run

sleap_nn.inference.run

Top-level predict — one-call inference from model paths to Labels.

This is the "I just want predictions" entry point. It builds a :class:Predictor, runs inference, and returns sio.Labels. For more control (streaming, raw Outputs, custom filtering), use :class:Predictor directly.

Usage::

from sleap_nn.inference import predict

# Simplest call — returns sio.Labels
labels = predict("video.mp4", model_paths=["/path/to/model"])

# With prediction-time overrides
labels = predict(
    "video.mp4",
    model_paths=["/path/to/centroid", "/path/to/centered_instance"],
    peak_threshold=0.3,
    centroid_threshold=0.5,
    keypoint_threshold=0.1,
)

# Save to disk
labels = predict("video.mp4", model_paths=[...], output_path="preds.slp")

Functions:

Name	Description
predict	Build a predictor, run inference, return Labels.
save_analysis_h5_files	Write SLEAP Analysis HDF5 file(s) from a predicted Labels object.
save_predictions	Save predicted Labels to disk in the requested format(s).

predict(source, *, model_paths=None, export_dir=None, device='auto', batch_size=4, runtime='auto', backbone_ckpt_path=None, head_ckpt_path=None, preprocess_config=None, anchor_part=None, paf_workers=0, centroid_only=False, emit_centroid='instance', max_edge_length_ratio=0.25, dist_penalty_weight=1.0, n_points=10, min_instance_peaks=0, min_line_scores=0.25, fg_threshold=0.5, min_mask_area=0, center_nms_kernel=3, mask_cleanup=False, mask_cleanup_radius=0, distance_gate_alpha=None, merge_fragments=False, merge_method='greedy', merge_thresholds=(0.85, 0.6, 0.4), merge_w_valley=1.0, merge_w_offset=0.25, merge_dilate=1, full_res_masks=False, mask_output='mask', polygon_epsilon=0.01, mask_backend=None, sam_checkpoint=None, sam_model_type='vit_h', sam3_model_id='facebook/sam3', sam_prompt_mode='pose', sam_anchor_ind=None, sam_disjointify_masks=False, overlay_path=None, frames=None, peak_threshold=None, centroid_threshold=None, keypoint_threshold=None, max_instances=None, integral_refinement=None, integral_patch_size=None, return_confmaps=False, return_crops=False, return_pafs=False, return_paf_graph=False, return_class_maps=False, return_class_vectors=False, filter_config=None, tracker_config=None, output_path=None, output_format='slp', embed='false', restore_source_videos=False, clean_empty_frames=False, progress_callback=None, tracking_progress_callback=None)

Build a predictor, run inference, return Labels.

Exactly one of model_paths or export_dir must be provided.

Parameters:

