Skip to content

Latest commit

 

History

History
48 lines (30 loc) · 2.65 KB

README.md

File metadata and controls

48 lines (30 loc) · 2.65 KB
Raw

Overview

bigtracks is an attempt to provide a somewhat friendly front-end for tracking particles in a series of video images. It uses trackpy, Tom Caswell's Python implementation of the Crocker-Grier particle-tracking algorithm.

Its principal virtues are

  • Like trackpy, it is free and open-source (under the GPL) and runs in a free environment.
  • It scales efficiently to large datasets, limited only by disk space. In principle, available RAM limits only the size of a single frame.
  • It outputs to a standard numerical file format, HDF5, which is readable by MATLAB, IDL, etc. (although there, you may be limited by available RAM).
  • It includes tools for efficiently reading its particle tracks databases, which may be used as a foundation for your own analysis.

bigtracks was written by Nathan Keim, a member of the Penn Complex Fluids Lab.

Installation

The easiest route is to first install the free Anaconda Python distribution from Continuum Analytics.

Otherwise, the following Python packages are needed for bigtracks and the required version of trackpy (see below):

  • numba
  • the Python Imaging Library (PIL)
  • pip (for easy installation)
  • scipy and numpy
  • pandas
  • pytables
  • ipython and pyzmq for parallel computing
  • tornado to display the example IPython notebooks
  • matplotlib (optional)

At present, the also-excellent Enthought EPD or Canopy include all of these except numba, though it is possible to install that package and its several requirements manually, by following the instructions.

Installing pytracks

bigtracks uses a special version of pytracks that has been accelerated with numba, and given a slightly modified API to permit handling of large datasets. This is currently found on GitHub. The easiest way to install it is with pip:

pip 'git+http://github.com/nkeim/trackpy/@numba#egg=trackpy'

Tip for novices: Be sure that the pip you are running belongs to the Python installation you'll use for tracking (e.g. anaconda).

Installing bigtracks

The easiest method is

pip 'git+http://github.com/nkeim/bigtracks/#egg=bigtracks'

Or, instead of the GitHub URL, use the path to a local directory or .zip file that contains the downloaded source code.

If you choose not to use pip or easy_install, you will need to make sure that the path.py package is installed.