openlifu

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.. SPHINX-START

openlifu is a toolbox for planning and controlling focused ultrasound treatments. It generally replicates the functionality developed in the MATLAB open-TFUS toolbox <https://github.com/OpenwaterHealth/opw_neuromod_sw>__.

Installation

Requirements

Python 3.9 or later on Windows or Linux.

Create Virtual Environment

Windows:

.. code:: sh

C:\Users\\AppData\Local\Programs\Python\Python311\python.exe -m venv env .\env\Scripts\activate

Linux:

.. code:: sh

python3.11 -m venv env

Install project (editable)

With this repo as the working directory:

Basic mode
^^^^^^^^^^
.. code:: sh

   pip install -e .

Dev mode
^^^^^^^^
.. code:: sh

   pip install -e .[dev]

Version control of database using DVC (Data Version Control)
-------------------------------------------------------------

Data Version Control (DVC) is a data management tool that is meant to be run alongside Git.
In this project, DVC is used to link changes in the code to specific versions of a sample database containing example project files.
DVC can be used when this project is installed in Dev mode. You can read more about DVC and how to use it `here <https://dvc.org/doc/start>`_.
**Note:** Remote access to the sample database stored on google drive is currently restricted. Access requires a :code:`gdrive_client_secret`
for user access authentication to be shared by developers.

DVC usage

To download the sample database:

.. code:: sh

git pull dvc remote modify --local shared_gdrive gdrive_client_secret # Contact developers for grive_client_secret dvc pull # Requires access to remote storage

This will download a directory 'db_dvc' in the repo directory that contains the corresponding version of example database files.

To commit updates to the sample database:

.. code:: sh

dvc add db_dvc git commit -m "Describe updates to database" git push dvc push #Requires access to remote storage

Disclaimer

CAUTION - Investigational device. Limited by Federal (or United States) law to investigational use. The system described here has not been evaluated by the FDA and is not designed for the treatment or diagnosis of any disease. It is provided AS-IS, with no warranties. User assumes all liability and responsibility for identifying and mitigating risks associated with using this software.

.. |Actions Status| image:: https://github.com/OpenwaterHealth/OpenLIFU-python/workflows/CI/badge.svg :target: https://github.com/OpenwaterHealth/OpenLIFU-python/actions .. |Documentation Status| image:: https://readthedocs.org/projects/openlifu/badge/?version=latest :target: https://openlifu.readthedocs.io/en/latest/?badge=latest .. |PyPI version| image:: https://img.shields.io/pypi/v/openlifu :target: https://pypi.org/project/openlifu/ .. |PyPI platforms| image:: https://img.shields.io/pypi/pyversions/openlifu :target: https://pypi.org/project/openlifu/ .. |GitHub Discussion| image:: https://img.shields.io/static/v1?label=Discussions&message=Ask&color=blue&logo=github :target: https://github.com/OpenwaterHealth/OpenLIFU-python/discussions