implement FiniteDiffs submodule: gradient, divergence and laplacian o…

…perators (#22) New operators: - gradient and adjoint gradient: `fgradient` - divergence: `fdiv` - laplacian: `flaplacian` To better organize the symbols, I deprecate two entrypoints: * `ImageBase.fdiff` => `ImageBase.FiniteDiff.fdiff` * `ImageBase.fdiff!` => `ImageBase.FiniteDiff.fdiff!` * disable meta quality test in old Julia versions Maintaining old compatibility becomes quite troublesome especially when we have 1.6 as the new LTS version now. * CI compatibility fix for Julia < 1.3 Co-authored-by: Tim Holy <[email protected]>
JuliaImages · Oct 18, 2021 · 5687005 · 5687005
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diff --git a/.github/workflows/UnitTest.yml b/.github/workflows/UnitTest.yml
@@ -48,6 +48,14 @@ jobs:
             ${{ runner.os }}-test-
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
+      - name: "Compat fix for Julia < v1.3.0"
+        if: ${{ matrix.version == '1.0' }}
+        run: |
+          using Pkg
+          Pkg.add([
+            PackageSpec(name="AbstractFFTs", version="0.5"),
+          ])
+        shell: julia --project=. --startup=no --color=yes {0}
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v1

diff --git a/Project.toml b/Project.toml
@@ -14,6 +14,7 @@ julia = "1"
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
 ImageIO = "82e4d734-157c-48bb-816b-45c225c6df19"
 ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
@@ -23,4 +24,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TestImages = "5e47fb64-e119-507b-a336-dd2b206d9990"
 
 [targets]
-test = ["Aqua", "Documenter", "Test", "ImageIO", "ImageMagick", "OffsetArrays", "Statistics", "StackViews", "TestImages"]
+test = ["Aqua", "Documenter", "Test", "ImageFiltering", "ImageIO", "ImageMagick", "OffsetArrays", "Statistics", "StackViews", "TestImages"]
diff --git a/src/ImageBase.jl b/src/ImageBase.jl
@@ -5,11 +5,6 @@ export
     # originally from ImageTransformations.jl
     restrict,
 
-    # finite difference on one-dimension
-    # originally from Images.jl
-    fdiff,
-    fdiff!,
-
     # basic image statistics, from Images.jl
     minimum_finite,
     maximum_finite,
@@ -26,13 +21,11 @@ using Reexport
 using Base.Cartesian: @nloops
 @reexport using ImageCore
 using ImageCore.OffsetArrays
-using ImageCore.MappedArrays: of_eltype
 
 include("diff.jl")
 include("restrict.jl")
 include("utils.jl")
 include("statistics.jl")
-include("compat.jl")
 include("deprecated.jl")
 
 if VERSION >= v"1.4.2" # work around https://github.com/JuliaLang/julia/issues/34121

diff --git a/src/compat.jl b/src/compat.jl
diff --git a/src/deprecated.jl b/src/deprecated.jl
@@ -8,4 +8,9 @@
 @deprecate maxfinite(A; kwargs...) maximum_finite(A; kwargs...)
 @deprecate maxabsfinite(A; kwargs...) maximum_finite(abs, A; kwargs...)
 
+# These two symbols are exported by previous ImageBase versions and now organized in the
+# FiniteDiff submodule.
+@deprecate fdiff(args...; kwargs...) ImageBase.FiniteDiff.fdiff(args...; kwargs...)
+@deprecate fdiff!(args...; kwargs...) ImageBase.FiniteDiff.fdiff!(args...; kwargs...)
+
 # END 0.1 deprecation
diff --git a/src/diff.jl b/src/diff.jl
@@ -1,5 +1,36 @@
-# TODO: add keyword `shrink` to give a consistant result on Base
-#       when this is done, then we can propose this change to upstream Base
+# Because there exists the `FiniteDiff.jl` package with quite different purposes,
+# this module is not expected to be reexported.
+module FiniteDiff
+
+using ImageCore
+using ImageCore.MappedArrays: of_eltype
+
+"""
+Although stored as an array, image can also be viewed as a function from discrete grid space
+Zᴺ to continuous space R if it is gray image, to C if it is complex-valued image
+(MRI rawdata), to Rᴺ if it is colorant image, etc.
+This module provides the discrete
+version of gradient-related operators by viewing image arrays as functions.
+
+This module provides:
+
+- forward/backward difference [`fdiff`](@ref) are the Images-flavor of `Base.diff`
+- gradient operator [`fgradient`](@ref) and its adjoint via keyword `adjoint=true`.
+- divergence operator [`fdiv`](@ref) computes the sum of discrete derivatives of vector
+  fields.
+- laplacian operator [`flaplacian`](@ref) is the divergence of the gradient fields.
+
+Every function in this module has its in-place version.
+"""
+FiniteDiff
+
+export
+    fdiff, fdiff!,
+    fdiv, fdiv!,
+    fgradient, fgradient!,
+    flaplacian, flaplacian!
+
+
 """
     fdiff(A::AbstractArray; dims::Int, rev=false, boundary=:periodic)
 
