allensdk.brain_observatory.behavior package

Subpackages

• allensdk.brain_observatory.behavior.behavior_project_cache package
  • Subpackages
    • allensdk.brain_observatory.behavior.behavior_project_cache.project_metadata_writer package
      • Submodules
      • Module contents
    • allensdk.brain_observatory.behavior.behavior_project_cache.tables package
      • Subpackages
      • Submodules
      • Module contents
  • Submodules
    • allensdk.brain_observatory.behavior.behavior_project_cache.behavior_neuropixels_project_cache module
      • VisualBehaviorNeuropixelsProjectCache
    • allensdk.brain_observatory.behavior.behavior_project_cache.behavior_project_cache module
      • UpdatedStimulusPresentationTableWarning
      • VBOLimsCache
      • VisualBehaviorOphysProjectCache
    • allensdk.brain_observatory.behavior.behavior_project_cache.project_cache_base module
      • ProjectCacheBase
    • allensdk.brain_observatory.behavior.behavior_project_cache.utils module
      • BehaviorCloudCacheVersionException
      • version_check()
  • Module contents
• 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
      • DemixFile
      • from_json_cache_key()
      • from_lims_cache_key()
    • allensdk.brain_observatory.behavior.data_files.dff_file module
      • DFFFile
      • from_json_cache_key()
      • from_lims_cache_key()
    • allensdk.brain_observatory.behavior.data_files.event_detection_file module
      • EventDetectionFile
      • from_json_cache_key()
      • from_lims_cache_key()
    • allensdk.brain_observatory.behavior.data_files.eye_tracking_file module
      • EyeTrackingFile
    • allensdk.brain_observatory.behavior.data_files.eye_tracking_metadata_file module
      • EyeTrackingMetadataFile
    • allensdk.brain_observatory.behavior.data_files.eye_tracking_video module
      • EyeTrackingVideo
    • allensdk.brain_observatory.behavior.data_files.max_projection_file module
    • allensdk.brain_observatory.behavior.data_files.neuropil_corrected_file module
      • NeuropilCorrectedFile
      • from_json_cache_key()
      • from_lims_cache_key()
    • allensdk.brain_observatory.behavior.data_files.neuropil_file module
      • NeuropilFile
      • from_json_cache_key()
      • from_lims_cache_key()
    • allensdk.brain_observatory.behavior.data_files.rigid_motion_transform_file module
      • RigidMotionTransformFile
      • from_json_cache_key()
      • from_lims_cache_key()
    • allensdk.brain_observatory.behavior.data_files.stimulus_file module
      • BehaviorStimulusFile
      • MalformedStimulusFileError
      • MappingStimulusFile
      • ReplayStimulusFile
      • StimulusFileLookup
      • StimulusFileReadableInterface
      • from_json_cache_key()
      • from_lims_cache_key()
      • stimulus_lookup_from_json()
    • allensdk.brain_observatory.behavior.data_files.sync_file module
      • SyncFile
      • SyncFileReadableInterface
      • from_json_cache_key()
      • from_lims_cache_key()
  • Module contents
• allensdk.brain_observatory.behavior.data_objects package
  • Subpackages
    • allensdk.brain_observatory.behavior.data_objects.cell_specimens package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.brain_observatory.behavior.data_objects.eye_tracking package
      • Submodules
      • Module contents
    • allensdk.brain_observatory.behavior.data_objects.metadata package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.brain_observatory.behavior.data_objects.running_speed package
