allensdk package

Subpackages

• allensdk.api package
  • Subpackages
    • allensdk.api.cloud_cache package
      • Submodules
      • Module contents
    • allensdk.api.queries package
      • Submodules
      • Module contents
    • allensdk.api.warehouse_cache package
      • Submodules
      • Module contents
  • Submodules
    • allensdk.api.api module
      • Api
      • stream_file_over_http()
      • stream_zip_directory_over_http()
  • Module contents
• allensdk.brain_observatory package
  • Subpackages
    • allensdk.brain_observatory.behavior package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.brain_observatory.data_release_utils package
      • Subpackages
      • Module contents
    • allensdk.brain_observatory.ecephys package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.brain_observatory.extract_running_speed package
      • Module contents
    • allensdk.brain_observatory.gaze_mapping package
      • Module contents
    • allensdk.brain_observatory.multi_stimulus_running_speed package
      • Submodules
      • Module contents
    • allensdk.brain_observatory.nwb package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.brain_observatory.ophys package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.brain_observatory.receptive_field_analysis package
      • Submodules
      • Module contents
    • allensdk.brain_observatory.sync_utilities package
      • Module contents
    • allensdk.brain_observatory.vbn_2022 package
      • Subpackages
      • Module contents
    • allensdk.brain_observatory.visualization package
      • Module contents
  • Submodules
    • allensdk.brain_observatory.argschema_utilities module
      • ArgSchemaParserPlus
      • InputFile
      • OutputFile
      • RaisingSchema
      • check_read_access()
      • check_write_access()
      • check_write_access_dir()
      • check_write_access_overwrite()
      • optional_lims_inputs()
      • write_or_print_outputs()
    • allensdk.brain_observatory.brain_observatory_exceptions module
      • BrainObservatoryAnalysisException
      • EpochSeparationException
      • MissingStimulusException
      • NoEyeTrackingException
    • allensdk.brain_observatory.brain_observatory_plotting module
      • plot_drifting_grating_traces()
      • plot_lsn_traces()
      • plot_ns_traces()
      • plot_running_a()
      • plot_sg_traces()
    • allensdk.brain_observatory.chisquare_categorical module
      • advance_combination()
      • chisq_from_stim_table()
      • compute_chi()
      • compute_chi_shuffle()
      • compute_expected()
      • compute_observed()
      • make_category_dummy()
      • stim_table_to_categories()
    • allensdk.brain_observatory.circle_plots module
      • CoronaPlotter
      • FanPlotter
      • PolarPlotter
      • TrackPlotter
      • add_angle_labels()
      • add_arrow()
      • angle_lines()
      • build_hex_pack()
      • hex_pack()
      • make_pincushion_plot()
      • polar_line_circles()
      • polar_linspace()
      • polar_to_xy()
      • radial_arcs()
      • radial_circles()
      • reset_hex_pack()
      • rings_in_hex_pack()
      • spiral_trials()
      • spiral_trials_polar()
      • wedge_ring()
    • allensdk.brain_observatory.comparison_utils module
      • compare_fields()
    • allensdk.brain_observatory.demixer module
      • demix_time_dep_masks()
      • find_negative_baselines()
      • find_negative_transients_threshold()
      • find_zero_baselines()
      • identify_valid_masks()
      • plot_negative_baselines()
      • plot_negative_transients()
      • plot_overlap_masks_lengthOne()
      • plot_traces()
      • plot_transients()
      • rolling_window()
    • allensdk.brain_observatory.dff module
      • calculate_dff()
      • compute_dff_windowed_median()
      • compute_dff_windowed_mode()
      • main()
      • movingaverage()
      • movingmode_fast()
      • noise_std()
      • plot_onetrace()
      • robust_std()
    • allensdk.brain_observatory.drifting_gratings module
      • DriftingGratings
    • allensdk.brain_observatory.findlevel module
      • findlevel()
    • allensdk.brain_observatory.locally_sparse_noise module
      • LocallySparseNoise
    • allensdk.brain_observatory.natural_movie module
      • NaturalMovie
    • allensdk.brain_observatory.natural_scenes module
      • NaturalScenes
    • allensdk.brain_observatory.observatory_plots module
      • DimensionPatchHandler
      • figure_in_px()
      • finalize_no_axes()
      • finalize_no_labels()
      • finalize_with_axes()
      • float_label()
      • plot_cell_correlation()
      • plot_combined_speed()
      • plot_condition_histogram()
      • plot_mask_outline()
      • plot_pupil_location()
      • plot_radial_histogram()
