	)

static

Creates a PyNN 0.9 Connector

Parameters

connector_name	name of the pyNN connector
pynn	Reference to the pynn module
additional_parameter	Additional parameter needed by the connector
allow_self_connections	flag to allow self connections if source and target populations are the same

Returns: py::object reference to the connector

static py::object cypress::PyNN::get_connector7	(	const ConnectionDescriptor &	conn,
		const py::module &	pynn
	)

static

Creates a PyNN 0.7 Connector

Parameters

connector_name	name of the pyNN connector
group_conn	Group connection description
pynn	Reference to the pynn module

Returns: py::object reference to the connector

static std::string cypress::PyNN::get_import	(	const std::vector< std::string > &	imports,
		const std::string &	simulator
	)

static

Returns a string containing the import for given simulator. Throws an error is simualator could not be found

Parameters

imports	list of possible/supported imports
simulator	simulator string

static int cypress::PyNN::get_neo_version ( )

static

Returns the neo version, 5 represents version 0.5.x

Returns: integer representing the neo version

static std::string cypress::PyNN::get_neuron_class ( const NeuronType & neuron_type )

static

Given a NeuronType, this function returns the name of the PyNN neuron_type

Parameters

neuron_type Reference to the NeuronType of the population

Returns: PyNN class name of the neuron type

static py::object cypress::PyNN::get_pop_view	(	const py::module &	pynn,
		const py::object &	py_pop,
		const PopulationBase &	c_pop,
		const size_t &	start,
		const size_t &	end
	)

static

Get a handler for a part of a population

Parameters

pynn	handler for the PyNN instance
py_pop	PyNN population
c_pop	Cypress population
start	id of the first neuron
end	id of the last neuron

Returns: handler for PopulationView object

static int cypress::PyNN::get_pynn_version ( )

static

Returns the PyNN version, 8 represents version 0.8.x

Returns: integer representing the pyNN version

static py::object cypress::PyNN::group_connect	(	const std::vector< PopulationBase > &	populations,
		const std::vector< py::object > &	pypopulations,
		const ConnectionDescriptor &	conn,
		const py::module &	pynn,
		const bool	nest_flag,
		const Real	timestep = `0.0`
	)

static

Connect based on an existing PyNN connector

Parameters

populations	vector of cypress populations
pypopulations	vector of PyNN populations
conn	Cypress connection descriptor
pynn	Handler for PyNN module
nest_flag	use sign of weight and ignore receptor_type for nest and current based neurons
timestep	timestep of the simulator

Returns: Handler for the connector

static py::object cypress::PyNN::group_connect	(	const std::vector< PopulationBase > &	populations,
		const std::vector< py::object > &	pypopulations,
		const ConnectionDescriptor &	conn,
		const py::module &	pynn,
		const Real	nest_flag
	)

staticdelete

static py::object cypress::PyNN::group_connect7	(	const std::vector< PopulationBase > &	populations,
		const std::vector< py::object > &	pypopulations,
		const ConnectionDescriptor &	conn,
		const py::module &	pynn
	)

static

Connect based on an existing PyNN connector

Parameters

populations	vector of cypress populations
pypopulations	vector of PyNN populations
conn	Cypress connection descriptor
pynn	Handler for PyNN module

Returns: Handler for the connector

const std::vector<std::string>& cypress::PyNN::imports ( ) const

inline

Returns the Python imports that tried to be used when starting the platform.

static void cypress::PyNN::init_logger ( )

static

Intitialize the logger, still TODO

static py::dict cypress::PyNN::json_to_dict ( Json json )

static

Converting a Json object to a py::dict. Make sure that the python interpreter is already started before calling this function

Parameters

json	The json object which will be converted

Returns: python dictionary

static std::tuple<py::object, py::object> cypress::PyNN::list_connect	(	const std::vector< py::object > &	pypopulations,
		const ConnectionDescriptor	conn,
		const py::module &	pynn,
		const bool	current_based,
		const Real	timestep = `0.0`
	)

static

Creates a PyNN FromList Connection

Parameters

pypopulations	list of python populations
conn	ConnectionDescriptor of the List connection
pynn	Handler for PyNN python module
current_based	true if target population is current_based
timestep	Timestep of the simulator, default 0

Returns: tuple of the excitatory,inhibitory connection. List is separated for compatibility reasons

static std::tuple<py::object, py::object> cypress::PyNN::list_connect	(	const std::vector< py::object > &	pypopulations,
		const ConnectionDescriptor	conn,
		const py::module &	pynn,
		const Real	current_based
	)

staticdelete

static std::tuple<py::object, py::object> cypress::PyNN::list_connect7	(	const std::vector< py::object > &	pypopulations,
		const ConnectionDescriptor	conn,
		const py::module &	pynn
	)

static

Creates a PyNN6/7 FromList Connection

Parameters

pypopulations	list of python populations
conn	ConnectionDescriptor of the List connection
pynn	Handler for PyNN python module

Returns: tuple of the excitatory,inhibitory connection. List is separated for compatibility reasons

template<typename T >

static Matrix<T> cypress::PyNN::matrix_from_numpy	(	const py::object &	object,
		bool	transposed = `false`
	)

static

Given a numpy object, this method creates the (transposed) C++ matrix without creating a copy. The python dtype is checked and compared to

Parameters

T.	Matrix sizes are caught in Python, because the py::buffer_info seems to be misleading in some cases.
T	Type of the matrix
object	handler for numpy array
transposed	matrix dimensions are swapped (hack for NEO)

Returns: C++ matrix of the numpy array

std::string cypress::PyNN::name ( ) const

inlineoverridevirtual

Returns the canonical name of the backend.

