bug fixes and help file additions

Author: RainerHeintzmann

Project.toml

@@ -1,7 +1,7 @@
 name = "SeparableFunctions"
 uuid = "c8c7ead4-852c-491e-a42d-3d43bc74259e"
 authors = ["RainerHeintzmann <heintzmann@gmail.com>"]
-version = "0.4"
+version = "0.4.1"
 
 [deps]
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"

src/specific.jl

@@ -263,7 +263,7 @@ end
 
 ## Here some individual versions based on copy_corners! stuff. They only exist in the _cor version as they are not separable in X and Y.
 """
-    propagator_col([]::Type{TA},] sz::NTuple{N, Int}; Δz=one(eltype(TA)), k_max=0.5f0, scale=0.5f0 ./ (max.(sz ./ 2, 1))) where{TA, N}
+    propagator_col([]::Type{TA},] sz::NTuple{N, Int}; Δz=one(eltype(TA)), k_max=0.5f0, scale=0.5f0 ./ (max.(sz ./ 2, 1)), ref_idx = (length(sz) < 3) ? 1 : sz[3]÷2+1, use_sep=use_sep) where{TA, N}
 
 generates a propagator for propagating optical fields via exp(i kz Δz) with kz=sqrt(k0^2-kx^2-ky^2). The k-space radius is stated by
 k_max relative to the Nyquist frequency, as long as the scale remains to be 1 ./ (2 max.(sz ./ 2, 1))).
@@ -279,18 +279,21 @@ Note that there is no `propagator_sep` version of this function, since this prop
 + `Δz`:     distance in Z to propagate per slice.
 + `k_max`:  maximum propagation radius in k-space. I.e. limit of the k-sphere. This is not the aperture limit!
 + `scale`:  specifies how to interpret k-space positions. Should remain to be 1 ./ (2 max.(sz ./ 2, 1))).
++ `ref_idx`: reference index at which the propagator has no effect. E.g. `ref_idx=1` means the first slice of the result array does not propagate. By default, the (Fourier space) center position along Z is chosen.
++ `use_sep`: This boolean flag switches to an algorithm using rr2_sep and no corner copies. In CUDA this is a little faster.
+
 """
-function propagator_col(::Type{TA}, sz::NTuple{N, Int}; Δz=one(eltype(TA)), k_max=0.5f0, scale=0.5f0 ./ (max.(sz ./ 2, 1)), ref_idx = (length(sz) < 3) ? 1 : sz[3]÷2+1) where{TA, N}
+function propagator_col(::Type{TA}, sz::NTuple{N, Int}; Δz=one(eltype(TA)), k_max=0.5f0, scale=0.5f0 ./ (max.(sz ./ 2, 1)), ref_idx = (length(sz) < 3) ? 1 : sz[3]÷2+1, use_sep=false) where{TA, N}
 # function propagator_col(::Type{TA}, sz::NTuple{N, Int}; Δz=1.0, k_max=0.5, scale=0.5 ./ (max.(sz ./ 2, 1))) where{TA, N}
     if length(sz) > 3
         error("propagators are only allowed up to the third dimension. If you need to propagate several stacks, use broadcasting.")
     end
     arr = TA(undef, sz)
-    propagator_col!(arr; Δz=Δz, k_max=k_max, scale=scale, ref_idx = ref_idx) 
+    propagator_col!(arr; Δz=Δz, k_max=k_max, scale=scale, ref_idx = ref_idx, use_sep=use_sep) 
 end
 
-function propagator_col(sz::NTuple{N, Int}; Δz=1.0, k_max=0.5, scale=0.5 ./ (max.(sz ./ 2, 1)), ref_idx =  (length(sz) < 3) ? 1 : sz[3]÷2+1) where{N}
-    propagator_col(DefaultComplexArrType, sz; Δz=Δz, k_max=k_max, scale=scale, ref_idx = ref_idx)
+function propagator_col(sz::NTuple{N, Int}; Δz=1.0, k_max=0.5, scale=0.5 ./ (max.(sz ./ 2, 1)), ref_idx =  (length(sz) < 3) ? 1 : sz[3]÷2+1, use_sep=false) where{N}
+    propagator_col(DefaultComplexArrType, sz; Δz=Δz, k_max=k_max, scale=scale, ref_idx = ref_idx, use_sep=use_sep)
 end
 
