bmtk.utils.brain_observatory.ecephys package#

Submodules#

bmtk.utils.brain_observatory.ecephys.ecephys_project_cache module#

class bmtk.utils.brain_observatory.ecephys.ecephys_project_cache.EcephysProjectCache(fetch_api=None, fetch_tries=2, stream_writer=None, manifest=None, version=None, cache=True)[source]#

Bases: Cache

CHANNELS_KEY = 'channels'#
MANIFEST_VERSION = '0.3.0'#
NATURAL_MOVIE_DIR_KEY = 'movie_dir'#
NATURAL_MOVIE_KEY = 'natural_movie'#
NATURAL_SCENE_DIR_KEY = 'natural_scene_dir'#
NATURAL_SCENE_KEY = 'natural_scene'#
PROBES_KEY = 'probes'#
PROBE_LFP_NWB_KEY = 'probe_lfp_nwb'#
SESSIONS_KEY = 'sessions'#
SESSION_ANALYSIS_METRICS_KEY = 'session_analysis_metrics'#
SESSION_DIR_KEY = 'session_data'#
SESSION_NWB_KEY = 'session_nwb'#
SUPPRESS_FROM_PROBES = ('air_channel_index', 'surface_channel_index', 'date_of_acquisition', 'published_at', 'specimen_id', 'session_type', 'isi_experiment_id', 'age_in_days', 'sex', 'genotype', 'has_nwb', 'lfp_temporal_subsampling_factor')#
TYPEWISE_ANALYSIS_METRICS_KEY = 'typewise_analysis_metrics'#
UNITS_KEY = 'units'#
add_manifest_paths(manifest_builder)[source]#
classmethod from_warehouse(scheme=None, host=None, asynchronous=False, manifest=None, version=None, cache=True, fetch_tries=2, timeout=1200)[source]#
get_channels(suppress=None)[source]#
get_probes(suppress=None)[source]#
get_session_data(session_id, force_overwrite=False)[source]#

Obtain an EcephysSession object containing detailed data for a single session

get_unit_analysis_metrics_for_session(session_id, annotate: bool = True, filter_by_validity: bool = True, **unit_filter_kwargs)[source]#
class bmtk.utils.brain_observatory.ecephys.ecephys_project_cache.EcephysProjectWarehouseApi(rma_engine=None)[source]#

Bases: object

classmethod default(asynchronous=False, **rma_kwargs)[source]#
get_channels(channel_ids=None, probe_ids=None)[source]#
get_probe_lfp_data(probe_id)[source]#
get_probes(probe_ids=None, session_ids=None)[source]#
get_rig_metadata()[source]#
get_session_data(session_id, **kwargs)[source]#
get_sessions(session_ids=None, has_eye_tracking=None, stimulus_names=None)[source]#
get_unit_analysis_metrics(unit_ids=None, ecephys_session_ids=None, session_types=None)[source]#
get_units(unit_ids=None, channel_ids=None, probe_ids=None, session_ids=None, *a, **k)[source]#
class bmtk.utils.brain_observatory.ecephys.ecephys_project_cache.EcephysSession(nwb_path)[source]#

Bases: object

Module contents#