@@ -19,7 +50,7 @@ Take vector as an example, it computes `(A[2]-A[1], A[3]-A[2], ..., A[1]-A[end])
 
 # Examples
 
-```jldoctest; setup=:(using ImageBase: fdiff)
+```jldoctest; setup=:(using ImageBase.FiniteDiff: fdiff)
 julia> A = [2 4 8; 3 9 27; 4 16 64]
 3×3 $(Matrix{Int}):
  2   4   8
@@ -106,3 +137,111 @@ _fdiff_default_dims(A::AbstractVector) = 1
 maybe_floattype(::Type{T}) where T = T
 maybe_floattype(::Type{T}) where T<:FixedPoint = floattype(T)
 maybe_floattype(::Type{CT}) where CT<:Color = base_color_type(CT){maybe_floattype(eltype(CT))}
+
+
+"""
+    fdiv(Vs...)
+
+Compute the divergence of vector fields `Vs`.
+
+See also [`fdiv!`](@ref) for the in-place version.
+"""
+function fdiv(V₁::AbstractArray{T}, Vs::AbstractArray{T}...) where T
+    fdiv!(similar(V₁, maybe_floattype(T)), V₁, Vs...)
+end
+fdiv(Vs::Tuple) = fdiv(Vs...)
+
+"""
+    fdiv!(out, Vs...)
+
+The in-place version of divergence operator [`fdiv`](@ref).
+"""
+function fdiv!(out::AbstractArray, V₁::AbstractArray, Vs::AbstractArray...)
+    # This is the optimized version of `sum(v->fgradient(v; ajoint=true), (V₁, Vs...))`
+    # by removing unnecessary memory allocations.
+    all(v->axes(v) == axes(out), (V₁, Vs...)) || throw(ArgumentError("All axes of vector fields Vs and X should be the same."))
+
+    # TODO(johnnychen94): for better performance, we can eliminate this `tmp` allocation by fusing multiple `fdiff` in the inner loop.
+    out .= fdiff(V₁; dims=1, rev=true, boundary=:periodic)
+    tmp = similar(out)
+    for i in 1:length(Vs)
+        out .+= fdiff!(tmp, Vs[i]; dims=i+1, rev=true, boundary=:periodic)
+    end
+    return out
+end
+fdiv!(out::AbstractArray, Vs::Tuple) = fdiv!(out, Vs...)
+
+"""
+    flaplacian(X::AbstractArray)
+
+The discrete laplacian operator, i.e., the divergence of the gradient fields of `X`.
+
+See also [`flaplacian!`](@ref) for the in-place version.
+"""
+flaplacian(X::AbstractArray) = flaplacian!(similar(X, maybe_floattype(eltype(X))), X)
+
+"""
+    flaplacian!(out, X)
+    flaplacian!(out, ∇X::Tuple, X)
+
+The in-place version of the laplacian operator [`flaplacian`](@ref).
+
+!!! tip Avoiding allocations
+    The two-argument method will allocate memory to store the intermediate
+    gradient fields `∇X`. If you call this repeatedly with images of consistent size and type,
+    consider using the three-argument form with pre-allocated memory for `∇X`,
+    which will eliminate allocation by this function.
+"""
+flaplacian!(out, X::AbstractArray) = fdiv!(out, fgradient(X))
+flaplacian!(out, ∇X::Tuple, X::AbstractArray) = fdiv!(out, fgradient!(∇X, X))
+
+
+"""
+    fgradient(X::AbstractArray; adjoint=false) -> (∂₁X, ∂₂X, ..., ∂ₙX)
+
+Computes the gradient fields of `X`. If `adjoint==true` then it computes the adjoint gradient
+fields.
+