      • Submodules
      • Module contents
    • allensdk.brain_observatory.behavior.data_objects.stimuli package
      • Submodules
      • Module contents
    • allensdk.brain_observatory.behavior.data_objects.timestamps package
      • Subpackages
      • Submodules
      • Module contents
    • allensdk.brain_observatory.behavior.data_objects.trials package
      • Submodules
      • Module contents
  • Submodules
    • allensdk.brain_observatory.behavior.data_objects.licks module
      • Licks
    • allensdk.brain_observatory.behavior.data_objects.motion_correction module
      • MotionCorrection
    • allensdk.brain_observatory.behavior.data_objects.projections module
      • Projections
    • allensdk.brain_observatory.behavior.data_objects.rewards module
      • Rewards
    • allensdk.brain_observatory.behavior.data_objects.task_parameters module
      • BehaviorStimulusType
      • StimulusDistribution
      • TaskParameters
      • TaskType
  • Module contents
• allensdk.brain_observatory.behavior.sync package
  • Submodules
    • allensdk.brain_observatory.behavior.sync.process_sync module
      • calculate_delay()
      • filter_digital()
  • Module contents
    • get_behavior_monitoring()
    • get_eye_tracking()
    • get_lick_times()
    • get_ophys_frames()
    • get_raw_stimulus_frames()
    • get_stim_photodiode()
    • get_sync_data()
    • get_trigger()
• allensdk.brain_observatory.behavior.utils package
  • Submodules
    • allensdk.brain_observatory.behavior.utils.metadata_parsers module
      • parse_behavior_context()
      • parse_num_cortical_structures()
      • parse_num_depths()
      • parse_stimulus_set()
  • Module contents
• allensdk.brain_observatory.behavior.write_nwb package
  • Subpackages
    • allensdk.brain_observatory.behavior.write_nwb.behavior package
      • Submodules
      • Module contents
    • allensdk.brain_observatory.behavior.write_nwb.extensions package
      • Subpackages
      • Module contents
    • allensdk.brain_observatory.behavior.write_nwb.ophys package
      • Submodules
      • Module contents
  • Submodules
    • allensdk.brain_observatory.behavior.write_nwb.nwb_writer_utils module
      • OphysNwbWriter
  • Module contents

Submodules

• allensdk.brain_observatory.behavior.behavior_ophys_analysis module
  • BehaviorOphysAnalysis
    • BehaviorOphysAnalysis.plot_example_traces_and_behavior()
  • plot_example_traces_and_behavior()
  • plot_trace()
• allensdk.brain_observatory.behavior.behavior_ophys_experiment module
  • BehaviorOphysExperiment
    • BehaviorOphysExperiment.average_projection
    • BehaviorOphysExperiment.cell_specimen_table
    • BehaviorOphysExperiment.corrected_fluorescence_traces
    • BehaviorOphysExperiment.demixed_traces
    • BehaviorOphysExperiment.dff_traces
    • BehaviorOphysExperiment.events
    • BehaviorOphysExperiment.from_json()
    • BehaviorOphysExperiment.from_lims()
    • BehaviorOphysExperiment.from_nwb()
    • BehaviorOphysExperiment.get_cell_specimen_ids()
    • BehaviorOphysExperiment.get_cell_specimen_indices()
    • BehaviorOphysExperiment.get_dff_traces()
    • BehaviorOphysExperiment.get_segmentation_mask_image()
    • BehaviorOphysExperiment.max_projection
    • BehaviorOphysExperiment.metadata
    • BehaviorOphysExperiment.motion_correction
    • BehaviorOphysExperiment.neuropil_traces
    • BehaviorOphysExperiment.ophys_experiment_id
    • BehaviorOphysExperiment.ophys_session_id
    • BehaviorOphysExperiment.ophys_timestamps
