allensdk.brain_observatory.behavior.session_apis.abcs.data_extractor_base.behavior_ophys_data_extractor_base module

class allensdk.brain_observatory.behavior.session_apis.abcs.data_extractor_base.behavior_ophys_data_extractor_base.BehaviorOphysDataExtractorBase

Bases: allensdk.brain_observatory.behavior.session_apis.abcs.data_extractor_base.behavior_data_extractor_base.BehaviorDataExtractorBase

Abstract base class implementing required methods for extracting data (from LIMS or from JSON) that will be transformed or passed on to fill behavior + ophys session data.

get_average_intensity_projection_image_file(self) → str

Get the avg intensity project image filepath associated with an ophys experiment

get_demix_file(self) → str

Get the filepath of the demixed traces file associated with an ophys experiment

get_dff_file(self) → str

Get the filepath of the dff trace file associated with an ophys experiment.

get_event_detection_filepath(self) → str

Get the filepath of the .h5 events file associated with an ophys experiment

get_eye_tracking_filepath(self) → dict

Get the eye tracking filepath containing ellipse fits

get_eye_tracking_rig_geometry(self) → dict

Get the eye tracking rig geometry associated with an ophys experiment

get_field_of_view_shape(self) → Dict[str, int]

Get a field of view dictionary for a given ophys experiment. ex: {“width”: int, “height”: int}

get_imaging_depth(self) → int

Get the imaging depth for an ophys experiment (ex: 400, 500, etc.)

get_imaging_plane_group(self) → Union[int, NoneType]

Get the imaging plane group number. This is a numeric index that indicates the order that the frames were acquired when there is more than one frame acquired concurrently. Relevant for mesoscope data timestamps, as the laser jumps between plane groups during the scan. Will be None for non-mesoscope data.

get_max_projection_file(self) → str

Get the filepath of the max projection image associated with the ophys experiment

get_ophys_cell_segmentation_run_id(self) → int

Get the ophys cell segmentation run id associated with an ophys experiment id

get_ophys_container_id(self) → int

Get the experiment container id associated with an ophys experiment

get_ophys_experiment_id(self) → int

Return the ophys experiment id (experiments are an internal alias for an imaging plane)

get_ophys_session_id(self) → int

Return the ophys session id

get_plane_group_count(self) → int

Gets the total number of plane groups in the session. This is required for resampling ophys timestamps for mesoscope data. Will be 0 if the scope did not capture multiple concurrent frames. See get_imaging_plane_group for more info.

get_project_code(self) → str

Get the project code.

get_raw_cell_specimen_table_dict(self) → dict

Get the cell_rois table from LIMS in dictionary form

get_rigid_motion_transform_file(self) → str

Get the filepath for the motion transform file (.csv) associated with an ophys experiment

get_surface_2p_pixel_size_um(self) → float

Get the pixel size for 2-photon movies in micrometers

get_sync_file(self) → str

Get the filepath of the sync timing file associated with the ophys experiment

get_targeted_structure(self) → str

Get the targeted structure (acronym) for an ophys experiment (ex: “Visp”)