NonuniformFFTs.jl
Yet another package for computing multidimensional non-uniform fast Fourier transforms (NUFFTs) in Julia.
Like other existing packages, computations are parallelised using threads. By default, all available Julia threads are used.
Installation
NonuniformFFTs.jl can be simply installed from the Julia REPL with:
julia> ] add NonuniformFFTs
Conventions
Transform definitions
This package evaluates type-1 (non-uniform to uniform) and type-2 (uniform to non-uniform) non-uniform fast Fourier transforms (NUFFTs). These are sometimes also called the adjoint and direct NUFFTs, respectively.
In one dimension, the type-1 NUFFT computed by this package is defined as follows:
\[û(k) = ∑_{j = 1}^{M} v_j \, e^{-i k x_j} \quad \text{ for } \quad k = -\frac{N}{2}, …, \frac{N}{2} - 1\]
where the $x_j ∈ [0, 2π)$ are the non-uniform points and the $v_j$ are the input values at those points, and $k$ are the associated Fourier wavenumbers (or frequencies). Here $M$ is the number of non-uniform points, and $N$ is the number of Fourier modes that are kept (taken to be even here, but can also be odd).
Similarly, the type-2 NUFFT is defined as:
\[v_j = ∑_{k = -N/2}^{N/2 + 1} û(k) \, e^{+i k x_j}\]
for $x_j ∈ [0, 2π)$. The type-2 transform can be interpreted as an interpolation of a Fourier series onto a given location.
If the points are uniformly distributed in $[0, 2π)$, i.e. $x_j = 2π (j - 1) / M$, then these definitions exactly correspond to the forward and backward DFTs computed by FFTW. Note in particular that the type-1 transform is not normalised. In applications, one usually wants to normalise the obtained Fourier coefficients by the size $N$ of the transform (see examples below).
Ordering of data in frequency space
This package follows the FFTW convention of storing frequency-space data starting from the non-negative frequencies $(k = 0, 1, …, N/2 - 1)$, followed by the negative frequencies $(k = -N/2, ..., -2, -1)$. Note that this package also allows the non-uniform data ($v_j$ values) to be purely real, in which case real-to-complex FFTs are performed and only the non-negative wavenumbers are kept (in one dimension).
One can use the fftfreq
function from the AbstractFFTs package to conveniently obtain the Fourier frequencies in the right order. For real data transforms, rfftfreq
should be used instead.
Alternatively, for complex non-uniform data, one can use fftshift
and ifftshift
from the same package to switch between this convention and the more "natural" convention of storing frequencies in increasing order $(k = -N/2, …, N/2 - 1)$.
Basic usage
Type-1 (or adjoint) NUFFT in one dimension
using NonuniformFFTs
using AbstractFFTs: rfftfreq # can be used to obtain the associated Fourier wavenumbers
N = 256 # number of Fourier modes
Np = 100 # number of non-uniform points
ks = rfftfreq(N, N) # Fourier wavenumbers
# Generate some non-uniform random data
T = Float64 # non-uniform data is real (can also be complex)
xp = rand(T, Np) .* 2π # non-uniform points in [0, 2π]
vp = randn(T, Np) # random values at points
# Create plan for data of type T
plan_nufft = PlanNUFFT(T, N; m = HalfSupport(8)) # larger support increases accuracy
# Set non-uniform points
set_points!(plan_nufft, xp)
# Perform type-1 NUFFT on preallocated output
ûs = Array{Complex{T}}(undef, size(plan_nufft))
exec_type1!(ûs, plan_nufft, vp)
@. ûs = ûs / N # normalise transform
Type-2 (or direct) NUFFT in one dimension
using NonuniformFFTs
N = 256 # number of Fourier modes
Np = 100 # number of non-uniform points
# Generate some uniform random data
T = Float64 # non-uniform data is real (can also be complex)
xp = rand(T, Np) .* 2π # non-uniform points in [0, 2π]
ûs = randn(Complex{T}, N ÷ 2 + 1) # random values at points (we need to store roughly half the Fourier modes for complex-to-real transform)
# Create plan for data of type T
plan_nufft = PlanNUFFT(T, N; m = HalfSupport(8))
# Set non-uniform points
set_points!(plan_nufft, xp)
# Perform type-2 NUFFT on preallocated output
vp = Array{T}(undef, Np)
exec_type2!(vp, plan_nufft, ûs)
