API Reference: PyNN.brainscales2¶
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pynn_brainscales.brainscales2.populations.Assembly : public pyNN.common.Assembly
Private Static Attributes
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_simulator
= simulator¶
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-
class
pynn_brainscales.brainscales2.simulator.
BackgroundSpikeSourcePlacement
¶ Tracks assignment of pyNN IDs of SpikeSourcePoissonOnChip based populations to the corresponding hardware entity, i.e.
BackgroundSpikeSourceOnDLS. We use one source on each hemisphere to ensure arbitrary routing works. Default constructed with reversed 1 to 1 permutation to yield better distribution for small networks.
:cvar default_permutation: Default permutation, where allocation is ordered to start at the highest-enum PADI-bus to reduce overlap with allocated neurons.
Public Functions
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__init__
(self, List[int] permutation=None)¶ :param permutation: Look up table for permutation.
Index: HW related population neuron enumeration. Value: HW neuron enumeration.
Private Static Functions
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_check_and_transform
(list lut)¶
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pynn_brainscales.brainscales2.projections.Connection : public pyNN.common.Connection
Store an individual plastic connection and information about it.
Provide an interface that allows access to the connection’s weight, delay and other attributes.
Public Functions
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__init__
(self, projection, pre_index, post_index, **parameters)¶
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as_tuple
(self, *attribute_names)¶
Public Members
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changed_since_last_run
¶
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parameters
¶
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pop_post_index
¶
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pop_pre_index
¶
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postsynaptic_index
¶
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presynaptic_index
¶
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projection
¶
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cells.HXNeuron : public StandardCellType , public cells.NetworkAddableCell
One to one representation of subset of parameter space of a lola.AtomicNeuron.
Parameter hierarchy is flattened. Defaults to “silent” neuron.
:param parameters: Mapping of parameters and corresponding values, e.g. dict. Either 1-dimensional or population size dimensions. Default values are overwritten for specified parameters.
Public Functions
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__init__
(self, **parameters)¶ parameters
should be a mapping object, e.g.a dict
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apply_config
(self, List[halco.AtomicNeuronOnDLS] coords)¶ Extract and apply config according to provided chip object.
:param coords: List of coordinates to look up coco. Needs same order and dimensions as parameter_space.
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can_record
(self, str variable)¶
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create_hw_entity
(cls, dict pynn_parameters)¶ Builds a Lola Neuron with the values from the dict ‘pynn_parameters’.
Public Static Functions
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add_to_input_generator
(Population population, grenade.InputGenerator builder)¶ Add external events to input generator.
:param population: Population to add featuring this cell’s celltype. :param builder: Input builder to add external events to.
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add_to_network_graph
(Population population, grenade.NetworkBuilder builder)¶ Add population to network builder.
:param population: Population to add featuring this cell’s celltype. :param builder: Network builder to add population to. :return: Descriptor of added population
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get_default_values
()¶ Get the default values of a LoLa Neuron.
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get_values
(lola.AtomicNeuron() atomic_neuron)¶ Get values of a LoLa Neuron instance as a dict.
Private Functions
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_generate_hw_entity_setters
(cls)¶ Builds setters for creation of Lola Neuron.
Private Static Functions
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_create_translation
()¶
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pynn_brainscales.brainscales2.simulator.ID : public int , public IDMixin
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Private Static Attributes
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__doc__
= IDMixin.__doc__¶
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class
pynn_brainscales.brainscales2.
InjectedConfiguration
¶ User defined injected configuration.
:param pre_non_realtime: Injection written prior to the non realtime configuration. :param pre_realtime: Injection written prior to the realtime configuration. :param post_realtime: Injection written after the the realtime configuration.
Public Static Attributes
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default_factory
¶
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class
pynn_brainscales.brainscales2.
InjectedReadout
¶ User defined injected readout.
:param pre_realtime: Injection of reads after the the pre_realtime configuration. :param post_realtime: Injection of reads after the the post_realtime configuration.