Name	Type	Description	Default
source	Any	Video path, sio.Video, sio.Labels, or a Provider.	required
model_paths	Optional[List[str]]	Trained model directories — or a path to a model's best.ckpt or training_config.{yaml,json} file, which resolves to its directory (#575). One for single-instance / bottom-up, two for top-down.	None
export_dir	Optional[str]	Path to an exported ONNX/TRT directory (alternative to model_paths).	None
device	str	"auto", "cpu", "cuda", "mps", etc.	'auto'
batch_size	int	Frames per batch.	4
runtime	str	Runtime for an exported model: "auto" (prefer TensorRT, fall back to ONNX), "onnx", or "tensorrt". Ignored when model_paths is given (checkpoints).	'auto'
backbone_ckpt_path	Optional[str]	Optional backbone weight override.	None
head_ckpt_path	Optional[str]	Optional head weight override.	None
preprocess_config	Optional[Any]	Optional OmegaConf preprocessing overrides.	None
anchor_part	Optional[str]	Override centroid anchor node name.	None
paf_workers	int	CPU worker processes for bottom-up PAF grouping.	0
centroid_only	bool	Force centroid-only output even when a centered-instance model is among model_paths.	False
emit_centroid	str	Centroid-only output representation: "instance" (default; single-node PredictedInstance, frontend-compatible), "centroid" (sio.PredictedCentroid), or "both".	'instance'
max_edge_length_ratio	float	Bottom-up PAF max edge length ratio.	0.25
dist_penalty_weight	float	Bottom-up PAF distance penalty weight.	1.0
n_points	int	Bottom-up PAF line integration sample count.	10
min_instance_peaks	float	Bottom-up min peaks for a valid instance.	0
min_line_scores	float	Bottom-up per-edge match threshold. (These five apply only to plain bottom-up models.)	0.25
fg_threshold	float	Foreground probability threshold for binarizing the segmentation map (bottom-up segmentation only).	0.5
min_mask_area	int	Minimum predicted-mask area in original-image pixels; smaller masks are dropped to suppress over-segmentation. 0 disables it (bottom-up segmentation only).	0
center_nms_kernel	int	Odd window size for center-peak NMS; larger merges nearby duplicate centers (bottom-up segmentation only).	3
mask_cleanup	bool	Keep-largest-CC + hole-fill per mask (bottom-up segmentation only).	False
mask_cleanup_radius	int	Morphological open->close radius (output-stride pixels) applied during mask_cleanup; 0 keeps keep-largest + fill only (bottom-up segmentation only).	0
distance_gate_alpha	Optional[float]	Adaptive distance-gate strength; None (default) keeps the byte-for-byte argmin grouping. When set, foreground pixels whose offset-predicted center exceeds alpha*sqrt(area/pi) from their assigned center are dropped (bottom-up segmentation only).	None
merge_fragments	bool	Enable the RAG fragment-merge that re-fuses over-segmented animal halves while keeping touching distinct animals apart; False (default) is byte-for-byte today (bottom-up segmentation only).	False
merge_method	str	"greedy" (default) or "multicut" agglomeration; inert when merge_fragments=False (bottom-up segmentation only).	'greedy'
merge_thresholds	tuple	Greedy-merge decreasing affinity thresholds (default (0.85, 0.6, 0.4)); inert when off (bottom-up segmentation only).	(0.85, 0.6, 0.4)
merge_w_valley	float	Center-valley merge-term weight (default 1.0); inert when off (bottom-up segmentation only).	1.0
merge_w_offset	float	Offset-agreement merge-term weight (default 0.25); inert when off (bottom-up segmentation only).	0.25
merge_dilate	int	Merge contact-test dilation iterations (default 1); inert when off (bottom-up segmentation only).	1
full_res_masks	bool	Encode masks at full original resolution instead of the output-stride grid (default False: stride encoding is ~stride^2 smaller and lossless at model resolution; bottom-up segmentation only).	False