 """
@@ -307,10 +310,10 @@ Note that there is no `propagator_sep` version of this function, since this prop
 # Arguments
 + `arr`:    the array to fill with propagators. If a 3rd dimension is present, a stack a propagators is returned, one for each multiple of Δz.
 + `Δz`:     distance in Z to propagate per slice in relation to the wavelength. Nyquist sampling would be 0.5.
-+ `ref_idx`: reference index at which the propagator has no effect. E.g. `ref_idx=1` means the first slice of the result array does not propagate. By default, the (Fourier space) center position along Z is chosen.
 + `k_max`:  maximum propagation radius in k-space. I.e. limit of the k-sphere in relation to sampling frequency. This is not the aperture limit!
             k_max = 0.5 corresponds to the Nyquist limit.
 + `scale`:  specifies how to interpret k-space positions. Should remain to be 1 ./ (2 max.(sz ./ 2, 1))).
++ `ref_idx`: reference index at which the propagator has no effect. E.g. `ref_idx=1` means the first slice of the result array does not propagate. By default, the (Fourier space) center position along Z is chosen.
 + `use_sep`: This boolean flag switches to an algorithm using rr2_sep and no corner copies. In CUDA this is a little faster.
 
 # Example
@@ -459,7 +462,7 @@ julia> # Note that a 2D propagator is always propagating by one Δz, thus corres
 julia> p = propagator_col((100,50,30), sampling, λ)
 ```
 """    
-function propagator_col(::Type{TA}, sz::NTuple{N, Int}, sampling::NTuple{3}, λ; ref_idx = size(arr,3)÷2+1, use_sep=false) where{TA, N}
+function propagator_col(::Type{TA}, sz::NTuple{N, Int}, sampling::NTuple{3}, λ; ref_idx = sz[3]÷2+1, use_sep=false) where{TA, N}
     if length(sz) > 3
         error("propagators are only allowed up to the third dimension. If you need to propagate several stacks, use broadcasting.")
     end

test/runtests.jl

@@ -149,22 +149,24 @@ end
     w = propagator_col!(rand(ComplexF32, 10,10,10), Δz = Δz)
     q = propagator_col!(zeros(ComplexF32, 10,10,1), Δz = Δz)
     q1 = propagator_col!(ones(ComplexF32, 10,10,10), Δz = Δz, ref_idx=1)
-    q2 = propagator_col!(rand(ComplexF32, 10,10,10), Δz = Δz, ref_idx=10, use_sep=true)
+    q2 = propagator_col((10,10,10), Δz = Δz, ref_idx=10, use_sep=true)
     @test q[:,:,1] == w[:,:,7]
     @test q[:,:,1] == q1[:,:,2]
     @test q[:,:,1] ≈ conj.(q2[:,:,9])
     w1 = propagator_col((10,10,10), Δz = Δz)
     @test w1 == w
-    q1 = propagator_col((10,10,1), Δz = Δz)
-    @test q1 == q
+    q1 = propagator_col((10,10), Δz = Δz)
+    @test q1[:,:,1] ≈ q
 
     sampling = (0.25,0.25,0.25)
     λ = 0.5
     q2 = propagator_col((10, 10, 10), sampling, λ)
     tmp = rand(ComplexF32, 10,10,10)
     q3 = propagator_col!(tmp, sampling, λ)
+    q4 = propagator_col((10,10,10), sampling, λ)
     @test w == q2
     @test w == q3
+    @test q4 == q3
     @test w == tmp
 end
 
@@ -175,14 +177,15 @@ end
     q1 = phase_kz_col!(ones(Float32, 10,10,10), Δz = Δz, ref_idx=1)
     q2 = phase_kz_col!(rand(Float32, 10,10,10), Δz = Δz, ref_idx=10, use_sep=true)
     @test q[:,:,1] == w[:,:,7]
-    @test q[:,:,1] == q1[:,:,2]
+    q = phase_kz_col!(rand(Float32, 10,10), Δz = Δz)
+    @test q[:,:] == q1[:,:,2]
     @test q[:,:,1] ≈ .-(q2[:,:,9])
 
     w1 = phase_kz_col((10,10,10), Δz = Δz)
     w = phase_kz_col!(rand(Float32, 10,10,10), Δz = Δz)
     @test w1 == w
-    q1 = phase_kz_col((10,10,1), Δz = Δz)
-    @test q1 == q
+    q1 = phase_kz_col((10,10), Δz = Δz)
+    @test q1 == q[:,:,1]
     # does phase_kz agree to propagator_col
 
     sampling = (0.25,0.25,0.25)