Improve error messages, formatting

src/QSM.jl

@@ -80,8 +80,7 @@ const FFTW_NTHREADS = Ref{Int}(known(num_cores()))
     end
 
     function fftw_set_threading(lib::Symbol = :FFTW)
-        lib ∈ (:FFTW, :Polyester, :Threads) ||
-            throw(ArgumentError("lib must be one of :FFTW, :Polyester or :Threads, got :$(lib)"))
+        checkopts(lib, (:FFTW, :Polyester, :Threads), :lib)
 
         if lib ∈ (:Polyester, :Threads) && nthreads() < 2
             @warn "Cannot use $lib with FFTW. Defaulting to FFTW multi-threading" Threads.nthreads()

src/bgremove/ismv.jl

@@ -88,24 +88,24 @@ function _ismv!(
     S = _smv_kernel!(S, F̂, s, vsz, r, P)
 
     # constants
-    _δ = one(eltype(s)) - sqrt(eps(eltype(s)))
+    δ = one(eltype(s)) - sqrt(eps(eltype(s)))
 
     # erode mask
     s = tcopyto!(s, m) # in-place type conversion, reuse smv var
     m0 = tcopyto!(m0, m)
 
     F̂ = mul!(F̂, P, s)
-    @inbounds @batch for I in eachindex(F̂)
+    @batch for I in eachindex(F̂)
         F̂[I] *= S[I]
     end
 
     s = mul!(s, iP, F̂)
-    @inbounds @batch for I in eachindex(m)
-        m[I] = s[I] > _δ
+    @batch for I in eachindex(m)
+        m[I] = s[I] > δ
     end
 
     # iSMV
-    @inbounds for t in axes(f, 4)
+    for t in axes(f, 4)
         if verbose && size(f, 4) > 1
             @printf("Echo: %d/%d\n", t, size(f, 4))
         end
@@ -135,7 +135,7 @@ end
 
 
 function __ismv!(f::AbstractArray{T}, f0, S, bc, m, iP, F̂, P, tol, maxit, verbose) where {T}
-    @inbounds @batch for I in eachindex(f0)
+    @batch for I in eachindex(f0)
         f0[I] = m[I]*f[I]
     end
 
@@ -146,7 +146,7 @@ function __ismv!(f::AbstractArray{T}, f0, S, bc, m, iP, F̂, P, tol, maxit, verb
         @printf("iter%6s\tresnorm\n", "")
     end
 
-    @inbounds for i in 1:maxit
+    for i in 1:maxit
         if nr ≤ ϵ
             break
         end

src/bgremove/lbv.jl

@@ -118,7 +118,7 @@ function _lbv!(
     end
 
     # set boundaries
-    @inbounds for t in axes(f, 4)
+    for t in axes(f, 4)
         fct = @view(f[Rc,t])
         @batch for I in eachindex(fct, mc)
             fct[I] *= mc[I]

src/bgremove/pdf.jl

@@ -85,8 +85,7 @@ function _pdf!(
         checkshape(W, f, (:W, :f))
     end
 
-    Dkernel ∈ (:k, :kspace, :i, :ispace) ||
-        throw(ArgumentError("Dkernel must be one of :k, :kspace, :i, :ispace, got :$(Dkernel)"))
+    checkopts(Dkernel, (:k, :kspace, :i, :ispace), :Dkernel)
 
     # pad to fast fft size
     fp = padfastfft(@view(f[:,:,:,1]), pad, rfft=true)
@@ -126,7 +125,7 @@ function _pdf!(
     D = _dipole_kernel!(D, F̂, b, sz0, vsz, bdir, P, Dkernel, :rfft)
 
     # background mask
-    @inbounds @batch for I in eachindex(m)
+    @batch for I in eachindex(m)
         M̃[I] = !m[I]
     end
 
@@ -138,7 +137,7 @@ function _pdf!(
     elseif ndims(W) == 3
         # same weights for all echoes
         b = padarray!(b, W)
-        @inbounds @batch for I in eachindex(MW)
+        @batch for I in eachindex(MW)
             MW[I] = m[I] * b[I]
         end
 
@@ -147,7 +146,7 @@ function _pdf!(
         # VOID
     end
 
-    @inbounds for t in axes(f, 4)
+    for t in axes(f, 4)
         if verbose && size(f, 4) > 1
             @printf("Echo: %d/%d\n", t, size(f, 4))
         end
@@ -205,17 +204,17 @@ function _A_pdf!(Av, v, W, iP, D, F̂, P, M̃)
     v = reshape(v, size(W))
     x = reshape(Av, size(W))
 
-    @inbounds @batch for I in eachindex(x)
+    @batch for I in eachindex(x)
         x[I] = M̃[I] * v[I]
     end
 
     F̂ = mul!(F̂, P, x)
-    @inbounds @batch for I in eachindex(F̂)
+    @batch for I in eachindex(F̂)
         F̂[I] *= D[I]
     end
 
     x = mul!(x, iP, F̂)
-    @inbounds @batch for I in eachindex(x)
+    @batch for I in eachindex(x)
         x[I] *= W[I]
     end
 