mask_output	str	Mask output representation — "mask" (default), "polygon" (sio.PredictedROI only), or "both" (bottom-up segmentation only).	'mask'
polygon_epsilon	float	Douglas-Peucker tolerance (fraction of perimeter) for mask_output polygon/both (bottom-up segmentation only).	0.01
mask_backend	Optional[str]	Explicit SAM mask backend (PLAN L2): "sam" (SAM1) / "sam3" (PR-B). When set, source is treated as a pose .slp and masks are predicted from its existing instances (no trained seg model, so model_paths / export_dir are not required). None (the default) leaves the model-driven path untouched.	None
sam_checkpoint	Optional[str]	SAM1 checkpoint path (required for mask_backend="sam").	None
sam_model_type	str	SAM1 model registry key.	'vit_h'
sam3_model_id	str	Hugging Face model id for the gated SAM3 path (mask_backend="sam3"); defaults to "facebook/sam3".	'facebook/sam3'
sam_prompt_mode	str	"pose" / "centroid" / "box" (PLAN §2.2).	'pose'
sam_anchor_ind	Optional[int]	Centroid anchor node index for sam_prompt_mode="centroid".	None
sam_disjointify_masks	bool	Make per-frame masks disjoint when >=2 instances.	False
overlay_path	Optional[str]	Optional review-overlay PNG path (PLAN L4; SAM path only).	None
frames	Optional[List[int]]	Frame indices to predict. None = all.	None
peak_threshold	Optional[float]	Override peak threshold for all stages.	None
centroid_threshold	Optional[float]	Override centroid-stage threshold (top-down).	None
keypoint_threshold	Optional[float]	Override centered-instance threshold (top-down).	None
max_instances	Optional[int]	Cap on instances per frame.	None
integral_refinement	Optional[str]	"integral" or "none".	None
integral_patch_size	Optional[int]	Refinement patch size.	None
return_confmaps	bool	Keep confidence maps on Outputs.	False
return_crops	bool	Keep per-instance crops on Outputs (top-down).	False
return_pafs	bool	Keep part-affinity fields on Outputs (bottom-up).	False
return_paf_graph	bool	Keep the PAF graph on Outputs (bottom-up).	False
return_class_maps	bool	Keep class maps on Outputs (multi-class bottom-up).	False
return_class_vectors	bool	Keep class vectors on Outputs (multi-class top-down).	False
filter_config	Optional['FilterConfig']	Post-inference :class:FilterConfig.	None
tracker_config	Optional['TrackerConfig']	:class:TrackerConfig for tracking.	None
output_path	Optional[str]	If set, save the Labels to this path.	None
output_format	Union[str, Sequence[str]]	Format to save the Labels in when output_path is set. One of "slp" (the default), "analysis_h5" (a SLEAP Analysis HDF5 file, one .analysis.h5 per video), or "both". Analysis HDF5 paths are derived from output_path.	'slp'
embed	Union[str, bool]	Image-embedding policy for a .slp output, one of "false" (the default; never embed, backreference source media — today's behavior), "true" (embed images into a self-contained .pkg.slp-style file), or "auto" (embed iff the input was itself an embedded .pkg.slp). Only applies to .slp output.	'false'
restore_source_videos	bool	On a non-embedding .slp save, False (the default) keeps references to the input .pkg.slp file(s) — the pixels are already there, and the pre-embedding source video is often unavailable. True instead restores references to the original pre-embedding source video files, when recorded. Ignored when embedding.	False
clean_empty_frames	bool	Drop frames with no instances.	False
progress_callback	Optional[Callable[[int, int], None]]	(processed_frames, total_frames) callback invoked after each batch (counts are in frames).	None
tracking_progress_callback	Optional[Callable[[int, int], None]]	(processed_frames, total_frames) callback per frame during tracking.	None

