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sleap_io.io.main

This module contains high-level wrappers for utilizing different I/O backends.

Modules:

Name Description
jabs

This module handles direct I/O operations for working with JABS files.
labelstudio

This module handles direct I/O operations for working with Labelstudio files.
nwb

Functions to write and read from the neurodata without borders (NWB) format.
slp

This module handles direct I/O operations for working with .slp files.
video_writing

Utilities for writing videos.

Functions:

Name Description
load_file

Load a file and return the appropriate object.
load_jabs

Read JABS-style predictions from a file and return a Labels object.
load_labelstudio

Read Label Studio-style annotations from a file and return a Labels object.
load_nwb

Load an NWB dataset as a SLEAP Labels object.
load_slp

Load a SLEAP dataset.
load_video

Load a video file.
save_file

Save a file based on the extension.
save_jabs

Save a SLEAP dataset to JABS pose file format.
save_labelstudio

Save a SLEAP dataset to Label Studio format.
save_nwb

Save a SLEAP dataset to NWB format.
save_slp

Save a SLEAP dataset to a .slp file.
save_video

Write a list of frames to a video file.

load_file(filename, format=None, **kwargs)

Load a file and return the appropriate object.

Parameters:

Name Type Description Default
filename str | Path

Path to a file.

 required
format Optional[str]

Optional format to load as. If not provided, will be inferred from the file extension. Available formats are: "slp", "nwb", "labelstudio", "jabs" and "video".

 None

Returns:

Type Description
Union[Labels, Video]

A Labels or Video object.
Source code in sleap_io/io/main.py 
def load_file(
    filename: str | Path, format: Optional[str] = None, **kwargs
) -> Union[Labels, Video]:
    """Load a file and return the appropriate object.

    Args:
        filename: Path to a file.
        format: Optional format to load as. If not provided, will be inferred from the
            file extension. Available formats are: "slp", "nwb", "labelstudio", "jabs"
            and "video".

    Returns:
        A `Labels` or `Video` object.
    """
    if isinstance(filename, Path):
        filename = filename.as_posix()

    if format is None:
        if filename.endswith(".slp"):
            format = "slp"
        elif filename.endswith(".nwb"):
            format = "nwb"
        elif filename.endswith(".json"):
            format = "json"
        elif filename.endswith(".h5"):
            format = "jabs"
        else:
            for vid_ext in Video.EXTS:
                if filename.endswith(vid_ext):
                    format = "video"
                    break
        if format is None:
            raise ValueError(f"Could not infer format from filename: '{filename}'.")

    if filename.endswith(".slp"):
        return load_slp(filename, **kwargs)
    elif filename.endswith(".nwb"):
        return load_nwb(filename, **kwargs)
    elif filename.endswith(".json"):
        return load_labelstudio(filename, **kwargs)
    elif filename.endswith(".h5"):
        return load_jabs(filename, **kwargs)
    elif format == "video":
        return load_video(filename, **kwargs)

load_jabs(filename, skeleton=None)

Read JABS-style predictions from a file and return a Labels object.

Parameters:

Name Type Description Default
filename str

Path to the jabs h5 pose file.

 required
skeleton Optional[Skeleton]

An optional Skeleton object.

 None

Returns:

Type Description
Labels

Parsed labels as a Labels instance.
Source code in sleap_io/io/main.py 
def load_jabs(filename: str, skeleton: Optional[Skeleton] = None) -> Labels:
    """Read JABS-style predictions from a file and return a `Labels` object.

    Args:
        filename: Path to the jabs h5 pose file.
        skeleton: An optional `Skeleton` object.

    Returns:
        Parsed labels as a `Labels` instance.
    """
    return jabs.read_labels(filename, skeleton=skeleton)

load_labelstudio(filename, skeleton=None)

Read Label Studio-style annotations from a file and return a Labels object.

Parameters:

Name Type Description Default
filename str

Path to the label-studio annotation file in JSON format.

 required
skeleton Optional[Union[Skeleton, list[str]]]

An optional Skeleton object or list of node names. If not provided (the default), skeleton will be inferred from the data. It may be useful to provide this so the keypoint label types can be filtered to just the ones in the skeleton.

