Installation of nDTomo software

Repository

The nDTomo project repository is available for download from GitHub: https://github.com/antonyvam/nDTomo

Installation instructions

To make your life easier, please install [Anaconda](https://www.anaconda.com/products/distribution). The nDTomo library and all associated ode can be installed by following the next three steps:

  1. Install astra-toolbox

An important part of the code is based on astra-toolbox, which is currently available through conda.

It is possible to install astra-toolbox from sources (i.e., if one wants to avoid using conda), but it is not a trivial task. We recommend creating a new conda environment for nDTomo.

Create a new environment and first install astra-toolbox:

` conda create --name ndtomo python=3.11 `

` conda activate ndtomo `

` conda install -c astra-toolbox -c nvidia astra-toolbox `

  1. Install nDTomo from GitHub

To install from git:

` pip install git+https://github.com/antonyvam/nDTomo.git `

For development work (editable install):

` git clone https://github.com/antonyvam/nDTomo.git && cd nDTomo `

` pip install -e . `

Navigate to where the setup.py file is located and run:

` pip install --user . `

or:

` python3 setup.py install --user `

  1. Install pytorch

The neural networks, as well as any GPU-based code, used in nDTomo require Pytorch which can be installed through pip.

For example, for Windows/Linux with CUDA 11.8:

` pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118 `

  1. Launching the nDTomoGUI

After installing nDTomo, the graphical user interface can be launched directly from the terminal:

` conda activate ndtomo `

` python -m nDTomo.gui.nDTomoGUI `

  1. Diamond Light Source

As a user at the Diamond Light Source, you can install nDTomo by doing:

` git clone https://github.com/antonyvam/nDTomo.git && cd nDTomo `

` module load python/3 `

` python setup.py install --user `