spynnaker.pyNN package

Subpackages

Submodules

spynnaker.pyNN.config_setup module

spynnaker.pyNN.config_setup.add_spynnaker_cfg()[source]
spynnaker.pyNN.config_setup.setup_configs()[source]

Sets up the configurations including the users configuration file.

Clears out any previous read configurations but does not load the new configurations so a warning is generated if a configuration is used before setup is called.

spynnaker.pyNN.config_setup.unittest_setup()[source]

Does all the steps that may be required before a unit-test.

Resets the configurations so only the local default configurations are included. The user configuration is not included!

Unsets any previous simulators and temporary directories

Note

This file should only be called from sPyNNaker tests that do not call sim.setup

spynnaker.pyNN.exceptions module

exception spynnaker.pyNN.exceptions.DelayExtensionException[source]

Bases: ConfigurationException

Raised when a delay extension vertex fails.

exception spynnaker.pyNN.exceptions.FilterableException[source]

Bases: SpynnakerException

Raised when it is not possible to determine if an edge should be filtered.

exception spynnaker.pyNN.exceptions.InvalidParameterType[source]

Bases: SpynnakerException

Raised when a parameter is not recognised.

exception spynnaker.pyNN.exceptions.MemReadException[source]

Bases: SpynnakerException

Raised when the PyNN front end fails to read a certain memory region.

exception spynnaker.pyNN.exceptions.SpynnakerException[source]

Bases: Exception

Superclass of all exceptions from the PyNN module.

exception spynnaker.pyNN.exceptions.SpynnakerSplitterConfigurationException[source]

Bases: ConfigurationException

Raised when a splitter configuration fails.

exception spynnaker.pyNN.exceptions.SynapseRowTooBigException(max_size, message)[source]

Bases: SpynnakerException

Raised when a synapse row is bigger than is allowed.

Parameters:

  • max_size – the maximum permitted size of row

  • message – the exception message

property max_size

The maximum size allowed.

exception spynnaker.pyNN.exceptions.SynapticBlockGenerationException[source]

Bases: ConfigurationException

Raised when the synaptic manager fails to generate a synaptic block.

exception spynnaker.pyNN.exceptions.SynapticBlockReadException[source]

Bases: ConfigurationException

Raised when the synaptic manager fails to read a synaptic block or convert it into readable values.

exception spynnaker.pyNN.exceptions.SynapticConfigurationException[source]

Bases: ConfigurationException

Raised when the synaptic manager fails for some reason.

exception spynnaker.pyNN.exceptions.SynapticMaxIncomingAtomsSupportException[source]

Bases: ConfigurationException

Raised when a synaptic sublist exceeds the max atoms possible to be supported.

spynnaker.pyNN.random_distribution module

spynnaker.pyNN.setup_pynn module

This script installs sPyNNaker so that it usable as the pyNN.spiNNaker module.

Note

This modifies your pyNN installation!

spynnaker.pyNN.setup_pynn.install_sPyNNaker_into(module)[source]

Do the actual installation by creating a package within the given module’s implementation. This is very nasty!

Parameters:

module (ModuleType) –

spynnaker.pyNN.setup_pynn.version_satisfies(module, requirement)[source]

Perform a version check. This code could be smarter…

Parameters:
Returns:

Whether the module’s version satisfies the given requirement

Return type:

bool

spynnaker.pyNN.spinnaker module

spynnaker.pyNN.spynnaker_external_device_plugin_manager module

class spynnaker.pyNN.spynnaker_external_device_plugin_manager.SpynnakerExternalDevicePluginManager[source]

Bases: object

User-level interface for the external device plug-in manager.

static activate_live_output_for(population, database_notify_host=None, database_notify_port_num=None, database_ack_port_num=None, port=None, host=None, tag=None, strip_sdp=True, use_prefix=False, key_prefix=None, prefix_type=None, message_type=EIEIOType.KEY_32_BIT, right_shift=0, payload_as_time_stamps=True, notify=True, use_payload_prefix=True, payload_prefix=None, payload_right_shift=0, number_of_packets_sent_per_time_step=0, translate_keys=False)[source]

Output the spikes from a given population from SpiNNaker as they occur in the simulation.

Parameters:

  • population (Population) – The population to activate the live output for

  • database_notify_host (str) – The hostname for the device which is listening to the database notification.

  • database_ack_port_num (int) – The port number to which a external device will acknowledge that they have finished reading the database and are ready for it to start execution

  • database_notify_port_num (int) – The port number to which a external device will receive the database is ready command

  • key_prefix (int or None) – the prefix to be applied to the key

  • prefix_type (EIEIOPrefix) – if the prefix type is 32 bit or 16 bit

  • message_type (EIEIOType) – If the message is a EIEIO command message, or an EIEIO data message with 16 bit or 32 bit keys.

  • payload_as_time_stamps (bool) –

  • right_shift (int) –

  • use_payload_prefix (bool) –

  • notify (bool) –

  • payload_prefix (int or None) –

  • payload_right_shift (int) –

  • number_of_packets_sent_per_time_step (int) –

  • port (int) – The UDP port to which the live spikes will be sent. If not specified, the port will be taken from the “live_spike_port” parameter in the “Recording” section of the sPyNNaker configuration file.

  • host (str) – The host name or IP address to which the live spikes will be sent. If not specified, the host will be taken from the “live_spike_host” parameter in the “Recording” section of the sPyNNaker configuration file.

  • tag (int) – The IP tag to be used for the spikes. If not specified, one will be automatically assigned

  • strip_sdp (bool) – Determines if the SDP headers will be stripped from the transmitted packet.

  • use_prefix (bool) – Determines if the spike packet will contain a common prefix for the spikes

  • label (str) – The label of the gatherer vertex

  • partition_ids (list(str)) – The names of the partitions to create edges for

  • translate_keys (bool) – Whether the incoming keys from the cores should be translated to global keys rather than core-based keys

static activate_live_output_to(population, device, partition_id='SPIKE')[source]

Activate the output of spikes from a population to an external device.

Note

All spikes will be sent to the device.

Parameters:

  • population (Population) – The pyNN population object from which spikes will be sent.

  • device (Population or ApplicationVertex) – The pyNN population or external device to which the spikes will be sent.

  • partition_id (str) – The partition ID to activate live output to.

static add_application_vertex(vertex)[source]
static add_database_socket_address(database_notify_host, database_notify_port_num, database_ack_port_num)[source]
Parameters:

  • database_notify_host (str or None) – Host to talk to tell that the database (and application) is ready.

  • database_notify_port_num (int or None) – Port to talk to tell that the database (and application) is ready.

  • database_ack_port_num (int or None) – Port on which to listen for an acknowledgement that the simulation should start.

static add_edge(vertex, device_vertex, partition_id)[source]

Add an edge between two vertices (often a vertex and a external device) on a given partition.

Parameters:

  • vertex (ApplicationVertex) – the pre-population vertex to connect the edge from

  • device_vertex (ApplicationVertex) – the post-population vertex to connect the edge to

  • partition_id (str) – the partition identifier for making nets

static add_poisson_live_rate_control(poisson_population, control_label_extension='_control', receive_port=None, database_notify_host=None, database_notify_port_num=None, database_ack_port_num=None, notify=True, reserve_reverse_ip_tag=False)[source]

Add a live rate controller to a Poisson population.

Parameters:

  • poisson_population (Population) – The population to control

  • control_label_extension (str) – An extension to add to the label of the Poisson source. Must match up with the equivalent in the SpynnakerPoissonControlConnection

  • receive_port (int) – The port that the SpiNNaker board should listen on

  • database_notify_host (str) – the hostname for the device which is listening to the database notification.

  • database_ack_port_num (int) – the port number to which a external device will acknowledge that they have finished reading the database and are ready for it to start execution

  • database_notify_port_num (int) – The port number to which an external device will receive the database is ready command

  • notify (bool) – adds to the notification protocol if set.

  • reserve_reverse_ip_tag (bool) – True if a reverse IP tag is to be used, False if SDP is to be used (default)

static update_live_packet_gather_tracker(vertex_to_record_from, params, partition_ids)[source]

Add an edge from a vertex to the live packet gatherer, builds as needed and has all the parameters for the creation of the live packet gatherer if needed.

Parameters:

Module contents

The spynnaker.pyNN package contains the front end specifications and implementation for the PyNN High-level API (https://neuralensemble.org/trac/PyNN).

This package contains the profile of that code for PyNN 0.9.

class spynnaker.pyNN.ACSource(start=0.0, stop=0.0, amplitude=0.0, offset=0.0, frequency=0.0, phase=0.0)

Bases: AbstractCurrentSource

AC current source (i.e. sine wave) turned on at “start” and off at “stop”, given (y-)offset, amplitude, frequency and phase.

Parameters:
property current_source_id

The ID of the current source.

Return type:

int

property get_parameter_types

The parameter types for the current source.

Return type:

dict(str, Any)

property get_parameters

The parameters of the current source.

Return type:

dict(str, Any)

get_sdram_usage_in_bytes()[source]

The SDRAM usage in bytes of the current source.

Return type:

int

set_parameters(**parameters)[source]

Set the current source parameters.

Parameters:

parameters – the parameters to set

spynnaker.pyNN.AdditiveWeightDependence

alias of WeightDependenceAdditive

class spynnaker.pyNN.AllToAllConnector(allow_self_connections=True, safe=True, verbose=None, callback=None)

Bases: AbstractGenerateConnectorOnMachine, AbstractGenerateConnectorOnHost

Connects all cells in the presynaptic population to all cells in the postsynaptic population.

Parameters:

  • allow_self_connections (bool) – if the connector is used to connect a Population to itself, this flag determines whether a neuron is allowed to connect to itself, or only to other neurons in the Population.