 None

Returns:

Type Description
Labels

Parsed labels as a Labels instance.
Source code in sleap_io/io/main.py 
def load_labelstudio(
    filename: str, skeleton: Optional[Union[Skeleton, list[str]]] = None
) -> Labels:
    """Read Label Studio-style annotations from a file and return a `Labels` object.

    Args:
        filename: Path to the label-studio annotation file in JSON format.
        skeleton: An optional `Skeleton` object or list of node names. If not provided
            (the default), skeleton will be inferred from the data. It may be useful to
            provide this so the keypoint label types can be filtered to just the ones in
            the skeleton.

    Returns:
        Parsed labels as a `Labels` instance.
    """
    return labelstudio.read_labels(filename, skeleton=skeleton)

load_nwb(filename)

Load an NWB dataset as a SLEAP Labels object.

Parameters:

Name Type Description Default
filename str

Path to a NWB file (.nwb).

 required

Returns:

Type Description
Labels

The dataset as a Labels object.
Source code in sleap_io/io/main.py 
def load_nwb(filename: str) -> Labels:
    """Load an NWB dataset as a SLEAP `Labels` object.

    Args:
        filename: Path to a NWB file (`.nwb`).

    Returns:
        The dataset as a `Labels` object.
    """
    return nwb.read_nwb(filename)

load_slp(filename, open_videos=True)

Load a SLEAP dataset.

Parameters:

Name Type Description Default
filename str

Path to a SLEAP labels file (.slp).

 required
open_videos bool

If True (the default), attempt to open the video backend for I/O. If False, the backend will not be opened (useful for reading metadata when the video files are not available).

 True

Returns:

Type Description
Labels

The dataset as a Labels object.
Source code in sleap_io/io/main.py 
def load_slp(filename: str, open_videos: bool = True) -> Labels:
    """Load a SLEAP dataset.

    Args:
        filename: Path to a SLEAP labels file (`.slp`).
        open_videos: If `True` (the default), attempt to open the video backend for
            I/O. If `False`, the backend will not be opened (useful for reading metadata
            when the video files are not available).

    Returns:
        The dataset as a `Labels` object.
    """
    return slp.read_labels(filename, open_videos=open_videos)

load_video(filename, **kwargs)

Load a video file.

Parameters:

Name Type Description Default
filename str

The filename(s) of the video. Supported extensions: "mp4", "avi", "mov", "mj2", "mkv", "h5", "hdf5", "slp", "png", "jpg", "jpeg", "tif", "tiff", "bmp". If the filename is a list, a list of image filenames are expected. If filename is a folder, it will be searched for images.

 required

Returns:

Type Description
Video

A Video object.
Source code in sleap_io/io/main.py 
def load_video(filename: str, **kwargs) -> Video:
    """Load a video file.

    Args:
        filename: The filename(s) of the video. Supported extensions: "mp4", "avi",
            "mov", "mj2", "mkv", "h5", "hdf5", "slp", "png", "jpg", "jpeg", "tif",
            "tiff", "bmp". If the filename is a list, a list of image filenames are
            expected. If filename is a folder, it will be searched for images.

    Returns:
        A `Video` object.
    """
    return Video.from_filename(filename, **kwargs)

save_file(labels, filename, format=None, **kwargs)

Save a file based on the extension.

Parameters:

Name Type Description Default
labels Labels

A SLEAP Labels object (see load_slp).

 required
filename str | Path

Path to save labels to.

 required
format Optional[str]

Optional format to save as. If not provided, will be inferred from the file extension. Available formats are: "slp", "nwb", "labelstudio" and "jabs".

 None
Source code in sleap_io/io/main.py 
def save_file(
    labels: Labels, filename: str | Path, format: Optional[str] = None, **kwargs
):
    """Save a file based on the extension.

