Direct identification of the human's control scheme during walking.
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README.rst

Introduction

This is the source repository for the paper:

Moore, J.K. and van den Bogert, A. " Direct Identification of Human Gait Control", 2015.

This repository contains or links to all of the information needed to reproduce the results in the paper.

The latest rendered version of the PDF can be viewed via the ShareLaTeX CI system:

License

The content of this repository is licensed under the Creative Commons Attribution 4.0 International License.

https://i.creativecommons.org/l/by/4.0/80x15.png

Supplementary Material

The repository contains various modules, scripts, and IPython notebooks that are included as supplementary material so that readers can explore the analysis themselves.

Software

The scripts used for the analysis is available in the src directory of this repository and depend primarily on two open source Python packages developed for this paper. The snapshots of the DynamicistToolKit 0.3.5 and the GaitAnalysisToolKit 0.1.2 are available via both Zenodo and PyPi:

Be sure to read the installation instructions for the two packages.

DynamicistToolKit
Latest Version
GaitAnalysisToolKit
Latest Version

Furthermore, there are a variety of dependencies that must be installed on your system to run the scripts. It is best to follow the installation instructions provided by each of the following software packages for your operating system.

  • Various unix tools [1]: cd, bash, gzip, make, mkdir, rm, tar, unzip, wget
  • The Anaconda Python distribution with Python 2.7 for ease of download and management of Python packages.
  • Various Python packages: pip, numpy 1.9.1, scipy 0.14.0, matplotlib 1.4.2, pytables 3.1.1, pandas 0.15.1, pyyaml 3.11, seaborn 0.5.0, pygments 2.0.1, oct2py 2.4.2, DynamicistToolKit 0.3.5, GaitAnalysisToolKit 0.1.2
  • Octave 3.8.1
  • A LaTeX distribution which includes pdflatex. For example: MikTeX [Win], TeX Live [Linux], MacTeX [Mac].
  • Various LaTeX Packages [2]: minted, lineno, graphicx, booktabs, cprotect, siunitx, inputenc, babel, ifthen, calc, microtype, times, mathptmx, ifpdf, amsmath, amsfonts, amssymb, xcolor, authblk, geometry, caption, natbib, fancyhdr, lastpage, titlesec, enumitem, bibtex
  • Git (optional)
[1]These are available by default in Linux distributions, provided by Xcode on the Mac, and can be obtained via Cygwin, MinGW, or individual install on Windows.
[2]Most packages will likely be installed with your LaTeX distribution, otherwise follow the installation instructions provided by the package. Note that minted has abnormal dependencies: Python and Pygments. On Debian based systems you will need to install texlive-humanities and texlive-science to get all of the necessary packages.

Interactive Notebooks

The notebooks can be viewed here:

http://nbviewer.ipython.org/github/csu-hmc/gait-control-direct-id-paper/tree/master/notebooks/

Note that the following notebooks are currently not working with the latest GATK:

  • data_munging.ipynb
  • perturbations.ipynb

Data

The data presented in the paper are available for download from Zenodo under the Creative Commons CC0 license.

Downloading the Repository

First, navigate to a desired location on your file system and either clone the repository with Git [3] and change into the new directory:

$ git clone https://github.com/csu-hmc/gait-control-direct-id-paper.git
$ cd gait-control-direct-id-paper

or download with wget, unpack the zip file, and change into the new directory:

$ wget https://github.com/csu-hmc/gait-control-direct-id-paper/archive/master.zip
$ unzip gait-control-direct-id-paper-master.zip
$ cd gait-control-direct-id-paper-master
[3]Please use Git if you wish to contribute back to the repository. See CONTRIBUTING.rst for information on how to contribute.

Basic LaTeX Build Instructions

To build the pdf from the LaTeX source using the pre-generated figures and tables in the repository, make sure you have an up-to-date LaTeX distribution installed and run make from within the repository. The default make target will build the document, i.e.:

$ make

You can then view the document with your preferred PDF viewer. For example, Evince can be used:

$ evince main.pdf