myogait 0.6.0

Markerless video-based gait analysis toolkit

myogait

Markerless video-based gait analysis toolkit.

Author: Frederic Fer, Institut de Myologie ([e-mail])

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Features

• Multi-model pose extraction — MediaPipe, YOLO, Sapiens (3 sizes), Sapiens 2 (4 sizes), ViTPose, RTMW, HRNet, RTMPose, OpenPose, AlphaPose, Detectron2
• Sapiens / Sapiens 2 depth estimation — monocular relative depth per landmark
• Sapiens / Sapiens 2 body segmentation — 28/29-class body-part labels per landmark
• Frame coherence scoring — per-frame biomechanical quality metric (z-score based)
• Butterworth, Savitzky-Golay, and Kalman filtering
• Joint angle computation (sagittal vertical axis, sagittal classic)
• 4 event detection methods (Zeni, crossing, velocity, O'Connor)
• Gait cycle segmentation and normalization
• Spatio-temporal analysis (cadence, stride time, stance%)
• Symmetry and variability indices
• Step length and walking speed estimation
• Harmonic ratio and regularity index
• Advanced pathology detection (Trendelenburg, spastic, steppage, crouch)
• Biomechanical validation against physiological ranges
• Publication-quality matplotlib plots
• Multi-page PDF clinical report
• Export to CSV, OpenSim (.mot/.trc), Excel
• YAML/JSON pipeline configuration
• CLI with extract, run, analyze, batch, download, and info commands

Installation

pip install myogait

Install with a specific pose estimation backend:

pip install myogait[mediapipe]   # MediaPipe (lightweight, CPU)
pip install myogait[yolo]        # YOLO via Ultralytics
pip install myogait[sapiens]     # Sapiens v1 (Meta AI) + Intel Arc GPU support
pip install myogait[sapiens2]    # Sapiens 2 (Meta AI, ICLR 2026) — see "Sapiens 2" section below for one-shot setup
pip install myogait[vitpose]     # ViTPose via HuggingFace Transformers
pip install myogait[rtmw]        # RTMW 133-keypoint whole-body
pip install myogait[mmpose]      # HRNet / RTMPose via MMPose
pip install myogait[alphapose]   # AlphaPose FastPose
pip install myogait[detectron2]  # Detectron2 Keypoint R-CNN
pip install myogait[all]         # All backends

Supported Pose Estimation Backends

Backend	Install	Notes
MediaPipe	pip install myogait[mediapipe]	Fast, good for real-time. 33 landmarks
YOLOv8-Pose	pip install myogait[yolo]	Fast, robust. 17 COCO keypoints
ViTPose	pip install myogait[vitpose]	State-of-the-art accuracy
Sapiens	pip install myogait[sapiens]	Meta model, depth estimation
Sapiens 2	pip install myogait[sapiens2]	Meta ICLR 2026, +4 mAP, 4K support
RTMPose/RTMLib	pip install myogait[rtmw]	Real-time, ONNX optimized
MMPose	pip install myogait[mmpose]	Academic reference, many models
OpenPose	Built-in (OpenCV DNN)	Historical baseline, bottom-up. 17 COCO keypoints
AlphaPose	pip install myogait[alphapose]	Top-down baseline, biomechanics standard
Detectron2	pip install myogait[detectron2]	Meta academic baseline, Keypoint R-CNN

GPU Support

All models support NVIDIA CUDA GPUs. Sapiens and ViTPose also support Intel Arc / Xe GPUs (via intel-extension-for-pytorch).

Model	CUDA	Intel Arc (XPU)	CPU
MediaPipe	—	—	yes
YOLO	yes	—	yes
Sapiens (pose, depth, seg)	yes	yes	yes
Sapiens 2 (pose, depth, seg)	yes	yes	yes
ViTPose	yes	yes	yes
RTMW	yes (onnxruntime)	—	yes
HRNet / RTMPose	yes	—	yes
OpenPose	yes (OpenCV DNN)	—	yes
AlphaPose	yes	yes	yes
Detectron2	yes	—	yes