Public Static Attributes
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default_factory
¶
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pynn_brainscales.brainscales2.recording.MADCRecorderSetting : public NamedTuple
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cells.NetworkAddableCell : public ABC
Subclassed by cells.HXNeuron, cells.SpikeSourceArray, cells.SpikeSourcePoisson, cells.SpikeSourcePoissonOnChip
Public Static Functions
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add_to_input_generator
(Population population, grenade.InputGenerator builder)¶ Add external events to input generator.
:param population: Population to add featuring this cell’s celltype. :param builder: Input builder to add external events to.
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add_to_network_graph
(Population population, grenade.NetworkBuilder builder)¶ Add population to network builder.
:param population: Population to add featuring this cell’s celltype. :param builder: Network builder to add population to. :return: Descriptor of added population
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class
pynn_brainscales.brainscales2.simulator.
NeuronPlacement
¶ Tracks assignment of pyNN IDs of HXNeuron based populations to the corresponding hardware entity, i.e.
AtomicNeuronOnDLS. Default constructed with 1 to 1 permutation.
:param neuron_id: Look up table for permutation. Index: HW related population neuron enumeration. Value: HW neuron enumeration.
Public Functions
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__init__
(self, List[int] permutation=None)¶
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id2atomicneuron
(self, Union[List[ID], ID] neuron_id)¶ Get hardware coordinate from pyNN ID.
:param neuron_id: pyNN neuron ID
Private Static Functions
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_check_and_transform
(list lut)¶
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class
pynn_brainscales.brainscales2.plasticity_rules.
PlasticityRule
¶ Plasticity rule base class.
Inheritance is to be used for actual implementations. Periodic timing information is provided via class
Timer
. The kernel implementation is required to be in the form of C++-based PPU kernel code.Public Functions
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__init__
(self, Timer timer)¶ Create a new plasticity rule with timing information.
:param timer: Timer object.
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add_to_network_graph
(self, grenade.NetworkBuilder builder)¶
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generate_kernel
(self)¶ Generate plasticity rule kernel to be compiled into PPU program.
The interface to be adhered to is the same as in the empty implementation below.
PLASTICITY_RULE_KERNEL
is the generic name of the kernel function, which will be expanded to a unique implementation-defined name upon compilation to allow for multiple kernels.:return: PPU-code of plasticity-rule kernel as string.
Public Members
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changed_since_last_run
¶
Properties
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timer
= property(_get_timer, _set_timer)¶
Private Functions
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_add_projection
(self, Projection new_projection)¶
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_get_timer
(self)¶
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_remove_projection
(self, Projection old_projection)¶
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_set_timer
(self, new_timer)¶
Private Static Attributes
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_simulator
= simulator¶
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pynn_brainscales.brainscales2.examples.plasticity_rule.PlasticSynapse : public pynn.PlasticityRule , public pynn.standardmodels.synapses.StaticSynapse
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pynn_brainscales.brainscales2.populations.Population : public pyNN.common.Population
-
Public Static Attributes
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changed_since_last_run
= True¶
Private Functions
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_create_cells
(self)¶
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_get_parameters
(self, *names)¶ Return a ParameterSpace containing native parameters.
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_get_view
(self, selector, label=None)¶
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_set_initial_value_array
(self, variable, value)¶
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_set_parameters
(self, parameter_space)¶ parameter_space should contain native parameters
Private Members
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_mask_local
¶
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pynn_brainscales.brainscales2.populations.PopulationView : public pyNN.common.PopulationView
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pynn_brainscales.brainscales2.projections.Projection : public pyNN.common.Projection
Public Functions
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__init__
(self, presynaptic_neurons, postsynaptic_neurons, connector, synapse_type=None, source=None, receptor_type=None, space=Space(), label=None)¶ Create a new projection, connecting the pre- and post-synaptic neurons.
:param presynaptic_neurons: Population, PopulationView or Assembly object.
:param postsynaptic_neurons: Population, PopulationView or Assembly object.
:param connector: a Connector object, encapsulating the algorithm to use for connecting the neurons.
