allensdk.brain_observatory.ecephys.ecephys_session_api package

Submodules

• allensdk.brain_observatory.ecephys.ecephys_session_api.ecephys_nwb1_session_api module
  • EcephysNwb1Api
    • EcephysNwb1Api.from_path()
    • EcephysNwb1Api.get_channels()
    • EcephysNwb1Api.get_ecephys_session_id()
    • EcephysNwb1Api.get_invalid_times()
    • EcephysNwb1Api.get_mean_waveforms()
    • EcephysNwb1Api.get_probes()
    • EcephysNwb1Api.get_running_speed()
    • EcephysNwb1Api.get_spike_times()
    • EcephysNwb1Api.get_stimulus_presentations()
    • EcephysNwb1Api.get_units()
    • EcephysNwb1Api.processing_grp
    • EcephysNwb1Api.running_speed_grp
  • IDCreator
    • IDCreator.get_id()
• allensdk.brain_observatory.ecephys.ecephys_session_api.ecephys_nwb_session_api module
  • EcephysNwbSessionApi
    • EcephysNwbSessionApi.get_channels()
    • EcephysNwbSessionApi.get_current_source_density()
    • EcephysNwbSessionApi.get_ecephys_session_id()
    • EcephysNwbSessionApi.get_lfp()
    • EcephysNwbSessionApi.get_mean_waveforms()
    • EcephysNwbSessionApi.get_metadata()
    • EcephysNwbSessionApi.get_optogenetic_stimulation()
    • EcephysNwbSessionApi.get_probes()
    • EcephysNwbSessionApi.get_pupil_data()
    • EcephysNwbSessionApi.get_raw_running_data()
    • EcephysNwbSessionApi.get_rig_metadata()
    • EcephysNwbSessionApi.get_running_speed()
    • EcephysNwbSessionApi.get_screen_gaze_data()
    • EcephysNwbSessionApi.get_session_start_time()
    • EcephysNwbSessionApi.get_spike_amplitudes()
    • EcephysNwbSessionApi.get_spike_times()
    • EcephysNwbSessionApi.get_stimulus_presentations()
    • EcephysNwbSessionApi.get_units()
    • EcephysNwbSessionApi.path
    • EcephysNwbSessionApi.test()
• allensdk.brain_observatory.ecephys.ecephys_session_api.ecephys_session_api module
  • EcephysSessionApi
    • EcephysSessionApi.get_channels()
    • EcephysSessionApi.get_ecephys_session_id()
    • EcephysSessionApi.get_invalid_times()
    • EcephysSessionApi.get_lfp()
    • EcephysSessionApi.get_mean_waveforms()
    • EcephysSessionApi.get_metadata()
    • EcephysSessionApi.get_optogenetic_stimulation()
    • EcephysSessionApi.get_probes()
    • EcephysSessionApi.get_pupil_data()
    • EcephysSessionApi.get_rig_metadata()
    • EcephysSessionApi.get_running_speed()
    • EcephysSessionApi.get_screen_gaze_data()
    • EcephysSessionApi.get_session_start_time()
    • EcephysSessionApi.get_spike_amplitudes()
    • EcephysSessionApi.get_spike_times()
    • EcephysSessionApi.get_stimulus_presentations()
    • EcephysSessionApi.get_units()
    • EcephysSessionApi.session_na
    • EcephysSessionApi.test()

Module contents

class allensdk.brain_observatory.ecephys.ecephys_session_api.EcephysNwb1Api(path, *args, **kwargs)

Bases: EcephysSessionApi

An EcephySession adaptor for reading NWB1.0 files.

Was created by sight using an assortment of existing NWB1 files. It is possible that parts of the NWB1 standard (?!) is missing or not properly implemented.

NWB1 vs NWB2 issues: * In NWB 1 there is no difference between global unit-ids and probe’s local-index. A unit is unique to one channel * Units are missing information about firing_rate, isi_violation, and quality.

• So that EcephysSession._build_units() actually return values I had

to set quality=good for all units

• NWB Stimulus_presentations missing stimulus_block, stimulus_index and

Image column

• To get EcephysSession.conditionwise_spikes() working had to make up

a block number for every stimulus type

• NWB1 missing a ‘valid_data’ tag for channels. Had to set to True

otherwise EcephysSession won’t see any channels * There were no ‘channels’ table/group in NWB1. Instead we had to iterate through all the units and pull out the

distinct channel info.

• In NWB2 each unit has a mean-waveform for every channel on the probe.

In NWB1 A unit only has a single waveform * The NWB1 identifier is a string

classmethod from_path(path, **kwargs)

get_channels() → DataFrame

get_ecephys_session_id() → int

get_invalid_times() → DataFrame

get_mean_waveforms() → Dict[int, ndarray]

get_probes() → DataFrame

get_running_speed()

get_spike_times() → Dict[int, ndarray]

get_stimulus_presentations() → DataFrame

get_units() → DataFrame

property processing_grp

property running_speed_grp

class allensdk.brain_observatory.ecephys.ecephys_session_api.EcephysNwbSessionApi(path, probe_lfp_paths: Dict[int, Callable[[], NWBFile]] | None = None, additional_unit_metrics=None, external_channel_columns=None, **kwargs)

Bases: NwbApi, EcephysSessionApi

get_channels() → DataFrame

get_current_source_density(probe_id)

get_ecephys_session_id() → int

get_lfp(probe_id: int) → DataArray

get_mean_waveforms() → Dict[int, ndarray]

get_metadata()

get_optogenetic_stimulation() → DataFrame

get_probes() → DataFrame

get_pupil_data() → DataFrame | None

get_raw_running_data()

get_rig_metadata() → dict | None

get_running_speed(include_rotation=False) → DataFrame

Gets the running speed Parameters ———- lowpass: bool

Whether to return the running speed with lowpass filter applied or without

Returns:

RunningSpeed:

The running speed

get_screen_gaze_data(include_filtered_data=False) → DataFrame | None

get_session_start_time()

get_spike_amplitudes() → Dict[int, ndarray]

get_spike_times() → Dict[int, ndarray]

get_stimulus_presentations()

get_units() → DataFrame

path

test()

A minimal test to make sure that this API’s NWB file exists and is readable. Ecephys NWB files use the required session identifier field to store the session id, so this is guaranteed to be present for any uncorrupted NWB file.

Of course, this does not ensure that the file as a whole is correct.

class allensdk.brain_observatory.ecephys.ecephys_session_api.EcephysSessionApi(*args, **kwargs)

Bases: object

get_channels() → DataFrame

get_ecephys_session_id() → int

get_invalid_times() → DataFrame

get_lfp(probe_id: int) → DataArray

get_mean_waveforms() → Dict[int, ndarray]

get_metadata()

get_optogenetic_stimulation() → DataFrame

get_probes() → DataFrame

get_pupil_data() → DataFrame | None

get_rig_metadata() → dict | None

get_running_speed() → RunningSpeed

get_screen_gaze_data(include_filtered_data=False) → DataFrame | None

get_session_start_time() → datetime

get_spike_amplitudes() → Dict[int, ndarray]

get_spike_times() → Dict[int, ndarray]

get_stimulus_presentations() → DataFrame

get_units() → DataFrame

session_na = -1

test() → bool