Supported Pose Models

Name	Keypoints	Format	Backend	Install
mediapipe	33	MediaPipe	Google MediaPipe Tasks (heavy)	pip install myogait[mediapipe]
yolo	17	COCO	Ultralytics YOLOv8-Pose	pip install myogait[yolo]
sapiens-quick	17 COCO + 308 Goliath	COCO	Meta Sapiens 0.3B (336M params)	pip install myogait[sapiens]
sapiens-mid	17 COCO + 308 Goliath	COCO	Meta Sapiens 0.6B (664M params)	pip install myogait[sapiens]
sapiens-top	17 COCO + 308 Goliath	COCO	Meta Sapiens 1B (1.1B params)	pip install myogait[sapiens]
sapiens2-quick	17 COCO + 308 Goliath	COCO	Meta Sapiens 2 0.4B (ICLR 2026)	pip install myogait[sapiens2]
sapiens2-mid	17 COCO + 308 Goliath	COCO	Meta Sapiens 2 0.8B	pip install myogait[sapiens2]
sapiens2-top	17 COCO + 308 Goliath	COCO	Meta Sapiens 2 1B	pip install myogait[sapiens2]
sapiens2-ultra	17 COCO + 308 Goliath	COCO	Meta Sapiens 2 5B	pip install myogait[sapiens2]
vitpose	17	COCO	ViTPose-base (HuggingFace)	pip install myogait[vitpose]
vitpose-large	17	COCO	ViTPose+-large (HuggingFace)	pip install myogait[vitpose]
vitpose-huge	17	COCO	ViTPose+-huge (HuggingFace)	pip install myogait[vitpose]
rtmw	17 COCO + 133 whole-body	COCO	RTMW via rtmlib	pip install myogait[rtmw]
hrnet	17	COCO	HRNet-W48 via MMPose	pip install myogait[mmpose]
mmpose	17	COCO	RTMPose-m via MMPose	pip install myogait[mmpose]
openpose	17	COCO	CMU OpenPose via OpenCV DNN	Built-in
alphapose	17	COCO	AlphaPose FastPose (ResNet-50)	pip install myogait[alphapose]
detectron2	17	COCO	Keypoint R-CNN (R50-FPN, 3x)	pip install myogait[detectron2]

Sapiens Auxiliary Models

In addition to pose, Sapiens provides depth estimation and body-part segmentation. These run alongside any Sapiens pose model to enrich per-landmark data.

Depth Estimation

Monocular relative depth. Per-landmark depth values (closer = higher) are stored in each frame as landmark_depths.

Size	HuggingFace repo
0.3b	facebook/sapiens-depth-0.3b-torchscript
0.6b	facebook/sapiens-depth-0.6b-torchscript
1b	facebook/sapiens-depth-1b-torchscript
2b	facebook/sapiens-depth-2b-torchscript

Body-Part Segmentation

28-class segmentation (face, torso, arms, legs, hands, feet, clothing...). Per-landmark body-part labels are stored in each frame as landmark_body_parts.

Size	mIoU	HuggingFace repo
0.3b	76.7	facebook/sapiens-seg-0.3b-torchscript
0.6b	77.8	facebook/sapiens-seg-0.6b-torchscript
1b	79.9	facebook/sapiens-seg-1b-torchscript

Sapiens 2 (ICLR 2026)

Sapiens 2 improves over v1 with +4 mAP (pose), +24.3 mIoU (seg), and 45.6% lower angular error (normals). Same Goliath 308 keypoint layout as v1. Requires torch>=2.7 and safetensors.

Size	HuggingFace pose repo	HuggingFace depth repo	HuggingFace seg repo
0.4b	facebook/sapiens2-pose-0.4b	facebook/sapiens2-depth-0.4b	facebook/sapiens2-seg-0.4b
0.8b	facebook/sapiens2-pose-0.8b	facebook/sapiens2-depth-0.8b	facebook/sapiens2-seg-0.8b
1b	facebook/sapiens2-pose-1b	facebook/sapiens2-depth-1b	facebook/sapiens2-seg-1b
5b	facebook/sapiens2-pose-5b	facebook/sapiens2-depth-5b	facebook/sapiens2-seg-5b

Sapiens 2 segmentation uses 29 classes (adds Eyeglass at index 2).

