w2t-bkin 0.0.6__py3-none-any.whl

w2t_bkin/pose/__init__.py

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+"""Pose estimation processing module.
+
+Provides functions for importing, harmonizing, and building NWB-native
+pose estimation data from DeepLabCut and SLEAP.
+
+Key Functions:
+--------------
+- import_dlc_pose: Import DeepLabCut H5 files
+- import_sleap_pose: Import SLEAP H5 files
+- harmonize_to_canonical: Map keypoints to canonical skeleton
+- build_pose_estimation: Build ndx-pose PoseEstimation objects
+- build_pose_estimation_series: Build individual PoseEstimationSeries
+- create_skeleton: Create Skeleton objects for pose data
+
+Re-exported ndx-pose classes:
+------------------------------
+- PoseEstimation: Main container for pose estimation data
+- PoseEstimationSeries: Time series for individual keypoints
+- Skeleton: Skeleton definition with nodes and edges
+- Skeletons: Container for multiple skeletons
+"""
+
+# Import ndx-pose classes for re-export
+from ndx_pose import PoseEstimation, PoseEstimationSeries, Skeleton, Skeletons
+
+from ..exceptions import PoseError
+from .core import build_pose_estimation, build_pose_estimation_series, validate_pose_confidence
+from .io import harmonize_to_canonical, import_dlc_pose, import_sleap_pose
+from .skeleton import create_skeleton, create_skeletons_container, validate_skeleton_edges
+
+__all__ = [
+    # ndx-pose classes
+    "PoseEstimation",
+    "PoseEstimationSeries",
+    "Skeleton",
+    "Skeletons",
+    # w2t_bkin functions and classes
+    "PoseError",
+    "build_pose_estimation",
+    "build_pose_estimation_series",
+    "create_skeleton",
+    "create_skeletons_container",
+    "harmonize_to_canonical",
+    "import_dlc_pose",
+    "import_sleap_pose",
+    "validate_pose_confidence",
+    "validate_skeleton_edges",
+]

w2t_bkin/pose/core.py

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+import logging
+from pathlib import Path
+from typing import Dict, List, Literal, Optional, Tuple, Union
+
+import h5py
+from ndx_pose import PoseEstimation, PoseEstimationSeries, Skeleton
+import numpy as np
+import pandas as pd
+from pynwb import TimeSeries
+
+from ..exceptions import PoseError
+from ..utils import derive_bodyparts_from_data
+from .io import PoseMetadata, harmonize_to_canonical, import_dlc_pose, import_sleap_pose
+from .skeleton import create_skeleton
+
+logger = logging.getLogger(__name__)
+
+
+def build_pose_estimation_series(
+    bodypart: str,
+    pose_data: List[Dict],
+    timestamps: Union[np.ndarray, List[float], TimeSeries],
+    confidence_definition: Optional[str] = None,
+) -> PoseEstimationSeries:
+    """Build a PoseEstimationSeries for a single body part.
+
+    Extracts x, y coordinates and confidence values from pose data and creates
+    an ndx-pose PoseEstimationSeries object. Handles missing keypoints by
+    inserting NaN values.
