bluecellulab.circuit.circuit_access.bluepy_circuit_access

Classes

BluepyCircuitAccess(simulation_config)

Bluepy implementation of CircuitAccess protocol.

class bluecellulab.circuit.circuit_access.bluepy_circuit_access.BluepyCircuitAccess(simulation_config)[source]

Bluepy implementation of CircuitAccess protocol.

Parameters:

simulation_config (str | Path | SimulationConfig)

property available_cell_properties: set

Retrieve the available properties from connectome.

extract_synapses(cell_id, projections)[source]

Extract the synapses of a cell.

Return type:

DataFrame

Returns:

synapses dataframes indexed by projection, edge and synapse ids

Parameters:

• cell_id (CellId)

• projections (Union[list[str], str, None])

fetch_cell_info(cell_id)[source]

Fetch bluepy cell info of a gid.

Parameters:

cell_id (CellId)

Return type:

Series

fetch_mini_frequencies(cell_id)[source]

Get inhibitory frequency of gid.

Parameters:

cell_id (CellId)

Return type:

tuple[float | None, float | None]

get_cell_ids_of_targets(targets)[source]

Return all the gids belonging to one of the input targets.

Parameters:

targets (list[str])

Return type:

set[CellId]

get_cell_properties(cell_id, properties)[source]

Get a property of a cell.

Parameters:

• cell_id (CellId)

• properties (list[str] | str)

Return type:

Series

get_emodel_properties(cell_id)[source]

Get emodel_properties either from node properties or mecombo tsv.

Parameters:

cell_id (CellId)

Return type:

Optional[EmodelProperties]

get_gids_of_mtypes(mtypes)[source]

Returns all the gids belonging to one of the input mtypes.

Parameters:

mtypes (list[str])

Return type:

set[CellId]

get_population_ids(edge_name)[source]

Retrieve the population ids of a projection.

Parameters:

edge_name (str)

Return type:

tuple[int, int]

get_target_cell_ids(target)[source]

Return GIDs in target as a set.

Parameters:

target (str)

Return type:

set[CellId]

get_template_format()[source]

Return the template format.

Return type:

Optional[str]

is_valid_group(group)[source]

Check if target is a group of cells.

Parameters:

group (str)

Return type:

bool

property node_properties_available: bool

Checks if the node properties are available and can be used.

target_contains_cell(target, cell_id)[source]

Check if target contains the cell or target is the cell.

Parameters:

• target (str)

• cell_id (CellId)

Return type:

bool

property use_mecombo_tsv: bool

Property that decides whether to use mecombo_tsv.

virtual_population_sizes()[source]

Return full sizes for virtual populations.

Return type:

dict[str, int]