Plug-and-play setup

Meta ships Sapiens 2 weights as .safetensors and the Python package that rebuilds the model architecture lives only on GitHub (not PyPI). myogait ships a one-shot helper that handles the bridge:

# 1) myogait + Sapiens 2 runtime deps
pip install myogait[sapiens2]

# 2) one-shot setup: installs Meta `sapiens` from GitHub, downloads the
#    weights, traces a TorchScript .pt2 cached in ~/.myogait/models/.
#    From now on inference no longer needs the Meta package.
myogait setup-sapiens2 --size 0.4b --cleanup-safetensors

Once that command finishes, mg.extract(..., model="sapiens2-quick") loads the cached .pt2 directly — no Meta package required, no internet on subsequent runs. Repeat for --size 0.8b, 1b, 5b if you want the larger variants. The .pt2 is device-specific (constants get baked at trace time), so the helper traces on the device myogait will use at inference (CUDA > XPU > CPU, in that order).

If you prefer to keep the Meta sapiens package around (e.g. for research code that imports it directly), drop the --uninstall-sapiens flag — it stays installed but is not on the inference path anymore.

Usage

# Sapiens v1 — pose + depth + segmentation
myogait extract video.mp4 -m sapiens-quick --with-depth --with-seg

# Sapiens 2 — same API, better accuracy
myogait extract video.mp4 -m sapiens2-top --with-depth --with-seg

# Python
from myogait import extract
data = extract("video.mp4", model="sapiens2-top", with_depth=True, with_seg=True)

End-to-end demo (extract + overlay + side-by-side + angle plots)

python examples/sapiens2_compare_pipeline.py path/to/video.mp4 --out-dir out

Produces in out/:

• <stem>_<model>.json — pivot data per model (mediapipe, sapiens-quick, sapiens2-quick), reused on subsequent runs
• <stem>_<model>.mp4 — skeleton overlay per model
• compare_3way_slow.mp4 — three panels side-by-side at half-speed with legends and a darkened background so the skeleton stands out
• compare_angles.png — per-cycle hip / knee / ankle curves on left and right side, every cycle thin + each model's mean thick

The skeleton-on-video alignment honours data["frames"][i]["frame_idx"], so the auto-cropped intro of long recordings is rendered correctly across all models.

Experimental AIM Benchmark Input Degradation

myogait includes an experimental pre-extraction degradation layer for robustness benchmarking in the AIM benchmark context only. By default, it is disabled and applies no modification.

Python API:

from myogait import extract

data = extract(
    "video.mp4",
    model="mediapipe",
    experimental={
        "enabled": True,
        "target_fps": 15.0,    # frame-rate degradation
        "downscale": 0.6,      # spatial degradation
        "contrast": 0.7,       # contrast degradation
        "aspect_ratio": 1.2,   # non-square stretch
        "perspective_x": 0.2,  # side-like perspective skew
        "perspective_y": 0.1,  # forward/backward tilt skew
    },
)

CLI:

myogait extract video.mp4 \
  --exp-enable \
  --exp-target-fps 15 \
  --exp-downscale 0.6 \
  --exp-contrast 0.7 \
  --exp-aspect-ratio 1.2 \
  --exp-perspective-x 0.2 \
  --exp-perspective-y 0.1

Experimental VICON Alignment (Single Video)

For AIM benchmark workflows, you can align one myogait result with one VICON trial and attach ground-truth comparison metrics to the JSON. This is experimental and disabled by default in the standard pipeline.

from myogait import run_single_trial_vicon_benchmark

data = run_single_trial_vicon_benchmark(
    data,                               # myogait result dict
    trial_dir="/path/to/trial_01_1",   # contains *.mat files
    vicon_fps=200.0,
    max_lag_seconds=10.0,
)

# Results in data["experimental"]["vicon_benchmark"]

Experimental Single-Pair Benchmark Runner (AIM Only)

You can run a full benchmark grid on one (video, vicon_trial) pair and generate:

• one JSON per run (<output_dir>/runs/*.json)
• one CSV summary (<output_dir>/benchmark_summary.csv)
• one manifest (<output_dir>/benchmark_manifest.json)

from myogait import run_single_pair_benchmark

manifest = run_single_pair_benchmark(
    video_path="video.mp4",
    vicon_trial_dir="/path/to/trial_01_1",
    output_dir="./benchmark_out",
    benchmark_config={
        "models": ["mediapipe", "yolo"],         # or "all"
        "event_methods": "all",                  # or ["zeni", "gk_zeni", ...]
        "normalization_variants": [
            {"name": "none", "enabled": False, "kwargs": {}},
            {"name": "butterworth", "enabled": True, "kwargs": {"filters": ["butterworth"]}},
        ],
        "degradation_variants": [
            {"name": "none", "experimental": {"enabled": False}},
            {"name": "lowres", "experimental": {"enabled": True, "downscale": 0.7, "target_fps": 15.0}},
        ],
        "continue_on_error": True,
    },
)

print(manifest["summary_csv"])

This runner is experimental and intended only for AIM benchmark workflows.