  • safe (bool) – If True, check that weights and delays have valid values. If False, this check is skipped.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

property allow_self_connections
Return type:

bool

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

property gen_connector_id

The ID of the connection generator on the machine.

Return type:

int

gen_connector_params()[source]

Get the parameters of the on machine generation.

Return type:

ndarray(uint32)

property gen_connector_params_size_in_bytes

The size of the connector parameters, in bytes.

Return type:

int

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

class spynnaker.pyNN.ArrayConnector(array, safe=True, callback=None, verbose=False)

Bases: AbstractConnector, AbstractGenerateConnectorOnHost

Make connections using an array of integers based on the IDs of the neurons in the pre- and post-populations.

Parameters:

  • array (ndarray(2, uint8)) – An explicit boolean matrix that specifies the connections between the pre- and post-populations (see PyNN documentation). Must be 2D in practice.

  • safe (bool) – Whether to check that weights and delays have valid values. If False, this check is skipped.

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

class spynnaker.pyNN.Assembly(*populations, **kwargs)

Bases: Assembly

A group of neurons, may be heterogeneous, in contrast to a Population where all the neurons are of the same type.

Parameters:

  • populations (Population or PopulationView) – the populations or views to form the assembly out of

  • kwargs – may contain label (a string describing the assembly)

Create an Assembly of Populations and/or PopulationViews.

class spynnaker.pyNN.CSAConnector(cset, safe=True, callback=None, verbose=False)

Bases: AbstractConnector, AbstractGenerateConnectorOnHost

Make connections using a Connection Set Algebra (Djurfeldt 2012) description between the neurons in the pre- and post-populations.

Note

If you get TypeError in Python 3 see: https://github.com/INCF/csa/issues/10

Parameters:

  • cset (csa.connset.CSet) – A description of the connection set between populations

  • safe (bool) – If True, check that weights and delays have valid values. If False, this check is skipped.

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

Raises:

ImportError – if the csa library isn’t present; it’s tricky to install in some environments so we don’t force it to be present unless you want to actually use this class.

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

show_connection_set(n_pre_neurons, n_post_neurons)[source]
Parameters:

  • n_pre_neurons (int) –

  • n_post_neurons (int) –

spynnaker.pyNN.Convolution

alias of LocalOnlyConvolution

class spynnaker.pyNN.ConvolutionConnector(kernel_weights, kernel_shape=None, strides=None, padding=None, pool_shape=None, pool_stride=None, positive_receptor_type='excitatory', negative_receptor_type='inhibitory', safe=True, verbose=False, callback=None)

Bases: AbstractConnector

Where the pre- and post-synaptic populations are considered as a 2D array. Connect every post(row, column) neuron to many pre(row, column, kernel) through a (kernel) set of weights and/or delays.

Parameters:

  • kernel_weights (int or list or ndarray or RandomDistribution) –

    The synaptic strengths, shared by neurons in the post population. Can be:

    • single value: kernel_shape must be provided; the same value will be used for all weights

    • simple list: kernel_shape must be provided; the list must be sized shape width * height

    • 2D list: If kernel_shape is provided, it must match

    • ndarray: As above for simple or 2D list

    • RandomDistribution: kernel_shape must be provided; weights will be drawn from the distribution

  • kernel_shape (int or tuple(int,int)) – The shape of the kernel if it cannot be determined from kernel_weights. If a single value is provided, a square kernel will be assumed. If two values are provided, it will be assumed to be (n_rows, n_columns)

  • strides (int or tuple(int, int)) – Spatial sampling frequency, jumps between the post neurons. This matches the meaning of standard ML packages. If a single value is provided, the same stride will be used for rows and columns. If two values are provided it will be assumed to be (stride_rows, stride_columns)

  • padding (bool or int or tuple(int, int) or None) – How many ‘extra pixels’ around the pre-population will be added, only zero-valued pixels are currently supported. If a single value is provided, the same padding will be used for rows and columns. If two values are provided it will be assumed to be (padding_rows, padding_columns). If True, automatic padding will be used based on the kernel shape. If False or None, no padding will be used.

  • pool_shape (int or tuple(int, int) or None) – Area of pooling, only average pooling is supported (and seems to make sense). If a single value is provided, the pooling area will be square. If two values are provided it will be assumed to be (pooling_rows, pooling_columns).

  • pool_stride (int or tuple(int, int) or None) – Jumps between pooling regions. If a single value is provided, the same stride will be used for rows and columns. If two values are provided it will be assumed to be (stride_rows, stride_columns)

  • positive_receptor_type (str) – The receptor type to add the positive weights to. By default this is “excitatory”.

  • negative_receptor_type (str) – The receptor type to add the negative weights to. By default this is “inhibitory”.

  • safe (bool) – (ignored)

  • verbose (bool) – (ignored)

  • callback (callable) – (ignored)

get_connected_vertices(s_info, source_vertex, target_vertex)[source]

Get the machine vertices that are connected to each other with this connector

Parameters:
Returns:

A list of tuples of (target machine vertex, list of sources)

Return type:

list(tuple(MachineVertex, list(AbstractVertex)))

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_encoded_kernel_weights(app_edge, weight_scales)[source]
get_local_only_data(app_edge, vertex_slice, key, mask, n_colour_bits, delay, weight_index)[source]
get_max_n_incoming_slices(source_vertex, target_vertex)[source]
get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_post_shape(shape)[source]

Get the shape of the post image given the pre-image shape.

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

property kernel_n_bytes
property kernel_n_weights
property kernel_weights
property negative_receptor_type
property parameters_n_bytes
property positive_receptor_type
validate_connection(application_edge, synapse_info)[source]

Checks that the edge supports the connector. By default this does nothing i.e. assumes the edge is OK, but can be overridden if the connector has rules that need to be checked. Returns nothing; it is assumed that an Exception will be raised if anything is wrong.

Parameters:
class spynnaker.pyNN.Cuboid(width, height, depth)[source]

Bases: Shape

Represents a cuboidal volume within which neurons may be distributed.

Arguments:
height:

extent in y direction

width:

extent in x direction

depth:

extent in z direction

sample(n, rng)[source]

Return n points distributed randomly with uniform density within the cuboid.

class spynnaker.pyNN.DCSource(amplitude=0.0, start=0.0, stop=0.0)

Bases: AbstractCurrentSource

Current source with amplitude turned on at “start” and off at “stop”.

Parameters:
property current_source_id

The ID of the current source.

Return type:

int

property get_parameter_types

The parameter types for the current source.

Return type:

dict(str, Any)

property get_parameters

The parameters of the current source.

Return type:

dict(str, Any)

get_sdram_usage_in_bytes()[source]

The SDRAM usage in bytes of the current source.

Return type:

int

set_parameters(**parameters)[source]

Set the current source parameters.

Parameters:

parameters – the parameters to set

class spynnaker.pyNN.DistanceDependentFormation(grid=(16, 16), p_form_forward=0.16, sigma_form_forward=2.5, p_form_lateral=1.0, sigma_form_lateral=1.0)

Bases: AbstractFormation

Formation rule that depends on the physical distance between neurons.

Parameters:

  • grid (tuple(int,int) or list(int) or ndarray(int)) – (x, y) dimensions of the grid of distance

  • p_form_forward (float) – The peak probability of formation on feed-forward connections

  • sigma_form_forward (float) – The spread of probability with distance of formation on feed-forward connections

  • p_form_lateral (float) – The peak probability of formation on lateral connections

  • sigma_form_lateral (float) – The spread of probability with distance of formation on lateral connections

distance(x0, x1, metric)[source]

Compute the distance between points x0 and x1 place on the grid using periodic boundary conditions.

Parameters:

  • x0 (ndarray(int)) – first point in space

  • x1 (ndarray(int)) – second point in space

  • grid (ndarray(int)) – shape of grid

  • metric (str) – distance metric, i.e. euclidian or manhattan or equidistant

Returns:

the distance

Return type:

float

generate_distance_probability_array(probability, sigma)[source]

Generate the exponentially decaying probability LUTs.

Parameters:

  • probability (float) – peak probability

  • sigma (float) – spread

Returns:

distance-dependent probabilities

Return type:

ndarray(float)

get_parameter_names()[source]

Return the names of the parameters supported by this rule.

Return type:

iterable(str)

get_parameters_sdram_usage_in_bytes()[source]

Get the amount of SDRAM used by the parameters of this rule.

Return type:

int

property vertex_executable_suffix

The suffix to be appended to the vertex executable for this rule.

Return type:

str

write_parameters(spec)[source]

Write the parameters of the rule to the spec.

Parameters:

spec (DataSpecificationGenerator) –

class spynnaker.pyNN.DistanceDependentProbabilityConnector(d_expression, allow_self_connections=True, safe=True, verbose=False, n_connections=None, rng=None, callback=None)

Bases: AbstractConnector, AbstractGenerateConnectorOnHost

Make connections using a distribution which varies with distance.

Parameters:

  • d_expression (str) – the right-hand side of a valid python expression for probability, involving d, (e.g. "exp(-abs(d))", or "d < 3"), that can be parsed by eval(), that computes the distance dependent distribution.

  • allow_self_connections (bool) – if the connector is used to connect a Population to itself, this flag determines whether a neuron is allowed to connect to itself, or only to other neurons in the Population.

  • safe (bool) – if True, check that weights and delays have valid values. If False, this check is skipped.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

  • n_connections (int or None) – The number of efferent synaptic connections per neuron.

  • rng (NumpyRNG or None) – Seeded random number generator, or None to make one when needed.

  • callback (callable) –

property allow_self_connections
Return type:

bool

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

property d_expression

The distance expression.

Return type:

str

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

set_projection_information(synapse_info)[source]

Sets a connectors projection info.

