Stride - A modelling and optimisation framework for medical ultrasound

Stride is an open-source library for ultrasound modelling and tomography that provides flexibility and scalability together with production-grade performance.

Key features

High-performance modelling

We provide high-performance, finite-difference, time-domain solvers for modelling ultrasound propagation in the human body, including:

Variable speed of sound, density, and attenuation.
Off-grid sources and receivers.
A variety of absorbing boundary conditions.
Targeting both CPUs and GPUs with the same code.

Intuitive inversion algorithms

Stride also lets users easily prototype medical tomography algorithms with only a few lines of Python code by providing:

Composable, automatic gradient calculations.
State-of-the-art reconstruction algorithms.
The flexibility to (re)define every step of the optimisation.

Flexibility

Solvers in Stride are written in Devito, using math-like symbolic expressions. This means that anyone can easily add new physics to Stride, which will also run on both CPUs and GPUs.

Scalability

Stride can scale seamlessly from a Jupyter notebook in a local workstation, to a multi-node CPU cluster or a GPU cluster with production-grade performance.

Quickstart

Jump right in using a Jupyter notebook directly in your browser, using binder.

Otherwise, the recommended way to install Stride is through Anaconda's package manager (version >=4.9), which can be downloaded in Anaconda or Miniconda. A Python version above 3.7 is recommended to run Stride.

To install Stride, follow these steps:

git clone https://github.com/trustimaging/stride.git
cd stride
conda env create -f environment.yml
conda activate stride
pip install -e .

Running the examples

The easiest way to start working with Stride is to open the Jupyter notebooks under stride_examples/tutorials.

You can also check fully worked examples of breast imaging in 2D and 3D under stride_examples/breast2D and stride_examples/breast2D. To perform a forward run on the breast2D example, you can execute from any terminal:

cd stride_examples/examples/breast2D
mrun python 01_script_forward.py

You can control the number of workers and threads per worker by running:

mrun -nw 2 -nth 5 python 01_script_forward.py

You can configure the devito solvers using environment variables. For example, to run the same code on a GPU with OpenACC you can:

export DEVITO_COMPILER=pgcc
export DEVITO_LANGUAGE=openacc
export DEVITO_PLATFORM=nvidiaX
mrun -nw 1 -nth 5 python 01_script_forward.py

Once you've run it forward, you can run the corresponding inverse problem by doing:

mrun python 02_script_inverse.py

You can also open our interactive Jupyter notebooks in the public binder.

Additional packages

To access the 3D visualisation capabilities, we also recommend installing MayaVi:

conda install -c conda-forge mayavi

and installing Jupyter notebook is recommended to access all the examples:

conda install -c conda-forge notebook

GPU support

To run a solver using the GPU, simply add the option platform="nvidia-acc":

pde = IsoAcousticDevito(...)
await pde(..., platform="nvidia-acc")

The Devito library uses OpenACC to generate GPU code. The recommended way to access the necessary compilers is to install the NVIDIA HPC SDK.

wget https://developer.download.nvidia.com/hpc-sdk/21.2/nvhpc_2021_212_Linux_x86_64_cuda_multi.tar.gz
tar xpzf nvhpc_2021_212_Linux_x86_64_cuda_multi.tar.gz
cd nvhpc_2021_212_Linux_x86_64_cuda_multi/
sudo ./install

During the installation, select the single system install option.

Once the installation is done, you can add the following lines to your ~/.bashrc:

export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/2021/compilers/bin/:$PATH
export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/2021/compilers/lib/:$LD_LIBRARY_PATH
export PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/2021/comm_libs/mpi/bin/:$PATH
export LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/Linux_x86_64/2021/comm_libs/mpi/lib/:$LD_LIBRARY_PATH

Citing Stride

If you use Stride in your research, please cite our paper:

@misc{cueto2021-stride,
	title          =    { Stride: a flexible platform for high-performance ultrasound computed tomography  },
	author         =    { Carlos Cueto and Oscar Bates and George Strong and Javier Cudeiro and Fabio Luporini
				and Oscar Calderon Agudo and Gerard Gorman and Lluis Guasch and Meng-Xing Tang },
	year           =    { 2021 },
	eprint         =    { 2110.03345 },
	archivePrefix  =    { arXiv },
	primaryClass   =    { physics.med-ph },
	url            =    { https://arxiv.org/abs/2110.03345 }
}

Contact us

Join the conversation to share your projects, contribute, and get your questions answered.

Documentation

For details about the Stride API, check our latest documentation.

rehmanali1994/stride