allensdk.brain_observatory package¶
Subpackages¶
- allensdk.brain_observatory.behavior package
- Subpackages
- allensdk.brain_observatory.behavior.behavior_project_cache package
- allensdk.brain_observatory.behavior.data_files package
- allensdk.brain_observatory.behavior.data_objects package
- allensdk.brain_observatory.behavior.sync package
- allensdk.brain_observatory.behavior.utils package
- allensdk.brain_observatory.behavior.write_nwb package
- Submodules
- allensdk.brain_observatory.behavior.behavior_ophys_analysis module
- allensdk.brain_observatory.behavior.behavior_ophys_experiment module
- allensdk.brain_observatory.behavior.behavior_ophys_session module
- allensdk.brain_observatory.behavior.behavior_session module
- allensdk.brain_observatory.behavior.criteria module
- allensdk.brain_observatory.behavior.dprime module
- allensdk.brain_observatory.behavior.event_detection module
- allensdk.brain_observatory.behavior.eye_tracking_processing module
- allensdk.brain_observatory.behavior.image_api module
- allensdk.brain_observatory.behavior.mtrain module
- allensdk.brain_observatory.behavior.rewards_processing module
- allensdk.brain_observatory.behavior.schemas module
- allensdk.brain_observatory.behavior.session_metrics module
- allensdk.brain_observatory.behavior.stimulus_processing module
- allensdk.brain_observatory.behavior.trial_masks module
- allensdk.brain_observatory.behavior.trials_processing module
- Module contents
- Subpackages
- allensdk.brain_observatory.data_release_utils package
- allensdk.brain_observatory.ecephys package
- Subpackages
- allensdk.brain_observatory.ecephys.align_timestamps package
- allensdk.brain_observatory.ecephys.copy_utility package
- allensdk.brain_observatory.ecephys.current_source_density package
- allensdk.brain_observatory.ecephys.data_objects package
- allensdk.brain_observatory.ecephys.ecephys_project_api package
- allensdk.brain_observatory.ecephys.ecephys_session_api package
- allensdk.brain_observatory.ecephys.file_io package
- allensdk.brain_observatory.ecephys.lfp_subsampling package
- allensdk.brain_observatory.ecephys.nwb package
- allensdk.brain_observatory.ecephys.optotagging_table package
- allensdk.brain_observatory.ecephys.stimulus_analysis package
- allensdk.brain_observatory.ecephys.stimulus_table package
- allensdk.brain_observatory.ecephys.visualization package
- allensdk.brain_observatory.ecephys.write_nwb package
- Submodules
- allensdk.brain_observatory.ecephys.behavior_ecephys_session module
- allensdk.brain_observatory.ecephys.ecephys_project_cache module
- allensdk.brain_observatory.ecephys.ecephys_session module
- allensdk.brain_observatory.ecephys.nwb_util module
- allensdk.brain_observatory.ecephys.optotagging module
- allensdk.brain_observatory.ecephys.probes module
- allensdk.brain_observatory.ecephys.stimulus_sync module
- allensdk.brain_observatory.ecephys.utils module
- Module contents
- Subpackages
- allensdk.brain_observatory.extract_running_speed package
- allensdk.brain_observatory.gaze_mapping package
- allensdk.brain_observatory.multi_stimulus_running_speed package
- allensdk.brain_observatory.nwb package
- Subpackages
- Submodules
- Module contents
add_average_image()add_cell_specimen_table()add_corrected_fluorescence_traces()add_dff_traces()add_eye_gaze_data_interfaces()add_eye_gaze_mapping_data_to_nwbfile()add_eye_tracking_ellipse_fit_data_to_nwbfile()add_image()add_invalid_times()add_licks()add_max_projection()add_metadata()add_motion_correction()add_rewards()add_running_acquisition_to_nwbfile()add_running_speed_to_nwbfile()add_segmentation_mask_image()add_stimulus_timestamps()add_task_parameters()add_trials()check_nwbfile_version()create_eye_gaze_mapping_dataframe()create_eye_tracking_nwb_processing_module()create_gaze_mapping_nwb_processing_modules()create_stimulus_presentation_time_interval()eye_tracking_data_is_valid()read_eye_dlc_tracking_ellipses()read_eye_gaze_mappings()setup_table_for_epochs()setup_table_for_invalid_times()
- allensdk.brain_observatory.ophys package
- allensdk.brain_observatory.receptive_field_analysis package
- Submodules
- allensdk.brain_observatory.receptive_field_analysis.chisquarerf module
- allensdk.brain_observatory.receptive_field_analysis.eventdetection module