    Args:
        labels: A SLEAP `Labels` object (see `load_slp`).
        filename: Path to save labels to.
        format: Optional format to save as. If not provided, will be inferred from the
            file extension. Available formats are: "slp", "nwb", "labelstudio" and
            "jabs".
    """
    if isinstance(filename, Path):
        filename = str(filename)

    if format is None:
        if filename.endswith(".slp"):
            format = "slp"
        elif filename.endswith(".nwb"):
            format = "nwb"
        elif filename.endswith(".json"):
            format = "labelstudio"
        elif "pose_version" in kwargs:
            format = "jabs"

    if format == "slp":
        save_slp(labels, filename, **kwargs)
    elif format == "nwb":
        save_nwb(labels, filename, **kwargs)
    elif format == "labelstudio":
        save_labelstudio(labels, filename, **kwargs)
    elif format == "jabs":
        pose_version = kwargs.pop("pose_version", 5)
        root_folder = kwargs.pop("root_folder", filename)
        save_jabs(labels, pose_version=pose_version, root_folder=root_folder)
    else:
        raise ValueError(f"Unknown format '{format}' for filename: '{filename}'.")

save_jabs(labels, pose_version, root_folder=None)

Save a SLEAP dataset to JABS pose file format.

Parameters:

Name Type Description Default
labels Labels

SLEAP Labels object.

 required
pose_version int

The JABS pose version to write data out.

 required
root_folder Optional[str]

Optional root folder where the files should be saved.

 None
Note

Filenames for JABS poses are based on video filenames.

Source code in sleap_io/io/main.py 
def save_jabs(labels: Labels, pose_version: int, root_folder: Optional[str] = None):
    """Save a SLEAP dataset to JABS pose file format.

    Args:
        labels: SLEAP `Labels` object.
        pose_version: The JABS pose version to write data out.
        root_folder: Optional root folder where the files should be saved.

    Note:
        Filenames for JABS poses are based on video filenames.
    """
    jabs.write_labels(labels, pose_version, root_folder)

save_labelstudio(labels, filename)

Save a SLEAP dataset to Label Studio format.

Parameters:

Name Type Description Default
labels Labels

A SLEAP Labels object (see load_slp).

 required
filename str

Path to save labels to ending with .json.

 required
Source code in sleap_io/io/main.py 
def save_labelstudio(labels: Labels, filename: str):
    """Save a SLEAP dataset to Label Studio format.

    Args:
        labels: A SLEAP `Labels` object (see `load_slp`).
        filename: Path to save labels to ending with `.json`.
    """
    labelstudio.write_labels(labels, filename)

save_nwb(labels, filename, append=True)

Save a SLEAP dataset to NWB format.

Parameters:

Name Type Description Default
labels Labels

A SLEAP Labels object (see load_slp).

 required
filename str

Path to NWB file to save to. Must end in .nwb.

 required
append bool

If True (the default), append to existing NWB file. File will be created if it does not exist.

 True

See also: nwb.write_nwb, nwb.append_nwb

Source code in sleap_io/io/main.py 
def save_nwb(labels: Labels, filename: str, append: bool = True):
    """Save a SLEAP dataset to NWB format.

    Args:
        labels: A SLEAP `Labels` object (see `load_slp`).
        filename: Path to NWB file to save to. Must end in `.nwb`.
        append: If `True` (the default), append to existing NWB file. File will be
            created if it does not exist.

    See also: nwb.write_nwb, nwb.append_nwb
    """
    if append and Path(filename).exists():
        nwb.append_nwb(labels, filename)
    else:
        nwb.write_nwb(labels, filename)

save_slp(labels, filename, embed=None)

Save a SLEAP dataset to a .slp file.

Parameters:

Name Type Description Default
labels Labels

A SLEAP Labels object (see load_slp).

 required
filename str

Path to save labels to ending with .slp.

 required
embed bool | str | list[tuple[Video, int]] | None

Frames to embed in the saved labels file. One of None, True, "all", "user", "suggestions", "user+suggestions", "source" or list of tuples of (video, frame_idx).

If None is specified (the default) and the labels contains embedded frames, those embedded frames will be re-saved to the new file.