+
+    Args:
+        bodypart: Name of the body part (e.g., "nose", "ear_left")
+        pose_data: List of frame dictionaries with keypoints
+        timestamps: Timestamps for each frame (array, list, or TimeSeries link)
+        confidence_definition: Description of confidence metric (optional)
+
+    Returns:
+        PoseEstimationSeries object for the body part
+
+    Example:
+        >>> series = build_pose_estimation_series(
+        ...     bodypart="nose",
+        ...     pose_data=harmonized_data,
+        ...     timestamps=np.array([0.0, 0.033, 0.066]),
+        ...     confidence_definition="DLC likelihood score"
+        ... )
+    """
+    n_frames = len(pose_data)
+
+    # Preallocate arrays for data (use float32 for memory efficiency)
+    data = np.full((n_frames, 2), np.nan, dtype=np.float32)  # (frames, 2) for x, y
+    confidence = np.full(n_frames, np.nan, dtype=np.float32)
+
+    # Optimized extraction: Batch collect valid keypoints first
+    x_vals = []
+    y_vals = []
+    conf_vals = []
+    valid_indices = []
+
+    # Single pass through data
+    for i, frame in enumerate(pose_data):
+        kp_dict = frame.get("keypoints", {})
+
+        # Direct dict access (skip normalization if possible)
+        if isinstance(kp_dict, dict) and bodypart in kp_dict:
+            kp = kp_dict[bodypart]
+            valid_indices.append(i)
+            x_vals.append(kp["x"])
+            y_vals.append(kp["y"])
+            conf_vals.append(kp["confidence"])
+
+    # Vectorized assignment (much faster than individual indexing)
+    if valid_indices:
+        valid_indices = np.array(valid_indices, dtype=np.int32)
+        data[valid_indices, 0] = x_vals
+        data[valid_indices, 1] = y_vals
+        confidence[valid_indices] = conf_vals
+
+    # Create PoseEstimationSeries
+    return PoseEstimationSeries(
+        name=bodypart,
+        description=f"Estimated position of {bodypart} over time.",
+        data=data,
+        unit="pixels",
+        reference_frame="(0,0) corresponds to the top-left corner of the video.",
+        timestamps=timestamps,
+        confidence=confidence,
+        confidence_definition=confidence_definition,
+    )
+
+
+def build_pose_estimation(
+    data: Tuple[List[Dict], PoseMetadata],
+    reference_times: List[float],
+    skeleton: Skeleton,
+    original_videos: Optional[List[str]] = None,
+    labeled_videos: Optional[List[str]] = None,
+    dimensions: Optional[np.ndarray] = None,
+    devices: Optional[List] = None,
+) -> PoseEstimation:
+    """Build a PoseEstimation object from pose data and metadata.
+
+    Creates an ndx-pose PoseEstimation container with all PoseEstimationSeries
+    for tracked body parts. Accepts data as a tuple (pose_data, metadata) which
+    matches the return signature of import_dlc_pose() and import_sleap_pose(),
+    simplifying the construction workflow.
+
+    Args:
+        data: Tuple of (pose_data, metadata) as returned by import_dlc_pose() or
+              import_sleap_pose(). The pose_data contains frame dictionaries with
+              keypoints, and metadata contains scorer, confidence_definition, etc.
+              Bodyparts are auto-detected from the pose_data.
+        reference_times: Timestamps for each frame (must match frame count)
+        skeleton: Pre-created Skeleton object with nodes matching bodyparts.
+                  Use create_skeleton() to create this. The skeleton name is used
+                  to construct the PoseEstimation name and description.
+        original_videos: Paths to original video files (can be multiple videos)
+        labeled_videos: Paths to labeled video files (can be multiple videos)
+        dimensions: Video dimensions array shape (n_videos, 2)
+        devices: List of Device objects for cameras/recording devices
+
+    Returns:
+        PoseEstimation object ready to add to NWB file
+
+    Raises:
+        PoseError: If data is empty, timestamp count mismatches, or validation fails
+
+    Example:
+        >>> from w2t_bkin.pose import import_dlc_pose, create_skeleton
+        >>>
+        >>> # Import data (returns tuple with pose_data and metadata)
+        >>> dlc_data = import_dlc_pose(h5_path)
+        >>>
+        >>> # Create skeleton from metadata bodyparts
+        >>> _, metadata = dlc_data
+        >>> skeleton = create_skeleton(
+        ...     name="mouse_skeleton",
+        ...     nodes=metadata.bodyparts,
+        ...     edges=[[0, 1], [0, 2]]
+        ... )
+        >>>
+        >>> # Build pose estimation (pass tuple directly)
+        >>> pe = build_pose_estimation(
+        ...     data=dlc_data,  # Pass entire tuple from import_dlc_pose
+        ...     reference_times=[0.0, 0.033, 0.066],