Returns:

Type	Description
Labels	sio.Labels with predicted instances.

Raises:

Type	Description
ValueError	If neither model_paths nor export_dir is given, or if both are given.

Source code in sleap_nn/inference/run.py

def predict(
    source: Any,
    *,
    model_paths: Optional[List[str]] = None,
    export_dir: Optional[str] = None,
    # Construction-time (model/device)
    device: str = "auto",
    batch_size: int = 4,
    runtime: str = "auto",
    backbone_ckpt_path: Optional[str] = None,
    head_ckpt_path: Optional[str] = None,
    preprocess_config: Optional[Any] = None,
    anchor_part: Optional[str] = None,
    paf_workers: int = 0,
    centroid_only: bool = False,
    emit_centroid: str = "instance",
    # Bottom-up PAF grouping knobs (construction-time; plain bottom-up only)
    max_edge_length_ratio: float = 0.25,
    dist_penalty_weight: float = 1.0,
    n_points: int = 10,
    min_instance_peaks: float = 0,
    min_line_scores: float = 0.25,
    # Bottom-up segmentation knobs (construction-time; segmentation only)
    fg_threshold: float = 0.5,
    min_mask_area: int = 0,
    center_nms_kernel: int = 3,
    mask_cleanup: bool = False,
    mask_cleanup_radius: int = 0,
    distance_gate_alpha: Optional[float] = None,
    merge_fragments: bool = False,
    merge_method: str = "greedy",
    merge_thresholds: tuple = (0.85, 0.6, 0.4),
    merge_w_valley: float = 1.0,
    merge_w_offset: float = 0.25,
    merge_dilate: int = 1,
    full_res_masks: bool = False,
    mask_output: str = "mask",
    polygon_epsilon: float = 0.01,
    # SAM prompted-mask producer (explicit, no default; PLAN L2). When set, masks
    # are produced from the existing poses in ``source`` (no trained seg model).
    mask_backend: Optional[str] = None,
    sam_checkpoint: Optional[str] = None,
    sam_model_type: str = "vit_h",
    sam3_model_id: str = "facebook/sam3",
    sam_prompt_mode: str = "pose",
    sam_anchor_ind: Optional[int] = None,
    sam_disjointify_masks: bool = False,
    overlay_path: Optional[str] = None,
    # Prediction-time (can vary per call)
    frames: Optional[List[int]] = None,
    peak_threshold: Optional[float] = None,
    centroid_threshold: Optional[float] = None,
    keypoint_threshold: Optional[float] = None,
    max_instances: Optional[int] = None,
    integral_refinement: Optional[str] = None,
    integral_patch_size: Optional[int] = None,
    return_confmaps: bool = False,
    return_crops: bool = False,
    return_pafs: bool = False,
    return_paf_graph: bool = False,
    return_class_maps: bool = False,
    return_class_vectors: bool = False,
    # Filtering
    filter_config: Optional["FilterConfig"] = None,
    # Tracking
    tracker_config: Optional["TrackerConfig"] = None,
    # Output
    output_path: Optional[str] = None,
    output_format: Union[str, Sequence[str]] = "slp",
    embed: Union[str, bool] = "false",
    restore_source_videos: bool = False,
    clean_empty_frames: bool = False,
    progress_callback: Optional[Callable[[int, int], None]] = None,
    tracking_progress_callback: Optional[Callable[[int, int], None]] = None,
) -> sio.Labels:
    """Build a predictor, run inference, return Labels.

