allensdk.brain_observatory.ecephys package

Subpackages

• allensdk.brain_observatory.ecephys.align_timestamps package
  • Submodules
    • allensdk.brain_observatory.ecephys.align_timestamps.barcode module
      • extract_barcodes_from_times()
      • find_matching_index()
      • get_probe_time_offset()
      • linear_transform_from_intervals()
      • match_barcodes()
    • allensdk.brain_observatory.ecephys.align_timestamps.barcode_sync_dataset module
      • BarcodeSyncDataset
    • allensdk.brain_observatory.ecephys.align_timestamps.channel_states module
      • extract_barcodes_from_states()
      • extract_splits_from_barcode_times()
      • extract_splits_from_states()
    • allensdk.brain_observatory.ecephys.align_timestamps.probe_synchronizer module
      • ProbeSynchronizer
  • Module contents
• allensdk.brain_observatory.ecephys.copy_utility package
  • Module contents
• allensdk.brain_observatory.ecephys.current_source_density package
  • Module contents
• allensdk.brain_observatory.ecephys.data_objects package
  • Submodules
    • allensdk.brain_observatory.ecephys.data_objects.trials module
      • VBNTrial
      • VBNTrials
  • Module contents
• allensdk.brain_observatory.ecephys.ecephys_project_api package
  • Submodules
    • allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_api module
      • EcephysProjectApi
    • allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_fixed_api module
      • EcephysProjectFixedApi
      • MissingDataError
    • allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_lims_api module
      • EcephysProjectLimsApi
      • SplitPublishedAt
    • allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_warehouse_api module
      • EcephysProjectWarehouseApi
    • allensdk.brain_observatory.ecephys.ecephys_project_api.http_engine module
      • AsyncHttpEngine
      • HttpEngine
      • write_bytes_from_coroutine()
      • write_from_stream()
    • allensdk.brain_observatory.ecephys.ecephys_project_api.rma_engine module
      • AsyncRmaEngine
      • RmaEngine
      • 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
    • 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()
    • 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()
    • 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()
    • 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
    • MissingDataError
• allensdk.brain_observatory.ecephys.ecephys_session_api package
  • Submodules
    • allensdk.brain_observatory.ecephys.ecephys_session_api.ecephys_nwb1_session_api module
      • EcephysNwb1Api
      • IDCreator
    • allensdk.brain_observatory.ecephys.ecephys_session_api.ecephys_nwb_session_api module
      • EcephysNwbSessionApi
    • allensdk.brain_observatory.ecephys.ecephys_session_api.ecephys_session_api module
      • EcephysSessionApi
  • Module contents
    • 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
    • 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()
    • 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()
• allensdk.brain_observatory.ecephys.file_io package
  • Submodules
    • allensdk.brain_observatory.ecephys.file_io.continuous_file module
      • ContinuousFile
    • allensdk.brain_observatory.ecephys.file_io.ecephys_sync_dataset module
      • EcephysSyncDataset
    • allensdk.brain_observatory.ecephys.file_io.stim_file module
      • CamStimOnePickleStimFile
  • Module contents
• allensdk.brain_observatory.ecephys.lfp_subsampling package
  • Submodules
    • allensdk.brain_observatory.ecephys.lfp_subsampling.subsampling module
      • remove_lfp_noise()
      • remove_lfp_offset()
      • select_channels()
      • subsample_lfp()
      • subsample_timestamps()
  • Module contents
• allensdk.brain_observatory.ecephys.nwb package
  • Submodules
    • allensdk.brain_observatory.ecephys.nwb.ecephys_nwb_extension_builder module
  • Module contents
• allensdk.brain_observatory.ecephys.optotagging_table package
  • Module contents
• allensdk.brain_observatory.ecephys.stimulus_analysis package
  • Submodules
    • allensdk.brain_observatory.ecephys.stimulus_analysis.dot_motion module
