Merge pull request #44 from JuliaDSP/gfa/julia-compat-update

Julia compatibility update

.travis.yml

@@ -4,11 +4,17 @@ os:
   - linux
 julia:
   - 0.6
+  - 0.7
+  - 1.0
   - nightly
 matrix:
   allow_failures:
     - julia: nightly
 notifications:
   email: false
 after_success:
-  - julia -e 'cd(Pkg.dir("Wavelets")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
+  - julia -e 'VERSION >= v"0.7.0-DEV.5183" && using Pkg;
+      VERSION >= v"0.7.0-DEV.5183" || cd(Pkg.dir("Wavelets"));
+      Pkg.add("Coverage");
+      using Coverage;
+      Coveralls.submit(Coveralls.process_folder())'

README.md

@@ -216,13 +216,13 @@ m = 50
 threshold!(xtb, BiggestTH(), m)
 threshold!(xt, BiggestTH(), m)
 # compare sparse approximations in ell_2 norm
-vecnorm(x - iwpt(xtb, wt, tree), 2) # best basis wpt
-vecnorm(x - idwt(xt, wt), 2)        # regular dwt
+norm(x - iwpt(xtb, wt, tree), 2) # best basis wpt
+norm(x - idwt(xt, wt), 2)        # regular dwt
 ```
 ```
-julia> vecnorm(x - iwpt(xtb, wt, tree), 2)
+julia> norm(x - iwpt(xtb, wt, tree), 2)
 0.008941070750964843
-julia> vecnorm(x - idwt(xt, wt), 2)
+julia> norm(x - idwt(xt, wt), 2)
 0.05964431178940861
 ```
 

REQUIRE

@@ -1,4 +1,4 @@
 julia 0.6
 Reexport 0.0.3
 DSP 0.3.4
-Compat 0.65
+Compat 0.70

src/mod/Plot.jl

@@ -3,6 +3,7 @@ export wplotdots, wplotim
 using ..Util, ..WT, ..Transforms
 using Compat.LinearAlgebra
 using Compat: Nothing, undef
+import Compat
 
 # PLOTTING UTILITIES
 
@@ -86,7 +87,7 @@ function wplotim(x::AbstractArray, L::Integer, wt::Union{DiscreteWavelet,Nothing
     xts[1:nsc,1:nsc,:] .= 0
     scale01!(xts)
     for j=1:n, i=1:n
-        @inbounds xts[i,j,:] .= vecnorm(xts[i,j,:],pnorm).^(power)
+        @inbounds xts[i,j,:] .= Compat.norm(xts[i,j,:],pnorm).^(power)
     end
 
     # merge and reshape final image

src/mod/Threshold.jl

@@ -26,7 +26,9 @@ export
 using ..Util, ..WT, ..Transforms
 
 using Compat.LinearAlgebra
+using Compat.Statistics: median!
 using Compat: copyto!, Nothing, undef, rmul!
+import Compat
 
 # THRESHOLD TYPES AND FUNCTIONS
 
@@ -191,7 +193,7 @@ function denoise(x::AbstractArray,
         if ndims(x) == 1
             z = similar(x)
             for i = 1:pns
-                shift = nspin2circ(nspin, i)[1]
+                shift = i - 1
                 Util.circshift!(z, x, shift)
 
                 Transforms.dwt_oop!(xt, z, wt, L)
@@ -261,15 +263,11 @@ function mad!(y::AbstractArray)
     end
     return median!(y)
 end
-#function mad(x::AbstractArray)
-#    y = copy(x)
-#    mad!(y)
-#end
 
 # convert index i to a circshift array starting at 0 shift
 nspin2circ(nspin::Int, i::Int) = nspin2circ((nspin,), i)
 function nspin2circ(nspin::Tuple, i::Int)
-    c1 = ind2sub(nspin,i)
+    c1 = Compat.CartesianIndices(nspin)[i].I
     c = Vector{Int}(undef, length(c1))
     for k in 1:length(c1)
         c[k] = c1[k]-1
@@ -302,7 +300,7 @@ function matchingpursuit(x::AbstractVector, f::Function, ft::Function, tol::Real
     spat = zeros(eltype(x), length(y))  # sparse for atom computation
     nmax == -1 && (nmax = length(y))
 
-    while vecnorm(r) > tol && n <= nmax
+    while Compat.norm(r) > tol && n <= nmax
         # find largest inner product
         !oop && (ftr = ft(r))
         oop  && ft(ftr, r, tmp)
@@ -362,7 +360,7 @@ function coefentropy(x::T, et::LogEnergyEntropy, nrm::T) where T<:AbstractFloat
         return -log(s)
     end
 end
-function coefentropy(x::AbstractArray{T}, et::Entropy, nrm::T=vecnorm(x)) where T<:AbstractFloat
+function coefentropy(x::AbstractArray{T}, et::Entropy, nrm::T=Compat.norm(x)) where T<:AbstractFloat
     @assert nrm >= 0
     sum = zero(T)
     nrm == sum && return sum
@@ -389,7 +387,7 @@ function bestbasistree(y::AbstractVector{T}, wt::DiscreteWavelet, tree::BitVecto
     tmp = Vector{T}(undef, n)
     ntree = length(tree)
     entr_bf = Vector{T}(undef, ntree)
-    nrm = vecnorm(y)
+    nrm = Compat.norm(y)
 
     Lmax = maxtransformlevels(n)
     L = Lmax

