sleap.io.format.ndx_pose#

Adaptor to read and write ndx-pose files.

class sleap.io.format.ndx_pose.NDXPoseAdaptor[source]#

Adaptor to read and write ndx-pose files.

property all_exts: List[str]#

List of all file extensions supported by adaptor.

can_read_file(file: FileHandle) → bool[source]#

Returns whether this adaptor can read this file.

can_write_filename(filename: str) → bool[source]#

Returns whether this adaptor can write format of this filename.

property default_ext: str#

The default file extension, e.g., ‘json’ (without ‘.’).

does_read() → bool[source]#

Returns whether this adaptor supports reading.

does_write() → bool[source]#

Returns whether this adaptor supports writing.

property handles: SleapObjectType#

Returns the type of object that can be read/written.

The Dispatch class calls this method on all registered adaptors to determine which to use for reading/writing.

property name: str#

Human-reading name of the file format

read(file: FileHandle) → Labels[source]#

Read the NWB file and returns the appropriate deserialized Labels object.

Parameters:

file – FileHandle object for the NWB file to read.

Returns:

A Labels object.

write(filename: str, labels: Labels, overwrite: bool = False, session_description: str = 'Processed SLEAP pose data', identifier: Optional[str] = None, session_start_time: Optional[datetime] = None)[source]#

Write all PredictedInstance objects in a Labels object to an NWB file.

Use Labels.numpy to create a pynwb.NWBFile with a separate pynwb.ProcessingModule for each Video in the Labels object.

To access the pynwb.ProcessingModule for a specific Video, use the key ‘SLEAP_VIDEO_{video_idx:03}_{video_fn.stem}’ where isinstance(video_fn, pathlib.PurePath). Ex:

video: ‘path_to_video/my_video.mp4’ video index: 3/5 key: ‘003_my_video’

Within each pynwb.ProcessingModule is a ndx_pose.PoseEstimation for each unique track in the Video.

The ndx_pose.PoseEstimation for each unique Track is stored under the key ‘track{track_idx:03}’ if tracks are set or ‘untrack{track_idx:03}’ if untracked where track_idx ranges from 0 to (number of tracks) - 1. Ex:

track_idx: 1 key: ‘track001’

Each ndx_pose.PoseEstimation has a ndx_pose.PoseEstimationSeries for every Node in the Skeleton.

The ndx_pose.PoseEstimationSeries for a specific Node is stored under the key ‘Node.name’. Ex:

node name: ‘head’ key: ‘head’

Parameters:

  • filename – Output path for the NWB format file.

  • labels – The Labels object to covert to a NWB format file.

  • overwrite – Boolean that overwrites existing NWB file if True. If False, data will be appended to existing NWB file.

  • session_description – Description for entire project. Stored under NWBFile “session_description” key. If appending data to a preexisting file, then the session_description will not be used.

  • identifier – Unique identifier for project. If no identifier is specified, then will generate a GUID. If appending data to a preexisting file, then the identifier will not be used.

  • session_start_time – THe datetime associated with the project. If no session_start_time is given, then the current datetime will be used. If appending data to a preexisting file, then the session_start_time will not be used.

Returns:

A pynwb.NWBFile with a separate pynwb.ProcessingModule for each Video in the Labels object.