      • DotMotion
    • allensdk.brain_observatory.ecephys.stimulus_analysis.drifting_gratings module
      • DriftingGratings
      • c50()
      • f1_f0()
      • modulation_index()
    • allensdk.brain_observatory.ecephys.stimulus_analysis.flashes module
      • Flashes
    • allensdk.brain_observatory.ecephys.stimulus_analysis.natural_movies module
      • NaturalMovies
    • allensdk.brain_observatory.ecephys.stimulus_analysis.natural_scenes module
      • NaturalScenes
      • image_selectivity()
    • allensdk.brain_observatory.ecephys.stimulus_analysis.receptive_field_mapping module
      • ReceptiveFieldMapping
      • convert_azimuth_to_degrees()
      • convert_elevation_to_degrees()
      • convert_pixel_area_to_degrees()
      • convert_pixels_to_degrees()
      • fit_2d_gaussian()
      • gaussian_moments_2d()
      • invert_rf()
      • is_rf_inverted()
      • rf_on_screen()
      • threshold_rf()
    • allensdk.brain_observatory.ecephys.stimulus_analysis.static_gratings module
      • StaticGratings
      • exp_function()
      • fit_sf_tuning()
      • gauss_function()
      • get_sfdi()
    • allensdk.brain_observatory.ecephys.stimulus_analysis.stimulus_analysis module
      • StimulusAnalysis
      • calculate_time_delayed_correlation()
      • deg2rad()
      • dsi()
      • fano_factor()
      • fit_exp()
      • get_fr()
      • lifetime_sparseness()
      • osi()
      • overall_firing_rate()
      • reliability()
      • running_modulation()
  • Module contents
    • DotMotion
      • DotMotion.METRICS_COLUMNS
      • DotMotion.directions
      • DotMotion.known_spontaneous_keys
      • DotMotion.known_stimulus_keys()
      • DotMotion.metrics
      • DotMotion.name
      • DotMotion.null_condition
      • DotMotion.number_directions
      • DotMotion.number_speeds
      • DotMotion.speeds
    • DriftingGratings
      • DriftingGratings.METRICS_COLUMNS
      • DriftingGratings.conditionwise_statistics_contrast
      • DriftingGratings.contrastvals
      • DriftingGratings.known_stimulus_keys()
      • DriftingGratings.make_star_plot()
      • DriftingGratings.metrics
      • DriftingGratings.name
      • DriftingGratings.null_condition
      • DriftingGratings.number_contrast
      • DriftingGratings.number_ori
      • DriftingGratings.number_tf
      • DriftingGratings.orivals
      • DriftingGratings.plot_raster()
      • DriftingGratings.plot_response_summary()
      • DriftingGratings.stim_table_contrast
      • DriftingGratings.stimulus_conditions_contrast
      • DriftingGratings.tfvals
    • Flashes
      • Flashes.METRICS_COLUMNS
      • Flashes.colors
      • Flashes.known_stimulus_keys()
      • Flashes.metrics
      • Flashes.name
      • Flashes.null_condition
      • Flashes.number_colors
      • Flashes.plot_raster()
      • Flashes.plot_response()
    • NaturalMovies
      • NaturalMovies.METRICS_COLUMNS
      • NaturalMovies.known_stimulus_keys()
      • NaturalMovies.metrics
      • NaturalMovies.name
      • NaturalMovies.null_condition
    • NaturalScenes
      • NaturalScenes.METRICS_COLUMNS
      • NaturalScenes.frames
      • NaturalScenes.images
      • NaturalScenes.images_nonblank
      • NaturalScenes.known_stimulus_keys()
      • NaturalScenes.metrics
      • NaturalScenes.name
      • NaturalScenes.null_condition
      • NaturalScenes.number_images
      • NaturalScenes.number_nonblank
    • ReceptiveFieldMapping
      • ReceptiveFieldMapping.METRICS_COLUMNS
      • ReceptiveFieldMapping.azimuths
      • ReceptiveFieldMapping.elevations
      • ReceptiveFieldMapping.get_receptive_field()
      • ReceptiveFieldMapping.known_stimulus_keys()
      • ReceptiveFieldMapping.metrics
      • ReceptiveFieldMapping.name
      • ReceptiveFieldMapping.null_condition
      • ReceptiveFieldMapping.number_azimuths
      • ReceptiveFieldMapping.number_elevations
      • ReceptiveFieldMapping.plot_raster()
      • ReceptiveFieldMapping.plot_rf()
      • ReceptiveFieldMapping.receptive_fields
    • StaticGratings
      • StaticGratings.METRICS_COLUMNS
