Merge pull request #661 from juliohm/image-morphology

Add ImageMorphology as a dependency

REQUIRE

@@ -6,6 +6,7 @@ FixedPointNumbers 0.3.0
 ImageCore
 ImageTransformations 0.2.2
 ImageFiltering
+ImageMorphology
 AxisArrays
 ImageAxes
 ImageMetadata

src/Images.jl

@@ -49,6 +49,7 @@ const is_little_endian = ENDIAN_BOM == 0x04030201
 @reexport using ImageAxes
 @reexport using ImageMetadata
 @reexport using ImageFiltering
+@reexport using ImageMorphology
 
 import ImageTransformations: restrict
 using ImageMetadata: ImageMetaAxis

src/algorithms.jl

@@ -607,109 +607,7 @@ function imROF(img::AbstractArray, lambda::Number, iterations::Integer)
 end
 
 
-### Morphological operations
-
-# Erode and dilate support 3x3 regions only (and higher-dimensional generalizations).
-"""
-```
-imgd = dilate(img, [region])
-```
-
-perform a max-filter over nearest-neighbors. The
-default is 8-connectivity in 2d, 27-connectivity in 3d, etc. You can specify the
-list of dimensions that you want to include in the connectivity, e.g., `region =
-[1,2]` would exclude the third dimension from filtering.
-"""
-dilate(img::ImageMeta, region=coords_spatial(img)) = shareproperties(img, dilate!(copy(data(img)), region))
-"""
-```
-imge = erode(img, [region])
-```
-
-perform a min-filter over nearest-neighbors. The
-default is 8-connectivity in 2d, 27-connectivity in 3d, etc. You can specify the
-list of dimensions that you want to include in the connectivity, e.g., `region =
-[1,2]` would exclude the third dimension from filtering.
-"""
-erode(img::ImageMeta, region=coords_spatial(img)) = shareproperties(img, erode!(copy(data(img)), region))
-dilate(img::AbstractArray, region=coords_spatial(img)) = dilate!(copy(img), region)
-erode(img::AbstractArray, region=coords_spatial(img)) = erode!(copy(img), region)
-
-dilate!(maxfilt, region=coords_spatial(maxfilt)) = extremefilt!(maxfilt, max, region)
-erode!(minfilt, region=coords_spatial(minfilt)) = extremefilt!(minfilt, min, region)
-function extremefilt!(A::AbstractArray, select::Function, region=coords_spatial(A))
-    inds = indices(A)
-    for d = 1:ndims(A)
-        if size(A, d) == 1 || !in(d, region)
-            continue
-        end
-        Rpre = CartesianRange(inds[1:d-1])
-        Rpost = CartesianRange(inds[d+1:end])
-        _extremefilt!(A, select, Rpre, inds[d], Rpost)
-    end
-    A
-end
-
-@noinline function _extremefilt!(A, select, Rpre, inds, Rpost)
-    # TODO: improve the cache efficiency
-    for Ipost in Rpost, Ipre in Rpre
-        # first element along dim
-        i1 = first(inds)
-        a2, a3 = A[Ipre, i1, Ipost], A[Ipre, i1+1, Ipost]
-        A[Ipre, i1, Ipost] = select(a2, a3)
-        # interior along dim
-        for i = i1+2:last(inds)
-            a1, a2 = a2, a3
-            a3 = A[Ipre, i, Ipost]
-            A[Ipre, i-1, Ipost] = select(select(a1, a2), a3)
-        end
-        # last element along dim
-        A[Ipre, last(inds), Ipost] = select(a2, a3)
-    end
-    A
-end
-
-"""
-`imgo = opening(img, [region])` performs the `opening` morphology operation, equivalent to `dilate(erode(img))`.
-`region` allows you to control the dimensions over which this operation is performed.
-"""
-opening(img::AbstractArray, region=coords_spatial(img)) = opening!(copy(img), region)
-opening!(img::AbstractArray, region=coords_spatial(img)) = dilate!(erode!(img, region),region)
-
-"""
-`imgc = closing(img, [region])` performs the `closing` morphology operation, equivalent to `erode(dilate(img))`.
-`region` allows you to control the dimensions over which this operation is performed.
-"""
-closing(img::AbstractArray, region=coords_spatial(img)) = closing!(copy(img), region)
-closing!(img::AbstractArray, region=coords_spatial(img)) = erode!(dilate!(img, region),region)
-
-"""
-`imgth = tophat(img, [region])` performs `top hat` of an image,
-which is defined as the image minus its morphological opening.
-`region` allows you to control the dimensions over which this operation is performed.
-"""
-tophat(img::AbstractArray, region=coords_spatial(img)) = img - opening(img, region)
-
-"""
-`imgbh = bothat(img, [region])` performs `bottom hat` of an image,
-which is defined as its morphological closing minus the original image.
-`region` allows you to control the dimensions over which this operation is performed.
-"""
-bothat(img::AbstractArray, region=coords_spatial(img)) = closing(img, region) - img
-
-"""
-`imgmg = morphogradient(img, [region])` returns morphological gradient of the image,
-which is the difference between the dilation and the erosion of a given image.
-`region` allows you to control the dimensions over which this operation is performed.
-"""
-morphogradient(img::AbstractArray, region=coords_spatial(img)) = dilate(img, region) - erode(img, region)
-
-"""
-`imgml = morpholaplace(img, [region])` performs `Morphological Laplacian` of an image,
-which is defined as the arithmetic difference between the internal and the external gradient.
-`region` allows you to control the dimensions over which this operation is performed.
-"""
-morpholaplace(img::AbstractArray, region=coords_spatial(img)) = dilate(img, region) + erode(img, region) - 2img
+# what are these `extr` functions? TODO: documentation
 
 extr(order::ForwardOrdering, x::Real, y::Real) = max(x,y)
 extr(order::ForwardOrdering, x::Real, y::Real, z::Real) = max(x,y,z)