gaitalytics 0.1.2

Description:

gaitalytics 0.1.2

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.