tracker

sleap_nn.tracking.tracker

Module for tracking.

Classes:

Name	Description
FlowShiftTracker	Module for tracking using optical flow shift matching.
KalmanShiftTracker	Tracker that predicts candidate poses with per-track Kalman filters.
RateColumn	Renders the progress rate.
Tracker	Simple Pose Tracker.

Functions:

Name	Description
connect_single_breaks	Merge single-frame breaks in tracks by connecting single lost track with single new track.
run_tracker	Run tracking on a given set of frames.

FlowShiftTracker

Bases: Tracker

Module for tracking using optical flow shift matching.

This module handles tracking instances across frames by creating new track IDs (or) assigning track IDs to each instance when the .track() is called using optical flow based track matching. This is a sub-class of the Tracker module, which configures the update_candidates() method specific to optical flow shift matching. This class is initialized in the Tracker.from_config() method.

Attributes:

Name	Type	Description
candidates		Either FixedWindowCandidates or LocalQueueCandidates object.
min_match_points	int	Minimum non-NaN points for match candidates. Default: 0.
features	str	One of [keypoints, centroids, bboxes, image]. Default: keypoints.
scoring_method	str	Method to compute association score between features from the current frame and the previous tracks. One of [oks, cosine_sim, iou, euclidean_dist]. Default: oks.
scoring_reduction	str	Method to aggregate and reduce multiple scores if there are several detections associated with the same track. One of [mean, max, robust_quantile]. Default: mean.
robust_best_instance	float	If the value is between 0 and 1 (excluded), use a robust quantile similarity score for the track. If the value is 1, use the max similarity (non-robust). For selecting a robust score, 0.95 is a good value.
track_matching_method	str	track matching algorithm. One of hungarian, greedy. Default:hungarian`.
use_flow	bool	If True, FlowShiftTracker is used, where the poses are matched using optical flow. Default: False.
is_local_queue	bool	True if LocalQueueCandidates is used else False.
img_scale	float	Factor to scale the images by when computing optical flow. Decrease this to increase performance at the cost of finer accuracy. Sometimes decreasing the image scale can improve performance with fast movements. Default: 1.0.
of_window_size	int	Optical flow window size to consider at each pyramid scale level. Default: 21.
of_max_levels	int	Number of pyramid scale levels to consider. This is different from the scale parameter, which determines the initial image scaling. Default: 3
tracking_target_instance_count	Optional[int]	Target number of instances to track per frame. (default: None)
tracking_pre_cull_to_target	int	If non-zero and target_instance_count is also non-zero, then cull instances over target count per frame before tracking. (default: 0)
tracking_pre_cull_iou_threshold	float	If non-zero and pre_cull_to_target also set, then use IOU threshold to remove overlapping instances over count before tracking. (default: 0)

Methods:

Name	Description
get_shifted_instances_from_prv_frames	Generate shifted instances onto the new frame by applying optical flow.
update_candidates	Return dictionary with the features of tracked instances.

Source code in sleap_nn/tracking/tracker.py

@attrs.define
class FlowShiftTracker(Tracker):
    """Module for tracking using optical flow shift matching.

    This module handles tracking instances across frames by creating new track IDs (or)
    assigning track IDs to each instance when the `.track()` is called using optical flow
    based track matching. This is a sub-class of the `Tracker` module, which configures
    the `update_candidates()` method specific to optical flow shift matching. This class is
    initialized in the `Tracker.from_config()` method.

    Attributes:
        candidates: Either `FixedWindowCandidates` or `LocalQueueCandidates` object.
        min_match_points: Minimum non-NaN points for match candidates. Default: 0.
        features: One of [`keypoints`, `centroids`, `bboxes`, `image`].
            Default: `keypoints`.
        scoring_method: Method to compute association score between features from the
            current frame and the previous tracks. One of [`oks`, `cosine_sim`, `iou`,
            `euclidean_dist`]. Default: `oks`.
        scoring_reduction: Method to aggregate and reduce multiple scores if there are
            several detections associated with the same track. One of [`mean`, `max`,
            `robust_quantile`]. Default: `mean`.
        robust_best_instance: If the value is between 0 and 1
                (excluded), use a robust quantile similarity score for the
                track. If the value is 1, use the max similarity (non-robust).
                For selecting a robust score, 0.95 is a good value.
        track_matching_method: track matching algorithm. One of `hungarian`, `greedy.
                Default: `hungarian`.
        use_flow: If True, `FlowShiftTracker` is used, where the poses are matched using
            optical flow. Default: `False`.
        is_local_queue: `True` if `LocalQueueCandidates` is used else `False`.
        img_scale: Factor to scale the images by when computing optical flow. Decrease
            this to increase performance at the cost of finer accuracy. Sometimes
            decreasing the image scale can improve performance with fast movements.
            Default: 1.0.
        of_window_size: Optical flow window size to consider at each pyramid scale
            level. Default: 21.
        of_max_levels: Number of pyramid scale levels to consider. This is different
            from the scale parameter, which determines the initial image scaling.
            Default: 3
        tracking_target_instance_count: Target number of instances to track per frame. (default: None)
        tracking_pre_cull_to_target: If non-zero and target_instance_count is also non-zero, then cull instances over target count per frame *before* tracking. (default: 0)
        tracking_pre_cull_iou_threshold: If non-zero and pre_cull_to_target also set, then use IOU threshold to remove overlapping instances over count *before* tracking. (default: 0)

    """

    img_scale: float = 1.0
    of_window_size: int = 21
    of_max_levels: int = 3

    def _compute_optical_flow(
        self, ref_pts: np.ndarray, ref_img: np.ndarray, new_img: np.ndarray
    ):
        """Compute instances on new frame using optical flow displacements."""
        ref_img, new_img = self._preprocess_imgs(ref_img, new_img)
        shifted_pts, status, errs = cv2.calcOpticalFlowPyrLK(
            ref_img,
            new_img,
            (np.concatenate(ref_pts, axis=0)).astype("float32") * self.img_scale,
            None,
            winSize=(self.of_window_size, self.of_window_size),
            maxLevel=self.of_max_levels,
            criteria=(cv2.TERM_CRITERIA_EPS | cv2.TERM_CRITERIA_COUNT, 30, 0.01),
        )
        shifted_pts /= self.img_scale
        return shifted_pts, status, errs

    def _preprocess_imgs(self, ref_img: np.ndarray, new_img: np.ndarray):
        """Pre-process images for optical flow."""
        # Convert to uint8 for cv2.calcOpticalFlowPyrLK
        if np.issubdtype(ref_img.dtype, np.floating):
            ref_img = ref_img.astype("uint8")
        if np.issubdtype(new_img.dtype, np.floating):
            new_img = new_img.astype("uint8")

        # Ensure images are rank 2 in case there is a singleton channel dimension.
        if ref_img.ndim > 3:
            ref_img = np.squeeze(ref_img)
            new_img = np.squeeze(new_img)

        # Convert RGB to grayscale.
        if ref_img.ndim > 2 and ref_img.shape[0] == 3:
            ref_img = cv2.cvtColor(ref_img, cv2.COLOR_BGR2GRAY)
            new_img = cv2.cvtColor(new_img, cv2.COLOR_BGR2GRAY)

        # Input image scaling.
        if self.img_scale != 1:
            ref_img = cv2.resize(ref_img, None, None, self.img_scale, self.img_scale)
            new_img = cv2.resize(new_img, None, None, self.img_scale, self.img_scale)

        return ref_img, new_img

    def get_shifted_instances_from_prv_frames(
        self,
        candidates_list: Union[Deque, DefaultDict[int, Deque]],
        new_img: np.ndarray,
        feature_method,
    ) -> Dict[int, List[TrackedInstanceFeature]]:
        """Generate shifted instances onto the new frame by applying optical flow."""
        shifted_instances_prv_frames = defaultdict(list)

        if self.is_local_queue:
            # for local queue
            ref_candidates = self.candidate.get_instances_groupby_frame_idx(
                candidates_list
            )
            for fidx, ref_candidate_list in ref_candidates.items():
                ref_pts = [x.src_instance.numpy() for x in ref_candidate_list]
                if not ref_pts:
                    continue
                shifted_pts, status, errs = self._compute_optical_flow(
                    ref_pts=ref_pts,
                    ref_img=ref_candidate_list[0].image,
                    new_img=new_img,
                )

                sections = np.cumsum([len(x) for x in ref_pts])[:-1]
                shifted_pts = np.split(shifted_pts, sections, axis=0)
                status = np.split(status, sections, axis=0)
                errs = np.split(errs, sections, axis=0)

                # Create shifted instances.
                for idx, (ref_candidate, pts, found) in enumerate(
                    zip(ref_candidate_list, shifted_pts, status)
                ):
                    # Exclude points that weren't found by optical flow.
                    found = found.squeeze().astype(bool)
                    pts[~found] = np.nan

                    # Create a shifted instance.
                    shifted_instances_prv_frames[ref_candidate.track_id].append(
                        TrackedInstanceFeature(
                            feature=feature_method(pts),
                            src_predicted_instance=ref_candidate.src_instance,
                            frame_idx=fidx,
                            tracking_score=ref_candidate.tracking_score,
                            shifted_keypoints=pts,
                        )
                    )

        else:
            # for fixed window
            candidates_list = (
                candidates_list
                if candidates_list is not None
                else self.candidate.tracker_queue
            )
            for ref_candidate in candidates_list:
                ref_pts = [x.numpy() for x in ref_candidate.src_instances]
                if not ref_pts:
                    continue
                shifted_pts, status, errs = self._compute_optical_flow(
                    ref_pts=ref_pts, ref_img=ref_candidate.image, new_img=new_img
                )

                sections = np.cumsum([len(x) for x in ref_pts])[:-1]
                shifted_pts = np.split(shifted_pts, sections, axis=0)
                status = np.split(status, sections, axis=0)
                errs = np.split(errs, sections, axis=0)

                # Create shifted instances.
                for idx, (pts, found) in enumerate(zip(shifted_pts, status)):
                    # Exclude points that weren't found by optical flow.
                    found = found.squeeze().astype(bool)
                    pts[~found] = np.nan

                    # Create a shifted instance.
                    shifted_instances_prv_frames[ref_candidate.track_ids[idx]].append(
                        TrackedInstanceFeature(
                            feature=feature_method(pts),
                            src_predicted_instance=ref_candidate.src_instances[idx],
                            frame_idx=ref_candidate.frame_idx,
                            tracking_score=ref_candidate.tracking_scores[idx],
                            shifted_keypoints=pts,
                        )
                    )

        return shifted_instances_prv_frames

    def update_candidates(
        self,
        candidates_list: Union[Deque, DefaultDict[int, Deque]],
        image: np.ndarray,
    ) -> Dict[int, TrackedInstanceFeature]:
        """Return dictionary with the features of tracked instances.

        In this method, the tracked instances in the tracker queue are shifted on to the
        current frame using optical flow. The features are then computed from the shifted
        instances.

        Args:
            candidates_list: Tracker queue from the candidate class.
            image: Image of the current untracked frame. (used for flow shift tracker)

        Returns:
            Dictionary with keys as track IDs and values as the list of `TrackedInstanceFeature`.
        """
        # get feature method for the shifted instances
        if self.features not in self._feature_methods:
            message = "Invalid `features` argument. Please provide one of `keypoints`, `centroids`, `bboxes`, `masks` and `image`"
            logger.error(message)
            raise ValueError(message)
        feature_method = self._feature_methods[self.features]

        # get shifted instances from optical flow
        shifted_instances_prv_frames = self.get_shifted_instances_from_prv_frames(
            candidates_list=candidates_list,
            new_img=image,
            feature_method=feature_method,
        )

        return shifted_instances_prv_frames

get_shifted_instances_from_prv_frames(candidates_list, new_img, feature_method)

Generate shifted instances onto the new frame by applying optical flow.

Source code in sleap_nn/tracking/tracker.py

def get_shifted_instances_from_prv_frames(
    self,
    candidates_list: Union[Deque, DefaultDict[int, Deque]],
    new_img: np.ndarray,
    feature_method,
) -> Dict[int, List[TrackedInstanceFeature]]:
    """Generate shifted instances onto the new frame by applying optical flow."""
    shifted_instances_prv_frames = defaultdict(list)

    if self.is_local_queue:
        # for local queue
        ref_candidates = self.candidate.get_instances_groupby_frame_idx(
            candidates_list
        )
        for fidx, ref_candidate_list in ref_candidates.items():
            ref_pts = [x.src_instance.numpy() for x in ref_candidate_list]
            if not ref_pts:
                continue
            shifted_pts, status, errs = self._compute_optical_flow(
                ref_pts=ref_pts,
                ref_img=ref_candidate_list[0].image,
                new_img=new_img,
            )

            sections = np.cumsum([len(x) for x in ref_pts])[:-1]
            shifted_pts = np.split(shifted_pts, sections, axis=0)
            status = np.split(status, sections, axis=0)
            errs = np.split(errs, sections, axis=0)

            # Create shifted instances.
            for idx, (ref_candidate, pts, found) in enumerate(
                zip(ref_candidate_list, shifted_pts, status)
            ):
                # Exclude points that weren't found by optical flow.
                found = found.squeeze().astype(bool)
                pts[~found] = np.nan

                # Create a shifted instance.
                shifted_instances_prv_frames[ref_candidate.track_id].append(
                    TrackedInstanceFeature(
                        feature=feature_method(pts),
                        src_predicted_instance=ref_candidate.src_instance,
                        frame_idx=fidx,
                        tracking_score=ref_candidate.tracking_score,
                        shifted_keypoints=pts,
                    )
                )

    else:
        # for fixed window
        candidates_list = (
            candidates_list
            if candidates_list is not None
            else self.candidate.tracker_queue
        )
        for ref_candidate in candidates_list:
            ref_pts = [x.numpy() for x in ref_candidate.src_instances]
            if not ref_pts:
                continue
            shifted_pts, status, errs = self._compute_optical_flow(
                ref_pts=ref_pts, ref_img=ref_candidate.image, new_img=new_img
            )

            sections = np.cumsum([len(x) for x in ref_pts])[:-1]
            shifted_pts = np.split(shifted_pts, sections, axis=0)
            status = np.split(status, sections, axis=0)
            errs = np.split(errs, sections, axis=0)

            # Create shifted instances.
            for idx, (pts, found) in enumerate(zip(shifted_pts, status)):
                # Exclude points that weren't found by optical flow.
                found = found.squeeze().astype(bool)
                pts[~found] = np.nan

                # Create a shifted instance.
                shifted_instances_prv_frames[ref_candidate.track_ids[idx]].append(
                    TrackedInstanceFeature(
                        feature=feature_method(pts),
                        src_predicted_instance=ref_candidate.src_instances[idx],
                        frame_idx=ref_candidate.frame_idx,
                        tracking_score=ref_candidate.tracking_scores[idx],
                        shifted_keypoints=pts,
                    )
                )

    return shifted_instances_prv_frames

update_candidates(candidates_list, image)

Return dictionary with the features of tracked instances.

In this method, the tracked instances in the tracker queue are shifted on to the current frame using optical flow. The features are then computed from the shifted instances.

Parameters:

Name	Type	Description	Default
candidates_list	Union[Deque, DefaultDict[int, Deque]]	Tracker queue from the candidate class.	required
image	ndarray	Image of the current untracked frame. (used for flow shift tracker)	required

Returns:

Type	Description
Dict[int, TrackedInstanceFeature]	Dictionary with keys as track IDs and values as the list of TrackedInstanceFeature.

Source code in sleap_nn/tracking/tracker.py

def update_candidates(
    self,
    candidates_list: Union[Deque, DefaultDict[int, Deque]],
    image: np.ndarray,
) -> Dict[int, TrackedInstanceFeature]:
    """Return dictionary with the features of tracked instances.

