NeuronIO conversion

Module contract

The converter reads raw NeuronIO teacher traces and creates deterministic shards. Standard soma normalization clips at -55 mV and applies (v_mV-bias)*scale with bias=-67.7 and scale=0.1. Preserve conversion metadata: normalized targets cannot recover clipped spike peaks.

Source revision: 306a51ed950b. Public export index.

RawNeuronIO

Source

RawNeuronIO(inputs: np.ndarray, spikes: np.ndarray, soma: np.ndarray, metadata: dict[str, object]) -> None

Fields

Parameter	Type	Default
inputs	np.ndarray	required
spikes	np.ndarray	required
soma	np.ndarray	required
metadata	dict[str, object]	required

metadata: Caller metadata stored with model state.

parse_neuronio_pickle

Source

parse_neuronio_pickle(path: str | Path) -> RawNeuronIO

Parse a public NeuronIO simulation pickle into (sim, time, channel) arrays.

Parameter	Type	Default
path	str | Path	required

Returns RawNeuronIO.

convert_neuronio_pickles

Source

convert_neuronio_pickles(input_path: str | Path, output_dir: str | Path, *, shard_size: int=128, window_size: int | None=None, window_stride: int | None=None, ignore_start: int=0, y_soma_threshold: float=DEFAULT_Y_SOMA_THRESHOLD, y_train_soma_bias: float=DEFAULT_Y_TRAIN_SOMA_BIAS, y_train_soma_scale: float=DEFAULT_Y_TRAIN_SOMA_SCALE) -> list[Path]

Convert raw NeuronIO pickle files to deterministic .npz shards.

Parameter	Type	Default
input_path	str | Path	required
output_dir	str | Path	required
shard_size	int	128
window_size	int | None	None
window_stride	int | None	None
ignore_start	int	0
y_soma_threshold	float	DEFAULT_Y_SOMA_THRESHOLD = -55.0
y_train_soma_bias	float	DEFAULT_Y_TRAIN_SOMA_BIAS = -67.7
y_train_soma_scale	float	DEFAULT_Y_TRAIN_SOMA_SCALE = 0.1

ignore_start: Initial native timesteps excluded by the declared path.

Returns list[Path].

create_neuronio_input_type

Source

create_neuronio_input_type(num_input: int) -> np.ndarray

Parameter	Type	Default
num_input	int	required

num_input: Input-channel count.

Returns np.ndarray.

normalize_soma

Source

normalize_soma(soma: np.ndarray, threshold: float=DEFAULT_Y_SOMA_THRESHOLD, bias: float=DEFAULT_Y_TRAIN_SOMA_BIAS, scale: float=DEFAULT_Y_TRAIN_SOMA_SCALE) -> np.ndarray

Returns normalized soma targets after clipping teacher voltage at threshold and applying (voltage-bias)*scale. The default threshold is -55.0 mV, bias is -67.7 mV, and scale is 0.1.

Parameter	Type	Default
soma	np.ndarray	required
threshold	float	DEFAULT_Y_SOMA_THRESHOLD = -55.0
bias	float	DEFAULT_Y_TRAIN_SOMA_BIAS = -67.7
scale	float	DEFAULT_Y_TRAIN_SOMA_SCALE = 0.1

Returns np.ndarray.