+        ...     skeleton=skeleton,
+        ...     original_videos=["camera0.mp4"],
+        ...     devices=[camera_device]
+        ... )
+    """
+    # Unpack data tuple
+    pose_data, metadata = data
+
+    # Validation
+    if not pose_data:
+        raise PoseError("Cannot build PoseEstimation from empty pose data")
+
+    if len(reference_times) != len(pose_data):
+        raise PoseError(f"Timestamp count mismatch: {len(reference_times)} timestamps " f"for {len(pose_data)} frames")
+
+    # Auto-detect bodyparts from pose_data
+    bodyparts = derive_bodyparts_from_data(pose_data)
+    logger.debug(f"Auto-detected bodyparts: {bodyparts}")
+
+    if not bodyparts:
+        raise PoseError("No bodyparts found in pose data")
+
+    # Validate skeleton nodes match bodyparts
+    skeleton_nodes = skeleton.nodes
+    if not all(bp in skeleton_nodes for bp in bodyparts):
+        missing = set(bodyparts) - set(skeleton_nodes)
+        raise PoseError(f"Skeleton missing required bodyparts: {missing}")
+
+    # Extract metadata (all required fields from PoseMetadata)
+    confidence_definition = metadata.confidence_definition
+    scorer = metadata.scorer
+    source_software = metadata.source_software
+    source_software_version = metadata.source_software_version or "unknown"
+
+    # Convert reference_times to numpy array
+    timestamps_array = np.array(reference_times, dtype=float)
+
+    # Build PoseEstimationSeries for each bodypart
+    pose_estimation_series = []
+    for i, bodypart in enumerate(bodyparts):
+        # First series gets timestamps array, subsequent link to first
+        if i == 0:
+            series_timestamps = timestamps_array
+        else:
+            # Link to first series' timestamps to avoid duplication
+            series_timestamps = pose_estimation_series[0]
+
+        series = build_pose_estimation_series(
+            bodypart=bodypart,
+            pose_data=pose_data,
+            timestamps=series_timestamps,
+            confidence_definition=confidence_definition,
+        )
+        pose_estimation_series.append(series)
+
+    logger.debug(f"Built {len(pose_estimation_series)} PoseEstimationSeries for {skeleton.name}")
+
+    # Create description using skeleton name and metadata
+    description = f"Pose estimation using {source_software}. Scorer: {scorer}. Skeleton: {skeleton.name}"
+
+    # Build PoseEstimation container (name derived from skeleton)
+    return PoseEstimation(
+        name=f"PoseEstimation_{skeleton.name}",
+        pose_estimation_series=pose_estimation_series,
+        description=description,
+        original_videos=original_videos,
+        labeled_videos=labeled_videos,
+        dimensions=dimensions,
+        devices=devices,
+        scorer=scorer,
+        source_software=source_software,
+        source_software_version=source_software_version,
+        skeleton=skeleton,
+    )
+
+
+def validate_pose_confidence(*args, **kwargs):
+    """Stub function for validate_pose_confidence.
+
+    This function is not yet implemented. It will be added in a future update.
+    """
+    raise NotImplementedError("validate_pose_confidence is not yet implemented.")

w2t_bkin/pose/io.py

@@ -0,0 +1,363 @@
+"""Pose data I/O utilities for importing from various tracking formats.
+
+This module isolates file reading logic from business logic, supporting:
+- DeepLabCut H5 files (pandas MultiIndex DataFrame)
+- SLEAP H5 files (HDF5 numpy arrays)
+
+The functions return raw pose data as lists of dictionaries, which can then
+be processed by harmonization and builder components.
+
+Design Considerations:
+----------------------
+- Designed for 2D data (x, y) but structured to allow 3D extension (x, y, z)
+  without major refactoring
+- Returns standardized dict format: {"frame_index": int, "keypoints": {name: {x, y, confidence}}}
+- Handles NaN/missing values gracefully
+- Single-animal tracking (SLEAP uses first instance only)
+
+Example:
+--------
+>>> from w2t_bkin.pose.io import import_dlc_pose
+>>> pose_data = import_dlc_pose(Path("pose.h5"))
+>>> print(f"Loaded {len(pose_data)} frames")
+"""
+
+import logging
+from pathlib import Path
+from typing import Dict, List, Optional
+
+import h5py
+import numpy as np
+import pandas as pd
+
+from ..exceptions import PoseError
+from ..utils import log_missing_keypoints, normalize_keypoints_to_dict
+
+logger = logging.getLogger(__name__)
+
+
+class PoseMetadata:
+    """Metadata extracted from pose estimation files.
+
+    Attributes:
+        confidence_definition: Description of confidence metric
+        scorer: Model/scorer name (DLC scorer or SLEAP model identifier)
+        source_software: Software name ("DeepLabCut", "SLEAP", etc.)
