Acoustic Radiation Force FEM Tools

Finite Element Method (FEM) tools to simulate acoustic radiation force excitations and resultant shear wave propagation.

All software in this repository is licensed under the Apache v2.0 license, as detailed in the LICENSE file.

If you are using the FEM simulation tools in work that you publish, then please consider citing the following manuscript:

Palmeri ML, Sharma AC, Bouchard RR, Nightingale RW, Nightingale KR. "A Finite-Element Method Model of Soft Tissue Response to Impulsive Acoustic Radiation Force," IEEE UFFC, 52(10): 1699-1712, 2005

Also please cite the following manuscript if you use Field II:

J.A. Jensen and N. B. Svendsen: Calculation of pressure fields from arbitrarily shaped, apodized, and excited ultrasound transducers, IEEE Trans. Ultrason., Ferroelec., Freq. Contr., 39, pp. 262-267, 1992.

Installation

These tools have been developed in a Linux environment, which is the recommended platform for usage. Most of the Python code, and some of the C code, will work on Windows and Mac platforms, but build tools for these systems is not outlined here and robust testing does not exist for those environments (i.e., use at your own risk). The Python tools require a version >= 3.8.

There are three different methods to use/install this package:

1. [RECOMMENDED] Install this with pip in a local virtualenv: pip install --prefer-binary -e git+https://github.com/mlp6/fem.git#egg=fem. If swig is not available on your machine, install with pip install --prefer-binary -e git+https://github.com/mlp6/fem.git@no-swig#egg=fem.
2. Clone this source directory and manually install it in your local virtualenv: pip install -e .
3. Clone this source directory and work directly with it by defining PYTHONPATH to include the root directory this repository was cloned into. This is the easiest method if you are planning to actively edit/develop the codebase. You can do this on-the-fly for a given interactive ipython session with syntax like: PYTHONPATH=$HOME/fem ipython.

Documentation

The latest documentation is automatically generated from package docstrings using Sphinx and can be built in docs/. That directory also contains static HTML files that can be included in the documentation, as defined in docs/index.rst. The documentation synced to the root docs/ directory level are also rendered at https://mlp6.github.io/fem/.

To build the documentation:

1. Make sure that PYTHONPATH includes the fem package.
2. Make sure that the virtualenv in activated, which includes the sphinx-build package.
3. Within the docs/ directory: make html
4. Run docs/rsync_build.sh to bring the newly-built HTML files and associated source files into docs/.

Issues

Please file any bug reports, features requests, etc. using the GitHub Issues.

Contributors

• Mark Palmeri (mlp6@duke.edu)
• Joey Richardson (@jrichardson97)
• Anna Phillips (@annap2277)
• Ningrui Li (nl91@duke.edu)
• Mallory Selzo (UNC-CH)
• Chris Moore (chrisjmoore@unc.edu)
• David Bradway (david.bradway@duke.edu)
• Nick Bottenus (nbb5@duke.edu)
• Brian Bigler (brian.bigler@duke.edu)
• Carl Herickhoff (cdh14@duke.edu)
• Sam Lipman (sll16@duke.edu)
• Anna Knight (aek27@duke.edu)
• Matthew Huber (@matthew-huber)
• Felix Jin (@fqjin)