bsb.simulation package

Submodules

bsb.simulation.simulation module

class bsb.simulation.simulation.ProgressEvent(progression, duration, time)

Bases: object

class bsb.simulation.simulation.Simulation(*args, _parent=None, _key=None, **kwargs)

Bases: object

cell_models: cfgdict[CellModel]

connection_models: cfgdict[ConnectionModel]

devices: cfgdict[DeviceModel]

duration: float

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

get_connectivity_sets() → Mapping[ConnectionModel, ConnectivitySet]

Return type:

Mapping[ConnectionModel, ConnectivitySet]

get_model_of(type: CellType | ConnectionStrategy) → CellModel | ConnectionModel | None

Parameters:

type (CellType | ConnectionStrategy)

Return type:

CellModel | ConnectionModel | None

get_node_name()

name: str

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

post_prepare: cfglist[Callable[[Simulation, Any], None]]

scaffold: Scaffold

simulator: str

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

bsb.simulation.adapter module

class bsb.simulation.adapter.AdapterProgress(duration)

Bases: object

complete()

steps(step=1)

tick(step)

Report simulation progress.

class bsb.simulation.adapter.SimulationData(simulation: Simulation, result=None)

Bases: object

Parameters:

simulation (Simulation)

class bsb.simulation.adapter.SimulatorAdapter

Bases: ABC

add_progress_listener(listener)

collect(simulation, simdata, simresult, comm=None)

Collect the output of a simulation that completed

abstract prepare(simulation, comm=None)

Reset the simulation backend and prepare for the given simulation.

Parameters:

• simulation (Simulation) – The simulation configuration to prepare.

• comm – The mpi4py MPI communicator to use. Only nodes in the communicator will participate in the simulation. The first node will idle as the main node.

abstract run(*simulations, comm=None)

Fire up the prepared adapter.

simulate(*simulations, post_prepare=None, comm=None)

Simulate the given simulations.

bsb.simulation.cell module

class bsb.simulation.cell.CellModel(*args, _parent=None, _key=None, **kwargs)

Bases: SimulationComponent

Cell models are simulator specific representations of a cell type.

cell_type: CellType

The cell type that this model represents

get_node_name()

get_placement_set(chunks=None)

parameters: cfglist[Parameter]

The parameters of the model.

bsb.simulation.component module

class bsb.simulation.component.SimulationComponent(*args, _parent=None, _key=None, **kwargs)

Bases: ABC

get_node_name()

name: str

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

property simulation

bsb.simulation.connection module

class bsb.simulation.connection.ConnectionModel(*args, _parent=None, _key=None, **kwargs)

Bases: SimulationComponent

get_connectivity_set()

get_node_name()

tag: str

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

bsb.simulation.device module

class bsb.simulation.device.DeviceModel(*args, _parent=None, _key=None, **kwargs)

Bases: SimulationComponent

get_node_name()

implement(adapter, simulation, simdata)

bsb.simulation.parameter module

class bsb.simulation.parameter.Parameter(*args, _parent=None, _key=None, **kwargs)

Bases: object

get_node_name()

type

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

value: ParameterValue

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

class bsb.simulation.parameter.ParameterValue(*args, _parent=None, _key=None, **kwargs)

Bases: object

get_node_name()

type

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

bsb.simulation.results module

class bsb.simulation.results.SimulationRecorder

Bases: object

flush(segment: neo.core.Segment)

Parameters:

segment (neo.core.Segment)

class bsb.simulation.results.SimulationResult(simulation)

Bases: object

add(recorder)

property analogsignals

create_recorder(flush: Callable[[neo.core.Segment], None])

Parameters:

flush (Callable[[neo.core.Segment], None])

flush()

property spiketrains

write(filename, mode)

bsb.simulation.targetting module

class bsb.simulation.targetting.BranchLocTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: LabelTargetting

get_locations(cell)

get_node_name()

x

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

class bsb.simulation.targetting.ByIdTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: FractionFilter, CellTargetting

Targets all given identifiers.

get_node_name()

get_targets(adapter, simulation, simdata)

ids: dict[str, list[int]]

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

class bsb.simulation.targetting.ByLabelTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all given labels.

get_node_name()

get_targets(adapter, simulation, simdata)

labels: list[str]

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

class bsb.simulation.targetting.CellModelFilter

Bases: object

cell_models: list[CellModel]

get_targets(adapter, simulation, simdata)

class bsb.simulation.targetting.CellModelTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all cells of certain cell models.

cell_models: list[CellModel]

get_node_name()

get_targets(adapter, simulation, simdata)

class bsb.simulation.targetting.CellTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: Targetting

get_node_name()

get_targets(adapter, simulation, simdata)

type: Literal['cell', 'connection']

class bsb.simulation.targetting.ConnectionTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: Targetting

get_node_name()

get_targets(adapter, simulation, simdata)

type: Literal['cell', 'connection']

class bsb.simulation.targetting.CylindricalTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all cells in a cylinder along specified axis.

axis: Literal['x', 'y', 'z']

Main axis of the cylinder

get_node_name()

get_targets(adapter, simulation, simdata)

Target all or certain cells within a cylinder of specified radius.

origin: ndarray[float]

Coordinates of the base of the cylinder for each non main axis

radius: float

Radius of the cylinder

class bsb.simulation.targetting.FractionFilter

Bases: object

count

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

static filter(f)

fraction

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

satisfy_fractions(targets)

class bsb.simulation.targetting.LabelTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: LocationTargetting

get_locations(cell)

get_node_name()

labels

class bsb.simulation.targetting.LocationTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: object

get_locations(cell)

get_node_name()

strategy

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

class bsb.simulation.targetting.RepresentativesTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all identifiers of certain cell types.

get_node_name()

get_targets(adapter, simulation, simdata)

n: int

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

class bsb.simulation.targetting.SomaTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: LocationTargetting

get_locations(cell)

get_node_name()

class bsb.simulation.targetting.SphericalTargetting(*args, _parent=None, _key=None, **kwargs)

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all cells in a sphere.

get_node_name()

get_targets(adapter, simulation, simdata)

Target all or certain cells within a sphere of specified radius.

origin: list[float]

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

radius: float

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

class bsb.simulation.targetting.Targetting(*args, _parent=None, _key=None, **kwargs)

Bases: object

get_node_name()

get_targets(adapter, simulation, simdata)

strategy

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

type: Literal['cell', 'connection']

Base implementation of all the different configuration attributes. Call the factory function attr() instead.

Module contents

class bsb.simulation.SimulationBackendPlugin(Adapter: bsb.simulation.adapter.SimulatorAdapter, Simulation: bsb.simulation.simulation.Simulation)

Bases: object

Parameters:

• Adapter (SimulatorAdapter)

• Simulation (Simulation)

Adapter: SimulatorAdapter

Simulation: Simulation

bsb.simulation.get_simulation_adapter(name: str)

Parameters:

name (str)