If True or "all", all labeled frames and suggested frames will be embedded.

If "source" is specified, no images will be embedded and the source video will be restored if available.

This argument is only valid for the SLP backend.

 None
Source code in sleap_io/io/main.py 
def save_slp(
    labels: Labels,
    filename: str,
    embed: bool | str | list[tuple[Video, int]] | None = None,
):
    """Save a SLEAP dataset to a `.slp` file.

    Args:
        labels: A SLEAP `Labels` object (see `load_slp`).
        filename: Path to save labels to ending with `.slp`.
        embed: Frames to embed in the saved labels file. One of `None`, `True`,
            `"all"`, `"user"`, `"suggestions"`, `"user+suggestions"`, `"source"` or list
            of tuples of `(video, frame_idx)`.

            If `None` is specified (the default) and the labels contains embedded
            frames, those embedded frames will be re-saved to the new file.

            If `True` or `"all"`, all labeled frames and suggested frames will be
            embedded.

            If `"source"` is specified, no images will be embedded and the source video
            will be restored if available.

            This argument is only valid for the SLP backend.
    """
    return slp.write_labels(filename, labels, embed=embed)

save_video(frames, filename, fps=30, pixelformat='yuv420p', codec='libx264', crf=25, preset='superfast', output_params=None)

Write a list of frames to a video file.

Parameters:

Name Type Description Default
frames ndarray | Video

Sequence of frames to write to video. Each frame should be a 2D or 3D numpy array with dimensions (height, width) or (height, width, channels).

 required
filename str | Path

Path to output video file.

 required
fps float

Frames per second. Defaults to 30.

 30
pixelformat str

Pixel format for video. Defaults to "yuv420p".

 'yuv420p'
codec str

Codec to use for encoding. Defaults to "libx264".

 'libx264'
crf int

Constant rate factor to control lossiness of video. Values go from 2 to 32, with numbers in the 18 to 30 range being most common. Lower values mean less compressed/higher quality. Defaults to 25. No effect if codec is not "libx264".

 25
preset str

H264 encoding preset. Defaults to "superfast". No effect if codec is not "libx264".

 'superfast'
output_params list | None

Additional output parameters for FFMPEG. This should be a list of strings corresponding to command line arguments for FFMPEG and libx264. Use ffmpeg -h encoder=libx264 to see all options for libx264 output_params.

 None

See also: sio.VideoWriter

Source code in sleap_io/io/main.py 
def save_video(
    frames: np.ndarray | Video,
    filename: str | Path,
    fps: float = 30,
    pixelformat: str = "yuv420p",
    codec: str = "libx264",
    crf: int = 25,
    preset: str = "superfast",
    output_params: list | None = None,
):
    """Write a list of frames to a video file.

    Args:
        frames: Sequence of frames to write to video. Each frame should be a 2D or 3D
            numpy array with dimensions (height, width) or (height, width, channels).
        filename: Path to output video file.
        fps: Frames per second. Defaults to 30.
        pixelformat: Pixel format for video. Defaults to "yuv420p".
        codec: Codec to use for encoding. Defaults to "libx264".
        crf: Constant rate factor to control lossiness of video. Values go from 2 to 32,
            with numbers in the 18 to 30 range being most common. Lower values mean less
            compressed/higher quality. Defaults to 25. No effect if codec is not
            "libx264".
        preset: H264 encoding preset. Defaults to "superfast". No effect if codec is not
            "libx264".
        output_params: Additional output parameters for FFMPEG. This should be a list of
            strings corresponding to command line arguments for FFMPEG and libx264. Use
            `ffmpeg -h encoder=libx264` to see all options for libx264 output_params.

    See also: `sio.VideoWriter`
    """
    if output_params is None:
        output_params = []

    with video_writing.VideoWriter(
        filename,
        fps=fps,
        pixelformat=pixelformat,
        codec=codec,
        crf=crf,
        preset=preset,
        output_params=output_params,
    ) as writer:
        for frame in frames:
            writer(frame)