.. docs-include-ref

MBIRJAX

Model-Based Iterative Reconstruction (MBIR) for tomographic reconstruction that is based on the JAX <https://github.com/google/jax>__ library. Full documentation is available at https://mbirjax.readthedocs.io .

Installing from PyPI

For CPU only:

.. code-block::

    pip install mbirjax

For CPU with a CUDA12-enabled GPU:

.. code-block::

    pip install --upgrade mbirjax[cuda12]

Installing from Source

1. Clone the repository:

   .. code-block::

    git clone git@github.com:cabouman/mbirjax.git
   

2. Install the conda environment and package

   a. Option 1: Clean install using dev_scripts - We provide bash scripts that will do a clean install of MBIRJAX in a new conda environment using the commands:

    .. code-block::
   
        cd dev_scripts
        source clean_install_all.sh
   

   b. Option 2: Manual install - You can also manually install MBIRJAX from the main directory of the repository with the following commands:

    .. code-block::
   
        conda create --name mbirjax python=3.10
        conda activate mbirjax
        pip install -r requirements.txt
        pip install .
   

Optional Pixi Development Environment

For contributors who use Pixi <https://pixi.sh>__, MBIRJAX also provides an optional reproducible development environment. This does not replace the conda installation workflow above.

For the default CPU environment on Linux or Apple Silicon macOS:

.. code-block::

    pixi run smoke
    pixi run test-fast

For a CUDA-enabled Linux system:

.. code-block::

    pixi run -e cuda smoke-jax
    pixi run -e cuda test-fast

Additional useful tasks include:

.. code-block::

    pixi run test
    pixi run test-data
    pixi run docs

Running Demo(s)

Run any of the available demo scripts with something like the following:

.. code-block::

    python demo/<demo_file>.py