+Each gradient vector is computed as forward difference along specific dimension, e.g.,
+[`∂ᵢX = fdiff(X, dims=i)`](@ref fdiff).
+
+Mathematically, the adjoint operator ∂ᵢ' of ∂ᵢ is defined as `<∂ᵢu, v> := <u, ∂ᵢ'v>`.
+
+See also the in-place version [`fgradient!(X)`](@ref) to reuse the allocated memory.
+"""
+function fgradient(X::AbstractArray{T,N}; adjoint::Bool=false) where {T,N}
+    fgradient!(ntuple(i->similar(X, maybe_floattype(T)), N), X; adjoint=adjoint)
+end
+
+"""
+    fgradient!(∇X::Tuple, X::AbstractArray; adjoint=false)
+
+The in-place version of (adjoint) gradient operator [`fgradient`](@ref).
+
+The input `∇X = (∂₁X, ∂₂X, ..., ∂ₙX)` is a tuple of arrays that are similar to `X`, i.e.,
+`eltype(∂ᵢX) == eltype(X)` and `axes(∂ᵢX)  == axes(X)` for all `i`.
+"""
+function fgradient!(∇X::NTuple{N, <:AbstractArray}, X; adjoint::Bool=false) where N
+    all(v->axes(v) == axes(X), ∇X) || throw(ArgumentError("All axes of vector fields ∇X and X should be the same."))
+    for i in 1:N
+        if adjoint
+            # the negative adjoint of gradient operator for forward difference is the backward difference
+            # see also
+            # Getreuer, Pascal. "Rudin-Osher-Fatemi total variation denoising using split Bregman." _Image Processing On Line_ 2 (2012): 74-95.
+            fdiff!(∇X[i], X, dims=i, rev=true)
+            # TODO(johnnychen94): ideally we can get avoid flipping the signs for better performance.
+            @. ∇X[i] = -∇X[i]
+        else
+            fdiff!(∇X[i], X, dims=i)
+        end
+    end
+    return ∇X
+end
+
+
+
+if VERSION < v"1.1"
+    isnothing(x) = x === nothing
+end
+
+end # module
diff --git a/test/deprecated.jl b/test/deprecated.jl
@@ -14,4 +14,11 @@
         @test maxabsfinite(A) == maximum_finite(abs, A)
         @test maxabsfinite(A, dims=1) == maximum_finite(abs, A, dims=1)
     end
+
+    @testset "fdiff entrypoints" begin
+        A = rand(Float32, 5)
+        @test ImageBase.fdiff(A, rev=true) == ImageBase.FiniteDiff.fdiff(A, rev=true)
+        out = similar(A)
+        @test ImageBase.fdiff!(out, A, rev=false) == ImageBase.FiniteDiff.fdiff!(out, A, rev=false)
+    end
 end
diff --git a/test/diff.jl b/test/diff.jl
@@ -1,8 +1,12 @@
+using ImageBase.FiniteDiff
+# TODO(johnnychen94): remove this after we delete `Imagebase.fdiff` and `ImageBase.fdiff!` entrypoints
+using ImageBase.FiniteDiff: fdiff, fdiff!
+
 @testset "fdiff" begin
     # Base.diff doesn't promote integer to float
-    @test ImageBase.maybe_floattype(Int) == Int
-    @test ImageBase.maybe_floattype(N0f8) == Float32
-    @test ImageBase.maybe_floattype(RGB{N0f8}) == RGB{Float32}
+    @test ImageBase.FiniteDiff.maybe_floattype(Int) == Int
+    @test ImageBase.FiniteDiff.maybe_floattype(N0f8) == Float32
+    @test ImageBase.FiniteDiff.maybe_floattype(RGB{N0f8}) == RGB{Float32}
 