    In this method, the tracked instances in the tracker queue are shifted on to the
    current frame using optical flow. The features are then computed from the shifted
    instances.

    Args:
        candidates_list: Tracker queue from the candidate class.
        image: Image of the current untracked frame. (used for flow shift tracker)

    Returns:
        Dictionary with keys as track IDs and values as the list of `TrackedInstanceFeature`.
    """
    # get feature method for the shifted instances
    if self.features not in self._feature_methods:
        message = "Invalid `features` argument. Please provide one of `keypoints`, `centroids`, `bboxes`, `masks` and `image`"
        logger.error(message)
        raise ValueError(message)
    feature_method = self._feature_methods[self.features]

    # get shifted instances from optical flow
    shifted_instances_prv_frames = self.get_shifted_instances_from_prv_frames(
        candidates_list=candidates_list,
        new_img=image,
        feature_method=feature_method,
    )

    return shifted_instances_prv_frames

KalmanShiftTracker

Bases: Tracker

Tracker that predicts candidate poses with per-track Kalman filters.

KalmanShiftTracker mirrors FlowShiftTracker: it subclasses Tracker and overrides only update_candidates() (plus a thin track() that records the current frame index). Instead of shifting previous-frame keypoints with optical flow, it advances one constant-velocity pykalman.KalmanFilter per track to predict where each tracked instance should be in the current frame. The shared scoring/matching path (get_scores -> scores_to_cost_matrix -> assign_tracks) is reused unchanged.

The tracker runs in two phases:

1. Warm-up. For the first kf_init_frame_count frames, update_candidates delegates to the base keypoint-feature path (i.e. behaves like a plain fixed-window / local-queue tracker) while accumulating a per-track keypoint history. Because the candidate queue is bounded to window_size, the history is kept in a separate buffer (_obs_history) so warm-up can span more frames than the queue holds.
2. Motion model. Once kf_init_frame_count frames have been seen, one constant-velocity Kalman filter is fit per track over the warm-up window — on the per-track CENTROID (state [cx, vcx, cy, vcy]), not every keypoint independently (a per-keypoint fit overfits noise into non-physical poses). Each frame thereafter, update_candidates: (a) resets tracks unseen beyond kf_reset_gap_size frames; (b) corrects each matched filter with its newly observed centroid subject to a distance gate (rejecting false positives / mismatches), coasting across multi-frame gaps so elapsed motion is not dumped into velocity; © lazily (re)fits filters for tracks that lack one (entrants / post-reset, from a contiguous fresh window); and (d) projects the centroid forward and builds the candidate by RIGIDLY translating the last observed pose by a fraction (kf_prediction_blend) of the predicted centroid displacement — translating the real body keeps the candidate geometrically valid so the similarity score stays meaningful.

Robustness knobs (kf_prediction_blend, the measurement-gate and velocity-cap parameters; tuned defaults, overridable via Tracker.from_config(...)) make the motion model net-beneficial where association is ambiguous — crossing / converging / fast-smooth motion — and neutral on clean, false-positive, and occluded scenes. Under heavy detection noise with frequent missed detections it can slightly reduce IDF1 vs the memoryless base tracker (lower kf_prediction_blend, e.g. 0.25, to favor the last observation there).

Kalman tracking requires a known target identity count (tracking_target_instance_count, or one derived from max_tracks/max_instances) and is mutually exclusive with use_flow; both are validated in Tracker.from_config.

Attributes:

Name	Type	Description
kf_init_frame_count	int	Number of warm-up frames tracked with the base path before the per-track Kalman filters are fit via EM. Default: 10.
kf_node_indices	Optional[List[int]]	Skeleton node (row) indices to track with the motion model. None (default) uses all nodes.
kf_reset_gap_size	int	Number of consecutive missed frames after which a stale track's filter is reset (and later re-fit). Default: 5.
kf_prediction_blend	float	Weight of the motion prediction when blending it with the last observation to form the scoring candidate (w*pred + (1-w)*last_obs). 0 = pure last-observation (no motion model at scoring), 1 = pure prediction. Scales toward pure prediction during gaps. Default: 0.5.
kf_gate_step_mult	float	Measurement gate as a multiple of the track's median step; an observation farther than max(kf_min_gate_px, kf_gate_step_mult*step) from the prediction is rejected (treated as a miss). Default: 8.0.
kf_min_gate_px	float	Floor (px) for the measurement gate. Default: 40.0.
kf_velocity_cap_mult	float	Cap on learned per-coordinate velocity as a multiple of the track's median step. Default: 3.0.
kf_min_velocity_cap_px	float	Floor (px/frame) for the velocity cap. Default: 15.0.

Methods:

Name	Description
track	Record the frame index, run base tracking, then ingest the assignment.
update_candidates	Return Kalman-predicted candidate features for the current frame.

Source code in sleap_nn/tracking/tracker.py

@attrs.define
class KalmanShiftTracker(Tracker):
    """Tracker that predicts candidate poses with per-track Kalman filters.

    `KalmanShiftTracker` mirrors `FlowShiftTracker`: it subclasses `Tracker` and
    overrides only `update_candidates()` (plus a thin `track()` that records the
    current frame index). Instead of shifting previous-frame keypoints with optical
    flow, it advances one constant-velocity `pykalman.KalmanFilter` per track to
    predict where each tracked instance should be in the current frame. The shared
    scoring/matching path (`get_scores` -> `scores_to_cost_matrix` -> `assign_tracks`)
    is reused unchanged.

    The tracker runs in two phases:

    1. **Warm-up.** For the first `kf_init_frame_count` frames, `update_candidates`
       delegates to the base keypoint-feature path (i.e. behaves like a plain
       fixed-window / local-queue tracker) while accumulating a per-track keypoint
       history. Because the candidate queue is bounded to `window_size`, the history
       is kept in a separate buffer (`_obs_history`) so warm-up can span more frames
       than the queue holds.
    2. **Motion model.** Once `kf_init_frame_count` frames have been seen, one
       constant-velocity Kalman filter is fit per track over the warm-up window — on the
       per-track CENTROID (state ``[cx, vcx, cy, vcy]``), not every keypoint
       independently (a per-keypoint fit overfits noise into non-physical poses). Each
       frame thereafter, `update_candidates`: (a) resets tracks unseen beyond
       `kf_reset_gap_size` frames; (b) corrects each matched filter with its newly
       observed centroid subject to a distance gate (rejecting false positives /
       mismatches), coasting across multi-frame gaps so elapsed motion is not dumped into
       velocity; (c) lazily (re)fits filters for tracks that lack one (entrants /
       post-reset, from a contiguous fresh window); and (d) projects the centroid forward
       and builds the candidate by RIGIDLY translating the last observed pose by a
       fraction (`kf_prediction_blend`) of the predicted centroid displacement —
       translating the real body keeps the candidate geometrically valid so the
       similarity score stays meaningful.

    Robustness knobs (`kf_prediction_blend`, the measurement-gate and velocity-cap
    parameters; tuned defaults, overridable via `Tracker.from_config(...)`) make the
    motion model net-beneficial where association is ambiguous — crossing / converging /
    fast-smooth motion — and neutral on clean, false-positive, and occluded scenes.
    Under heavy detection noise with frequent missed detections it can slightly reduce
    IDF1 vs the memoryless base tracker (lower `kf_prediction_blend`, e.g. 0.25, to
    favor the last observation there).

    Kalman tracking requires a known target identity count
    (`tracking_target_instance_count`, or one derived from `max_tracks`/`max_instances`)
    and is mutually exclusive with `use_flow`; both are validated in
    `Tracker.from_config`.

    Attributes:
        kf_init_frame_count: Number of warm-up frames tracked with the base path
            before the per-track Kalman filters are fit via EM. Default: 10.
        kf_node_indices: Skeleton node (row) indices to track with the motion model.
            `None` (default) uses all nodes.
        kf_reset_gap_size: Number of consecutive missed frames after which a stale
            track's filter is reset (and later re-fit). Default: 5.
        kf_prediction_blend: Weight of the motion prediction when blending it with the
            last observation to form the scoring candidate (`w*pred + (1-w)*last_obs`).
            0 = pure last-observation (no motion model at scoring), 1 = pure prediction.
            Scales toward pure prediction during gaps. Default: 0.5.
        kf_gate_step_mult: Measurement gate as a multiple of the track's median step;
            an observation farther than `max(kf_min_gate_px, kf_gate_step_mult*step)`
            from the prediction is rejected (treated as a miss). Default: 8.0.
        kf_min_gate_px: Floor (px) for the measurement gate. Default: 40.0.
        kf_velocity_cap_mult: Cap on learned per-coordinate velocity as a multiple of
            the track's median step. Default: 3.0.
        kf_min_velocity_cap_px: Floor (px/frame) for the velocity cap. Default: 15.0.
    """

    kf_track_features: str = "centroid"
    kf_init_frame_count: int = 10
    kf_node_indices: Optional[List[int]] = None
    kf_reset_gap_size: int = 5
    kf_prediction_blend: float = 0.5
    kf_gate_step_mult: float = 8.0
    kf_min_gate_px: float = 40.0
    kf_velocity_cap_mult: float = 3.0
    kf_min_velocity_cap_px: float = 15.0

    # Per-instance Kalman state (never passed to the constructor).
    _kalman_filters: Dict[int, Any] = attrs.field(init=False, factory=dict)
    _last_results: Dict[int, Dict[str, Any]] = attrs.field(init=False, factory=dict)
    _last_frame_for_track: Dict[int, int] = attrs.field(init=False, factory=dict)
    _last_corrected_frame: Dict[int, int] = attrs.field(init=False, factory=dict)
    _obs_history: Dict[int, List[Dict[str, Any]]] = attrs.field(
        init=False, factory=dict
    )
    _resolved_node_indices: Optional[List[int]] = attrs.field(init=False, default=None)
    _n_nodes: Optional[int] = attrs.field(init=False, default=None)
    _frames_seen: int = attrs.field(init=False, default=0)
    _initialized: bool = attrs.field(init=False, default=False)
    _current_frame_idx: int = attrs.field(init=False, default=0)
    # Per-track robust inter-frame centroid step, used for the measurement gate and
    # the velocity cap (set at filter init).
    _median_step: Dict[int, float] = attrs.field(init=False, factory=dict)
    # Frame index at which a track was last reset; (re)fit windows only use
    # observations strictly after this, so a refit never straddles an occlusion gap.
    _reset_frame: Dict[int, int] = attrs.field(init=False, factory=dict)

    def track(
        self,
        untracked_instances: List[sio.PredictedInstance],
        frame_idx: int,
        image: np.ndarray = None,
    ) -> List[sio.PredictedInstance]:
        """Record the frame index, run base tracking, then ingest the assignment.

        Observations are recorded into `_obs_history` AFTER `super().track()` (i.e.
        after the current frame's track assignment is finalized) so each track id is
        associated with the instance it was actually matched to this frame, not a
        pre-assignment queue snapshot.
        """
        self._current_frame_idx = int(frame_idx)
        result = super().track(untracked_instances, frame_idx, image)
        self._ingest_observations(self.candidate.tracker_queue)
        return result

    def update_candidates(
        self,
        candidates_list: Union[Deque, DefaultDict[int, Deque]],
        image: np.ndarray,
    ) -> Dict[int, List[TrackedInstanceFeature]]:
        """Return Kalman-predicted candidate features for the current frame.

        During warm-up this delegates to the base keypoint-feature path. Once the
        filters are initialized, each track's filter is corrected (with measurement
        gating) by its newly observed keypoints, stale tracks are reset, filters are
        lazily (re)fit for tracks that lack one, and a motion-predicted pose blended
        with the last observation is returned as the candidate feature.

        Args:
            candidates_list: Tracker queue from the candidate class.
            image: Image of the current untracked frame (unused; Kalman tracking does
                not use image features).

        Returns:
            Dictionary with keys as track IDs and values as lists of
            `TrackedInstanceFeature`.
        """
        if self.features not in self._feature_methods:
            message = "Invalid `features` argument. Please provide one of `keypoints`, `centroids`, `bboxes`, `masks` and `image`"
            logger.error(message)
            raise ValueError(message)
        feature_method = self._feature_methods[self.features]

        if not self._initialized:
            self._frames_seen += 1
            if self._frames_seen >= self.kf_init_frame_count:
                self._init_filters()
            if not self._initialized:
                # Still warming up: behave exactly like the base tracker.
                return super().update_candidates(candidates_list, image)

        # Reset tracks that have gone stale (no *accepted* observation within
        # `kf_reset_gap_size` frames) BEFORE correcting, so a track that is only
        # receiving gated-out observations is dropped to the base path rather than
        # eventually corrupted by a stale-extrapolation match. Then correct matched
        # filters with gated observations, lazily (re)fit filters for tracks that lack
        # one, and predict for scoring.
        self._reset_stale_tracks(self._current_frame_idx)
        self._correct_filters()
        self._init_missing_filters()
        return self._predict_candidates(candidates_list, feature_method)

    def _ingest_observations(
        self, candidates_list: Union[Deque, DefaultDict[int, Deque]]
    ) -> None:
        """Record the most recent observation per track into `_obs_history`.

        Uses the candidate class's own `get_features_from_track_id` accessor so this
        works for both fixed-window and local-queue tracker queues.
        """
        for track_id in self.candidate.current_tracks:
            feats = self.candidate.get_features_from_track_id(track_id, candidates_list)
            if not feats:
                continue
            newest = max(
                feats,
                key=lambda tf: (tf.frame_idx if tf.frame_idx is not None else -1),
            )
            frame_idx = (
                int(newest.frame_idx)
                if newest.frame_idx is not None
                else self._current_frame_idx
            )
            history = self._obs_history.setdefault(track_id, [])
            if history and history[-1]["frame_idx"] >= frame_idx:
                continue  # already recorded this (or a newer) observation
            keypoints = newest.src_predicted_instance.numpy()
            history.append(
                {
                    "frame_idx": frame_idx,
                    "keypoints": keypoints,
                    "src": newest.src_predicted_instance,
                    "score": newest.tracking_score,
                }
            )
            if self._n_nodes is None:
                self._n_nodes = keypoints.shape[0]

    def _resolve_node_indices(self) -> List[int]:
        """Resolve `kf_node_indices` to a concrete list of node-row indices.

        These nodes define the per-track *centroid* the motion model tracks; the
        predicted centroid displacement is applied rigidly to the whole body.
        """
        if self.kf_node_indices is not None:
            return [i for i in self.kf_node_indices if i < (self._n_nodes or 0)]
        return list(range(self._n_nodes)) if self._n_nodes else []

    def _num_track_points(self) -> int:
        """Number of points the motion model tracks per instance.

        1 for ``kf_track_features="centroid"`` (the per-track centroid); one per
        selected node for ``kf_track_features="keypoints"``.
        """
        if self.kf_track_features == "keypoints":
            return max(1, len(self._resolved_node_indices))
        return 1

    def _tracked_points(self, keypoints: np.ndarray) -> np.ndarray:
        """The points the motion model tracks for an instance, shape (P, 2).

        Centroid mode: the single (visibility-aware) centroid. Keypoints mode: the
        selected node coordinates as-is (NaN where a node is missing).
        """
        if self.kf_track_features == "keypoints":
            return np.asarray(keypoints, dtype=float)[self._resolved_node_indices, :]
        return self._centroid(keypoints).reshape(1, 2)

    def _build_matrices(self):
        """Build constant-velocity transition/observation matrices for P points.