:param synapse_type: a SynapseType object specifying which synaptic connection mechanisms to use, defaults to None
:param source: string specifying which attribute of the presynaptic cell signals action potentials. This is only needed for multicompartmental cells with branching axons or dendrodendritic synapses. All standard cells have a single source, and this is the default, defaults to None
:param receptor_type: string specifying which synaptic receptor_type type on the postsynaptic cell to connect to. For standard cells, this can be ‘excitatory’ or ‘inhibitory’. For non-standard cells, it could be ‘NMDA’, etc. If receptor_type is not given, the default values of ‘excitatory’ is used, defaults to None
:param space: Space object, determining how distances should be calculated for distance-dependent wiring schemes or parameter values, defaults to Space()
:param label: a name for the projection (one will be auto-generated if this is not supplied), defaults to None
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__getitem__
(self, i)¶ Return the *i*th connection within the Projection.
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__len__
(self)¶ Return the total number of local connections.
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__setattr__
(self, name, value)¶
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placed_connections
(self)¶ Query the last routing run for placement of this projection.
Public Static Functions
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add_to_network_graph
(List[Population] populations, Projection projection, grenade.NetworkBuilder builder)¶
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pynn_brainscales.brainscales2.recording.Recorder : public pyNN.recording.Recorder
Public Functions
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__init__
(self, population, file=None)¶
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record
(self, variables, ids, sampling_interval=None)¶
Public Members
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changed_since_last_run
¶
Public Static Attributes
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madc_variables
= ["v", "exc_synin", "inh_synin", "adaptation"]¶
Private Functions
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_clear_simulator
(self)¶
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_get_current_segment
(self, filter_ids=None, variables='all', clear=False)¶
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_local_count
(self, variable, filter_ids)¶
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_record
(self, variable, new_ids, sampling_interval=None)¶
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_reset
(self)¶
Private Static Functions
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_get_spiketimes
(ids, clear=None)¶ Returns a dict containing the neuron_id and its spiketimes.
Private Static Attributes
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_simulator
= simulator¶
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cells.SpikeSourceArray : public cells.NetworkAddableCell
Spike source generating spikes at the times [ms] given in the spike_times array.
Public Functions
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can_record
(self, str variable)¶
Public Static Functions
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add_to_input_generator
(Population population, grenade.InputGenerator builder)¶ Add external events to input generator.
:param population: Population to add featuring this cell’s celltype. :param builder: Input builder to add external events to.
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add_to_network_graph
(Population population, grenade.NetworkBuilder builder)¶ Add population to network builder.
:param population: Population to add featuring this cell’s celltype. :param builder: Network builder to add population to. :return: Descriptor of added population
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cells.SpikeSourcePoisson : public cells.NetworkAddableCell
Spike source, generating spikes according to a Poisson process.
Public Functions
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__init__
(self, start, rate, duration)¶
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can_record
(self, str variable)¶
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get_spike_times
(self)¶ When this function is called for the first time, the spike times for a Poisson stimulation are calculated and saved, so that all neurons connected to it receive the same stimulation.
When a parameter was changed (compared to the last calculation of the spike time), the times are recalculated.
:return: (unsorted) spike times for each neuron in the population.
Public Static Functions
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add_to_input_generator
(Population population, grenade.InputGenerator builder)¶ Add external events to input generator.
:param population: Population to add featuring this cell’s celltype. :param builder: Input builder to add external events to.
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add_to_network_graph
(Population population, grenade.NetworkBuilder builder)¶ Add population to network builder.
:param population: Population to add featuring this cell’s celltype. :param builder: Network builder to add population to. :return: Descriptor of added population
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cells.SpikeSourcePoissonOnChip : public StandardCellType , public cells.NetworkAddableCell
Spike source, generating spikes according to a Poisson process.
Public Static Functions
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add_to_input_generator
(Population population, grenade.InputGenerator builder)¶ Add external events to input generator.
:param population: Population to add featuring this cell’s celltype. :param builder: Input builder to add external events to.
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add_to_network_graph
(Population population, grenade.NetworkBuilder builder)¶ Add population to network builder.
:param population: Population to add featuring this cell’s celltype. :param builder: Network builder to add population to. :return: Descriptor of added population
Public Static Attributes
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recordable
= []¶
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translations
= build_translations(('rate', 'rate'),('seed', 'seed'),)¶
Private Static Attributes
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_simulator
= simulator¶
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pynn_brainscales.brainscales2.simulator.State : public BaseState
Represent the simulator state.