References

• Sapiens v1: Rawal et al., Sapiens: Foundation for Human Vision Models, ECCV 2024 — arXiv:2408.12569 — Code — Models
• Sapiens 2: Rawal et al., Sapiens 2: A Human Foundation Model, ICLR 2026 — arXiv:2604.21681 — Code — Models

ViTPose

Vision Transformer for pose estimation (NeurIPS 2022). Top-down architecture with RT-DETR person detector. Fully pip-installable via HuggingFace Transformers.

Variant	Size	HuggingFace repo
vitpose (base)	90M	usyd-community/vitpose-base-simple
vitpose-large	400M	usyd-community/vitpose-plus-large
vitpose-huge	900M	usyd-community/vitpose-plus-huge

• Paper: Xu et al., ViTPose: Simple Vision Transformer Baselines for Human Pose Estimation, NeurIPS 2022 — arXiv:2204.12484
• Paper: Xu et al., ViTPose++: Vision Transformer for Generic Body Pose Estimation, TPAMI 2024 — arXiv:2212.04246

RTMW (Whole-Body 133 Keypoints)

Real-Time Multi-person Whole-body estimation: body (17) + feet (6) + face (68) + hands (42) = 133 keypoints. Uses rtmlib (lightweight ONNX inference, no MMPose required).

Mode	Pose Model	Speed
performance	RTMW-x-l 384x288	Slower, most accurate
balanced	RTMW-x-l 256x192	Default
lightweight	RTMW-l-m 256x192	Fastest

• Paper: Jiang et al., RTMPose: Real-Time Multi-Person Pose Estimation based on MMPose, 2023
• RTMW configs: MMPose cocktail14
• rtmlib: github.com/Tau-J/rtmlib

Other Pose Models

MediaPipe

Google's MediaPipe PoseLandmarker — 33 landmarks with full-body coverage. Uses the heavy model variant (most accurate). Auto-downloaded on first use.

• Docs: developers.google.com/mediapipe

YOLO Pose

Ultralytics YOLOv8-Pose — 17 COCO keypoints, fast single-shot detection.

• Docs: docs.ultralytics.com

HRNet / RTMPose (MMPose)

HRNet-W48 and RTMPose-m via the OpenMMLab MMPose framework — 17 COCO keypoints.

• MMPose: github.com/open-mmlab/mmpose
• HRNet: Sun et al., Deep High-Resolution Representation Learning for Visual Recognition, TPAMI 2019
• RTMPose: Jiang et al., RTMPose: Real-Time Multi-Person Pose Estimation based on MMPose, 2023

OpenPose

CMU OpenPose — historical bottom-up baseline, 17 COCO keypoints via OpenCV DNN. No extra dependency needed (uses OpenCV DNN, included in core install). Model auto-downloaded on first use (~200 MB).

• Paper: Cao et al., Realtime Multi-Person 2D Pose Estimation using Part Affinity Fields, CVPR 2017
• Code: github.com/CMU-Perceptual-Computing-Lab/openpose

AlphaPose

AlphaPose FastPose (ResNet-50) — top-down baseline widely used in biomechanics. Uses YOLO person detection + heatmap-based pose estimation. Supports both the official AlphaPose library and a fallback PyTorch reimplementation.

• Paper: Fang et al., AlphaPose: Whole-Body Regional Multi-Person Pose Estimation and Tracking in Real-Time, TPAMI 2022
• Code: github.com/MVIG-SJTU/AlphaPose

Detectron2 / Keypoint R-CNN

Meta's Detectron2 with Keypoint R-CNN (ResNet-50-FPN, 3x schedule) — academic baseline. Built-in person detection and 17 COCO keypoint estimation in a single pass.