- allensdk.brain_observatory.receptive_field_analysis.fit_parameters module
- allensdk.brain_observatory.receptive_field_analysis.fitgaussian2D module
- allensdk.brain_observatory.receptive_field_analysis.postprocessing module
- allensdk.brain_observatory.receptive_field_analysis.receptive_field module
- allensdk.brain_observatory.receptive_field_analysis.tools module
- allensdk.brain_observatory.receptive_field_analysis.utilities module
- allensdk.brain_observatory.receptive_field_analysis.visualization module
- Module contents
- Submodules
- allensdk.brain_observatory.sync_utilities package
- allensdk.brain_observatory.vbn_2022 package
- allensdk.brain_observatory.visualization package
Submodules¶
- allensdk.brain_observatory.argschema_utilities module
- allensdk.brain_observatory.brain_observatory_exceptions module
- allensdk.brain_observatory.brain_observatory_plotting module
- allensdk.brain_observatory.chisquare_categorical module
- allensdk.brain_observatory.circle_plots module
CoronaPlotterFanPlotterPolarPlotterTrackPlotteradd_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
- allensdk.brain_observatory.demixer module
- allensdk.brain_observatory.dff module
- allensdk.brain_observatory.drifting_gratings module
DriftingGratingsDriftingGratings.from_analysis_file()DriftingGratings.get_noise_correlation()DriftingGratings.get_peak()DriftingGratings.get_representational_similarity()DriftingGratings.get_response()DriftingGratings.get_signal_correlation()DriftingGratings.number_oriDriftingGratings.number_tfDriftingGratings.open_star_plot()DriftingGratings.orivalsDriftingGratings.plot_direction_selectivity()DriftingGratings.plot_orientation_selectivity()DriftingGratings.plot_preferred_direction()DriftingGratings.plot_preferred_temporal_frequency()DriftingGratings.populate_stimulus_table()DriftingGratings.reshape_response_array()DriftingGratings.tfvals
- allensdk.brain_observatory.findlevel module
- allensdk.brain_observatory.locally_sparse_noise module
LocallySparseNoiseLocallySparseNoise.LSNLocallySparseNoise.LSN_GREYLocallySparseNoise.LSN_OFFLocallySparseNoise.LSN_OFF_SCREENLocallySparseNoise.LSN_ONLocallySparseNoise.LSN_maskLocallySparseNoise.cell_index_receptive_field_analysis_dataLocallySparseNoise.extralengthLocallySparseNoise.from_analysis_file()LocallySparseNoise.get_mean_response()LocallySparseNoise.get_peak()LocallySparseNoise.get_receptive_field()LocallySparseNoise.get_receptive_field_analysis_data()LocallySparseNoise.get_receptive_field_attribute_df()LocallySparseNoise.interlengthLocallySparseNoise.mean_responseLocallySparseNoise.merge_mean_response()LocallySparseNoise.open_pincushion_plot()LocallySparseNoise.plot_cell_receptive_field()LocallySparseNoise.plot_population_receptive_field()LocallySparseNoise.plot_receptive_field_analysis_data()LocallySparseNoise.populate_stimulus_table()LocallySparseNoise.read_cell_index_receptive_field_analysis()LocallySparseNoise.receptive_fieldLocallySparseNoise.save_cell_index_receptive_field_analysis()LocallySparseNoise.sort_trials()LocallySparseNoise.sweeplength
- allensdk.brain_observatory.natural_movie module
- allensdk.brain_observatory.natural_scenes module
NaturalScenesNaturalScenes.extralengthNaturalScenes.from_analysis_file()NaturalScenes.get_noise_correlation()NaturalScenes.get_peak()NaturalScenes.get_representational_similarity()NaturalScenes.get_response()NaturalScenes.get_signal_correlation()NaturalScenes.interlengthNaturalScenes.number_scenesNaturalScenes.open_corona_plot()NaturalScenes.plot_time_to_peak()NaturalScenes.populate_stimulus_table()NaturalScenes.reshape_response_array()NaturalScenes.sweeplength
- allensdk.brain_observatory.observatory_plots module
DimensionPatchHandlerfigure_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
- allensdk.brain_observatory.roi_masks module
- allensdk.brain_observatory.running_speed module
- allensdk.brain_observatory.session_analysis module
SessionAnalysisSessionAnalysis.append_experiment_metrics()SessionAnalysis.append_metadata()SessionAnalysis.append_metrics_drifting_grating()SessionAnalysis.append_metrics_locally_sparse_noise()SessionAnalysis.append_metrics_natural_movie_one()SessionAnalysis.append_metrics_natural_movie_three()SessionAnalysis.append_metrics_natural_movie_two()SessionAnalysis.append_metrics_natural_scene()SessionAnalysis.append_metrics_static_grating()SessionAnalysis.save_session_a()SessionAnalysis.save_session_b()SessionAnalysis.save_session_c()SessionAnalysis.save_session_c2()SessionAnalysis.session_a()SessionAnalysis.session_b()SessionAnalysis.session_c()SessionAnalysis.session_c2()SessionAnalysis.verify_roi_lists_equal()
