update codebase to 1.0 and 1.x (continue #27) (#31)

* add Project.toml

* update test for cache and minor fix

* update test for rotation and minor fix

* update flipdm to reverse

JuliaLang/julia#26369

* update test for crop and minor fix

* update test for resize

* update test for scale and minor fix

* update test for zoom and minor fix

* WIP: update test for distortion and minor fix

* update test for either and minor fix

* fix pipeline test

* update summary reference for distortedview

* WIP: fix tests for augment and operations

* drop julia 0.7 and update CI

* use FileIO v1.1.0

JuliaIO/FileIO.jl#245

* add 1.x tests to CI

* revert back unnecessary changes

* test windows in travis

* fix randomly failed test cases for inacuraccy reasons

* update to julia 1.1

* maybe_copy doesn't explain its usage
* replace Slice by OffsetArrays.IdentityUnitRange

JuliaArrays/OffsetArrays.jl#62

* update to julia 1.2 -- part I

* WIP: update to julia 1.2 -- part II

detect some type instable test cases, only the outmost wrapper is
instable here

* unify how types are displayed

Only meta operations such as Either, Pipeline doesn't have Agumentor
prefix

* add more test versions

* move safe_rand to compat.jl

rand is thread-safe in julia 1.3

* don't allow failures for julia 1.3

* fix commit "WIP: update 1.0"

* use explicit and intuitive CartesianIndex(1, 1)

* add method specialization for tweight

* allow FileIO 1.2

* fix type instability for Either

* update reference for FixedPointNumbers v0.7

* try: relax equality check for scale

* restore test cases in tst_scale.jl

* Revert "add method specialization for tweight"

This reverts commit a698382.

* Augmentor v0.6.0-pre

.gitignore

@@ -4,3 +4,4 @@
 _build/
 _static/
 _templates
+/Manifest.toml

.travis.yml

@@ -3,9 +3,12 @@ language: julia
 os:
   - linux
   - osx
+  - windows
 julia:
-  - 0.7
   - 1.0
+  - 1.1
+  - 1.2
+  - 1.3
   - nightly
 notifications:
   email: false
@@ -18,14 +21,6 @@ matrix:
   allow_failures:
     - julia: nightly
 
-## uncomment and modify the following lines to manually install system packages
-#addons:
-#  apt: # apt-get for linux
-#    packages:
-#    - gfortran
-#before_script: # homebrew for mac
-#  - if [ $TRAVIS_OS_NAME = osx ]; then brew install gcc; fi
-
 #jobs:
 #  include:
 #    - stage: deploy
@@ -36,10 +31,5 @@ matrix:
 #        - julia -e 'import Pkg; Pkg.add("Documenter")'
 #        - julia -e 'import Augmentor; ENV["DOCUMENTER_DEBUG"] = "true"; include(joinpath("docs","make.jl"))'
 
-## uncomment the following lines to override the default test script
-script:
-    - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-    - julia --check-bounds=yes --color=yes -e 'import Pkg; Pkg.clone(pwd()); Pkg.build("Augmentor"); Pkg.test("Augmentor"; coverage=true)';
-
 after_success:
   - julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Coveralls.submit(process_folder())'

Project.toml

@@ -0,0 +1,49 @@
+name = "Augmentor"
+uuid = "02898b10-1f73-11ea-317c-6393d7073e15"
+authors = ["Christof Stocker <stocker.christof@gmail.com>"]
+version = "0.6.0-pre"
+
+[deps]
+ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
+ComputationalResources = "ed09eef8-17a6-5b46-8889-db040fac31e3"
+CoordinateTransformations = "150eb455-5306-5404-9cee-2592286d6298"
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+IdentityRanges = "bbac6d45-d8f3-5730-bfe4-7a449cd117ca"
+ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
+ImageFiltering = "6a3955dd-da59-5b1f-98d4-e7296123deb5"
+ImageTransformations = "02fcd773-0e25-5acc-982a-7f6622650795"
+Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MLDataPattern = "9920b226-0b2a-5f5f-9153-9aa70a013f8b"
+MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900"
+OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
+Rotations = "6038ab10-8711-5258-84ad-4b1120ba62dc"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+
+[compat]
+ColorTypes = "0.7, 0.8"
+ComputationalResources = "0.3"
+CoordinateTransformations = "0.5"
+FileIO = "1"
+IdentityRanges = "0.3"
+ImageCore = "0.8.1"
+ImageFiltering = "0.4, 0.5, 0.6"
+ImageTransformations = "0.5, 0.6, 0.7, 0.8"
+Interpolations = "0.8, 0.9, 0.10, 0.11, 0.12"
+MLDataPattern = "0.4, 0.5"
+MappedArrays = "0.1, 0.2"
+OffsetArrays = "0.8, 0.9, 0.10, 0.11"
+Rotations = "0.7, 0.8, 0.9, 0.10, 0.11, 0.12"
+StaticArrays = "0.8, 0.9, 0.10, 0.11, 0.12"
+julia = "1"
+
+[extras]
+ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254"
+ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
+ReferenceTests = "324d217c-45ce-50fc-942e-d289b448e8cf"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestImages = "5e47fb64-e119-507b-a336-dd2b206d9990"
+
+[targets]
+test = ["ImageInTerminal", "ImageMagick", "ReferenceTests", "Statistics", "TestImages", "Test"]

