🧹 code organization and dead code elimination (#971)

Author: johnnychen94

.github/workflows/UnitTest.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version: ['1.0', '1', 'nightly']
+        julia-version: ['1.3', '1', 'nightly']
         os: [ubuntu-latest]
         arch: [x64]
         include:

Project.toml

@@ -3,11 +3,11 @@ uuid = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
 version = "0.24.1"
 
 [deps]
-AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 Graphics = "a2bd30eb-e257-5431-a919-1863eab51364"
 ImageAxes = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac"
+ImageBase = "c817782e-172a-44cc-b673-b171935fbb9e"
 ImageContrastAdjustment = "f332f351-ec65-5f6a-b3d1-319c6670881a"
 ImageCore = "a09fc81d-aa75-5fe9-8630-4744c3626534"
 ImageDistances = "51556ac3-7006-55f5-8cb3-34580c88182d"
@@ -20,7 +20,7 @@ ImageQualityIndexes = "2996bd0c-7a13-11e9-2da2-2f5ce47296a9"
 ImageShow = "4e3cecfd-b093-5904-9786-8bbb286a6a31"
 ImageTransformations = "02fcd773-0e25-5acc-982a-7f6622650795"
 IndirectArrays = "9b13fd28-a010-5f03-acff-a1bbcff69959"
-OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
+IntegralArrays = "1d092043-8f09-5a30-832f-7509e371ab51"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
@@ -30,29 +30,29 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 TiledIteration = "06e1c1a7-607b-532d-9fad-de7d9aa2abac"
 
 [compat]
-AxisArrays = "0.3, 0.4"
 FileIO = "1"
 Graphics = "0.4, 1.0"
-ImageAxes = "0.6"
+ImageAxes = "0.6.9"
+ImageBase = "0.1.5"
 ImageContrastAdjustment = "0.3.3"
-ImageCore = "0.9"
+ImageCore = "0.9.3"
 ImageDistances = "0.2.5"
-ImageFiltering = "0.6.3"
-ImageIO = "0.0.1, 0.3, 0.4, 0.5"
-ImageMagick = "0.7.5, 1"
-ImageMetadata = "0.6, 0.7, 0.8, 0.9"
-ImageMorphology = "0.2.7"
-ImageQualityIndexes = "0.1.3, 0.2"
-ImageShow = "0.1, 0.2, 0.3"
-ImageTransformations = "0.4, 0.5, 0.6, 0.7, 0.8"
-IndirectArrays = "0.5"
-OffsetArrays = "0.8, 0.9, 0.10, 0.11, 1.0.1"
-Reexport = "0.2, 1.0"
+ImageFiltering = "0.7.1"
+ImageIO = "0.3, 0.4, 0.5"
+ImageMagick = "1"
+ImageMetadata = "0.9.7"
+ImageMorphology = "0.3"
+ImageQualityIndexes = "0.3"
+ImageShow = "0.3"
+ImageTransformations = "0.9"
+IndirectArrays = "0.5, 1"
+IntegralArrays = "0.1"
+Reexport = "1.1"
 StaticArrays = "0.8, 0.9, 0.10, 0.11, 0.12, 1.0"
 StatsBase = "0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30, 0.31, 0.32, 0.33"
 Suppressor = "0.2"
 TiledIteration = "0.2, 0.3"
-julia = "1"
+julia = "1.3"
 
 [extras]
 FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"

src/Images.jl

@@ -1,48 +1,21 @@
 module Images
 
-import Base.Iterators.take
-import Base: +, -, *
-import Base: abs, atan, clamp, convert, copy, copy!, delete!,
-             eltype, get, getindex, haskey, hypot,
-             imag, length, map, map!, maximum,
-             minimum, ndims, one, parent, permutedims, real, reinterpret,
-             reshape, resize!,
-             setindex!, show, similar, size, sqrt,
-             strides, sum, write, zero
-
-export float32, float64
 export HomogeneousPoint
 