        State is ``[x0, vx0, y0, vy0, x1, vx1, y1, vy1, ...]`` (4*P dims); the
        observation is the P point positions ``[x0, y0, x1, y1, ...]`` (2*P dims).
        For ``kf_track_features="centroid"`` P=1 (a single stable centroid filter,
        whose predicted displacement is applied rigidly to the whole body); for
        ``"keypoints"`` P is the number of tracked nodes (each node gets its own
        constant-velocity filter — noisier, but uses the pose directly).
        """
        n_points = self._num_track_points()
        state_dim = 4 * n_points
        obs_dim = 2 * n_points
        transition = [[0.0] * state_dim for _ in range(state_dim)]
        observation = [[0.0] * state_dim for _ in range(obs_dim)]
        for p in range(n_points):
            b = 4 * p
            transition[b][b] = 1.0  # x' = x + vx
            transition[b][b + 1] = 1.0
            transition[b + 1][b + 1] = 1.0  # vx' = vx
            transition[b + 2][b + 2] = 1.0  # y' = y + vy
            transition[b + 2][b + 3] = 1.0
            transition[b + 3][b + 3] = 1.0  # vy' = vy
            observation[2 * p][b] = 1.0  # observe x
            observation[2 * p + 1][b + 2] = 1.0  # observe y
        return transition, observation

    def _centroid(self, keypoints: np.ndarray) -> np.ndarray:
        """NaN-ignoring centroid of the tracked nodes, shape (2,).

        Returns NaN when fewer than half the tracked nodes are visible: a centroid
        built from a small, changing subset of nodes is biased (it shifts as different
        nodes drop), which would otherwise feed the filter a spurious displacement.
        A NaN centroid is treated as a missing observation (the filter coasts) rather
        than a corrupting one.
        """
        import warnings

        pts = np.asarray(keypoints)[self._resolved_node_indices, :]
        visible = int((~np.isnan(pts).any(axis=1)).sum())
        if visible == 0 or visible * 2 < pts.shape[0]:
            return np.array([np.nan, np.nan])
        with warnings.catch_warnings():
            warnings.simplefilter("ignore", category=RuntimeWarning)
            return np.nanmean(pts, axis=0)

    def _obs_vector(self, keypoints: np.ndarray) -> np.ndarray:
        """Masked observation vector of the tracked points, shape (2*P,)."""
        return np.ma.masked_invalid(
            np.ma.asarray(self._tracked_points(keypoints).flatten(), dtype=float)
        )

    @staticmethod
    def _predicted_points(mean: np.ndarray) -> np.ndarray:
        """Extract predicted point positions ``[[x0,y0],...]`` from a state mean."""
        return np.asarray(mean)[::2].reshape(-1, 2)

    def _predicted_centroid(self, mean: np.ndarray) -> np.ndarray:
        """Centroid of the predicted tracked points, shape (2,) (used for gating)."""
        import warnings

        with warnings.catch_warnings():
            warnings.simplefilter("ignore", category=RuntimeWarning)
            return np.nanmean(self._predicted_points(mean), axis=0)

    @staticmethod
    def _cap_velocity(mean: np.ndarray, cap: float) -> np.ndarray:
        """Clip the per-axis velocity entries (vcx, vcy) of a state mean to +/- cap."""
        mean = np.asarray(mean, dtype=float).copy()
        mean[1::2] = np.clip(mean[1::2], -cap, cap)
        return mean

    def _window_median_step(self, window: List[Dict[str, Any]]) -> float:
        """Noise-robust estimate of the per-frame centroid step over a window.

        Uses the endpoint displacement divided by the number of elapsed FRAMES
        between the first and last valid centroids (not the count of valid intervals):
        dividing by interval count would overestimate the per-frame step by up to the
        gap length when centroids drop out mid-window, which would loosen the velocity
        cap and gate in exactly the noisy regime they protect. The endpoint baseline
        averages per-frame measurement noise out for a roughly constant-velocity track.
        """
        valid = [
            (h["frame_idx"], self._centroid(h["keypoints"]))
            for h in window
            if not np.isnan(self._centroid(h["keypoints"])).any()
        ]
        if len(valid) < 2:
            return 0.0
        span = valid[-1][0] - valid[0][0]
        if span <= 0:
            return 0.0
        baseline = float(np.linalg.norm(valid[-1][1] - valid[0][1])) / span
        return baseline

    def _velocity_cap(self, track_id: int) -> float:
        med = self._median_step.get(track_id, 0.0)
        return max(self.kf_min_velocity_cap_px, self.kf_velocity_cap_mult * med)

    def _gate_distance(self, track_id: int) -> float:
        med = self._median_step.get(track_id, 0.0)
        return max(self.kf_min_gate_px, self.kf_gate_step_mult * med)

    def _contiguous_fresh_window(self, track_id: int) -> List[Dict[str, Any]]:
        """Longest suffix of a track's history that is contiguous and post-reset.

        Observations from before the track's last reset are excluded, and the window
        is broken at any frame-index gap > 1, so a (re)fit never straddles an
        occlusion and the median-step / velocity-cap estimates stay physical.
        """
        history = self._obs_history.get(track_id, [])
        reset_frame = self._reset_frame.get(track_id, -1)
        fresh = [h for h in history if h["frame_idx"] > reset_frame]
        if not fresh:
            return []
        window = [fresh[-1]]
        for h in reversed(fresh[:-1]):
            if window[0]["frame_idx"] - h["frame_idx"] == 1:
                window.insert(0, h)
            else:
                break
        return window

    def _fit_track_filter(self, track_id: int) -> bool:
        """Fit a centroid Kalman filter for a track from a contiguous fresh window.

        Returns True on success. Seeds the initial state from the first *finite*
        centroid (and a capped finite-difference velocity), keeps the initial mean
        fixed during EM, and caps the learned velocity so a short/noisy window cannot
        produce a runaway state.
        """
        window = self._contiguous_fresh_window(track_id)
        if len(window) < 3:
            return False  # need a few contiguous frames for a stable velocity fit
        window = window[-self.kf_init_frame_count :]
        n_points = self._num_track_points()
        obs_dim = 2 * n_points
        rows = np.asarray(
            [self._tracked_points(h["keypoints"]).flatten() for h in window],
            dtype=float,
        )  # (T, 2P), NaN where a tracked point is missing
        obs = np.ma.masked_invalid(rows)

        median_step = self._window_median_step(window)
        velocity_cap = max(
            self.kf_min_velocity_cap_px, self.kf_velocity_cap_mult * median_step
        )

        # Need at least two frames with any usable observation.
        if int(np.sum(~np.isnan(rows).all(axis=1))) < 2:
            return False

        # Per-coordinate seed: position from the first finite value; velocity from the
        # first consecutive finite pair (capped) so a dropout does not mislabel a
        # multi-frame step as a one-frame velocity. Coordinates never seen in the
        # window are filled with the same-axis mean (never the image origin).
        first = np.full(obs_dim, np.nan)
        seed_vel = np.zeros(obs_dim)
        for c in range(obs_dim):
            finite_t = np.where(~np.isnan(rows[:, c]))[0]
            if len(finite_t) == 0:
                continue
            first[c] = rows[finite_t[0], c]
            for t in finite_t:
                if t + 1 < len(rows) and not np.isnan(rows[t + 1, c]):
                    seed_vel[c] = np.clip(
                        rows[t + 1, c] - rows[t, c], -velocity_cap, velocity_cap
                    )
                    break
        if np.isnan(first).all():
            return False
        if np.isnan(first).any():
            fx = np.nanmean(first[0::2]) if not np.isnan(first[0::2]).all() else 0.0
            fy = np.nanmean(first[1::2]) if not np.isnan(first[1::2]).all() else 0.0
            first[0::2] = np.where(np.isnan(first[0::2]), fx, first[0::2])
            first[1::2] = np.where(np.isnan(first[1::2]), fy, first[1::2])
        initial_state_mean = [0.0] * (4 * n_points)
        for p in range(n_points):
            initial_state_mean[4 * p] = float(first[2 * p])
            initial_state_mean[4 * p + 1] = float(seed_vel[2 * p])
            initial_state_mean[4 * p + 2] = float(first[2 * p + 1])
            initial_state_mean[4 * p + 3] = float(seed_vel[2 * p + 1])

        transition, observation = self._build_matrices()
        kalman_filter_cls = _get_kalman_filter_cls()
        try:
            kf = kalman_filter_cls(
                transition_matrices=transition,
                observation_matrices=observation,
                initial_state_mean=initial_state_mean,
            )
            # Learn only the noise covariances; keep the structural matrices and the
            # initial state mean fixed.
            kf = kf.em(
                obs,
                n_iter=20,
                em_vars=[
                    "transition_covariance",
                    "observation_covariance",
                    "initial_state_covariance",
                ],
            )
            means, covariances = kf.filter(obs)
        except Exception as e:  # pragma: no cover - numerical edge cases
            logger.warning(
                f"Kalman filter initialization failed for track {track_id}: {e}"
            )
            return False

        self._kalman_filters[track_id] = kf
        self._last_results[track_id] = {
            "means": self._cap_velocity(means[-1], velocity_cap),
            "covariances": covariances[-1],
        }
        self._last_corrected_frame[track_id] = window[-1]["frame_idx"]
        self._last_frame_for_track[track_id] = window[-1]["frame_idx"]
        self._median_step[track_id] = median_step
        return True

    def _init_filters(self) -> None:
        """Fit a centroid Kalman filter per track at the end of warm-up."""
        self._resolved_node_indices = self._resolve_node_indices()
        if len(self._resolved_node_indices) == 0:
            # Nothing to track with a motion model; fall back to the base path.
            self._initialized = True
            return
        for track_id in list(self._obs_history.keys()):
            self._fit_track_filter(track_id)
        self._initialized = True

    def _init_missing_filters(self) -> None:
        """Lazily (re)fit filters for active tracks that lack one.

        Covers identities that spawn after warm-up and tracks whose filter was reset.
        A filter is fit only once `kf_init_frame_count` CONTIGUOUS fresh (post-reset)
        observations have accumulated, so a just-reset track is not immediately re-fit
        (no thrashing) and the fit window never straddles the occlusion gap.
        """
        if not self._resolved_node_indices:
            return
        for track_id in self.candidate.current_tracks:
            if track_id in self._kalman_filters:
                continue
            window = self._contiguous_fresh_window(track_id)
            if len(window) >= self.kf_init_frame_count:
                self._fit_track_filter(track_id)

    def _correct_filters(self) -> None:
        """Advance each matched filter with gated centroid observations.

        Coasts the filter across multi-frame gaps (one masked predict per missed
        frame) before applying the reappearance observation, so the elapsed motion is
        not dumped into the velocity state. Rejects observations whose centroid is
        beyond the measurement gate from the prediction (e.g. false positives),
        treating them as a miss.
        """
        for track_id, kf in list(self._kalman_filters.items()):
            history = self._obs_history.get(track_id, [])
            last_corrected = self._last_corrected_frame.get(track_id, -1)
            new_observations = [h for h in history if h["frame_idx"] > last_corrected]
            velocity_cap = self._velocity_cap(track_id)
            gate = self._gate_distance(track_id)
            for h in new_observations:
                prior = self._last_results[track_id]
                mean = prior["means"]
                covariance = prior["covariances"]
                gap = h["frame_idx"] - self._last_corrected_frame.get(track_id, -1)
                try:
                    # Coast across missed frames so the single reappearance update
                    # does not absorb the whole gap displacement as velocity.
                    for _ in range(max(0, gap - 1)):
                        mean, covariance = kf.filter_update(
                            mean, covariance, observation=np.ma.masked
                        )
                        mean = self._cap_velocity(mean, velocity_cap)
                    # Predict the observation frame to gate the measurement.
                    pred_mean, pred_cov = kf.filter_update(
                        mean, covariance, observation=np.ma.masked
                    )
                    pred_centroid = self._predicted_centroid(pred_mean)
                    obs_centroid = self._centroid(h["keypoints"])
                    gated_out = (
                        not np.isnan(pred_centroid).any()
                        and not np.isnan(obs_centroid).any()
                        and float(np.linalg.norm(pred_centroid - obs_centroid)) > gate
                    )
                    if gated_out:
                        # Reject the observation (likely a false positive / mismatch);
                        # carry the predict-only state forward as a miss.
                        mean, covariance = pred_mean, pred_cov
                    else:
                        mean, covariance = kf.filter_update(
                            mean,
                            covariance,
                            observation=self._obs_vector(h["keypoints"]),
                        )
                except Exception as e:  # pragma: no cover - numerical edge cases
                    logger.warning(
                        f"Kalman filter update failed for track {track_id}: {e}"
                    )
                    break
                self._last_results[track_id] = {
                    "means": self._cap_velocity(mean, velocity_cap),
                    "covariances": covariance,
                }
                self._last_corrected_frame[track_id] = h["frame_idx"]
                if not gated_out:
                    self._last_frame_for_track[track_id] = h["frame_idx"]

    def _reset_stale_tracks(self, frame_idx: int) -> None:
        """Reset filters for any track unseen for more than `kf_reset_gap_size` frames.

        A reset track drops its (now-unreliable) filter and falls back to the base
        feature path; `_init_missing_filters` re-fits it once it re-accumulates enough
        fresh contiguous history. Unlike the legacy `tracks_with_gap` rule, a single
        long occlusion is reset too, so a stale extrapolation cannot mis-associate the
        reappearing animal. `_reset_frame` is stamped so the next fit window starts
        fresh.
        """
        stale = [
            track_id
            for track_id, last in self._last_frame_for_track.items()
            if frame_idx - last > self.kf_reset_gap_size
        ]
        for track_id in stale:
            self._kalman_filters.pop(track_id, None)
            self._last_results.pop(track_id, None)
            self._last_frame_for_track.pop(track_id, None)
            self._last_corrected_frame.pop(track_id, None)
            self._median_step.pop(track_id, None)
            self._reset_frame[track_id] = frame_idx

    def _predict_candidates(
        self,
        candidates_list: Union[Deque, DefaultDict[int, Deque]],
        feature_method,
    ) -> Dict[int, List[TrackedInstanceFeature]]:
        """Build candidate features by rigidly translating the last observed pose.

        The centroid filter is projected forward from the last corrected state to the
        current frame (coasting across any gap), and the last observed body is
        translated by (a fraction of) the predicted centroid displacement. Translating
        the *real* last pose keeps the candidate rigid and geometrically valid, so the
        OKS / similarity score stays meaningful (predicting each keypoint
        independently produced non-physical poses that scored ~0 and randomized the
        assignment). Tracks without an active filter fall back to the base feature
        path so they remain trackable.
        """
        predicted = defaultdict(list)
        for track_id in self.candidate.current_tracks:
            kf = self._kalman_filters.get(track_id)
            prior = self._last_results.get(track_id)
            history = self._obs_history.get(track_id)
            if kf is None or prior is None or not history:
                predicted[track_id].extend(
                    self.candidate.get_features_from_track_id(track_id, candidates_list)
                )
                continue

            steps = max(
                1,
                self._current_frame_idx
                - self._last_corrected_frame.get(track_id, self._current_frame_idx - 1),
            )
            velocity_cap = self._velocity_cap(track_id)
            try:
                mean = prior["means"]
                covariance = prior["covariances"]
                for _ in range(steps):
                    mean, covariance = kf.filter_update(
                        mean, covariance, observation=np.ma.masked
                    )
                    mean = self._cap_velocity(mean, velocity_cap)
            except Exception as e:  # pragma: no cover - numerical edge cases
                logger.warning(f"Kalman prediction failed for track {track_id}: {e}")
                predicted[track_id].extend(
                    self.candidate.get_features_from_track_id(track_id, candidates_list)
                )
                continue

            ref = history[-1]
            last_keypoints = np.asarray(ref["keypoints"], dtype=float)
            blend = self.kf_prediction_blend
            pred_centroid = self._predicted_centroid(mean)
            last_centroid = self._centroid(last_keypoints)

            if np.isnan(pred_centroid).any() or np.isnan(last_centroid).any():
                candidate_keypoints = last_keypoints  # hold last (no valid prediction)
            elif self.kf_track_features == "keypoints":
                # Per-node mode: blend each tracked node's predicted position with its
                # last observed position; non-tracked nodes are translated rigidly by
                # the mean tracked displacement. Uses the pose directly (noisier than
                # the rigid centroid candidate), with a tolerant similarity score
                # (`oks_stddev`) or bbox/iou recommended.
                idx = self._resolved_node_indices
                pred_points = self._predicted_points(mean)  # (K, 2)
                last_tracked = last_keypoints[idx]
                disp = pred_points - last_tracked
                blended = last_tracked + blend * disp
                blended = np.where(np.isnan(blended), pred_points, blended)
                candidate_keypoints = last_keypoints.copy()
                candidate_keypoints[idx] = blended
                with warnings.catch_warnings():
                    warnings.simplefilter("ignore", category=RuntimeWarning)
                    mean_disp = np.nanmean(disp, axis=0)
                if not np.isnan(mean_disp).any():
                    mask = np.ones(self._n_nodes, dtype=bool)
                    mask[idx] = False
                    candidate_keypoints[mask] = last_keypoints[mask] + blend * mean_disp
            else:
                # Centroid mode: rigidly translate the last observed pose by a fraction
                # of the predicted centroid displacement. The weight is constant (NOT
                # scaled up with staleness): a coasting prediction is *less* reliable,
                # so amplifying it during gaps just injects swaps under noise.
                displacement = blend * (pred_centroid - last_centroid)
                candidate_keypoints = last_keypoints + displacement

            predicted[track_id].append(
                TrackedInstanceFeature(
                    feature=feature_method(candidate_keypoints),
                    src_predicted_instance=ref["src"],
                    frame_idx=ref["frame_idx"],
                    tracking_score=ref["score"] if ref["score"] is not None else 1.0,
                    shifted_keypoints=candidate_keypoints,
                )
            )
        return predicted

track(untracked_instances, frame_idx, image=None)

Record the frame index, run base tracking, then ingest the assignment.

