allensdk.brain_observatory.ecephys.ecephys_project_api package

Submodules

• allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_api module
  • EcephysProjectApi
    • EcephysProjectApi.get_channels()
    • EcephysProjectApi.get_isi_experiments()
    • EcephysProjectApi.get_natural_movie_template()
    • EcephysProjectApi.get_natural_scene_template()
    • EcephysProjectApi.get_probe_lfp_data()
    • EcephysProjectApi.get_probes()
    • EcephysProjectApi.get_session_data()
    • EcephysProjectApi.get_sessions()
    • EcephysProjectApi.get_unit_analysis_metrics()
    • EcephysProjectApi.get_units()
• allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_fixed_api module
  • EcephysProjectFixedApi
    • EcephysProjectFixedApi.get_channels()
    • EcephysProjectFixedApi.get_isi_experiments()
    • EcephysProjectFixedApi.get_natural_movie_template()
    • EcephysProjectFixedApi.get_natural_scene_template()
    • EcephysProjectFixedApi.get_probe_lfp_data()
    • EcephysProjectFixedApi.get_probes()
    • EcephysProjectFixedApi.get_session_data()
    • EcephysProjectFixedApi.get_sessions()
    • EcephysProjectFixedApi.get_targeted_regions()
    • EcephysProjectFixedApi.get_units()
  • MissingDataError
• allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_lims_api module
  • EcephysProjectLimsApi
    • EcephysProjectLimsApi.STIMULUS_TEMPLATE_NAMESPACE
    • EcephysProjectLimsApi.default()
    • EcephysProjectLimsApi.get_channels()
    • EcephysProjectLimsApi.get_natural_movie_template()
    • EcephysProjectLimsApi.get_natural_scene_template()
    • EcephysProjectLimsApi.get_probe_lfp_data()
    • EcephysProjectLimsApi.get_probes()
    • EcephysProjectLimsApi.get_session_data()
    • EcephysProjectLimsApi.get_sessions()
    • EcephysProjectLimsApi.get_unit_analysis_metrics()
    • EcephysProjectLimsApi.get_units()
  • SplitPublishedAt
    • SplitPublishedAt.published_at
    • SplitPublishedAt.published_at_not_null
• allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_warehouse_api module
  • EcephysProjectWarehouseApi
    • EcephysProjectWarehouseApi.default()
    • EcephysProjectWarehouseApi.get_channels()
    • EcephysProjectWarehouseApi.get_natural_movie_template()
    • EcephysProjectWarehouseApi.get_natural_scene_template()
    • EcephysProjectWarehouseApi.get_probe_lfp_data()
    • EcephysProjectWarehouseApi.get_probes()
    • EcephysProjectWarehouseApi.get_session_data()
    • EcephysProjectWarehouseApi.get_sessions()
    • EcephysProjectWarehouseApi.get_unit_analysis_metrics()
    • EcephysProjectWarehouseApi.get_units()
    • EcephysProjectWarehouseApi.movie_re
    • EcephysProjectWarehouseApi.scene_re
    • EcephysProjectWarehouseApi.stimulus_templates
• allensdk.brain_observatory.ecephys.ecephys_project_api.http_engine module
  • AsyncHttpEngine
    • AsyncHttpEngine.session
    • AsyncHttpEngine.stream()
    • AsyncHttpEngine.write_bytes()
  • HttpEngine
    • HttpEngine.stream()
    • HttpEngine.write_bytes()
  • write_bytes_from_coroutine()
  • write_from_stream()
• allensdk.brain_observatory.ecephys.ecephys_project_api.rma_engine module
  • AsyncRmaEngine
  • RmaEngine
    • RmaEngine.add_page_params()
    • RmaEngine.format_query_string
    • RmaEngine.get_rma()
    • RmaEngine.get_rma_list()
    • RmaEngine.get_rma_tabular()
  • RmaRequestError
  • infer_column_types()
• allensdk.brain_observatory.ecephys.ecephys_project_api.utilities module
  • build_and_execute()
  • build_environment()
  • execute_templated()
  • macros()
  • postgres_macros()
  • rma_macros()