-using Base: depwarn
-using Base.Order: Ordering, ForwardOrdering, ReverseOrdering
-
 using StaticArrays
-using Base64: Base64EncodePipe
-
-# CHECKME: use this or follow deprecation and substitute?
-using SparseArrays: findnz
-
-# "deprecated imports" are below
 
 using Reexport
 @reexport using ImageCore
-if isdefined(ImageCore, :permuteddimsview)
-    export permuteddimsview
-end
+using ImageCore: NumberLike
+using ImageCore.OffsetArrays
+@reexport using ImageBase
 
-using FileIO
-export load, save
-import .Colors: Fractional
-import Graphics
-import Graphics: width, height, Point
-using StatsBase  # TODO: eliminate this dependency
+@reexport using FileIO: load, save
+import Graphics # TODO: eliminate this direct dependency
+import StatsBase  # TODO: eliminate this dependency
 using IndirectArrays, ImageCore.MappedArrays
 
-# TODO: can we get rid of these definitions?
-const NumberLike = Union{Number,AbstractGray}
-const RealLike = Union{Real,AbstractGray}
-
-const is_little_endian = ENDIAN_BOM == 0x04030201
+const is_little_endian = ENDIAN_BOM == 0x04030201 # CHECKME(johnnychen94): is this still used?
 
 @reexport using ImageTransformations
 @reexport using ImageAxes
@@ -52,104 +25,43 @@ const is_little_endian = ENDIAN_BOM == 0x04030201
 @reexport using ImageDistances
 @reexport using ImageContrastAdjustment
 @reexport using ImageQualityIndexes
+@reexport using IntegralArrays
+@reexport using IntegralArrays.IntervalSets.EllipsisNotation
 
-if isdefined(ImageQualityIndexes, :assess_psnr)
-    # deprecated since ImageQualityIndexes v0.1.4
-    Base.@deprecate_binding psnr assess_psnr
-    Base.@deprecate_binding ssim assess_ssim
-else
-    const psnr = ImageQualityIndexes.psnr
-    export psnr
-end
-
-# Both ImageMetadata v0.9.0 and ImageAxes v0.6.0 deprecate the symbol data and
-# this causes a name conflict
-if isdefined(ImageMetadata, :arraydata)
-    Base.@deprecate_binding data arraydata
-end
-# ImageMetadata < v0.9.0 compatibility
-if !hasmethod(arraydata, (ImageMeta, ) )
-    ImageAxes.arraydata(img::ImageMeta) = ImageMetadata.data(img)
-end
-
-# Non-exported symbol bindings to ImageShow
-import ImageShow
-if isdefined(ImageShow, :play)
-    @doc (@doc ImageShow.play)
-    const play = ImageShow.play
-else
-    play(args...; kwargs...) = error("The `Images.play` function requires ImageShow at least 0.3.0.")
-end
-if isdefined(ImageShow, :explore)
-    @doc (@doc ImageShow.explore)
-    const explore = ImageShow.explore
-else
-    explore(args...; kwargs...) = error("The `Images.explore` function requires ImageShow at least 0.3.0.")
-end
-if isdefined(ImageShow, :gif)
-    @doc (@doc ImageShow.gif)
-    const gif = ImageShow.gif
-else
-    gif(args...; kwargs...) = error("The `Images.gif` function requires ImageShow at least 0.3.0.")
-end
+# Non-exported symbol bindings to ImageShow so that we can use, e.g., `Images.gif`
+import ImageShow: play, explore, gif
 
 # While we are bridging the old API and the new API in ImageContrastAdjustment
 # we need to import these functions because we make new definitions for them
 # in deprecations.jl
 import ImageContrastAdjustment: build_histogram, adjust_histogram, adjust_histogram!
 
-using ImageMetadata: ImageMetaAxis
-import ImageMorphology: dilate, erode
-import ImageTransformations: restrict
 using TiledIteration: EdgeIterator
 
