NWBFileSaveConfig

class movement.io.nwb.NWBFileSaveConfig(*, nwbfile_kwargs=NOTHING, processing_module_kwargs=NOTHING, subject_kwargs=NOTHING, pose_estimation_series_kwargs=NOTHING, pose_estimation_kwargs=NOTHING, skeleton_kwargs=NOTHING)

Bases: object

Configuration for saving movement poses dataset to NWBFile(s).

This class is used with movement.io.save_poses.to_nwb_file() to add custom metadata to the NWBFile(s) created from a given movement dataset.

nwbfile_kwargs

Keyword arguments for pynwb.file.NWBFile.

If nwbfile_kwargs is a single dictionary, the same keyword arguments will be applied to all NWBFile objects except for identifier.

If nwbfile_kwargs is a dictionary of dictionaries, the outer keys should correspond to individual names in the movement dataset, and the inner dictionaries will be passed as keyword arguments to the pynwb.file.NWBFile constructor.

The following arguments cannot be overwritten:

• subject: pynwb.file.Subject created for the individual using subject_kwargs

The following arguments will have default values if not set:

• session_description: “not set”

• session_start_time: current UTC time

identifier will be set in the following order of precedence:

1. identifier in the inner dictionary

2. nwbfile_kwargs["identifier"] (single-individual dataset only)

3. individual name in the movement dataset

Type:

dict[str, Any] or dict[str, dict[str, Any]], optional

processing_module_kwargs

Keyword arguments for pynwb.base.ProcessingModule.

If processing_module_kwargs is a single dictionary, the same keyword arguments will be applied to all ProcessingModules.

If processing_module_kwargs is a dictionary of dictionaries, the outer keys should correspond to individual names in the movement dataset, and the inner dictionaries will be passed as keyword arguments to the pynwb.file.ProcessingModule constructor.

The following arguments will have default values if not set:

• name: “behavior”

• description: “processed behavioral data”

Type:

dict[str, Any] or dict[str, dict[str, Any]], optional

subject_kwargs

Keyword arguments for pynwb.file.Subject.

If subject_kwargs is a single dictionary, the same keyword arguments will be applied to all Subjects except for subject_id.

If subject_kwargs is a dictionary of dictionaries, the outer keys should correspond to individual names in the movement dataset, and the inner dictionaries will be passed as keyword arguments to the pynwb.file.Subject constructor.

subject_id will be set in the following order of precedence:

1. subject_id in the inner dictionary

2. subject_kwargs["subject_id"] (single-individual dataset only)

3. individual name in the movement dataset

Type:

dict[str, Any] or dict[str, dict[str, Any]], optional

pose_estimation_series_kwargs

Keyword arguments for ndx_pose.PoseEstimationSeries [1].

If pose_estimation_series_kwargs is a single dictionary, the same keyword arguments will be applied to all PoseEstimationSeries objects.

If pose_estimation_series_kwargs is a dictionary of dictionaries, the outer keys should correspond to keypoint names in the movement dataset, and the inner dictionaries will be passed as keyword arguments to the ndx_pose.PoseEstimationSeries constructor.

The following arguments will be set based on the dataset and cannot be overwritten:

• data: position data for the keypoint

• confidence: confidence data for the keypoint

• timestamps: time data for the keypoint

The following arguments will have default values if not set:

• unit: “pixels”

• reference_frame: “(0,0,0) corresponds to …”

name will be set in the following order of precedence:

1. name in the inner dictionary

2. pose_estimation_series_kwargs["name"] (single-keypoint dataset only)

3. keypoint name in the movement dataset

Type:

dict[str, Any] or dict[str, dict[str, Any]], optional

pose_estimation_kwargs

Keyword arguments for ndx_pose.PoseEstimation [1].

If pose_estimation_kwargs is a single dictionary, the same keyword arguments will be applied to all PoseEstimation objects.

If pose_estimation_kwargs is a dictionary of dictionaries, the outer keys should correspond to individual names in the movement dataset, and the inner dictionaries will be passed as keyword arguments to the ndx_pose.PoseEstimation constructor.

The following arguments cannot be overwritten:

• pose_estimation_series: list of PoseEstimationSeries objects

• skeleton: Skeleton object

The following arguments will have default values if not set:

• source_software: source_software attribute from the movement dataset

• description: “Estimated positions of <keypoints> for <individual> using <source_software>.”

If specified, name will be set in the following order of precedence:

1. name in the inner dictionary

2. pose_estimation_kwargs["name"] (single-individual dataset only)

3. individual name in the movement dataset

Type:

dict[str, Any] or dict[str, dict[str, Any]], optional

skeleton_kwargs

Keyword arguments for ndx_pose.Skeleton [1].

If skeleton_kwargs is a single dictionary, the same keyword arguments will be applied to all Skeleton objects.

If skeleton_kwargs is a dictionary of dictionaries, the outer keys should correspond to individual names in the movement dataset, and the inner dictionaries will be passed as keyword arguments to the ndx_pose.Skeleton constructor.

The following arguments cannot be overwritten:

• subject: pynwb.file.Subject created for the individual using subject_kwargs

The following arguments will have default values if not set:

• name: “<individual>_skeleton”

• nodes: list of keypoint names in the dataset

name will be set in the following order of precedence:

1. name in the inner dictionary

2. skeleton_kwargs["name"] (single-individual dataset only)

3. individual name in the movement dataset

Type:

dict[str, Any] or dict[str, dict[str, Any]], optional

References

[1] (1,2,3)

rly/ndx-pose

See also

movement.io.save_poses.to_nwb_file

Example usage of this class to save a movement dataset to an NWB file.