PATATO: PhotoAcoustic Tomography Analysis TOolkit
=====================================================================

.. image:: https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7/status.svg
    :target: https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7
    :alt: Journal of Open Source Software
.. image:: https://readthedocs.org/projects/patato/badge/?version=latest
    :target: https://patato.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
.. image:: https://img.shields.io/badge/License-MIT-yellow.svg
    :target: https://github.com/tomelse/patato/blob/main/LICENSE.MD
    :alt: MIT License
.. image:: https://badge.fury.io/py/patato.svg
    :target: https://badge.fury.io/py/patato
    :alt: PyPI version

PATATO is an open-source project to enable the analysis of photoacoustic (PA)
imaging data in a transparent, reproducible and extendable way.
We provide efficient, GPU-optimised implementations of common PA
algorithms written around standard Python libraries, including
filtered backprojection, model-based reconstruction and spectral
unmixing.

The project supports many file formats, such as the `International
Photoacoustic Standardisation Consortium (IPASC) data format <https://www.sciencedirect.com/science/article/pii/S2213597922000106>`_,
and it can be extended to support custom data formats. At present, the project
contains functions to handle data generated by commercial PA systems
by iThera Medical GmbH. The examples will thus be drawn from applications
and geometries suitable for those systems. The data used in the examples is freely available
`online <https://doi.org/10.17863/CAM.93181>`_. By providing
PATATO as an open-source project, we encourage others to contribute their
own algorithms that handle both alternative commercial PA systems and custom home-built
systems.

Our goal in providing this toolkit is to provide a framework than can enable faster and
wider dissemination of state-of-the-art analysis methods for PA imaging and thus be a useful tool
for the community as we translate photoacoustics to the clinic.

* Please report any bugs or issues you find to our GitHub repository
* Please do get involved! Contact Thomas Else (thomas.else@cruk.cam.ac.uk).

The logo was designed by `Elly Pugh <https://ellypugh.com/>`_.

Cite PATATO
"""""""""""""""

To cite PATATO, please reference our Journal of Open Source Software paper `here <https://joss.theoj.org/papers/456eaf591244858915ad8730dcbc19d7>`_. 

.. only:: latex

    User Guide
    """""""""""""""""""""

.. toctree::
   :maxdepth: 1
   :caption: User Guide
   :glob:

   intro/*

.. only:: latex

    Examples
    """""""""""""""""""""

.. toctree::
   :maxdepth: 2
   :caption: Examples
   :glob:

   examples/*

.. only:: latex

    Developers
    """"""""""""""""""""

.. toctree::
   :maxdepth: 2
   :caption: Developers
   :glob:

   dev/*
   CONTRIBUTING.md

.. only:: latex

    API Reference
    """""""""""""""""""""

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   Analysis Code <api/analysis_code>
   Convenience Scripts <api/convenience_scripts>
   Useful Utilities <api/useful_utilities>