Parameters:

synapse_info (SynapseInformation) – the synapse info

class spynnaker.pyNN.FixedNumberPostConnector(n, allow_self_connections=True, safe=True, verbose=False, with_replacement=False, rng=None, callback=None)

Bases: AbstractGenerateConnectorOnMachine, AbstractGenerateConnectorOnHost

Connects a fixed number of post-synaptic neurons selected at random, to all pre-synaptic neurons.

Parameters:

  • n (int) – number of random post-synaptic neurons connected to pre-neurons.

  • allow_self_connections (bool) – if the connector is used to connect a Population to itself, this flag determines whether a neuron is allowed to connect to itself, or only to other neurons in the Population.

  • safe (bool) – Whether to check that weights and delays have valid values; if False, this check is skipped.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

  • with_replacement (bool) – this flag determines how the random selection of post-synaptic neurons is performed; if True, then every post-synaptic neuron can be chosen on each occasion, and so multiple connections between neuron pairs are possible; if False, then once a post-synaptic neuron has been connected to a pre-neuron, it can’t be connected again.

  • rng (NumpyRNG or None) – Seeded random number generator, or None to make one when needed.

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

property allow_self_connections
create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

property gen_connector_id

The ID of the connection generator on the machine.

Return type:

int

gen_connector_params()[source]

Get the parameters of the on machine generation.

Return type:

ndarray(uint32)

property gen_connector_params_size_in_bytes

The size of the connector parameters, in bytes.

Return type:

int

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

set_projection_information(synapse_info)[source]

Sets a connectors projection info.

Parameters:

synapse_info (SynapseInformation) – the synapse info

validate_connection(application_edge, synapse_info)[source]

Checks that the edge supports the connector. By default this does nothing i.e. assumes the edge is OK, but can be overridden if the connector has rules that need to be checked. Returns nothing; it is assumed that an Exception will be raised if anything is wrong.

Parameters:
class spynnaker.pyNN.FixedNumberPreConnector(n, allow_self_connections=True, safe=True, verbose=False, with_replacement=False, rng=None, callback=None)

Bases: AbstractGenerateConnectorOnMachine, AbstractGenerateConnectorOnHost

Connects a fixed number of pre-synaptic neurons selected at random, to all post-synaptic neurons.

Parameters:

  • n (int) – number of random pre-synaptic neurons connected to output

  • allow_self_connections (bool) – if the connector is used to connect a Population to itself, this flag determines whether a neuron is allowed to connect to itself, or only to other neurons in the Population.

  • safe (bool) – Whether to check that weights and delays have valid values. If False, this check is skipped.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

  • with_replacement (bool) – this flag determines how the random selection of pre-synaptic neurons is performed; if true, then every pre-synaptic neuron can be chosen on each occasion, and so multiple connections between neuron pairs are possible; if false, then once a pre-synaptic neuron has been connected to a post-neuron, it can’t be connected again.

  • rng (NumpyRNG or None) – Seeded random number generator, or None to make one when needed

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

property allow_self_connections
create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

property gen_connector_id

The ID of the connection generator on the machine.

Return type:

int

gen_connector_params()[source]

Get the parameters of the on machine generation.

Return type:

ndarray(uint32)

property gen_connector_params_size_in_bytes

The size of the connector parameters, in bytes.

Return type:

int

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

set_projection_information(synapse_info)[source]

Sets a connectors projection info.

Parameters:

synapse_info (SynapseInformation) – the synapse info

validate_connection(application_edge, synapse_info)[source]

Checks that the edge supports the connector. By default this does nothing i.e. assumes the edge is OK, but can be overridden if the connector has rules that need to be checked. Returns nothing; it is assumed that an Exception will be raised if anything is wrong.

Parameters:
class spynnaker.pyNN.FixedProbabilityConnector(p_connect, allow_self_connections=True, safe=True, verbose=False, rng=None, callback=None)

Bases: AbstractGenerateConnectorOnMachine, AbstractGenerateConnectorOnHost

For each pair of pre-post cells, the connection probability is constant.

Parameters:

  • p_connect (float) – a value between zero and one. Each potential connection is created with this probability.

  • allow_self_connections (bool) – if the connector is used to connect a Population to itself, this flag determines whether a neuron is allowed to connect to itself, or only to other neurons in the Population.

  • safe (bool) – If True, check that weights and delays have valid values. If False, this check is skipped.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

  • rng (NumpyRNG or None) – Seeded random number generator, or None to make one when needed

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

property gen_connector_id

The ID of the connection generator on the machine.

Return type:

int

gen_connector_params()[source]

Get the parameters of the on machine generation.

Return type:

ndarray(uint32)

property gen_connector_params_size_in_bytes

The size of the connector parameters, in bytes.

Return type:

int

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

property p_connect
validate_connection(application_edge, synapse_info)[source]

Checks that the edge supports the connector. By default this does nothing i.e. assumes the edge is OK, but can be overridden if the connector has rules that need to be checked. Returns nothing; it is assumed that an Exception will be raised if anything is wrong.

Parameters:
spynnaker.pyNN.FixedTotalNumberConnector

alias of MultapseConnector

class spynnaker.pyNN.FromFileConnector(file, distributed=False, safe=True, callback=None, verbose=False)

Bases: FromListConnector

Make connections according to a list read from a file.

Parameters:

  • file (str or FileIO) –

    Either an open file object or the filename of a file containing a list of connections, in the format required by FromListConnector. Column headers, if included in the file, must be specified using a list or tuple, e.g.:

    # columns = ["i", "j", "weight", "delay", "U", "tau_rec"]

    Note

    The header requires # at the beginning of the line.

  • distributed (bool) –

    Basic pyNN says:

    if this is True, then each node will read connections from a file called filename.x, where x is the MPI rank. This speeds up loading connections for distributed simulations.

    Note

    Always leave this as False with sPyNNaker, which is not MPI-based.

  • safe (bool) – Whether to check that weights and delays have valid values. If False, this check is skipped.

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

get_reader(file)[source]

Get a file reader object using the PyNN methods.

Returns:

A pynn StandardTextFile or similar

Return type:

StandardTextFile

class spynnaker.pyNN.FromListConnector(conn_list, safe=True, verbose=False, column_names=None, callback=None)

Bases: AbstractConnector, AbstractGenerateConnectorOnHost

Make connections according to a list.

Parameters:

  • conn_list (ndarray or list(tuple(int,int,...))) –

    A numpy array or a list of tuples, one tuple for each connection. Each tuple should contain:

    (pre_idx, post_idx, p1, p2, ..., pn)

    where pre_idx is the index (i.e. order in the Population, not the ID) of the presynaptic neuron, post_idx is the index of the postsynaptic neuron, and p1, p2, etc. are the synaptic parameters (e.g., weight, delay, plasticity parameters). All tuples/rows must have the same number of items.

  • safe (bool) – if True, check that weights and delays have valid values. If False, this check is skipped.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

  • column_names (None or tuple(str) or list(str)) – the names of the parameters p1, p2, etc. If not provided, it is assumed the parameters are weight, delay (for backwards compatibility).

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

property column_names

The names of the columns in the array after the first two. Of particular interest is whether weight and delay columns are present.

Return type:

list(str)

property conn_list

The connection list.

Return type:

ndarray

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

get_connected_vertices(s_info, source_vertex, target_vertex)[source]

Get the machine vertices that are connected to each other with this connector

Parameters:
Returns:

A list of tuples of (target machine vertex, list of sources)

Return type:

list(tuple(MachineVertex, list(AbstractVertex)))

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_delay_variance(delays, synapse_info)[source]

Get the variance of the delays.

Parameters:

delays (RandomDistribution or int or float of str) –

Return type:

float

get_extra_parameter_names()[source]

Get the names of the extra parameters.

Return type:

list(str)

get_extra_parameters()[source]

Getter for the extra parameters. Excludes weight and delay columns.

Returns:

The extra parameters

Return type:

ndarray

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

get_weight_mean(weights, synapse_info)[source]

Get the mean of the weights.

Parameters:

weights (RandomDistribution or int or float or str) –

Return type:

float

get_weight_variance(weights, synapse_info)[source]

Get the variance of the weights.

Parameters:

weights (RandomDistribution or int or float or str) –

Return type:

float

class spynnaker.pyNN.Grid2D(aspect_ratio=1.0, dx=1.0, dy=1.0, x0=0.0, y0=0.0, z=0, fill_order='sequential', rng=None)[source]

Bases: BaseStructure

Represents a structure with neurons distributed on a 2D grid.

Arguments:
dx, dy:

distances between points in the x, y directions.

x0, y0:

coordinates of the starting corner of the grid.

z:

the z-coordinate of all points in the grid.

aspect_ratio:

ratio of the number of grid points per side (not the ratio of the side lengths, unless dx == dy)

fill_order:

may be ‘sequential’ or ‘random’

calculate_size(n)[source]

docstring goes here

generate_positions(n)[source]

Calculate and return the positions of n neurons positioned according to this structure.

parameter_names = ('aspect_ratio', 'dx', 'dy', 'x0', 'y0', 'z', 'fill_order')
class spynnaker.pyNN.Grid3D(aspect_ratioXY=1.0, aspect_ratioXZ=1.0, dx=1.0, dy=1.0, dz=1.0, x0=0.0, y0=0.0, z0=0, fill_order='sequential', rng=None)[source]

Bases: BaseStructure

Represents a structure with neurons distributed on a 3D grid.

Arguments:
dx, dy, dz:

distances between points in the x, y, z directions.

x0, y0. z0:

coordinates of the starting corner of the grid.

aspect_ratioXY, aspect_ratioXZ:

ratios of the number of grid points per side (not the ratio of the side lengths, unless dx == dy == dz)

fill_order:

may be ‘sequential’ or ‘random’.

