PyQuantUS is the pip-accessible backend engine for QuantUS written in Python. It contains all data loading and analytical capabilities of QuantUS, enabling scalable batch processing through a command-line interface.
Complete software documentation for QuantUS and PyQuantUS can be found here.
Requires Python>=3.10.0.
pip install git+https://github.com/TUL-Dev/PyQuantUSRequires Python>=3.10.0. We will refer to the path of such a Python version as $PYTHON below.
Below are steps to create a new python virtual environment for PyQuantUS. Note lines commented with # Unix should only be run on MacOS or Linux while lines commented with # Windows (cmd) should only be run on the Windows command prompt. These commands should be run from the directory of this repository.
$PYTHON -m pip install virtualenv
$PYTHON -m virtualenv .venv
source .venv/bin/activate # Unix
.venv\Scripts\activate # Windows (cmd)
sudo apt-get update & sudo apt-get install python3-dev # Linux
pip install -r requirements.txtThis environment is activated using source .venv/bin/activate | .venv\Scripts\activate and deactivated using the deactivate command.
lzop is required to unzip .tar files generated by Clarius systems. Ensure this is installed using your preferred package manager.
See the notebooks in the CLI-Demos folder for examples of analysis for different ultrasound systems. Also note slight differences between examples scan-converted (sc) and non-scan-converted images. Data required to reproduce these examples is stored here. When using these notebooks, the Python environment should match the environment created for QuantUS.
- MBF
- SS
- SI
- Attenuation Coefficient
- Nakagami Parameters (w, u)
- Backscatter Coefficient
- Effective Scatterer Diameter
- Effective Scatterer Concentration