Observations are recorded into _obs_history AFTER super().track() (i.e. after the current frame's track assignment is finalized) so each track id is associated with the instance it was actually matched to this frame, not a pre-assignment queue snapshot.

Source code in sleap_nn/tracking/tracker.py

def track(
    self,
    untracked_instances: List[sio.PredictedInstance],
    frame_idx: int,
    image: np.ndarray = None,
) -> List[sio.PredictedInstance]:
    """Record the frame index, run base tracking, then ingest the assignment.

    Observations are recorded into `_obs_history` AFTER `super().track()` (i.e.
    after the current frame's track assignment is finalized) so each track id is
    associated with the instance it was actually matched to this frame, not a
    pre-assignment queue snapshot.
    """
    self._current_frame_idx = int(frame_idx)
    result = super().track(untracked_instances, frame_idx, image)
    self._ingest_observations(self.candidate.tracker_queue)
    return result

update_candidates(candidates_list, image)

Return Kalman-predicted candidate features for the current frame.

During warm-up this delegates to the base keypoint-feature path. Once the filters are initialized, each track's filter is corrected (with measurement gating) by its newly observed keypoints, stale tracks are reset, filters are lazily (re)fit for tracks that lack one, and a motion-predicted pose blended with the last observation is returned as the candidate feature.

Parameters:

Name	Type	Description	Default
candidates_list	Union[Deque, DefaultDict[int, Deque]]	Tracker queue from the candidate class.	required
image	ndarray	Image of the current untracked frame (unused; Kalman tracking does not use image features).	required

Returns:

Type	Description
Dict[int, List[TrackedInstanceFeature]]	Dictionary with keys as track IDs and values as lists of TrackedInstanceFeature.

Source code in sleap_nn/tracking/tracker.py

def update_candidates(
    self,
    candidates_list: Union[Deque, DefaultDict[int, Deque]],
    image: np.ndarray,
) -> Dict[int, List[TrackedInstanceFeature]]:
    """Return Kalman-predicted candidate features for the current frame.

    During warm-up this delegates to the base keypoint-feature path. Once the
    filters are initialized, each track's filter is corrected (with measurement
    gating) by its newly observed keypoints, stale tracks are reset, filters are
    lazily (re)fit for tracks that lack one, and a motion-predicted pose blended
    with the last observation is returned as the candidate feature.

    Args:
        candidates_list: Tracker queue from the candidate class.
        image: Image of the current untracked frame (unused; Kalman tracking does
            not use image features).

    Returns:
        Dictionary with keys as track IDs and values as lists of
        `TrackedInstanceFeature`.
    """
    if self.features not in self._feature_methods:
        message = "Invalid `features` argument. Please provide one of `keypoints`, `centroids`, `bboxes`, `masks` and `image`"
        logger.error(message)
        raise ValueError(message)
    feature_method = self._feature_methods[self.features]

    if not self._initialized:
        self._frames_seen += 1
        if self._frames_seen >= self.kf_init_frame_count:
            self._init_filters()
        if not self._initialized:
            # Still warming up: behave exactly like the base tracker.
            return super().update_candidates(candidates_list, image)

    # Reset tracks that have gone stale (no *accepted* observation within
    # `kf_reset_gap_size` frames) BEFORE correcting, so a track that is only
    # receiving gated-out observations is dropped to the base path rather than
    # eventually corrupted by a stale-extrapolation match. Then correct matched
    # filters with gated observations, lazily (re)fit filters for tracks that lack
    # one, and predict for scoring.
    self._reset_stale_tracks(self._current_frame_idx)
    self._correct_filters()
    self._init_missing_filters()
    return self._predict_candidates(candidates_list, feature_method)

RateColumn

Bases: ProgressColumn

Renders the progress rate.

Methods:

Name	Description
render	Show progress rate.

Source code in sleap_nn/tracking/tracker.py

class RateColumn(rich.progress.ProgressColumn):
    """Renders the progress rate."""

    def render(self, task: "Task") -> rich.progress.Text:
        """Show progress rate."""
        speed = task.speed
        if speed is None:
            return rich.progress.Text("?", style="progress.data.speed")
        return rich.progress.Text(f"{speed:.1f} frames/s", style="progress.data.speed")

render(task)

Show progress rate.

Source code in sleap_nn/tracking/tracker.py

def render(self, task: "Task") -> rich.progress.Text:
    """Show progress rate."""
    speed = task.speed
    if speed is None:
        return rich.progress.Text("?", style="progress.data.speed")
    return rich.progress.Text(f"{speed:.1f} frames/s", style="progress.data.speed")

Tracker

Simple Pose Tracker.

This is the base class for all Trackers. This module handles tracking instances across frames by creating new track IDs (or) assigning track IDs to each predicted instance when the .track() is called. This class is initialized in the Predictor classes.

Attributes:

Name	Type	Description
candidate	Union[FixedWindowCandidates, LocalQueueCandidates]	Instance of either FixedWindowCandidates or LocalQueueCandidates.
min_match_points	int	Minimum support for match candidates: non-NaN keypoints, or foreground area (px) for features="masks". Default: 0.
features	str	Feature representation for the candidates to update current detections. One of [keypoints, centroids, bboxes, masks, image]. masks tracks bottom-up segmentation PredictedSegmentationMask objects. Default: keypoints.
scoring_method	str	Method to compute association score between features from the current frame and the previous tracks. One of [oks, cosine_sim, iou, mask_iou, euclidean_dist]. mask_iou is the pixel IoU between two segmentation masks (pair with features="masks"). Default: oks.
scoring_reduction	str	Method to aggregate and reduce multiple scores if there are several detections associated with the same track. One of [mean, max, robust_quantile]. Default: mean.
track_matching_method	str	Track matching algorithm. One of hungarian, greedy. Default:hungarian`.
robust_best_instance	float	If the value is between 0 and 1 (excluded), use a robust quantile similarity score for the track. If the value is 1, use the max similarity (non-robust). For selecting a robust score, 0.95 is a good value.
use_flow	bool	If True, FlowShiftTracker is used, where the poses are matched using optical flow shifts. Default: False.
is_local_queue	bool	True if LocalQueueCandidates is used else False.

Methods:

Name	Description
assign_tracks	Assign track IDs using Hungarian method.
from_config	Create Tracker from config.
generate_candidates	Get the tracked instances from tracker queue.
get_features	Get features for the current untracked instances.
get_scores	Compute association score between untracked and tracked instances.
scores_to_cost_matrix	Converts scores matrix to cost matrix for track assignments.
track	Assign track IDs to the untracked list of sio.PredictedInstance objects.
update_candidates	Return dictionary with the features of tracked instances.

Source code in sleap_nn/tracking/tracker.py

@attrs.define
class Tracker:
    """Simple Pose Tracker.

    This is the base class for all Trackers. This module handles tracking instances
    across frames by creating new track IDs (or) assigning track IDs to each predicted
    instance when the `.track()` is called. This class is initialized in the `Predictor`
    classes.

    Attributes:
        candidate: Instance of either `FixedWindowCandidates` or `LocalQueueCandidates`.
        min_match_points: Minimum support for match candidates: non-NaN keypoints,
            or foreground area (px) for `features="masks"`. Default: 0.
        features: Feature representation for the candidates to update current detections.
            One of [`keypoints`, `centroids`, `bboxes`, `masks`, `image`]. `masks`
            tracks bottom-up segmentation `PredictedSegmentationMask` objects.
            Default: `keypoints`.
        scoring_method: Method to compute association score between features from the
            current frame and the previous tracks. One of [`oks`, `cosine_sim`, `iou`,
            `mask_iou`, `euclidean_dist`]. `mask_iou` is the pixel IoU between two
            segmentation masks (pair with `features="masks"`). Default: `oks`.
        scoring_reduction: Method to aggregate and reduce multiple scores if there are
            several detections associated with the same track. One of [`mean`, `max`,
            `robust_quantile`]. Default: `mean`.
        track_matching_method: Track matching algorithm. One of `hungarian`, `greedy.
            Default: `hungarian`.
        robust_best_instance: If the value is between 0 and 1
            (excluded), use a robust quantile similarity score for the
            track. If the value is 1, use the max similarity (non-robust).
            For selecting a robust score, 0.95 is a good value.
        use_flow: If True, `FlowShiftTracker` is used, where the poses are matched using
            optical flow shifts. Default: `False`.
        is_local_queue: `True` if `LocalQueueCandidates` is used else `False`.

    """

    candidate: Union[FixedWindowCandidates, LocalQueueCandidates] = (
        FixedWindowCandidates()
    )
    min_match_points: int = 0
    features: str = "keypoints"
    scoring_method: str = "oks"
    scoring_reduction: str = "mean"
    track_matching_method: str = "hungarian"
    robust_best_instance: float = 1.0
    oks_stddev: float = 0.025
    use_flow: bool = False
    is_local_queue: bool = False
    tracking_target_instance_count: Optional[int] = None
    tracking_pre_cull_to_target: int = 0
    tracking_pre_cull_iou_threshold: float = 0
    _scoring_functions: Dict[str, Any] = {
        "oks": compute_oks,
        "iou": compute_iou,
        "mask_iou": compute_mask_iou,
        "cosine_sim": compute_cosine_sim,
        "euclidean_dist": compute_euclidean_distance,
    }
    _scoring_reduction_methods: Dict[str, Any] = {
        "mean": np.nanmean,
        "max": np.nanmax,
        # `robust_quantile` is resolved per-instance in `get_scores` so it honors
        # `self.robust_best_instance`; this entry only registers the valid key
        # (a class-level functools.partial would freeze `q` at the class default).
        "robust_quantile": np.nanmax,
    }
    _feature_methods: Dict[str, Any] = {
        "keypoints": get_keypoints,
        "centroids": get_centroid,
        "bboxes": get_bbox,
        "masks": get_mask,
    }
    _track_matching_methods: Dict[str, Any] = {
        "hungarian": hungarian_matching,
        "greedy": greedy_matching,
    }
    _track_objects: Dict[int, sio.Track] = attrs.field(factory=dict)

    @classmethod
    def from_config(
        cls,
        window_size: int = 5,
        min_new_track_points: int = 0,
        candidates_method: str = "fixed_window",
        min_match_points: int = 0,
        features: str = "keypoints",
        scoring_method: str = "oks",
        scoring_reduction: str = "mean",
        robust_best_instance: float = 1.0,
        oks_stddev: Optional[float] = None,
        track_matching_method: str = "hungarian",
        max_tracks: Optional[int] = None,
        use_flow: bool = False,
        of_img_scale: float = 1.0,
        of_window_size: int = 21,
        of_max_levels: int = 3,
        use_kalman: bool = False,
        kf_track_features: str = "centroid",
        kf_init_frame_count: int = 10,
        kf_node_indices: Optional[List[int]] = None,
        kf_reset_gap_size: int = 5,
        kf_prediction_blend: float = 0.5,
        kf_gate_step_mult: float = 8.0,
        kf_min_gate_px: float = 40.0,
        kf_velocity_cap_mult: float = 3.0,
        kf_min_velocity_cap_px: float = 15.0,
        tracking_target_instance_count: Optional[int] = None,
        tracking_pre_cull_to_target: int = 0,
        tracking_pre_cull_iou_threshold: float = 0,
    ):
        """Create `Tracker` from config.

        Args:
            window_size: Number of frames to look for in the candidate instances to match
                with the current detections. Default: 5.
            min_new_track_points: We won't spawn a new track for an instance with
                fewer than this many non-nan points (for `features="masks"`, this
                is read as a foreground-area floor in px). Default: 0.
            candidates_method: Either of `fixed_window` or `local_queues`. In fixed window
                method, candidates from the last `window_size` frames. In local queues,
                last `window_size` instances for each track ID is considered for matching
                against the current detection. Default: `fixed_window`.
            min_match_points: Minimum support for match candidates: non-NaN
                keypoints, or foreground area (px) for `features="masks"`. Default: 0.
            features: Feature representation for the candidates to update current detections.
                One of [`keypoints`, `centroids`, `bboxes`, `masks`, `image`].
                Default: `keypoints`.
            scoring_method: Method to compute association score between features from the
                current frame and the previous tracks. One of [`oks`, `cosine_sim`, `iou`,
                `mask_iou`, `euclidean_dist`]. Default: `oks`.
            scoring_reduction: Method to aggregate and reduce multiple scores if there are
                several detections associated with the same track. One of [`mean`, `max`,
                `robust_quantile`]. Default: `mean`.
            robust_best_instance: If the value is between 0 and 1
                (excluded), use a robust quantile similarity score for the
                track. If the value is 1, use the max similarity (non-robust).
                For selecting a robust score, 0.95 is a good value.
            track_matching_method: Track matching algorithm. One of `hungarian`, `greedy.
                Default: `hungarian`.
            max_tracks: Maximum number of new tracks to be created to avoid redundant
                tracks. Honored only by the `local_queues` candidate maker; setting it
                with `candidates_method="fixed_window"` auto-switches the method to
                `local_queues` (logged at INFO) so the cap is enforced. Default: None.
            use_flow: If True, `FlowShiftTracker` is used, where the poses are matched using
            optical flow shifts. Default: `False`.
            of_img_scale: Factor to scale the images by when computing optical flow. Decrease
                this to increase performance at the cost of finer accuracy. Sometimes
                decreasing the image scale can improve performance with fast movements.
                Default: 1.0. (only if `use_flow` is True)
            of_window_size: Optical flow window size to consider at each pyramid scale
                level. Default: 21. (only if `use_flow` is True)
            of_max_levels: Number of pyramid scale levels to consider. This is different
                from the scale parameter, which determines the initial image scaling.
                Default: 3. (only if `use_flow` is True)
            oks_stddev: Keypoint-spread normalization constant for `oks` scoring;
                larger is more tolerant of localization error. `None` (default)
                auto-resolves to 0.1 for `kf_track_features="keypoints"` (whose per-node
                prediction is noisier) and 0.025 otherwise.
            use_kalman: If True, `KalmanShiftTracker` is used, where poses are predicted
                with a per-track constant-velocity Kalman filter. Requires
                `tracking_target_instance_count` (or `max_tracks`) and is mutually
                exclusive with `use_flow`. Default: `False`.
            kf_track_features: What the Kalman motion model tracks: `centroid` (default;
                rigid translation of the last pose) or `keypoints` (per-node poses;
                noisier, pair with a larger `oks_stddev` or `features="bboxes"` +
                `scoring_method="iou"`). (only if `use_kalman` is True)
            kf_init_frame_count: Number of warm-up frames tracked with the base path
                before the Kalman filters are fit via EM. Default: 10.
                (only if `use_kalman` is True)
            kf_node_indices: Skeleton node (row) indices to track with the motion model.
                `None` uses all nodes. Default: None. (only if `use_kalman` is True)
            kf_reset_gap_size: Number of consecutive missed frames after which a stale
                track's filter is reset. Default: 5. (only if `use_kalman` is True)
            kf_prediction_blend: Weight of the motion prediction when blending with the
                last observation to form the scoring candidate. Default: 0.5.
                (only if `use_kalman` is True)
            kf_gate_step_mult: Measurement gate as a multiple of the track's median
                step. Default: 8.0. (only if `use_kalman` is True)
            kf_min_gate_px: Floor (px) for the measurement gate. Default: 40.0.
                (only if `use_kalman` is True)
            kf_velocity_cap_mult: Cap on learned velocity as a multiple of the track's
                median step. Default: 3.0. (only if `use_kalman` is True)
            kf_min_velocity_cap_px: Floor (px/frame) for the velocity cap. Default: 15.0.
                (only if `use_kalman` is True)
            tracking_target_instance_count: Target number of instances to track per frame. (default: None)
            tracking_pre_cull_to_target: If non-zero and target_instance_count is also non-zero, then cull instances over target count per frame *before* tracking. (default: 0)
            tracking_pre_cull_iou_threshold: If non-zero and pre_cull_to_target also set, then use IOU threshold to remove overlapping instances over count *before* tracking. (default: 0)