If fill_order is ‘sequential’, the z-index will be filled first, then y then x, i.e. the first cell will be at (0,0,0) (given default values for the other arguments), the second at (0,0,1), etc.

calculate_size(n)[source]

docstring goes here

generate_positions(n)[source]

Calculate and return the positions of n neurons positioned according to this structure.

parameter_names = ('aspect_ratios', 'dx', 'dy', 'dz', 'x0', 'y0', 'z0', 'fill_order')
spynnaker.pyNN.IF_cond_exp

alias of IFCondExpBase

spynnaker.pyNN.IF_curr_alpha

alias of IFCurrAlpha

spynnaker.pyNN.IF_curr_delta

alias of IFCurrDelta

spynnaker.pyNN.IF_curr_exp

alias of IFCurrExpBase

class spynnaker.pyNN.IndexBasedProbabilityConnector(index_expression, allow_self_connections=True, rng=None, safe=True, callback=None, verbose=False)

Bases: AbstractConnector, AbstractGenerateConnectorOnHost

Make connections using a probability distribution which varies dependent upon the indices of the pre- and post-populations.

Parameters:

  • index_expression (str) – the right-hand side of a valid python expression for probability, involving the indices of the pre- and post-populations, that can be parsed by eval(), that computes a probability distribution; the indices will be given as variables i and j when the expression is evaluated.

  • allow_self_connections (bool) – if the connector is used to connect a Population to itself, this flag determines whether a neuron is allowed to connect to itself, or only to other neurons in the Population.

  • rng (NumpyRNG or None) – Seeded random number generator, or None to make one when needed.

  • safe (bool) – Whether to check that weights and delays have valid values. If False, this check is skipped.

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

property allow_self_connections

When the connector is used to connect a Population to itself, this flag determines whether a neuron is allowed to connect to itself, or only to other neurons in the Population.

Return type:

bool

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

property index_expression

The right-hand side of a valid python expression for probability, involving the indices of the pre- and post-populations, that can be parsed by eval(), that computes a probability distribution.

Return type:

str

spynnaker.pyNN.Izhikevich

alias of IzkCurrExpBase

class spynnaker.pyNN.KernelConnector(shape_pre, shape_post, shape_kernel, weight_kernel=None, delay_kernel=None, shape_common=None, pre_sample_steps_in_post=None, pre_start_coords_in_post=None, post_sample_steps_in_pre=None, post_start_coords_in_pre=None, safe=True, space=None, verbose=False, callback=None)

Bases: AbstractGenerateConnectorOnMachine, AbstractGenerateConnectorOnHost

Where the pre- and post-synaptic populations are considered as a 2D array. Connect every post(row, column) neuron to many pre(row, column, kernel) through a (kernel) set of weights and/or delays.

TODO

Should these include allow_self_connections and with_replacement?

Parameters:

  • shape_pre (list(int) or tuple(int,int)) – 2D shape of the pre-population (rows/height, columns/width, usually the input image shape)

  • shape_post (list(int) or tuple(int,int)) – 2D shape of the post-population (rows/height, columns/width)

  • shape_kernel (list(int) or tuple(int,int)) – 2D shape of the kernel (rows/height, columns/width)

  • weight_kernel (ndarray or RandomDistribution or int or float or list(int) or list(float) or None) – (optional) 2D matrix of size shape_kernel describing the weights

  • delay_kernel (ndarray or RandomDistribution or int or float or list(int) or list(float) or None) – (optional) 2D matrix of size shape_kernel describing the delays

  • shape_common (list(int) or tuple(int,int) or None) – (optional) 2D shape of common coordinate system (for both pre- and post-, usually the input image sizes)

  • pre_sample_steps_in_post (None or list(int) or tuple(int,int)) – (optional) Sampling steps/jumps for pre-population <=> (stepX, stepY)

  • pre_start_coords_in_post (None or list(int) or tuple(int,int)) – (optional) Starting row/column for pre-population sampling <=> (offX, offY)

  • post_sample_steps_in_pre (None or list(int) or tuple(int,int)) – (optional) Sampling steps/jumps for post-population <=> (stepX, stepY)

  • post_start_coords_in_pre (None or list(int) or tuple(int,int)) – (optional) Starting row/column for post-population sampling <=> (offX, offY)

  • safe (bool) – Whether to check that weights and delays have valid values. If False, this check is skipped.

  • space (Space) – Currently ignored; for future compatibility.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

  • callback (callable) – (ignored)

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

property gen_connector_id

The ID of the connection generator on the machine.

Return type:

int

gen_connector_params()[source]

Get the parameters of the on machine generation.

Return type:

ndarray(uint32)

property gen_connector_params_size_in_bytes

The size of the connector parameters, in bytes.

Return type:

int

get_connected_vertices(s_info, source_vertex, target_vertex)[source]

Get the machine vertices that are connected to each other with this connector

Parameters:
Returns:

A list of tuples of (target machine vertex, list of sources)

Return type:

list(tuple(MachineVertex, list(AbstractVertex)))

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_delay_variance(delays, synapse_info)[source]

Get the variance of the delays.

Parameters:

delays (RandomDistribution or int or float of str) –

Return type:

float

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

get_weight_mean(weights, synapse_info)[source]

Get the mean of the weights.

Parameters:

weights (RandomDistribution or int or float or str) –

Return type:

float

get_weight_variance(weights, synapse_info)[source]

Get the variance of the weights.

Parameters:

weights (RandomDistribution or int or float or str) –

Return type:

float

class spynnaker.pyNN.LastNeuronSelection(spike_buffer_size=64)

Bases: AbstractPartnerSelection

Partner selection that picks a random source neuron from the neurons that spiked in the last timestep.

Parameters:

spike_buffer_size – The size of the buffer for holding spikes

get_parameter_names()[source]

Return the names of the parameters supported by this rule.

Return type:

iterable(str)

get_parameters_sdram_usage_in_bytes()[source]

Get the amount of SDRAM used by the parameters of this rule.

Return type:

str

property vertex_executable_suffix

The suffix to be appended to the vertex executable for this rule.

Return type:

str

write_parameters(spec)[source]

Write the parameters of the rule to the spec.

Parameters:

spec (DataSpecificationGenerator) –

class spynnaker.pyNN.Line(dx=1.0, x0=0.0, y=0.0, z=0.0)[source]

Bases: BaseStructure

Represents a structure with neurons distributed evenly on a straight line.

Arguments:
dx:

distance between points in the line.

y, z,:

y- and z-coordinates of all points in the line.

x0:

x-coordinate of the first point in the line.

generate_positions(n)[source]

Calculate and return the positions of n neurons positioned according to this structure.

parameter_names = ('dx', 'x0', 'y', 'z')
spynnaker.pyNN.MultiplicativeWeightDependence

alias of WeightDependenceMultiplicative

class spynnaker.pyNN.NoisyCurrentSource(mean=0.0, stdev=0.0, start=0.0, stop=0.0, dt=1.0, rng=None)

Bases: AbstractCurrentSource

A noisy current source beginning at “start” and ending at “stop”, with noise simulated based on the given mean and standard deviation, and updating every dt (dt should default to the machine time step).

Parameters:
property current_source_id

The ID of the current source.

Return type:

int

property get_parameter_types

The parameter types for the current source.

Return type:

dict(str, Any)

property get_parameters

The parameters of the current source.

Return type:

dict(str, Any)

get_sdram_usage_in_bytes()[source]

The SDRAM usage in bytes of the current source.

Return type:

int

set_parameters(**parameters)[source]

Set the current source parameters.

Parameters:

parameters – the parameters to set

class spynnaker.pyNN.NumpyRNG(seed=None, parallel_safe=True)[source]

Bases: WrappedRNG

Wrapper for the np.random.RandomState class (Mersenne Twister PRNG).

normal_clipped(mu=0.0, sigma=1.0, low=-inf, high=inf, size=None)[source]
normal_clipped_to_boundary(mu=0.0, sigma=1.0, low=-inf, high=inf, size=None)[source]
translations = {'binomial': ('binomial', {'n': 'n', 'p': 'p'}), 'exponential': ('exponential', {'beta': 'scale'}), 'gamma': ('gamma', {'k': 'shape', 'theta': 'scale'}), 'lognormal': ('lognormal', {'mu': 'mean', 'sigma': 'sigma'}), 'normal': ('normal', {'mu': 'loc', 'sigma': 'scale'}), 'normal_clipped': ('normal_clipped', {'high': 'high', 'low': 'low', 'mu': 'mu', 'sigma': 'sigma'}), 'normal_clipped_to_boundary': ('normal_clipped_to_boundary', {'high': 'high', 'low': 'low', 'mu': 'mu', 'sigma': 'sigma'}), 'poisson': ('poisson', {'lambda_': 'lam'}), 'uniform': ('uniform', {'high': 'high', 'low': 'low'}), 'uniform_int': ('randint', {'high': 'high', 'low': 'low'}), 'vonmises': ('vonmises', {'kappa': 'kappa', 'mu': 'mu'})}
class spynnaker.pyNN.OneToOneConnector(safe=True, callback=None, verbose=False)

Bases: AbstractGenerateConnectorOnMachine, AbstractGenerateConnectorOnHost

Where the pre- and postsynaptic populations have the same size, connect cell i in the presynaptic population to cell i in the postsynaptic population, for all i.

Parameters:

  • safe (bool) – If True, check that weights and delays have valid values. If False, this check is skipped.

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

property gen_connector_id

The ID of the connection generator on the machine.

Return type:

int

gen_connector_params()[source]

Get the parameters of the on machine generation.

Return type:

ndarray(uint32)

property gen_connector_params_size_in_bytes

The size of the connector parameters, in bytes.