      • plot_receptive_field()
      • plot_representational_similarity()
      • plot_selectivity_cumulative_histogram()
      • plot_speed()
      • plot_time_to_peak()
      • population_correlation_scatter()
    • allensdk.brain_observatory.r_neuropil module
      • NeuropilSubtract
      • ab_from_T()
      • ab_from_diagonals()
      • alpha_filter()
      • error_calc()
      • error_calc_outlier()
      • estimate_contamination_ratios()
      • get_diagonals_from_sparse()
      • normalize_F()
      • synthesize_F()
      • validate_with_synthetic_F()
    • allensdk.brain_observatory.roi_masks module
      • Mask
      • NeuropilMask
      • RoiMask
      • calculate_roi_and_neuropil_traces()
      • calculate_traces()
      • create_neuropil_mask()
      • create_roi_mask()
      • create_roi_mask_array()
      • validate_mask()
    • allensdk.brain_observatory.running_speed module
      • RunningSpeed
    • allensdk.brain_observatory.session_analysis module
      • SessionAnalysis
      • main()
      • multi_dataframe_merge()
      • run_session_analysis()
    • allensdk.brain_observatory.session_api_utils module
      • ParamsMixin
      • is_equal()
      • sessions_are_equal()
    • allensdk.brain_observatory.static_gratings module
      • StaticGratings
    • allensdk.brain_observatory.stimulus_analysis module
      • StimulusAnalysis
      • nonraising_ks_2samp()
    • allensdk.brain_observatory.stimulus_info module
      • BinaryIntervalSearchTree
      • BrainObservatoryMonitor
      • ExperimentGeometry
      • Monitor
      • StimulusSearch
      • all_stimuli()
      • get_spatial_grating()
      • get_spatio_temporal_grating()
      • lsn_coordinate_to_monitor_coordinate()
      • make_display_mask()
      • map_monitor_coordinate_to_stimulus_coordinate()
      • map_monitor_coordinate_to_template_coordinate()
      • map_stimulus()
      • map_stimulus_coordinate_to_monitor_coordinate()
      • map_template_coordinate_to_monitor_coordinate()
      • mask_stimulus_template()
      • monitor_coordinate_to_lsn_coordinate()
      • monitor_coordinate_to_natural_movie_coordinate()
      • natural_movie_coordinate_to_monitor_coordinate()
      • natural_scene_coordinate_to_monitor_coordinate()
      • rotate()
      • sessions_with_stimulus()
      • stimuli_in_session()
      • translate_image_and_fill()
      • warp_stimulus_coords()
    • allensdk.brain_observatory.sync_dataset module
      • Dependencies
      • Dataset
      • get_bit()
      • unpack_uint32()
    • allensdk.brain_observatory.sync_stim_aligner module
  • Module contents
    • JSONEncoder
      • JSONEncoder.default()
    • dict_to_indexed_array()
    • hook()
• allensdk.config package
  • Subpackages
    • allensdk.config.app package
      • Submodules
      • Module contents
    • allensdk.config.model package
      • Subpackages
      • Submodules
      • Module contents
  • Submodules
    • allensdk.config.manifest module
      • Manifest
      • ManifestVersionError
    • allensdk.config.manifest_builder module
      • ManifestBuilder
  • Module contents
    • enable_console_log()
• allensdk.core package
  • Subpackages
    • allensdk.core.lazy_property package
      • Submodules
      • Module contents
  • Submodules
    • allensdk.core.auth_config module
    • allensdk.core.authentication module
      • CredentialProvider
      • DbCredentials
      • EnvCredentialProvider
      • credential_injector()
      • get_credential_provider()
      • set_credential_provider()
    • allensdk.core.brain_observatory_cache module
    • allensdk.core.brain_observatory_nwb_data_set module
      • BrainObservatoryNwbDataSet
      • align_running_speed()
      • get_epoch_mask_list()
    • allensdk.core.cache_method_utilities module
      • CachedInstanceMethodMixin
    • allensdk.core.cell_types_cache module
      • CellTypesCache
      • ReporterStatus
    • allensdk.core.dat_utilities module
      • DatUtilities
    • allensdk.core.dataframe_utils module
      • INT_NULL
      • enforce_df_column_order()
      • enforce_df_int_typing()
      • patch_df_from_other()
      • return_one_dataframe_row_only()
    • allensdk.core.exceptions module
      • DataFrameIndexError
      • DataFrameKeyError
      • MissingDataError
    • allensdk.core.h5_utilities module
      • decode_bytes()
      • h5_object_matcher_relname_in()
      • keyed_locate_h5_objects()
      • load_datasets_by_relnames()
      • locate_h5_objects()
      • traverse_h5_file()
    • allensdk.core.json_utilities module
      • JsonComments
      • json_handler()
      • read()
      • read_url()
      • read_url_get()
      • read_url_post()
      • write()
      • write_string()
    • allensdk.core.mouse_connectivity_cache module