@@ -227,17 +226,17 @@ function _At_pdf!(Atu, u, M̃, iP, D, F̂, P, W)
     u = reshape(u, size(W))
     x = reshape(Atu, size(W))
 
-    @inbounds @batch for I in eachindex(x)
+    @batch for I in eachindex(x)
         x[I] = W[I] * u[I]
     end
 
     F̂ = mul!(F̂, P, x)
-    @inbounds @batch for I in eachindex(F̂)
+    @batch for I in eachindex(F̂)
         F̂[I] *= D[I] # conj(D), D is real
     end
 
     x = mul!(x, iP, F̂)
-    @inbounds @batch for I in eachindex(x)
+    @batch for I in eachindex(x)
         x[I] *= M̃[I]
     end
 

src/bgremove/sharp.jl

@@ -80,27 +80,27 @@ function _sharp!(
     S = _smv_kernel!(S, F̂, s, vsz, r, P)
 
     # constants
-    _thr  = convert(eltype(S), thr)
-    _one  = one(eltype(S))
-    _zero = zero(eltype(F̂))
-    _δ    = one(eltype(s)) - sqrt(eps(eltype(s)))
+    thrT  = convert(eltype(S), thr)
+    oneT  = one(eltype(S))
+    zeroT = zero(eltype(F̂))
+    δ     = one(eltype(s)) - sqrt(eps(eltype(s)))
 
     # erode mask
     s = tcopyto!(s, m) # in-place type conversion, reuse smv var
 
     F̂ = mul!(F̂, P, s)
-    @inbounds @batch for I in eachindex(F̂)
+    @batch for I in eachindex(F̂)
         F̂[I] *= S[I]
-        S[I] = _one - S[I]
+        S[I] = oneT - S[I]
     end
 
     s = mul!(s, iP, F̂)
-    @inbounds @batch for I in eachindex(m)
-        m[I] = s[I] > _δ
+    @batch for I in eachindex(m)
+        m[I] = s[I] > δ
     end
 
     # SHARP
-    @inbounds for t in axes(f, 4)
+    for t in axes(f, 4)
         if t > 1
             fp = padarray!(fp, @view(f[Rc,t]))
         end
@@ -117,7 +117,7 @@ function _sharp!(
 
         F̂ = mul!(F̂, P, fp)
         @batch for I in eachindex(F̂)
-            F̂[I] = ifelse(abs(S[I]) < _thr, _zero, F̂[I]*inv(S[I]))
+            F̂[I] = ifelse(abs(S[I]) < thrT, zeroT, F̂[I]*inv(S[I]))
         end
 
         fp = mul!(fp, iP, F̂)
@@ -226,34 +226,34 @@ function _sharp!(
     fp = tfill!(fp, 0)
 
     # constants
-    _thr  = convert(eltype(S), thr)
-    _one  = one(eltype(S))
-    _zero = zero(eltype(F̂))
-    _δ    = one(eltype(s)) - sqrt(eps(eltype(s)))
+    thrT  = convert(eltype(S), thr)
+    oneT  = one(eltype(S))
+    zeroT = zero(eltype(F̂))
+    δ     = one(eltype(s)) - sqrt(eps(eltype(s)))
 
     # fft of original mask
     s = tcopyto!(s, mr) # in-place type conversion
     M̂ = mul!(M̂, P, s)
 
-    @inbounds for (i, r) in enumerate(rs)
+    for (i, r) in enumerate(rs)
         # get smv kernel
         S = _smv_kernel!(S, F̂, s, vsz, r, P)
 
         # erode mask
         @batch for I in eachindex(F̂)
             F̂[I] = S[I] * M̂[I]
-            S[I] = _one - S[I]
+            S[I] = oneT - S[I]
         end
 
         s = mul!(s, iP, F̂)
         @batch for I in eachindex(mr)
-            mr[I] = s[I] > _δ
+            mr[I] = s[I] > δ
         end
 
         # high-pass filter first (largest) kernel for deconvolution
         if i == 1
             @batch for I in eachindex(iS)
-                iS[I] = ifelse(abs(S[I]) < _thr, _zero, inv(S[I]))
+                iS[I] = ifelse(abs(S[I]) < thrT, zeroT, inv(S[I]))
             end
         end
 
@@ -301,7 +301,7 @@ function _sharp!(
     checkshape(fl, f, (:fl, :f))
     checkshape(smask, mask, (:smask, :mask))
     checkshape(axes(mask), axes(f)[1:3], (:mask, :f))
-    length(r) > 0 || throw(ArgumentError("r must not be empty"))
+    !isempty(r) || throw(ArgumentError("r must not be empty"))
 
     rs = sort!(unique(collect(r)), rev=true)
 
@@ -338,34 +338,34 @@ function _sharp!(
     fp = tfill!(fp, 0)
 
     # constants
-    _thr  = convert(eltype(S), thr)
-    _one  = one(eltype(S))
-    _zero = zero(eltype(F̂))
-    _δ    = one(eltype(s)) - sqrt(eps(eltype(s)))
+    thrT  = convert(eltype(S), thr)
+    oneT  = one(eltype(S))
+    zeroT = zero(eltype(F̂))
+    δ     = one(eltype(s)) - sqrt(eps(eltype(s)))
 