    Exactly one of ``model_paths`` or ``export_dir`` must be provided.

    Args:
        source: Video path, ``sio.Video``, ``sio.Labels``, or a Provider.
        model_paths: Trained model directories — or a path to a model's
            ``best.ckpt`` or ``training_config.{yaml,json}`` file, which resolves
            to its directory (#575). One for single-instance / bottom-up, two for
            top-down.
        export_dir: Path to an exported ONNX/TRT directory (alternative
            to ``model_paths``).
        device: ``"auto"``, ``"cpu"``, ``"cuda"``, ``"mps"``, etc.
        batch_size: Frames per batch.
        runtime: Runtime for an exported model: ``"auto"`` (prefer TensorRT,
            fall back to ONNX), ``"onnx"``, or ``"tensorrt"``. Ignored when
            ``model_paths`` is given (checkpoints).
        backbone_ckpt_path: Optional backbone weight override.
        head_ckpt_path: Optional head weight override.
        preprocess_config: Optional OmegaConf preprocessing overrides.
        anchor_part: Override centroid anchor node name.
        paf_workers: CPU worker processes for bottom-up PAF grouping.
        centroid_only: Force centroid-only output even when a
            centered-instance model is among ``model_paths``.
        emit_centroid: Centroid-only output representation: ``"instance"``
            (default; single-node ``PredictedInstance``, frontend-compatible),
            ``"centroid"`` (``sio.PredictedCentroid``), or ``"both"``.
        max_edge_length_ratio: Bottom-up PAF max edge length ratio.
        dist_penalty_weight: Bottom-up PAF distance penalty weight.
        n_points: Bottom-up PAF line integration sample count.
        min_instance_peaks: Bottom-up min peaks for a valid instance.
        min_line_scores: Bottom-up per-edge match threshold. (These five
            apply only to plain bottom-up models.)
        fg_threshold: Foreground probability threshold for binarizing the
            segmentation map (bottom-up segmentation only).
        min_mask_area: Minimum predicted-mask area in original-image pixels;
            smaller masks are dropped to suppress over-segmentation. ``0``
            disables it (bottom-up segmentation only).
        center_nms_kernel: Odd window size for center-peak NMS; larger merges
            nearby duplicate centers (bottom-up segmentation only).
        mask_cleanup: Keep-largest-CC + hole-fill per mask (bottom-up
            segmentation only).
        mask_cleanup_radius: Morphological open->close radius (output-stride
            pixels) applied during ``mask_cleanup``; ``0`` keeps keep-largest +
            fill only (bottom-up segmentation only).
        distance_gate_alpha: Adaptive distance-gate strength; ``None`` (default)
            keeps the byte-for-byte argmin grouping. When set, foreground pixels
            whose offset-predicted center exceeds ``alpha*sqrt(area/pi)`` from
            their assigned center are dropped (bottom-up segmentation only).
        merge_fragments: Enable the RAG fragment-merge that re-fuses
            over-segmented animal halves while keeping touching distinct animals
            apart; ``False`` (default) is byte-for-byte today (bottom-up
            segmentation only).
        merge_method: ``"greedy"`` (default) or ``"multicut"`` agglomeration;
            inert when ``merge_fragments=False`` (bottom-up segmentation only).
        merge_thresholds: Greedy-merge decreasing affinity thresholds (default
            ``(0.85, 0.6, 0.4)``); inert when off (bottom-up segmentation only).
        merge_w_valley: Center-valley merge-term weight (default ``1.0``); inert
            when off (bottom-up segmentation only).
        merge_w_offset: Offset-agreement merge-term weight (default ``0.25``);
            inert when off (bottom-up segmentation only).
        merge_dilate: Merge contact-test dilation iterations (default ``1``);
            inert when off (bottom-up segmentation only).
        full_res_masks: Encode masks at full original resolution instead of the
            output-stride grid (default ``False``: stride encoding is ~stride^2
            smaller and lossless at model resolution; bottom-up segmentation only).
        mask_output: Mask output representation — ``"mask"`` (default),
            ``"polygon"`` (``sio.PredictedROI`` only), or ``"both"`` (bottom-up
            segmentation only).
        polygon_epsilon: Douglas-Peucker tolerance (fraction of perimeter) for
            ``mask_output`` polygon/both (bottom-up segmentation only).
        mask_backend: **Explicit** SAM mask backend (PLAN L2): ``"sam"`` (SAM1) /
            ``"sam3"`` (PR-B). When set, ``source`` is treated as a pose ``.slp``
            and masks are predicted from its existing instances (no trained seg
            model, so ``model_paths`` / ``export_dir`` are not required). ``None``
            (the default) leaves the model-driven path untouched.
        sam_checkpoint: SAM1 checkpoint path (required for ``mask_backend="sam"``).
        sam_model_type: SAM1 model registry key.
        sam3_model_id: Hugging Face model id for the gated SAM3 path
            (``mask_backend="sam3"``); defaults to ``"facebook/sam3"``.
        sam_prompt_mode: ``"pose"`` / ``"centroid"`` / ``"box"`` (PLAN §2.2).
        sam_anchor_ind: Centroid anchor node index for ``sam_prompt_mode="centroid"``.
        sam_disjointify_masks: Make per-frame masks disjoint when >=2 instances.
        overlay_path: Optional review-overlay PNG path (PLAN L4; SAM path only).
        frames: Frame indices to predict. ``None`` = all.
        peak_threshold: Override peak threshold for all stages.
        centroid_threshold: Override centroid-stage threshold (top-down).
        keypoint_threshold: Override centered-instance threshold (top-down).
        max_instances: Cap on instances per frame.
        integral_refinement: ``"integral"`` or ``"none"``.
        integral_patch_size: Refinement patch size.
        return_confmaps: Keep confidence maps on Outputs.
        return_crops: Keep per-instance crops on Outputs (top-down).
        return_pafs: Keep part-affinity fields on Outputs (bottom-up).
        return_paf_graph: Keep the PAF graph on Outputs (bottom-up).
        return_class_maps: Keep class maps on Outputs (multi-class bottom-up).
        return_class_vectors: Keep class vectors on Outputs (multi-class top-down).
        filter_config: Post-inference :class:`FilterConfig`.
        tracker_config: :class:`TrackerConfig` for tracking.
        output_path: If set, save the Labels to this path.
        output_format: Format to save the Labels in when ``output_path`` is set.
            One of ``"slp"`` (the default), ``"analysis_h5"`` (a SLEAP Analysis
            HDF5 file, one ``.analysis.h5`` per video), or ``"both"``. Analysis
            HDF5 paths are derived from ``output_path``.
        embed: Image-embedding policy for a ``.slp`` output, one of ``"false"``
            (the default; never embed, backreference source media — today's
            behavior), ``"true"`` (embed images into a self-contained
            ``.pkg.slp``-style file), or ``"auto"`` (embed iff the input was
            itself an embedded ``.pkg.slp``). Only applies to ``.slp`` output.
        restore_source_videos: On a non-embedding ``.slp`` save, ``False`` (the
            default) keeps references to the input ``.pkg.slp`` file(s) — the
            pixels are already there, and the pre-embedding source video is
            often unavailable. ``True`` instead restores references to the
            original pre-embedding source video files, when recorded.
            Ignored when embedding.
        clean_empty_frames: Drop frames with no instances.
        progress_callback: ``(processed_frames, total_frames)`` callback
            invoked after each batch (counts are in frames).
        tracking_progress_callback: ``(processed_frames, total_frames)``
            callback per frame during tracking.