Public Functions
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__init__
(self)¶
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clear
(self)¶
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prepare_static_config
(self)¶
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reset
(self)¶ Reset the state of the current network to time t = 0.
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run
(self, Optional[float] runtime)¶ Performs a hardware run for
runtime
milliseconds.If runtime is
None
, we only perform preparatory steps.
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run_until
(self, tstop)¶
Public Members
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background_spike_source_placement
¶
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conn
¶
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conn_comes_from_outside
¶
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conn_manager
¶
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current_sources
¶
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grenade_chip_config
¶
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grenade_network
¶
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grenade_network_graph
¶
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id_counter
¶
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initial_config
¶
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injected_config
¶
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injected_readout
¶
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injection_post_realtime
¶
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injection_pre_realtime
¶
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injection_pre_static_config
¶
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log
¶
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madc_recorder
¶
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madc_samples
¶
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max_delay
¶
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min_delay
¶
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mpi_rank
¶
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neuron_placement
¶
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num_processes
¶
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plasticity_rules
¶
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populations
¶
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post_realtime_read
¶
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post_realtime_tickets
¶
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pre_realtime_read
¶
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pre_realtime_tickets
¶
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projections
¶
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recorders
¶
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running
¶
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segment_counter
¶
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spikes
¶
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t
¶
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t_start
¶
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times
¶
Private Functions
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_configure_hxneuron
(self, lola.Chip config, ID neuron_id, dict parameters, bool enable_spike_output)¶ Places Neuron in Population “pop” on chip and configures spike and v recording.
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_configure_recorders_populations
(self, lola.Chip config)¶
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_generate_inputs
(self, grenade.NetworkGraph network_graph)¶ Generate external input events from the routed network graph representation.
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_generate_network_graph
(self)¶ Generate placed and routed executable network graph representation.
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_generate_playback_hooks
(self)¶
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_get_post_realtime_read
(self)¶ Redeem tickets of injected readout after post_realtime section to get information after execution.
:return: Dictionary with coordinates as keys and read container as values.
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_get_pre_realtime_read
(self)¶ Redeem tickets of injected readout after pre_realtime section to get information after execution.
:return: Dictionary with coordinates as keys and read container as values.
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_prepare_post_realtime_read
(self, sta.PlaybackProgramBuilder builder)¶ Prepare injected readout after post_realtime configuration.
This generates tickets to access the read information and ensures completion via a barrier. :param builder: Builder to append instructions to.
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_prepare_pre_realtime_read
(self, sta.PlaybackProgramBuilder builder)¶ Prepare injected readout after pre_realtime configuration and before realtime experiment section.
This generates tickets to access the read information and ensures completion via a barrier. :param builder: Builder to append instructions to.
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_recorders_populations_changed
(self)¶ Collect populations which configurations were changed.
This includes changes in:
neuron parameters
recorder settings
out-going synaptic connections
:return: Populations which were subject to a change mentioned above.
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_reset_changed_since_last_run
(self)¶ Reset changed_since_last_run flag to track incremental changes for the next run.
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_spike_source_indices
(self)¶ Collect all neurons which serve as a spike source.
Check each projection and collect populations and their neurons which serve as spike sources.
:return: Sets cell ids of neurons which serve as spike sources. These sets are organized in populations which they belong to.
Private Static Functions
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_configure_routing
(lola.Chip config)¶ Configure global routing-related but static parameters.
:param config: Chip configuration to add configuration to :return: Altered chip configuration
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_get_spikes
(grenade.NetworkGraph network_graph, grenade.IODataMap outputs)¶ Get spikes indexed via neuron IDs.
:param network_graph: Network graph to use for lookup of spike label <-> ID relation :param outputs: All outputs of a single execution to extract spikes from :return: Spikes as dict with atomic neuron enum value as key and numpy array of times as value
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_get_v
(grenade.NetworkGraph network_graph, grenade.IODataMap outputs)¶ Get MADC samples with times in ms.
:param network_graph: Network graph to use for lookup of MADC output vertex descriptor :param outputs: All outputs of a single execution to extract samples from :return: Times and sample values as numpy array
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class
synapses.
