Array functions and settings

The bartorch namespace holds array functions on tensors, most of them calling BART’s commands, and the process-wide settings of the embedded library. Axis arguments are indices into a C-order shape; results are not recorded by autograd.

Fourier transforms

Object	Description
fft	Fourier transform along axes; centred and unnormalized by default, unitary with unitary=True
ifft	Inverse of fft
fftshift	Cyclic shift of the zero frequency to the centre, or back
fftmod	Multiplication by the alternating phase relating centred and uncentred transforms
nufft	Non-uniform Fourier transform of an image along a trajectory
nufft_adjoint	Adjoint non-uniform Fourier transform, from samples to an image
estimate_density	Sampling density compensation weights of a trajectory (Pipe-Menon iteration)

K-space windows and readout

Object	Description
hann_window	Radial or separable Hann window on a k-space grid
fermi_window	Radial or separable Fermi window on a k-space grid
apodize	Multiplication of k-space by a Hann or Fermi window over its trailing axes
remove_readout_oversampling	Cropping of the readout field of view in image space

Wavelet transforms

Object	Description
fwt	Multi-level discrete wavelet transform along axes
iwt	Inverse of fwt

Thresholding

Object	Description
soft_thresh	Soft thresholding of the modulus, \(x \max(1 - \lambda/\lvert x\rvert, 0)\)
hard_thresh	Hard thresholding, keeping entries with \(\lvert x\rvert > \lambda\)

Array utilities

Object	Description
resize	Cropping or zero padding to a shape, anchored at the centre, the front or the start
flip	Reversal along axes
circshift	Cyclic shift along axes
conv	Cyclic convolution with a kernel
median_filter	Moving median along one axis
moving_average	Moving average along one axis
normalize	Division by the \(\ell_2\) or \(\ell_1\) norm over axes
mip	Maximum or minimum intensity projection
unwrap	Unwrapping of the real part along one axis, for a given period
casorati	Casorati matrix of overlapping blocks
rss	Root sum of squares over axes

Interpolation

Object	Description
interpolate	Sampling of an array at fractional voxel positions

Coil kernels

Object	Description
maps_to_kernels	Sensitivities as their low-frequency k-space kernels
kernels_to_maps	Sensitivities from k-space kernels

Errors

Object	Description
BartError	Exception raised when a BART command or operator fails, carrying BART’s message

Runtime settings

Object	Description
set_num_threads	Threads used by BART, its FFT and FINUFFT’s host transforms
set_copy_inputs	Whether commands work on copies of their inputs (default)
set_debug_level	BART’s verbosity
get_debug_level	Current verbosity

CUDA

Object	Description
cuda_available	Whether the library was built with CUDA and a device is present
set_cuda_streams	Number of CUDA streams BART uses
use_cuda_memcache	Whether BART caches freed device memory

Build information

Object	Description
bart_version	Version of the embedded BART
build_info	Compiler, nested-function mode, OpenMP and CUDA configuration of the library
backend_sources	Library serving each BLAS and LAPACK routine and the FFT