    Returns:
        ``sio.Labels`` with predicted instances.

    Raises:
        ValueError: If neither ``model_paths`` nor ``export_dir`` is given,
            or if both are given.
    """
    import torch

    from sleap_nn.inference.predictor import Predictor

    if device == "auto":
        device = (
            "cuda"
            if torch.cuda.is_available()
            else "mps" if torch.backends.mps.is_available() else "cpu"
        )

    # SAM prompted-mask producer (PLAN L2/L8): masks come from the existing poses
    # in ``source`` — there is no trained seg model, so this short-circuits the
    # model-driven path entirely. ``mask_backend`` is explicit / required to opt
    # in; ``None`` (the default) leaves everything below unchanged.
    if mask_backend is not None:
        if model_paths or export_dir:
            raise ValueError(
                "mask_backend produces masks from the poses in `source` and does "
                "not use a trained seg model; do not also pass model_paths / "
                "export_dir."
            )
        from sleap_nn.inference.sam import run_sam_segmentation

        # Segmentation masks only serialize to ``.slp``: the SLEAP Analysis HDF5
        # format stores poses/tracks, not ``PredictedSegmentationMask``, so it
        # would silently drop the masks (the actual output). Reject it up front
        # rather than write a mask-less ``.h5``.
        if output_path is not None and any(
            f != "slp" for f in _normalize_output_formats(output_format)
        ):
            raise ValueError(
                f"mask_backend output only supports output_format='slp' (got "
                f"{output_format!r}); the SLEAP Analysis HDF5 format stores "
                "poses/tracks, not segmentation masks."
            )
        # Save handling lives in ``run_sam_segmentation``, which mirrors the
        # regular prediction path: by default it backreferences the source media
        # via provenance and does not re-embed images (small output; see its
        # docs). The ``embed`` / ``restore_source_videos`` controls are forwarded.
        labels = run_sam_segmentation(
            source,
            mask_backend,
            prompt_mode=sam_prompt_mode,
            sam_checkpoint=sam_checkpoint,
            sam_model_type=sam_model_type,
            sam3_model_id=sam3_model_id,
            device=device,
            anchor_ind=sam_anchor_ind,
            disjointify_masks=sam_disjointify_masks,
            output_path=output_path,
            overlay_path=overlay_path,
            frames=frames,
            clean_empty_frames=clean_empty_frames,
            embed=embed,
            restore_source_videos=restore_source_videos,
        )
        return labels

    if model_paths and export_dir:
        raise ValueError("Provide model_paths or export_dir, not both.")
    if not model_paths and not export_dir:
        raise ValueError("Either model_paths or export_dir is required.")

    if tracker_config is not None and emit_centroid != "instance":
        raise ValueError(
            "Tracking is incompatible with emit_centroid="
            f"{emit_centroid!r}: tracking operates on sio.PredictedInstance "
            "objects, but this mode emits sio.PredictedCentroid objects. Use "
            "emit_centroid='instance' (the default) for tracking."
        )

    # Build predictor
    build_kwargs: dict = {
        "device": device,
        "batch_size": batch_size,
        "paf_workers": paf_workers,
    }
    if filter_config is not None:
        build_kwargs["filter_config"] = filter_config
    if tracker_config is not None:
        build_kwargs["tracker_config"] = tracker_config

    if model_paths:
        if backbone_ckpt_path is not None:
            build_kwargs["backbone_ckpt_path"] = backbone_ckpt_path
        if head_ckpt_path is not None:
            build_kwargs["head_ckpt_path"] = head_ckpt_path
        if preprocess_config is not None:
            build_kwargs["preprocess_config"] = preprocess_config
        if anchor_part is not None:
            build_kwargs["anchor_part"] = anchor_part
        if peak_threshold is not None:
            build_kwargs["peak_threshold"] = peak_threshold
        if max_instances is not None:
            build_kwargs["max_instances"] = max_instances
        if centroid_only:
            build_kwargs["centroid_only"] = True
        if emit_centroid != "instance":
            build_kwargs["emit_centroid"] = emit_centroid
        # Bottom-up PAF knobs configure the scorer at load time (#583); inert
        # for non-bottom-up models (load_model_assets forwards them only there).
        build_kwargs["max_edge_length_ratio"] = max_edge_length_ratio
        build_kwargs["dist_penalty_weight"] = dist_penalty_weight
        build_kwargs["n_points"] = n_points
        build_kwargs["min_instance_peaks"] = min_instance_peaks
        build_kwargs["min_line_scores"] = min_line_scores
        # Segmentation knobs configure the SegmentationLayer at load time; inert
        # for non-segmentation models (load_model_assets forwards them only there).
        build_kwargs["fg_threshold"] = fg_threshold
        build_kwargs["min_mask_area"] = min_mask_area
        build_kwargs["center_nms_kernel"] = center_nms_kernel
        build_kwargs["mask_cleanup"] = mask_cleanup
        build_kwargs["mask_cleanup_radius"] = mask_cleanup_radius
        build_kwargs["distance_gate_alpha"] = distance_gate_alpha
        build_kwargs["merge_fragments"] = merge_fragments
        build_kwargs["merge_method"] = merge_method
        build_kwargs["merge_thresholds"] = merge_thresholds
        build_kwargs["merge_w_valley"] = merge_w_valley
        build_kwargs["merge_w_offset"] = merge_w_offset
        build_kwargs["merge_dilate"] = merge_dilate
        build_kwargs["full_res_masks"] = full_res_masks
        build_kwargs["mask_output"] = mask_output
        build_kwargs["polygon_epsilon"] = polygon_epsilon
        predictor = Predictor.from_model_paths(model_paths, **build_kwargs)
    else:
        # Exported ONNX/TRT models bake most post-processing into the graph at
        # export time; only these construction-time knobs still apply.
        build_kwargs["runtime"] = runtime
        build_kwargs["min_instance_peaks"] = min_instance_peaks
        build_kwargs["min_line_scores"] = min_line_scores
        build_kwargs["emit_centroid"] = emit_centroid
        if max_instances is not None:
            build_kwargs["max_instances"] = max_instances
        predictor = Predictor.from_export_dir(export_dir, **build_kwargs)