src/Augmentor.jl

@@ -9,12 +9,18 @@ using CoordinateTransformations
 using Rotations
 using Interpolations
 using StaticArrays
-using OffsetArrays
 using IdentityRanges
 using MLDataPattern
 using ComputationalResources
 using FileIO
 using Base.PermutedDimsArrays: PermutedDimsArray
+using LinearAlgebra
+using OffsetArrays
+
+# axes(::OffsetArray) changes from Base.Slice to Base.IdentityUnitRange in julia 1.1
+# https://github.com/JuliaArrays/OffsetArrays.jl/pull/62
+# TODO: switch to Base.IdentityUnitRange when we decide to drop 1.0 compatibility
+using OffsetArrays: IdentityUnitRange
 
 export
 
@@ -67,6 +73,7 @@ export
 
     testpattern
 
+include("compat.jl")
 include("utils.jl")
 include("types.jl")
 include("operation.jl")
@@ -97,7 +104,10 @@ include("augment.jl")
 include("augmentbatch.jl")
 
 function __init__()
-    rand_mutex[] = Threads.Mutex()
+    if VERSION < v"1.3"
+        # see compat.jl
+        rand_mutex[] = Threads.Mutex()
+    end
 end
 
 end # module

src/augment.jl

@@ -110,14 +110,14 @@ augment!(out, img, op::Operation) = augment!(out, img, (op,))
 
 function augment!(out::AbstractArray, img::AbstractArray, pipeline::AbstractPipeline)
     out_lazy = _augment_avoid_eager(img, pipeline)
-    copy!(match_idx(out, axes(out_lazy)), out_lazy)
+    copyto!(match_idx(out, axes(out_lazy)), out_lazy)
     out
 end
 
 function augment!(outs::NTuple{N,AbstractArray}, imgs::NTuple{N,AbstractArray}, pipeline::AbstractPipeline) where N
     outs_lazy = _augment_avoid_eager(imgs, pipeline)
     map(outs, outs_lazy) do out, out_lazy
-        copy!(match_idx(out, axes(out_lazy)), out_lazy)
+        copyto!(match_idx(out, axes(out_lazy)), out_lazy)
     end
     outs
 end

src/compat.jl

@@ -0,0 +1,22 @@
+if VERSION >= v"1.3"
+    const safe_rand = rand
+else
+    # rand is thread safe after julia 1.3
+    # TODO: delete this when we decide to drop 1.0 compatibility
+
+    # --------------------------------------------------------------------
+    # rand() is not threadsafe (https://discourse.julialang.org/t/4683)
+
+    # Because we only require random numbers to sample parameters
+    # and not the actual expensive computation, this seems like a better
+    # approach than using separate RNG per thread.
+    const rand_mutex = Ref{Threads.Mutex}()
+
+    # constant overhead of about 80 ns compared to unsafe rand
+    function safe_rand(args...)
+        lock(rand_mutex[])
+        result = rand(args...)
+        unlock(rand_mutex[])
+        result
+    end
+end

src/distortedview.jl

@@ -6,14 +6,17 @@ struct DistortedView{T,P<:AbstractMatrix,E<:AbstractExtrapolation,G,D} <: Abstra
 
     function DistortedView(parent::AbstractMatrix{T}, grid::AbstractArray{Float64,3}) where T
         @assert size(grid,1) == 2
+        # to compare two DistortedViews, their `axes` should be the same
+        parent = plain_axes(parent)
         etp = ImageTransformations.box_extrapolation(parent, Flat())
         field = ImageTransformations.box_extrapolation(grid, 0.0)
         new{T,typeof(parent),typeof(etp),typeof(grid),typeof(field)}(parent, etp, grid, field)
     end
 end
 
 Base.parent(A::DistortedView) = A.parent
-Base.size(A::DistortedView) = map(length, axes(A.parent))
+Base.size(A::DistortedView) = map(length, axes(A))
+Base.axes(A::DistortedView) = axes(A.parent)
 
 function Base.showarg(io::IO, A::DistortedView, toplevel)
     print(io, typeof(A).name, '(')
@@ -22,7 +25,7 @@ function Base.showarg(io::IO, A::DistortedView, toplevel)
     Base.showarg(io, A.grid, false)
     print(io, " as ", size(A.field,2), '×', size(A.field,3), " vector field")
     print(io, ')')
-    toplevel && print(io, " with eltype ", eltype(v))
+    toplevel && print(io, " with eltype ", eltype(A))
 end
 
