Analysis of leg kinmatics data

How to use this repo

For more information on the structure of this repo, see this template repo.

Analysis pipelines

The notebook files notebooks/*.ipynb are workflows for the individual steps in the analysis pipeline.

notebook file	use case
ball_fitting_example.ipynb	fit ball to tarsal tips and predict swing and stance phase per frame and leg
ball_fitting_batch.ipynb	run ball fitting and stepcycle predictions in batch mode

Documentation

The analysis pipelines contain most information needed to understand how to work with the data. Some additional information is provided for:

file	content
data_structure.md	Data structure generated with DLC/anipose
3D_visualization.md	3D visualization using VMD molecular viewer

old scripts

These old scripts need to become part of the new code structure.

• notebooks/old_notebooks/feature_generation/coordinate_transformation.ipynb incl utils.py
• notebooks/old_notebooks/feature_extraction (i) BPN, (ii) P9LT, (iii), P9RT
• notebooks/old_notebooks/generate-dataset MATLAB code (port to python?)
• notebooks/old_notebooks/regression_model/model.ipynb

Installation

# create conda environment with necessary dependencies
conda env create -n kinematics_analysis -f environment.yml
conda activate kinematics_analysis

# get source code
git clone https://github.com/bidaye-lab/kinematics_analysis

# install code as local local python module
cd kinematics_analysis
pip install -e .