Bindings-NUFFT-pytorch

Bindings to use a Non-uniform Fourier Transform in pytorch with differentiation with respect to the input and to the positions.

Bindings with automatic differentiation are implemented for the following libraries:

• torchkbnufft: works on GPU
• cufinufft: works on GPU
• NFFT: works on CPU and it uses the PyNFFT library
• pykeops: works both on CPU and on GPU, a NUFFT is implemented in nufftbindings/pykeops.py as a reduction operation

This repository was initially created for personal use. Feel free to create a pull request and to propose any improvement.

Example

Import the nufft with the backend you want to use by executing one of the following lines:

import nufftbindings.kbnufft as nufft
import nufftbindings.cufinufft as nufft
import nufftbindings.nfft as nufft
import nufftbindings.pykeops as nufft

nx = ny = 320       # size of the image
K = int(nx*ny)      # number of points in the Fourier domain
Nb = 3              # size of the batch

# CUDA device if you use kbnufft, cufinufft or pykeops
device = torch.device("cuda:0")
# otherwise use
# device = torch.device("cpu")

dtype = torch.complex64

# define the positions in the Fourier domain
xi = torch.rand(K, 2, device=device)*2*np.pi-np.pi
xi.requires_grad = True

# precomputations
nufft.nufft.set_dims(K, (nx, ny), device, Nb=3)
nufft.nufft.precompute(xi)

f = torch.randn(Nb, nx, ny, device=device, dtype=dtype)
y = nufft.forward(xi, f)
g = nufft.adjoint(xi, y)
# you can define whatever cost function you want and compute the gradient with respect to the image f or to xi
loss = g.abs().pow(2).sum()
loss.backward()

Requirements

The codes were tested with the following configuration:

• CUDA 11.2
• Python 3.6.9 and 3.8.11
• PyTorch 1.3.0 and 1.9.0
• Numpy 1.17.2 and 1.20.3
• PyNFFT 1.3.2
• PyKeOps 1.2 and 1.5
• cuFINUFFT 1.2
• torchkbnufft 1.2.0

Note: This repository was previously using a hack of the cuFINUFFT library to avoid pycuda/pytorch transfers. This is no longer required and the memory leak has been fixed.

License

See the LICENSE file

Some technical material for debugging

These bindings are especially used in MRI for the optimization of the sampling locations (see [1,2] for example of such projects that use this library). In this kind of project we need to differentiate sequences of operations that rely on Non-uniform Fourier Transforms with respect to the frequencies. Instead of differentiating all the operations involved in the computation of the NUFFT, the codes in this repository use an explicit differentiation.

• [1] A. Gossard, F. de Gournay and P. Weiss. Off-the-grid data-driven optimization of sampling schemes in MRI. In international Traveling Work-shop on Interactions between low-complexity data models and Sensing Techniques (iTWIST) 2020. PDF
• [2] A. Gossard, F. de Gournay and P. Weiss. Bayesian Optimization of Sampling Densities in MRI. MELBA (Machine Learning for Biomedical Imaging) 2 (2023:009), 2023. PDF