Return type:

int

get_connected_vertices(s_info, source_vertex, target_vertex)[source]

Get the machine vertices that are connected to each other with this connector

Parameters:
Returns:

A list of tuples of (target machine vertex, list of sources)

Return type:

list(tuple(MachineVertex, list(AbstractVertex)))

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

use_direct_matrix(synapse_info)[source]
Parameters:

synapse_info (SynapseInformation) –

Return type:

bool

spynnaker.pyNN.PoolDense

alias of LocalOnlyPoolDense

class spynnaker.pyNN.PoolDenseConnector(weights, pool_shape=None, pool_stride=None, positive_receptor_type='excitatory', negative_receptor_type='inhibitory', safe=True, verbose=False, callback=None)

Bases: AbstractConnector

Where the pre- and post-synaptic populations are considered as a 2D array. Connect every post(row, column) neuron to many pre(row, column, kernel) through a (kernel) set of weights and/or delays.

Parameters:

  • weights (int or float or list(int or float) or ndarray or RandomDistribution) –

    The synaptic strengths. Can be:

    • single value: the same value will be used for all weights

    • list: the total number of elements must be (number after pooling * number post)

    • ndarray: As above for list

    • RandomDistribution: weights will be drawn at random

  • pool_shape (int or tuple(int) or None) – Shape of average pooling. If a single value is provided, it will be used for every dimension, otherwise must be the same number of values as there are dimensions in the source.

  • pool_stride (int or tuple(int) or None) – Jumps between pooling regions. If a single value is provided, the same stride will be used for all dimensions, otherwise must be the same number of values as there are dimensions in the source. If None, and pool_shape is provided, pool_stride will be set to pool_shape.

  • positive_receptor_type (str) – The receptor type to add the positive weights to. By default this is “excitatory”.

  • negative_receptor_type (str) – The receptor type to add the negative weights to. By default this is “inhibitory”.

  • safe (bool) – (ignored)

  • verbose (bool) – (ignored)

  • callback (callable) – (ignored)

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

static get_post_pool_shape(pre_shape, pool_shape=None, pool_stride=None)[source]
get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

local_only_n_bytes(incoming_slices, n_post_atoms)[source]
Parameters:

  • incoming_slices (iterable(Slice)) –

  • n_post_atoms (int) –

Return type:

int

property negative_receptor_type
Return type:

str

property positive_receptor_type
Return type:

str

validate_connection(application_edge, synapse_info)[source]

Checks that the edge supports the connector. By default this does nothing i.e. assumes the edge is OK, but can be overridden if the connector has rules that need to be checked. Returns nothing; it is assumed that an Exception will be raised if anything is wrong.

Parameters:
property weights
Return type:

ndarray

write_local_only_data(spec, app_edge, pre_vertex_slice, post_vertex_slice, key, mask, n_colour_bits, weight_scales)[source]
Parameters:

  • spec (DataSpecificationGenerator) –

  • app_edge (ApplicationEdge) –

  • pre_vertex_slice (Slice) –

  • post_vertex_slice (Slice) –

  • key (int) –

  • mask (int) –

  • n_colour_bits (int) –

  • weight_scales –

class spynnaker.pyNN.Population(size, cellclass, cellparams=None, structure=None, initial_values=None, label=None, additional_parameters=None, **additional_kwargs)

Bases: PopulationBase

PyNN 0.9 population object.

Parameters:

  • size (int) – The number of neurons in the population

  • cellclass (type or AbstractPyNNModel) – The implementation of the individual neurons.

  • cellparams (dict(str,object) or None) – Parameters to pass to cellclass if it is a class to instantiate. Must be None if cellclass is an instantiated object.

  • structure (BaseStructure) –

  • initial_values (dict(str,float)) – Initial values of state variables

  • label (str) – A label for the population

  • additional_parameters (dict(str, ...)) – Additional parameters to pass to the vertex creation function.

  • additional_kwargs (dict(str, ...)) – A nicer way of allowing additional things

add_placement_constraint(x, y, p=None)[source]

Add a placement constraint.

Parameters:

  • x (int) – The x-coordinate of the placement constraint

  • y (int) – The y-coordinate of the placement constraint

  • p (int) – The processor ID of the placement constraint (optional)

Raises:

  • SimulatorRunningException – If sim.run is currently running

  • SimulatorNotSetupException – If called before sim.setup

  • SimulatorShutdownException – If called after sim.end

all()[source]

Iterator over cell IDs on all MPI nodes.

Return type:

iterable(IDMixin)

property all_cells
Return type:

list(IDMixin)

property annotations

The annotations given by the end user.

Return type:

dict(str, …)

can_record(variable)[source]

Determine whether variable can be recorded from this population.

Parameters:

variable (str) – The variable to answer the question about

Return type:

bool

property celltype

Implements the PyNN expected celltype property.

Returns:

The cell type this property has been set to

Return type:

AbstractPyNNModel

property conductance_based

Whether the population uses conductance inputs

Return type:

bool

static create(cellclass, cellparams=None, n=1)[source]

Pass through method to the constructor defined by PyNN. Create n cells all of the same type.

Parameters:
Returns:

A New Population

Return type:

Population

property current_values

Get the current values of the state variables.

Return type:

ParameterHolder

describe(template='population_default.txt', engine='default')[source]

Returns a human-readable description of the population.

The output may be customized by specifying a different template together with an associated template engine (see pyNN.descriptions).

If template is None, then a dictionary containing the template context will be returned.

Parameters:

  • template (str) – Template filename

  • engine (str or TemplateEngine or None) – Template substitution engine

Return type:

str or dict

find_units(variable)[source]

Get the units of a variable.

Parameters:

variable (str) – The name of the variable

Returns:

The units of the variable

Return type:

str

property first_id

The ID of the first member of the population.

Return type:

int

get(parameter_names, gather=True, simplify=True)[source]

Get the values of a parameter for every local cell in the population.

Parameters:

  • parameter_names (str or iterable(str)) – Name of parameter. This is either a single string or a list of strings

  • gather (bool) – pointless on sPyNNaker

  • simplify (bool) – ignored

Returns:

A single list of values (or possibly a single value) if paramter_names is a string, or a dict of these if parameter names is a list.

Return type:

ParameterHolder

get_data(variables='all', gather=True, clear=False, annotations=None)[source]

Return a Neo Block containing the data (spikes, state variables) recorded from the Assembly.

Parameters:

  • variables (str or list(str)) – either a single variable name or a list of variable names. Variables must have been previously recorded, otherwise an Exception will be raised.

  • gather (bool) –

    Whether to collect data from all MPI nodes or just the current node.

    Note

    This is irrelevant on sPyNNaker, which always behaves as if this parameter is True.

  • clear (bool) – Whether recorded data will be deleted from the Assembly.

  • annotations (dict(str, ...)) – annotations to put on the neo block

Return type:

Block

Raises:

ConfigurationException – If the variable or variables have not been previously set to record.

get_spike_counts(gather=True)[source]

Return the number of spikes for each neuron.

Return type:

ndarray

id_to_index(id)[source]

Given the ID(s) of cell(s) in the Population, return its (their) index (order in the Population).

Defined by https://neuralensemble.org/docs/PyNN/reference/populations.html

Parameters:

id (int or iterable(int)) –

Return type:

int or iterable(int)

id_to_local_index(cell_id)[source]

Given the ID(s) of cell(s) in the Population, return its (their) index (order in the Population), counting only cells on the local MPI node.

Defined by https://neuralensemble.org/docs/PyNN/reference/populations.html

Parameters:

cell_id (int or iterable(int)) –

Return type:

int or iterable(int)

index_to_id(index)[source]

Given the index (order in the Population) of cell(s) in the Population, return their ID(s)

Parameters:

index (int or iterable(int)) –

Return type:

int or iterable(int)

property initial_values

The initial values of the state variables.

Note

These values will be the same as the values set with the last call to initialize rather than the actual initial values if this call has been made.

Return type:

ParameterHolder

initialize(**kwargs)[source]

Set initial values of state variables, e.g. the membrane potential. Values passed to initialize() may be:

  • single numeric values (all neurons set to the same value), or

  • RandomDistribution objects, or

  • lists / arrays of numbers of the same size as the population mapping functions, where a mapping function accepts a single argument (the cell index) and returns a single number.

Values should be expressed in the standard PyNN units (i.e. millivolts, nanoamps, milliseconds, microsiemens, nanofarads, event per second).

Examples:

p.initialize(v=-70.0)
p.initialize(v=rand_distr, gsyn_exc=0.0)
p.initialize(v=lambda i: -65 + i / 10.0)
inject(current_source)[source]

Connect a current source to all cells in the Population.

Defined by https://neuralensemble.org/docs/PyNN/reference/populations.html

property label

The label of the population.

Return type:

str

property last_id

The ID of the last member of the population.

Return type:

int

property local_size

The number of local cells.

Defined by https://neuralensemble.org/docs/PyNN/reference/populations.html

property position_generator
Return type:

callable((int), ndarray)

property positions

The position array for structured populations.

Returns:

a 3xN array

Return type:

ndarray

record(variables, to_file=None, sampling_interval=None)[source]

Record the specified variable or variables for all cells in the Population or view.

Parameters:

  • variables (str or list(str)) – either a single variable name or a list of variable names. For a given celltype class, celltype.recordable contains a list of variables that can be recorded for that celltype.

  • to_file (io or rawio or str) – a file to automatically record to (optional). write_data() will be automatically called when sim.end() is called.

  • sampling_interval (int) – a value in milliseconds, and an integer multiple of the simulation timestep.

sample(n, rng=None)[source]

Randomly sample n cells from the Population, and return a PopulationView object.

Parameters:

  • n (int) – The number of cells to put in the view.