    • BehaviorOphysExperiment.roi_masks
    • BehaviorOphysExperiment.segmentation_mask_image
    • BehaviorOphysExperiment.to_nwb()
    • BehaviorOphysExperiment.update_targeted_imaging_depth()
• allensdk.brain_observatory.behavior.behavior_ophys_session module
  • BehaviorOphysSession
• allensdk.brain_observatory.behavior.behavior_session module
  • BehaviorSession
    • BehaviorSession.behavior_session_id
    • BehaviorSession.eye_tracking
    • BehaviorSession.eye_tracking_rig_geometry
    • BehaviorSession.from_json()
    • BehaviorSession.from_lims()
    • BehaviorSession.from_nwb()
    • BehaviorSession.from_nwb_path()
    • BehaviorSession.get_performance_metrics()
    • BehaviorSession.get_reward_rate()
    • BehaviorSession.get_rolling_performance_df()
    • BehaviorSession.licks
    • BehaviorSession.list_data_attributes_and_methods()
    • BehaviorSession.metadata
    • BehaviorSession.raw_running_speed
    • BehaviorSession.rewards
    • BehaviorSession.running_speed
    • BehaviorSession.stimulus_presentations
    • BehaviorSession.stimulus_templates
    • BehaviorSession.stimulus_timestamps
    • BehaviorSession.task_parameters
    • BehaviorSession.to_nwb()
    • BehaviorSession.trials
• allensdk.brain_observatory.behavior.criteria module
  • consistency_is_key()
  • consistent_behavior_within_session()
  • meets_engagement_criteria()
  • mostly_useful()
  • n_complete()
  • no_response_bias()
  • summer_over()
  • two_out_of_three_aint_bad()
  • whole_lotta_trials()
  • yesterday_was_good()
• allensdk.brain_observatory.behavior.dprime module
  • get_catch_responses()
  • get_dprime()
  • get_false_alarm_rate()
  • get_go_responses()
  • get_hit_rate()
  • get_rolling_dprime()
  • get_trial_count_corrected_false_alarm_rate()
  • get_trial_count_corrected_hit_rate()
  • trial_number_limit()
• allensdk.brain_observatory.behavior.event_detection module
  • filter_events_array()
• allensdk.brain_observatory.behavior.eye_tracking_processing module
  • EyeTrackingError
  • compute_circular_area()
  • compute_elliptical_area()
  • determine_likely_blinks()
  • determine_outliers()
  • filter_on_blinks()
  • load_eye_tracking_hdf()
  • process_eye_tracking_data()
• allensdk.brain_observatory.behavior.image_api module
  • Image
    • Image.data
    • Image.spacing
    • Image.unit
  • ImageApi
    • ImageApi.deserialize()
    • ImageApi.serialize()
• allensdk.brain_observatory.behavior.mtrain module
  • ExtendedTrialSchema
    • ExtendedTrialSchema.dump_fields
    • ExtendedTrialSchema.exclude
    • ExtendedTrialSchema.fields
    • ExtendedTrialSchema.load_fields
    • ExtendedTrialSchema.opts
  • FriendlyDate
  • FriendlyDateTime
  • annotate_change_detect()
  • annotate_trials()
  • assign_session_id()
  • explode_response_window()
  • fix_change_time()
• allensdk.brain_observatory.behavior.rewards_processing module
  • get_rewards()
• allensdk.brain_observatory.behavior.schemas module
  • BehaviorMetadataSchema
    • BehaviorMetadataSchema.dump_fields
    • BehaviorMetadataSchema.exclude
    • BehaviorMetadataSchema.fields
    • BehaviorMetadataSchema.load_fields
    • BehaviorMetadataSchema.neurodata_doc
    • BehaviorMetadataSchema.neurodata_skip
    • BehaviorMetadataSchema.neurodata_type
    • BehaviorMetadataSchema.neurodata_type_inc
    • BehaviorMetadataSchema.opts
  • BehaviorTaskParametersSchema
    • BehaviorTaskParametersSchema.dump_fields
    • BehaviorTaskParametersSchema.exclude