main()multi_dataframe_merge()run_session_analysis()
- allensdk.brain_observatory.session_api_utils module
- allensdk.brain_observatory.static_gratings module
StaticGratingsStaticGratings.extralengthStaticGratings.from_analysis_file()StaticGratings.get_noise_correlation()StaticGratings.get_peak()StaticGratings.get_representational_similarity()StaticGratings.get_response()StaticGratings.get_signal_correlation()StaticGratings.interlengthStaticGratings.number_oriStaticGratings.number_phaseStaticGratings.number_sfStaticGratings.open_fan_plot()StaticGratings.orivalsStaticGratings.phasevalsStaticGratings.plot_orientation_selectivity()StaticGratings.plot_preferred_orientation()StaticGratings.plot_preferred_spatial_frequency()StaticGratings.plot_time_to_peak()StaticGratings.populate_stimulus_table()StaticGratings.reshape_response_array()StaticGratings.sfvalsStaticGratings.sweeplength
- allensdk.brain_observatory.stimulus_analysis module
StimulusAnalysisStimulusAnalysis.acquisition_rateStimulusAnalysis.binned_cells_spStimulusAnalysis.binned_cells_visStimulusAnalysis.binned_dx_spStimulusAnalysis.binned_dx_visStimulusAnalysis.cell_idStimulusAnalysis.celltracesStimulusAnalysis.dfftracesStimulusAnalysis.dxcmStimulusAnalysis.dxtimeStimulusAnalysis.get_fluorescence()StimulusAnalysis.get_peak()StimulusAnalysis.get_response()StimulusAnalysis.get_speed_tuning()StimulusAnalysis.get_sweep_response()StimulusAnalysis.mean_sweep_responseStimulusAnalysis.numbercellsStimulusAnalysis.peakStimulusAnalysis.peak_runStimulusAnalysis.plot_representational_similarity()StimulusAnalysis.plot_running_speed_histogram()StimulusAnalysis.plot_speed_tuning()StimulusAnalysis.populate_stimulus_table()StimulusAnalysis.pvalStimulusAnalysis.responseStimulusAnalysis.roi_idStimulusAnalysis.row_from_cell_id()StimulusAnalysis.stim_tableStimulusAnalysis.sweep_responseStimulusAnalysis.timestamps
nonraising_ks_2samp()
- allensdk.brain_observatory.stimulus_info module
BinaryIntervalSearchTreeBrainObservatoryMonitorExperimentGeometryMonitorMonitor.aspect_ratioMonitor.get_mask()Monitor.grating_to_screen()Monitor.heightMonitor.lsn_image_to_screen()Monitor.map_stimulus()Monitor.maskMonitor.natural_movie_image_to_screen()Monitor.natural_scene_image_to_screen()Monitor.panel_sizeMonitor.pixel_sizeMonitor.pixels_to_visual_degrees()Monitor.set_spatial_unit()Monitor.show_image()Monitor.spatial_frequency_to_pix_per_cycle()Monitor.visual_degrees_to_pixels()Monitor.width
StimulusSearchall_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
DatasetDataset.BEHAVIOR_TRACKING_KEYSDataset.DEPRECATED_KEYSDataset.EYE_TRACKING_KEYSDataset.FRAME_KEYSDataset.OPTOGENETIC_STIMULATION_KEYSDataset.PHOTODIODE_KEYSDataset.analog_meta_dataDataset.close()Dataset.duty_cycle()Dataset.frequency()Dataset.get_all_bits()Dataset.get_all_events()Dataset.get_all_times()Dataset.get_analog_channel()Dataset.get_analog_meta()Dataset.get_bit()Dataset.get_bit_changes()Dataset.get_edges()Dataset.get_events_by_bit()Dataset.get_events_by_line()Dataset.get_falling_edges()Dataset.get_line()Dataset.get_line_changes()Dataset.get_nearest()Dataset.get_rising_edges()Dataset.line_stats()Dataset.load()Dataset.period()Dataset.plot_all()Dataset.plot_bit()Dataset.plot_bits()Dataset.plot_line()Dataset.plot_lines()Dataset.sample_freqDataset.stats()
get_bit()unpack_uint32()
- allensdk.brain_observatory.sync_stim_aligner module
Module contents¶
- class allensdk.brain_observatory.JSONEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]¶
Bases:
JSONEncoder- default(o)[source]¶
Implement this method in a subclass such that it returns a serializable object for
o, or calls the base implementation (to raise aTypeError).For example, to support arbitrary iterators, you could implement default like this:
def default(self, o): try: iterable = iter(o) except TypeError: pass else: return list(iterable) # Let the base class default method raise the TypeError return JSONEncoder.default(self, o)