        """
        # `max_tracks` is enforced only by the `local_queues` candidate maker
        # (`LocalQueueCandidates.get_new_track_id` returns `None` past the cap);
        # `fixed_window` silently ignores it and mints unbounded track IDs. When a
        # caller asks for a track cap under `fixed_window`, switch to `local_queues`
        # -- the candidate method designed for a fixed identity count -- so the cap
        # is actually honored. This is the universal safety net: every tracking
        # entry point (CLI, `run_inference`/`run_tracker`, `apply_tracking`, direct
        # API use) flows through `from_config` (sleap#2720, #582).
        if max_tracks is not None and candidates_method == "fixed_window":
            logger.info(
                "max_tracks=%s was set with candidates_method='fixed_window', which "
                "ignores it; switching to candidates_method='local_queues' to honor "
                "the track cap.",
                max_tracks,
            )
            candidates_method = "local_queues"

        if candidates_method == "fixed_window":
            candidate = FixedWindowCandidates(
                window_size=window_size,
                min_new_track_points=min_new_track_points,
            )
            is_local_queue = False

        elif candidates_method == "local_queues":
            candidate = LocalQueueCandidates(
                window_size=window_size,
                max_tracks=max_tracks,
                min_new_track_points=min_new_track_points,
            )
            is_local_queue = True

        else:
            message = f"{candidates_method} is not a valid method. Please choose one of [`fixed_window`, `local_queues`]"
            logger.error(message)
            raise ValueError(message)

        if use_kalman and use_flow:
            message = (
                "`use_kalman` and `use_flow` are mutually exclusive; choose one "
                "tracker (Kalman tracking does not use optical flow)."
            )
            logger.error(message)
            raise ValueError(message)

        if use_kalman and tracking_target_instance_count is None and max_tracks is None:
            message = (
                "Kalman tracking requires a known target identity count: pass "
                "`tracking_target_instance_count` (or `max_tracks` / `--max_instances`)."
            )
            logger.error(message)
            raise ValueError(message)

        if use_kalman and kf_track_features not in ("centroid", "keypoints"):
            message = (
                f"Invalid kf_track_features={kf_track_features!r}; choose 'centroid' "
                "(default) or 'keypoints'."
            )
            logger.error(message)
            raise ValueError(message)

        # Resolve the OKS tolerance: the per-node 'keypoints' prediction is noisier, so
        # the strict default stddev (0.025) collapses its similarity scores; default it
        # to 0.1 (validated on synthetic + real data). Centroid/base keep 0.025. An
        # explicit oks_stddev always wins.
        if oks_stddev is None:
            oks_stddev = (
                0.1 if (use_kalman and kf_track_features == "keypoints") else 0.025
            )

        if use_kalman:
            return KalmanShiftTracker(
                candidate=candidate,
                min_match_points=min_match_points,
                features=features,
                scoring_method=scoring_method,
                scoring_reduction=scoring_reduction,
                robust_best_instance=robust_best_instance,
                oks_stddev=oks_stddev,
                track_matching_method=track_matching_method,
                kf_track_features=kf_track_features,
                kf_init_frame_count=kf_init_frame_count,
                kf_node_indices=kf_node_indices,
                kf_reset_gap_size=kf_reset_gap_size,
                kf_prediction_blend=kf_prediction_blend,
                kf_gate_step_mult=kf_gate_step_mult,
                kf_min_gate_px=kf_min_gate_px,
                kf_velocity_cap_mult=kf_velocity_cap_mult,
                kf_min_velocity_cap_px=kf_min_velocity_cap_px,
                is_local_queue=is_local_queue,
                tracking_target_instance_count=tracking_target_instance_count,
                tracking_pre_cull_to_target=tracking_pre_cull_to_target,
                tracking_pre_cull_iou_threshold=tracking_pre_cull_iou_threshold,
            )

        if use_flow:
            return FlowShiftTracker(
                candidate=candidate,
                min_match_points=min_match_points,
                features=features,
                scoring_method=scoring_method,
                scoring_reduction=scoring_reduction,
                robust_best_instance=robust_best_instance,
                oks_stddev=oks_stddev,
                track_matching_method=track_matching_method,
                img_scale=of_img_scale,
                of_window_size=of_window_size,
                of_max_levels=of_max_levels,
                is_local_queue=is_local_queue,
                tracking_target_instance_count=tracking_target_instance_count,
                tracking_pre_cull_to_target=tracking_pre_cull_to_target,
                tracking_pre_cull_iou_threshold=tracking_pre_cull_iou_threshold,
            )

        tracker = cls(
            candidate=candidate,
            min_match_points=min_match_points,
            features=features,
            scoring_method=scoring_method,
            scoring_reduction=scoring_reduction,
            robust_best_instance=robust_best_instance,
            oks_stddev=oks_stddev,
            track_matching_method=track_matching_method,
            use_flow=use_flow,
            is_local_queue=is_local_queue,
            tracking_target_instance_count=tracking_target_instance_count,
            tracking_pre_cull_to_target=tracking_pre_cull_to_target,
            tracking_pre_cull_iou_threshold=tracking_pre_cull_iou_threshold,
        )
        return tracker

    def track(
        self,
        untracked_instances: List[sio.PredictedInstance],
        frame_idx: int,
        image: np.ndarray = None,
    ) -> List[sio.PredictedInstance]:
        """Assign track IDs to the untracked list of `sio.PredictedInstance` objects.

        Args:
            untracked_instances: List of untracked `sio.PredictedInstance` objects.
            frame_idx: Frame index of the predicted instances.
            image: Source image if visual features are to be used (also when using flow).

        Returns:
            List of `sio.PredictedInstance` objects, each having an assigned track.
        """
        # Pre-cull is pose-only (cull_frame_instances uses same_pose_as / bbox);
        # segmentation masks are scoped out of cull for the MVP (apply_tracking
        # rejects the pre-cull flags in mask mode, so this is belt-and-braces).
        masks_input = bool(untracked_instances) and is_segmentation_mask(
            untracked_instances[0]
        )
        if (
            not masks_input
            and self.tracking_target_instance_count is not None
            and self.tracking_target_instance_count
            and self.tracking_pre_cull_to_target
        ):
            untracked_instances = cull_frame_instances(
                untracked_instances,
                self.tracking_target_instance_count,
                self.tracking_pre_cull_iou_threshold,
            )
        # get features for the untracked instances.
        current_instances = self.get_features(untracked_instances, frame_idx, image)

        candidates_list = (
            self.generate_candidates()
        )  # either Deque/ DefaultDict for FixedWindow/ LocalQueue candidate.

        if candidates_list:
            # if track queue is not empty

            # update candidates if needed and get the features from previous tracked instances.
            candidates_feature_dict = self.update_candidates(candidates_list, image)

            # scoring function
            scores = self.get_scores(current_instances, candidates_feature_dict)
            cost_matrix = self.scores_to_cost_matrix(scores)

            # track assignment
            current_tracked_instances = self.assign_tracks(
                current_instances, cost_matrix
            )

        else:
            # Initialize the tracker queue if empty.
            current_tracked_instances = self.candidate.add_new_tracks(current_instances)

        # convert the `current_instances` back to `List[sio.PredictedInstance]` objects.
        if self.is_local_queue:
            new_pred_instances = []
            for instance in current_tracked_instances:
                if instance.track_id is not None:
                    if instance.track_id not in self._track_objects:
                        self._track_objects[instance.track_id] = sio.Track(
                            f"track_{instance.track_id}"
                        )
                    instance.src_instance.track = self._track_objects[instance.track_id]
                    instance.src_instance.tracking_score = instance.tracking_score
                new_pred_instances.append(instance.src_instance)

        else:
            new_pred_instances = []
            for idx, inst in enumerate(current_tracked_instances.src_instances):
                track_id = current_tracked_instances.track_ids[idx]
                if track_id is not None:
                    if track_id not in self._track_objects:
                        self._track_objects[track_id] = sio.Track(f"track_{track_id}")
                    inst.track = self._track_objects[track_id]
                    inst.tracking_score = current_tracked_instances.tracking_scores[idx]
                    new_pred_instances.append(inst)

        return new_pred_instances

    def get_features(
        self,
        untracked_instances: List[sio.PredictedInstance],
        frame_idx: int,
        image: np.ndarray = None,
    ) -> Union[TrackInstances, List[TrackInstanceLocalQueue]]:
        """Get features for the current untracked instances.

        The feature can either be an embedding of cropped image around each instance (visual feature),
        the bounding box coordinates, or centroids, or the poses as a feature.

        Args:
            untracked_instances: List of untracked `sio.PredictedInstance` objects.
            frame_idx: Frame index of the current untracked instances.
            image: Image of the current frame if visual features are to be used.

        Returns:
            `TrackInstances` object or `List[TrackInstanceLocalQueue]` with the features
            assigned for the untracked instances and track_id set as `None`.
        """
        if self.features not in self._feature_methods:
            message = "Invalid `features` argument. Please provide one of `keypoints`, `centroids`, `bboxes`, `masks` and `image`"
            logger.error(message)
            raise ValueError(message)

        feature_method = self._feature_methods[self.features]
        feature_list = []
        for pred_instance in untracked_instances:
            feature_list.append(feature_method(pred_instance))

        current_instances = self.candidate.get_track_instances(
            feature_list, untracked_instances, frame_idx=frame_idx, image=image
        )

        return current_instances

    def generate_candidates(self):
        """Get the tracked instances from tracker queue."""
        return self.candidate.tracker_queue

    def update_candidates(
        self, candidates_list: Union[Deque, DefaultDict[int, Deque]], image: np.ndarray
    ) -> Dict[int, TrackedInstanceFeature]:
        """Return dictionary with the features of tracked instances.

        Args:
            candidates_list: List of tracked instances from tracker queue to consider.
            image: Image of the current untracked frame. (used for flow shift tracker)

        Returns:
            Dictionary with keys as track IDs and values as the list of `TrackedInstanceFeature`.
        """
        candidates_feature_dict = defaultdict(list)
        for track_id in self.candidate.current_tracks:
            candidates_feature_dict[track_id].extend(
                self.candidate.get_features_from_track_id(track_id, candidates_list)
            )
        return candidates_feature_dict

    def get_scores(
        self,
        current_instances: Union[TrackInstances, List[TrackInstanceLocalQueue]],
        candidates_feature_dict: Dict[int, TrackedInstanceFeature],
    ):
        """Compute association score between untracked and tracked instances.

        For visual feature vectors, this can be `cosine_sim`, for bounding boxes
        it could be `iou`, for centroids it could be `euclidean_dist`, and for poses it
        could be `oks`.

        Args:
            current_instances: `TrackInstances` object or `List[TrackInstanceLocalQueue]`
                with features and unassigned tracks.
            candidates_feature_dict: Dictionary with keys as track IDs and values as the
                list of `TrackedInstanceFeature`.

        Returns:
            scores: Score matrix of shape (num_new_instances, num_existing_tracks)
        """
        if self.scoring_method not in self._scoring_functions:
            message = "Invalid `scoring_method` argument. Please provide one of `oks`, `cosine_sim`, `iou`, `mask_iou`, and `euclidean_dist`."
            logger.error(message)
            raise ValueError(message)

        if self.scoring_reduction not in self._scoring_reduction_methods:
            message = "Invalid `scoring_reduction` argument. Please provide one of `mean`, `max`, and `robust_quantile`."
            logger.error(message)
            raise ValueError(message)

        scoring_method = self._scoring_functions[self.scoring_method]
        if self.scoring_method == "oks":
            # OKS tolerance is configurable: a larger stddev is more forgiving of
            # localization error, which matters for the noisier per-keypoint Kalman
            # prediction (`kf_track_features="keypoints"`).
            scoring_method = functools.partial(compute_oks, stddev=self.oks_stddev)
        scoring_reduction = self._scoring_reduction_methods[self.scoring_reduction]
        if self.scoring_reduction == "robust_quantile":
            # Resolve at runtime so the per-instance `robust_best_instance` is
            # honored (a class-level partial freezes `q` at the class default).
            # `nanquantile` matches the NaN-handling of `nanmean`/`nanmax`.
            scoring_reduction = functools.partial(
                np.nanquantile, q=self.robust_best_instance
            )

        # Get list of features for the `current_instances`.
        if self.is_local_queue:
            current_instances_features = [x.feature for x in current_instances]
        else:
            current_instances_features = [x for x in current_instances.features]

        scores = np.zeros(
            (len(current_instances_features), len(self.candidate.current_tracks))
        )

        for f_idx, f in enumerate(current_instances_features):
            for t_idx, track_id in enumerate(self.candidate.current_tracks):
                scores_trackid = [
                    scoring_method(f, x.feature)
                    for x in candidates_feature_dict[track_id]
                    if count_valid_points(x.src_predicted_instance)
                    > self.min_match_points  # candidates with min support (non-NaN
                    # keypoints, or mask area px for segmentation masks)
                ]
                # An empty candidate list (all filtered by `min_match_points`)
                # reduces to NaN (-> inf cost in `scores_to_cost_matrix`); guard
                # explicitly because `np.nanmax([])` raises (`np.nanmean([])` /
                # `np.nanquantile([])` return NaN, but `max` must not crash).
                score_trackid = (
                    np.nan if not scores_trackid else scoring_reduction(scores_trackid)
                )
                scores[f_idx][t_idx] = score_trackid

        return scores

    def scores_to_cost_matrix(self, scores: np.ndarray):
        """Converts `scores` matrix to cost matrix for track assignments."""
        cost_matrix = -scores
        cost_matrix[np.isnan(cost_matrix)] = np.inf
        return cost_matrix

    def assign_tracks(
        self,
        current_instances: Union[TrackInstances, List[TrackInstanceLocalQueue]],
        cost_matrix: np.ndarray,
    ) -> Union[TrackInstances, List[TrackInstanceLocalQueue]]:
        """Assign track IDs using Hungarian method.

        Args:
            current_instances: `TrackInstances` object or `List[TrackInstanceLocalQueue]`
                with features and unassigned tracks.
            cost_matrix: Cost matrix of shape (num_new_instances, num_existing_tracks).

        Returns:
            `TrackInstances` object or `List[TrackInstanceLocalQueue]`objects with
                track IDs assigned.
        """
        if self.track_matching_method not in self._track_matching_methods:
            message = "Invalid `track_matching_method` argument. Please provide one of `hungarian`, and `greedy`."
            logger.error(message)
            raise ValueError(message)

        matching_method = self._track_matching_methods[self.track_matching_method]

        row_inds, col_inds = matching_method(cost_matrix)
        tracking_scores = [
            -cost_matrix[row, col] for row, col in zip(row_inds, col_inds)
        ]

        # update the candidates tracker queue with the newly tracked instances and assign
        # track IDs to `current_instances`.
        current_tracked_instances = self.candidate.update_tracks(
            current_instances, row_inds, col_inds, tracking_scores
        )

        return current_tracked_instances

assign_tracks(current_instances, cost_matrix)

Assign track IDs using Hungarian method.

Parameters:

Name	Type	Description	Default
current_instances	Union[TrackInstances, List[TrackInstanceLocalQueue]]	TrackInstances object or List[TrackInstanceLocalQueue] with features and unassigned tracks.	required
cost_matrix	ndarray	Cost matrix of shape (num_new_instances, num_existing_tracks).	required

Returns:

Type	Description
Union[TrackInstances, List[TrackInstanceLocalQueue]]	TrackInstances object or List[TrackInstanceLocalQueue]objects with track IDs assigned.

Source code in sleap_nn/tracking/tracker.py

def assign_tracks(
    self,
    current_instances: Union[TrackInstances, List[TrackInstanceLocalQueue]],
    cost_matrix: np.ndarray,
) -> Union[TrackInstances, List[TrackInstanceLocalQueue]]:
    """Assign track IDs using Hungarian method.

    Args:
        current_instances: `TrackInstances` object or `List[TrackInstanceLocalQueue]`
            with features and unassigned tracks.
        cost_matrix: Cost matrix of shape (num_new_instances, num_existing_tracks).

    Returns:
        `TrackInstances` object or `List[TrackInstanceLocalQueue]`objects with
            track IDs assigned.
    """
    if self.track_matching_method not in self._track_matching_methods:
        message = "Invalid `track_matching_method` argument. Please provide one of `hungarian`, and `greedy`."
        logger.error(message)
        raise ValueError(message)

    matching_method = self._track_matching_methods[self.track_matching_method]

    row_inds, col_inds = matching_method(cost_matrix)
    tracking_scores = [
        -cost_matrix[row, col] for row, col in zip(row_inds, col_inds)
    ]

    # update the candidates tracker queue with the newly tracked instances and assign
    # track IDs to `current_instances`.
    current_tracked_instances = self.candidate.update_tracks(
        current_instances, row_inds, col_inds, tracking_scores
    )

    return current_tracked_instances

from_config(window_size=5, min_new_track_points=0, candidates_method='fixed_window', min_match_points=0, features='keypoints', scoring_method='oks', scoring_reduction='mean', robust_best_instance=1.0, oks_stddev=None, track_matching_method='hungarian', max_tracks=None, use_flow=False, of_img_scale=1.0, of_window_size=21, of_max_levels=3, use_kalman=False, kf_track_features='centroid', kf_init_frame_count=10, kf_node_indices=None, kf_reset_gap_size=5, kf_prediction_blend=0.5, kf_gate_step_mult=8.0, kf_min_gate_px=40.0, kf_velocity_cap_mult=3.0, kf_min_velocity_cap_px=15.0, tracking_target_instance_count=None, tracking_pre_cull_to_target=0, tracking_pre_cull_iou_threshold=0) classmethod

Create Tracker from config.

Parameters:

Name	Type	Description	Default
window_size	int	Number of frames to look for in the candidate instances to match with the current detections. Default: 5.	5
min_new_track_points	int	We won't spawn a new track for an instance with fewer than this many non-nan points (for features="masks", this is read as a foreground-area floor in px). Default: 0.	0
candidates_method	str	Either of fixed_window or local_queues. In fixed window method, candidates from the last window_size frames. In local queues, last window_size instances for each track ID is considered for matching against the current detection. Default: fixed_window.	'fixed_window'
min_match_points	int	Minimum support for match candidates: non-NaN keypoints, or foreground area (px) for features="masks". Default: 0.	0
features	str	Feature representation for the candidates to update current detections. One of [keypoints, centroids, bboxes, masks, image]. Default: keypoints.	'keypoints'
scoring_method	str	Method to compute association score between features from the current frame and the previous tracks. One of [oks, cosine_sim, iou, mask_iou, euclidean_dist]. Default: oks.	'oks'
scoring_reduction	str	Method to aggregate and reduce multiple scores if there are several detections associated with the same track. One of [mean, max, robust_quantile]. Default: mean.	'mean'
robust_best_instance	float	If the value is between 0 and 1 (excluded), use a robust quantile similarity score for the track. If the value is 1, use the max similarity (non-robust). For selecting a robust score, 0.95 is a good value.	1.0
track_matching_method	str	Track matching algorithm. One of hungarian, greedy. Default:hungarian`.	'hungarian'
max_tracks	Optional[int]	Maximum number of new tracks to be created to avoid redundant tracks. Honored only by the local_queues candidate maker; setting it with candidates_method="fixed_window" auto-switches the method to local_queues (logged at INFO) so the cap is enforced. Default: None.	None
use_flow	bool	If True, FlowShiftTracker is used, where the poses are matched using	False
optical flow shifts. Default		False.	required
of_img_scale	float	Factor to scale the images by when computing optical flow. Decrease this to increase performance at the cost of finer accuracy. Sometimes decreasing the image scale can improve performance with fast movements. Default: 1.0. (only if use_flow is True)	1.0
of_window_size	int	Optical flow window size to consider at each pyramid scale level. Default: 21. (only if use_flow is True)	21
of_max_levels	int	Number of pyramid scale levels to consider. This is different from the scale parameter, which determines the initial image scaling. Default: 3. (only if use_flow is True)	3
oks_stddev	Optional[float]	Keypoint-spread normalization constant for oks scoring; larger is more tolerant of localization error. None (default) auto-resolves to 0.1 for kf_track_features="keypoints" (whose per-node prediction is noisier) and 0.025 otherwise.	None
use_kalman	bool	If True, KalmanShiftTracker is used, where poses are predicted with a per-track constant-velocity Kalman filter. Requires tracking_target_instance_count (or max_tracks) and is mutually exclusive with use_flow. Default: False.	False
kf_track_features	str	What the Kalman motion model tracks: centroid (default; rigid translation of the last pose) or keypoints (per-node poses; noisier, pair with a larger oks_stddev or features="bboxes" + scoring_method="iou"). (only if use_kalman is True)	'centroid'
kf_init_frame_count	int	Number of warm-up frames tracked with the base path before the Kalman filters are fit via EM. Default: 10. (only if use_kalman is True)	10
kf_node_indices	Optional[List[int]]	Skeleton node (row) indices to track with the motion model. None uses all nodes. Default: None. (only if use_kalman is True)	None
kf_reset_gap_size	int	Number of consecutive missed frames after which a stale track's filter is reset. Default: 5. (only if use_kalman is True)	5
kf_prediction_blend	float	Weight of the motion prediction when blending with the last observation to form the scoring candidate. Default: 0.5. (only if use_kalman is True)	0.5
kf_gate_step_mult	float	Measurement gate as a multiple of the track's median step. Default: 8.0. (only if use_kalman is True)	8.0
kf_min_gate_px	float	Floor (px) for the measurement gate. Default: 40.0. (only if use_kalman is True)	40.0
kf_velocity_cap_mult	float	Cap on learned velocity as a multiple of the track's median step. Default: 3.0. (only if use_kalman is True)	3.0
kf_min_velocity_cap_px	float	Floor (px/frame) for the velocity cap. Default: 15.0. (only if use_kalman is True)	15.0
tracking_target_instance_count	Optional[int]	Target number of instances to track per frame. (default: None)	None
tracking_pre_cull_to_target	int	If non-zero and target_instance_count is also non-zero, then cull instances over target count per frame before tracking. (default: 0)	0
tracking_pre_cull_iou_threshold	float	If non-zero and pre_cull_to_target also set, then use IOU threshold to remove overlapping instances over count before tracking. (default: 0)	0

Source code in sleap_nn/tracking/tracker.py

@classmethod
def from_config(
    cls,
    window_size: int = 5,
    min_new_track_points: int = 0,
    candidates_method: str = "fixed_window",
    min_match_points: int = 0,
    features: str = "keypoints",
    scoring_method: str = "oks",
    scoring_reduction: str = "mean",
    robust_best_instance: float = 1.0,
    oks_stddev: Optional[float] = None,
    track_matching_method: str = "hungarian",
    max_tracks: Optional[int] = None,
    use_flow: bool = False,
    of_img_scale: float = 1.0,
    of_window_size: int = 21,
    of_max_levels: int = 3,
    use_kalman: bool = False,
    kf_track_features: str = "centroid",
    kf_init_frame_count: int = 10,
    kf_node_indices: Optional[List[int]] = None,
    kf_reset_gap_size: int = 5,
    kf_prediction_blend: float = 0.5,
    kf_gate_step_mult: float = 8.0,
    kf_min_gate_px: float = 40.0,
    kf_velocity_cap_mult: float = 3.0,
    kf_min_velocity_cap_px: float = 15.0,
    tracking_target_instance_count: Optional[int] = None,
    tracking_pre_cull_to_target: int = 0,
    tracking_pre_cull_iou_threshold: float = 0,
):
    """Create `Tracker` from config.

    Args:
        window_size: Number of frames to look for in the candidate instances to match
            with the current detections. Default: 5.
        min_new_track_points: We won't spawn a new track for an instance with
            fewer than this many non-nan points (for `features="masks"`, this
            is read as a foreground-area floor in px). Default: 0.
        candidates_method: Either of `fixed_window` or `local_queues`. In fixed window
            method, candidates from the last `window_size` frames. In local queues,
            last `window_size` instances for each track ID is considered for matching
            against the current detection. Default: `fixed_window`.
        min_match_points: Minimum support for match candidates: non-NaN
            keypoints, or foreground area (px) for `features="masks"`. Default: 0.
        features: Feature representation for the candidates to update current detections.
            One of [`keypoints`, `centroids`, `bboxes`, `masks`, `image`].
            Default: `keypoints`.
        scoring_method: Method to compute association score between features from the
            current frame and the previous tracks. One of [`oks`, `cosine_sim`, `iou`,
            `mask_iou`, `euclidean_dist`]. Default: `oks`.
        scoring_reduction: Method to aggregate and reduce multiple scores if there are
            several detections associated with the same track. One of [`mean`, `max`,
            `robust_quantile`]. Default: `mean`.
        robust_best_instance: If the value is between 0 and 1
            (excluded), use a robust quantile similarity score for the
            track. If the value is 1, use the max similarity (non-robust).
            For selecting a robust score, 0.95 is a good value.
        track_matching_method: Track matching algorithm. One of `hungarian`, `greedy.
            Default: `hungarian`.
        max_tracks: Maximum number of new tracks to be created to avoid redundant
            tracks. Honored only by the `local_queues` candidate maker; setting it
            with `candidates_method="fixed_window"` auto-switches the method to
            `local_queues` (logged at INFO) so the cap is enforced. Default: None.
        use_flow: If True, `FlowShiftTracker` is used, where the poses are matched using
        optical flow shifts. Default: `False`.
        of_img_scale: Factor to scale the images by when computing optical flow. Decrease
            this to increase performance at the cost of finer accuracy. Sometimes
            decreasing the image scale can improve performance with fast movements.
            Default: 1.0. (only if `use_flow` is True)
        of_window_size: Optical flow window size to consider at each pyramid scale
            level. Default: 21. (only if `use_flow` is True)
        of_max_levels: Number of pyramid scale levels to consider. This is different
            from the scale parameter, which determines the initial image scaling.
            Default: 3. (only if `use_flow` is True)
        oks_stddev: Keypoint-spread normalization constant for `oks` scoring;
            larger is more tolerant of localization error. `None` (default)
            auto-resolves to 0.1 for `kf_track_features="keypoints"` (whose per-node
            prediction is noisier) and 0.025 otherwise.
        use_kalman: If True, `KalmanShiftTracker` is used, where poses are predicted
            with a per-track constant-velocity Kalman filter. Requires
            `tracking_target_instance_count` (or `max_tracks`) and is mutually
            exclusive with `use_flow`. Default: `False`.
        kf_track_features: What the Kalman motion model tracks: `centroid` (default;
            rigid translation of the last pose) or `keypoints` (per-node poses;
            noisier, pair with a larger `oks_stddev` or `features="bboxes"` +
            `scoring_method="iou"`). (only if `use_kalman` is True)
        kf_init_frame_count: Number of warm-up frames tracked with the base path
            before the Kalman filters are fit via EM. Default: 10.
            (only if `use_kalman` is True)
        kf_node_indices: Skeleton node (row) indices to track with the motion model.
            `None` uses all nodes. Default: None. (only if `use_kalman` is True)
        kf_reset_gap_size: Number of consecutive missed frames after which a stale
            track's filter is reset. Default: 5. (only if `use_kalman` is True)
        kf_prediction_blend: Weight of the motion prediction when blending with the
            last observation to form the scoring candidate. Default: 0.5.
            (only if `use_kalman` is True)
        kf_gate_step_mult: Measurement gate as a multiple of the track's median
            step. Default: 8.0. (only if `use_kalman` is True)
        kf_min_gate_px: Floor (px) for the measurement gate. Default: 40.0.
            (only if `use_kalman` is True)
        kf_velocity_cap_mult: Cap on learned velocity as a multiple of the track's
            median step. Default: 3.0. (only if `use_kalman` is True)
        kf_min_velocity_cap_px: Floor (px/frame) for the velocity cap. Default: 15.0.
            (only if `use_kalman` is True)
        tracking_target_instance_count: Target number of instances to track per frame. (default: None)
        tracking_pre_cull_to_target: If non-zero and target_instance_count is also non-zero, then cull instances over target count per frame *before* tracking. (default: 0)
        tracking_pre_cull_iou_threshold: If non-zero and pre_cull_to_target also set, then use IOU threshold to remove overlapping instances over count *before* tracking. (default: 0)

    """
    # `max_tracks` is enforced only by the `local_queues` candidate maker
    # (`LocalQueueCandidates.get_new_track_id` returns `None` past the cap);
    # `fixed_window` silently ignores it and mints unbounded track IDs. When a
    # caller asks for a track cap under `fixed_window`, switch to `local_queues`
    # -- the candidate method designed for a fixed identity count -- so the cap
    # is actually honored. This is the universal safety net: every tracking
    # entry point (CLI, `run_inference`/`run_tracker`, `apply_tracking`, direct
    # API use) flows through `from_config` (sleap#2720, #582).
    if max_tracks is not None and candidates_method == "fixed_window":
        logger.info(
            "max_tracks=%s was set with candidates_method='fixed_window', which "
            "ignores it; switching to candidates_method='local_queues' to honor "
            "the track cap.",
            max_tracks,
        )
        candidates_method = "local_queues"

    if candidates_method == "fixed_window":
        candidate = FixedWindowCandidates(
            window_size=window_size,
            min_new_track_points=min_new_track_points,
        )
        is_local_queue = False

    elif candidates_method == "local_queues":
        candidate = LocalQueueCandidates(
            window_size=window_size,
            max_tracks=max_tracks,
            min_new_track_points=min_new_track_points,
        )
        is_local_queue = True

    else:
        message = f"{candidates_method} is not a valid method. Please choose one of [`fixed_window`, `local_queues`]"
        logger.error(message)
        raise ValueError(message)

    if use_kalman and use_flow:
        message = (
            "`use_kalman` and `use_flow` are mutually exclusive; choose one "
            "tracker (Kalman tracking does not use optical flow)."
        )
        logger.error(message)
        raise ValueError(message)

    if use_kalman and tracking_target_instance_count is None and max_tracks is None:
        message = (
            "Kalman tracking requires a known target identity count: pass "
            "`tracking_target_instance_count` (or `max_tracks` / `--max_instances`)."
        )
        logger.error(message)
        raise ValueError(message)

    if use_kalman and kf_track_features not in ("centroid", "keypoints"):
        message = (
            f"Invalid kf_track_features={kf_track_features!r}; choose 'centroid' "
            "(default) or 'keypoints'."
        )
        logger.error(message)
        raise ValueError(message)