      • StaticGratings.known_stimulus_keys()
      • StaticGratings.make_fan_plot()
      • StaticGratings.metrics
      • StaticGratings.name
      • StaticGratings.null_condition
      • StaticGratings.number_ori
      • StaticGratings.number_phase
      • StaticGratings.number_sf
      • StaticGratings.orivals
      • StaticGratings.phasevals
      • StaticGratings.plot_raster()
      • StaticGratings.plot_response_summary()
      • StaticGratings.sfvals
• allensdk.brain_observatory.ecephys.stimulus_table package
  • Subpackages
    • allensdk.brain_observatory.ecephys.stimulus_table.visualization package
      • Submodules
      • Module contents
  • Submodules
    • allensdk.brain_observatory.ecephys.stimulus_table.ephys_pre_spikes module
      • apply_display_sequence()
      • apply_frame_times()
      • assign_sweep_values()
      • build_stimuluswise_table()
      • create_stim_table()
      • make_spontaneous_activity_tables()
      • read_stimulus_name_from_path()
      • split_column()
    • allensdk.brain_observatory.ecephys.stimulus_table.naming_utilities module
      • add_number_to_shuffled_movie()
      • collapse_columns()
      • drop_empty_columns()
      • map_column_names()
      • map_stimulus_names()
      • standardize_movie_numbers()
    • allensdk.brain_observatory.ecephys.stimulus_table.output_validation module
      • validate_epoch_durations()
      • validate_epoch_order()
      • validate_max_spontaneous_epoch_duration()
    • allensdk.brain_observatory.ecephys.stimulus_table.stimulus_parameter_extraction module
      • extract_const_params_from_stim_repr()
      • extract_stim_class_from_repr()
      • parse_stim_repr()
  • Module contents
• allensdk.brain_observatory.ecephys.visualization package
  • Module contents
    • plot_mean_waveforms()
    • plot_spike_counts()
    • raster_plot()
• allensdk.brain_observatory.ecephys.write_nwb package
  • Subpackages
    • allensdk.brain_observatory.ecephys.write_nwb.vbn package
      • Module contents
  • Submodules
    • allensdk.brain_observatory.ecephys.write_nwb.nwb_writer module
      • BehaviorEcephysNwbWriter
    • allensdk.brain_observatory.ecephys.write_nwb.schemas module
      • BaseBehaviorSessionDataSchema
      • BaseNeuropixelsSchema
      • Channel
      • InvalidEpoch
      • Lfp
      • OutputSchema
      • Probe
      • ProbeOutputs
      • SessionMetadata
      • Unit
      • VCNInputSchema
  • Module contents

Submodules

• allensdk.brain_observatory.ecephys.behavior_ecephys_session module
  • BehaviorEcephysSession
    • BehaviorEcephysSession.behavior_data_class()
    • BehaviorEcephysSession.from_json()
    • BehaviorEcephysSession.from_nwb()
    • BehaviorEcephysSession.get_channels()
    • BehaviorEcephysSession.get_current_source_density()
    • BehaviorEcephysSession.get_lfp()
    • BehaviorEcephysSession.get_probes_obj()
    • BehaviorEcephysSession.get_units()
    • BehaviorEcephysSession.mean_waveforms
    • BehaviorEcephysSession.metadata
    • BehaviorEcephysSession.optotagging_table
    • BehaviorEcephysSession.probes
    • BehaviorEcephysSession.spike_amplitudes
    • BehaviorEcephysSession.spike_times
    • BehaviorEcephysSession.to_nwb()
  • VBNBehaviorSession
    • VBNBehaviorSession.from_lims()
• allensdk.brain_observatory.ecephys.ecephys_project_cache module
  • EcephysProjectCache
    • EcephysProjectCache.CHANNELS_KEY
    • EcephysProjectCache.MANIFEST_VERSION
    • EcephysProjectCache.NATURAL_MOVIE_DIR_KEY
    • EcephysProjectCache.NATURAL_MOVIE_KEY
    • EcephysProjectCache.NATURAL_SCENE_DIR_KEY
    • EcephysProjectCache.NATURAL_SCENE_KEY
    • EcephysProjectCache.PROBES_KEY
    • EcephysProjectCache.PROBE_LFP_NWB_KEY
    • EcephysProjectCache.SESSIONS_KEY
    • EcephysProjectCache.SESSION_ANALYSIS_METRICS_KEY
    • EcephysProjectCache.SESSION_DIR_KEY
    • EcephysProjectCache.SESSION_NWB_KEY
    • EcephysProjectCache.SUPPRESS_FROM_CHANNELS
    • EcephysProjectCache.SUPPRESS_FROM_PROBES
    • EcephysProjectCache.SUPPRESS_FROM_SESSION_TABLE
    • EcephysProjectCache.SUPPRESS_FROM_UNITS
    • EcephysProjectCache.TYPEWISE_ANALYSIS_METRICS_KEY