      • MouseConnectivityCache
    • allensdk.core.nwb_data_set module
      • NwbDataSet
    • allensdk.core.obj_utilities module
      • parse_obj()
      • read_obj()
    • allensdk.core.ontology module
      • Ontology
    • allensdk.core.ophys_experiment_session_id_mapping module
    • allensdk.core.pickle_utils module
      • load_and_sanitize_pickle()
    • allensdk.core.reference_space module
      • ReferenceSpace
    • allensdk.core.reference_space_cache module
      • ReferenceSpaceCache
    • allensdk.core.simple_tree module
      • SimpleTree
    • allensdk.core.sitk_utilities module
      • fix_array_dimensions()
      • get_sitk_image_information()
      • read_ndarray_with_sitk()
      • set_sitk_image_information()
      • write_ndarray_with_sitk()
    • allensdk.core.structure_tree module
      • StructureTree
    • allensdk.core.swc module
      • Compartment
      • Marker
      • Morphology
      • read_marker_file()
      • read_swc()
    • allensdk.core.typing module
      • SupportsStr
    • allensdk.core.utilities module
      • df_list_to_tuple()
      • literal_col_eval()
  • Module contents
• allensdk.ephys package
  • Submodules
    • allensdk.ephys.ephys_extractor module
      • EphysCellFeatureExtractor
      • EphysSweepFeatureExtractor
      • EphysSweepSetFeatureExtractor
      • cell_extractor_for_nwb()
      • extractor_for_nwb_sweeps()
      • fit_fi_slope()
      • input_resistance()
      • membrane_time_constant()
      • reset_long_squares_start()
    • allensdk.ephys.ephys_features module
      • FeatureError
      • adaptation_index()
      • analyze_trough_details()
      • average_rate()
      • average_voltage()
      • calculate_dvdt()
      • check_thresholds_and_peaks()
      • detect_bursts()
      • detect_pauses()
      • detect_putative_spikes()
      • estimate_adjusted_detection_parameters()
      • filter_putative_spikes()
      • find_downstroke_indexes()
      • find_peak_indexes()
      • find_time_index()
      • find_trough_indexes()
      • find_upstroke_indexes()
      • find_widths()
      • fit_membrane_time_constant()
      • fit_prespike_time_constant()
      • get_isis()
      • has_fixed_dt()
      • latency()
      • norm_diff()
      • norm_sq_diff()
      • refine_threshold_indexes()
    • allensdk.ephys.extract_cell_features module
      • extract_cell_features()
      • extract_sweep_features()
      • get_ramp_stim_characteristics()
      • get_square_stim_characteristics()
      • get_stim_characteristics()
      • mean_features_spike_zero()
    • allensdk.ephys.feature_extractor module
      • EphysFeatureExtractor
      • EphysFeatures
  • Module contents
• allensdk.internal package
  • Subpackages
    • allensdk.internal.api package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.internal.brain_observatory package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.internal.core package
      • Submodules
      • Module contents
    • allensdk.internal.ephys package
      • Submodules
      • Module contents
    • allensdk.internal.model package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.internal.morphology package
      • Submodules
      • Module contents
    • allensdk.internal.mouse_connectivity package
      • Subpackages
      • Module contents
    • allensdk.internal.notebooks package
      • Submodules
      • Module contents
    • allensdk.internal.pipeline_modules package
      • Subpackages
      • Submodules
      • Module contents
  • Module contents
• allensdk.model package
  • Subpackages
    • allensdk.model.biophys_sim package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.model.biophysical package
      • Submodules
      • Module contents
    • allensdk.model.glif package
      • Submodules
      • Module contents
  • Module contents
• allensdk.morphology package
  • Submodules
    • allensdk.morphology.validate_swc module
      • main()
      • validate_swc()
  • Module contents
• allensdk.mouse_connectivity package
  • Subpackages
    • allensdk.mouse_connectivity.grid package
      • Subpackages
      • Submodules
      • Module contents
  • Module contents
• allensdk.test_utilities package
  • Submodules
    • allensdk.test_utilities.custom_comparators module
      • WhitespaceStrippedString
      • safe_df_comparison()
      • stimulus_pickle_equivalence()
    • allensdk.test_utilities.regression_fixture module
      • get_list_of_path_dict()
    • allensdk.test_utilities.temp_dir module
      • temp_dir()
  • Module contents

Submodules

• allensdk.deprecated module
  • class_deprecated()
  • deprecated()
  • legacy()

Module contents

exception allensdk.OneResultExpectedError

Bases: RuntimeError

allensdk.one(x)