StaticSynapse
¶ Synaptic connection with fixed weight and delay.
Public Static Attributes
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translations
= build_translations(('weight', 'weight'),('delay', 'delay'))¶
Private Functions
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_get_minimum_delay
(self)¶
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class
pynn_brainscales.brainscales2.plasticity_rules.
Timer
¶ Periodic timer information for plasticity rule execution.
Public Members
-
parameters
¶
Properties
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num_periods
= property(_get_num_periods, _set_num_periods)¶
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period
= property(_get_period, _set_period)¶
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start
= property(_get_start, _set_start)¶
-
-
module
cells
¶
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namespace
pyNN
¶
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namespace
pynn
¶
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namespace
common
¶
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namespace
recording
¶
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namespace
standardmodels
¶
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namespace
synapses
¶
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module
pynn_brainscales
¶
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module
pynn_brainscales.
brainscales2
¶ Functions
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end
()¶ Do any necessary cleaning up before exiting.
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get_backend_statistics
()¶ Get statistics of placement and routing like amount of time spent and number of hardware entities used.
:raises RuntimeError: If the simulator is not active, i.e. pynn.setup() was not called. :raises RuntimeError: If the routing and placement step were not performed, i.e. pynn.run() was not called. :return: Statistics object.
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get_post_realtime_read
()¶ Get injected read results of after post_realtime section.
:return: Dictionary with coordinates as keys and read container as values.
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get_pre_realtime_read
()¶ Get injected read results of after pre_realtime section.
:return: Dictionary with coordinates as keys and read container as values.
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list_standard_models
()¶ Return a list of all the StandardCellType classes available for this simulator.
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run
(*args, **kwargs)¶
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setup
(timestep=simulator.State.dt, min_delay=DEFAULT_MIN_DELAY, **extra_params)¶ Should be called at the very beginning of a script.
:param extra_params: most params come from pynn.common.setup neuronPermutation: List providing lookup for custom pyNN neuron to hardware neuron. Index: HW related population neuron enumeration. Value: HW neuron enumeration. Can be shorter than total HW neuron count. E.g. [2,4,5] results in the first neuron of the first HXNeuron population to be assigned to AtomicNeuronOnDLS(Enum(2)) and so forth. backgroundPermutation: List providing lookup for custom pyNN background spike source to hardware entity. Index: HW related population source enumeration. Value: HW source enumeration. Can be shorter than total HW source count. E.g. [2,3] results in the first population to be assigned to PADIBusOnPADIBusBlock(2) and so forth. enable_neuron_bypass: Enable neuron bypass mode: neurons forward spikes arriving at the synaptic input (i.e. no leaky integration is happening); defaults to False. initial_config: Initial configuration of the entire chip. Can for example be used to manually apply a calibration result. injected_config: Optional user defined injected configuration. injected_readout: Optional user defined injected readout.
Variables
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__all__
= ["list_standard_models", "setup", "end", "run", "run_until","run_for", "reset", "initialize", "get_current_time", "create","connect", "set", "record", "logger"]¶
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connect
= common.build_connect(Projection, FixedProbabilityConnector, synapses.StaticSynapse)¶
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create
= common.build_create(Population)¶
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initialize
= common.initialize¶
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num_processes
¶
-
rank
¶
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record
= common.build_record(simulator)¶
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reset
= common.build_reset(simulator)¶
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run_for
= run¶
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set
= common.set¶
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-
module
examples
¶
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module
pynn_brainscales.brainscales2.examples.
crossbar_event_counter_read
¶ Functions
-
main
(int num_spikes=200, float runtime=20.)¶ This example shows readout of the event output counters in the routing crossbar via injected reads.
:param num_spikes: Number of spikes to inject during the experiment. :param runtime: Runtime of the experiment [ms]. :return: Difference between counter values before the experiment and after the experiment. The results are saved in a dictionary with an entry for each crossbar output.
