Fetching Synchronized Data

Fetching Synchronized Keypoints + Reconstruction Data

Overview

KinematicReconstruction qpos and 2D keypoints come from different DataJoint tables with independently managed timestamps. Naive timestamp matching silently produces frame offsets that corrupt downstream tasks (guidance, evaluation, metrics). The correct approach uses fetch_keypoints(only_detected=True) from BodyModels, which guarantees 1:1 frame correspondence with KR qpos by construction.

When to Use

• Fetching 2D keypoints that must align frame-by-frame with KR qpos
• Building inference/guidance pipelines that pair observations with reconstruction
• Debugging high reprojection error or misaligned 2D-3D data
• Writing any code that joins TopDownPerson keypoints with KinematicReconstruction

When NOT to use: Fetching keypoints for standalone 2D analysis (no KR alignment needed), or querying KR qpos without 2D observations.

The Correct Pattern

from body_models.datajoint.dataset import fetch_keypoints as bm_fetch_keypoints
from body_models.datajoint.kinematic_dj import KinematicReconstruction

trial_key = {
    "participant_id": participant_id,
    "session_date": session_date,
    "recording_timestamps": recording_timestamps,
}
full_key = {**trial_key, "kinematic_reconstruction_settings_num": 137}

# 1. Fetch qpos from KR
qpos = (KinematicReconstruction.Trial & full_key).fetch1("qpos")  # (T, 41)

# 2. Fetch keypoints using the SAME function that built the KR
timestamps, keypoints_raw = bm_fetch_keypoints(trial_key,
# timestamps: (T,) video-start-relative seconds
# keypoints_raw: (C, T, 87, 3) — (x, y, confidence) per camera/frame/marker

# 3. CRITICAL: verify 1:1 correspondence
assert qpos.shape[0] == keypoints_raw.shape[1], (
    f"Frame count mismatch: qpos={qpos.shape[0]} vs keypoints={keypoints_raw.shape[1]}"
)

# 4. Extract components
confidences = keypoints_raw[..., 2]    # (C, T, 87)
keypoints_2d = keypoints_raw[..., :2]  # (C, T, 87, 2)

Why this works: fetch_keypoints(only_detected=True) applies the exact same frame filtering as KeypointDataset used when building the KR. Both arrays share the same frame indices — qpos[i] corresponds to keypoints[:, i] by construction.

Camera Parameter Reordering

KinematicReconstruction.updated_calibration stores camera parameters in Calibration table order. Keypoints from fetch_keypoints are in alphabetical SingleCameraVideo order. These may differ.

from multi_camera.datajoint.calibrate_cameras import Calibration
from multi_camera.datajoint.multi_camera_dj import SingleCameraVideo

cal_camera_names = (Calibration & parent_key).fetch1("camera_names")
camera_rows = (SingleCameraVideo & trial_key).fetch(as_dict=True, order_by="camera_name")
kp_camera_names = [row["camera_name"] for row in camera_rows]

# Reindex camera_params to match keypoint camera order
cal_names_list = list(cal_camera_names)
reorder_idx = [cal_names_list.index(name) for name in kp_camera_names]
for pkey in ("mtx", "rvec", "tvec", "dist"):
    val = np.asarray(camera_params[pkey])
    if val.ndim > 1:
        camera_params[pkey] = val[reorder_idx]

Without this, camera i in keypoints_2d gets projected with the wrong camera's intrinsics/extrinsics.

Contiguous Segment Selection

After alignment, find the longest window with continuous detections and no time gaps:

detected = np.sum(confidences, axis=(0, 2))  # (T,) — sum across cameras and joints
dt = np.median(np.diff(timestamps))
time_gaps = np.concatenate([np.diff(timestamps), [dt]]) > (1.5 * dt)
valid = np.logical_and(detected > 0, ~time_gaps)

# find_longest_segment returns (start, end) exclusive
start, end = find_longest_segment(valid)
timestamps = timestamps[start:end]
qpos = qpos[start:end]
keypoints_2d = keypoints_2d[:, start:end]
confidences = confidences[:, start:end]

Anti-Patterns

Real-world impact: The timestamp-matching anti-pattern caused a 38-frame temporal offset on trial ASB_144 cam 8 (first detection at video frame 38), producing 900px reprojection error and unusable guidance.

Invariants

1. Frame correspondence: qpos.shape[0] == keypoints_raw.shape[1] — always assert this
2. Camera ordering: After reordering, camera_params index i matches keypoints_2d[i]
3. Timestamps are video-start-relative: Not zeroed by KR; usable directly for time-gap detection
4. only_detected=True is mandatory when aligning with KR qpos

Quick Reference

Complete reference implementation: BiomechanicalFlowModel/src/biomechanical_fm/datajoint/datajoint_fetcher.py:fetch_trial_data()

Related skills: rae:datajoint-biomechanics-schema for schema details, rae:camera-model for projection conventions.