[Morphology][Tasks] introduce generic fillholes algorithm

benchmark/benchmarks.jl

@@ -1,5 +1,5 @@
-# Usage:
-#     julia benchmark/run_benchmarks.jl
+Usage:
+    julia benchmark/run_benchmarks.jl
 using BenchmarkTools
 using ImageCore
 using ImageMorphology
@@ -91,8 +91,8 @@ end
 SUITE["connected"] = BenchmarkGroup()
 let grp = SUITE["connected"]
     grp["label_components"] = @benchmarkable label_components($blobs)
-    grp["label_flatzones"] = @benchmarkable label_flatzones($cameraman, trues(3,3))
-    grp["label_lambdaflatzones"] = @benchmarkable label_lambdaflatzones($cameraman, trues(3,3),Gray{N0f8}(1.0/255.0))
+    grp["label_flatzones"] = @benchmarkable label_flatzones($cameraman, trues(3, 3))
+    grp["label_lambdaflatzones"] = @benchmarkable label_lambdaflatzones($cameraman, trues(3, 3), Gray{N0f8}(1.0 / 255.0))
 end
 
 SUITE["Maxtree"] = BenchmarkGroup()
@@ -136,3 +136,13 @@ let grp = SUITE["extremum"]
         grp["regional_maxima"]["$sz×$sz"] = @benchmarkable regional_maxima($tst_img)
     end
 end
+
+SUITE["clearborder"] = BenchmarkGroup()
+let grp = SUITE["clearborder"]
+    grp["clearborder"] = @benchmarkable clearborder($blobs)
+end
+
+SUITE["fillhole"] = BenchmarkGroup()
+let grp = SUITE["fillhole"]
+    grp["fillhole"] = @benchmarkable fillhole($blobs)
+end

src/ImageMorphology.jl

@@ -24,6 +24,7 @@ include("connected.jl")
 include("clearborder.jl")
 include("extreme_filter.jl")
 include("extremum.jl")
+include("filholes.jl")
 include("ops/dilate.jl")
 include("ops/erode.jl")
 include("ops/closing.jl")
@@ -130,15 +131,22 @@ export
     #feature_transform.jl
     feature_transform,
     distance_transform,
+
+    #clearborder
     clearborder,
 
+    #fillhole
+    fillhole,
+    fillhole!,
+
     #leveling
     low_leveling,
     low_leveling!,
     high_leveling,
     high_leveling!,
     leveling,
     leveling!,
+
     #extremum
     hmaxima,
     hmaxima!,

src/filholes.jl

@@ -0,0 +1,58 @@
+"""
+    fillhole(img; [dims])
+    fillhole(img; se)
+
+Fill the holes in image 'img'. Could be binary or grascale
+
+The `dims` keyword is used to specify the dimension to process by constructing the box shape
+structuring element [`strel_box(img; dims)`](@ref strel_box). For generic structuring
+element, the half-size is expected to be either `0` or `1` along each dimension.
+
+The output has the same type as input image
+"""
+
+function fillhole(img; dims=coords_spatial(img))
+    return fillhole(img, strel_box(img, dims))
+end
+
+function fillhole(img, se)
+    return fillhole!(similar(img), img, se)
+end
+
+function fillhole!(out, img; dims=coords_spatial(img))
+    return fillhole!(out, img, strel_box(img, dims))
+end
+
+function fillhole!(out, img, se)
+    return _fillhole!(out, img, se)
+end
+
+function _fillhole!(out, img, se)
+    N = ndims(img)
+
+    axes(out) == axes(img) || throw(DimensionMismatch("images should have the same axes"))
+
+    se_size = strel_size(se)
+    if length(se_size) != N
+        msg = "the input structuring element is not for $N dimensional array, instead it is for $(length(se_size)) dimensional array"
+        throw(DimensionMismatch(msg))
+    end
+    if !all(x -> in(x, (1, 3)), strel_size(se))
+        msg = "structuring element with half-size larger than 1 is invalid"
+        throw(DimensionMismatch(msg))
+    end
+
+    tmp = similar(img)
+
+    # fill marker image with max
+    fill!(tmp, typemax(eltype(img)))
+    # fill borders with 0
+    dimensions = size(tmp)
+    outerrange = CartesianIndices(map(i -> 1:i, dimensions))
+    innerrange = CartesianIndices(map(i -> (1 + 1):(i - 1), dimensions))
+    for i in EdgeIterator(outerrange, innerrange)
+        tmp[i] = 0
+    end
+
+    return mreconstruct!(erode, out, tmp, img, se)
+end

test/fillholes.jl

@@ -0,0 +1,64 @@
+@testset "fillhole" begin
+    #binary
+    img = Bool[
+        0 0 0 0 0 0 0
+        0 1 1 1 1 1 0
+        0 1 0 0 0 1 0
+        0 1 0 0 0 1 0
+        0 1 0 0 0 1 0
+        0 1 1 1 1 1 0
+        0 0 0 0 0 0 0
+    ]
+
+    expected = Bool[
+        0 0 0 0 0 0 0
+        0 1 1 1 1 1 0
+        0 1 1 1 1 1 0
+        0 1 1 1 1 1 0
+        0 1 1 1 1 1 0
+        0 1 1 1 1 1 0
+        0 0 0 0 0 0 0
+    ]
+
+    out = fillhole(img)
+    @test eltype(out) == Bool
+    @test out == expected
+
+    # in place
+    out = similar(img)
+    out = fillhole!(out, img)
+    @test out == expected
+
+    # in place diamond
+    out = similar(img)
+    out = fillhole!(out, img, strel_diamond((3, 3)))
+    @test out == expected
+
+    #gray
+    img = [
+        3 3 3 3 3 3 3 3 3 3
+        3 4 4 4 3 3 4 4 4 3
+        3 4 1 4 3 3 4 1 4 3
+        3 4 4 4 3 3 4 4 4 3
+        3 3 3 3 3 3 3 3 3 3
+    ]
+
+    expected = [
+        3 3 3 3 3 3 3 3 3 3
+        3 4 4 4 3 3 4 4 4 3
+        3 4 4 4 3 3 4 4 4 3
+        3 4 4 4 3 3 4 4 4 3
+        3 3 3 3 3 3 3 3 3 3
+    ]
+
+    out = fillhole(img)
+    @test out == expected
+
+    msg = "the input structuring element is not for 1 dimensional array, instead it is for 2 dimensional array"
+    @test_throws DimensionMismatch(msg) fillhole(rand(10), strel_box((3, 3)))
+
+    se = strel_diamond((7, 7))
+    msg = "structuring element with half-size larger than 1 is invalid"
+    @test_throws DimensionMismatch(msg) fillhole(rand(10, 10), se)
+
+end

test/runtests.jl

@@ -37,6 +37,7 @@ include("testutils.jl")
     include("feature_transform.jl")
     include("leveling.jl")
     include("clearborder.jl")
+    include("fillholes.jl")
     @info "Beginning deprecation tests, warnings are expected"
     include("deprecations.jl")
 end