alignment.AlignmentResult

alignment.AlignmentResult(
    method,
    pid,
    channel_xyz,
    recorded,
    predicted_std,
    recorded_std,
    p_good,
    valid,
    trace_xyz,
    feature_names,
    cost_matrix=None,
    path=None,
    diagnostics=dict(),
    timings=dict(),
)

Where one probe’s channels are, according to one method.

Channel arrays are in row order (top of the probe first; see :mod:.geometry).

Attributes: method: "histology", "histology_unit" or "ephys_only". pid: Insertion id (’’ when unknown, e.g. a GUI probe without one). channel_xyz: [C, 3] estimated channel positions (m). recorded: [C, F] recorded features, feature units. predicted_std: [C, F] model prediction at channel_xyz, standardised. recorded_std: [C, F] recorded features, standardised. p_good: [C] probe-confidence p(good) at channel_xyz (NaN where invalid). valid: [C] channels carrying a signal (used by the method and the metrics). trace_xyz: [L, 3] the trace the channels lie on: the extended histology trace, or the inferred trace for the ephys-only method. feature_names: The F feature names. cost_matrix: Histology methods: [C_valid, L] alignment cost (valid channels x trace). path: Histology methods: [P, 2] (valid-channel row, trace index) warping path. diagnostics: Method-specific values, e.g. candidate_scores / candidate_distance_um for the ephys-only method, the unit-cost summary for the channel + unit method. timings: Seconds spent per step.

Methods

Name	Description
save	Write the arrays and scalar diagnostics to a compressed .npz.

save

alignment.AlignmentResult.save(path)

Write the arrays and scalar diagnostics to a compressed .npz.