openlifu 0.2.1

Openwater Focused Ultrasound Toolkit

openlifu is a toolbox for planning and controlling focused ultrasound treatments. It generally replicates the functionality developed in the MATLAB open-TFUS toolbox.

Installation

Requirements

Python 3.9 or later on Windows or Linux.

Create Virtual Environment

Windows:

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

Linux:

python3.11 -m venv env

Install project (editable)

With this repo as the working directory:

Basic mode

pip install -e .

Dev mode

pip install -e '.[dev]'

Installing Meshroom

If you are using openlifu.nav.photoscan to reconstruct meshes from photo collections, then you will need to set up Meshroom.

Ubuntu

Download and Extract

1. Download Meshroom for Linux from https://alicevision.org/#meshroom.

2. Extract the downloaded archive:

   tar -xvf Meshroom-2023.3.0.tar.gz

Add Meshroom to PATH

Temporary (Current Session) Run:

export PATH="<path-to-meshroom>/Meshroom-2023.3.0:$PATH"

Replace <path-to-meshroom> with the actual path where Meshroom was extracted.

Permanent (Persistent Across Sessions) For Bash users:

echo 'export PATH="<path-to-meshroom>/Meshroom-2023.3.0:$PATH"' >> ~/.bashrc
source ~/.bashrc

Windows

Download and Extract

1. Download Meshroom for Windows from https://alicevision.org/#meshroom.

2. Extract the downloaded archive to a directory of your choice.

Add Meshroom to PATH

1. Open Edit environment variables for your account from the Start menu.

2. In the Environment Variables window, under User variables, select Path and click Edit.

3. Click New, and add the path to the folder containing Meshroom.exe.

4. Click OK to save the changes.

Enable GPU Acceleration

To ensure Meshroom uses your NVIDIA GPU:

1. Open NVIDIA Control Panel.

2. In the left sidebar under 3D Settings, click Manage 3D settings.

3. Go to the Program Settings tab.

4. Click Add, then browse to and select Meshroom.exe from the folder where you extracted Meshroom.

5. Under Select the preferred graphics processor for this program, choose High-performance NVIDIA processor.

6. Click Apply.

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. Note: Remote access to the sample database stored on google drive is currently restricted. Access requires a gdrive_client_secret for user access authentication to be shared by developers.

DVC usage

To download the sample database:

git pull
dvc remote modify --local shared_gdrive gdrive_client_secret <client_secret_here> # 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:

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.