    # Run inference with prediction-time overrides
    labels = predictor.predict(
        source,
        frames=frames,
        make_labels=True,
        clean_empty_frames=clean_empty_frames,
        progress_callback=progress_callback,
        tracking_progress_callback=tracking_progress_callback,
        peak_threshold=peak_threshold,
        centroid_threshold=centroid_threshold,
        keypoint_threshold=keypoint_threshold,
        max_instances=max_instances,
        integral_refinement=integral_refinement,
        integral_patch_size=integral_patch_size,
        return_confmaps=return_confmaps,
        return_crops=return_crops,
        return_pafs=return_pafs,
        return_paf_graph=return_paf_graph,
        return_class_maps=return_class_maps,
        return_class_vectors=return_class_vectors,
    )

    if output_path is not None:
        save_predictions(
            labels,
            output_path,
            output_format=output_format,
            embed=embed,
            restore_source_videos=restore_source_videos,
        )

    return labels

save_analysis_h5_files(labels, slp_output_path, video_index=None)

Write SLEAP Analysis HDF5 file(s) from a predicted Labels object.

Analysis HDF5 files store a single video each, so one file is written per video. The video name is embedded in the filename when more than one video is exported (mirroring the multi-video .slp naming). Videos with no predicted frames are skipped.

Parameters:

Name	Type	Description	Default
labels	Labels	Predicted sio.Labels to export.	required
slp_output_path	Union[str, Path]	Path to the canonical .slp predictions file. The HDF5 path(s) are derived from it by replacing the trailing .predictions.slp (or .slp) suffix with .analysis.h5.	required
video_index	Optional[int]	If not None, only this video is exported. Otherwise all videos with at least one predicted frame are exported.	None

Returns:

Type	Description
List[Path]	List of Paths that were written.

Source code in sleap_nn/inference/run.py

def save_analysis_h5_files(
    labels: sio.Labels,
    slp_output_path: Union[str, Path],
    video_index: Optional[int] = None,
) -> List[Path]:
    """Write SLEAP Analysis HDF5 file(s) from a predicted ``Labels`` object.

    Analysis HDF5 files store a single video each, so one file is written per
    video. The video name is embedded in the filename when more than one video
    is exported (mirroring the multi-video ``.slp`` naming). Videos with no
    predicted frames are skipped.

    Args:
        labels: Predicted ``sio.Labels`` to export.
        slp_output_path: Path to the canonical ``.slp`` predictions file. The
            HDF5 path(s) are derived from it by replacing the trailing
            ``.predictions.slp`` (or ``.slp``) suffix with ``.analysis.h5``.
        video_index: If not ``None``, only this video is exported. Otherwise all
            videos with at least one predicted frame are exported.

    Returns:
        List of ``Path``s that were written.
    """
    slp_output_path = Path(slp_output_path)

    # Derive the base name by stripping the predictions/slp suffix.
    name = slp_output_path.name
    for suffix in (".predictions.slp", ".slp"):
        if name.endswith(suffix):
            base_stem = name[: -len(suffix)]
            break
    else:
        base_stem = slp_output_path.stem
    base = slp_output_path.parent / base_stem

    # Count predicted frames per video (using identity to avoid relying on
    # Video equality semantics).
    frames_per_video = [0] * len(labels.videos)
    for lf in labels.labeled_frames:
        for i, video in enumerate(labels.videos):
            if lf.video is video:
                frames_per_video[i] += 1
                break

    # Determine which videos to export.
    if video_index is not None:
        candidate_indices = (
            [video_index] if 0 <= video_index < len(labels.videos) else []
        )
    else:
        candidate_indices = list(range(len(labels.videos)))

    target_indices = [i for i in candidate_indices if frames_per_video[i] > 0]
    skipped_indices = [i for i in candidate_indices if frames_per_video[i] == 0]
    if skipped_indices:
        logger.warning(
            f"Skipping Analysis HDF5 export for {len(skipped_indices)} video(s) "
            f"with no predicted frames: {skipped_indices}."
        )

