allensdk.brain_observatory package¶
Subpackages¶
- allensdk.brain_observatory.behavior package
- Subpackages
- allensdk.brain_observatory.behavior.behavior_project_cache package
- Subpackages
- allensdk.brain_observatory.behavior.behavior_project_cache.external package
- allensdk.brain_observatory.behavior.behavior_project_cache.tables package
- Subpackages
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.util package
- Submodules
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.util.experiments_table_utils module
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.util.image_presentation_utils module
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.util.prior_exposure_processing module
- Module contents
- Submodules
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.util package
- Submodules
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.experiments_table module
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.ophys_mixin module
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.ophys_sessions_table module
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.project_table module
- allensdk.brain_observatory.behavior.behavior_project_cache.tables.sessions_table module
- Module contents
- Subpackages
- Submodules
- allensdk.brain_observatory.behavior.behavior_project_cache.behavior_neuropixels_project_cache module
- allensdk.brain_observatory.behavior.behavior_project_cache.behavior_project_cache module
- allensdk.brain_observatory.behavior.behavior_project_cache.project_cache_base module
- allensdk.brain_observatory.behavior.behavior_project_cache.utils module
- Module contents
- Subpackages
- allensdk.brain_observatory.behavior.data_files package
- Submodules
- allensdk.brain_observatory.behavior.data_files.avg_projection_file module
- allensdk.brain_observatory.behavior.data_files.demix_file module
- allensdk.brain_observatory.behavior.data_files.dff_file module
- allensdk.brain_observatory.behavior.data_files.event_detection_file module
- allensdk.brain_observatory.behavior.data_files.eye_tracking_file module
- allensdk.brain_observatory.behavior.data_files.eye_tracking_metadata_file module
- allensdk.brain_observatory.behavior.data_files.eye_tracking_video module
- allensdk.brain_observatory.behavior.data_files.max_projection_file module
- allensdk.brain_observatory.behavior.data_files.neuropil_corrected_file module
- allensdk.brain_observatory.behavior.data_files.neuropil_file module
- allensdk.brain_observatory.behavior.data_files.rigid_motion_transform_file module
- allensdk.brain_observatory.behavior.data_files.stimulus_file module
- allensdk.brain_observatory.behavior.data_files.sync_file module
- Module contents
- Submodules
- allensdk.brain_observatory.behavior.data_objects package
- Subpackages
- allensdk.brain_observatory.behavior.data_objects.cell_specimens package
- Subpackages
- allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces package
- Submodules
- allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces.corrected_fluorescence_traces module
- allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces.demixed_traces module
- allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces.dff_traces module
- allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces.neuropil_traces module
- Module contents
- Submodules
- allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces package
- Submodules
- Module contents
- Subpackages
- allensdk.brain_observatory.behavior.data_objects.eye_tracking package
- allensdk.brain_observatory.behavior.data_objects.metadata package
- Subpackages
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata package
- Submodules
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.behavior_metadata module
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.behavior_session_id module
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.behavior_session_uuid module
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.date_of_acquisition module
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.equipment module
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.foraging_id module
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.project_code module
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.session_type module
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.stimulus_frame_rate module
- Module contents
- Submodules
- allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata package
- Subpackages
- Submodules
- allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.field_of_view_shape module
- allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.imaging_depth module
- allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.imaging_plane module
- allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_container_id module
- allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_experiment_metadata module
- allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_project_code module
- allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_session_id module
- allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.targeted_imaging_depth module
- Module contents
- allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata package
- Submodules
- allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.age module
- allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.driver_line module
- allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.full_genotype module
- allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.mouse_id module
- allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.reporter_line module
- allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.sex module
- allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.subject_metadata module
- Module contents
- Submodules
- allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata package
- Submodules
- Module contents
- Subpackages
- allensdk.brain_observatory.behavior.data_objects.running_speed package
- Submodules
- allensdk.brain_observatory.behavior.data_objects.running_speed.multi_stim_running_processing module
- allensdk.brain_observatory.behavior.data_objects.running_speed.running_acquisition module
- allensdk.brain_observatory.behavior.data_objects.running_speed.running_processing module
- allensdk.brain_observatory.behavior.data_objects.running_speed.running_speed module
- Module contents
- Submodules
- allensdk.brain_observatory.behavior.data_objects.stimuli package
- Submodules
- allensdk.brain_observatory.behavior.data_objects.stimuli.fingerprint_stimulus module
- allensdk.brain_observatory.behavior.data_objects.stimuli.presentations module
- allensdk.brain_observatory.behavior.data_objects.stimuli.stimuli module
- allensdk.brain_observatory.behavior.data_objects.stimuli.stimulus_templates module
- allensdk.brain_observatory.behavior.data_objects.stimuli.templates module
- allensdk.brain_observatory.behavior.data_objects.stimuli.util module
- Module contents
- Submodules
- allensdk.brain_observatory.behavior.data_objects.timestamps package
- allensdk.brain_observatory.behavior.data_objects.trials package
- allensdk.brain_observatory.behavior.data_objects.cell_specimens package
- Submodules
- allensdk.brain_observatory.behavior.data_objects.licks module
- allensdk.brain_observatory.behavior.data_objects.motion_correction module
- allensdk.brain_observatory.behavior.data_objects.projections module
- allensdk.brain_observatory.behavior.data_objects.rewards module
- allensdk.brain_observatory.behavior.data_objects.task_parameters module
- Module contents
- Subpackages
- allensdk.brain_observatory.behavior.sync package
- allensdk.brain_observatory.behavior.write_behavior_nwb package
- allensdk.brain_observatory.behavior.write_nwb package
- allensdk.brain_observatory.behavior.behavior_project_cache 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
- Submodules
- allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_api module
- allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_fixed_api module
- allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_lims_api module
- allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_warehouse_api module
- allensdk.brain_observatory.ecephys.ecephys_project_api.http_engine module
- allensdk.brain_observatory.ecephys.ecephys_project_api.rma_engine module
- allensdk.brain_observatory.ecephys.ecephys_project_api.utilities module
- Module contents
- Submodules
- 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
- Submodules
- allensdk.brain_observatory.ecephys.stimulus_analysis.dot_motion module
- allensdk.brain_observatory.ecephys.stimulus_analysis.drifting_gratings module
- allensdk.brain_observatory.ecephys.stimulus_analysis.flashes module
- allensdk.brain_observatory.ecephys.stimulus_analysis.natural_movies module
- allensdk.brain_observatory.ecephys.stimulus_analysis.natural_scenes module
- allensdk.brain_observatory.ecephys.stimulus_analysis.receptive_field_mapping module
- allensdk.brain_observatory.ecephys.stimulus_analysis.static_gratings module
- allensdk.brain_observatory.ecephys.stimulus_analysis.stimulus_analysis module
- Module contents
- Submodules
- allensdk.brain_observatory.ecephys.stimulus_table package
- Subpackages
- Submodules
- allensdk.brain_observatory.ecephys.stimulus_table.ephys_pre_spikes module
- allensdk.brain_observatory.ecephys.stimulus_table.naming_utilities module
- allensdk.brain_observatory.ecephys.stimulus_table.output_validation module
- allensdk.brain_observatory.ecephys.stimulus_table.stimulus_parameter_extraction module
- Module contents
- 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
- 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
- allensdk.brain_observatory.comparison_utils module
- allensdk.brain_observatory.demixer module
- allensdk.brain_observatory.dff module
- allensdk.brain_observatory.drifting_gratings module
- allensdk.brain_observatory.findlevel module
- allensdk.brain_observatory.locally_sparse_noise module
- allensdk.brain_observatory.natural_movie module
- allensdk.brain_observatory.natural_scenes module
- allensdk.brain_observatory.observatory_plots module
- allensdk.brain_observatory.r_neuropil module
- allensdk.brain_observatory.roi_masks module
- allensdk.brain_observatory.running_speed module
- allensdk.brain_observatory.session_analysis module
- allensdk.brain_observatory.session_api_utils module
- allensdk.brain_observatory.static_gratings module
- allensdk.brain_observatory.stimulus_analysis module
- allensdk.brain_observatory.stimulus_info module
- allensdk.brain_observatory.sync_dataset module
- 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:
json.encoder.JSONEncoder
-
default
(self, 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)
-