lucaSchilling/MasterThesis

Image Registration using Deep Learning

Author: Luca S.

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Requirements

• Python 3.8
• Poetry 1.1
• cmake 3.2.1
• git
• build-essentials

Setup (tested on Ubuntu 20.04 only)

1. Download & install the latest python 3.8 release from here

2. Download and install poetry as explained here

3. Download and compile SimpleElastix as explained here

4. Run poetry install -vvv in the root of the repository to create a virtual environment and install all dependencies listed in the pyproject.toml. -vvv activates the debug mode which somehow is needed to install airlab as development dependency correctly.

5. From within poetry's venv console navigate to {BUILD_DIRECTORY}/SimpleITK-build/Wrapping/Python and execute python Packaging/setup.py install

Hint: To enter poetry's venv u can use poetry shell if poetry is added correctly to your path otherwise use source {path_to_venv}/bin/activate.

On Ubuntu Poetry's venvs are located under ~/.cache/pypoetry/virtualenvs/

6. Run any of the run scripts...

   6.1 ... using the command line

   poetry shell
   
   poetry run python validation.py
   
   

   6.2 ... using an IDE:

   • Select the poetry venv as interpreter and run/debug one of the scripts as usual