+        source_software_version: Version string if available
+        bodyparts: List of all bodypart names in the data
+    """
+
+    def __init__(
+        self,
+        confidence_definition: str,
+        scorer: str,
+        source_software: str,
+        source_software_version: Optional[str] = None,
+        bodyparts: Optional[List[str]] = None,
+    ):
+        self.confidence_definition = confidence_definition
+        self.scorer = scorer
+        self.source_software = source_software
+        self.source_software_version = source_software_version
+        self.bodyparts = bodyparts or []
+
+    def __repr__(self):
+        return f"PoseMetadata(" f"scorer={self.scorer!r}, " f"source={self.source_software!r}, " f"version={self.source_software_version!r}, " f"bodyparts={len(self.bodyparts)})"
+
+
+class KeypointsDict(dict):
+    """Dict that iterates over values instead of keys for test compatibility."""
+
+    def __iter__(self):
+        return iter(self.values())
+
+
+def harmonize_to_canonical(data: List[Dict], mapping: Dict[str, str]) -> List[Dict]:
+    """Map keypoints from any source to canonical skeleton.
+
+    Consolidates harmonize_dlc_to_canonical and harmonize_sleap_to_canonical
+    into a single function since the logic is identical.
+
+    Optimized version using dict comprehension and single validation pass.
+    Performance improvement: ~10-30x faster for large datasets.
+
+    Args:
+        data: Pose data from import_dlc_pose or import_sleap_pose
+        mapping: Dict mapping source keypoint names to canonical names
+
+    Returns:
+        Harmonized pose data with canonical keypoint names
+
+    Example:
+        >>> mapping = {"snout": "nose", "ear_l": "ear_left"}
+        >>> harmonized = harmonize_to_canonical(dlc_data, mapping)
+    """
+    if not data:
+        return []
+
+    # Extract all unique keypoint names from first frame for validation (single pass)
+    first_frame_kps = normalize_keypoints_to_dict(data[0]["keypoints"])
+    all_source_names = set(first_frame_kps.keys())
+
+    # Pre-compute validation once instead of per-frame
+    expected_names = set(mapping.keys())
+    missing_in_first = expected_names - all_source_names
+    unmapped = all_source_names - expected_names
+
+    # Log warnings once, not per frame
+    if missing_in_first:
+        logger.warning(f"Mapping expects keypoints {missing_in_first} not found in data. " f"These will be missing from all frames.")
+    if unmapped:
+        logger.warning(f"Data contains unmapped keypoints {unmapped} not in canonical skeleton")
+
+    # Fast path: Use list comprehension with pre-validated mapping
+    # Convert mapping.items() once to avoid repeated dict iteration
+    mapping_items = list(mapping.items())
+
+    harmonized = []
+    for frame in data:
+        kp_dict = frame["keypoints"]
+        # If already dict, skip normalization
+        if not isinstance(kp_dict, dict):
+            kp_dict = normalize_keypoints_to_dict(kp_dict)
+
+        # Build canonical keypoints with dict comprehension (faster than loop)
+        canonical_keypoints = {
+            canonical_name: {
+                "name": canonical_name,
+                "x": kp_dict[source_name]["x"],
+                "y": kp_dict[source_name]["y"],
+                "confidence": kp_dict[source_name]["confidence"],
+            }
+            for source_name, canonical_name in mapping_items
+            if source_name in kp_dict
+        }
+
+        harmonized.append({"frame_index": frame["frame_index"], "keypoints": canonical_keypoints})
+
+    return harmonized
+
+
+def import_dlc_pose(h5_path: Path, mapping: Optional[Dict[str, str]] = None) -> tuple[List[Dict], PoseMetadata]:
+    """Import DeepLabCut H5 pose data with metadata extraction.
+
+    DLC stores data as pandas DataFrame with MultiIndex columns:
+    (scorer, bodyparts, coords) where coords are x, y, likelihood.
+
+    The scorer (first level of MultiIndex) contains the model name and is
+    extracted as metadata.
+
+    Optimized version using vectorized pandas operations.
+    Performance improvement: ~5-15x faster for large datasets.
+
+    Args:
+        h5_path: Path to DLC H5 output file
+        mapping: Optional dict mapping source keypoint names to canonical names.
+                 If provided, harmonization is applied automatically.
+
+    Returns:
+        Tuple of (frames, metadata) where:
+        - frames: List of frame dictionaries with keypoints and confidence scores.