Implements cypress::Backend.

std::string cypress::PyNN::nmpi_platform ( ) const

Returns the NMPI platform name corresponding to the currently chosen PyNN backend.

const std::string& cypress::PyNN::normalised_simulator ( ) const

inline

Returns the canonical simulator name.

void cypress::Backend::run	(	NetworkBase &	network,
		Real	duration = `0.0`
	)		const

inherited

Simulates the given spiking neural network for the given duration.

Parameters

network	is the network that should be simulated. The simulation result will be written to the network instance.
duration	is the duration for which the network should be simulated.

static void cypress::PyNN::set_homogeneous_rec	(	const PopulationBase &	pop,
		py::object &	pypop
	)

static

Set recording for a full population

Parameters

pop	Source cypress population
pypop	Target PyNN population

static void cypress::PyNN::set_inhomogeneous_parameters	(	const PopulationBase &	pop,
		py::object &	pypop,
		bool	init_available = `false`
	)

static

Sets parameters of an existing population

Parameters

pop	Source cypress population
pypop	Target PyNN population
init_available	flag for initializing the population

static void cypress::PyNN::set_inhomogenous_rec	(	const PopulationBase &	pop,
		py::object &	pypop,
		py::module &	pynn
	)

static

Set mixed recordings for a population

Parameters

pop	Source cypress population
pypop	Target PyNN population

Json cypress::PyNN::setup ( ) const

inline

Return the system config

const std::string& cypress::PyNN::simulator ( ) const

inline

Returns the simulator name as provided by the user.

static std::vector<std::string> cypress::PyNN::simulators ( )

static

Lists available PyNN simulators.

static py::object cypress::PyNN::spikey_create_homogeneous_pop	(	const PopulationBase &	pop,
		py::module &	pynn
	)

static

Creates a PyNN population with homogeneous parameters for Spikey, inhomogeneous parameters can be set with set_inhomogeneous_parameters afterwards.

Parameters

pop	The cypress population
pynn	the PyNN instance

Returns: handler for the PyNN population

static py::object cypress::PyNN::spikey_create_source_population	(	const PopulationBase &	pop,
		py::module &	pynn
	)

static

Creates a PyNN source population for Spikey

Parameters

pop	The cypress population
pynn	the PyNN instance

Returns: handler for the PyNN population

static void cypress::PyNN::spikey_get_spikes	(	PopulationBase	pop,
		py::object &	pypop
	)

static

Fetches spikes and saves them to pop

Parameters

pop	cypress population
pypop	PyNN population

static void cypress::PyNN::spikey_get_voltage	(	NeuronBase	neuron,
		py::module &	pynn
	)

static

Fetch membrane voltage for a neuron in Spikey

Parameters

neuron	The cypress neuron recording the membrane
pynn	pointer to PyNN module

static void cypress::PyNN::spikey_run	(	NetworkBase &	source,
		Real	duration,
		py::module &	pynn,
		py::dict	dict
	)

static

Special run function for the Spikey system

Parameters

source	The Network description
duration	Simulation duration
pynn	Module pointer to PyNN.hardware.spikey

static void cypress::PyNN::spikey_set_homogeneous_rec	(	const PopulationBase &	pop,
		py::object &	pypop,
		py::module &	pynn
	)

static

Sets parameters of an existing population for spikey

Parameters

pop	Source cypress population
pypop	Target PyNN population
init_available	flag for initializing the population

static void cypress::PyNN::spikey_set_inhomogeneous_parameters	(	const PopulationBase &	pop,
		py::object &	pypop
	)

static

Set mixed recordings for a population for the Spikey system

Parameters

pop	Source cypress population
pypop	Target PyNN population

static void cypress::PyNN::spikey_set_inhomogeneous_rec	(	const PopulationBase &	pop,
		py::object &	pypop,
		py::module	pynn
	)

static

Set recording for a full population for spikey

Parameters

pop	Source cypress population
pypop	Target PyNN population

std::unordered_set<const NeuronType *> cypress::PyNN::supported_neuron_types ( ) const

overridevirtual

Returns a set of neuron types which are supported by this backend. Trying to execute a network with other neurons than the ones specified in the result of this function will result in an exception.

Returns: a set of neuron types supported by this particular backend instance.

Implements cypress::Backend.

Real cypress::PyNN::timestep ( )

Calculates the timestep the simulation will be running with. This does not make any sense for analogue hardware, why zero is returned in this case.

Returns: the simulation timestep in milliseconds.

Member Data Documentation

std::vector<std::string> cypress::PyNN::m_imports

protected

bool cypress::PyNN::m_keep_log

protected

std::string cypress::PyNN::m_normalised_simulator

protected

Json cypress::PyNN::m_setup

protected

std::string cypress::PyNN::m_simulator

protected

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

cypress/backend/pynn/pynn.hpp

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation