Installation Guide

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. ToMoBAR can run with CuPy or using normal routines using pre-built CUDA modules of the Regularisation Toolkit.

Note

CuPy-enabled ToMoBAR is the development in progress. Methods like FISTA can normally run several times faster, however, not every method variation is supported.

Python#

Install ToMoBAR as a pre-built conda Python package:#

Minimal installation that skips most of Dependencies:

$ 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 CuPy conda install conda-forge::cupy if you need CuPy-enabled modules and pip install pypwt if you are planning to use wavelet regularisation.

If the installation above does not work, one can also try:

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

Warning

Note that packages installed from the CCPi channel might be of different versions and incompatible with the demos. Please create an issue on GitHub if there is a problem with an installation from the httomo channel.

Install ToMoBAR from PyPi:#

One can install ToMoBAR from PyPi, however, not all dependencies might be at PyPi yet.

$ pip install tomobar
$ pip install ccpi-regularisation-cupy

Using conda environment:#

One can also create a new conda environment by using the 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 .

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 all tests

Conda builds#

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#