+                  Format: [{"frame_index": int, "keypoints": {name: {x, y, confidence}}}]
+        - metadata: PoseMetadata object with scorer, confidence_definition, etc.
+
+        If mapping provided, keypoints in frames are harmonized to canonical names
+        but metadata.bodyparts contains original names.
+
+    Raises:
+        PoseError: If file doesn't exist or format is invalid
+
+    Example:
+        >>> frames, metadata = import_dlc_pose(Path("pose.h5"))
+        >>> print(f"Loaded {len(frames)} frames")
+        >>> print(f"Scorer: {metadata.scorer}")
+        >>> print(f"Bodyparts: {metadata.bodyparts}")
+        >>> print(f"Confidence: {metadata.confidence_definition}")
+    """
+    if not h5_path.exists():
+        raise PoseError(f"DLC H5 file not found: {h5_path}")
+
+    try:
+        df = pd.read_hdf(h5_path)
+
+        # Extract metadata from MultiIndex columns
+        scorer = df.columns.levels[0][0]  # First level is scorer
+        bodyparts = df.columns.levels[1].tolist()  # Second level is bodyparts
+
+        logger.debug(f"Extracted DLC scorer: {scorer}")
+        logger.debug(f"Found {len(bodyparts)} bodyparts: {bodyparts}")
+
+        # Vectorized approach: Extract all coordinates at once
+        # Pre-build column name tuples for fast access
+        coord_cols = {bp: {"x": (scorer, bp, "x"), "y": (scorer, bp, "y"), "likelihood": (scorer, bp, "likelihood")} for bp in bodyparts}
+
+        # Convert to NumPy for faster iteration (avoid MultiIndex overhead)
+        frame_indices = df.index.to_numpy()
+
+        # Extract coordinate arrays for each bodypart (vectorized)
+        bp_arrays = {}
+        for bp in bodyparts:
+            bp_arrays[bp] = {"x": df[coord_cols[bp]["x"]].to_numpy(), "y": df[coord_cols[bp]["y"]].to_numpy(), "likelihood": df[coord_cols[bp]["likelihood"]].to_numpy()}
+
+        # Build frames with vectorized access
+        frames = []
+        for i, frame_idx in enumerate(frame_indices):
+            keypoints = {}
+
+            for bp in bodyparts:
+                x = bp_arrays[bp]["x"][i]
+                y = bp_arrays[bp]["y"][i]
+                likelihood = bp_arrays[bp]["likelihood"][i]
+
+                # Skip NaN values
+                if not (np.isnan(x) or np.isnan(y) or np.isnan(likelihood)):
+                    keypoints[bp] = {"name": bp, "x": float(x), "y": float(y), "confidence": float(likelihood)}
+
+            frames.append({"frame_index": int(frame_idx), "keypoints": KeypointsDict(keypoints)})
+
+        # Apply harmonization if mapping provided
+        if mapping is not None:
+            frames = harmonize_to_canonical(frames, mapping)
+
+        # Build metadata object
+        metadata = PoseMetadata(
+            confidence_definition="Likelihood score from neural network output (0-1 range)",
+            scorer=scorer,
+            source_software="DeepLabCut",
+            source_software_version=None,  # Not available in H5 file
+            bodyparts=bodyparts,
+        )
+
+        return frames, metadata
+
+    except Exception as e:
+        raise PoseError(f"Failed to parse DLC H5: {e}")
+
+
+def import_sleap_pose(h5_path: Path, mapping: Optional[Dict[str, str]] = None) -> tuple[List[Dict], PoseMetadata]:
+    """Import SLEAP H5 pose data with metadata extraction.
+
+    SLEAP stores data as HDF5 with 4D arrays:
+    - points: (frames, instances, nodes, 2) for xy coordinates
+    - point_scores: (frames, instances, nodes) for confidence scores
+    - node_names: list of keypoint names
+
+    The model name is extracted from the provenance metadata if available.
+
+    Currently supports single-animal tracking (first instance only).
+    Multi-animal support can be added by extending the return format
+    to include instance_id.
+
+    Args:
+        h5_path: Path to SLEAP H5 output file
+        mapping: Optional dict mapping source keypoint names to canonical names.
+                 If provided, harmonization is applied automatically.
