gaitalytics 0.1.2

Python package to extract gait analytic parameters for different kind of recordings (i.e. MOCAP, Force Plate)

This Python package provides a comprehensive set of tools and advanced algorithms for analyzing 3D motion capture data. It is specifically designed to process gait data stored in c3d format. Prior to utilizing the features of gaitalytics, it is necessary to perform data labeling, modeling, and filtering procedures.

The library’s versatility allows it to be adaptable to various marker sets and modeling algorithms, offering high configurability.

Current pre-release is only tested with data acquired with Motek Caren, HBM2 Lower Body Trunk and PIG.

Free software: MIT license

Functionalities

Event Detection

Method	Description	options	checked
Marker	Zenis 2006	min_distance = 100: minimum of frames between same event on same context foot_strike_offset = 0: Amount of frames to offset foot strike foot_off_offset = 0: Amount of frames to offset foot off	X
Forceplate	Split-Belt

Event Detection Check

Method	Description	options	checked
context	Checks gait event sequences HS->TO-HS-TO
spacing	Checks Frames between same event on same context

Modelling

Method	Description	options	checked
com	creates Center of Mass Marker
xcom	creates extrapolated Center of Mass Marker	belt_speed = 1 : speed of treadmill dominant_leg_length = 0.1 : length of dominant leg (mm)
cmos	create Continuous Margin of Stability

Analysis

Method	Description	options	checked
angels	min max mean sd amplitude min velocity max velocity sd velocity	by_phase = True If metrics should be calculated by standing and swinging phase
forces	min max mean sd amplitude	by_phase = True If metrics should be calculated by standing and swinging phase
moments	min max mean sd amplitude	by_phase = True If metrics should be calculated by standing and swinging phase
powers	min max mean sd amplitude	by_phase = True If metrics should be calculated by standing and swinging phase
cmos	min max mean sd amplitude	by_phase = True If metrics should be calculated by standing and swinging phase
mos	Mos at FS Mos at TO Mos at contra HS
Spatio-temporal	step_length stride_length cycle_duration swing_duration_perc stance_duration_perc step_height step_width limb_circumduction [1] single_support_duration_percent [2] double_support_duration_percent [2]		X
Toe Clearance	minimal toe clearance Percentage in cycle where minimal toe clearance happened minimal toe clearance at FS

References

[1] Michael D. Lewek et al. (2012), “The influence of mechanically and physiologically imposed stiff-knee gait patterns on the energy cost of walking”, vol. 93, no.1, pp. 123-128. Publisher: Archives of Physical Medicine and Rehabilitation.

[2] A. Gouelle and F. Mégrot (2017), “Interpreting spatiotemporal parameters, symmetry, and variability in clinical gait analysis”, Handbook of Human Motion pp. 1-20, Publisher: Springer International Publishing.

Usage

Installation

Please be aware of the dependency of gaitalytics to Biomechanical-ToolKit (BTK). To install follow the instructions here or use conda-forge version here

Fast install with anaconda:

pip install gaitalytics
conda install -c conda-forge btk

You can also install the in-development version with:

pip install https://github.com/DART-Lab-LLUI/python-gaitalytics/archive/main.zip
conda install -c conda-forge btk

Configuration

Gaitalytics can be used with any marker set, which at least includes four hip markers (left front/back, right front/back) and four foot markers (left heel/toe, right heel/toe) and four ankle makers (left medial/lateral, right medial lateral).

All functionalities in the libraries only take points into account which are configured in as specific yaml file. Working example file can be found here

Minimal requirements would look like this:

marker_set_mapping:
  left_back_hip: LASIS
  right_back_hip: RASIS
  left_front_hip: LPSIS
  right_front_hip: RPSIS

  left_lat_malleoli: LLM
  right_lat_malleoli: RLM
  left_med_malleoli: LMM
  right_med_malleoli: RMM

  right_heel: RHEE
  left_heel: LHEE
  right_meta_2: RMT2
  left_meta_2: LMT2

  com: COM
  left_cmos: cmos_left
  right_cmos: cmos_right

model_mapping:

Warning Do not rename keys of the minimal setting

Pipeline

Please take the resources in the example folder for advice.

Documentation

https://python-gaitalytics.readthedocs.org

Development

To run all the tests run:

tox

Note, to combine the coverage data from all the tox environments run:

Windows	set PYTEST_ADDOPTS=--cov-append tox
Other	PYTEST_ADDOPTS=--cov-append tox

Release

https://github.com/ionelmc/cookiecutter-pylibrary

Changelog

0.0.0 (2024-02-09)

• First release on PyPI.