-
-
module
pynn_brainscales.brainscales2.examples.
external_input
¶ Functions
-
main
(dict params)¶
Variables
-
cell_params
= {"threshold_v_threshold": 300,"leak_v_leak": 750,"leak_i_bias": 420,"leak_enable_division": True,"reset_v_reset": 200,"reset_i_bias": 950,"reset_enable_multiplication": True,"threshold_enable": True,"membrane_capacitance_capacitance": 4,"refractory_period_refractory_time": 250,"excitatory_input_enable": True,"excitatory_input_i_bias_tau": 150,"excitatory_input_i_bias_gm": 200,# FIXME: replace by i_drop_input and i_shift_reference# "excitatory_input_v_syn": 700}¶
-
level
¶
-
log
= pynn.logger.get("external_input")¶
-
spiketimes
= main(cell_params)¶
-
-
module
pynn_brainscales.brainscales2.examples.
isi_calib
¶
-
module
pynn_brainscales.brainscales2.examples.
plasticity_rule
¶ Functions
-
main
(dict params)¶
Variables
-
cell_params
= {"threshold_v_threshold": 300,"leak_v_leak": 750,"leak_i_bias": 420,"leak_enable_division": True,"reset_v_reset": 200,"reset_i_bias": 950,"reset_enable_multiplication": True,"threshold_enable": True,"membrane_capacitance_capacitance": 4,"refractory_period_refractory_time": 250,"excitatory_input_enable": True,"excitatory_input_i_bias_tau": 150,"excitatory_input_i_bias_gm": 200,# FIXME: replace by i_drop_input and i_shift_reference# "excitatory_input_v_syn": 700}¶
-
level
¶
-
log
= pynn.logger.get("plasticity_rule")¶
-
spiketimes
= main(cell_params)¶
-
-
module
pynn_brainscales.brainscales2.examples.
single_neuron_demo
¶ Functions
-
plot_membrane_dynamics
(Population population, segment_id=-1)¶ Plot the membrane potential of the neuron in a given population view.
Only population views of size 1 are supported. :param population: Population, membrane traces and spikes are plotted for. :param segment_id: Index of the neo segment to be plotted. Defaults to -1, encoding the last recorded segment.
Variables
-
exc_spiketimes
= [0.01, 0.05, 0.07, 0.08]¶
-
exc_stim_pop
= pynn.Population(1, SpikeSourceArray(spike_times=exc_spiketimes))¶
-
inh_spiketimes
= [0.03]¶
-
inh_stim_pop
= pynn.Population(1, SpikeSourceArray(spike_times=inh_spiketimes))¶
-
level
¶
-
logger
= pynn.logger.get("single_neuron_demo")¶
-
p_view
= pynn.PopulationView(pop, [neuron_id])¶
-
pop
= pynn.Population(1, pynn.cells.HXNeuron(# Leak potential, range: 300-1000leak_v_leak=700,# Leak conductance, range: 0-1022leak_i_bias=1022))¶
-
receptor_type
¶
-
stimulated_p
¶
-
synapse_type
¶
-
-
module
pynn_brainscales.brainscales2.
helper
¶ Functions
-
chip_from_file
(str path)¶ Extract chip config from coco file dump.
:param path: path to file containing coco dump.
-
chip_from_nightly
()¶ Extract chip config from nightly calibration.
-
chip_from_portable_binary
(bytes data)¶ Convert portable binary data to chip object.
:param data: Coco list in portable binary format. :return: lola chip configuration.
-
get_unique_identifier
()¶ Retrieve the unique identifier of the current chip.
Set by Slurm when allocating resources.
-
nightly_calib_path
()¶ Find path for nightly calibration.
-
nightly_calib_url
()¶ Find url for nightly calibration.
-
-
module
plasticity_rules
¶
-
module
populations
¶
-
module
projections
¶
-
module
recording
¶
-
namespace
std
STL namespace.
-
module
synapses
¶
-
file
__init__.py
-
file
__init__.py
-
file
__init__.py
-
file
crossbar_event_counter_read.py
-
file
external_input.py
-
file
internal_projections.py
-
file
isi_calib.py
-
file
leak_over_threshold.py
-
file
plasticity_rule.py
-
file
single_neuron_demo.py
-
file
helper.py
-
file
plasticity_rules.py
-
file
populations.py
-
file
projections.py
-
file
recording.py
-
file
simulator.py
-
file
cells.py
-
file
synapses.py
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dir
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