    # Resolve the OKS tolerance: the per-node 'keypoints' prediction is noisier, so
    # the strict default stddev (0.025) collapses its similarity scores; default it
    # to 0.1 (validated on synthetic + real data). Centroid/base keep 0.025. An
    # explicit oks_stddev always wins.
    if oks_stddev is None:
        oks_stddev = (
            0.1 if (use_kalman and kf_track_features == "keypoints") else 0.025
        )

    if use_kalman:
        return KalmanShiftTracker(
            candidate=candidate,
            min_match_points=min_match_points,
            features=features,
            scoring_method=scoring_method,
            scoring_reduction=scoring_reduction,
            robust_best_instance=robust_best_instance,
            oks_stddev=oks_stddev,
            track_matching_method=track_matching_method,
            kf_track_features=kf_track_features,
            kf_init_frame_count=kf_init_frame_count,
            kf_node_indices=kf_node_indices,
            kf_reset_gap_size=kf_reset_gap_size,
            kf_prediction_blend=kf_prediction_blend,
            kf_gate_step_mult=kf_gate_step_mult,
            kf_min_gate_px=kf_min_gate_px,
            kf_velocity_cap_mult=kf_velocity_cap_mult,
            kf_min_velocity_cap_px=kf_min_velocity_cap_px,
            is_local_queue=is_local_queue,
            tracking_target_instance_count=tracking_target_instance_count,
            tracking_pre_cull_to_target=tracking_pre_cull_to_target,
            tracking_pre_cull_iou_threshold=tracking_pre_cull_iou_threshold,
        )

    if use_flow:
        return FlowShiftTracker(
            candidate=candidate,
            min_match_points=min_match_points,
            features=features,
            scoring_method=scoring_method,
            scoring_reduction=scoring_reduction,
            robust_best_instance=robust_best_instance,
            oks_stddev=oks_stddev,
            track_matching_method=track_matching_method,
            img_scale=of_img_scale,
            of_window_size=of_window_size,
            of_max_levels=of_max_levels,
            is_local_queue=is_local_queue,
            tracking_target_instance_count=tracking_target_instance_count,
            tracking_pre_cull_to_target=tracking_pre_cull_to_target,
            tracking_pre_cull_iou_threshold=tracking_pre_cull_iou_threshold,
        )

    tracker = cls(
        candidate=candidate,
        min_match_points=min_match_points,
        features=features,
        scoring_method=scoring_method,
        scoring_reduction=scoring_reduction,
        robust_best_instance=robust_best_instance,
        oks_stddev=oks_stddev,
        track_matching_method=track_matching_method,
        use_flow=use_flow,
        is_local_queue=is_local_queue,
        tracking_target_instance_count=tracking_target_instance_count,
        tracking_pre_cull_to_target=tracking_pre_cull_to_target,
        tracking_pre_cull_iou_threshold=tracking_pre_cull_iou_threshold,
    )
    return tracker

generate_candidates()

Get the tracked instances from tracker queue.

Source code in sleap_nn/tracking/tracker.py

def generate_candidates(self):
    """Get the tracked instances from tracker queue."""
    return self.candidate.tracker_queue

get_features(untracked_instances, frame_idx, image=None)

Get features for the current untracked instances.

The feature can either be an embedding of cropped image around each instance (visual feature), the bounding box coordinates, or centroids, or the poses as a feature.

Parameters:

Name	Type	Description	Default
untracked_instances	List[PredictedInstance]	List of untracked sio.PredictedInstance objects.	required
frame_idx	int	Frame index of the current untracked instances.	required
image	ndarray	Image of the current frame if visual features are to be used.	None

Returns:

Type	Description
Union[TrackInstances, List[TrackInstanceLocalQueue]]	TrackInstances object or List[TrackInstanceLocalQueue] with the features assigned for the untracked instances and track_id set as None.

Source code in sleap_nn/tracking/tracker.py

def get_features(
    self,
    untracked_instances: List[sio.PredictedInstance],
    frame_idx: int,
    image: np.ndarray = None,
) -> Union[TrackInstances, List[TrackInstanceLocalQueue]]:
    """Get features for the current untracked instances.

    The feature can either be an embedding of cropped image around each instance (visual feature),
    the bounding box coordinates, or centroids, or the poses as a feature.

    Args:
        untracked_instances: List of untracked `sio.PredictedInstance` objects.
        frame_idx: Frame index of the current untracked instances.
        image: Image of the current frame if visual features are to be used.

    Returns:
        `TrackInstances` object or `List[TrackInstanceLocalQueue]` with the features
        assigned for the untracked instances and track_id set as `None`.
    """
    if self.features not in self._feature_methods:
        message = "Invalid `features` argument. Please provide one of `keypoints`, `centroids`, `bboxes`, `masks` and `image`"
        logger.error(message)
        raise ValueError(message)

    feature_method = self._feature_methods[self.features]
    feature_list = []
    for pred_instance in untracked_instances:
        feature_list.append(feature_method(pred_instance))

    current_instances = self.candidate.get_track_instances(
        feature_list, untracked_instances, frame_idx=frame_idx, image=image
    )

    return current_instances

get_scores(current_instances, candidates_feature_dict)

Compute association score between untracked and tracked instances.

For visual feature vectors, this can be cosine_sim, for bounding boxes it could be iou, for centroids it could be euclidean_dist, and for poses it could be oks.

Parameters:

Name	Type	Description	Default
current_instances	Union[TrackInstances, List[TrackInstanceLocalQueue]]	TrackInstances object or List[TrackInstanceLocalQueue] with features and unassigned tracks.	required
candidates_feature_dict	Dict[int, TrackedInstanceFeature]	Dictionary with keys as track IDs and values as the list of TrackedInstanceFeature.	required

Returns:

Name	Type	Description
scores		Score matrix of shape (num_new_instances, num_existing_tracks)

Source code in sleap_nn/tracking/tracker.py

def get_scores(
    self,
    current_instances: Union[TrackInstances, List[TrackInstanceLocalQueue]],
    candidates_feature_dict: Dict[int, TrackedInstanceFeature],
):
    """Compute association score between untracked and tracked instances.

    For visual feature vectors, this can be `cosine_sim`, for bounding boxes
    it could be `iou`, for centroids it could be `euclidean_dist`, and for poses it
    could be `oks`.

    Args:
        current_instances: `TrackInstances` object or `List[TrackInstanceLocalQueue]`
            with features and unassigned tracks.
        candidates_feature_dict: Dictionary with keys as track IDs and values as the
            list of `TrackedInstanceFeature`.

    Returns:
        scores: Score matrix of shape (num_new_instances, num_existing_tracks)
    """
    if self.scoring_method not in self._scoring_functions:
        message = "Invalid `scoring_method` argument. Please provide one of `oks`, `cosine_sim`, `iou`, `mask_iou`, and `euclidean_dist`."
        logger.error(message)
        raise ValueError(message)

    if self.scoring_reduction not in self._scoring_reduction_methods:
        message = "Invalid `scoring_reduction` argument. Please provide one of `mean`, `max`, and `robust_quantile`."
        logger.error(message)
        raise ValueError(message)

    scoring_method = self._scoring_functions[self.scoring_method]
    if self.scoring_method == "oks":
        # OKS tolerance is configurable: a larger stddev is more forgiving of
        # localization error, which matters for the noisier per-keypoint Kalman
        # prediction (`kf_track_features="keypoints"`).
        scoring_method = functools.partial(compute_oks, stddev=self.oks_stddev)
    scoring_reduction = self._scoring_reduction_methods[self.scoring_reduction]
    if self.scoring_reduction == "robust_quantile":
        # Resolve at runtime so the per-instance `robust_best_instance` is
        # honored (a class-level partial freezes `q` at the class default).
        # `nanquantile` matches the NaN-handling of `nanmean`/`nanmax`.
        scoring_reduction = functools.partial(
            np.nanquantile, q=self.robust_best_instance
        )

    # Get list of features for the `current_instances`.
    if self.is_local_queue:
        current_instances_features = [x.feature for x in current_instances]
    else:
        current_instances_features = [x for x in current_instances.features]

    scores = np.zeros(
        (len(current_instances_features), len(self.candidate.current_tracks))
    )

    for f_idx, f in enumerate(current_instances_features):
        for t_idx, track_id in enumerate(self.candidate.current_tracks):
            scores_trackid = [
                scoring_method(f, x.feature)
                for x in candidates_feature_dict[track_id]
                if count_valid_points(x.src_predicted_instance)
                > self.min_match_points  # candidates with min support (non-NaN
                # keypoints, or mask area px for segmentation masks)
            ]
            # An empty candidate list (all filtered by `min_match_points`)
            # reduces to NaN (-> inf cost in `scores_to_cost_matrix`); guard
            # explicitly because `np.nanmax([])` raises (`np.nanmean([])` /
            # `np.nanquantile([])` return NaN, but `max` must not crash).
            score_trackid = (
                np.nan if not scores_trackid else scoring_reduction(scores_trackid)
            )
            scores[f_idx][t_idx] = score_trackid

    return scores

scores_to_cost_matrix(scores)

Converts scores matrix to cost matrix for track assignments.

Source code in sleap_nn/tracking/tracker.py

def scores_to_cost_matrix(self, scores: np.ndarray):
    """Converts `scores` matrix to cost matrix for track assignments."""
    cost_matrix = -scores
    cost_matrix[np.isnan(cost_matrix)] = np.inf
    return cost_matrix

track(untracked_instances, frame_idx, image=None)

Assign track IDs to the untracked list of sio.PredictedInstance objects.

Parameters:

Name	Type	Description	Default
untracked_instances	List[PredictedInstance]	List of untracked sio.PredictedInstance objects.	required
frame_idx	int	Frame index of the predicted instances.	required
image	ndarray	Source image if visual features are to be used (also when using flow).	None

Returns:

Type	Description
List[PredictedInstance]	List of sio.PredictedInstance objects, each having an assigned track.

Source code in sleap_nn/tracking/tracker.py

def track(
    self,
    untracked_instances: List[sio.PredictedInstance],
    frame_idx: int,
    image: np.ndarray = None,
) -> List[sio.PredictedInstance]:
    """Assign track IDs to the untracked list of `sio.PredictedInstance` objects.

    Args:
        untracked_instances: List of untracked `sio.PredictedInstance` objects.
        frame_idx: Frame index of the predicted instances.
        image: Source image if visual features are to be used (also when using flow).

    Returns:
        List of `sio.PredictedInstance` objects, each having an assigned track.
    """
    # Pre-cull is pose-only (cull_frame_instances uses same_pose_as / bbox);
    # segmentation masks are scoped out of cull for the MVP (apply_tracking
    # rejects the pre-cull flags in mask mode, so this is belt-and-braces).
    masks_input = bool(untracked_instances) and is_segmentation_mask(
        untracked_instances[0]
    )
    if (
        not masks_input
        and self.tracking_target_instance_count is not None
        and self.tracking_target_instance_count
        and self.tracking_pre_cull_to_target
    ):
        untracked_instances = cull_frame_instances(
            untracked_instances,
            self.tracking_target_instance_count,
            self.tracking_pre_cull_iou_threshold,
        )
    # get features for the untracked instances.
    current_instances = self.get_features(untracked_instances, frame_idx, image)

    candidates_list = (
        self.generate_candidates()
    )  # either Deque/ DefaultDict for FixedWindow/ LocalQueue candidate.

    if candidates_list:
        # if track queue is not empty

        # update candidates if needed and get the features from previous tracked instances.
        candidates_feature_dict = self.update_candidates(candidates_list, image)

        # scoring function
        scores = self.get_scores(current_instances, candidates_feature_dict)
        cost_matrix = self.scores_to_cost_matrix(scores)

        # track assignment
        current_tracked_instances = self.assign_tracks(
            current_instances, cost_matrix
        )

    else:
        # Initialize the tracker queue if empty.
        current_tracked_instances = self.candidate.add_new_tracks(current_instances)

    # convert the `current_instances` back to `List[sio.PredictedInstance]` objects.
    if self.is_local_queue:
        new_pred_instances = []
        for instance in current_tracked_instances:
            if instance.track_id is not None:
                if instance.track_id not in self._track_objects:
                    self._track_objects[instance.track_id] = sio.Track(
                        f"track_{instance.track_id}"
                    )
                instance.src_instance.track = self._track_objects[instance.track_id]
                instance.src_instance.tracking_score = instance.tracking_score
            new_pred_instances.append(instance.src_instance)

    else:
        new_pred_instances = []
        for idx, inst in enumerate(current_tracked_instances.src_instances):
            track_id = current_tracked_instances.track_ids[idx]
            if track_id is not None:
                if track_id not in self._track_objects:
                    self._track_objects[track_id] = sio.Track(f"track_{track_id}")
                inst.track = self._track_objects[track_id]
                inst.tracking_score = current_tracked_instances.tracking_scores[idx]
                new_pred_instances.append(inst)

    return new_pred_instances

update_candidates(candidates_list, image)

Return dictionary with the features of tracked instances.

Parameters:

Name	Type	Description	Default
candidates_list	Union[Deque, DefaultDict[int, Deque]]	List of tracked instances from tracker queue to consider.	required
image	ndarray	Image of the current untracked frame. (used for flow shift tracker)	required

Returns:

Type	Description
Dict[int, TrackedInstanceFeature]	Dictionary with keys as track IDs and values as the list of TrackedInstanceFeature.

Source code in sleap_nn/tracking/tracker.py

def update_candidates(
    self, candidates_list: Union[Deque, DefaultDict[int, Deque]], image: np.ndarray
) -> Dict[int, TrackedInstanceFeature]:
    """Return dictionary with the features of tracked instances.

    Args:
        candidates_list: List of tracked instances from tracker queue to consider.
        image: Image of the current untracked frame. (used for flow shift tracker)

    Returns:
        Dictionary with keys as track IDs and values as the list of `TrackedInstanceFeature`.
    """
    candidates_feature_dict = defaultdict(list)
    for track_id in self.candidate.current_tracks:
        candidates_feature_dict[track_id].extend(
            self.candidate.get_features_from_track_id(track_id, candidates_list)
        )
    return candidates_feature_dict

connect_single_breaks(lfs, max_instances)

Merge single-frame breaks in tracks by connecting single lost track with single new track.

Parameters:

Name	Type	Description	Default
lfs	List[LabeledFrame]	List of LabeledFrame objects with predicted instances.	required
max_instances	int	The maximum number of instances we want per frame.	required

Returns:

Type	Description
List[LabeledFrame]	Updated list of labeled frames with modified track IDs.

Source code in sleap_nn/tracking/tracker.py

def connect_single_breaks(
    lfs: List[sio.LabeledFrame], max_instances: int
) -> List[sio.LabeledFrame]:
    """Merge single-frame breaks in tracks by connecting single lost track with single new track.