Module contents

class allensdk.brain_observatory.ecephys.ecephys_project_api.EcephysProjectApi

Bases: object

get_channels(channel_ids: ArrayLike | None = None, probe_ids: ArrayLike | None = None, session_ids: ArrayLike | None = None, published_at: str | None = None)

get_isi_experiments(*args, **kwargs)

get_natural_movie_template(number) → Iterable

get_natural_scene_template(number) → Iterable

get_probe_lfp_data(probe_id: int) → Iterable

get_probes(probe_ids: ArrayLike | None = None, session_ids: ArrayLike | None = None, published_at: str | None = None)

get_session_data(session_id: int) → Iterable

get_sessions(session_ids: ArrayLike | None = None, published_at: str | None = None)

get_unit_analysis_metrics(unit_ids: ArrayLike | None = None, ecephys_session_ids: ArrayLike | None = None, session_types: ArrayLike | None = None) → DataFrame

get_units(unit_ids: ArrayLike | None = None, channel_ids: ArrayLike | None = None, probe_ids: ArrayLike | None = None, session_ids: ArrayLike | None = None, published_at: str | None = None)

class allensdk.brain_observatory.ecephys.ecephys_project_api.EcephysProjectFixedApi

Bases: EcephysProjectApi

get_channels(*args, **kwargs)

get_isi_experiments(*args, **kwargs)

get_natural_movie_template(number, *args, **kwargs)

get_natural_scene_template(number, *args, **kwargs)

get_probe_lfp_data(probe_id, *args, **kwargs)

get_probes(*args, **kwargs)

get_session_data(session_id, *args, **kwargs)

get_sessions(*args, **kwargs)

get_targeted_regions(*args, **kwargs)

get_units(*args, **kwargs)

class allensdk.brain_observatory.ecephys.ecephys_project_api.EcephysProjectLimsApi(postgres_engine, app_engine)

Bases: EcephysProjectApi

STIMULUS_TEMPLATE_NAMESPACE = 'brain_observatory_1.1'

classmethod default(lims_credentials: DbCredentials | None = None, app_kwargs=None, asynchronous=False)

Construct a “straightforward” lims api that can fetch data from lims2.

Parameters:

lims_credentialsDbCredentials

Credentials and configuration for postgres queries against the LIMS database. If left unspecified will attempt to provide credentials from environment variables.

app_kwargsdict

High-level configuration for http requests. See allensdk.brain_observatory.ecephys.ecephys_project_api.http_engine.HttpEngine and AsyncHttpEngine for details.

asynchronousbool

If true, (http) queries will be made asynchronously.

Returns:

EcephysProjectLimsApi

get_channels(channel_ids: ArrayLike | None = None, probe_ids: ArrayLike | None = None, session_ids: ArrayLike | None = None, published_at: str | None = None) → DataFrame

Download a table of ecephys channel records.

Parameters:

channel_ids

A collection of integer identifiers for ecephys channels. If provided, results will be filtered to these channels.

probe_ids

A collection of integer identifiers for ecephys probes. If provided, results will be filtered to channels on these probes.

session_ids

A collection of integer identifiers for ecephys sessions. If provided, results will be filtered to channels recorded from during these sessions.

published_at

A date (rendered as “YYYY-MM-DD”). If provided, only channels recorded from during sessions published before this date will be returned.

Returns:

a pd.DataFrame whose rows are ecephys channels.

get_natural_movie_template(number: int) → Iterable[bytes]

Download a template for the natural movie stimulus. This is the actual movie that was shown during the recording session.

Parameters:

number

idenfifier for this movie (note that this is an integer, so to get the template for natural_movie_three you should pass in 3)

Returns:

An iterable yielding an npy file as bytes

get_natural_scene_template(number: int) → Iterable[bytes]

Download a template for the natural scene stimulus. This is the actual image that was shown during the recording session.

Parameters:

number

idenfifier for this scene

Returns:

An iterable yielding a tiff file as bytes.

get_probe_lfp_data(probe_id: int) → Iterable[bytes]

Download an NWB file containing detailed data for the local field potential recorded from an ecephys probe.

Parameters:

probe_id

Download an NWB file for this probe’s LFP

Returns:

An iterable yielding an NWB file as bytes.

get_probes(probe_ids: ArrayLike | None = None, session_ids: ArrayLike | None = None, published_at: str | None = None) → DataFrame

Download a table of ecephys probe records.