  • rng (NumpyRNG) – The random number generator to use

Return type:

PopulationView

set(**parameters)[source]

Set one or more parameters for every cell in the population.

parameter can be a dict, in which case value should not be supplied, or a string giving the parameter name, in which case value is the parameter value. value can be a numeric value, or list of such (e.g. for setting spike times):

p._set("tau_m", 20.0).
p._set({'tau_m':20, 'v_rest':-65})
Parameters:
Raises:

  • SimulatorRunningException – If sim.run is currently running

  • SimulatorNotSetupException – If called before sim.setup

  • SimulatorShutdownException – If called after sim.end

set_max_atoms_per_core(max_atoms_per_core)[source]

Supports the setting of this population’s max atoms per dimension per core.

Parameters:

max_atoms_per_core (int) – the new value for the max atoms per dimension per core.

Raises:

  • SimulatorRunningException – If sim.run is currently running

  • SimulatorNotSetupException – If called before sim.setup

  • SimulatorShutdownException – If called after sim.end

set_state(**kwargs)[source]

Set current values of state variables, e.g. the membrane potential. Values passed to set_state() may be:

  • single numeric values (all neurons set to the same value), or

  • RandomDistribution objects, or

  • lists / arrays of numbers of the same size as the population mapping functions, where a mapping function accepts a single argument (the cell index) and returns a single number.

Values should be expressed in the standard PyNN units (i.e. millivolts, nanoamps, milliseconds, microsiemens, nanofarads, event per second).

Examples:

p.set_state(v=-70.0)
p.set_state(v=rand_distr, gsyn_exc=0.0)
p.set_state(v=lambda i: -65 + i / 10.0)
property size

The number of neurons in the population.

Return type:

int

spinnaker_get_data(variable, as_matrix=False, view_indexes=None)[source]

Public accessor for getting data as a numpy array, instead of the Neo-based object

Parameters:

  • variable (str or list(str)) – a single variable name.

  • as_matrix (bool) – If set True the data is returned as a 2d matrix

  • view_indexes – The indexes for which data should be returned. If None, all data (view_index = data_indexes)

Returns:

array of the data

Return type:

ndarray

property structure

The structure for the population.

Return type:

BaseStructure or None

write_data(io, variables='all', gather=True, clear=False, annotations=None)[source]

Write recorded data to file, using one of the file formats supported by Neo.

Parameters:

  • io (neo.io.baseio.BaseIO or str) – a Neo IO instance, or a string for where to put a neo instance

  • variables (str or list(str)) – either a single variable name or a list of variable names. Variables must have been previously recorded, otherwise an Exception will be raised.

  • gather (bool) –

    Whether to bring all relevant data together.

    Note

    SpiNNaker always gathers.

  • clear (bool) – clears the storage data if set to true after reading it back

  • annotations (dict(str, ...)) – annotations to put on the neo block

Raises:

ConfigurationException – If the variable or variables have not been previously set to record.

class spynnaker.pyNN.PopulationView(parent, selector, label=None)

Bases: PopulationBase

A view of a subset of neurons within a Population.

In most ways, Populations and PopulationViews have the same behaviour, i.e., they can be recorded, connected with Projections, etc. It should be noted that any changes to neurons in a PopulationView will be reflected in the parent Population and vice versa.

It is possible to have views of views.

Note

Selector to Id is actually handled by AbstractSized.

Parameters:

  • parent (Population or PopulationView) – the population or view to make the view from

  • vertex (PopulationApplicationVertex) – The actual underlying vertex

  • recorder (Recorder) – The recorder of the Population

  • selector (None or slice or int or list(bool) or list(int) or ndarray(bool) or ndarray(int)) –

    a slice or numpy mask array. The mask array should either be a boolean array (ideally) of the same size as the parent, or an integer array containing cell indices, i.e. if p.size == 5 then:

    PopulationView(p, array([False, False, True, False, True]))
PopulationView(p, array([2, 4]))
PopulationView(p, slice(2, 5, 2))

    will all create the same view.

  • label (str) – A label for the view

all()[source]

Iterator over cell IDs (on all MPI nodes).

Return type:

iterable(IDMixin)

property all_cells

An array containing the cell IDs of all neurons in the Population (all MPI nodes).

Return type:

list(IDMixin)

can_record(variable)[source]

Determine whether variable can be recorded from this population.

Return type:

bool

property celltype

The type of neurons making up the underlying Population.

Return type:

AbstractPyNNModel

property conductance_based

Whether the post-synaptic response is modelled as a change in conductance or a change in current.

Return type:

bool

property current_values

A dict containing the current values of the state variables.

Return type:

InitialValuesHolder

describe(template='populationview_default.txt', engine='default')[source]

Returns a human-readable description of the population view.

The output may be customized by specifying a different template together with an associated template engine (see pyNN.descriptions).

If template is None, then a dictionary containing the template context will be returned.

Parameters:

  • template (str) – Template filename

  • engine (str or TemplateEngine or None) – Template substitution engine

Return type:

str or dict

find_units(variable)[source]

Get the units of a variable

Warning

No PyNN description of this method.

Parameters:

variable (str) – The name of the variable

Returns:

The units of the variable

Return type:

str

get(parameter_names, gather=False, simplify=True)[source]

Get the values of the given parameters for every local cell in the population, or, if gather=True, for all cells in the population.

Values will be expressed in the standard PyNN units (i.e. millivolts, nanoamps, milliseconds, microsiemens, nanofarads, event per second).

Note

SpiNNaker always gathers.

Parameters:
Return type:

ParameterHolder

get_data(variables='all', gather=True, clear=False, annotations=None)[source]

Return a Neo Block containing the data(spikes, state variables) recorded from the Population.

Parameters:

  • variables (str or list(str)) – Either a single variable name or a list of variable names. Variables must have been previously recorded, otherwise an Exception will be raised.

  • gather (bool) –

    For parallel simulators, if gather is True, all data will be gathered to all nodes and the Neo Block will contain data from all nodes. Otherwise, the Neo Block will contain only data from the cells simulated on the local node.

    Note

    SpiNNaker always gathers.

  • clear (bool) – If True, recorded data will be deleted from the Population.

  • annotations (dict(str, ...)) – annotations to put on the neo block

Return type:

Block

Raises:

ConfigurationException – If the variable or variables have not been previously set to record.

get_spike_counts(gather=True)[source]

Returns a dict containing the number of spikes for each neuron.

The dict keys are neuron IDs, not indices.

Note

Implementation of this method is different to Population as the Populations uses PyNN 7 version of the get_spikes method which does not support indexes.

Parameters:

gather (bool) –

Note

SpiNNaker always gathers.

Return type:

dict(int,int)

property grandparent

The parent Population at the root of the tree (since the immediate parent may itself be a PopulationView).

The name “grandparent” is of course a little misleading, as it could be just the parent, or the great, great, great, …, grandparent.

Return type:

Population

id_to_index(id)[source]

Given the ID(s) of cell(s) in the PopulationView, return its / their index / indices(order in the PopulationView).

assert pv.id_to_index(pv[3]) == 3

Parameters:

id (int or list(int)) –

Return type:

int or list(int)

index_in_grandparent(indices)[source]

Given an array of indices, return the indices in the parent population at the root of the tree.

Parameters:

indices (list(int)) –

Return type:

list(int)

property initial_values

A dict containing the initial values of the state variables.

Return type:

InitialValuesHolder

initialize(**initial_values)[source]

Set initial values of state variables, e.g. the membrane potential. Values passed to initialize() may be:

  • single numeric values (all neurons set to the same value), or

  • RandomDistribution objects, or

  • lists / arrays of numbers of the same size as the population mapping functions, where a mapping function accepts a single argument (the cell index) and returns a single number.

Values should be expressed in the standard PyNN units (i.e. millivolts, nanoamps, milliseconds, microsiemens, nanofarads, events per second).

Examples:

p.initialize(v=-70.0)
p.initialize(v=rand_distr, gsyn_exc=0.0)
p.initialize(v=lambda i: -65 + i / 10.0)
inject(current_source)[source]

Injects the specified current_source into this PopulationView.

Parameters:

current_source (AbstractCurrentSource) – the current source to be injected

property label

A label for the Population View.

Return type:

str

property mask

The selector mask that was used to create this view.

Return type:

None or slice or int or list(bool) or list(int) or ndarray(bool) or ndarray(int)

property parent

A reference to the parent Population (that this is a view of).

Return type:

Population

record(variables, to_file=None, sampling_interval=None)[source]

Record the specified variable or variables for all cells in the Population or view.

Parameters:

  • variables (str or list(str)) – either a single variable name, or a list of variable names, or all to record everything. For a given celltype class, celltype.recordable contains a list of variables that can be recorded for that celltype.

  • to_file (io or rawio or str) – If specified, should be a Neo IO instance and write_data() will be automatically called when sim.end() is called.

  • sampling_interval (int) – should be a value in milliseconds, and an integer multiple of the simulation timestep.

sample(n, rng=None)[source]

Randomly sample n cells from the Population view, and return a new PopulationView object.

Parameters:

  • n (int) – The number of cells to select

  • rng (NumpyRNG) – Random number generator

Return type:

PopulationView

set(**parameters)[source]

Set one or more parameters for every cell in the population. Values passed to set() may be:

  • single values,

  • RandomDistribution objects, or

  • lists / arrays of values of the same size as the population mapping functions, where a mapping function accepts a single argument (the cell index) and returns a single value.

Here, a “single value” may be either a single number or a list / array of numbers (e.g. for spike times).

Values should be expressed in the standard PyNN units (i.e. millivolts, nanoamps, milliseconds, microsiemens, nanofarads, event per second).