• Paper: Wu et al., Detectron2, 2019 ; He et al., Mask R-CNN, ICCV 2017
• Code: github.com/facebookresearch/detectron2

Tutorials & Examples

Basic Pipeline

The core workflow extracts pose landmarks from video, preprocesses the signal, computes joint kinematics, detects gait events, and derives spatio-temporal parameters.

from myogait import extract, normalize, compute_angles, detect_events
from myogait import segment_cycles, analyze_gait

# 1. Extract landmarks from video
data = extract("walking_video.mp4", model="mediapipe")

# 2. Preprocess: filter noise, handle gaps
data = normalize(data, filters=["butterworth"])

# 3. Compute joint angles (sagittal + frontal if depth available)
data = compute_angles(data)

# 4. Detect gait events (heel strikes, toe offs)
data = detect_events(data, method="gk_bike")  # uses gaitkit Bayesian detector

# 5. Segment into gait cycles
cycles = segment_cycles(data)

# 6. Compute spatio-temporal parameters
stats = analyze_gait(data, cycles)
print(f"Cadence: {stats['spatiotemporal']['cadence_steps_per_min']:.1f} steps/min")
print(f"Walking speed: {stats['walking_speed']['speed_mean']:.2f} m/s")

Clinical Scores

Compute standardized gait quality indices used in clinical gait analysis laboratories worldwide.

from myogait import gait_profile_score_2d, sagittal_deviation_index
from myogait import gait_variable_scores, movement_analysis_profile

# GPS-2D: overall gait quality score (RMS deviation from normative)
gps = gait_profile_score_2d(cycles)
print(f"GPS-2D: {gps['gps_2d_overall']:.1f}")

# SDI: Sagittal Deviation Index (0-120, 100 = normal)
# Note: This is a z-score based index, NOT the GDI (Schwartz & Rozumalski 2008).
sdi = sagittal_deviation_index(cycles)
print(f"SDI: {sdi['gdi_2d_overall']:.1f}")

# Per-joint deviation scores
gvs = gait_variable_scores(cycles)
for side in ("left", "right"):
    for joint, score in gvs[side].items():
        print(f"  {side} {joint}: {score:.1f}")

Data Quality Assessment

Evaluate landmark detection confidence and flag outliers before running the analysis pipeline.

from myogait import confidence_filter, detect_outliers, data_quality_score
from myogait import frame_coherence_score

# Filter low-confidence landmarks
data = confidence_filter(data, threshold=0.3)

# Detect and interpolate outliers
data = detect_outliers(data, z_thresh=3.0)

# Quality report
quality = data_quality_score(data)
print(f"Quality score: {quality['score']}/100")

# Per-frame coherence scoring (z-score based, adapts to any FPS)
data = frame_coherence_score(data)
print(f"Mean coherence: {data['coherence_summary']['mean']:.3f}")
print(f"Low frames: {data['coherence_summary']['low_coherence_frames']}")

Normative Comparison

Compare patient kinematics against published normative reference bands (Perry & Burnfield).

from myogait import plot_normative_comparison, get_normative_band

# Plot patient vs normative bands (Perry & Burnfield)
fig = plot_normative_comparison(data, cycles, plane="both")
fig.savefig("normative_comparison.png", dpi=150)

# Access raw normative data
band = get_normative_band("hip", stratum="adult")
mean, lower, upper = band["mean"], band["lower"], band["upper"]

Event Detection with gaitkit

myogait integrates multiple gait event detection algorithms, including Bayesian and ensemble methods from the gaitkit library.

from myogait import detect_events, event_consensus, list_event_methods

# List all available methods
print(list_event_methods())
# ['zeni', 'velocity', 'crossing', 'oconnor',
#  'gk_bike', 'gk_zeni', 'gk_ensemble', ...]

# Single method (gaitkit Bayesian BIS -- best F1 score)
data = detect_events(data, method="gk_bike")

# Consensus: vote across multiple detectors
data = event_consensus(data, methods=["gk_bike", "gk_zeni", "gk_oconnor"])

Export to OpenSim / Pose2Sim

Export landmarks and kinematics in formats compatible with OpenSim musculoskeletal modeling and Pose2Sim multi-camera triangulation.

from myogait import export_trc, export_mot, export_openpose_json
from myogait import export_opensim_scale_setup, export_ik_setup

# OpenSim .trc markers file (with height-based unit conversion)
export_trc(data, "markers.trc", opensim_model="gait2392")

