add jabs-cli command for converting jabs pose file to nwb pose file

CLAUDE.md

@@ -151,6 +151,7 @@ cache invalidation logic (version mismatch, pose hash, distance scale).
 - `__init__.py` files: unused imports (F401) are allowed
 - **Naming**: `PascalCase` classes, `snake_case` functions/methods/files,
   `UPPER_SNAKE_CASE` constants, `_` prefix for private members
+- Prefer American English spelling (e.g., "behavior" not "behaviour").
 
 ## Coding Standards
 

CONTRIBUTING.md

@@ -109,7 +109,7 @@ For detailed information about JABS architecture, development setup, and impleme
 
 - **General questions**: Open an issue on GitHub
 - **Security issues**: Email jabs@jax.org (do not open public issues)
-- **Development questions**: See [DEVELOPMENT.md](docs/DEVELOPMENT.md) or contact jabs@jax.org
+- **Development questions**: See [DEVELOPMENT.md](docs/development/DEVELOPMENT.md) or contact jabs@jax.org
 
 ## Code of Conduct
 

packages/jabs-core/src/jabs/core/abstract/pose_est.py

@@ -8,6 +8,7 @@
 import numpy as np
 from shapely.geometry import MultiPoint
 
+from jabs.core.types import DynamicObjectData
 from jabs.core.utils import hash_file
 
 MINIMUM_CONFIDENCE = 0.3
@@ -132,7 +133,8 @@ def __init__(self, file_path: Path, cache_dir: Path | None = None, fps: int = 30
         self._hash = hash_file(file_path)
         self._fps = fps
 
-        self._static_objects = {}
+        self._static_objects: dict = {}
+        self._dynamic_objects: dict[str, DynamicObjectData] = {}
 
         # check cache version, if it doesn't match, clear the cache file for this pose file
         if self._cache_dir is not None and not self.check_cache_version():
@@ -270,6 +272,28 @@ def static_objects(self):
         """get static objects from the pose file"""
         return self._static_objects
 
+    @property
+    def dynamic_objects(self) -> dict[str, DynamicObjectData]:
+        """Get dynamic objects from the pose file.
+
+        Returns:
+            Mapping of object name to jabs.core.types.DynamicObjectData.
+            Empty for pose versions that do not support dynamic objects (v2-v6).
+        """
+        return self._dynamic_objects
+
+    def get_dynamic_object(self, name: str) -> DynamicObjectData | None:
+        """Get a named dynamic object from the pose file.
+
+        Args:
+            name: Name of the dynamic object (e.g. "fecal_boli").
+
+        Returns:
+            DynamicObjectData for the requested object, or None if not present.
+            Always None for pose versions that do not support dynamic objects (v2-v6).
+        """
+        return self._dynamic_objects.get(name)
+
     def get_identity_convex_hulls(self, identity):
         """get a list of length #frames containing convex hulls for the given identity.
 
@@ -419,3 +443,11 @@ def _cache_file_path(self) -> Path | None:
             return None
         filename = self._path.name.replace(".h5", "_cache.h5")
         return self._cache_dir / filename
+
+    def get_bounding_boxes(self, identity: int) -> np.ndarray | None:
+        """Get bounding box array for an identity index.
+
+        Default implementation returns None, indicating no bounding box data.
+        Bounding boxes are not available in pose file versions <8, this is included for interface consistency.
+        """
+        return None

packages/jabs-core/src/jabs/core/types/__init__.py

@@ -3,7 +3,7 @@
 from .inference import AggregationSpec, InferenceSampling
 from .keypoints import FrameKeypoints, FrameKeypointsData, KeypointAnnotation
 from .model import ModelInfo
-from .pose import PoseData
+from .pose import DynamicObjectData, PoseData
 from .prediction import BehaviorPrediction, ClassifierMetadata
 from .results import InferenceRunMetadata, KeypointInferenceResult
 from .video import VideoInfo
@@ -12,6 +12,7 @@
     "AggregationSpec",
     "BehaviorPrediction",
     "ClassifierMetadata",
+    "DynamicObjectData",
     "FrameKeypoints",
     "FrameKeypointsData",
     "InferenceRunMetadata",

packages/jabs-core/src/jabs/core/types/pose.py

@@ -2,6 +2,33 @@
 from typing import Any
 
 import numpy as np
+import numpy.typing as npt
+
+
+@dataclass(frozen=True)
+class DynamicObjectData:
+    """Container for a single dynamic object read from a pose file.
+
+    Dynamic objects are objects that may change position or count over time, but
+    are not predicted every frame.  Only frames listed in sample_indices have
+    valid predictions.  Coordinates are always stored in (x, y) order.
+
+    points is always 4-D regardless of how many keypoints each object
+    instance has.  Single-keypoint objects (e.g. fecal boli) have
+    n_keypoints=1 after normalization on read.
+
+    Attributes:
+        points: Detected keypoint coordinates in (x, y) order, shape
+            (n_predictions, max_count, n_keypoints, 2).
+        counts: Number of valid detected objects for each prediction, shape
+            (n_predictions,).
+        sample_indices: Frame indices at which each prediction was made, shape
+            (n_predictions,).
+    """
+
+    points: npt.NDArray[np.float64]
+    counts: npt.NDArray[np.int64]
+    sample_indices: npt.NDArray[np.int64]
 
 
 @dataclass(frozen=True)
@@ -20,8 +47,13 @@ class PoseData:
             Format is [[upper_left_x, upper_left_y], [lower_right_x, lower_right_y]].
         segmentation_data: Optional segmentation masks or data.
         static_objects: Dictionary of static objects (e.g., 'lixit') and their positions.
+        dynamic_objects: Dictionary of dynamic objects (e.g., 'fecal_boli') and their data.
         external_ids: Optional list of external identifiers for each identity.
             Maps an identity index to an external ID string.
+        subjects: Optional per-animal biological metadata, keyed by identity name
+            (matching the values in external_ids).  Each value is a free-form
+            dict; standard keys are subject_id, sex, genotype,
+            strain, age, weight, species, description.
         metadata: Dictionary for any additional provenance or experimental metadata.
     """
 
@@ -35,7 +67,9 @@ class PoseData:
     bounding_boxes: np.ndarray | None = None
     segmentation_data: np.ndarray | None = None
     static_objects: dict[str, np.ndarray] = field(default_factory=dict)
+    dynamic_objects: dict[str, DynamicObjectData] = field(default_factory=dict)
     external_ids: list[str] | None = None
+    subjects: dict[str, dict] | None = None
     metadata: dict[str, Any] = field(default_factory=dict)
 
     def __post_init__(self):

packages/jabs-io/pyproject.toml

@@ -14,7 +14,6 @@ authors = [
 
 dependencies = [
     "jabs-core",
-    "ndx-pose>=0.2.2",
     "numpy>=2.0.0,<3.0.0",
 ]
 

packages/jabs-io/src/jabs/io/internal/pose/__init__.py

@@ -1,4 +1,4 @@
-"""Pose estimation NWB adapters."""
+"""Pose estimation adapters (NWB requires the [nwb] extra)."""
 
 from jabs.io.internal.pose.nwb import PoseNWBAdapter