Parameters:

probe_ids

A collection of integer identifiers for ecephys probes. If provided, results will be filtered to these probes.

session_ids

A collection of integer identifiers for ecephys sessions. If provided, results will be filtered to probes recorded from during these sessions.

published_at

A date (rendered as “YYYY-MM-DD”). If provided, only probes recorded from during sessions published before this date will be returned.

Returns:

a pd.DataFrame whose rows are ecephys probes.

get_session_data(session_id: int) → Iterable[bytes]

Download an NWB file containing detailed data for an ecephys session.

Parameters:

session_id

Download an NWB file for this session

Returns:

An iterable yielding an NWB file as bytes.

get_sessions(session_ids: ArrayLike | None = None, published_at: str | None = None) → DataFrame

Download a table of ecephys session records.

Parameters:

session_ids

A collection of integer identifiers for ecephys sessions. If provided, results will be filtered to these sessions.

published_at

A date (rendered as “YYYY-MM-DD”). If provided, only sessions published before this date will be returned.

Returns:

a pd.DataFrame whose rows are ecephys sessions.

get_unit_analysis_metrics(unit_ids: ArrayLike | None = None, ecephys_session_ids: ArrayLike | None = None, session_types: ArrayLike | None = None) → DataFrame

Fetch analysis metrics (stimulus set-specific characterizations of unit response patterns) for ecephys units. Note that the metrics returned depend on the stimuli that were presented during recording ( and thus on the session_type)

Parameters

unit_ids :

integer identifiers for a set of ecephys units. If provided, the response will only include metrics calculated for these units

ecephys_session_ids :

integer identifiers for a set of ecephys sessions. If provided, the response will only include metrics calculated for units identified during these sessions

session_types :

string names identifying ecephys session types (e.g. “brain_observatory_1.1” or “functional_connectivity”)

Returns:

a pandas dataframe indexed by ecephys unit id whose columns are

metrics.

get_units(unit_ids: ArrayLike | None = None, channel_ids: ArrayLike | None = None, probe_ids: ArrayLike | None = None, session_ids: ArrayLike | None = None, published_at: str | None = None) → DataFrame

Download a table of records describing sorted ecephys units.

Parameters:

unit_ids

A collection of integer identifiers for sorted ecephys units. If provided, only return records describing these units.

channel_ids

A collection of integer identifiers for ecephys channels. If provided, results will be filtered to units recorded from these channels.

probe_ids

A collection of integer identifiers for ecephys probes. If provided, results will be filtered to units recorded from these probes.

session_ids

A collection of integer identifiers for ecephys sessions. If provided, results will be filtered to units recorded during these sessions.

published_at

A date (rendered as “YYYY-MM-DD”). If provided, only units recorded during sessions published before this date will be returned.

Returns:

a pd.DataFrame whose rows are ecephys channels.

class allensdk.brain_observatory.ecephys.ecephys_project_api.EcephysProjectWarehouseApi(rma_engine=None)

Bases: EcephysProjectApi

classmethod default(asynchronous=False, **rma_kwargs)

get_channels(channel_ids=None, probe_ids=None)

get_natural_movie_template(number)

get_natural_scene_template(number)

get_probe_lfp_data(probe_id)

get_probes(probe_ids=None, session_ids=None)

get_session_data(session_id, **kwargs)

get_sessions(session_ids=None, has_eye_tracking=None, stimulus_names=None)

get_unit_analysis_metrics(unit_ids=None, ecephys_session_ids=None, session_types=None)

Download analysis metrics - precalculated descriptions of unitwise responses to visual stimulation.

Parameters:

unit_idsarray-like of int, optional

Unique identifiers for ecephys units. If supplied, only download metrics for these units.

ecephys_session_idsarray-like of int, optional

Unique identifiers for ecephys sessions. If supplied, only download metrics for units collected during these sessions.

session_typesarray-like of str, optional

Names of session types. e.g. “brain_observatory_1.1” or “functional_connectivity”. If supplied, only download metrics for units collected during sessions of these types

Returns:

pd.DataFrame

A table of analysis metrics, indexed by unit_id.

get_units(unit_ids=None, channel_ids=None, probe_ids=None, session_ids=None, *a, **k)

movie_re = re.compile('.*natural_movie_(?P<num>\\d+).npy')

scene_re = re.compile('.*/(?P<num>\\d+).tiff')

property stimulus_templates

exception allensdk.brain_observatory.ecephys.ecephys_project_api.MissingDataError

Bases: ValueError