torchkbnufft works primarily via PyTorch modules. You create a module with
the properties of your imaging setup. The module will calculate a Kaiser-Bessel
kernel and some interpolation parameters based on your inputs. Then, you apply
the module to your data stored as PyTorch tensors. NUFFT operations are wrapped in
torch.autograd.Function classes for backpropagation and training
The following code loads a Shepp-Logan phantom and computes a single radial spoke of k-space data:
import torch import torchkbnufft as tkbn import numpy as np from skimage.data import shepp_logan_phantom x = shepp_logan_phantom().astype(np.complex) im_size = x.shape # convert to tensor, unsqueeze batch and coil dimension # output size: (1, 1, ny, nx) x = torch.tensor(x).unsqueeze(0).unsqueeze(0).to(torch.complex64) klength = 64 ktraj = np.stack( (np.zeros(64), np.linspace(-np.pi, np.pi, klength)) ) # convert to tensor, unsqueeze batch dimension # output size: (2, klength) ktraj = torch.tensor(ktraj).to(torch.float) nufft_ob = tkbn.KbNufft(im_size=im_size) # outputs a (1, 1, klength) vector of k-space data kdata = nufft_ob(x, ktraj)
The package also includes utilities for working with SENSE-NUFFT operators. The above code can be modified to include sensitivity maps.
smaps = torch.rand(1, 8, 400, 400) + 1j * torch.rand(1, 8, 400, 400) sense_data = nufft_ob(x, ktraj, smaps=smaps.to(x))
This code first multiplies by the sensitivity coils in
computes a 64-length radial spoke for each coil. All operations are broadcast
across coils, which minimizes interaction with the Python interpreter, helping
Sparse matrices are an alternative to table interpolation. Their speed can vary, but they are a bit more accurate than standard table mode. The following code calculates sparse interpolation matrices and uses them to compute a single radial spoke of k-space data:
adjnufft_ob = tkbn.KbNufftAdjoint(im_size=im_size) # precompute the sparse interpolation matrices interp_mats = tkbn.calc_tensor_spmatrix( ktraj, im_size=im_size ) # use sparse matrices in adjoint image = adjnufft_ob(kdata, ktraj, interp_mats)
Sparse matrix multiplication is only implemented for real numbers in PyTorch, which can limit their speed.
The package includes routines for calculating embedded Toeplitz kernels and using them as FFT filters for the forward/backward NUFFT operations. This is very useful for gradient descent algorithms that must use the forward/backward ops in calculating the gradient. The following code shows an example:
toep_ob = tkbn.ToepNufft() # precompute the embedded Toeplitz FFT kernel kernel = tkbn.calc_toeplitz_kernel(ktraj, im_size) # use FFT kernel from embedded Toeplitz matrix image = toep_ob(image, kernel)
All of the examples included in this repository can be run on the GPU by sending the NUFFT object and data to the GPU prior to the function call, e.g.,
adjnufft_ob = adjnufft_ob.to(torch.device('cuda')) kdata = kdata.to(torch.device('cuda')) ktraj = ktraj.to(torch.device('cuda')) image = adjnufft_ob(kdata, ktraj)
Similar to programming low-level code, PyTorch will throw errors if the
device of all objects are not matching. Be
sure to make sure your data and NUFFT objects are on the right device and in
the right format to avoid these errors.
For more details, please examine the API in torchkbnufft or check out the notebooks below on Google Colab.