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
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
- allensdk.brain_observatory.demixer module
- allensdk.brain_observatory.dff module
- allensdk.brain_observatory.drifting_gratings module
DriftingGratings
DriftingGratings.from_analysis_file()
DriftingGratings.get_noise_correlation()
DriftingGratings.get_peak()
DriftingGratings.get_representational_similarity()
DriftingGratings.get_response()
DriftingGratings.get_signal_correlation()
DriftingGratings.number_ori
DriftingGratings.number_tf
DriftingGratings.open_star_plot()
DriftingGratings.orivals
DriftingGratings.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
LocallySparseNoise
LocallySparseNoise.LSN
LocallySparseNoise.LSN_GREY
LocallySparseNoise.LSN_OFF
LocallySparseNoise.LSN_OFF_SCREEN
LocallySparseNoise.LSN_ON
LocallySparseNoise.LSN_mask
LocallySparseNoise.cell_index_receptive_field_analysis_data
LocallySparseNoise.extralength
LocallySparseNoise.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.interlength
LocallySparseNoise.mean_response
LocallySparseNoise.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_field
LocallySparseNoise.save_cell_index_receptive_field_analysis()
LocallySparseNoise.sort_trials()
LocallySparseNoise.sweeplength
- allensdk.brain_observatory.natural_movie module
- allensdk.brain_observatory.natural_scenes module
NaturalScenes
NaturalScenes.extralength
NaturalScenes.from_analysis_file()
NaturalScenes.get_noise_correlation()
NaturalScenes.get_peak()
NaturalScenes.get_representational_similarity()
NaturalScenes.get_response()
NaturalScenes.get_signal_correlation()
NaturalScenes.interlength
NaturalScenes.number_scenes
NaturalScenes.open_corona_plot()
NaturalScenes.plot_time_to_peak()
NaturalScenes.populate_stimulus_table()
NaturalScenes.reshape_response_array()
NaturalScenes.sweeplength
- 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
- allensdk.brain_observatory.roi_masks module
- allensdk.brain_observatory.running_speed module
- allensdk.brain_observatory.session_analysis module
SessionAnalysis
SessionAnalysis.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
StaticGratings
StaticGratings.extralength
StaticGratings.from_analysis_file()
StaticGratings.get_noise_correlation()
StaticGratings.get_peak()
StaticGratings.get_representational_similarity()
StaticGratings.get_response()
StaticGratings.get_signal_correlation()
StaticGratings.interlength
StaticGratings.number_ori
StaticGratings.number_phase
StaticGratings.number_sf
StaticGratings.open_fan_plot()
StaticGratings.orivals
StaticGratings.phasevals
StaticGratings.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.sfvals
StaticGratings.sweeplength
- allensdk.brain_observatory.stimulus_analysis module
StimulusAnalysis
StimulusAnalysis.acquisition_rate
StimulusAnalysis.binned_cells_sp
StimulusAnalysis.binned_cells_vis
StimulusAnalysis.binned_dx_sp
StimulusAnalysis.binned_dx_vis
StimulusAnalysis.cell_id
StimulusAnalysis.celltraces
StimulusAnalysis.dfftraces
StimulusAnalysis.dxcm
StimulusAnalysis.dxtime
StimulusAnalysis.get_fluorescence()
StimulusAnalysis.get_peak()
StimulusAnalysis.get_response()
StimulusAnalysis.get_speed_tuning()
StimulusAnalysis.get_sweep_response()
StimulusAnalysis.mean_sweep_response
StimulusAnalysis.numbercells
StimulusAnalysis.peak
StimulusAnalysis.peak_run
StimulusAnalysis.plot_representational_similarity()
StimulusAnalysis.plot_running_speed_histogram()
StimulusAnalysis.plot_speed_tuning()
StimulusAnalysis.populate_stimulus_table()
StimulusAnalysis.pval
StimulusAnalysis.response
StimulusAnalysis.roi_id
StimulusAnalysis.row_from_cell_id()
StimulusAnalysis.stim_table
StimulusAnalysis.sweep_response
StimulusAnalysis.timestamps
nonraising_ks_2samp()
- allensdk.brain_observatory.stimulus_info module
BinaryIntervalSearchTree
BrainObservatoryMonitor
ExperimentGeometry
Monitor
Monitor.aspect_ratio
Monitor.get_mask()
Monitor.grating_to_screen()
Monitor.height
Monitor.lsn_image_to_screen()
Monitor.map_stimulus()
Monitor.mask
Monitor.natural_movie_image_to_screen()
Monitor.natural_scene_image_to_screen()
Monitor.panel_size
Monitor.pixel_size
Monitor.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
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
Dataset.BEHAVIOR_TRACKING_KEYS
Dataset.DEPRECATED_KEYS
Dataset.EYE_TRACKING_KEYS
Dataset.FRAME_KEYS
Dataset.OPTOGENETIC_STIMULATION_KEYS
Dataset.PHOTODIODE_KEYS
Dataset.analog_meta_data
Dataset.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_freq
Dataset.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)