+# TODO(johnnychen94): (v1.0.0) remove these entry points
+# Entry points that isn't used by JuliaImages at all (except for deprecations)
+# They used to be accessible by, e.g., `Images.metadata`
+import .Colors: Fractional
+import FileIO: metadata
+import Graphics: Point
+
 include("compat.jl")
 include("misc.jl")
 include("labeledarrays.jl")
 include("algorithms.jl")
-include("exposure.jl")
 include("deprecations.jl")
 include("corner.jl")
 include("edge.jl")
 
 export
     # types
-    BlobLoG,
     ColorizedArray,
     Percentile,
 
     # macros
     @test_approx_eq_sigma_eps,
 
-    # core functions
-    assert_timedim_last,
-    colordim,
-    coords_spatial,
-    copyproperties,
-    data,
-    height,
-    maxabsfinite,
-    maxfinite,
-    minfinite,
-    nimages,
-    pixelspacing,
-    properties,
-    restrict,
-    sdims,
-    size_spatial,
-    shareproperties,
-    spacedirections,
-    spatialorder,
-    spatialproperties,
-    timedim,
-    width,
-    widthheight,
-
     # algorithms
-    backdiffx,
-    backdiffy,
-    forwarddiffx,
-    forwarddiffy,
     imcorner,
     imcorner_subpixel,
     corner2subpixel,
@@ -160,17 +72,11 @@ export
     meancovs,
     gammacovs,
     imedge,  # TODO: deprecate?
-    blob_LoG,
-    findlocalmaxima,
-    findlocalminima,
     imgaussiannoise,
-    imlineardiffusion,
-    imROF,
     otsu_threshold,
     yen_threshold,
 
     #Exposure
-    complement,
     imhist,
     histeq,
     adjust_gamma,
@@ -182,27 +88,18 @@ export
 
     magnitude,
     magnitude_phase,
-    meanfinite,
-    entropy,
     orientation,
-    padarray,
     phase,
     thin_edges,
     thin_edges_subpix,
     thin_edges_nonmaxsup,
     thin_edges_nonmaxsup_subpix,
     canny,
-    integral_image,
-    boxdiff,
-    bilinear_interpolation,
     gaussian_pyramid,
 
     # phantoms
     shepp_logan
 
-_length(A::AbstractArray) = length(eachindex(A))
-_length(A) = length(A)
-
 """
 Constructors, conversions, and traits:
 
@@ -216,18 +113,17 @@ Contrast/coloration:
 
 Algorithms:
 
-    - Reductions: `maxfinite`, `maxabsfinite`, `minfinite`, `meanfinite`, `integral_image`, `boxdiff`, `gaussian_pyramid`
+    - Reductions: `maxfinite`, `maxabsfinite`, `minfinite`, `meanfinite`, `IntegralArray`, `gaussian_pyramid`
     - Resizing: `restrict`, `imresize` (not yet exported)
     - Filtering: `imfilter`, `imfilter!`, `mapwindow`, `imROF`, `padarray`
-    - Filtering kernels: `Kernel.` or `KernelFactors.`, followed by `ando[345]`, `guassian2d`, `imaverage`, `imdog`, `imlaplacian`, `prewitt`, `sobel`
+    - Filtering kernels: `Kernel.` or `KernelFactors.`, followed by `ando[345]`, `guassian`, `Laplacian', `DoG`, `prewitt`, `sobel`, etc.
     - Exposure : `imhist`, `histeq`, `adjust_gamma`, `histmatch`, `imadjustintensity`, `imstretch`, `imcomplement`, `clahe`, `cliphist`
     - Gradients: `backdiffx`, `backdiffy`, `forwarddiffx`, `forwarddiffy`, `imgradients`
     - Edge detection: `imedge`, `imgradients`, `thin_edges`, `magnitude`, `phase`, `magnitudephase`, `orientation`, `canny`
     - Corner detection: `imcorner`,`imcorner_subpixel`, `harris`, `shi_tomasi`, `kitchen_rosenfeld`, `meancovs`, `gammacovs`, `fastcorners`
     - Blob detection: `blob_LoG`, `findlocalmaxima`, `findlocalminima`
     - Morphological operations: `dilate`, `erode`, `closing`, `opening`, `tophat`, `bothat`, `morphogradient`, `morpholaplace`, `feature_transform`, `distance_transform`, `convexhull`
     - Connected components: `label_components`, `component_boxes`, `component_lengths`, `component_indices`, `component_subscripts`, `component_centroids`
-    - Interpolation: `bilinear_interpolation`
 
 Test images and phantoms (see also TestImages.jl):