A python package for medical ultrasound imaging
Load experimental setup (probe details, sequence, scanning region) and compute imaging in Plane Wave Compounding mode. See the wiki
You will need a distribution of Python (v 3.5+) and several classic python packages, that most likely come with the distribution of Python, or can be easily installed with Pip Install Packages pip see here.
- Python 3.5+ - A python distribution (Anaconda comes with the conda package facility and is highly recommended)
- numpy The classic array library.
- scipy Not less classic scientific computation library.
- matplotlib A Python plotting/charting library.
- click A powerful command line utility
For file I/O we use the hdf5 format, so that python package is required aswell:
Depending on your system, the install should be as easy as:
pip install numpy
Download the repo to a location of your choice /Users/YourSelf/projects/pymus.
In order for python to have access to different modules at startup, one convenient solution is to create a pymus.pth file that would be located at a location of the style:
/Users/YourSelf/miniconda2/lib/python2.7/site-packages/pymus.pth
To find out about your specific prefix (/Users/YourSelf/miniconda2/), run python and then import sys and then sys.prefix.
The pymus.pth file should have just one line that is the absolute path to your pymus directory.
The following test should run a Plane-Wave simplified beamforming and display an echogeinicity of a phantom image.
python experiment/test_pymus.py
- Pierre Garapon - Initial work - pgarapon
This project is based on porting to python the matlab project Picmus. The Plane Wave Imaging Challenge in Medical UltraSound. See the following paper:
Liebgott, H., Rodriguez-Molares, A., Jensen, J.A., Bernard, O., "Plane-Wave Imaging Challenge in Medical Ultrasound", in IEEE International Ultrasonics Symposium, Tours, France., 2016, p. accepted
See also the list of contributors who participated in this project.
This project is licensed under the MIT License - see the LICENSE.md file for details
- The Medical ultrasound community and the folks at INSA Lyon for exposing some datasets. Creatis
- The Python community for an ever growing suite of efficient tools.