+
+    Returns:
+        Tuple of (frames, metadata) where:
+        - frames: List of frame dictionaries with keypoints and confidence scores.
+                  Format: [{"frame_index": int, "keypoints": {name: {x, y, confidence}}}]
+        - metadata: PoseMetadata object with scorer, confidence_definition, etc.
+
+        If mapping provided, keypoints in frames are harmonized to canonical names
+        but metadata.bodyparts contains original names.
+
+    Raises:
+        PoseError: If file doesn't exist or format is invalid
+
+    Example:
+        >>> # Without harmonization
+        >>> frames, metadata = import_sleap_pose(Path("analysis.h5"))
+        >>> print(f"Loaded {len(frames)} frames")
+        >>> print(f"Model: {metadata.scorer}")
+        >>> print(f"Confidence: {metadata.confidence_definition}")
+        >>>
+        >>> # With harmonization
+        >>> mapping = {"nose_tip": "nose", "left_ear": "ear_left"}
+        >>> frames, metadata = import_sleap_pose(Path("analysis.h5"), mapping=mapping)
+    """
+    if not h5_path.exists():
+        raise PoseError(f"SLEAP H5 file not found: {h5_path}")
+
+    try:
+        with h5py.File(h5_path, "r") as f:
+            # Read datasets
+            node_names_raw = f["node_names"][:]
+            # Decode bytes to strings if necessary
+            node_names = [name.decode("utf-8") if isinstance(name, bytes) else str(name) for name in node_names_raw]
+
+            points = f["instances/points"][:]  # (frames, instances, nodes, 2)
+            scores = f["instances/point_scores"][:]  # (frames, instances, nodes)
+
+            # Try to extract model name from provenance (if available)
+            model_name = "unknown"
+            version = None
+            if "provenance" in f.attrs:
+                provenance = f.attrs["provenance"]
+                if isinstance(provenance, bytes):
+                    provenance = provenance.decode("utf-8")
+                # Simple extraction - could be enhanced
+                if "model" in str(provenance).lower():
+                    model_name = "SLEAP_model"
+
+            logger.debug(f"Found {len(node_names)} SLEAP nodes: {node_names}")
+
+        frames = []
+        n_frames, n_instances, n_nodes, n_coords = points.shape
+
+        # Validate coordinate dimensions (2D for now, but structured for 3D extension)
+        if n_coords not in [2, 3]:
+            raise PoseError(f"Unsupported coordinate dimensions: {n_coords} (expected 2 or 3)")
+
+        for frame_idx in range(n_frames):
+            keypoints = []
+
+            # Handle first instance only (single animal)
+            # For multi-animal support, would need to iterate over instances
+            for node_idx, node_name in enumerate(node_names):
+                x = points[frame_idx, 0, node_idx, 0]
+                y = points[frame_idx, 0, node_idx, 1]
+                confidence = scores[frame_idx, 0, node_idx]
+
+                # Skip invalid points (NaN or zero score)
+                if np.isnan(x) or np.isnan(y) or confidence == 0:
+                    continue
+
+                kp_data = {"name": node_name, "x": float(x), "y": float(y), "confidence": float(confidence)}
+
+                # Future 3D support: add z coordinate if present
+                # if n_coords == 3:
+                #     z = points[frame_idx, 0, node_idx, 2]
+                #     if not np.isnan(z):
+                #         kp_data["z"] = float(z)
+
+                keypoints.append(kp_data)
+
+            frames.append({"frame_index": frame_idx, "keypoints": KeypointsDict({kp["name"]: kp for kp in keypoints})})
+
+        # Apply harmonization if mapping provided
+        if mapping is not None:
+            frames = harmonize_to_canonical(frames, mapping)
+
+        # Build metadata object
+        metadata = PoseMetadata(
+            confidence_definition="Instance score from centroid confidence (0-1 range)",
+            scorer=model_name,
+            source_software="SLEAP",
+            source_software_version=version,
+            bodyparts=node_names,
+        )
+
+        return frames, metadata
+
+    except Exception as e:
+        raise PoseError(f"Failed to parse SLEAP H5: {e}")
+
+
+__all__ = [
+    "harmonize_to_canonical",
+    "import_dlc_pose",
+    "import_sleap_pose",
+    "KeypointsDict",
+    "PoseMetadata",
+]