    Args:
        lfs: List of `LabeledFrame` objects with predicted instances.
        max_instances: The maximum number of instances we want per frame.

    Returns:
        Updated list of labeled frames with modified track IDs.
    """
    if not lfs:
        return lfs

    # Move instances in new tracks into tracks that disappeared on previous frame
    fix_track_map = dict()
    last_good_frame_tracks = {inst.track for inst in lfs[0].instances}
    for lf in lfs:
        frame_tracks = {inst.track for inst in lf.instances}

        tracks_fixed_before = frame_tracks.intersection(set(fix_track_map.keys()))
        if tracks_fixed_before:
            for inst in lf.instances:
                if (
                    inst.track in fix_track_map
                    and fix_track_map[inst.track] not in frame_tracks
                ):
                    inst.track = fix_track_map[inst.track]
                    frame_tracks = {inst.track for inst in lf.instances}

        extra_tracks = frame_tracks - last_good_frame_tracks
        missing_tracks = last_good_frame_tracks - frame_tracks

        if len(extra_tracks) == 1 and len(missing_tracks) == 1:
            for inst in lf.instances:
                if inst.track in extra_tracks:
                    old_track = inst.track
                    new_track = missing_tracks.pop()
                    fix_track_map[old_track] = new_track
                    inst.track = new_track

                    break
        else:
            # Update last_good_frame_tracks when we have at least as many instances
            # as before. This prevents stale reference when max_instances doesn't
            # match actual count or when first frame has fewer instances.
            if len(frame_tracks) >= len(last_good_frame_tracks):
                last_good_frame_tracks = frame_tracks

    return lfs

run_tracker(untracked_frames, window_size=5, min_new_track_points=0, candidates_method='fixed_window', min_match_points=0, features='keypoints', scoring_method='oks', scoring_reduction='mean', robust_best_instance=1.0, oks_stddev=None, track_matching_method='hungarian', max_tracks=None, use_flow=False, of_img_scale=1.0, of_window_size=21, of_max_levels=3, use_kalman=False, kf_track_features='centroid', kf_init_frame_count=10, kf_node_indices=None, kf_reset_gap_size=5, post_connect_single_breaks=False, tracking_target_instance_count=None, tracking_pre_cull_to_target=0, tracking_pre_cull_iou_threshold=0, tracking_clean_instance_count=0, tracking_clean_iou_threshold=0)

Run tracking on a given set of frames.

Parameters:

Name	Type	Description	Default
untracked_frames	List[LabeledFrame]	List of labeled frames with predicted instances to be tracked.	required
window_size	int	Number of frames to look for in the candidate instances to match with the current detections. Default: 5.	5
min_new_track_points	int	We won't spawn a new track for an instance with fewer than this many points. Default: 0.	0
candidates_method	str	Either of fixed_window or local_queues. In fixed window method, candidates from the last window_size frames. In local queues, last window_size instances for each track ID is considered for matching against the current detection. Default: fixed_window.	'fixed_window'
min_match_points	int	Minimum non-NaN points for match candidates. Default: 0.	0
features	str	Feature representation for the candidates to update current detections. One of [keypoints, centroids, bboxes, image]. Default: keypoints.	'keypoints'
scoring_method	str	Method to compute association score between features from the current frame and the previous tracks. One of [oks, cosine_sim, iou, euclidean_dist]. Default: oks.	'oks'
scoring_reduction	str	Method to aggregate and reduce multiple scores if there are several detections associated with the same track. One of [mean, max, robust_quantile]. Default: mean.	'mean'
robust_best_instance	float	If the value is between 0 and 1 (excluded), use a robust quantile similarity score for the track. If the value is 1, use the max similarity (non-robust). For selecting a robust score, 0.95 is a good value.	1.0
track_matching_method	str	Track matching algorithm. One of hungarian, greedy. Default:hungarian`.	'hungarian'
max_tracks	Optional[int]	Meaximum number of new tracks to be created to avoid redundant tracks. (only for local queues candidate) Default: None.	None
use_flow	bool	If True, FlowShiftTracker is used, where the poses are matched using	False
optical flow shifts. Default		False.	required
of_img_scale	float	Factor to scale the images by when computing optical flow. Decrease this to increase performance at the cost of finer accuracy. Sometimes decreasing the image scale can improve performance with fast movements. Default: 1.0. (only if use_flow is True)	1.0
of_window_size	int	Optical flow window size to consider at each pyramid scale level. Default: 21. (only if use_flow is True)	21
of_max_levels	int	Number of pyramid scale levels to consider. This is different from the scale parameter, which determines the initial image scaling. Default: 3. (only if use_flow is True).	3
oks_stddev	Optional[float]	Keypoint-spread normalization constant for oks scoring; larger is more tolerant of localization error. None (default) auto-resolves to 0.1 for kf_track_features="keypoints" and 0.025 otherwise.	None
use_kalman	bool	If True, KalmanShiftTracker is used, where poses are predicted with a per-track constant-velocity Kalman filter. Requires tracking_target_instance_count (or max_tracks) and is mutually exclusive with use_flow. Default: False.	False
kf_track_features	str	What the Kalman motion model tracks: centroid (default) or keypoints (per-node poses; noisier). (only if use_kalman is True)	'centroid'
kf_init_frame_count	int	Number of warm-up frames tracked with the base path before the Kalman filters are fit via EM. Default: 10. (only if use_kalman is True)	10
kf_node_indices	Optional[List[int]]	Skeleton node (row) indices to track with the motion model. None uses all nodes. Default: None. (only if use_kalman is True)	None
kf_reset_gap_size	int	Number of consecutive missed frames after which a stale track's filter is reset. Default: 5. (only if use_kalman is True)	5
post_connect_single_breaks	bool	If True and max_tracks is not None with local queues candidate method, connects track breaks when exactly one track is lost and exactly one new track is spawned in the frame.	False
tracking_target_instance_count	Optional[int]	Target number of instances to track per frame. (default: None)	None
tracking_pre_cull_to_target	int	If non-zero and target_instance_count is also non-zero, then cull instances over target count per frame before tracking. (default: 0)	0
tracking_pre_cull_iou_threshold	float	If non-zero and pre_cull_to_target also set, then use IOU threshold to remove overlapping instances over count before tracking. (default: 0)	0
tracking_clean_instance_count	int	Target number of instances to clean after tracking. (default: 0)	0
tracking_clean_iou_threshold	float	IOU to use when culling instances after tracking. (default: 0)	0

Returns:

Type	Description
List[LabeledFrame]	sio.Labels object with tracked instances.

Source code in sleap_nn/tracking/tracker.py

def run_tracker(
    untracked_frames: List[sio.LabeledFrame],
    window_size: int = 5,
    min_new_track_points: int = 0,
    candidates_method: str = "fixed_window",
    min_match_points: int = 0,
    features: str = "keypoints",
    scoring_method: str = "oks",
    scoring_reduction: str = "mean",
    robust_best_instance: float = 1.0,
    oks_stddev: Optional[float] = None,
    track_matching_method: str = "hungarian",
    max_tracks: Optional[int] = None,
    use_flow: bool = False,
    of_img_scale: float = 1.0,
    of_window_size: int = 21,
    of_max_levels: int = 3,
    use_kalman: bool = False,
    kf_track_features: str = "centroid",
    kf_init_frame_count: int = 10,
    kf_node_indices: Optional[List[int]] = None,
    kf_reset_gap_size: int = 5,
    post_connect_single_breaks: bool = False,
    tracking_target_instance_count: Optional[int] = None,
    tracking_pre_cull_to_target: int = 0,
    tracking_pre_cull_iou_threshold: float = 0,
    tracking_clean_instance_count: int = 0,
    tracking_clean_iou_threshold: float = 0,
) -> List[sio.LabeledFrame]:
    """Run tracking on a given set of frames.

    Args:
        untracked_frames: List of labeled frames with predicted instances to be tracked.
        window_size: Number of frames to look for in the candidate instances to match
                with the current detections. Default: 5.
        min_new_track_points: We won't spawn a new track for an instance with
            fewer than this many points. Default: 0.
        candidates_method: Either of `fixed_window` or `local_queues`. In fixed window
            method, candidates from the last `window_size` frames. In local queues,
            last `window_size` instances for each track ID is considered for matching
            against the current detection. Default: `fixed_window`.
        min_match_points: Minimum non-NaN points for match candidates. Default: 0.
        features: Feature representation for the candidates to update current detections.
            One of [`keypoints`, `centroids`, `bboxes`, `image`]. Default: `keypoints`.
        scoring_method: Method to compute association score between features from the
            current frame and the previous tracks. One of [`oks`, `cosine_sim`, `iou`,
            `euclidean_dist`]. Default: `oks`.
        scoring_reduction: Method to aggregate and reduce multiple scores if there are
            several detections associated with the same track. One of [`mean`, `max`,
            `robust_quantile`]. Default: `mean`.
        robust_best_instance: If the value is between 0 and 1
            (excluded), use a robust quantile similarity score for the
            track. If the value is 1, use the max similarity (non-robust).
            For selecting a robust score, 0.95 is a good value.
        track_matching_method: Track matching algorithm. One of `hungarian`, `greedy.
            Default: `hungarian`.
        max_tracks: Meaximum number of new tracks to be created to avoid redundant tracks.
            (only for local queues candidate) Default: None.
        use_flow: If True, `FlowShiftTracker` is used, where the poses are matched using
        optical flow shifts. Default: `False`.
        of_img_scale: Factor to scale the images by when computing optical flow. Decrease
            this to increase performance at the cost of finer accuracy. Sometimes
            decreasing the image scale can improve performance with fast movements.
            Default: 1.0. (only if `use_flow` is True)
        of_window_size: Optical flow window size to consider at each pyramid scale
            level. Default: 21. (only if `use_flow` is True)
        of_max_levels: Number of pyramid scale levels to consider. This is different
            from the scale parameter, which determines the initial image scaling.
                Default: 3. (only if `use_flow` is True).
        oks_stddev: Keypoint-spread normalization constant for `oks` scoring; larger is
            more tolerant of localization error. `None` (default) auto-resolves to 0.1
            for `kf_track_features="keypoints"` and 0.025 otherwise.
        use_kalman: If True, `KalmanShiftTracker` is used, where poses are predicted with
            a per-track constant-velocity Kalman filter. Requires
            `tracking_target_instance_count` (or `max_tracks`) and is mutually exclusive
            with `use_flow`. Default: `False`.
        kf_track_features: What the Kalman motion model tracks: `centroid` (default) or
            `keypoints` (per-node poses; noisier). (only if `use_kalman` is True)
        kf_init_frame_count: Number of warm-up frames tracked with the base path before
            the Kalman filters are fit via EM. Default: 10. (only if `use_kalman` is True)
        kf_node_indices: Skeleton node (row) indices to track with the motion model.
            `None` uses all nodes. Default: None. (only if `use_kalman` is True)
        kf_reset_gap_size: Number of consecutive missed frames after which a stale track's
            filter is reset. Default: 5. (only if `use_kalman` is True)
        post_connect_single_breaks: If True and `max_tracks` is not None with local queues candidate method,
            connects track breaks when exactly one track is lost and exactly one new track is spawned in the frame.
        tracking_target_instance_count: Target number of instances to track per frame. (default: None)
        tracking_pre_cull_to_target: If non-zero and target_instance_count is also non-zero, then cull instances over target count per frame *before* tracking. (default: 0)
        tracking_pre_cull_iou_threshold: If non-zero and pre_cull_to_target also set, then use IOU threshold to remove overlapping instances over count *before* tracking. (default: 0)
        tracking_clean_instance_count: Target number of instances to clean *after* tracking. (default: 0)
        tracking_clean_iou_threshold: IOU to use when culling instances *after* tracking. (default: 0)

    Returns:
        `sio.Labels` object with tracked instances.

    """
    tracker = Tracker.from_config(
        window_size=window_size,
        min_new_track_points=min_new_track_points,
        candidates_method=candidates_method,
        min_match_points=min_match_points,
        features=features,
        scoring_method=scoring_method,
        scoring_reduction=scoring_reduction,
        robust_best_instance=robust_best_instance,
        oks_stddev=oks_stddev,
        track_matching_method=track_matching_method,
        max_tracks=max_tracks,
        use_flow=use_flow,
        of_img_scale=of_img_scale,
        of_window_size=of_window_size,
        of_max_levels=of_max_levels,
        use_kalman=use_kalman,
        kf_track_features=kf_track_features,
        kf_init_frame_count=kf_init_frame_count,
        kf_node_indices=kf_node_indices,
        kf_reset_gap_size=kf_reset_gap_size,
        tracking_target_instance_count=tracking_target_instance_count,
        tracking_pre_cull_to_target=tracking_pre_cull_to_target,
        tracking_pre_cull_iou_threshold=tracking_pre_cull_iou_threshold,
    )

    try:
        with Progress(
            "{task.description}",
            BarColumn(),
            "[progress.percentage]{task.percentage:>3.0f}%",
            MofNCompleteColumn(),
            "ETA:",
            TimeRemainingColumn(),
            "Elapsed:",
            TimeElapsedColumn(),
            RateColumn(),
            auto_refresh=False,
            refresh_per_second=4,
            speed_estimate_period=5,
        ) as progress:
            task = progress.add_task("Tracking...", total=len(untracked_frames))
            last_report = time()

            tracked_lfs = []
            for lf in untracked_frames:
                # prefer user instances over predicted instance
                instances = []
                if lf.has_user_instances:
                    instances_to_track = lf.user_instances
                    if lf.has_predicted_instances:
                        instances = lf.predicted_instances
                else:
                    instances_to_track = lf.predicted_instances

                instances.extend(
                    tracker.track(
                        untracked_instances=instances_to_track,
                        frame_idx=lf.frame_idx,
                        image=lf.image,
                    )
                )
                tracked_lfs.append(
                    sio.LabeledFrame(
                        video=lf.video, frame_idx=lf.frame_idx, instances=instances
                    )
                )

                progress.update(task, advance=1)

                if time() - last_report > 0.25:
                    progress.refresh()
                    last_report = time()

    except KeyboardInterrupt:
        logger.info("Tracking interrupted by user")
        raise KeyboardInterrupt

    if not tracked_lfs:
        logger.info("0 frames to track; skipping tracking post-processing.")
        return tracked_lfs

    if tracking_clean_instance_count > 0:
        logger.info("Post-processing: Culling instances...")
        tracked_lfs = cull_instances(
            tracked_lfs, tracking_clean_instance_count, tracking_clean_iou_threshold
        )
        if not post_connect_single_breaks:
            logger.info("Post-processing: Connecting single breaks...")
            tracked_lfs = connect_single_breaks(
                tracked_lfs, tracking_clean_instance_count
            )

    if post_connect_single_breaks:
        if (
            tracking_target_instance_count is None
            or tracking_target_instance_count == 0
        ):
            if max_tracks is not None:
                suggestion = f"Add --tracking_target_instance_count {max_tracks} to your command (using your --max_tracks value)."
            else:
                suggestion = "Add --tracking_target_instance_count N where N is the expected number of instances per frame."
            message = (
                f"--post_connect_single_breaks requires --tracking_target_instance_count to be set. "
                f"{suggestion}"
            )
            logger.error(message)
            raise ValueError(message)
        start_final_pass_time = time()
        start_fp_timestamp = str(datetime.now())
        logger.info(
            f"Started final-pass (connecting single breaks) at: {start_fp_timestamp}"
        )
        tracked_lfs = connect_single_breaks(
            tracked_lfs, max_instances=tracking_target_instance_count
        )
        finish_fp_timestamp = str(datetime.now())
        total_fp_elapsed = time() - start_final_pass_time
        logger.info(
            f"Finished final-pass (connecting single breaks) at: {finish_fp_timestamp}"
        )
        logger.info(f"Total runtime: {total_fp_elapsed} secs")

    return tracked_lfs