Examples:

p.set(tau_m=20.0, v_rest=-65).
p.set(spike_times=[0.3, 0.7, 0.9, 1.4])
p.set(cm=rand_distr, tau_m=lambda i: 10 + i / 10.0)
set_state(**initial_values)[source]

Set current values of state variables, e.g. the membrane potential. Values passed to initialize() may be:

  • single numeric values (all neurons set to the same value), or

  • RandomDistribution objects, or

  • lists / arrays of numbers of the same size as the population mapping functions, where a mapping function accepts a single argument (the cell index) and returns a single number.

Values should be expressed in the standard PyNN units (i.e. millivolts, nanoamps, milliseconds, microsiemens, nanofarads, events per second).

Examples:

p.set_state(v=-70.0)
p.set_state(v=rand_distr, gsyn_exc=0.0)
p.set_state(v=lambda i: -65 + i / 10.0)
property size

The total number of neurons in the Population View.

Return type:

int

spinnaker_get_data(variable, as_matrix=False)[source]

Public accessor for getting data as a numpy array, instead of the Neo-based object

Parameters:

  • variable (str) – a single variable name

  • as_matrix (bool) – If set True the data is returned as a 2d matrix

Returns:

array of the data

Return type:

ndarray

spinnaker_get_spikes()[source]

Public accessor for getting spikes as a numpy array, instead of the Neo-based object

write_data(io, variables='all', gather=True, clear=False, annotations=None)[source]

Write recorded data to file, using one of the file formats supported by Neo.

Parameters:

  • io (neo.io.BaseIO or str) – a Neo IO instance or the name of a file to write

  • variables (str or list(str)) – either a single variable name or a list of variable names. These must have been previously recorded, otherwise an Exception will be raised.

  • gather (bool) –

    For parallel simulators, if this is True, all data will be gathered to the master node and a single output file created there. Otherwise, a file will be written on each node, containing only data from the cells simulated on that node.

    Note

    SpiNNaker always gathers.

  • clear (bool) – If this is True, recorded data will be deleted from the Population.

  • annotations (dict(str, ...)) – should be a dict containing simple data types such as numbers and strings. The contents will be written into the output data file as metadata.

Raises:

ConfigurationException – If the variable or variables have not been previously set to record.

spynnaker.pyNN.Projection(presynaptic_population, postsynaptic_population, connector, synapse_type=None, source=None, receptor_type='excitatory', space=None, label=None)[source]

Used to support PEP 8 spelling correctly.

Parameters:

  • presynaptic_population (Population) – the source pop

  • postsynaptic_population (Population) – the destination population

  • connector (AbstractConnector) – the connector type

  • synapse_type (AbstractStaticSynapseDynamics) – the synapse type

  • source (None) – Unsupported; must be None

  • receptor_type (str) – the receptor type

  • space (Space or None) – the space object

  • label (str or None) – the label

Returns:

a projection object for SpiNNaker

Return type:

Projection

class spynnaker.pyNN.RandomByWeightElimination(threshold, prob_elim_depressed=0.0245, prob_elim_potentiated=0.00013600000000000003)

Bases: AbstractElimination

Elimination Rule that depends on the weight of a synapse.

Parameters:

  • threshold (float) – Below this weight is considered depression, above or equal to this weight is considered potentiation (or the static weight of the connection on static weight connections)

  • prob_elim_depressed (float) – The probability of elimination if the weight has been depressed (ignored on static weight connections)

  • prob_elim_potentiated (float) – The probability of elimination of the weight has been potentiated or has not changed (and also used on static weight connections)

get_parameter_names()[source]

Return the names of the parameters supported by this rule.

Return type:

iterable(str)

get_parameters_sdram_usage_in_bytes()[source]

Get the amount of SDRAM used by the parameters of this rule.

Return type:

int

property vertex_executable_suffix

The suffix to be appended to the vertex executable for this rule.

Return type:

str

write_parameters(spec, weight_scale)[source]

Write the parameters of the rule to the spec.

Parameters:

  • spec (DataSpecificationGenerator) –

  • weight_scale (float) –

class spynnaker.pyNN.RandomDistribution(distribution, parameters_pos=None, rng=None, **parameters_named)

Bases: RandomDistribution

Class which defines a next(n) method which returns an array of n random numbers from a given distribution.

Examples:

>>> rd = RandomDistribution('uniform', (-70, -50))
>>> rd = RandomDistribution('normal', mu=0.5, sigma=0.1)
>>> rng = NumpyRNG(seed=8658764)
>>> rd = RandomDistribution('gamma', k=2.0, theta=5.0, rng=rng)
Available distributions

Name

Parameters

Comments

binomial

n, p

gamma

k, theta

exponential

beta

lognormal

mu, sigma

normal

mu, sigma

normal_clipped

mu, sigma, low, high

Values outside (low, high) are redrawn

normal_clipped_to_boundary

mu, sigma, low, high

Values below/above low/high are set to low/high

poisson

lambda_

Trailing underscore since lambda is a Python keyword

uniform

low, high

uniform_int

low, high

Only generates integer values

vonmises

mu, kappa
Parameters:

  • distribution (str) – the name of a random number distribution.

  • parameters_pos (tuple or None) – parameters of the distribution, provided as a tuple. For the correct ordering, see random.available_distributions.

  • rng (NumpyRNG or GSLRNG or NativeRNG or None) – the random number generator to use, if a specific one is desired (e.g., to provide a seed).

  • parameters_named – parameters of the distribution, provided as keyword arguments.

Parameters may be provided either through parameters_pos or through parameters_named, but not both. All parameters must be provided, there are no default values. Parameter names are, in general, as used in Wikipedia.

class spynnaker.pyNN.RandomSelection

Bases: AbstractPartnerSelection

Partner selection that picks a random source neuron from all sources.

get_parameter_names()[source]

Return the names of the parameters supported by this rule.

Return type:

iterable(str)

get_parameters_sdram_usage_in_bytes()[source]

Get the amount of SDRAM used by the parameters of this rule.

Return type:

str

property vertex_executable_suffix

The suffix to be appended to the vertex executable for this rule.

Return type:

str

write_parameters(spec)[source]

Write the parameters of the rule to the spec.

Parameters:

spec (DataSpecificationGenerator) –

class spynnaker.pyNN.RandomStructure(boundary, origin=(0.0, 0.0, 0.0), rng=None)[source]

Bases: BaseStructure

Represents a structure with neurons distributed randomly within a given volume.

Arguments:

boundary - a subclass of Shape. origin - the coordinates (x,y,z) of the centre of the volume.

generate_positions(n)[source]

Calculate and return the positions of n neurons positioned according to this structure.

parameter_names = ('boundary', 'origin', 'rng')
spynnaker.pyNN.STDPMechanism

alias of SynapseDynamicsSTDP

class spynnaker.pyNN.SmallWorldConnector(degree, rewiring, allow_self_connections=True, n_connections=None, rng=None, safe=True, callback=None, verbose=False)

Bases: AbstractConnector, AbstractGenerateConnectorOnHost

A connector that uses connection statistics based on the Small World network connectivity model.

Note

This is typically used from a population to itself.

Parameters:

  • degree (float) – the region length where nodes will be connected locally

  • rewiring (float) – the probability of rewiring each edge

  • allow_self_connections (bool) – if the connector is used to connect a Population to itself, this flag determines whether a neuron is allowed to connect to itself, or only to other neurons in the Population.

  • n_connections (int or None) – if specified, the number of efferent synaptic connections per neuron

  • rng (NumpyRNG or None) – Seeded random number generator, or None to make one when needed.

  • safe (bool) – If True, check that weights and delays have valid values. If False, this check is skipped.

  • callback (callable) –

    if given, a callable that display a progress bar on the terminal.

    Note

    Not supported by sPyNNaker.

  • verbose (bool) – Whether to output extra information about the connectivity to a CSV file

create_synaptic_block(post_slices, post_vertex_slice, synapse_type, synapse_info)[source]

Create a synaptic block from the data.

Parameters:
Returns:

The synaptic matrix data to go to the machine, as a Numpy array

Return type:

ndarray

get_delay_maximum(synapse_info)[source]

Get the maximum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) – the synapse info

Return type:

int or None

get_delay_minimum(synapse_info)[source]

Get the minimum delay specified by the user in ms, or None if unbounded.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int or None

get_n_connections_from_pre_vertex_maximum(n_post_atoms, synapse_info, min_delay=None, max_delay=None)[source]

Get the maximum number of connections from any neuron in the pre vertex to the neurons in the post_vertex_slice, for connections with a delay between min_delay and max_delay (inclusive) if both specified (otherwise all connections).

Parameters:
Return type:

int

get_n_connections_to_post_vertex_maximum(synapse_info)[source]

Get the maximum number of connections to any neuron in the post vertex from neurons in the pre vertex.

Parameters:

synapse_info (SynapseInformation) –

Return type:

int

get_weight_maximum(synapse_info)[source]

Get the maximum of the weights for this connection.

Parameters:

synapse_info (SynapseInformation) –

Return type:

float

set_projection_information(synapse_info)[source]

Sets a connectors projection info.

Parameters:

synapse_info (SynapseInformation) – the synapse info

class spynnaker.pyNN.Space(axes=None, scale_factor=1.0, offset=0.0, periodic_boundaries=None)[source]

Bases: object

Class representing a space within distances can be calculated. The space is Cartesian, may be 1-, 2- or 3-dimensional, and may have periodic boundaries in any of the dimensions.

Arguments:
axes:

if not supplied, then the 3D distance is calculated. If supplied, axes should be a string containing the axes to be used, e.g. ‘x’, or ‘yz’. axes=’xyz’ is the same as axes=None.

scale_factor:

it may be that the pre and post populations use different units for position, e.g. degrees and µm. In this case, scale_factor can be specified, which is applied to the positions in the post-synaptic population.

offset:

if the origins of the coordinate systems of the pre- and post- synaptic populations are different, offset can be used to adjust for this difference. The offset is applied before any scaling.

periodic_boundaries:

either None, or a tuple giving the boundaries for each dimension, e.g. ((x_min, x_max), None, (z_min, z_max)).

