Installation Guide

ToMoBAR is a Python package with several Dependencies. To ensure its full functionality it is recommended to install them. It mostly relies on the GPU-enabled computations and therefore we suggest using a decent NVIDIA graphics card to support it.

Python

Install ToMoBAR as a pre-built Python package:

Minimal installation as a conda pre-built package:

$ conda install -c httomo tomobar

or install with the dependencies into a new environment (tested on Linux and Windows):

$ conda install -c httomo -c conda-forge tomophantom tomobar astra-toolbox ccpi-regulariser

In addition you can install pip install pypwt if you are planning to use wavelet regularisation.

Conda environment + pip install:

One can also create a new conda environment by using provided environment YAML file, and then pip install ToMoBAR into the environment.

$ git clone git@github.com/dkazanc/ToMoBAR.git # clone the repo
$ conda env create --name tomobar --file conda-recipe/environment/environment.yml
$ conda activate tomobar
$ pip install .

Install ToMoBAR from PyPi:

One can install ToMoBAR from PyPi into venv or conda` environments. It is the quickest way, however, this approach suits best if CuPy-enabled part of ToMoBAR (modules tomobar.methodsDIR_CuPy and tomobar.methodsIR_CuPy) is mainly used.

$ python -m venv tomobar
$ source tomobar/bin/activate
$ pip install tomobar # one can also install into conda environment

Note

CuPy-enabled ToMoBAR is currently actively developed. With CuPy support and device-to-device transfer features, iterative nethods like FISTA can normally run several times faster.

Developers environment

This sets the development environment to work in-place on the code.

$ git clone git@github.com/dkazanc/ToMoBAR.git # clone the repo
$ conda env create --name tomobar --file conda-recipe/environment/environment.yml
$ conda activate tomobar
$ pip install -e .[dev] # the editable environment
$ pytest tests/test_RecToolsDIR.py tests/test_RecToolsIR.py
$ pytest tests/ # you'll need CuPy to run those tests

Conda build

If one needs to conda-build the package, please follow the steps bellow:

$ export VERSION=$(date +%Y.%m) # OR set VERSION=2025.01 for Windows
$ git clone git@github.com/dkazanc/ToMoBAR.git # clone the repo
$ conda build conda-recipe/
$ conda install path/to/the/tarball

Matlab

Warning

Matlab’s part of ToMoBAR is not currently maintained and will be deprecated in future releases. The code and demos were tested with Matlab 2018 and ASTRA-Toolbox version v1.8.3.