Multidimensional transforms
using NonuniformFFTs
using StaticArrays: SVector # for convenience
Ns = (256, 256) # number of Fourier modes in each direction
Np = 1000 # number of non-uniform points
# Generate some non-uniform random data
T = Float64 # non-uniform data is real (can also be complex)
d = length(Ns) # number of dimensions (d = 2 here)
xp = [2π * rand(SVector{d, T}) for _ ∈ 1:Np] # non-uniform points in [0, 2π]ᵈ
vp = randn(T, Np) # random values at points
# Create plan for data of type T
plan_nufft = PlanNUFFT(T, Ns; m = HalfSupport(8))
# Set non-uniform points
set_points!(plan_nufft, xp)
# Perform type-1 NUFFT on preallocated output
ûs = Array{Complex{T}}(undef, size(plan_nufft))
exec_type1!(ûs, plan_nufft, vp)
ûs ./= prod(Ns) # normalise transform
# Perform type-2 NUFFT on preallocated output
exec_type2!(vp, plan_nufft, ûs)
Multiple transforms on the same non-uniform points
using NonuniformFFTs
N = 256 # number of Fourier modes
Np = 100 # number of non-uniform points
ntrans = Val(3) # number of simultaneous transforms
# Generate some non-uniform random data
T = Float64 # non-uniform data is real (can also be complex)
xp = rand(T, Np) .* 2π # non-uniform points in [0, 2π]
vp = ntuple(_ -> randn(T, Np), ntrans) # random values at points (one vector per transformed quantity)
# Create plan for data of type T
plan_nufft = PlanNUFFT(T, N; ntransforms = ntrans)
# Set non-uniform points
set_points!(plan_nufft, xp)
# Perform type-1 NUFFT on preallocated output (one array per transformed quantity)
ûs = ntuple(_ -> Array{Complex{T}}(undef, size(plan_nufft)), ntrans)
exec_type1!(ûs, plan_nufft, vp)
@. ûs = ûs / N # normalise transform
# Perform type-2 NUFFT on preallocated output (one vector per transformed quantity)
vp_interp = map(similar, vp)
exec_type2!(vp, plan_nufft, ûs)
More details on optional parameters and on tuning accuracy is coming soon.
Differences with other packages
This package roughly follows the same notation and conventions of the FINUFFT library and its Julia interface, with a few differences detailed below.
Conventions used by this package
We try to preserve as much as possible the conventions used in FFTW3. In particular, this means that:
The FFT outputs are ordered starting from mode $k = 0$ to $k = N/2 - 1$ (for even $N$) and then from $-N/2$ to $-1$. Wavenumbers can be obtained in this order by calling
AbstractFFTs.fftfreq(N, N)
. UseAbstractFFTs.fftshift
to get Fourier modes in increasing order $-N/2, …, -1, 0, 1, …, N/2 - 1$. In FINUFFT, one should setmodeord = 1
to get this order.The type-1 NUFFT (non-uniform to uniform) is defined with a minus sign in the exponential. This is the same convention as the forward DFT in FFTW3. In particular, this means that performing a type-1 NUFFT on uniform points gives the same output than performing a FFT using FFTW3. In FINUFFT, this corresponds to setting
iflag = -1
in type-1 transforms. Conversely, type-2 NUFFTs (uniform to non-uniform) are defined with a plus sign, equivalently to the backward DFT in FFTW3.
Differences with NFFT.jl
This package allows changing the non-uniform points associated to a NUFFT plan. In other words, once a plan already exists, computing a NUFFT for a different set of points is efficient and doesn't need to allocate a new plan.
This package allows NUFFTs of purely real non-uniform data.
Different convention is used: non-uniform points are expected to be in $[0, 2π]$.
This package allows performing transforms of multiple quantities at the same non-uniform values at once.
Differences with FINUFFT / FINUFFT.jl
This package is written in "pure" Julia (besides the FFTs themselves which rely on the FFTW3 library, via their Julia interface).
This package allows NUFFTs of purely real non-uniform data. Moreover, transforms can be performed in for an arbitrary number of dimensions.
A different smoothing kernel function is used (backwards Kaiser–Bessel kernel by default).
It is possible to use the same plan for type-1 and type-2 transforms, reducing memory requirements in cases where one wants to perform both.