AXES = {'x': [0], 'xy': [0, 1], 'xyz': range(0, 3), 'xz': [0, 2], 'y': [1], 'yz': [1, 2], 'z': [2], None: range(0, 3)}
distance_generator(f, g)[source]
distances(A, B, expand=False)[source]

Calculate the distance matrix between two sets of coordinates, given the topology of the current space. From http://projects.scipy.org/pipermail/numpy-discussion/2007-April/027203.html

class spynnaker.pyNN.Sphere(radius)[source]

Bases: Shape

Represents a spherical volume within which neurons may be distributed.

sample(n, rng)[source]

Return n points distributed randomly with uniform density within the sphere.

spynnaker.pyNN.SpiNNakerProjection

alias of Projection

spynnaker.pyNN.SpikePairRule

alias of TimingDependenceSpikePair

class spynnaker.pyNN.SpikeSourceArray(spike_times=None)

Bases: AbstractPyNNModel

create_vertex(n_neurons, label, splitter, n_colour_bits)[source]

Create a vertex for a population of the model.

Parameters:

  • n_neurons (int) – The number of neurons in the population

  • label (str) – The label to give to the vertex

  • splitter (AbstractSplitterCommon or None) –

  • n_colour_bits (int) –

Returns:

An application vertex for the population

Return type:

PopulationApplicationVertex

default_population_parameters = {'n_colour_bits': None, 'splitter': None}
class spynnaker.pyNN.SpikeSourcePoisson(rate=1.0, start=0, duration=None)

Bases: AbstractPyNNModel

absolute_max_atoms_per_core = 500
create_vertex(n_neurons, label, seed, max_rate, splitter, n_colour_bits)[source]

Create a vertex for a population of the model.

Parameters:

  • n_neurons (int) – The number of neurons in the population

  • label (str) – The label to give to the vertex

  • seed (float) –

  • max_rate (float) –

  • splitter (AbstractSplitterCommon or None) –

  • n_colour_bits (int) –

Returns:

An application vertex for the population

Return type:

PopulationApplicationVertex

default_population_parameters = {'max_rate': None, 'n_colour_bits': None, 'seed': None, 'splitter': None}
spynnaker.pyNN.StaticSynapse

alias of SynapseDynamicsStatic

class spynnaker.pyNN.StepCurrentSource(times=None, amplitudes=None)

Bases: AbstractCurrentSource

Current source where the amplitude changes based on a time array.

Parameters:
property current_source_id

The ID of the current source.

Return type:

int

property get_parameter_types

The parameter types for the current source.

Return type:

dict(str, Any)

property get_parameters

The parameters of the current source.

Return type:

dict(str, Any)

get_sdram_usage_in_bytes()[source]

The SDRAM usage in bytes of the current source.

Return type:

int

set_parameters(**parameters)[source]

Set the current source parameters.

Parameters:

parameters – the parameters to set

spynnaker.pyNN.StructuralMechanismSTDP

alias of SynapseDynamicsStructuralSTDP

spynnaker.pyNN.StructuralMechanismStatic

alias of SynapseDynamicsStructuralStatic

spynnaker.pyNN.connect(pre, post, weight=0.0, delay=None, receptor_type=None, p=1, rng=None)[source]

Builds a projection.

Parameters:

  • pre (Population) – source pop

  • post (Population) – destination pop

  • weight (float) – weight of the connections

  • delay (float) – the delay of the connections

  • receptor_type (str) – excitatory / inhibitory

  • p (float) – probability

  • rng (NumpyRNG) – random number generator

spynnaker.pyNN.create(cellclass, cellparams=None, n=1)[source]

Builds a population with certain parameters.

Parameters:

  • cellclass (type or AbstractPyNNModel) – population class

  • cellparams – population parameters.

  • n (int) – number of neurons

Return type:

Population

spynnaker.pyNN.distance(src_cell, tgt_cell, mask=None, scale_factor=1.0, offset=0.0, periodic_boundaries=None)[source]

Return the Euclidean distance between two cells.

Parameters:

  • src_cell – Measure from this cell

  • tgt_cell – To this cell

  • mask (ndarray) –

    allows only certain dimensions to be considered, e.g.:

    • to ignore the z-dimension, use mask=array([0,1])

    • to ignore y, mask=array([0,2])

    • to just consider z-distance, mask=array([2])

  • scale_factor (float) – allows for different units in the pre- and post-position (the post-synaptic position is multiplied by this quantity).

  • offset (float) –

  • periodic_boundaries –

spynnaker.pyNN.end(_=True)[source]

Cleans up the SpiNNaker machine and software

Parameters:

_ – was named compatible_output, which we don’t care about, so is a non-existent parameter

spynnaker.pyNN.get_current_time()[source]

Gets the time within the simulation.

Returns:

returns the current time

spynnaker.pyNN.get_machine()[source]

Get the SpiNNaker machine in use.

Returns:

the machine object

Return type:

Machine

spynnaker.pyNN.get_max_delay()[source]

Part of the PyNN API but does not make sense for sPyNNaker as different Projection, Vertex splitter combination could have different delays they can support.

Most likely value is timestep * 144

Raises:

NotImplementedError – As there is no system wide max_delay

spynnaker.pyNN.get_min_delay()[source]

The minimum allowed synaptic delay; delays will be clamped to be at least this.

Returns:

returns the min delay of the simulation

Return type:

int

spynnaker.pyNN.get_time_step()[source]

The integration time step.

Returns:

get the time step of the simulation (in ms)

Return type:

float

spynnaker.pyNN.initialize(cells, **initial_values)[source]

Sets cells to be initialised to the given values.

Parameters:

  • cells (Population or PopulationView) – the cells to change parameters on

  • initial_values – the parameters and their values to change

spynnaker.pyNN.list_standard_models()[source]

Return a list of all the StandardCellType classes available for this simulator.

Return type:

list(str)

spynnaker.pyNN.name()[source]

Returns the name of the simulator.

Return type:

str

spynnaker.pyNN.num_processes()[source]

The number of MPI processes.

Note

Always 1 on SpiNNaker, which doesn’t use MPI.

Returns:

the number of MPI processes

Return type:

int

spynnaker.pyNN.rank()[source]

The MPI rank of the current node.

Note

Always 0 on SpiNNaker, which doesn’t use MPI.

Returns:

MPI rank

Return type:

int

spynnaker.pyNN.record(variables, source, filename, sampling_interval=None, annotations=None)[source]

Sets variables to be recorded.

Parameters:

  • variables (str or list(str)) – may be either a single variable name or a list of variable names. For a given celltype class, celltype.recordable contains a list of variables that can be recorded for that celltype.

  • source (Population or PopulationView) – where to record from

  • filename (str) – file name to write data to

  • sampling_interval – how often to sample the recording, not ignored so far

  • annotations (dict(str, ...)) – the annotations to data writers

Returns:

neo object

Return type:

Block

spynnaker.pyNN.reset(annotations=None)[source]

Resets the simulation to t = 0.

Parameters:

annotations (dict(str, ...)) – the annotations to the data objects

spynnaker.pyNN.run(simtime, callbacks=None)[source]

The run() function advances the simulation for a given number of milliseconds.

Parameters:

  • simtime (float) – time to run for (in milliseconds)

  • callbacks – callbacks to run

Returns:

the actual simulation time that the simulation stopped at

Return type:

float

spynnaker.pyNN.run_for(simtime, callbacks=None)

The run() function advances the simulation for a given number of milliseconds.

Parameters:

  • simtime (float) – time to run for (in milliseconds)

  • callbacks – callbacks to run

Returns:

the actual simulation time that the simulation stopped at

Return type:

float

spynnaker.pyNN.run_until(tstop)[source]

Run until a (simulation) time period has completed.

Parameters:

tstop (float) – the time to stop at (in milliseconds)

Returns:

the actual simulation time that the simulation stopped at

Return type:

float

spynnaker.pyNN.set_number_of_neurons_per_core(neuron_type, max_permitted)[source]

Sets a ceiling on the number of neurons of a given model that can be placed on a single core. This can be overridden by the individual Population.

The new value can be None, meaning that the maximum is the same as the number of atoms, an int, meaning all Populations of this model must have one dimension, or a tuple of n integers, meaning all Populations of this model must have n dimensions. If not all Populations of this model have the same number of dimensions, it is recommended to set this to None here and then set the maximum on each Population.

Parameters:
spynnaker.pyNN.setup(timestep=0.1, min_delay='auto', max_delay=None, database_socket_addresses=None, time_scale_factor=None, n_chips_required=None, n_boards_required=None, **extra_params)[source]

The main method needed to be called to make the PyNN 0.8 setup. Needs to be called before any other function

Parameters:

  • timestep (float or None) – the time step of the simulations in microseconds; if None, the configuration value is used

  • min_delay (float or str) – the minimum delay of the simulation

  • max_delay (float or str or None) – Ignored and logs a warning if provided

  • database_socket_addresses (iterable(SocketAddress)) – the sockets used by external devices for the database notification protocol

  • time_scale_factor (int or None) – multiplicative factor to the machine time step (does not affect the neuron models accuracy)

  • n_chips_required (int or None) – Deprecated! Use n_boards_required instead. Must be None if n_boards_required specified.

  • n_boards_required (int or None) – if you need to be allocated a machine (for spalloc) before building your graph, then fill this in with a general idea of the number of boards you need so that the spalloc system can allocate you a machine big enough for your needs.

  • extra_params – other keyword arguments used to configure PyNN

Returns:

MPI rank (always 0 on SpiNNaker)

Return type:

int

Raises:

ConfigurationException – if both n_chips_required and n_boards_required are used.