Installation

Supported python versions : python version

Also python 3.5, 3.6, 3.7 are supported but not tested

The full list of prerequisites is the following:

  • numpy>=1.17

  • opencv-python

  • tdqm

  • SimpleITK

And, for testing:

  • PyTest>=3.0.7

  • Hypothesis>=4.13.0

The lung extraction is performed by using pre-trained UNet, so please ensure to have installed the lungmask package. For more information about how the network is trained, please refers here

Installation

First of all, ensure to have the right python version and the package for the lung extraction correctly installed

To install this package first of all you have to clone the repositories from GitHub:

git clone https://github.com/RiccardoBiondi/segmentation

Now you can install tha package using pip

pip install segmentation/

Testing

Testing routines use pytest and hypothesis packages. please install these packages to perform the test:

pip install pytest>=3.0.7
pip install hypothesis>=4.13.0

Warning

Pytest versions above 6.1.2 are not available for python 3.5

All the full set of test is provided in the testing directory. You can run the full list of test from the segmentation folder:

cd segmentation
python -m pytest