    • EcephysProjectCache.UNITS_KEY
    • EcephysProjectCache.add_manifest_paths()
    • EcephysProjectCache.fixed()
    • EcephysProjectCache.from_lims()
    • EcephysProjectCache.from_warehouse()
    • EcephysProjectCache.get_all_ages()
    • EcephysProjectCache.get_all_full_genotypes()
    • EcephysProjectCache.get_all_session_types()
    • EcephysProjectCache.get_all_sexes()
    • EcephysProjectCache.get_channels()
    • EcephysProjectCache.get_natural_movie_template()
    • EcephysProjectCache.get_natural_scene_template()
    • EcephysProjectCache.get_probes()
    • EcephysProjectCache.get_session_data()
    • EcephysProjectCache.get_session_table()
    • EcephysProjectCache.get_structure_acronyms()
    • EcephysProjectCache.get_unit_analysis_metrics_by_session_type()
    • EcephysProjectCache.get_unit_analysis_metrics_for_session()
    • EcephysProjectCache.get_units()
  • count_owned()
  • get_grouped_uniques()
  • read_csv()
  • read_metrics_csv()
  • read_movie()
  • read_nwb()
  • read_scene()
  • write_csv()
  • write_metrics_csv()
• allensdk.brain_observatory.ecephys.ecephys_session module
  • EcephysSession
    • EcephysSession.DETAILED_STIMULUS_PARAMETERS
    • EcephysSession.age_in_days
    • EcephysSession.channel_structure_intervals()
    • EcephysSession.conditionwise_spike_statistics()
    • EcephysSession.from_nwb_path()
    • EcephysSession.full_genotype
    • EcephysSession.get_current_source_density()
    • EcephysSession.get_inter_presentation_intervals_for_stimulus()
    • EcephysSession.get_invalid_times()
    • EcephysSession.get_lfp()
    • EcephysSession.get_parameter_values_for_stimulus()
    • EcephysSession.get_pupil_data()
    • EcephysSession.get_screen_gaze_data()
    • EcephysSession.get_stimulus_epochs()
    • EcephysSession.get_stimulus_parameter_values()
    • EcephysSession.get_stimulus_table()
    • EcephysSession.metadata
    • EcephysSession.num_channels
    • EcephysSession.num_probes
    • EcephysSession.num_stimulus_presentations
    • EcephysSession.num_units
    • EcephysSession.presentationwise_spike_counts()
    • EcephysSession.presentationwise_spike_times()
    • EcephysSession.rig_equipment_name
    • EcephysSession.rig_geometry_data
    • EcephysSession.session_type
    • EcephysSession.sex
    • EcephysSession.specimen_name
    • EcephysSession.spike_times
    • EcephysSession.stimulus_conditions
    • EcephysSession.stimulus_names
    • EcephysSession.stimulus_presentations
    • EcephysSession.structure_acronyms
    • EcephysSession.structurewise_unit_counts
    • EcephysSession.units
  • array_intervals()
  • build_spike_histogram()
  • build_time_window_domain()
  • coerce_scalar()
  • is_distinct_from()
  • nan_intervals()
  • removed_unused_stimulus_presentation_columns()
• allensdk.brain_observatory.ecephys.nwb_util module
  • add_ecephys_electrodes()
  • add_probe_to_nwbfile()
  • add_ragged_data_to_dynamic_table()
• allensdk.brain_observatory.ecephys.optotagging module
  • OptotaggingTable
    • OptotaggingTable.from_json()
    • OptotaggingTable.from_nwb()
    • OptotaggingTable.to_nwb()
    • OptotaggingTable.value
• allensdk.brain_observatory.ecephys.probes module
  • Probes
    • Probes.from_json()
    • Probes.from_nwb()
    • Probes.get_units_table()
    • Probes.mean_waveforms
    • Probes.probes
    • Probes.spike_amplitudes
    • Probes.spike_times
    • Probes.to_dataframe()
    • Probes.to_nwb()
• allensdk.brain_observatory.ecephys.stimulus_sync module
  • allocate_by_vsync()
  • assign_to_last()
  • compute_frame_times()
  • correct_on_off_effects()
  • estimate_frame_duration()
  • fix_unexpected_edges()
  • flag_unexpected_edges()
  • separate_vsyncs_and_photodiode_times()
  • trim_border_pulses()
  • trim_discontiguous_vsyncs()
  • trimmed_stats()
• allensdk.brain_observatory.ecephys.utils module
  • clobbering_merge()
  • group_1d_by_unit()
  • load_and_squeeze_npy()
  • scale_amplitudes()
  • strip_substructure_acronym()

Module contents

allensdk.brain_observatory.ecephys.get_unit_filter_value(key, pop=True, replace_none=True, **source)