    • BehaviorTaskParametersSchema.fields
    • BehaviorTaskParametersSchema.load_fields
    • BehaviorTaskParametersSchema.neurodata_doc
    • BehaviorTaskParametersSchema.neurodata_type
    • BehaviorTaskParametersSchema.neurodata_type_inc
    • BehaviorTaskParametersSchema.opts
  • CompleteOphysBehaviorMetadataSchema
    • CompleteOphysBehaviorMetadataSchema.dump_fields
    • CompleteOphysBehaviorMetadataSchema.exclude
    • CompleteOphysBehaviorMetadataSchema.fields
    • CompleteOphysBehaviorMetadataSchema.load_fields
    • CompleteOphysBehaviorMetadataSchema.opts
  • EyeTrackingRigGeometry
    • EyeTrackingRigGeometry.dump_fields
    • EyeTrackingRigGeometry.exclude
    • EyeTrackingRigGeometry.fields
    • EyeTrackingRigGeometry.load_fields
    • EyeTrackingRigGeometry.opts
  • NwbOphysMetadataSchema
    • NwbOphysMetadataSchema.dump_fields
    • NwbOphysMetadataSchema.exclude
    • NwbOphysMetadataSchema.fields
    • NwbOphysMetadataSchema.load_fields
    • NwbOphysMetadataSchema.opts
  • OphysBehaviorMetadataSchema
    • OphysBehaviorMetadataSchema.dump_fields
    • OphysBehaviorMetadataSchema.exclude
    • OphysBehaviorMetadataSchema.fields
    • OphysBehaviorMetadataSchema.load_fields
    • OphysBehaviorMetadataSchema.neurodata_doc
    • OphysBehaviorMetadataSchema.neurodata_skip
    • OphysBehaviorMetadataSchema.neurodata_type
    • OphysBehaviorMetadataSchema.neurodata_type_inc
    • OphysBehaviorMetadataSchema.opts
  • OphysEyeTrackingRigMetadataSchema
    • OphysEyeTrackingRigMetadataSchema.dump_fields
    • OphysEyeTrackingRigMetadataSchema.exclude
    • OphysEyeTrackingRigMetadataSchema.fields
    • OphysEyeTrackingRigMetadataSchema.load_fields
    • OphysEyeTrackingRigMetadataSchema.neurodata_doc
    • OphysEyeTrackingRigMetadataSchema.neurodata_type
    • OphysEyeTrackingRigMetadataSchema.neurodata_type_inc
    • OphysEyeTrackingRigMetadataSchema.opts
  • OphysMetadataSchema
    • OphysMetadataSchema.dump_fields
    • OphysMetadataSchema.exclude
    • OphysMetadataSchema.fields
    • OphysMetadataSchema.load_fields
    • OphysMetadataSchema.opts
  • RaisingSchema
    • RaisingSchema.Meta
      • RaisingSchema.Meta.unknown
    • RaisingSchema.dump_fields
    • RaisingSchema.exclude
    • RaisingSchema.fields
    • RaisingSchema.load_fields
    • RaisingSchema.opts
  • SubjectMetadataSchema
    • SubjectMetadataSchema.dump_fields
    • SubjectMetadataSchema.exclude
    • SubjectMetadataSchema.fields
    • SubjectMetadataSchema.load_fields
    • SubjectMetadataSchema.neurodata_doc
    • SubjectMetadataSchema.neurodata_skip
    • SubjectMetadataSchema.neurodata_type
    • SubjectMetadataSchema.neurodata_type_inc
    • SubjectMetadataSchema.opts
• allensdk.brain_observatory.behavior.session_metrics module
  • num_contingent_trials()
  • response_bias()
• allensdk.brain_observatory.behavior.stimulus_processing module
  • add_active_flag()
  • compute_is_sham_change()
  • compute_trials_id_for_stimulus()
  • fix_omitted_end_frame()
  • get_flashes_since_change()
  • get_gratings_metadata()
  • get_image_names()
  • get_images_dict()
  • get_stimulus_metadata()
  • get_stimulus_presentations()
  • get_stimulus_templates()
  • get_visual_stimuli_df()
  • is_change_event()
  • load_pickle()
  • produce_stimulus_block_names()
  • unpack_change_log()
• allensdk.brain_observatory.behavior.trial_masks module
  • contingent_trials()
  • reward_rate()
  • trial_types()
• allensdk.brain_observatory.behavior.trials_processing module

Module contents