     # fft of original mask
     s = tcopyto!(s, mr) # in-place type conversion
     M̂ = mul!(M̂, P, s)
 
-    @inbounds for (i, r) in enumerate(rs)
+    for (i, r) in enumerate(rs)
         # get smv kernel
         S = _smv_kernel!(S, F̂, s, vsz, r, P)
 
         # erode mask
         @batch for I in eachindex(F̂)
             F̂[I] = S[I] * M̂[I]
-            S[I] = _one - S[I]
+            S[I] = oneT - S[I]
         end
 
         s = mul!(s, iP, F̂)
         @batch for I in eachindex(mr)
-            mr[I] = s[I] > _δ
+            mr[I] = s[I] > δ
         end
 
         # high-pass filter first (largest) kernel for deconvolution
         if i == 1
             @batch for I in eachindex(iS)
-                iS[I] = ifelse(abs(S[I]) < _thr, _zero, inv(S[I]))
+                iS[I] = ifelse(abs(S[I]) < thrT, zeroT, inv(S[I]))
             end
         end
 
@@ -391,15 +391,15 @@ function _sharp!(
 
     # deconvolution + high-pass filter
     F̂p = mul!(F̂p, P4, fp)
-    @inbounds for t in axes(F̂p, 4)
+    for t in axes(F̂p, 4)
         F̂t = @view(F̂p[:,:,:,t])
         @batch for I in eachindex(F̂t)
             F̂t[I] *= iS[I]
         end
     end
 
     fp = mul!(fp, iP4, F̂p)
-    @inbounds for t in axes(fp, 4)
+    for t in axes(fp, 4)
         ft = @view(fp[:,:,:,t])
         @batch for I in eachindex(ft)
             ft[I] *= m[I]

src/inversion/direct.jl

@@ -175,16 +175,9 @@ function _kdiv!(
     checkshape(x, f, (:x, :f))
     checkshape(axes(mask), axes(f)[1:3])
 
-    Dkernel ∈ (:k, :kspace, :i, :ispace) ||
-        throw(ArgumentError("Dkernel must be one of :k, :kspace, :i, :ispace, got :$(Dkernel)"))
-
-    method ∈ (:tkd, :tsvd, :tikh) ||
-        throw(ArgumentError("method must be one of :tkd, :tsvd, got :$(method)"))
-
-    if method == :tikh
-        reg ∈ (:identity, :gradient, :laplacian) ||
-            throw(ArgumentError("reg must be one of :identity, :gradient, :laplacian, got :$(reg)"))
-    end
+    checkopts(Dkernel, (:k, :kspace, :i, :ispace), :Dkernel)
+    checkopts(method, (:tkd, :tsvd, :tikh), :method)
+    method == :tikh && checkopts(reg, (:identity, :gradient, :laplacian), :reg)
 
     # pad to fast fft size
     fp = padfastfft(@view(f[:,:,:,1]), pad, rfft=true)
@@ -208,7 +201,7 @@ function _kdiv!(
     # inverse k-space kernel
     iD = _kdiv_ikernel!(D, F̂, fp, vsz, P, lambda, reg, method)
 
-    @inbounds for t in axes(f, 4)
+    for t in axes(f, 4)
         fp = padarray!(fp, @view(f[:,:,:,t]))
 
         F̂ = mul!(F̂, P, fp)
@@ -243,22 +236,22 @@ function _kdiv_ikernel!(
         δ = convert(T, lambda)
         iδ = inv(δ)
 
-        @inbounds @batch for I in eachindex(D)
+        @batch for I in eachindex(D)
             D[I] = ifelse(abs(D[I]) ≤ δ, copysign(iδ, D[I]), inv(D[I]))
         end
 
     elseif method == :tsvd
         δ = convert(T, lambda)
-        _zero = zero(T)
+        zeroT = zero(T)
 
-        @inbounds @batch for I in eachindex(D)
-            D[I] = ifelse(abs(D[I]) ≤ δ, _zero, inv(D[I]))
+        @batch for I in eachindex(D)
+            D[I] = ifelse(abs(D[I]) ≤ δ, zeroT, inv(D[I]))
         end
 
 
     elseif method == :tikh
         λ = convert(T, lambda)
-        _zero = zero(T)
+        zeroT = zero(T)
 
         Γ = similar(D)
 
@@ -273,8 +266,8 @@ function _kdiv_ikernel!(
             Γ = tmap!(abs2, Γ)
         end
 
-        @inbounds @batch for I in eachindex(D)
-            D[I] = ifelse(iszero(D[I]) && iszero(Γ[I]), _zero, inv(D[I]*D[I] + λ*Γ[I])*D[I])
+        @batch for I in eachindex(D)
+            D[I] = ifelse(iszero(D[I]) && iszero(Γ[I]), zeroT, inv(D[I]*D[I] + λ*Γ[I])*D[I])
         end
 
     end