 # inline speeds up ~30%
@@ -39,8 +42,8 @@ end
     # map array indices to grid indices
     gi, gj = (i-1)/(leny-1)*(gh-1)+1, (j-1)/(lenx-1)*(gw-1)+1
     # compute parent indices offset
-    @inbounds dy = field[1, gi, gj] * leny
-    @inbounds dx = field[2, gi, gj] * lenx
+    @inbounds dy = field(1, gi, gj) * leny
+    @inbounds dx = field(2, gi, gj) * lenx
     # compute parent indices and return value
     # Note: we subtract instead of add, because the vector field is
     #       specified in forward mode (i.e. in reference to the source
@@ -50,6 +53,6 @@ end
     checkbounds(indsx, j)
     @inbounds y = indsy[i] - dy
     @inbounds x = indsx[j] - dx
-    @inbounds res = etp[y, x]
+    @inbounds res = etp(y, x)
     res
 end

src/operation.jl

@@ -63,7 +63,9 @@ for FUN in (:applyeager, :applylazy, :applypermute,
 end
 
 function applyeager(op::Operation, img::AbstractArray, param)
-    maybe_copy(applylazy(op, img, param))
+    # TODO: we don't need wrappers for eager mode, so we might want to
+    # add plain_array to it as well for the sake of simplicity
+    contiguous(applylazy(op, img, param))
 end
 
 function applyaffineview(op::Operation, img::AbstractArray, param)
@@ -116,7 +118,7 @@ end
 @generated function toaffinemap_common(op::AffineOperation, img::AbstractArray{T,N}, param) where {T,N}
     quote
         tfm = toaffinemap(op, img, param)
-        AffineMap(SMatrix(tfm.m), SVector(tfm.v))::AffineMap{SArray{Tuple{$N,$N},Float64,$N,$(N*N)},SVector{$N,Float64}}
+        AffineMap(SMatrix(tfm.linear), SVector(tfm.translation))::AffineMap{SArray{Tuple{$N,$N},Float64,$N,$(N*N)},SVector{$N,Float64}}
     end
 end
 

src/operations/cache.jl

@@ -53,7 +53,7 @@ pl = ElasticDistortion(3,3) |> zeros(20,20) |> Rotate(-10:10)
 """
 struct CacheImage <: ImageOperation end
 
-applyeager(op::CacheImage, img::AbstractArray, param) = maybe_copy(img)
+applyeager(op::CacheImage, img::AbstractArray, param) = contiguous(img)
 
 function showconstruction(io::IO, op::CacheImage)
     print(io, typeof(op).name.name, "()")
@@ -92,12 +92,12 @@ function applylazy(op::CacheImageInto, img::Tuple)
 end
 
 function applylazy(op::CacheImageInto{<:AbstractArray}, img::AbstractArray, param)
-    copy!(match_idx(op.buffer, axes(img)), img)
+    copyto!(match_idx(op.buffer, axes(img)), img)
 end
 
 function applylazy(op::CacheImageInto{<:Tuple}, imgs::Tuple)
     map(op.buffer, imgs) do buffer, img
-        copy!(match_idx(buffer, axes(img)), img)
+        copyto!(match_idx(buffer, axes(img)), img)
     end
 end
 
@@ -130,7 +130,7 @@ function Base.show(io::IO, op::CacheImageInto{<:AbstractArray})
         print(io, summary(op.buffer))
     else
         print(io, typeof(op).name, "(")
-        showarg(io, op.buffer)
+        Base.showarg(io, op.buffer, false)
         print(io, ")")
     end
 end
@@ -142,7 +142,7 @@ function Base.show(io::IO, op::CacheImageInto{<:Tuple})
     else
         print(io, typeof(op).name, "((")
         for (i, buffer) in enumerate(op.buffer)
-            showarg(io, buffer)
+            Base.showarg(io, buffer, false)
             i < length(op.buffer) && print(io, ", ")
         end
         print(io, "))")

src/operations/convert.jl

@@ -52,7 +52,7 @@ end
 @inline supports_lazy(::Type{<:ConvertEltype}) = true
 
 function applyeager(op::ConvertEltype{T}, img::AbstractArray, param) where T
-    maybe_copy(convert(AbstractArray{T}, img))
+    contiguous(convert(AbstractArray{T}, img))
 end
 
 function applylazy(op::ConvertEltype{T}, img::AbstractArray, param) where T