bsb.simulation package#

Submodules#

bsb.simulation.simulation module#

class bsb.simulation.simulation.ProgressEvent(progression, duration, time)[source]#: Bases: object

class bsb.simulation.simulation.Simulation(*args, _parent=None, _key=None, **kwargs)[source]#

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][source]#

get_model_of(type: CellType | ConnectionStrategy) → CellModel | ConnectionModel | None[source]#

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)[source]#

Bases: object

complete()[source]#

steps(step=1)[source]#

tick(step)[source]#: Report simulation progress.

class bsb.simulation.adapter.SimulationData(simulation: Simulation, result=None)[source]#: Bases: object

class bsb.simulation.adapter.SimulatorAdapter[source]#

Bases: ABC

add_progress_listener(listener)[source]#

collect(simulation, simdata, simresult, comm=None)[source]#: Collect the output of a simulation that completed

abstract prepare(simulation, comm=None)[source]#

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)[source]#: Fire up the prepared adapter.

simulate(*simulations, post_prepare=None, comm=None)[source]#: Simulate the given simulations.

bsb.simulation.cell module#

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

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)[source]#

parameters: cfglist[Parameter]#: The parameters of the model.

bsb.simulation.component module#

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

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)[source]#

Bases: SimulationComponent

get_connectivity_set()[source]#

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)[source]#

Bases: SimulationComponent

get_node_name()#

implement(adapter, simulation, simdata)[source]#

bsb.simulation.parameter module#

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

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)[source]#

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[source]#

Bases: object

flush(segment: neo.core.Segment)[source]#

class bsb.simulation.results.SimulationResult(simulation)[source]#

Bases: object

add(recorder)[source]#

property analogsignals#

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

flush()[source]#

property spiketrains#

write(filename, mode)[source]#

bsb.simulation.targetting module#

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

Bases: LabelTargetting

get_locations(cell)[source]#

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)[source]#

Bases: FractionFilter, CellTargetting

Targets all given identifiers.

get_node_name()#

get_targets(adapter, simulation, simdata)[source]#

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)[source]#

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all given labels.

get_node_name()#

get_targets(adapter, simulation, simdata)[source]#

labels: list[str]#: Base implementation of all the different configuration attributes. Call the factory function attr() instead.

class bsb.simulation.targetting.CellModelFilter[source]#

Bases: object

cell_models: list[CellModel]#

get_targets(adapter, simulation, simdata)[source]#

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

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all cells of certain cell models.

cell_models: list[CellModel]#

get_node_name()#

get_targets(adapter, simulation, simdata)[source]#

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

Bases: Targetting

get_node_name()#

get_targets(adapter, simulation, simdata)[source]#

type: Literal['cell'] | Literal['connection']#

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

Bases: Targetting

get_node_name()#

get_targets(adapter, simulation, simdata)[source]#

type: Literal['cell'] | Literal['connection']#

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

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all cells in a cylinder along specified axis.

axis: Literal['x'] | Literal['y'] | Literal['z']#: Base implementation of all the different configuration attributes. Call the factory function attr() instead.

get_node_name()#

get_targets(adapter, simulation, simdata)[source]#: Target all or certain cells within a cylinder 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.FractionFilter[source]#

Bases: object

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

static filter(f)[source]#

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

satisfy_fractions(targets)[source]#

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

Bases: LocationTargetting

get_locations(cell)[source]#

get_node_name()#

labels#

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

Bases: object

get_locations(cell)[source]#

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)[source]#

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all identifiers of certain cell types.

get_node_name()#

get_targets(adapter, simulation, simdata)[source]#

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)[source]#

Bases: LocationTargetting

get_locations(cell)[source]#

get_node_name()#

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

Bases: CellModelFilter, FractionFilter, CellTargetting

Targets all cells in a sphere.

get_node_name()#

get_targets(adapter, simulation, simdata)[source]#: 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)[source]#

Bases: object

get_node_name()#

get_targets(adapter, simulation, simdata)[source]#

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

type: Literal['cell'] | Literal['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)[source]#

Bases: object

Adapter: SimulatorAdapter#

Simulation: Simulation#

bsb.simulation.get_simulation_adapter(name: str)[source]#