src/mod/transforms_maximal_overlap.jl

@@ -11,8 +11,8 @@ function modwt_step(v::AbstractVector{T}, j::Integer, h::Array{S,1},
         g::Array{S,1}) where {T <: Number, S <: Number}
     N = length(v)
     L = length(h)
-    v1 = zeros(v)
-    w1 = zeros(v)
+    v1 = zeros(T, N)
+    w1 = zeros(T, N)
     for t in 1:N
         k = t
         w1[t] = h[1] * v[k]
@@ -52,7 +52,7 @@ function modwt(x::AbstractVector{T}, wt::OrthoFilter,
     g /= sqrt(2)
     h /= sqrt(2)
     N = length(x)
-    W = zeros(N, L)
+    W = zeros(T, N, L)
     V = deepcopy(x)
     for j in 1:L
         V[:], W[:, j] = modwt_step(V, j, h, g)
@@ -75,7 +75,7 @@ function imodwt_step(v::AbstractVector{T}, w::AbstractVector{T}, j::Integer,
         throw(DimensionMismatch("Filter sizes must match"))
     N = length(v)
     L = length(h)
-    v0 = zeros(N)
+    v0 = zeros(T, N)
     for t in 1:N
         k = t
         v0[t] = h[1] * w[k] + g[1] * v[k]

test/plot.jl

@@ -1,14 +1,12 @@
 
-let
-    print("plot: execute functions ...\n")
+@testset "Utils" begin
     J = 8
     n = 2^J
     x = testfunction(n, "Bumps")
     y = dwt(x, wavelet(WT.cdf97, WT.Lifting))
     d,l = wplotdots(y, 0.1, n)
     A = wplotim(y)
 
-
     x = randn(64,64)
     L = 2
     xts = wplotim(x, L, wavelet(WT.db3, WT.Filter))

test/runtests.jl

@@ -1,32 +1,33 @@
 using Wavelets
-using Base.Test
+using Compat.Test
 using Compat.LinearAlgebra
 using Compat.DelimitedFiles
 using Compat: ComplexF64, copyto!, range
+import Compat
 
 # modified from Base.Test
-function test_vecnorm_eq(va, vb, Eps, astr, bstr)
+function vecnorm_eq(va, vb, Eps, astr="a", bstr="b")
     if length(va) != length(vb)
-        error("lengths of ", astr, " and ", bstr, " do not match: ",
-              "\n  ", astr, " (length $(length(va))) = ", va,
-              "\n  ", bstr, " (length $(length(vb))) = ", vb)
+        #error("lengths of ", astr, " and ", bstr, " do not match: ",
+        #      "\n  ", astr, " (length $(length(va))) = ", va,
+        #      "\n  ", bstr, " (length $(length(vb))) = ", vb)
+        return false
     end
-    diff = vecnorm(va - vb)
 
-    if !isnan(Eps) && !(diff <= Eps)
-        sdiff = string("|", astr, " - ", bstr, "| <= ", Eps)
-        error("assertion failed: ", sdiff,
-              "\n  difference = ", diff, " > ", Eps)
+    diff = Compat.norm(va - vb)
+    if !isnan(Eps) && diff > Eps
+        #sdiff = string("|", astr, " - ", bstr, "| <= ", Eps)
+        #error("assertion failed: ", sdiff,
+        #      "\n  difference = ", diff, " > ", Eps)
+        return false
     end
+    return true
 end
-macro test_vecnorm_eq_eps(a, b, c)
-    :(test_vecnorm_eq($(esc(a)), $(esc(b)), $(esc(c)), $(string(a)), $(string(b))))
+macro vecnorm_eq_eps(a, b, c)
+    :(vecnorm_eq($(esc(a)), $(esc(b)), $(esc(c)), $(string(a)), $(string(b))))
 end
 
-
-include("util.jl")
-include("transforms.jl")
-include("threshold.jl")
-include("plot.jl")
-
-print("\ntesting: success\n")
+@testset "Util" begin include("util.jl") end
+@testset "Transforms" begin include("transforms.jl") end
+@testset "Threshold" begin include("threshold.jl") end
+@testset "Plot" begin include("plot.jl") end

test/threshold.jl

@@ -1,8 +1,5 @@
 
-print("threshold: execute functions ...\n")
-
-#threshold
-let
+@testset "Threshold" begin # TODO @test something
     x = randn(200)*2
     for th in (BiggestTH(), HardTH(), SoftTH(), SemiSoftTH(), SteinTH())
         threshold(x, th, 2)
@@ -12,8 +9,7 @@ let
     end
 end
 
-# denoising
-let
+@testset "Denoising" begin
     vs = VisuShrink(10)
     n = 2^8
     x0 = testfunction(n, "Doppler")
@@ -25,8 +21,7 @@ let
     y = denoise(randn(32,32), TI=true)
 end
 
-# best basis
-let
+@testset "Best basis" begin
     wt = wavelet(WT.db4)
     x = sin.(4*range(0, stop=2*pi-eps(), length=1024))
     tree = bestbasistree(x, wt)
@@ -39,8 +34,7 @@ let
     @test iwpt(xtb, wt, tree) ≈ x
 end
 
-#matching pursuit
-let
+@testset "Matching pursuit" begin
     N = 128
     M = 64
     y=randn(N)