    # Build the video name embedded in each filename, disambiguating any videos
    # that share a filename stem by appending the video index.
    def _video_name(i):
        filename = labels.videos[i].filename
        return Path(filename).stem if isinstance(filename, str) else f"video_{i}"

    video_names = {i: _video_name(i) for i in target_indices}
    name_counts = {}
    for vname in video_names.values():
        name_counts[vname] = name_counts.get(vname, 0) + 1
    video_names = {
        i: (f"{vname}_{i}" if name_counts[vname] > 1 else vname)
        for i, vname in video_names.items()
    }

    written_paths = []
    embed_video_name = len(target_indices) > 1
    for i in target_indices:
        if embed_video_name:
            h5_path = base.parent / f"{base.name}.{video_names[i]}.analysis.h5"
        else:
            h5_path = base.parent / f"{base.name}.analysis.h5"
        sio.save_analysis_h5(
            labels,
            h5_path.as_posix(),
            video=i,
            labels_path=slp_output_path.as_posix(),
        )
        written_paths.append(h5_path)
        logger.info(f"Analysis HDF5 output path: {h5_path}")
    return written_paths

save_predictions(labels, output_path, output_format='slp', video_index=None, embed='false', restore_source_videos=False)

Save predicted Labels to disk in the requested format(s).

Parameters:

Name	Type	Description	Default
labels	Labels	Predicted sio.Labels to save.	required
output_path	Union[str, Path]	Canonical .slp output path. Analysis HDF5 paths are derived from it.	required
output_format	Union[str, Sequence[str]]	One format or several — "slp" (the default), "analysis_h5", or a sequence like ["slp", "analysis_h5"] to write both. (The CLI exposes this as a repeatable --output_format.)	'slp'
video_index	Optional[int]	Restrict the analysis HDF5 export to a single video index; None exports every video with predicted frames.	None
embed	Union[str, bool]	Image-embedding policy for the .slp output, one of "false" (the default; never embed, backreference source media — today's behavior), "true" (embed images into a self-contained .pkg.slp-style file), or "auto" (embed iff the input was itself an embedded .pkg.slp). A bool passes through unchanged. Only applies to .slp output.	'false'
restore_source_videos	bool	On a non-embedding .slp save, False (the default) keeps references to the input .pkg.slp file(s) — the pixels are already there, and the pre-embedding source video is often unavailable. True instead restores references to the original pre-embedding source video files, when recorded. Maps to sleap-io's restore_original_videos and is ignored when embedding.	False

Returns:

Type	Description
List[Path]	The list of analysis HDF5 paths written (empty unless "analysis_h5" was requested).

Raises:

Type	Description
ValueError	If any requested format is not "slp" or "analysis_h5".

Source code in sleap_nn/inference/run.py

def save_predictions(
    labels: sio.Labels,
    output_path: Union[str, Path],
    output_format: Union[str, Sequence[str]] = "slp",
    video_index: Optional[int] = None,
    embed: Union[str, bool] = "false",
    restore_source_videos: bool = False,
) -> List[Path]:
    """Save predicted ``Labels`` to disk in the requested format(s).

    Args:
        labels: Predicted ``sio.Labels`` to save.
        output_path: Canonical ``.slp`` output path. Analysis HDF5 paths are
            derived from it.
        output_format: One format or several — ``"slp"`` (the default),
            ``"analysis_h5"``, or a sequence like ``["slp", "analysis_h5"]`` to
            write both. (The CLI exposes this as a repeatable ``--output_format``.)
        video_index: Restrict the analysis HDF5 export to a single video index;
            ``None`` exports every video with predicted frames.
        embed: Image-embedding policy for the ``.slp`` output, one of
            ``"false"`` (the default; never embed, backreference source media —
            today's behavior), ``"true"`` (embed images into a self-contained
            ``.pkg.slp``-style file), or ``"auto"`` (embed iff the input was
            itself an embedded ``.pkg.slp``). A bool passes through unchanged.
            Only applies to ``.slp`` output.
        restore_source_videos: On a non-embedding ``.slp`` save, ``False`` (the
            default) keeps references to the input ``.pkg.slp`` file(s) — the
            pixels are already there, and the pre-embedding source video is
            often unavailable. ``True`` instead restores references to the
            original pre-embedding source video files, when recorded. Maps to
            sleap-io's ``restore_original_videos`` and is ignored when
            embedding.

    Returns:
        The list of analysis HDF5 paths written (empty unless ``"analysis_h5"``
        was requested).

    Raises:
        ValueError: If any requested format is not ``"slp"`` or ``"analysis_h5"``.
    """
    formats = _normalize_output_formats(output_format)

    if "slp" in formats:
        labels.save(
            Path(output_path).as_posix(),
            embed=_resolve_embed(embed, labels),
            restore_original_videos=restore_source_videos,
        )
        logger.info(f"Predictions output path: {output_path}")
        logger.info(f"Saved file at: {datetime.now()}")

    h5_paths: List[Path] = []
    if "analysis_h5" in formats:
        h5_paths = save_analysis_h5_files(labels, output_path, video_index=video_index)
    return h5_paths