# OpenSim .mot kinematics
export_mot(data, "kinematics.mot")

# OpenSim Scale Tool setup XML
export_opensim_scale_setup(data, "scale_setup.xml", model_file="gait2392.osim")

# OpenSim IK setup XML
export_ik_setup("markers.trc", "ik_setup.xml", model_file="scaled_model.osim")

# Pose2Sim: export OpenPose-format JSON for triangulation
export_openpose_json(data, "./openpose_output/", model="BODY_25")

Video Overlay & Visualization

Generate annotated videos, anonymized stick-figure animations, and publication-ready dashboards.

from myogait import render_skeleton_video, render_stickfigure_animation
from myogait import plot_summary, plot_gvs_profile

# Skeleton overlay on original video
render_skeleton_video("video.mp4", data, "overlay.mp4", show_angles=True)

# Anonymized stick figure GIF
render_stickfigure_animation(data, "stickfigure.gif")

# Summary dashboard
fig = plot_summary(data, cycles, stats)
fig.savefig("dashboard.png", dpi=150)

# MAP barplot (Movement Analysis Profile)
fig = plot_gvs_profile(gvs)
fig.savefig("gvs_profile.png", dpi=150)

PDF Report

Generate a multi-page clinical report with kinematic plots, spatio-temporal tables, and normative comparisons.

from myogait import generate_report

# Generate clinical PDF report (French or English)
generate_report(data, cycles, stats, "rapport_marche.pdf", language="fr")

Multiple Export Formats

Export analysis results to a variety of tabular and structured formats for downstream processing and archival.

from myogait import export_csv, export_excel, to_dataframe, export_summary_json

# CSV files (one per data type)
export_csv(data, "./csv_output/", cycles, stats)

# Excel workbook
export_excel(data, "gait_analysis.xlsx", cycles, stats)

# Pandas DataFrame for custom analysis
df = to_dataframe(data, what="angles")
print(df.head())

# Compact summary JSON
export_summary_json(data, cycles, stats, "summary.json")

CLI Usage

Run the full pipeline on a video:

myogait run video.mp4                                    # MediaPipe (default)
myogait run video.mp4 -m sapiens-quick                   # Sapiens 0.3B
myogait run video.mp4 -m sapiens-top --with-depth        # Sapiens 1B + depth
myogait run video.mp4 -m sapiens2-top --with-depth       # Sapiens 2 1B + depth
myogait run video.mp4 -m sapiens2-ultra                  # Sapiens 2 5B
myogait run video.mp4 -m vitpose                         # ViTPose
myogait run video.mp4 -m rtmw                            # RTMW 133 keypoints

Extract landmarks only:

myogait extract video.mp4 -m sapiens-top --with-depth --with-seg

Analyze previously extracted results:

myogait analyze result.json --csv --pdf

Optional lateral-label correction:

from myogait import correct_lateral_labels

# Default: conservative global inversion correction
data = correct_lateral_labels(data)

# Opt-in: recover isolated ankle/knee/heel swaps during crossings
data = correct_lateral_labels(data, mode="partial")

Batch process multiple videos:

myogait batch *.mp4 -o results/

Download models:

myogait download --list                 # list all available models
myogait download sapiens-0.3b           # Sapiens v1 pose 0.3B
myogait download sapiens-depth-1b       # Sapiens v1 depth 1B
myogait download sapiens2-1b            # Sapiens 2 pose 1B
myogait download sapiens2-ultra         # Sapiens 2 pose 5B

Inspect a result file:

myogait info result.json

API Reference

All functions operate on a single data dict that flows through the pipeline.

