Stage Overview¶

monomech keeps each major operation explicit. You can run only the stage you need, inspect its output, and continue later.

Pipeline overview

Video-First Path¶

flowchart LR
    video["Video file"] --> pose["mm.estimate_pose"]
    pose --> clean["mm.smooth + mm.gap_fill"]
    clean --> preview["vis_2d / vis_3d"]
    clean --> csv["CSV export"]
    clean --> trc["TRC export"]
    clean --> opensim["OpenSim scale / IK / ID"]

Marker-First Path¶

flowchart LR
    trc["TRC file"] --> clean["mm.gap_fill + mm.smooth"]
    clean --> export["TRC / CSV export"]
    export --> opensim["OpenSim scale / IK / ID"]

Main APIs¶

Stage	API	Notes
Estimate global pose	`mm.estimate_pose(path)`	Requires `monomech[pose]`.
Smooth data	`mm.smooth(result_or_trc)`	Works with pose, marker results, and TRC files.
Fill gaps	`mm.gap_fill(result_or_trc)`	Interpolates short gaps.
Preview pose	`pose.vis_2d()`, `pose.vis_3d()`	Notebook-friendly frame checks.
Scale model	`mm.run_scaling(...)`	Requires OpenSim-compatible bindings.
Inverse kinematics	`mm.run_ik(...)`	Returns an IK `StorageResult`.
Inverse dynamics	`mm.run_id(...)`	Accepts measured or estimated external loads.
Visualize	`mm.animate(...)`	Creates a notebook-ready HTML viewer.

Stage Outputs¶

Stage	Main result	What to inspect
2D pose	`Pose2DResult`	Source-frame overlay, landmark confidence, missing frames.
Global 3D pose	`Pose3DGlobalResult`	Floor alignment, foot clearance, landmark trajectories.
TRC export	`.trc`	Marker names, units, axes, and time range.
IK	`StorageResult` and `.mot`	Joint coordinate curves and marker errors.
External loads	`.xml` and `.mot`	Force signs, application points, and time coverage.
ID	`StorageResult` and `.sto`	Joint forces and moments.
Viewer	`OpenSimVisualizerResult`	Motion, forces, IK, and ID in one synchronized page.

IK coordinate signals

Estimated external-load signals

Inverse-dynamics output signals

For a visual walkthrough, open the pipeline tour.