aind_ephys_utils package

Subpackages

• aind_ephys_utils.accessors package
  • Submodules
    • aind_ephys_utils.accessors.dataarray module
      • EphysDataArrayAccessor
  • Module contents
• aind_ephys_utils.adapters package
  • Submodules
    • aind_ephys_utils.adapters.dataframe module
      • Supported patterns
      • FromDataFrameError
      • from_dataframe()
  • Module contents
    • from_dataframe()
• aind_ephys_utils.metrics package
  • Submodules
    • aind_ephys_utils.metrics.ccg module
      • Lag convention
      • NN_to_pair_vec()
      • TrialSegments
      • cc_leads_over_std()
      • ccg()
      • ccg_allpairs_sparse()
      • ccg_between_sets_sparse()
      • ccg_trial_paired()
      • ccg_trial_surrogates()
      • clip_spikes_to_trials()
      • clip_to_window()
      • derangements()
      • jitter_spikes_times()
      • measure_fwhm()
      • measure_per_pair()
      • measure_prominence()
      • monte_carlo_pvalue()
      • pair_vec_to_NN()
      • peak_contributing_spikes()
      • rescale_ccgs()
      • rescale_ccgs_zero_mean()
      • smooth_ccgs()
    • aind_ephys_utils.metrics.connectivity module
      • build_shape_prefilter()
      • run_surrogates()
      • run_two_stage_mc()
    • aind_ephys_utils.metrics.latency module
      • spike_latency()
  • Module contents
    • NN_to_pair_vec()
    • build_shape_prefilter()
    • ccg()
    • ccg_allpairs_sparse()
    • ccg_between_sets_sparse()
    • ccg_trial_paired()
    • ccg_trial_surrogates()
    • clip_spikes_to_trials()
    • measure_fwhm()
    • measure_prominence()
    • monte_carlo_pvalue()
    • pair_vec_to_NN()
    • rescale_ccgs()
    • run_surrogates()
    • run_two_stage_mc()
    • smooth_ccgs()
    • spike_latency()
• aind_ephys_utils.ops package
  • Submodules
    • aind_ephys_utils.ops.align module
      • EphysAlignError
      • align()
    • aind_ephys_utils.ops.baseline module
      • baseline()
    • aind_ephys_utils.ops.bin module
      • bin()
    • aind_ephys_utils.ops.normalize module
      • normalize()
    • aind_ephys_utils.ops.pseudopop module
      • pseudopop()
    • aind_ephys_utils.ops.psth module
      • psth()
    • aind_ephys_utils.ops.reduce module
      • reduce()
    • aind_ephys_utils.ops.restrict module
      • restrict()
    • aind_ephys_utils.ops.smooth module
      • smooth()
  • Module contents
    • align()
    • baseline()
    • bin()
    • normalize()
    • pseudopop()
    • psth()
    • reduce()
    • restrict()
    • smooth()
• aind_ephys_utils.plots package
  • Submodules
    • aind_ephys_utils.plots.annotations module
      • add_scale_bars()
      • annotate_events()
    • aind_ephys_utils.plots.colors module
      • get_color_for_region()
    • aind_ephys_utils.plots.psth module
      • psth()
    • aind_ephys_utils.plots.raster module
      • raster()
    • aind_ephys_utils.plots.trajectory module
      • trajectory()
  • Module contents
    • annotate_events()
    • get_color_for_region()
    • psth()
    • raster()
    • trajectory()
• aind_ephys_utils.standards package
  • Submodules
    • aind_ephys_utils.standards.conventions module
      • Conventions
    • aind_ephys_utils.standards.validate module
      • EphysValidationError
      • ValidationResult
      • infer_kind()
      • is_binned_spikes()
      • is_continuous()
      • is_events()
      • is_ragged_spikes()
      • validate()
  • Module contents

Submodules

• aind_ephys_utils.align module
  • align_to_events()
  • events_to_dataset()
  • to_events()
• aind_ephys_utils.config module
  • configure_defaults()

Module contents

Helpful methods for exploring in vivo electrophysiology data.

aind_ephys_utils.configure_defaults(*, plot: bool = True, display: bool = True, print_options: bool = True, savefig_dpi: int | None = 300) → None

Apply recommended global defaults explicitly.

Parameters:

• plot – If True, apply matplotlib defaults for export-friendly figures.

• display – If True, set xarray display options for compact DataArray rendering.

• print_options – If True, set numpy print options for concise array display.

• savefig_dpi – Save DPI to set when plot=True. If None, leaves current value.

aind_ephys_utils.validate(da: DataArray, *, kind: str | None = None, require_time_coord: bool = True, check_ragged_contents: bool = True) → ValidationResult

Validate that a DataArray conforms to the conventions expected by .ephys.

Parameters:

• da – The DataArray to validate.

• kind – If provided, require that the DataArray matches this inferred kind. One of: “spikes_ragged”, “continuous”, “binned”, “events”.

• require_time_coord – If True, require a ‘time’ coordinate whenever there is a time dimension.

• check_ragged_contents – If True, sample-check ragged spike contents for basic shape/dtype sanity.

Return type:

ValidationResult