     @testset "API" begin
         # fdiff! works the same as fdiff
@@ -107,3 +111,77 @@
         @test fdiff(A, dims=1) == fdiff(float.(A), dims=1)
     end
 end
+
+@testset "fgradient" begin
+    for T in generate_test_types([N0f8, Float32], [Gray, RGB])
+        for sz in [(7, ), (7, 5), (7, 5, 3)]
+            A = rand(T, sz...)
+
+            ∇A = fgradient(A)
+            for i in 1:length(sz)
+                @test ∇A[i] == fdiff(A, dims=i)
+            end
+            ∇A = map(similar, ∇A)
+            @test fgradient!(∇A, A) == fgradient(A)
+
+            ∇tA = fgradient(A, adjoint=true)
+            for i in 1:length(sz)
+                @test ∇tA[i] == .-fdiff(A, dims=i, rev=true)
+            end
+            ∇tA = map(similar, ∇tA)
+            @test fgradient!(∇tA, A, adjoint=true) == fgradient(A, adjoint=true)
+        end
+    end
+end
+
+@testset "fdiv/flaplacian" begin
+    ref_laplacian(X) = imfilter(X, Kernel.Laplacian(ntuple(x->true, ndims(X))), "circular")
+
+    X = [
+        5  3  8  1  2  2  3
+        5  5  1  3  3  1  1
+        1  8  2  9  1  2  7
+        7  3  4  5  8  1  5
+        1  4  1  8  8  9  7
+    ]
+    ΔX_ref = [
+        -8   10  -26   17    6    7    3
+        -8   -3   14    2   -5    4   12
+        23  -21   14  -25   18    2  -19
+       -18   11   -5    9  -17   20    2
+        19   -8   20  -17   -5  -18  -10
+    ]
+    ΔX = ref_laplacian(X)
+    # Base.diff doesn't promote Int to floats so we should probably do the same for laplacian
+    @test eltype(ΔX) == Int
+    @test ΔX_ref == ΔX
+
+    for T in generate_test_types([N0f8, Float32], [Gray, RGB])
+        for sz in [(7,), (7, 7), (7, 7, 7)]
+            A = rand(T, sz...)
+            ∇A = fgradient(A)
+            out = fdiv(∇A)
+            @test out ≈ ref_laplacian(A)
+
+            fill!(out, zero(T))
+            fdiv!(out, ∇A...)
+            @test out == fdiv(∇A)
+        end
+    end
+
+    for T in generate_test_types([N0f8, Float32], [Gray, RGB])
+        for sz in [(7,), (7, 7), (7, 7, 7)]
+            A = rand(T, sz...)
+            out = flaplacian(A)
+            @test out ≈ ref_laplacian(A)
+
+            ∇A = fgradient(A)
+            foreach((out, ∇A...)) do x
+                fill!(x, zero(T))
+            end
+            flaplacian!(out, ∇A, A)
+            @test out == flaplacian(A)
+            @test ∇A == fgradient(A)
+        end
+    end
+end
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,23 +1,23 @@
 using ImageBase, OffsetArrays, StackViews
+using ImageFiltering
 using Test, TestImages, Aqua, Documenter
 
 using OffsetArrays: IdentityUnitRange
 include("testutils.jl")
 
 @testset "ImageBase.jl" begin
-
     @testset "Project meta quality checks" begin
-        # Not checking compat section for test-only dependencies
-        Aqua.test_ambiguities(ImageBase)
-        Aqua.test_all(ImageBase;
-            ambiguities=false,
-            project_extras=true,
-            deps_compat=true,
-            stale_deps=true,
-            project_toml_formatting=true
-        )
-        if VERSION >= v"1.2"
-            doctest(ImageBase,manual = false)
+        if VERSION >= v"1.3"
+            # Not checking compat section for test-only dependencies
+            Aqua.test_ambiguities(ImageBase)
+            Aqua.test_all(ImageBase;
+                ambiguities=false,
+                project_extras=true,
+                deps_compat=true,
+                stale_deps=true,
+                project_toml_formatting=true
+            )
+            doctest(ImageBase, manual = false)
         end
     end