Function	Description
Core pipeline
extract(video, model, experimental=None)	Extract pose landmarks from video
normalize(data, filters)	Filter and normalize landmark trajectories
compute_angles(data)	Compute sagittal joint angles
compute_frontal_angles(data)	Compute frontal plane angles (requires depth)
detect_events(data, method)	Detect gait events (15 methods incl. gaitkit)
event_consensus(data, methods)	Multi-method voting for robust event detection
segment_cycles(data)	Segment into individual gait cycles
analyze_gait(data, cycles)	Compute spatio-temporal parameters
run_single_trial_vicon_benchmark(data, trial_dir)	Experimental VICON alignment + metrics (single trial)
run_single_pair_benchmark(video, trial_dir, output_dir, benchmark_config=None)	Experimental benchmark grid runner (single video + single VICON trial)
Clinical scores
gait_profile_score_2d(cycles)	GPS-2D: overall gait deviation (sagittal + frontal)
sagittal_deviation_index(cycles)	SDI (Sagittal Deviation Index): z-score based 0-120 index (100 = normal). Not the GDI.
gait_variable_scores(cycles)	Per-joint deviation vs normative
movement_analysis_profile(cycles)	MAP barplot data
Quality
confidence_filter(data)	Remove low-confidence landmarks
detect_outliers(data)	Detect and interpolate spikes
data_quality_score(data)	Composite quality score 0-100
frame_coherence_score(data)	Per-frame biomechanical coherence [0,1] (z-score based)
fill_gaps(data)	Interpolate missing landmark gaps
Analysis
walking_speed(data, cycles)	Estimated walking speed
step_length(data, cycles)	Step/stride length estimation
stride_variability(data, cycles)	CV of spatio-temporal parameters
arm_swing_analysis(data, cycles)	Arm swing amplitude and asymmetry
segment_lengths(data)	Anthropometric segment lengths
detect_pathologies(data, cycles)	Pattern detection (equinus, antalgic, etc.)
Visualization
plot_summary(data, cycles, stats)	Summary dashboard
plot_normative_comparison(data, cycles)	Patient vs normative bands
plot_gvs_profile(gvs)	Movement Analysis Profile barplot
render_skeleton_video(video, data, out)	Skeleton overlay on video
render_stickfigure_animation(data, out)	Anonymized stick figure GIF
Export
export_csv(data, dir, cycles, stats)	CSV files
export_mot(data, path)	OpenSim .mot kinematics
export_trc(data, path)	OpenSim .trc markers
load_c3d(path)	Load VICON C3D file into myogait data dict
export_openpose_json(data, dir)	OpenPose JSON for Pose2Sim
export_opensim_scale_setup(data, path)	OpenSim Scale Tool XML
export_ik_setup(trc, path)	OpenSim IK setup XML
to_dataframe(data, what)	Pandas DataFrame
generate_report(data, cycles, stats, path)	Multi-page clinical PDF report
validate_biomechanical(data, cycles)	Validate against physiological ranges

Configuration

myogait supports YAML and JSON pipeline configuration files:

from myogait import load_config, save_config

config = load_config("pipeline.yaml")
config["filter"]["method"] = "butterworth"
config["filter"]["cutoff"] = 6.0
save_config(config, "pipeline_updated.yaml")

Experimental degradation can also be set in config (disabled by default):

extract:
  model: mediapipe
  experimental:
    enabled: false
    target_fps: null
    downscale: 1.0
    contrast: 1.0
    aspect_ratio: 1.0
    perspective_x: 0.0
    perspective_y: 0.0

JSON Output Format

When using Sapiens (v1 or v2) with depth and segmentation:

{
  "extraction": {
    "model": "sapiens2-top",
    "depth_model": "sapiens2-depth-1b",
    "seg_model": "sapiens2-seg-1b",
    "auxiliary_format": "goliath308",
    "seg_classes": ["Background", "Apparel", "Eyeglass", "Face_Neck", "..."]
  },
  "frames": [
    {
      "frame_idx": 0,
      "landmarks": { "NOSE": {"x": 0.52, "y": 0.31, "visibility": 0.95} },
      "goliath308": [[0.52, 0.31, 0.95], "..."],
      "landmark_depths": { "NOSE": 0.73, "LEFT_HIP": 0.45, "..." : 0.0 },
      "landmark_body_parts": { "NOSE": "Face_Neck", "LEFT_HIP": "Left_Upper_Leg" }
    }
  ]
}

Acknowledgments

myogait is developed at the Institut de Myologie (Paris, France) by the PhysioEvalLab / IDMDataHub team.

This work is supported by:

• AFM-Téléthon — French Muscular Dystrophy Association
• Fondation Myologie — Research foundation for muscle diseases
• Téléthon — Annual fundraising event for rare disease research

     

Citation

If you use myogait in your research, please cite:

@software{myogait,
  author = {Fer, Frederic},
  title = {myogait: Markerless video-based gait analysis toolkit},
  year = {2025},
  institution = {Institut de Myologie, Paris, France},
  publisher = {GitHub},
  url = {https://github.com/IDMDataHub/myogait}
}

A peer-reviewed publication is in preparation.

License

This project is licensed under the MIT License. See LICENSE for details.